US20120329113A1

US20120329113A1 - Microorganisms for Producing 1,3-Butanediol and Methods Related Thereto

Info

Publication number: US20120329113A1
Application number: US13/528,593
Authority: US
Inventors: Anthony P. Burgard; Mark J. Burk; Robin E. Osterhout; Jun Sun; Priti Pharkya
Original assignee: Genomatica Inc
Current assignee: Genomatica Inc
Priority date: 2011-06-22
Filing date: 2012-06-20
Publication date: 2012-12-27
Also published as: AU2012273177A1; US9982281B2; US11708589B2; WO2012177619A2; US20160076060A1; US20210123078A1; WO2012177619A3; US20190085363A1

Abstract

Provided herein is a non-naturally occurring microbial organism having a 1,3-butanediol (1,3-BDO) pathway and comprising at least one exogenous nucleic acid encoding a 1,3-BDO pathway enzyme expressed in a sufficient amount to produce 1,3-BDO. In some embodiments, the pathway includes reducing equivalents from CO or hydrogen. In certain embodiments, a 1,3-BDO pathway proceeds by way of central metabolites pyruvate, succinate or alpha-ketoglutarate. Also provided herein is a method for producing 1,3-BDO, includes culturing such microbial organisms under conditions and for a sufficient period of time to produce 1,3-BDO.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims the benefit of priority to U.S. Ser. Nos. 61/500,131, filed Jun. 22, 2011, and 61/502,702, filed Jun. 29, 2011, the contents of which are herein incorporated by reference in their entirety.

BACKGROUND

The present invention relates generally to biosynthetic processes and organisms capable of producing organic compounds. More specifically, the invention relates to non-naturally occurring organisms that can produce the commodity chemical 1,3-butanediol.
1,3-butanediol (1,3-BDO) is a four carbon diol traditionally produced from acetylene via its hydration. The resulting acetaldehyde is then converted to 3-hydroxybutyraldehdye which is subsequently reduced to form 1,3-BDO. In more recent years, acetylene has been replaced by the less expensive ethylene as a source of acetaldehyde. 1,3-BDO is commonly used as an organic solvent for food flavoring agents. It is also used as a co-monomer for polyurethane and polyester resins and is widely employed as a hypoglycaemic agent. Optically active 1,3-BDO is a useful starting material for the synthesis of biologically active compounds and liquid crystals. A substantial commercial use of 1,3-butanediol is subsequent dehydration to afford 1,3-butadiene (Ichikawa et al., J. of Molecular Catalysis A-Chemical, 256:106-112 (2006); Ichikawa et al., J. of Molecular Catalysis A-Chemical, 231:181-189 (2005)), a 25 billion lb/yr petrochemical used to manufacture synthetic rubbers (e.g., tires), latex, and resins. The reliance on petroleum based feedstocks for either acetylene or ethylene warrants the development of a renewable feedstock based route to 1,3-butanediol and to butadiene.
Thus, there exists a need to develop microorganisms and methods of their use to produce 1,3-BDO. The present invention satisfies this need and provides related advantages as well.

SUMMARY

In some embodiments, the present invention is directed to a non-naturally occurring microbial organism that includes a microbial organism having a 1,3-butanediol (1,3-BDO) pathway having at least one exogenous nucleic acid encoding a 1,3-BDO pathway enzyme expressed in a sufficient amount to produce 1,3-BDO. The 1,3-BDO pathway includes an enzyme selected from the group consisting of a 2-amino-4-ketopentanoate (AKP) thiolase, an AKP dehydrogenase, a 2-amino-4-hydroxypentanoate aminotransferase, a 2-amino-4-hydroxypentanoate oxidoreductase (deaminating), a 2-oxo-4-hydroxypentanoate decarboxylase, a 3-hydroxybutyraldehyde reductase, an AKP aminotransferase, an AKP oxidoreductase (deaminating), a 2,4-dioxopentanoate decarboxylase, a 3-oxobutyraldehyde reductase (ketone reducing), a 3-oxobutyraldehyde reductase (aldehyde reducing), a 4-hydroxy-2-butanone reductase, an AKP decarboxylase, a 4-aminobutan-2-one aminotransferase, a 4-aminobutan-2-one oxidoreductase (deaminating), a 4-aminobutan-2-one ammonia-lyase, a butenone hydratase, an AKP ammonia-lyase, an acetylacrylate decarboxylase, an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming), an acetoacetyl-CoA reductase (CoA-dependent, alcohol forming), an acetoacetyl-CoA reductase (ketone reducing), a 3-hydroxybutyryl-CoA reductase (aldehyde forming), a 3-hydroxybutyryl-CoA reductase (alcohol forming), a 4-hydroxybutyryl-CoA dehydratase, and a crotonase.
In some embodiments, the present invention is directed to a method for producing 1,3-BDO that includes culturing such a non-naturally occurring microbial organism, under conditions and for a sufficient period of time to produce 1,3-BDO.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows pathways to 1,3-BDO from alanine. Enzymes are: A) AKP thiolase, B) AKP aminotransferase or AKP oxidoreductase (deaminating), C) 2,4-dioxopentanoate decarboxylase, D) 3-oxobutyraldehyde reductase (aldehyde reducing), E) AKP decarboxylase, F) 4-aminobutan-2-one ammonia-lyase, G) Butenone hydratase, H) 4-hydroxy,2-butanone reductase, I) AKP ammonia-lyase, J) acetylacrylate decarboxylase, K) 4-aminobutan-2-one aminotransferase or 4-aminobutan-2-one oxidoreductase (deaminating), L) AKP dehydrogenase, M) 2-amino-4-hydroxypentanoate aminotransferase or 2-amino-4-hydroxypentanoate oxidoreductase (deaminating), N) 2-oxo-4-hydroxypentanoate decarboxylase, O) 3-oxobutyraldehyde reductase (ketone reducing), and P) 3-hydroxybutyraldehdye reductase.

FIG. 2 shows pathways from acetoacetyl-CoA to 1,3-butanediol. Enzymes are: A) acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming), B) 3-oxobutyraldehyde reductase (ketone reducing), C) 3-hydroxybutyraldehyde reductase, D) acetoacetyl-CoA reductase (CoA-dependent, alcohol forming), E) 3-oxobutyraldehyde reductase (aldehyde reducing), F) 4-hydroxy,2-butanone reductase, G) acetoacetyl-CoA reductase (ketone reducing), H) 3-hydroxybutyryl-CoA reductase (aldehyde forming), and I) 3-hydroxybutyryl-CoA reductase (alcohol forming).

FIG. 3 shows pathways from 4-hydroxybutyryl-CoA to 1,3-butanediol. Enzymes are: A) 4-hydroxybutyryl-CoA dehydratase, B) crotonase, C) 3-hydroxybutyryl-CoA reductase (aldehyde forming), D) 3-hydroxybutyraldehyde reductase, and E) 3-hydroxybutyryl-CoA reductase (alcohol forming).

FIG. 4 shows aldehyde dehydrogenases showing significant activity on 3-hydroxybutyl-CoA.

FIG. 5 shows the specific activity of bld from Clostridium saccharoperbutylacetonicum on 3-Hydroxybutyryl-CoA before and after dialysis.

FIG. 6 shows 1,3-BDO concentrations when 3-hydroxybutyraldehyde was added as a substrate and in the control samples with no substrate. The GI numbers for the alcohol dehydrogenases are shown.

FIG. 7 shows 1,3-BDO concentrations when 3-hydroxybutyryl-CoA was added as a substrate and in the control samples with no substrate. The GI numbers for the alcohol dehydrogenases are shown. The GI number for the aldehyde dehydrogenase tested in conjunction is 163762382.

FIG. 8A shows the pathways for fixation of CO₂to pyruvate using the reductive TCA cycle.

FIG. 8B shows exemplary pathways for the biosynthesis of 1,3-butanediol from pyruvate; pyruvate is converted to alanine by alanine dehydrogenase alanine aminotransferase; the remaining enzymatic transformations shown are carried out by the following enzymes: A) AKP thiolase, B) AKP aminotransferase or AKP oxidoreductase (deaminating), C) 2,4-dioxopentanoate decarboxylase, D) 3-oxobutyraldehyde reductase (aldehyde reducing), E) AKP decarboxylase, F) 4-aminobutan-2-one ammonia-lyase, G) Butenone hydratase, H) 4-hydroxy,2-butanone reductase, I) AKP ammonia-lyase, J) acetylacrylate decarboxylase, K) 4-aminobutan-2-one aminotransferase or 4-aminobutan-2-one oxidoreductase (deaminating), L) AKP dehydrogenase, M) 2-amino-4-hydroxypentanoate aminotransferase or 2-amino-4-hydroxypentanoate oxidoreductase (deaminating), N) 2-oxo-4-hydroxypentanoate decarboxylase, O) 3-oxobutyraldehyde reductase (ketone reducing), and P) 3-hydroxybutyraldehdye reductase.

FIG. 9A shows the pathways for fixation of CO₂to alpha-ketoglutarate, succinate and succinyl-CoA using the reductive TCA cycle.

FIG. 9B shows exemplary pathways for the biosynthesis of 1,3-butanediol from alpha-ketoglutarate, succinate and succinyl-CoA; the enzymatic transformations shown are carried out by the following enzymes: A. Succinyl-CoA transferase, or Succinyl-CoA synthetase (or succinyl-CoA ligase), B. Succinyl-CoA reductase (aldehyde forming), C. 4-Hydroxybutyrate dehydrogenase, D. 4-Hydroxybutyrate kinase, E. Phosphotrans-4-hydroxybutyrylase, F. Succinate reductase, G. Succinyl-CoA reductase (alcohol forming), H. 4-Hydroxybutyryl-CoA transferase, or 4-Hydroxybutyryl-CoA synthetase, or 4-Hydroxybutyryl-CoA ligase I. Alpha-ketoglutarate decarboxylase, J. 4-hydroxybutyryl-CoA dehydratase, K. crotonase, L. 3-hydroxybutyryl-CoA reductase (aldehyde forming), M. 3-hydroxybutanal reductase, N. 3-hydroxybutyryl-CoA reductase (alcohol forming), O. 3-hydroxybutyryl-CoA hydrolase, transferase, or synthetase, P. 3-hydroxybutyrate reductase, Q. Glutamate dehydrogenase and/or R. Glutamate transaminase; S. Glutamate decarboxylase; T. 4-aminobutyrate dehydrogenase and/or U. 4-aminobutyrate transaminase and V. Alpha-ketoglutarate dehydrogenase.

FIG. 10 shows Western blots of 10 micrograms ACS90 (lane 1), ACS91 (lane2), Mta98/99 (lanes 3 and 4) cell extracts with size standards (lane 5) and controls of M. thermoacetica CODH (Moth_—1202/1203) or Mtr (Moth_—1197) proteins (50, 150, 250, 350, 450, 500, 750, 900, and 1000 ng).

FIG. 11 shows CO oxidation assay results. Cells (M. thermoacetica or E. coli with the CODH/ACS operon; ACS90 or ACS91 or empty vector: pZA33S) were grown and extracts prepared. Assays were performed at 55° C. at various times on the day the extracts were prepared. Reduction of methylviologen was followed at 578 nm over a 120 sec time course.

FIG. 12A shows the nucleotide sequence (SEQ ID NO:1) of carboxylic acid reductase from Nocardia iowensis (GNM_—720), and FIG. 12B shows the encoded amino acid sequence (SEQ ID NO:2).

FIG. 13A shows the nucleotide sequence (SEQ ID NO:3) of phosphpantetheine transferase, which was codon optimized, and FIG. 13B shows the encoded amino acid sequence (SEQ ID NO:4).

FIG. 14A shows the nucleotide sequence (SEQ ID NO:5) of carboxylic acid reductase from Mycobacterium smegmatis mc(2)155 (designated 890), and FIG. 14B shows the encoded amino acid sequence (SEQ ID NO:6).

FIG. 15A shows the nucleotide sequence (SEQ ID NO:7) of carboxylic acid reductase from Mycobacterium avium subspecies paratuberculosis K-10 (designated 891), and FIG. 15B shows the encoded amino acid sequence (SEQ ID NO:8).

FIG. 16A shows the nucleotide sequence (SEQ ID NO:9) of carboxylic acid reductase from Mycobacterium marinum M (designated 892), and FIG. 16B shows the encoded amino acid sequence (SEQ ID NO:10).

FIG. 17A shows the nucleotide sequence (SEQ ID NO:11) of carboxylic acid reductase designated 891GA, and FIG. 17B shows the encoded amino acid sequence (SEQ ID NO:12).

DETAILED DESCRIPTION

This invention is directed, in part, to non-naturally occurring microorganisms that express genes encoding enzymes that catalyze 1,3-butanediol (1,3-BDO) production. Pathways for the production of 1,3-butanediol disclosed herein are based on three precursors: (i) D-alanine, (ii) acetoacetyl-CoA, and (iii) 4-hydroxybutyryl-CoA. Successfully engineering these pathways entails identifying an appropriate set of enzymes with sufficient activity and specificity, cloning their corresponding genes into a production host, optimizing fermentation conditions, and assaying for product formation following fermentation.
The conversion of alanine to 1,3-BDO can be accomplished by a number of pathways in about five enzymatic steps as shown in FIG. 1. In the first step of all pathways (Step A), alanine and acetyl-CoA are combined by 2-amino-4-ketopentanoate thiolase, a highly selective enzyme. The product of this reaction, 2-amino-4-oxopentanoate (AKP) can then be transaminated, reduced, decarboxylated or deaminated as shown in FIG. 1. Further synthetic steps for the production of 1,3-BDO are discussed in detail below. The theoretical yield of 1,3-BDO from each of these pathways is calculated to be about 1.09 mole/mole of glucose consumed.
FIG. 2 outlines multiple routes for producing 1,3-BDO from acetoacetyl-CoA. Each of these pathways from acetoacetyl-CoA to 1,3-BDO utilizes three reducing equivalents and provides a theoretical yield of 1 mole of 1,3-BDO per mole of glucose consumed. Other carbon substrates such as syngas can also be used for the production of acetoacetyl-CoA. Gasification of glucose to form syngas will result in the maximum theoretical yield of 1.09 moles of 1,3-BDO per mole of glucose consumed, assuming that 6 moles of CO and 6 moles of H₂are obtained from glucose
6CO+6H₂→1.091C₄H₁₀O₂+1.636CO₂+0.545H₂
4-Hydroxybutyryl-CoA is an important starting metabolite from which a number of industrially useful compounds can be made, including 1,3-BDO as shown in FIG. 3. Although 4-hydroxybutyryl-CoA is not a highly common central metabolite, methods for engineering strains that synthesize 4-hydroxybutyryl-CoA have been described previously by Applicants in U.S. Patent Application No. 2009/0075351. The 4-hydroxybutyryl-CoA to 1,3-butanediol pathway has a theoretical yield of 1.09 mol/mol product yield assuming glucose as the carbohydrate feedstock.
This invention is also directed, in part, to methods for producing 1,3-BDO through culturing of these non-naturally occurring microbial organisms. Dehydration of 1,3-BDO produced by the organisms and methods described herein, provides an opportunity to produce renewable butadiene in small end-use facilities obviating the need to transport this flammable and reactive chemical.
As used herein, the term “non-naturally occurring” when used in reference to a microbial organism or microorganism of the invention is intended to mean that the microbial organism has at least one genetic alteration not normally found in a naturally occurring strain of the referenced species, including wild-type strains of the referenced species. Genetic alterations include, for example, modifications introducing expressible nucleic acids encoding metabolic polypeptides, other nucleic acid additions, nucleic acid deletions and/or other functional disruption of the microbial organism's genetic material. Such modifications include, for example, coding regions and functional fragments thereof, for heterologous, homologous or both heterologous and homologous polypeptides for the referenced species. Additional modifications include, for example, non-coding regulatory regions in which the modifications alter expression of a gene or operon. Exemplary metabolic polypeptides include enzymes or proteins within a 1,3-butanediol biosynthetic pathway.
A metabolic modification refers to a biochemical reaction that is altered from its naturally occurring state. Therefore, non-naturally occurring microorganisms can have genetic modifications to nucleic acids encoding metabolic polypeptides or, functional fragments thereof. Exemplary metabolic modifications are disclosed herein.
As used herein, the term “isolated” when used in reference to a microbial organism is intended to mean an organism that is substantially free of at least one component as the referenced microbial organism is found in nature. The term includes a microbial organism that is removed from some or all components as it is found in its natural environment. The term also includes a microbial organism that is removed from some or all components as the microbial organism is found in non-naturally occurring environments. Therefore, an isolated microbial organism is partly or completely separated from other substances as it is found in nature or as it is grown, stored or subsisted in non-naturally occurring environments. Specific examples of isolated microbial organisms include partially pure microbes, substantially pure microbes and microbes cultured in a medium that is non-naturally occurring.
As used herein, the terms “microbial,” “microbial organism” or “microorganism” are intended to mean any organism that exists as a microscopic cell that is included within the domains of archaea, bacteria or eukarya. Therefore, the term is intended to encompass prokaryotic or eukaryotic cells or organisms having a microscopic size and includes bacteria, archaea and eubacteria of all species as well as eukaryotic microorganisms such as yeast and fungi. The term also includes cell cultures of any species that can be cultured for the production of a biochemical.
As used herein, the term “CoA” or “coenzyme A” is intended to mean an organic cofactor or prosthetic group (nonprotein portion of an enzyme) whose presence is required for the activity of many enzymes (the apoenzyme) to form an active enzyme system. Coenzyme A functions in certain condensing enzymes, acts in acetyl or other acyl group transfer and in fatty acid synthesis and oxidation, pyruvate oxidation and in other acetylation.
As used herein, the term “substantially anaerobic” when used in reference to a culture or growth condition is intended to mean that the amount of oxygen is less than about 10% of saturation for dissolved oxygen in liquid media. The term also is intended to include sealed chambers of liquid or solid medium maintained with an atmosphere of less than about 1% oxygen.
“Exogenous” as it is used herein is intended to mean that the referenced molecule or the referenced activity is introduced into the host microbial organism. The molecule can be introduced, for example, by introduction of an encoding nucleic acid into the host genetic material such as by integration into a host chromosome or as non-chromosomal genetic material such as a plasmid. Therefore, the term as it is used in reference to expression of an encoding nucleic acid refers to introduction of the encoding nucleic acid in an expressible form into the microbial organism. When used in reference to a biosynthetic activity, the term refers to an activity that is introduced into the host reference organism. The source can be, for example, a homologous or heterologous encoding nucleic acid that expresses the referenced activity following introduction into the host microbial organism. Therefore, the term “endogenous” refers to a referenced molecule or activity that is present in the host. Similarly, the term when used in reference to expression of an encoding nucleic acid refers to expression of an encoding nucleic acid contained within the microbial organism. The term “heterologous” refers to a molecule or activity derived from a source other than the referenced species whereas “homologous” refers to a molecule or activity derived from the host microbial organism. Accordingly, exogenous expression of an encoding nucleic acid of the invention can utilize either or both a heterologous or homologous encoding nucleic acid.
It is understood that when more than one exogenous nucleic acid is included in a microbial organism that the more than one exogenous nucleic acids refers to the referenced encoding nucleic acid or biosynthetic activity, as discussed above. It is further understood, as disclosed herein, that such more than one exogenous nucleic acids can be introduced into the host microbial organism on separate nucleic acid molecules, on polycistronic nucleic acid molecules, or a combination thereof, and still be considered as more than one exogenous nucleic acid. For example, as disclosed herein a microbial organism can be engineered to express two or more exogenous nucleic acids encoding a desired pathway enzyme or protein. In the case where two exogenous nucleic acids encoding a desired activity are introduced into a host microbial organism, it is understood that the two exogenous nucleic acids can be introduced as a single nucleic acid, for example, on a single plasmid, on separate plasmids, can be integrated into the host chromosome at a single site or multiple sites, and still be considered as two exogenous nucleic acids. Similarly, it is understood that more than two exogenous nucleic acids can be introduced into a host organism in any desired combination, for example, on a single plasmid, on separate plasmids, can be integrated into the host chromosome at a single site or multiple sites, and still be considered as two or more exogenous nucleic acids, for example three exogenous nucleic acids. Thus, the number of referenced exogenous nucleic acids or biosynthetic activities refers to the number of encoding nucleic acids or the number of biosynthetic activities, not the number of separate nucleic acids introduced into the host organism.
The non-naturally occurring microbal organisms of the invention can contain stable genetic alterations, which refers to microorganisms that can be cultured for greater than five generations without loss of the alteration. Generally, stable genetic alterations include modifications that persist greater than 10 generations, particularly stable modifications will persist more than about 25 generations, and more particularly, stable genetic modifications will be greater than 50 generations, including indefinitely.
Those skilled in the art will understand that the genetic alterations, including metabolic modifications exemplified herein, are described with reference to a suitable host organism such as E. coli and their corresponding metabolic reactions or a suitable source organism for desired genetic material such as genes for a desired metabolic pathway. However, given the complete genome sequencing of a wide variety of organisms and the high level of skill in the area of genomics, those skilled in the art will readily be able to apply the teachings and guidance provided herein to essentially all other organisms. For example, the E. coli metabolic alterations exemplified herein can readily be applied to other species by incorporating the same or analogous encoding nucleic acid from species other than the referenced species. Such genetic alterations include, for example, genetic alterations of species homologs, in general, and in particular, orthologs, paralogs or nonorthologous gene displacements.
An ortholog is a gene or genes that are related by vertical descent and are responsible for substantially the same or identical functions in different organisms. For example, mouse epoxide hydrolase and human epoxide hydrolase can be considered orthologs for the biological function of hydrolysis of epoxides. Genes are related by vertical descent when, for example, they share sequence similarity of sufficient amount to indicate they are homologous, or related by evolution from a common ancestor. Genes can also be considered orthologs if they share three-dimensional structure but not necessarily sequence similarity, of a sufficient amount to indicate that they have evolved from a common ancestor to the extent that the primary sequence similarity is not identifiable. Genes that are orthologous can encode proteins with sequence similarity of about 25% to 100% amino acid sequence identity. Genes encoding proteins sharing an amino acid similarity less that 25% can also be considered to have arisen by vertical descent if their three-dimensional structure also shows similarities. Members of the serine protease family of enzymes, including tissue plasminogen activator and elastase, are considered to have arisen by vertical descent from a common ancestor.
Orthologs include genes or their encoded gene products that through, for example, evolution, have diverged in structure or overall activity. For example, where one species encodes a gene product exhibiting two functions and where such functions have been separated into distinct genes in a second species, the three genes and their corresponding products are considered to be orthologs. For the production of a biochemical product, those skilled in the art will understand that the orthologous gene harboring the metabolic activity to be introduced or disrupted is to be chosen for construction of the non-naturally occurring microorganism. An example of orthologs exhibiting separable activities is where distinct activities have been separated into distinct gene products between two or more species or within a single species. A specific example is the separation of elastase proteolysis and plasminogen proteolysis, two types of serine protease activity, into distinct molecules as plasminogen activator and elastase. A second example is the separation of mycoplasma 5′-3′ exonuclease and Drosophila DNA polymerase III activity. The DNA polymerase from the first species can be considered an ortholog to either or both of the exonuclease or the polymerase from the second species and vice versa.
In contrast, paralogs are homologs related by, for example, duplication followed by evolutionary divergence and have similar or common, but not identical functions. Paralogs can originate or derive from, for example, the same species or from a different species. For example, microsomal epoxide hydrolase (epoxide hydrolase I) and soluble epoxide hydrolase (epoxide hydrolase II) can be considered paralogs because they represent two distinct enzymes, co-evolved from a common ancestor, that catalyze distinct reactions and have distinct functions in the same species. Paralogs are proteins from the same species with significant sequence similarity to each other suggesting that they are homologous, or related through co-evolution from a common ancestor. Groups of paralogous protein families include HipA homologs, luciferase genes, peptidases, and others.
A nonorthologous gene displacement is a nonorthologous gene from one species that can substitute for a referenced gene function in a different species. Substitution includes, for example, being able to perform substantially the same or a similar function in the species of origin compared to the referenced function in the different species. Although generally, a nonorthologous gene displacement will be identifiable as structurally related to a known gene encoding the referenced function, less structurally related but functionally similar genes and their corresponding gene products nevertheless will still fall within the meaning of the term as it is used herein. Functional similarity requires, for example, at least some structural similarity in the active site or binding region of a nonorthologous gene product compared to a gene encoding the function sought to be substituted. Therefore, a nonorthologous gene includes, for example, a paralog or an unrelated gene.
Therefore, in identifying and constructing the non-naturally occurring microbial organisms of the invention having 1,3-BDO biosynthetic capability, those skilled in the art will understand with applying the teaching and guidance provided herein to a particular species that the identification of metabolic modifications can include identification and inclusion or inactivation of orthologs. To the extent that paralogs and/or nonorthologous gene displacements are present in the referenced microorganism that encode an enzyme catalyzing a similar or substantially similar metabolic reaction, those skilled in the art also can utilize these evolutionally related genes.
Orthologs, paralogs and nonorthologous gene displacements can be determined by methods well known to those skilled in the art. For example, inspection of nucleic acid or amino acid sequences for two polypeptides will reveal sequence identity and similarities between the compared sequences. Based on such similarities, one skilled in the art can determine if the similarity is sufficiently high to indicate the proteins are related through evolution from a common ancestor. Algorithms well known to those skilled in the art, such as Align, BLAST, Clustal W and others compare and determine a raw sequence similarity or identity, and also determine the presence or significance of gaps in the sequence which can be assigned a weight or score. Such algorithms also are known in the art and are similarly applicable for determining nucleotide sequence similarity or identity. Parameters for sufficient similarity to determine relatedness are computed based on well known methods for calculating statistical similarity, or the chance of finding a similar match in a random polypeptide, and the significance of the match determined. A computer comparison of two or more sequences can, if desired, also be optimized visually by those skilled in the art. Related gene products or proteins can be expected to have a high similarity, for example, 25% to 100% sequence identity. Proteins that are unrelated can have an identity which is essentially the same as would be expected to occur by chance, if a database of sufficient size is scanned (about 5%). Sequences between 5% and 24% may or may not represent sufficient homology to conclude that the compared sequences are related. Additional statistical analysis to determine the significance of such matches given the size of the data set can be carried out to determine the relevance of these sequences.
Exemplary parameters for determining relatedness of two or more sequences using the BLAST algorithm, for example, can be as set forth below. Briefly, amino acid sequence alignments can be performed using BLASTP version 2.0.8 (Jan. 5, 1999) and the following parameters: Matrix: 0 BLOSUM62; gap open: 11; gap extension: 1; x_dropoff: 50; expect: 10.0; wordsize: 3; filter: on. Nucleic acid sequence alignments can be performed using BLASTN version 2.0.6 (Sep. 16, 1998) and the following parameters: Match: 1; mismatch: −2; gap open: 5; gap extension: 2; x_dropoff: 50; expect: 10.0; wordsize: 11; filter: off. Those skilled in the art will know what modifications can be made to the above parameters to either increase or decrease the stringency of the comparison, for example, and determine the relatedness of two or more sequences.
In some embodiments, the present invention provides a non-naturally occurring microbial organism that includes a microbial organism having a 1,3-butanediol (1,3-BDO) pathway with at least one exogenous nucleic acid encoding a 1,3-BDO pathway enzyme expressed in a sufficient amount to produce 1,3-BDO. The 1,3-BDO pathway includes an enzyme selected from the group consisting of a 2-amino-4-ketopentanoate (AKP) thiolase, an AKP dehydrogenase, a 2-amino-4-hydroxypentanoate aminotransferase, a 2-amino-4-hydroxypentanoate oxidoreductase (deaminating), a 2-oxo-4-hydroxypentanoate decarboxylase, a 3-hydroxybutyraldehyde reductase, an AKP aminotransferase, an AKP oxidoreductase (deaminating), a 2,4-dioxopentanoate decarboxylase, a 3-oxobutyraldehyde reductase (ketone reducing), a 3-oxobutyraldehyde reductase (aldehyde reducing), a 4-hydroxy-2-butanone reductase, an AKP decarboxylase, a 4-aminobutan-2-one aminotransferase, a 4-aminobutan-2-one oxidoreductase (deaminating), a 4-aminobutan-2-one ammonia-lyase, a butenone hydratase, an AKP ammonia-lyase, an acetylacrylate decarboxylase, an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming), an acetoacetyl-CoA reductase (CoA-dependent, alcohol forming), an acetoacetyl-CoA reductase (ketone reducing), a 3-hydroxybutyryl-CoA reductase (aldehyde forming), a 3-hydroxybutyryl-CoA reductase (alcohol forming), a 4-hydroxybutyryl-CoA dehydratase, and a crotonase.
Any combination and any number of the aforementioned enzymes can be introduced into a host microbial organism to complete a 1,3-BDO pathway, as exemplified in FIGS. 1-3. For example, the non-naturally occurring microbial organism can include one, two, three, four, five, up to all of the nucleic acids in a 1,3-BDO pathway, each nucleic acid encoding a 1,3-BDO pathway enzyme. Such nucleic acids can include heterologous nucleic acids, additional copies of existing genes, and gene regulatory elements, as explained further below. The pathways of the non-naturally occurring microbial organisms of the invention are also suitably engineered to be cultured in a substantially anaerobic culture medium.
In some embodiments, the non-naturally occurring microbial organisms having a 1,3-BDO pathway include a set of 1,3-BDO pathway enzymes. A set of 1,3-BDO pathway enzymes represents a group of enzymes that can convert alanine, acetoacetyl-CoA, or 4-hydroxybutyryl-CoA to 1,3-BDO, as show in FIGS. 1-3. Exemplary sets of 1,3-BDO pathway enzymes to convert alanine to 1,3-BDO, according to FIG. 1 include (a) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP dehydrogenase; (3) a 2-amino-4-hydroxypentanoate aminotransferase or oxidoreductase (deaminating); (4) a 2-oxo-4-hydroxypentanoate decarboxylase; and (5) a 3-hydroxybutyraldehyde reductase; (b) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP aminotransferase or oxidoreductase (deaminating); (3) a 2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase; (c) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP aminotransferase or oxidoreductase (deaminating); (3) a 2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase; (d) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase; (e) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase; (f) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one ammonia-lyase; (4) a butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase; and (g) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP ammonia-lyase; (3) an acetylacrylate decarboxylase; (4) a butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase;
Exemplary sets of 1,3-BDO pathway enzymes to convert acetoacetyl-CoA to 1,3-BDO, according to FIG. 2 include (h) (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde reductase (ketone reducing); and (3) a 3-hydroxybutyraldehyde reductase; (i) (1) an acetoacetyl-CoA reductase (CoA dependent, alcohol forming) and (2) a 4-hydroxy-2-butanone reductase; (j) (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (3) a 4-hydroxy-2-butanone reductase; (k) (1) an acetoacetyl-CoA reductase (ketone reducing) and (2) a 3-hydroxybutyryl-CoA reductase (alcohol forming); and (l) (1) an acetoacetyl-CoA reductase (ketone reducing); (2) a 3-hydroxybutyryl-CoA reductase (aldehyde forming); and (3) a 3-hydroxybutyraldehyde reductase;
Exemplary sets of 1,3-BDO pathway enzymes to convert 4-hydroxybutyryl-CoA to 1,3-BDO, according to FIG. 3 include (m) (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; and (3) a 3-hydroxybutyryl-CoA reductase (alcohol forming); and (n) (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; (3) a 3-hydroxybutyryl-CoA reductase (aldehyde forming); and (4) a 3-hydroxybutyraldehyde reductase.
The conversion of alanine to 1,3-BDO can be accomplished by a number of pathways involving about five enzymatic steps as shown in FIG. 1. In the first step of all pathways (Step A), alanine and acetyl-CoA are combined by 2-amino-4-ketopentanoate thiolase, a highly selective enzyme. The product of this reaction, 2-amino-4-oxopentanoate (AKP) can then be transaminated, reduced, decarboxylated or deaminated as shown in FIG. 1.
In one route, AKP converted to 2,4-dioxopentanoate, a 2-keto acid similar in structure to alpha-ketoglutarate, by an aminotransferase or deaminating oxidoreductase (Step B). 2,4-Dioxopentanoate is then converted to 3-oxobutyraldehyde by a 2-ketoacid decarboxylase (Step C). Reduction of the ketone and aldehyde groups to their corresponding alcohols yields 1,3-butanediol. These reductions can occur in either order to form the intermediates 3-hydroxybutyraldehyde (Steps O and P) or 4-hydroxy,2-butanone (Steps D and H).
In another route, the 4-oxo group of AKP is first reduced to a secondary alcohol by AKP dehydrogenase (Step L). The product, 2-amino-4-hydroxypentanoate, is then converted to 2-oxo-4-hydroxypentanoate (Step M). The resulting 2-ketoacid is decarboxylated to 3-hydroxybutyraldehyde (Step N). In the final step of this route, the aldehyde of 3-hydroxybutyraldehyde is reduced to a primary alcohol by 3-hydroxybutyraldehyde reductase, forming 1,3-butanediol (Step P).
Yet another route involves decarboxylation of AKP by an amino acid decarboxylase (Step E). The decarboxylation product, 4-aminobutan-2-one, can either be transaminated or oxidatively deaminated to 3-oxobutyraldehyde (Step K) or deaminated to butenone (Step F). When 3-oxobutyraldehyde is formed, two alcohol-forming reduction steps are used to form 1,3-butanediol, as described previously (Steps O and P, or Steps D and H). The deamination product, butenone, is then hydrolyzed to 4-hydroxy,2-butanone (Step G), which is reduced to 1,3-butanediol by 4-hydroxy-2-butanone reductase (Step H).
Yet another route involves the deamination of AKP to acetylacrylate (Step I). Acetylacrylate is decarboxylated to butenone (Step J), which is then converted to 1,3-butandiol by butenone hydratase (Step G) and 4-hydroxy,2-butanone reductase (Step H).
Based on the routes described above for the production 1,3-BDO from alanine, in some embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP dehydrogenase; (3) a 2-amino-4-hydroxypentanoate aminotransferase or oxidoreductase (deaminating); (4) a 2-oxo-4-hydroxypentanoate decarboxylase; and (5) a 3-hydroxybutyraldehyde reductase. Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one, two, three, four, up to all five of the nucleic acids that encode these enzymes. Where one, two, three, or four exogenous nucleic acids are introduced, such nucleic acids can be any permutation of the five nucleic acids.
In other embodiments non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP aminotransferase or oxidoreductase (deaminating); (3) a 2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase. Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one, two, three, four, up to all five of the nucleic acids that encode these enzymes. Where one, two, three, or four exogenous nucleic acids are introduced, such nucleic acids can be any permutation of the five nucleic acids.
In still other embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP aminotransferase or oxidoreductase (deaminating); (3) a 2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase. Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one, two, three, four, up to all five of the nucleic acids that encode these enzymes. Where one, two, three, or four exogenous nucleic acids are introduced, such nucleic acids can be any permutation of the five nucleic acids.
In yet further embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase. Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one, two, three, four, up to all five of the nucleic acids that encode these enzymes. Where one, two, three, or four exogenous nucleic acids are introduced, such nucleic acids can be any permutation of the five nucleic acids.
In yet still further embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase. Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one, two, three, four, up to all five of the nucleic acids that encode these enzymes. Where one, two, three, or four exogenous nucleic acids are introduced, such nucleic acids can be any permutation of the five nucleic acids.
In still further embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one ammonia-lyase; (4) a butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase. Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one, two, three, four, up to all five of the nucleic acids that encode these enzymes. Where one, two, three, or four exogenous nucleic acids are introduced, such nucleic acids can be any permutation of the five nucleic acids.
In yet still further embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP ammonia-lyase; (3) an acetylacrylate decarboxylase; (4) a butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase. Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one, two, three, four, up to all five of the nucleic acids that encode these enzymes. Where one, two, three, or four exogenous nucleic acids are introduced, such nucleic acids can be any permutation of the five nucleic acids.
FIG. 2 outlines multiple routes for producing 1,3-butanediol from acetoacetyl-CoA. One route through steps A, B and C utilizes (i) CoA-dependent, aldehyde forming acetoacetyl-CoA reductase to convert acetoacetyl-CoA into 3-oxobutyraldehyde (FIG. 2, Step A), (ii) 3-oxobutyraldehyde reductase to reduce 3-oxobutyraldehyde to 3-hydroxybutyraldehyde (FIG. 2, Step B), and (iii) finally, 3-hydroxybutyraldehyde reductase to foam 1,3-butanediol (FIG. 2, Step C).
Alternatively, acetoacetyl-CoA can be reduced via the aldehyde forming acetoacetyl-CoA reductase to form 4-hydroxy,2-butanone (FIG. 2, Step D). 4-hydroxy,2-butanone can also be formed by the reduction of 3-oxobutyraldehyde by the aldehyde reducing 3-oxobutyraldehyde reductase (FIG. 2, Step E). Eventually, 4-hydroxy,2-butanone can be reduced to form 1,3-BDO by 4-hydroxy-2-butanone reductase (FIG. 2, Step F).
Yet another set of 1,3-BDO forming routes rely on the reduction of acetoacetyl-CoA to 3-hydroxybutyryl-CoA by the ketone reducing acetoacetyl-CoA reductase (FIG. 2, Step G). This enzyme reduces the ketone function in acetoacetyl-CoA to a hydroxyl group. 3-hydroxybutyryl-CoA can be reduced by the bifunctional alcohol-forming 3-hydroxybutyryl-CoA reductase to form 1,3-butanediol (FIG. 2, Step I). Alternatively, it can first be reduced to 3-hydroxybutyraldehyde via the aldehyde forming 3-hydroxybutyryl-CoA reductase (Step H) and 3-hydroxybutyraldehyde can then be reduced as shown in Step C.
Based on the routes described above for the production 1,3-BDO from acetoacetyl-CoA, in some embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde reductase (ketone reducing); and (3) a 3-hydroxybutyraldehyde reductase. Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one, two up to all three of the nucleic acids that encode these enzymes. Where one or two exogenous nucleic acids are introduced, such nucleic acids can be any permutation of the three nucleic acids.
In other embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) an acetoacetyl-CoA reductase (CoA dependent, alcohol forming) and (2) a 4-hydroxy-2-butanone reductase. Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one or both of the nucleic acids that encode these enzymes. Where one exogenous nucleic acid is introduced, such a nucleic acid can be either of the two nucleic acids.
In further embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (3) a 4-hydroxy-2-butanone reductase. Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one, two up to all three of the nucleic acids that encode these enzymes. Where one or two exogenous nucleic acids are introduced, such nucleic acids can be any permutation of the three nucleic acids.
In yet further embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) an acetoacetyl-CoA reductase (ketone reducing) and (2) a 3-hydroxybutyryl-CoA reductase (alcohol forming). Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one or both of the nucleic acids that encode these enzymes. Where one exogenous nucleic acid is introduced, such a nucleic acid can be either of the two nucleic acids.
In still further embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) an acetoacetyl-CoA reductase (ketone reducing); (2) a 3-hydroxybutyryl-CoA reductase (aldehyde forming); and (3) a 3-hydroxybutyraldehyde reductase. Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one, two up to all three of the nucleic acids that encode these enzymes. Where one or two exogenous nucleic acids are introduced, such nucleic acids can be any permutation of the three nucleic acids.
4-hydroxybutyryl-CoA is an important starting metabolite from which a number of industrially useful compounds can be made. Although 4-hydroxybutyryl-CoA is not a highly common central metabolite, methods for engineering strains that synthesize 4-hydroxybutyryl-CoA have been described in Burk et al. (US 20090075351). An exemplary method involves synthesizing 4-hydroxybutyryl-CoA from succinyl-CoA by employing genes encoding succinic semialdehyde dehydrogenase (CoA-dependent), 4-hydroxybutyrate dehydrogenase, 4-hydroxybutyrate kinase, and phosphotransbutyrylase activities.
The first step in the pathway involves the dehydration of 4-hydroxybutyryl-CoA (Step A, FIG. 3) followed by the hydration of crotonoyl-CoA to form 3-hydroxybutyryl-CoA (Step B). 3-hydroxybutyryl-CoA then undergoes two reduction steps to form 1,3-butanediol carried out by either two enzymes (Steps C and D) or a single dual-function enzyme (Step E).
Thus, in some embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; and (3) a 3-hydroxybutyryl-CoA reductase (alcohol forming). Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one, two up to all three of the nucleic acids that encode these enzymes. Where one or two exogenous nucleic acids are introduced, such nucleic acids can be any permutation of the three nucleic acids.
In other embodiments, the non-naturally occurring microbial organism has a set of 1,3-BDO pathway enzymes that includes (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; (3) a 3-hydroxybutyryl-CoA reductase (aldehyde forming); and (4) a 3-hydroxybutyraldehyde reductase. Any number of nucleic acids encoding these enzymes can be introduced into a host microbial organism including one, two, three up to all four of the nucleic acids that encode these enzymes. Where one, two, or three exogenous nucleic acids are introduced, such nucleic acids can be any permutation of the four nucleic acids.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of alanine to 2-amino-4-oxopentanoate, 2-amino-4-oxopentanoate to 2-amino-4-hydroxypentanoate, 2-amino-4-hydroxypentanoate to 2-oxo-4-hydroxypentanoate, 2-oxo-4-hydroxypentanoate to 3-hydroxybutyraldehyde, and 3-hydroxybutyraldehyde to 1,3-BDO.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of alanine to 2-amino-4-oxopentanoate, 2-amino-4-oxopentanoate to 2,4-dioxopentanoate, 2,4-dioxopentanoate to 3-oxobutyraldehyde, 3-oxobutyraldehyde to 3-hydroxybutyraldehyde, and 3-hydroxybutyraldehyde to 1,3-BDO.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of alanine to 2-amino-4-oxopentanoate, 2-amino-4-oxopentanoate to 2,4-dioxopentanoate, 2,4-dioxopentanoate to 3-oxobutyraldehyde, 3-oxobutyraldehyde to 4-hydroxy-2-butanone, and 4-hydroxy-2-butanone to 1,3-BDO.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of alanine to 2-amino-4-oxopentanoate, 2-amino-4-oxopentanoate to 4-aminobutan-2-one, 4-aminobutan-2-one to 3-oxobutyraldehyde, 3-oxobutyraldehyde to 3-hydroxybutyraldehyde, and 3-hydroxybutyraldehyde to 1,3-BDO.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of alanine to 2-amino-4-oxopentanoate, 2-amino-4-oxopentanoate to 4-aminobutan-2-one, 4-aminobutan-2-one to 3-oxobutyraldehyde, 3-oxobutyraldehyde to 4-hydroxy-2-butanone, and 4-hydroxy-2-butanone to 1,3-BDO.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of alanine to 2-amino-4-oxopentanoate, 2-amino-4-oxopentanoate to 4-aminobutan-2-one, 4-aminobutan-2-one to butenone, butenone to 4-hydroxy-2-butanone, and 4-hydroxy-2-butanone to 1,3-BDO.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of alanine to 2-amino-4-oxopentanoate, 2-amino-4-oxopentanoate to acetylacrylate, acetylacrylate to butenone, butenone to 4-hydroxy-2-butanone, and 4-hydroxy-2-butanone to 1,3-BDO.
Thus, the invention provides a non-naturally occurring microbial organism containing at least one exogenous nucleic acid encoding an enzyme or protein, where the enzyme or protein converts the substrates and products of a 1,3-BDO pathway converting alanine to 1,3-BDO, as exemplified by the pathways shown in FIG. 1.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of acetoacetyl-CoA to 4-hydroxy-2-butanone, and 4-hydroxy-2-butanone to 1,3-BDO.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of acetoacetyl-CoA to 3-oxobutyraldehyde, 3-oxobutyraldehyde to 4-hydroxy-2-butanone, and 4-hydroxy-2-butanone to 1,3-BDO.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3 BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of acetoacetyl-CoA to 3-oxobutyraldehyde, 3-oxobutyraldehyde to 3-hydroxybutryaldehyde, and 3-hydroxybutryaldehyde to 1,3-BDO.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of acetoacetyl-CoA to 3-hydroxybutyryl-CoA, 3-hydroxybutyryl-CoA to 3-hydroxybutryaldehyde, and 3-hydroxybutryaldehyde to 1,3-BDO.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of acetoacetyl-CoA to 3-hydroxybutyryl-CoA, and 3-hydroxybutyryl-CoA to 1,3-BDO.
Thus, the invention provides a non-naturally occurring microbial organism containing at least one exogenous nucleic acid encoding an enzyme or protein, where the enzyme or protein converts the substrates and products of a 1,3-BDO pathway converting acetoacetyl-CoA to 1,3-BDO, as exemplified by the pathways shown in FIG. 2.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of 4-hydroxybutyryl-CoA to crotonoyl-CoA, crotonoyl-CoA to 3-hydroxybutyryl-CoA, 3-hydroxybutyryl-CoA to 3-hydroxybutryaldehyde, and 3-hydroxybutryaldehyde to 1,3-BDO.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-BDO pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of 4-hydroxybutyryl-CoA to crotonoyl-CoA, crotonoyl-CoA to 3-hydroxybutyryl-CoA, and 3-hydroxybutyryl-CoA to 1,3-BDO.
Thus, the invention provides a non-naturally occurring microbial organism containing at least one exogenous nucleic acid encoding an enzyme or protein, where the enzyme or protein converts the substrates and products of a 1,3-BDO pathway, the pathway converting 4-hydroxybutyryl-CoA to 1,3-BDO, as exemplified by the pathways shown in FIG. 3.
This invention is also directed, in part to engineered biosynthetic pathways to improve carbon flux through a central metabolism intermediate en route to 1,3-butanediol. The present invention provides non-naturally occurring microbial organisms having one or more exogenous genes encoding enzymes that can catalyze various enzymatic transformations en route to 1,3-butanediol. In some embodiments, these enzymatic transformations are part of the reductive tricarboxylic acid (RTCA) cycle and are used to improve product yields, including but not limited to, from carbohydrate-based carbon feedstock.
In numerous engineered pathways, realization of maximum product yields based on carbohydrate feedstock is hampered by insufficient reducing equivalents or by loss of reducing equivalents and/or carbon to byproducts. In accordance with some embodiments, the present invention increases the yields of 1,3-butanediol by (i) enhancing carbon fixation via the reductive TCA cycle, and/or (ii) accessing additional reducing equivalents from gaseous carbon sources and/or syngas components such as CO, CO₂, and/or H₂. In addition to syngas, other sources of such gases include, but are not limited to, the atmosphere, either as found in nature or generated.
The CO₂-fixing reductive tricarboxylic acid (RTCA) cycle is an endergenic anabolic pathway of CO₂assimilation which uses reducing equivalents and ATP (FIGS. 8 a and 9 a). One turn of the RTCA cycle assimilates two moles of CO₂into one mole of acetyl-CoA, or four moles of CO₂into one mole of oxaloacetate. This additional availability of acetyl-CoA improves the maximum theoretical yield of product molecules derived from carbohydrate-based carbon feedstock. Exemplary carbohydrates include but are not limited to glucose, sucrose, xylose, arabinose and glycerol.
In some embodiments, the reductive TCA cycle, coupled with carbon monoxide dehydrogenase and/or hydrogenase enzymes (FIGS. 8 a and 9 a insert), can be employed to allow syngas, CO₂, CO, H₂, and/or other gaseous carbon source utilization by microorganisms. Synthesis gas (syngas), in particular is a mixture of primarily H₂and CO, sometimes including some amounts of CO₂, that can be obtained via gasification of any organic feedstock, such as coal, coal oil, natural gas, biomass, or waste organic matter. Numerous gasification processes have been developed, and most designs are based on partial oxidation, where limiting oxygen avoids full combustion, of organic materials at high temperatures (500-1500° C.) to provide syngas as a 0.5:1-3:1 H₂/CO mixture. In addition to coal, biomass of many types has been used for syngas production and represents an inexpensive and flexible feedstock for the biological production of renewable chemicals and fuels. Carbon dioxide can be provided from the atmosphere or in condensed from, for example, from a tank cylinder, or via sublimation of solid CO₂. Similarly, CO and hydrogen gas can be provided in reagent form and/or mixed in any desired ratio. Other gaseous carbon forms can include, for example, methanol or similar volatile organic solvents.
The components of synthesis gas and/or other carbon sources can provide sufficient CO₂, reducing equivalents, and ATP for the reductive TCA cycle to operate. One turn of the RICA cycle assimilates two moles of CO₂into one mole of acetyl-CoA and requires 2 ATP and 4 reducing equivalents. CO and/or H₂can provide reducing equivalents by means of carbon monoxide dehydrogenase and hydrogenase enzymes, respectively. Reducing equivalents can come in the form of NADH, NADPH, FADH, reduced quinones, reduced ferredoxins, thioredoxins, and reduced flavodoxins. The reducing equivalents, particularly NADH, NADPH, and reduced ferredoxin, can serve as cofactors for the RTCA cycle enzymes, for example, malate dehydrogenase, fumarate reductase, alpha-ketoglutarate:ferredoxin oxidoreductase (alternatively known as 2-oxoglutarate:ferredoxin oxidoreductase, alpha-ketoglutarate synthase, or 2-oxoglutarate synthase), pyruvate:ferredoxin oxidoreductase and isocitrate dehydrogenase. The electrons from these reducing equivalents can alternatively pass through an ion-gradient producing electron transport chain where they are passed to an acceptor such as oxygen, nitrate, oxidized metal ions, protons, or an electrode. The ion-gradient can then be used for ATP generation via an ATP synthase or similar enzyme.
In some embodiments, a non-naturally occurring microbial organism has a 1,3-butanediol pathway and includes at least one exogenous nucleic acid encoding a 1,3-butanediol pathway enzyme expressed in a sufficient amount to produce 1,3-butanediol; wherein the non-naturally occurring microbial organism further includes:
A non-naturally occurring microbial organism having a 1,3-butanediol pathway, wherein said microbial organism comprises at least one exogenous nucleic acid encoding a 1,3-butanediol pathway enzyme expressed in a sufficient amount to produce 1,3-butanediol; said non-naturally occurring microbial organism further comprising:
(i) a reductive TCA pathway, wherein said microbial organism comprises at least one exogenous nucleic acid encoding a reductive TCA pathway enzyme selected from the group consisting of an ATP-citrate lyase, citrate lyase, a fumarate reductase, and an alpha-ketoglutarate:ferredoxin oxidoreductase;
(ii) a reductive TCA pathway, wherein said microbial organism comprises at least one exogenous nucleic acid encoding a reductive TCA pathway enzyme selected from the group consisting of a pyruvate:ferredoxin oxidoreductase, a phosphoenolpyruvate carboxylase, a phosphoenolpyruvate carboxykinase, a CO dehydrogenase, and an H₂hydrogenase; or
(iii) at least one exogenous nucleic acid encodes an enzyme selected from the group consisting of a CO dehydrogenase, an H₂hydrogenase, and combinations thereof;
wherein said 1,3-butanediol pathway comprises a pathway selected from the group consisting of:
(a) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP dehydrogenase; (3) a 2-amino-4-hydroxypentanoate aminotransferase or oxidoreductase (deaminating); (4) a 2-oxo-4-hydroxypentanoate decarboxylase; and (5) a 3-hydroxybutyraldehyde reductase;
(b) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP aminotransferase or oxidoreductase (deaminating); (3) a 2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase;
(c) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP aminotransferase or oxidoreductase (deaminating); (3) a 2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase;
(d) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase;
(e) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase;
(f) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one ammonia-lyase; (4) a butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase;
(g) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP ammonia-lyase; (3) an acetylacrylate decarboxylase; (4) a butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase;
(h) (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde reductase (ketone reducing); and (3) a 3-hydroxybutyraldehyde reductase;
(i) (1) an acetoacetyl-CoA reductase (CoA dependent, alcohol forming) and (2) a 4-hydroxy-2-butanone reductase;
(j) (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (3) a 4-hydroxy-2-butanone reductase;
(k) (1) an acetoacetyl-CoA reductase (ketone reducing) and (2) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(l) (1) an acetoacetyl-CoA reductase (ketone reducing); (2) a 3-hydroxybutyryl-CoA reductase (aldehyde forming); and (3) a 3-hydroxybutyraldehyde reductase;
(m) (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; and (3) a 3-hydroxybutyryl-CoA reductase (alcohol forming); and
(n) (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; (3) a 3-hydroxybutyryl-CoA reductase (aldehyde forming); and (4) a 3-hydroxybutyraldehyde reductase;
(o) (1) a succinyl-CoA transferase, a succinyl-CoA synthetase or a succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyrate kinase, (5) a phosphotrans-4-hydroxybutyrylase, (6) a 4-hydroxybutyryl-CoA dehydratase, (7) a crotonase, (8) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (9) a 3-hydroxybutanal reductase;
(p) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase; (6) a crotonase, (7) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (8) a 3-hydroxybutanal reductase;
(q) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (7) a 3-hydroxybutanal reductase;
(r) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, and (7) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(s) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, and (6) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(t) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (8) a 3-hydroxybutyrate reductase;
(u) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (7) a 3-hydroxybutyrate reductase.
(v) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (8) a 3-hydroxybutanal reductase;
(w) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), (7) a 3-hydroxybutanal reductase;
(x) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, and (7) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(y) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, and (6) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(z) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (8) a 3-hydroxybutyrate reductase;
(aa) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (7) a 3-hydroxybutyrate reductase;
(bb) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (5) a 4-hydroxybutyrate kinase, (6) a pPhosphotrans-4-hydroxybutyrylase, (7) a 4-hydroxybutyryl-CoA dehydratase, (8) a crotonase, and (9) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(cc) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyrate kinase, (5) a phosphotrans-4-hydroxybutyrylase, (6) a 4-hydroxybutyryl-CoA dehydratase, (7) a crotonase, (8) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (9) a 3-hydroxybutyrate reductase;
(dd) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (8) a 3-hydroxybutanal reductase;
(ee) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, and (7) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(ff) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (8) a 3-hydroxybutyrate reductase;
(gg) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyryl-CoA transferase, or 4-hydroxybutyryl-CoA synthetase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (8) a 3-hydroxybutanal reductase;
(hh) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde limning), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, and (7) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(ii) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, (8) a 3-hydroxybutyrate reductase;
(jj) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (7) a 3-hydroxybutanal reductase;
(kk) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, and (6) a 3-hydroxybutyryl-CoA reductase (alcohol forming); and
(ll) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (8) a 3-hydroxybutyrate reductase.
In some embodiments, the non-naturally occurring microbial organism (e.g., having pathway (i)) further includes an exogenous nucleic acid encoding an enzyme selected from a pyruvate:ferredoxin oxidoreductase, an aconitase, an isocitrate dehydrogenase, a succinyl-CoA synthetase, a succinyl-CoA transferase, a fumarase, a malate dehydrogenase, an acetate kinase, a phosphotransacetylase, an acetyl-CoA synthetase, an NAD(P)H:ferredoxin oxidoreductase, ferredoxin, and combinations thereof.
In some embodiments, the non-naturally occurring microbial organism (e.g., having pathway (ii)) further includes an exogenous nucleic acid encoding an enzyme selected from an aconitase, an isocitrate dehydrogenase, a succinyl-CoA synthetase, a succinyl-CoA transferase, a fumarase, a malate dehydrogenase, and combinations thereof.
In some embodiments, the non-naturally occurring microbial organism includes two, three, four, five, six, seven, eight or nine exogenous nucleic acids, each encoding a 1,3-BDO pathway enzyme.
In some embodiments, the non-naturally occurring microbial organism comprises exogenous nucleic acids encoding each of the enzymes of at least one of the 1,3-butanediol pathways selected from the group consisting of (a)-(ll).
In some embodiments, the non-naturally occurring microbial organism has at least one exogenous nucleic acid is a heterologous nucleic acid.
In some embodiments, the non-naturally occurring microbial organism is in a substantially anaerobic culture medium.
The reductive TCA cycle was first reported in the green sulfur photosynthetic bacterium Chlorobium limicola (Evans et al., Proc. Natl. Acad. Sci. U.S.A. 55:928-934 (1966)). Similar pathways have been characterized in some prokaryotes (proteobacteria, green sulfur bacteria and thermophillic Knallgas bacteria) and sulfur-dependent archaea (Hugler et al., J. Bacteriol. 187:3020-3027 (2005; Hugler et al., Environ. Microbiol. 9:81-92 (2007). In some cases, reductive and oxidative (Krebs) TCA cycles are present in the same organism (Hugler et al., supra (2007); Siebers et al., J. Bacteriol. 186:2179-2194 (2004)). Some methanogens and obligate anaerobes possess incomplete oxidative or reductive TCA cycles that may function to synthesize biosynthetic intermediates (Ekiel et al., J. Bacteriol. 162:905-908 (1985); Wood et al., FEMS Microbiol. Rev. 28:335-352 (2004)).
The key carbon-fixing enzymes of the reductive TCA cycle are alpha-ketoglutarate:ferredoxin oxidoreductase, pyruvate:ferredoxin oxidoreductase and isocitrate dehydrogenase. Additional carbon may be fixed during the conversion of phosphoenolpyruvate to oxaloacetate by phosphoenolpyruvate carboxylase or phosphoenolpyruvate carboxykinase or during the conversion of pyruvate to malate by malic enzyme and during the conversion of pyruvate to oxaloacetate by pyruvate carboxylase.
Many of the enzymes in the TCA cycle are reversible and can catalyze reactions in the reductive and oxidative directions. However, some TCA cycle reactions are irreversible in vivo and thus different enzymes are used to catalyze these reactions in the directions required for the reverse TCA cycle. These reactions are: (1) conversion of citrate to oxaloacetate and acetyl-CoA, (2) conversion of fumarate to succinate, and (3) conversion of succinyl-CoA to alpha-ketoglutarate. In the TCA cycle, citrate is formed from the condensation of oxaloacetate and acetyl-CoA. The reverse reaction, cleavage of citrate to oxaloacetate and acetyl-CoA, is ATP-dependent and catalyzed by ATP-citrate lyase, or citryl-CoA synthetase and citryl-CoA lyase. Alternatively, citrate lyase can be coupled to acetyl-CoA synthetase, an acetyl-CoA transferase, or phosphotransacetylase and acetate kinase to form acetyl-CoA and oxaloacetate from citrate. The conversion of succinate to fumarate is catalyzed by succinate dehydrogenase while the reverse reaction is catalyzed by fumarate reductase. In the TCA cycle succinyl-CoA is formed from the NAD(P)⁺ dependent decarboxylation of alpha-ketoglutarate by the alpha-ketoglutarate dehydrogenase complex. The reverse reaction is catalyzed by alpha-ketoglutarate:ferredoxin oxidoreductase.
An organism capable of utilizing the reverse tricarboxylic acid cycle to enable production of acetyl-CoA-derived products on 1) CO, 2) CO₂and H₂, 3) CO and CO₂, 4) synthesis gas comprising CO and H₂, and 5) synthesis gas or other gaseous carbon sources comprising CO, CO₂, and H₂can include any of the following enzyme activities: ATP-citrate lyase, citrate lyase, aconitase, isocitrate dehydrogenase, alpha-ketoglutarate:ferredoxin oxidoreductase, succinyl-CoA synthetase, succinyl-CoA transferase, fumarate reductase, fumarase, malate dehydrogenase, acetate kinase, phosphotransacetylase, acetyl-CoA synthetase, acetyl-CoA transferase, pyruvate:ferredoxin oxidoreductase, NAD(P)H:ferredoxin oxidoreductase, carbon monoxide dehydrogenase, hydrogenase, and ferredoxin (see FIGS. 8A and 9A). Enzymes and the corresponding genes required for these activities are described herein below.
Carbon from syngas or other gaseous carbon sources can be fixed via the reverse TCA cycle and components thereof. Specifically, the combination of certain carbon gas-utilization pathway components with the pathways for formation of 1,3-butanediol from acetyl-CoA results in high yields of these products by providing an efficient mechanism for fixing the carbon present in carbon dioxide, fed exogenously or produced endogenously from CO, into acetyl-CoA.
In some embodiments, a 1,3-butanediol pathway in a non-naturally occurring microbial organism of the invention can utilize any combination of (1) CO, (2) CO₂, (3) H₂, or mixtures thereof to enhance the yields of biosynthetic steps involving reduction, including addition to driving the reductive TCA cycle.
In some embodiments a non-naturally occurring microbial organism having a 1,3-butanediol pathway includes at least one exogenous nucleic acid encoding a reductive TCA pathway enzyme. The at least one exogenous nucleic acid is selected from an ATP-citrate lyase, citrate lyase, a fumarate reductase, an isocitrate dehydrogenase, an aconitase, an isocitrate dehydrogenase, and an alpha-ketoglutarate:ferredoxin oxidoreductase; and at least one exogenous enzyme selected from a carbon monoxide dehydrogenase, a hydrogenase, a NAD(P)H:ferredoxin oxidoreductase, and a ferredoxin, expressed in a sufficient amount to allow the utilization of (1) CO, (2) CO₂, (3) H₂, (4) CO₂and H₂, (5) CO and CO₂, (6) CO and H₂, or (7) CO, CO₂, and H₂.
In some embodiments a method includes culturing a non-naturally occurring microbial organism having a 1,3-butanediol pathway also comprising at least one exogenous nucleic acid encoding a reductive TCA pathway enzyme. The at least one exogenous nucleic acid is selected from an ATP-citrate lyase, citrate lyase, a fumarate reductase, an isocitrate dehydrogenase, an aconitase, an isocitrate dehydrogenase, and an alpha-ketoglutarate:ferredoxin oxidoreductase. Additionally, such an organism can also include at least one exogenous enzyme selected from a carbon monoxide dehydrogenase, a hydrogenase, a NAD(P)H:ferredoxin oxidoreductase, and a ferredoxin, expressed in a sufficient amount to allow the utilization of (1) CO, (2) CO₂, (3) H₂, (4) CO₂and H₂, (5) CO and CO₂, (6) CO and H₂, or (7) CO, CO₂, and H₂to produce a product.
In some embodiments a non-naturally occurring microbial organism having a 1,3-butanediol pathway further includes at least one exogenous nucleic acid encoding a reductive TCA pathway enzyme expressed in a sufficient amount to enhance carbon flux through acetyl-CoA. The at least one exogenous nucleic acid is selected from an ATP-citrate lyase, citrate lyase, a fumarate reductase, an isocitrate dehydrogenase, an aconitase, an isocitrate dehydrogenase, a pyruvate:ferredoxin oxidoreductase and an alpha-ketoglutarate:ferredoxin oxidoreductase.
In some embodiments a non-naturally occurring microbial organism having a 1,3-butanediol pathway includes at least one exogenous nucleic acid encoding an enzyme expressed in a sufficient amount to enhance the availability of reducing equivalents in the presence of carbon monoxide and/or hydrogen, thereby increasing the yield of redox-limited products via carbohydrate-based carbon feedstock. The at least one exogenous nucleic acid is selected from a carbon monoxide dehydrogenase, a hydrogenase, an NAD(P)H:ferredoxin oxidoreductase, and a ferredoxin. In some embodiments, the present invention provides a method for enhancing the availability of reducing equivalents in the presence of carbon monoxide or hydrogen thereby increasing the yield of redox-limited products via carbohydrate-based carbon feedstock, such as sugars or gaseous carbon sources, the method includes culturing this non-naturally occurring microbial organism under conditions and for a sufficient period of time to produce 1,3-butanediol.
In some embodiments, the non-naturally occurring microbial organism having a 1,3-butanediol pathway includes two exogenous nucleic acids each encoding a reductive TCA pathway enzyme. In some embodiments, the non-naturally occurring microbial organism having a 1,3-butanediol pathway includes three exogenous nucleic acids each encoding a reductive TCA pathway enzyme. In some embodiments, the non-naturally occurring microbial organism includes three exogenous nucleic acids encoding an ATP-citrate lyase, a fumarate reductase, and an alpha-ketoglutarate:ferredoxin oxidoreductase. In some embodiments, any one of the three exogenous nucleic acids can be an isocitrate dehydrogenase. In some embodiments, the non-naturally occurring microbial organism includes three exogenous nucleic acids encoding a citrate lyase, a fumarate reductase, and an alpha-ketoglutarate:ferredoxin oxidoreductase. In some embodiments, the non-naturally occurring microbial organism includes four exogenous nucleic acids encoding a pyruvate:ferredoxin oxidoreductase; a phosphoenolpyruvate carboxylase or a phosphoenolpyruvate carboxykinase, a CO dehydrogenase; and an H2 hydrogenase. In some embodiments, the non-naturally occurring microbial organism includes two exogenous nucleic acids encoding a CO dehydrogenase and an H2 hydrogenase.
In some embodiments, the non-naturally occurring microbial organisms having a 1,3-butanediol pathway further include an exogenous nucleic acid encoding an enzyme selected from a pyruvate:ferredoxin oxidoreductase, an aconitase, an isocitrate dehydrogenase, a succinyl-CoA synthetase, a succinyl-CoA transferase, a fumarase, a malate dehydrogenase, an acetate kinase, a phosphotransacetylase, an acetyl-CoA synthetase, an NAD(P)H:ferredoxin oxidoreductase, and combinations thereof.
In some embodiments, the non-naturally occurring microbial organism having a 1,3-butanediol pathway further includes an exogenous nucleic acid encoding an enzyme selected from carbon monoxide dehydrogenase, acetyl-CoA synthase, ferredoxin, NAD(P)H:ferredoxin oxidoreductase and combinations thereof.
In some embodiments, the non-naturally occurring microbial organism having a 1,3-butanediol pathway utilizes a carbon feedstock selected from (1) CO, (2) CO₂, (3) CO₂and H₂, (4) CO and H₂, or (5) CO, CO₂, and H₂. In some embodiments, the non-naturally occurring microbial organism having a 1,3-butanediol pathway utilizes hydrogen for reducing equivalents. In some embodiments, the non-naturally occurring microbial organism having a 1,3-butanediol pathway utilizes CO for reducing equivalents. In some embodiments, the non-naturally occurring microbial organism having a 1,3-butanediol pathway utilizes combinations of CO and hydrogen for reducing equivalents.
In some embodiments, the non-naturally occurring microbial organism having a 1,3-butanediol pathway further includes one or more nucleic acids encoding an enzyme selected from a phosphoenolpyruvate carboxylase, a phosphoenolpyruvate carboxykinase, a pyruvate carboxylase, and a malic enzyme.
In some embodiments, the non-naturally occurring microbial organism having a 1,3-butanediol pathway further includes one or more nucleic acids encoding an enzyme selected from a malate dehydrogenase, a fumarase, a fumarate reductase, a succinyl-CoA synthetase, and a succinyl-CoA transferase.
In some embodiments, the non-naturally occurring microbial organism having a 1,3-butanediol pathway further includes at least one exogenous nucleic acid encoding a citrate lyase, an ATP-citrate lyase, a citryl-CoA synthetase, a citryl-CoA lyase, an aconitase, an isocitrate dehydrogenase, a succinyl-CoA synthetase, a succinyl-CoA transferase, a fumarase, a malate dehydrogenase, an acetate kinase, a phosphotransacetylase, an acetyl-CoA synthetase, an acetyl-CoA transferase, and a ferredoxin.
It is understood by those skilled in the art that the above-described pathways for increasing product yield can be combined with any of the pathways disclosed herein, including those pathways depicted in the figures. One skilled in the art will understand that, depending on the pathway to a desired product and the precursors and intermediates of that pathway, a particular pathway for improving product yield, as discussed herein above and in the examples, or combination of such pathways, can be used in combination with a pathway to a desired product to increase the yield of that product or a pathway intermediate.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-butanediol pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of pyruvate to alanine, alanine to 2-amino-4-oxopentanoate, 2-amino-4-oxopentanoate to 2-amino-4-hydroxypentanoate, 2-amino-4-oxopentanoate to 2,4-dioxopentanoate, 2-amino-4-oxopentanoate to 4-aminobutan-2-one, 2-amino-4-oxopentanoate to acetylacrylate, 2-amino-4-hydroxypentanoate to 2-oxo-4-hydroxypentanoate, 2-oxo-4-hydroxypentanoate to 3-hydroxybutyraldehyde, 2,4-dioxopentanoate to 3-oxobutyraldehyde, 3-oxobutyraldehyde to 3-hydroxybutryaldehyde, 3-oxobutyraldehdye to 4-hydroxy-2-butanone, 4-aminobutan-2-one to 3-oxobutyraldehyde, 4-aminobutan-2-one to butanone, butanone to 4-hydroxy-2-butanone and acetylacrylate to butenone. One skilled in the art will understand that these are merely exemplary and that any of the substrate-product pairs disclosed herein suitable to produce a desired product and for which an appropriate activity is available for the conversion of the substrate to the product can be readily determined by one skilled in the art based on the teachings herein. Thus, the invention provides a non-naturally occurring microbial organism containing at least one exogenous nucleic acid encoding an enzyme or protein, where the enzyme or protein converts the substrates and products of a 1,3-butanediol pathway, such as that shown in FIG. 8B.
In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a 1,3-butanediol pathway, wherein the non-naturally occurring microbial organism comprises at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of succinate to succinyl-CoA, succinate to succinic semialdehyde, succinyl-CoA to succinic semialdehyde, alpha-ketoglutarate to succinic semialdehyde, succinyl-CoA to 4-hydroxybutyrate, succinic semialdehyde to 4-hydroxybutyrate, 4-hydroxybutyrate to 4-hydroxybutyryl phosphate, 4-hydroxybutyrate to 4-hydroxybutyryl-CoA, 4-hydroxybutyryl phosphate to 4-hydroxybutyryl CoA, 4-hydroxybutyryl-CoA to crotonyl-CoA, crotonyl-CoA to 3-hydroxybutyryl-CoA, 3-hydroxybutyryl-CoA to 3-hydroxybutyrate, 3-hydroxybutyrate to 1,3-butanediol, 3-hydroxybutyryl-CoA to 1,3-butanediol, 3-hydroxybutyryl-CoA to 3-hydroxybutanal, 3-hydroxybutanal to 1,3-butanediol. One skilled in the art will understand that these are merely exemplary and that any of the substrate-product pairs disclosed herein suitable to produce a desired product and for which an appropriate activity is available for the conversion of the substrate to the product can be readily determined by one skilled in the art based on the teachings herein. Thus, the invention provides a non-naturally occurring microbial organism containing at least one exogenous nucleic acid encoding an enzyme or protein, where the enzyme or protein converts the substrates and products of a 1,3-butanediol pathway, such as that shown in FIG. 9B.
While generally described herein as a microbial organism that contains a 1,3-butanediol pathway, it is understood that the invention additionally provides a non-naturally occurring microbial organism comprising at least one exogenous nucleic acid encoding a 1,3-butanediol pathway enzyme expressed in a sufficient amount to produce an intermediate of a 1,3-butanediol pathway. For example, as disclosed herein, a 1,3-butanediol pathway is exemplified in FIGS. 1-3, 8A/B, and 9A/B. Therefore, in addition to a microbial organism containing a 1,3-butanediol pathway that produces 1,3-butanediol, the invention additionally provides a non-naturally occurring microbial organism comprising at least one exogenous nucleic acid encoding a 1,3-butanediol pathway enzyme, where the microbial organism produces a 1,3-butanediol pathway intermediate, for example, alanine, 2-amino-4-pentanoate, 2-amino-4-hydroxypentanoate, 2-oxo-4-hydroxypentanoate, 3-hydroxybutyraldehyde, 2,4-dioxopentanoate, 3-oxobutyraldehyde, 4-aminobutan-2-one, acetylacrylate, butanone, 4-hydroxy-2-butanone, succinic semialdehyde, 4-hydroxybutyrate, 4-hydroxybutyryl phosphate, 4-hydroxybutyryl-CoA, crotonyl-CoA, 3-hydroxybutyryl-CoA, 3-hydroxybutyrate, and 3-hydroxybutanal.
It is understood that any of the pathways disclosed herein, as described in the Examples and exemplified in the Figures, including the pathways of FIGS. 1-3, 8A/B, and 9A/B can be utilized to generate a non-naturally occurring microbial organism that produces any pathway intermediate or product, as desired. As disclosed herein, such a microbial organism that produces an intermediate can be used in combination with another microbial organism expressing downstream pathway enzymes to produce a desired product. However, it is understood that a non-naturally occurring microbial organism that produces a 1,3-butanediol pathway intermediate can be utilized to produce the intermediate as a desired product.
Successfully engineering any of these pathways entails identifying an appropriate set of enzymes with sufficient activity and specificity, cloning their corresponding genes into a production host, optimizing fermentation conditions, and assaying for product formation following fermentation. To engineer a production host for the production of any of the aforementioned products, one or more exogenous DNA sequence(s) can be expressed in microorganisms. In addition, the microorganisms can have endogenous gene(s) functionally deleted. These modifications will enable the production of 1,3-BDO using renewable feedstocks.
Below, are described a number of biochemically characterized genes capable of encoding enzymes that catalyze each of the steps shown in FIGS. 1, 2 3, 8B, and 9B. Although we describe this method for E. coli, one skilled in the art can apply these teachings to essentially any other organism. Specifically, genes are listed that are native to E. coli in addition to genes in other organisms that can be applied to catalyze the appropriate transformations when properly cloned and expressed.
The invention is described herein with general reference to the metabolic reaction, reactant or product thereof, or with specific reference to one or more nucleic acids or genes encoding an enzyme associated with or catalyzing, or a protein associated with, the referenced metabolic reaction, reactant or product. Unless otherwise expressly stated herein, those skilled in the art will understand that reference to a reaction also constitutes reference to the reactants and products of the reaction. Similarly, unless otherwise expressly stated herein, reference to a reactant or product also references the reaction, and reference to any of these metabolic constituents also references the gene or genes encoding the enzymes that catalyze or proteins involved in the referenced reaction, reactant or product. Likewise, given the well known fields of metabolic biochemistry, enzymology and genomics, reference herein to a gene or encoding nucleic acid also constitutes a reference to the corresponding encoded enzyme and the reaction it catalyzes or a protein associated with the reaction as well as the reactants and products of the reaction.
As disclosed herein, intermediates en route to 1,3-butanediol can be carboxylic acids or CoA esters thereof, such as 4-hydroxy butyrate, 3-hydroxybutyrate, their CoA esters, as well as crotonyl-CoA. Any carboxylic acid intermediate can occur in various ionized forms, including fully protonated, partially protonated, and fully deprotonated forms. Accordingly, the suffix “-ate,” or the acid form, can be used interchangeably to describe both the free acid form as well as any deprotonated form, in particular since the ionized form is known to depend on the pH in which the compound is found. It is understood that carboxylate intermediates includes ester forms of carboxylate products or pathway intermediates, such as O-carboxylate and S-carboxylate esters. O- and S-carboxylates can include lower alkyl, that is C1 to C6, branched or straight chain carboxylates. Some such O- or S-carboxylates include, without limitation, methyl, ethyl, n-propyl, n-butyl, i-propyl, sec-butyl, and tert-butyl, pentyl, hexyl O- or S-carboxylates, any of which can further possess an unsaturation, providing for example, propenyl, butenyl, pentyl, and hexenyl O- or S-carboxylates. O-carboxylates can be the product of a biosynthetic pathway. Exemplary O-carboxylates accessed via biosynthetic pathways can include, without limitation, methyl 4-hydroxybutyrate, methyl-3-hydroxybutyrate, ethyl 4-hydroxybutyrate, ethyl 3-hydroxybutyrate, n-propyl 4-hydroxybutyrate, and n-propyl 3-hydroxybutyrate. Other biosynthetically accessible O-carboxylates can include medium to long chain groups, that is C7-C22, O-carboxylate esters derived from fatty alcohols, such heptyl, octyl, nonyl, decyl, undecyl, lauryl, tridecyl, myristyl, pentadecyl, cetyl, palmitolyl, heptadecyl, stearyl, nonadecyl, arachidyl, heneicosyl, and behenyl alcohols, any one of which can be optionally branched and/or contain unsaturations. O-carboxylate esters can also be accessed via a biochemical or chemical process, such as esterification of a free carboxylic acid product or transesterification of an O- or S-carboxylate. S-carboxylates are exemplified by CoA S-esters, cysteinyl S-esters, alkylthioesters, and various aryl and heteroaryl thioesters.
All transformations depicted in FIGS. 1-3, 8B and 9B fall into the 8 general categories of transformations shown in Table 1. Below is described a number of biochemically characterized genes in each category. Specifically listed are genes that can be applied to catalyze the appropriate transformations in FIGS. 1-3, 8B, and 9B when properly cloned and expressed. Exemplary genes for each of the steps in FIGS. 1-3, 8B and 9B are provided further below in Tables 35-37.
Table 1 shows the enzyme types useful to convert common central metabolic intermediates into 1,3-butanediol. The first three digits of each label correspond to the first three Enzyme Commission number digits which denote the general type of transformation independent of substrate specificity.

TABLE 1

LABEL	FUNCTION

1.1.1.a	Oxidoreductase (ketone to hydroxyl or aldehyde to alcohol)
1.1.1.c	Oxidoreductase (2 step, acyl-CoA to alcohol)
1.2.1.b	Oxidoreductase (acyl-CoA to aldehyde)
1.4.1.a	Oxidoreductase (deaminating)
2.3.1.b	Acyltransferase
2.6.1.a	Aminotransferase
4.1.1.a	Carboxy-lyase
4.2.1.a	Hydro-lyase
4.3.1.a	Ammonia-lyase

Numerous transformation in FIGS. 1, 2 and 3 fall into the category of oxidoreductases that reduce an aldehyde to alcohol. For example, Steps D and P in FIG. 1 catalyzed by 3-oxobutyraldehyde reductase (aldehyde reducing) and 3-hydroxybutyraldehyde reductase respectively fall into this category. Similarly, Steps C and E in FIG. 2 catalyzed by 3-hydroxybutyraldehyde reductase and 3-oxobutyraldehdye reductase (aldehyde reducing) respectively are also oxidoreductases that convert the aldehyde functionality to alcohol. Pathways in FIG. 3 involve oxidoreductases such as 3-hydroxybutyraldehdye reductase in Step D.
Exemplary genes encoding enzymes that catalyze the conversion of an aldehyde to alcohol (i.e., alcohol dehydrogenase or equivalently aldehyde reductase) include alrA encoding a medium-chain alcohol dehydrogenase for C2-C14 (Tani et al., Appl. Environ. Microbiol., 66:5231-5235 (2000)), ADH2 from Saccharomyces cerevisiae (Atsumi et al., Nature, 451:86-89 (2008)), yqhD from E. coli which has preference for molecules longer than C3 (Sulzenbacher et al., J. of Molecular Biology, 342:489-502 (2004)), and bdh I and bdh II from C. acetobutylicum which converts butyraldehyde into butanol (Walter et al., J. of Bacteriology, 174:7149-7158 (1992)). The gene product of yqhD catalyzes the reduction of acetaldehyde, malondialdehyde, propionaldehyde, butyraldehyde, and acrolein using NADPH as the cofactor (Perez et al., J. Biol. Chem., 283:7346-7353 (2008)). The adhA gene product from Zymomonas mobilis has been demonstrated to have activity on a number of aldehydes including formaldehyde, acetaldehyde, propionaldehyde, butyraldehyde, and acrolein (Kinoshita et al., Appl. Microbiol. Biotechnol, 22:249-254 (1985)). Additional aldehyde reductase candidates are encoded by bdh in C. saccharoperbutylacetonicum and Cbei_—1722, Cbei_—2181 and Cbei_—2421 in C. beijerinckii.
Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 2.

TABLE 2

Protein	GENBANK ID	GI NUMBER	ORGANISM

alrA	BAB12273.1	9967138	Acinetobacter sp.
			strain M-1
ADH2	NP_014032.1	6323961	Saccharomyces
			cerevisiae
yqhD	NP_417484.1	16130909	Escherichia coli
bdh I	NP_349892.1	15896543	Clostridium
			acetobutylicum
bdh II	NP_349891.1	15896542	Clostridium
			acetobutylicum
adhA	YP_162971.1	56552132	Zymomonas mobilis
bdh	BAF45463.1	124221917	Clostridium
			saccharoperbutyl-
			acetonicum
Cbei_1722	YP_001308850	150016596	Clostridium
			beijerinckii
Cbei_2181	YP_001309304	150017050	Clostridium
			beijerinckii
Cbei_2421	YP_001309535	150017281	Clostridium
			beijerinckii

Enzymes exhibiting 3-hydroxybutyraldehyde reductase activity (EC 1.1.1.61) also fall into this category. Such enzymes have been characterized in Ralstonia eutropha (Bravo et al., J. Forensic Sci., 49:379-387 (2004)), Clostridium kluyveri (Wolff et al., Protein Expr. Purif., 6:206-212 (1995)) and Arabidopsis thaliana (Breitkreuz et al., J. Biol. Chem., 278:41552-41556 (2003)). Yet another gene is the alcohol dehydrogenase adhI from Geobacillus thermoglucosidasius (Jeon et al., J. Biotechnol., 135:127-133 (2008)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 3.

TABLE 3

PROTEIN	GENBANK ID	GI NUMBER	ORGANISM

4hbd	YP_726053.1	113867564	Ralstonia eutropha H16
4hbd	L21902.1	146348486	Clostridium kluyveri
			DSM 555
4hbd	Q94B07	75249805	Arabidopsis thaliana
adhI	AAR91477.1	40795502	Geobacillus
			thermoglucosidasius
			M10EXG

Another exemplary enzyme is 3-hydroxyisobutyrate dehydrogenase which catalyzes the reversible oxidation of 3-hydroxyisobutyrate to methylmalonate semialdehyde. This enzyme participates in valine, leucine and isoleucine degradation and has been identified in bacteria, eukaryotes, and mammals. The enzyme encoded by P84067 from Thermus thermophilus HB8 has been structurally characterized (Lokanath et al., J. Mol. Biol., 352:905-917 (2005)). The reversibility of the human 3-hydroxyisobutyrate dehydrogenase was demonstrated using isotopically-labeled substrate (Manning et al., Biochem J., 231:481-484 (1985)). Additional genes encoding this enzyme include 3hidh in Homo sapiens (Hawes et al., Methods Enzymol, 324:218-228 (2000)) and Oryctolagus cuniculus (Hawes et al., supra; Chowdhury et al., Biosci. Biotechnol Biochem., 60:2043-2047 (1996)), mmsB in Pseudomonas aeruginosa and Pseudomonas putida (Liao et al., US patent 20050221466), and dhat in Pseudomonas putida (Aberhart et al., J. Chem. Soc., 6:1404-1406 (1979); Chowdhury et al., supra; Chowdhury et al., Biosci. Biotechnol Biochem., 67:438-441 (2003)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 4.

TABLE 4

PROTEIN	GENBANK ID	GI NUMBER	ORGANISM

P84067	P84067	75345323	Thermus thermophilus
3hidh	P31937.2	12643395	Homo sapiens
3hidh	P32185.1	416872	Oryctolagus cuniculus
mmsB	P28811.1	127211	Pseudomonas aeruginosa
mmsB	NP_746775.1	26991350	Pseudomonas putida
dhat	Q59477.1	2842618	Pseudomonas putida

Oxidoreductases that convert a ketone functionality to the corresponding hydroxyl group are also synthetic steps in the disclosed pathways. Notably, Reactions L, O and H in FIG. 1 catalyzed by AKP dehydrogenase, 3-oxobutyraldehyde reductase (ketone reducing), 4-hydroxy-2-butanone reductase respectively are transformations of this category. The two latter transformations are also encountered in Steps B and F respectively in FIG. 2. On similar lines, the acetoacetyl-CoA reductase in Step G of FIG. 2 reduces acetoacetyl-CoA to 3-hydroxybutyryl-CoA.
The reduction of 4-oxo group of 2-amino-4-oxopentanoate (AKP) by a dehydrogenase yields 2-amino-4-hydroxypentanoate (FIG. 1, step L). This reaction is very similar to the NAD(P)H-dependent reduction of aspartate semialdehyde to homoserine catalyzed by homoserine dehydrogenase (EC 1.1.13). In many organisms, including E. coli, homoserine dehydrogenase is a bifunctional enzyme that also catalyzes the ATP-dependent conversion of aspartate to aspartyl-4-phosphate (Starnes et al., Biochemistry, 11:677-687 (1973)). The functional domains are catalytically independent and connected by a linker region (Sibilli et al., J. Biol. Chem., 256:10228-10230 (1981)) and both domains are subject to allosteric inhibition by threonine. The homoserine dehydrogenase domain of the E. coli enzyme, encoded by thrA, was separated from the aspartate kinase domain, characterized, and found to exhibit high catalytic activity and reduced inhibition by threonine (James et al., Biochemistry, 41:3720-3725 (2002)). This can be applied to other bifunctional threonine kinases including, for example, hom1 of Lactobacillus plantarum (Cahyanto et al., Microbiology, 152:205-112 (2006)) and Arabidopsis thaliana. The monofunctional homoserine dehydrogenases encoded by hom6 in S. cerevisiae (Jacques et al., Biochem. Biophys. Acta, 1544:28-41 (2001)) and hom2 in Lactobacillus plantarum (Cahyanto et al., supra) have been functionally expressed and characterized in E. coli. Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 5.

TABLE 5

PROTEIN	GENBANK ID	GI NUMBER	ORGANISM

thrA	AAC73113.1	1786183	Escherichia coli K12
akthr2	O81852	75100442	Arabidopsis thaliana
hom6	CAA89671	1015880	Saccharomyces cerevisiae
hom1	CAD64819	28271914	Lactobacillus plantarum
hom2	CAD63186	28270285	Lactobacillus plantarum

Acetoacetyl-CoA reductase (Step G, FIG. 2) catalyzing the reduction of acetoacetyl-CoA to 3-hydroxybutyryl-CoA participates in the acetyl-CoA fermentation pathway to butyrate in several species of Clostridia and has been studied in detail (Jones et al., Microbiol. Rev., 50:484-524 (1986)). The enzyme from Clostridium acetobutylicum, encoded by hbd, has been cloned and functionally expressed in E. coli (Youngleson et al., J. Bacteriol., 171:6800-6807 (1989)). Additionally, subunits of two fatty acid oxidation complexes in E. coli, encoded by fadB and fadJ, function as 3-hydroxyacyl-CoA dehydrogenases (Binstock et al., Methods Enzymol., 71C:403-411 (1981)). Yet other genes demonstrated to reduce acetoacetyl-CoA to 3-hydroxybutyryl-CoA are phbB from Zoogloea ramigera (Ploux et al., Eur. J. Biochem., 174:177-182 (1988)) and phaB from Rhodobacter sphaeroides (Alber et al., Mol. Microbiol., 61:297-309 (2006)). The former gene is NADPH-dependent, its nucleotide sequence has been determined (Peoples et al., Mol. Microbiol. 3:349-357 (1989)) and the gene has been expressed in E. coli. Substrate specificity studies on the gene led to the conclusion that it could accept 3-oxopropionyl-CoA as a substrate besides acetoacetyl-CoA (Ploux et al., supra). Additional genes include Hbd1 (C-terminal domain) and Hbd2 (N-terminal domain) in Clostridium kluyveri (Hillmer and Gottschalk, Biochim. Biophys. Acta 3334:12-23 (1974)) and HSD17B10 in Bos taurus (Wakil et al., J. Biol. Chem., 207:631-638 (1954)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 6.

TABLE 6

Protein	GENBANK ID	GI NUMBER	ORGANISM

fadB	P21177.2	119811	Escherichia coli
fadJ	P77399.1	3334437	Escherichia coli
Hbd2	EDK34807.1	146348271	Clostridium kluyveri
Hbd1	EDK32512.1	146345976	Clostridium kluyveri
hbd	P52041.2		Clostridium
			acetobutylicum
HSD17B10	O02691.3	3183024	Bos Taurus
phbB	P23238.1	130017	Zoogloea ramigera
phaB	YP_353825.1	77464321	Rhodobacter sphaeroides

A number of similar enzymes have been found in other species of Clostridia and in Metallosphaera sedula (Berg et al., Archaea. Science, 318:1782-1786 (2007)) as shown in Table 7.

TABLE 7

Protein	GenBank ID	GI number	Organism

Hbd	NP_349314.1	NP_349314.1	Clostridium
			acetobutylicum
Hbd	AAM14586.1	AAM14586.1	Clostridium
			beijerinckii
Msed_1423	YP_001191505	YP_001191505	Metallosphaera
			sedula
Msed_0399	YP_001190500	YP_001190500	Metallosphaera
			sedula
Msed_0389	YP_001190490	YP_001190490	Metallosphaera
			sedula
Msed_1993	YP_001192057	YP_001192057	Metallosphaera
			sedula

An exemplary alcohol dehydrogenase that converts a ketone to a hydroxyl group is the secondary alcohol dehydrogenase that was shown to convert acetone to isopropanol in C. beijerinckii (Ismaiel et al., J. Bacteriol., 175:5097-5105 (1993)) and T. brockii (Lamed et al., Biochem. J., 195:183-190 (1981); Peretz et al., Biochemistry, 28:6549-6555 (1989)). The gene product of adhA from Pyrococcus furiosus, which exhibits maximum activity on 2-pentanol and pyruvaldehyde, was shown to have very broad specificity which includes isopropanol and acetone (Van der et al., Eur. J. Biochem., 268:3062-3068 (2001)). Yet another secondary alcohol dehydrogenase with activity on isopropanol and acetone is encoded by the gene product of adh-A from Rhodococcus ruber (Edegger et al., Chem. Commun. (Camb), 2402-2404 (2006); Kosjek et al., Biotechnol. Bioeng., 86:55-62 (2004)). These genes along with others are listed below in Table 8.

TABLE 8

Protein	GenBank ID	GI number	Organism

adh	AAA23199.2	60592974	Clostridium beijerinckii
			NRRL B593
adh	P14941.1	113443	Thermoanaerobacter brockii
			HTD4
adhA	AAC25556	3288810	Pyrococcus furiosus
adh-A	CAD36475	21615553	Rhodococcus ruber

Alternatively, there exist several exemplary alcohol dehydrogenases that convert a ketone to a hydroxyl functional group. Two such enzymes from E. coli are encoded by malate dehydrogenase (mdh) and lactate dehydrogenase (ldhA). In addition, lactate dehydrogenase from Ralstonia eutropha has been shown to demonstrate high activities on substrates of various chain lengths such as lactate, 2-oxobutyrate, 2-oxopentanoate and 2-oxoglutarate (Steinbuchel et al., Eur. J. Biochem., 130:329-334 (1983)). Conversion of the oxo functionality to the hydroxyl group can also be catalyzed by 2-keto-1,3-butanediol reductase, an enzyme reported to be found in rat and in human placenta (Suda et al., Arch. Biochem. Biophys., 176:610-620 (1976); Suda et al., Biochem. Biophys. Res. Commun., 77:586-591 (1977)). All of these enzymes can provide a 3-oxobutyraldehyde reductase, and a 4-hydroxy-2-butanone reductase. An additional enzyme for these steps is the mitochondrial 3-hydroxybutyrate dehydrogenase (bdh) from the human heart which has been cloned and characterized (Marks et al., J. Biol. Chem. 267:15459-15463 (1992)). This enzyme is a dehydrogenase that operates on a 3-hydroxyacid. Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 9.

TABLE 9

Protein	GenBank ID	GI number	Organism

mdh	AAC76268.1	1789632	Escherichia coli
ldhA	NP_415898.1	16129341	Escherichia coli
ldh	YP_725182.1	113866693	Ralstonia eutropha
bdh	AAA58352.1	177198	Homo sapiens

A number of organisms can catalyze the reduction of 4-hydroxy-2-butanone to 1,3-butanediol, including those belonging to the genus Bacillus, Brevibacterium, Candida, and Klebsiella among others, as described by Matsuyama et al. (1995).
Several transformations in FIGS. 2 and 3 rely on the two-step reduction of acyl-CoA to the corresponding alcohol. For example, Steps D and I in FIG. 2, involving the acetoacetyl-CoA reductase (CoA-dependent, alcohol forming) and 3-hydroxybutyryl-CoA reductase (alcohol forming), and Step E in FIG. 3 involving 3-hydroxybutyryl-CoA reductase (alcohol forming), shows such a transformation.
Exemplary two-step oxidoreductases that convert an acyl-CoA to alcohol include those that transform substrates such as acetyl-CoA to ethanol (e.g., adhE from E. coli (Kessler et al., FEBS. Lett., 281:59-63 (1991)) and butyryl-CoA to butanol (e.g. adhE2 from C. acetobutylicum (Fontaine et al., J. Bacteriol., 184:821-830 (2002)). In addition to reducing acetyl-CoA to ethanol, the enzyme encoded by adhE in Leuconostoc mesenteroides has been shown to oxidize the branched chain compound isobutyraldehyde to isobutyryl-CoA (Kazahaya et al., J. Gen. Appl. Microbiol., 18:43-55 (1972); Koo et al., Biotechnol. Lett., 27:505-510 (2005)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 10.

TABLE 10

Protein	GenBank ID	GI Number	Organism

adhE	NP_415757.1	16129202	Escherichia coli
adhE2	AAK09379.1	12958626	Clostridium acetobutylicum
adhE	AAV66076.1	55818563	Leuconostoc mesenteroides

Another exemplary enzyme can convert malonyl-CoA to 3-HP. An NADPH-dependent enzyme with this activity has characterized in Chloroflexus aurantiacus where it participates in the 3-hydroxypropionate cycle (Hugler et al., J. Bacteriol., 184:2404-2410 (2002); Strauss et al., Eur. J. Biochem., 215:633-643 (1993)). This enzyme, with a mass of 300 kDa, is highly substrate-specific and shows little sequence similarity to other known oxidoreductases (Hugler et al., supra). No enzymes in other organisms have been shown to catalyze this specific reaction; however there is bioinformatic evidence that other organisms can have similar pathways (Klatt et al., Environ. Microbiol., 9:2067-2078 (2007)). Enzymes in other organisms including Roseiflexus castenholzii, Erythrobacter sp. NAP1 and marine gamma proteobacterium HTCC2080 can be inferred by sequence similarity. Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 11.

TABLE 11

Protein	GenBank ID	GI Number	Organism

mcr	AAS20429.1	42561982	Chloroflexus
			aurantiacus
Rcas_2929	YP_001433009.1	156742880	Roseiflexus
			castenholzii
NAP1_02720	ZP_01039179.1	85708113	Erythrobacter
			sp. NAP1
MGP2080_00535	ZP_01626393.1	119504313	marine gamma
			proteobacterium
			HTCC2080

Longer chain acyl-CoA molecules can be reduced by enzymes such as the jojoba (Simmondsia chinensis) FAR which encodes an alcohol-forming fatty acyl-CoA reductase. Its overexpression in E. coli resulted in FAR activity and the accumulation of fatty alcohol (Metz et al., Plant Physiology, 122:635-644 (2000)) (FAR, AAD38039.1, 5020215, Simmondsia chinensis).
The pathways disclosed herein involve numerous oxidoreductase-type transformations that convert an acyl-CoA to an aldehyde. Specifically, Steps A and H in FIG. 2 catalyzed by acetoacetyl-CoA reductase (aldehyde forming) and 3-hydroxybutyryl-CoA reductase (aldehyde forming), and Step C from FIG. 3 showing the transformation catalyzed by 3-hydroxybutyryl-CoA reductase.
Several acyl-CoA dehydrogenases are capable of reducing an acyl-CoA to its corresponding aldehyde. Exemplary genes that encode such enzymes include the Acinetobacter calcoaceticus acr1 encoding a fatty acyl-CoA reductase (Reiser et al., J. of Bacteriology, 179:2969-2975 (1997)), the Acinetobacter sp. M-1 fatty acyl-CoA reductase (Ishige et al., Appl. Environ. Microbiol., 68:1192-1195 (2002)), and a CoA- and NADP-dependent succinate semialdehyde dehydrogenase encoded by the sucD gene in Clostridium kluyveri (Sohling et al., J. Bacteriol., 178:871-880 (1996)). SucD of P. gingivalis is another succinate semialdehyde dehydrogenase (Takahashi et al., J. Bacteriol., 182:4704-4710 (2000)). The enzyme acylating acetaldehyde dehydrogenase in Pseudomonas sp, encoded by bphG, is yet another enzyme demonstrated to oxidize and acylate acetaldehyde, propionaldehyde, butyraldehyde, isobutyraldehyde and formaldehyde (Powlowski et al., J. Bacteriol., 175:377-385 (1993)). In addition to reducing acetyl-CoA to ethanol, the enzyme encoded by adhE in Leuconostoc mesenteroides has been shown to oxidize the branched chain compound isobutyraldehyde to isobutyryl-CoA (Kazahaya et al., supra; Koo et al., supra). Butyraldehyde dehydrogenase catalyzes a similar reaction, conversion of butyryl-CoA to butyraldehyde, in solventogenic organisms such as Clostridium saccharoperbutylacetonicum (Kosaka et al., Biosci. Biotechnol. Biochem., 71:58-61 (2007)). Additional aldehyde dehydrogenase enzyme candidates are found in Desulfatibacillum alkenivorans, Citrobacter koseri, Salmonella enterica, Lactobacillus brevis and Bacillus selenitireducens. Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 12.

TABLE 12

Protein	GenBank ID	GI Number	Organism

acr1	YP_047869.1	50086359	Acinetobacter calcoaceticus
acr1	AAC45217	1684886	Acinetobacter baylyi
acr1	BAB85476.1	18857901	Acinetobacter sp. Strain M-1
sucD	P38947.1	172046062	Clostridium kluyveri
sucD	NP_904963.1	34540484	Porphyromonas gingivalis
bphG	BAA03892.1	425213	Pseudomonas sp
adhE	AAV66076.1	55818563	Leuconostoc mesenteroides
bld	AAP42563.1	31075383	Clostridium
			saccharoperbutylacetonicum
ald	ACL06658.1	218764192	Desulfatibacillum alkenivorans
			AK-01
ald	YP_001452373	157145054	Citrobacter koseri ATCC BAA-
			895
pduP	NP_460996.1	16765381	Salmonella enterica
			Typhimurium
pduP	ABJ64680.1	116099531	Lactobacillus brevis ATCC 367
BselDRAFT_1651	ZP_02169447
	163762382	Bacillus selenitireducens
			MLS10

An additional enzyme type that converts an acyl-CoA to its corresponding aldehyde is malonyl-CoA reductase which transforms malonyl-CoA to malonic semialdehyde. Malonyl-CoA reductase is a key enzyme in autotrophic carbon fixation via the 3-hydroxypropionate cycle in thermoacidophilic archaeal bacteria (Berg et al., supra; Thauer, R. K., Science, 318:1732-1733 (2007)). The enzyme utilizes NADPH as a cofactor and has been characterized in Metallosphaera and Sulfolobus spp (Alber et al., J. Bacteriol., 188:8551-8559 (2006); Hugler et al., supra). The enzyme is encoded by Msed_—0709 in Metallosphaera sedula (Alber et al., supra; Berg et al., supra). A gene encoding a malonyl-CoA reductase from Sulfolobus tokodaii was cloned and heterologously expressed in E. coli (Alber et al., supra). This enzyme has also been shown to catalyze the conversion of methylmalonyl-CoA to its corresponding aldehyde (2007). Although the aldehyde dehydrogenase functionality of these enzymes is similar to the bifunctional dehydrogenase from Chloroflexus aurantiacus, there is little sequence similarity. Both malonyl-CoA reductase enzymes have high sequence similarity to aspartate-semialdehyde dehydrogenase, an enzyme catalyzing the reduction and concurrent dephosphorylation of aspartyl-4-phosphate to aspartate semialdehyde. Additional genes can be found by sequence homology to proteins in other organisms including Sulfolobus solfataricus and Sulfolobus acidocaldarius and have been listed below. Yet another enzyme for CoA-acylating aldehyde dehydrogenase is the ald gene from Clostridium beijerinckii (Toth et al., Appl. Environ. Microbiol., 65:4973-4980 (1999)). This enzyme has been reported to reduce acetyl-CoA and butyryl-CoA to their corresponding aldehydes. This gene is very similar to eutE that encodes acetaldehyde dehydrogenase of Salmonella typhimurium and E. coli (Toth et al., supra). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 13.

TABLE 13

Protein	GenBank ID	GI Number	Organism

MSED_0709	YP_001190808.1	146303492	Metallosphaera sedula
mcr	NP_378167.1	15922498	Sulfolobus tokodaii
asd-2	NP_343563.1	15898958	Sulfolobus solfataricus
Saci_2370	YP_256941.1	70608071	Sulfolobus
			acidocaldarius
Ald	AAT66436	9473535	Clostridium
			beijerinckii
eutE	AAA80209	687645	Salmonella
			typhimurium
eutE	P77445	2498347	Escherichia coli

The oxidative deamination of amino groups to their corresponding oxo groups is catalyzed by deaminating oxidoreductases in the EC class 1.4.1. Such enzymes utilize NAD⁺, NADP⁺ or FAD⁺ as acceptor. Enzymes in this class can convert 2-amino-4-oxopentanoate to 2,4-dioxopentanoate (FIG. 1, Step B), 2-amino-4-hydroxypentanoate to 2-oxo-4-hydroxypentanoate (FIG. 1, Step M) and 4-aminobutan-2-one to 3-oxobutyraldehyde (FIG. 1, Step K). Exemplary oxidoreductases operating on similar substrates include glutamate dehydrogenase (deaminating), encoded by gdhA, leucine dehydrogenase (deaminating), encoded by ldh, and aspartate dehydrogenase (deaminating), encoded by nadX. The gdhA gene product from Escherichia coli (McPherson et al., Nucleic. Acids Res. 11:5257-5266 (1983); Korber et al., J. Mol. Biol. 234:1270-1273 (1993)), gdh from Thermotoga maritima (Kort et al., Extremophiles 1:52-60 (1997); Lebbink et al., J. Mol. Biol. 280:287-296 (1998); Lebbink et al., J. Mol. Biol. 289:357-369 (1999)), and gdhA1 from Halobacterium salinarum (Ingoldsby et al., Gene. 349:237-244 (2005)) catalyze the reversible interconversion of glutamate to 2-oxoglutarate and ammonia, while favoring NADP(H), NAD(H), or both, respectively. Additional glutamate dehydrogenase gene candidates are found in Bacillus subtilis (Khan et al., Biosci. Biotechnol Biochem. 69:1861-1870 (2005)), Nicotiana tabacum (Purnell et al., Planta 222:167-180 (2005)), Oryza sativa (Abiko et al., Plant Cell Physiol 46:1724-1734 (2005)), Haloferax mediterranei (Diaz et al., Extremophiles. 10:105-115 (2006)), Halobactreium salinarum (Hayden et al., FEMS Microbiol Lett. 211:37-41 (2002)) and yeast (Roca et al., Appl Environ. Microbiol 69:4732-4736 (2003)). The Nicotiana tabacum enzyme is composed of alpha and beta subunits encoded by gdh1 and gdh2 (Purnell et al., Planta 222:167-180 (2005)). The ldh gene of Bacillus cereus encodes the LeuDH protein that accepts a wide of range of substrates including leucine, isoleucine, valine, and 2-aminobutanoate (Stoyan et al., J. Biotechnol 54:77-80 (1997); Ansorge et al., Biotechnol Bioeng. 68:557-562 (2000)). The nadX gene from Thermotoga maritime encoding for the aspartate dehydrogenase is involved in the biosynthesis of NAD (Yang et al., J. Biol. Chem. 278:8804-8808 (2003)). Data related to the sequences for each of these exemplary gene products can be found using the GenBank accession numbers shown below in Table 14.

TABLE 14

Protein	GenBank ID	GI Number	Organism

gdhA	P00370	118547	Escherichia coli
gdh	P96110.4	6226595	Thermotoga maritima
gdhA1	NP_279651.1	15789827	Halobacterium salinarum
rocG	NP_391659.1	16080831	Bacillus subtilis
gdh1	AAR11534.1	38146335	Nicotiana tabacum
gdh2	AAR11535.1	38146337	Nicotiana tabacum
GDH	Q852M0	75243660	Oryza sativa
GDH	Q977U6	74499858	Haloferax mediterranei
GDH	P29051	118549	Halobactreium salinarum
GDH2	NP_010066.1	6319986	Saccharomyces cerevisiae
ldh	P0A393	61222614	Bacillus cereus
nadX	NP_229443.1	15644391	Thermotoga maritima

An enzyme with 4-aminobutan-2-one oxidoreductase (deaminating) activity is required to convert 4-aminobutan-2-one to its corresponding aldehyde (FIG. 1, Step K). Exemplary candidates include 3,5-diaminohexanoate dehydrogenase (EC 1.4.1.11) and lysine 6-dehydrogenase (EC 1.4.1.18). 3,5-Diaminohexanoate dehydrogenase interconverts 3-amino acids and 3-oxoacids and has been characterized in organisms that ferment lysine. The gene encoding 3,5-diaminohexanoate dehydrogenase, kdd, was recently identified in Fusobacterium nucleatum (Kreimeyer et al., J. Biol. Chem. 282:7191-7197 (2007)). The enzyme has been purified and characterized in other organisms (Baker et al., J Biol. Chem. 247:7724-7734 (1972); Baker et al., Biochemistry 13:292-299 (1974)) but the genes associated with these enzymes are not known. Candidates in other sequenced organisms can be inferred by sequence homology. Lysine 6-dehydrogenase, encoded by the lysDH genes, catalyzes the conversion of primary amines to their corresponding aldehydes. This enzyme naturally catalyzes the reversible oxidative deamination of the 6-amino group of L-lysine to form 2-aminoadipate-6-semialdehyde (Misono et al., J Bacteriol. 150:398-401 (1982)). Exemplary enzymes are found in Geobacillus stearothermophilus (Heydari et al., Appl Environ. Microbiol 70:937-942 (2004)), Agrobacterium tumefaciens (Hashimoto et al., J Biochem. 106:76-80 (1989); Misono and Nagasaki, J Bacteriol. 150:398-401 (1982)), and Achromobacter denitrificans (Ruldeekulthamrong et al., BMB. Rep. 41:790-795 (2008)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 15.

TABLE 15

Protein	GenBank ID	GI Number	Organism

kdd	AAL93966.1	19713113	Fusobacterium nucleatum
lysDH	BAB39707	13429872	Geobacillus stearothermophilus
lysDH	NP_353966	15888285	Agrobacterium tumefaciens
lysDH	AAZ94428	74026644	Achromobacter denitrificans

2-Amino-4-oxopentanoate (AKP) thiolase or AKP thiolase (AKPT) (Step 1, FIG. 1) is a pyridoxal phosphate-dependent enzyme participating in ornithine degradation in Clostridium sticklandii (Jeng et al., A. Biochemistry, 13:2898-2903 (1974); Kenklies et al., Microbiology, 145:819-826 (1999)). A gene cluster encoding the alpha and beta subunits of AKPT (or-2 (ortA) and or-3 (ortB)) was recently identified and the biochemical properties of the enzyme were characterized (Fonknechten et al., J. Bacteriol., In Press (2009)). The enzyme is capable of operating in both directions and reacts with the D-isomer of alanine. Enzyme engineering can be performed to optimize function with L-alanine as a substrate. AKPT from Clostridium sticklandii has been characterized but its protein sequence has not yet been published. Enzymes with high sequence homology are found in Clostridium difficile, Alkaliphilus metalliredigenes QYF, Thermoanaerobacter sp. X514, and Thermoanaerobacter tengcongensis MB4 (Fonknechten et al, supra). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 16.

TABLE 16

Protein	GenBank ID	GI Number	Organism

ortA (A)	YP_001086914.1	126698017	Clostridium
			difficile 630
ortB (β)	YP_001086915.1	126698018	Clostridium
			difficile 630
Amet_2368	YP_001320181.1	150390132	Alkaliphilus
(α)			metalliredigenes
			QYF
Amet_2369	YP_001320182.1	150390133	Alkaliphilus
(β)			metalliredigenes
			QYF
Teth514_1478	YP_001663101.1	167040116	Thermoanaerobacter
(α)			sp. X514
Teth514_1479	YP_001663102.1	167040117	Thermoanaerobacter
(β)			sp. X514
TTE1235 (α)	NP_622858.1	20807687	Thermoanaerobacter
			tengcongensis MB4
thrC (β)	NP_622859.1	20807688	Thermoanaerobacter
			tengcongensis MB4

The conversion of 2-amino-4-oxopentanoate (AKP) to 2,4-dioxopentanoate (Step B, FIG. 1) is accomplished by 2-amino-4-oxopentanoate aminotransferase or oxidoreductase (deaminating). Selection of an appropriate enzyme for this transformation is dependent on the stereochemistry of the substrate. For example, if the substrate is in the D-configuration, a D-amino acid aminotransferase (EC 2.6.1.21) can be utilized, whereas the L-stereoisomer can utilize an L-aminotransferase such as aspartate aminotransferase (EC 2.6.1.1).
Aspartate aminotransferase transfers an amino group from aspartate to alpha-ketoglutarate, forming glutamate and oxaloacetate. Aspartate is similar in structure to 2-amino-4-oxopentanoate. This conversion is catalyzed by, for example, the gene products of aspC from Escherichia coli (Yagi et al., FEBS Lett., 100:81-84 (1979); Yagi et al., Methods Enzymol., 133:83-89 (1985)), AAT2 from Saccharomyces cerevisiae (Yagi et al., J. Biochem., 92:35-43 (1982)) and ASP5 from Arabidopsis thaliana (Kwok et al., J. Exp. Bot., 55:595-604 (2004); De la et al., Plant J., 46:414-425 (2006); Wilkie et al., Protein Expr. Purif., 12:381-389 (1998)). The enzyme from Rattus norvegicus has been shown to transaminate alternate substrates such as 2-aminohexanedioic acid and 2,4-diaminobutyric acid (Recasens et al., Biochemistry, 19:4583-4589 (1980)). Aminotransferases that work on other amino-acid-like substrates can also catalyze this transformation. Valine aminotransferase catalyzes the conversion of valine and pyruvate to 2-ketoisovalerate and alanine. The E. coli gene, avtA, encodes one such enzyme (Whalen et al., J. Bacteriol., 150:739-746 (1982)). This gene product also catalyzes the amination of α-ketobutyrate to generate α-aminobutyrate, although the amine donor in this reaction has not been identified (Whalen et al., J. Bacteriol., 158:571-574 (1984)). An additional candidate is alpha-aminoadipate transaminase (EC 2.6.1.39), an enzyme that participates in lysine biosynthesis and degradation in some organisms. The enzyme from Thermus thermophilus, encoded by lysN, is active with several alternate substrates including oxaloacetate, 2-oxoisocaproate, 2-oxoisovalerate, and 2-oxo-3-methylvalerate (Miyazaki et al., Microbiol. 150:2327-2334 (2004)). A similar enzyme from Homo sapiens has been characterized (Okuno et al., Enz. Prot. 47:136-148 (1993)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 17.

TABLE 17

Protein	GenBank ID	GI Number	Organism

aspC	NP_415448.1	16128895	Escherichia coli
AAT2	P23542.3	1703040	Saccharomyces cerevisiae
ASP5	P46248.2	20532373	Arabidopsis thaliana
got2	P00507	112987	Rattus norvegicus
avtA	YP_026231.1	49176374	Escherichia coli
lysN	BAC76939.1	31096548	Thermus thermophilus
AadAT-II	Q8N5Z0.2	46395904	Homo sapiens

When the substrate is present as the D-stereoisomer, transamination can be catalyzed by D-aminotransferase (EC 2.6.1.21), also known as D-amino acid aminotransferase and D-alanine aminotransferase (DAAT). This class of enzymes is noted for its broad substrate specificity, which is species-specific. The D-aminotransferase from Bacillus species YM-1, encoded by dat, has been cloned, sequenced (Tanizawa et al., J. Biol. Chem., 264:2450-2454 (1989)) and the crystal structure has been solved (Peisach et al., Biochemistry, 37:4958-4967 (1998)). This enzyme has also been the subject of protein engineering studies to alter the substrate specificity (Gutierrez et al., Eur. J. Biochem, 267:7218-7223 (2000); Gutierrez et al., Protein Eng., 11:53-58 (1998)). Additional genes are found in Bacillus licheniformis ATCC 10716 (Taylor et al., Biochim. Biophys. Acta., 1350:38-40 (1997)), Staphylococcus haemolyticus (Pucci et al., J. Bacteriol., 177:336-342 (1995)) and Bacillus subtilis (Martinez-Carrion et al., J. Biol. Chem., 240:3538-3546 (1965)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 18.

TABLE 18

Protein	GenBank ID	GI Number	Organism

dat	P19938	118222	Bacillus sp. YM-1
dat	P54692	1706292	Bacillus licheniformis ATCC
			10716
dat	P54694	1706294	Staphylococcus haemolyticus
dat	O07597.1	3121979	Bacillus subtilis

In reaction K of FIG. 1, 4-aminobutan-2-one is transaminated to form 3-oxobutanal. This transformation can likely be catalyzed by an aminotransferase that interconverts terminal amines and aldehydes. Exemplary candidate enzymes are beta-alanine/alpha-ketoglutarate aminotransferase, GABA aminotransferase, 3-amino-2-methylpropionate transaminase, lysine-6-aminotransferase, 2,4-diaminobutanoate transaminase, putrescine aminotransferase and diamine aminotransferase.
Cargill has developed and patented a beta-alanine/alpha-ketoglutarate aminotransferase for producing 3-HP from beta-alanine via malonyl-semialdehyde (Chandra et al., ARch. Microbiol., 176:443-451 (2001)). The gene product of SkPYD4 in Saccharomyces kluyveri was also shown to preferentially use beta-alanine as the amino group donor (Aberhart et al., J. Chem. Soc. 6:1404-1406 (1979)). SkUGA1 encodes a homologue of Saccharomyces cerevisiae GABA aminotransferase, UGA1 (Ichikawa et al., J. Mol. Catalysis A-Chem., 256:106-112 (2006)), whereas SkPYD4 encodes an enzyme involved in both β-alanine and GABA transamination (Aberthart et al., Supra). 3-amino-2-methylpropionate transaminase catalyzes the transformation from methylmalonate semialdehyde to 3-amino-2-methylpropionate. The enzyme has been characterized in Rattus norvegicus and Sus scrofa and is encoded by Abat (Chopra et al., Protein Expr. Purif, 25:533-540 (2002), Kuznetsova et al., FEMS Microbiol. Rev., 29:263-279 (2005)). Enzyme candidates in other organisms with high sequence homology to 3-amino-2-methylpropionate transaminase include Gta-1 in C. elegans and gabT in Bacillus subtilus. Additionally, one of the native GABA aminotransferases in E. coli, encoded by gene gabT, has been shown to have broad substrate specificity (Fontaine et al., J. Bacteriol., 184:821-830 (2002), Kanamasa et al., Appl. Microbiol Biotechnol., 80:223-229 (2008)). The gene puuE encodes the other 4-aminobutyrate transaminase in E. coli (Drummond et al., J. Biol. Chem., 235:318-325 (1960)).
Lysine-6-aminotransferase converts lysine to alpha-aminoadipate semialdehyde. Candidate enzymes have been characterized in Candida utilis (Hammer et al., J Basic Microbiol 32:21-27 (1992)), Flavobacterium lutescens (Fujii et al., J Biochem. 128:391-397 (2000)) and Streptomyces clavuligenus (Romero et al., J Ind. Microbiol Biotechnol 18:241-246 (1997)). A recombinant lysine-6-aminotransferase from S. clavuligenus was functionally expressed in E. coli (Tobin et al., J Bacteriol. 173:6223-6229 (1991)). The F. lutescens enzyme is specific to alpha-ketoglutarate as the amino acceptor (Soda et al., Biochemistry 7:4110-4119 (1968)). An enzyme with diaminobutanoate transaminase activity is encoded by the dat gene product in Acinetobacter baumanii (Ikai et al., J Bacteriol. 179:5118-5125 (1997)). In addition to its natural substrate, 2,4-diaminobutyrate, DAT transaminates the terminal amines of lysine, 4-aminobutyrate and ornithine. Candidate putrescine aminotransferase enzymes are encoded by ygjG in E. coli and spuC of Pseudomonas aeruginosa (Lu et al., J Bacteriol. 184:3765-3773 (2002)). The ygiG gene product reacts with the alternate substrates cadaverine, spermidine and 1,7-diaminoheptanoate (Samsonova et al., BMC. Microbiol 3:2 (2003); Kim, J Biol. Chem. 239:783-786 (1964)).
Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 19.

TABLE 19

Protein	GenBank ID	GI Number	Organism

SkyPYD4	ABF58893.1	98626772	Saccharomyces kluyveri
SkUGA1	ABF58894.1	98626792	Saccharomyces kluyveri
UGA1	NP_011533.1	6321456	Saccharomyces cerevisiae
Abat	P50554.3	122065191	Rattus norvegicus
Abat	P80147.2	120968	Sus scrofa
Gta-1	Q21217.1	6016091	Caenorhabditis elegans
gabT	P94427.1	6016090	Bacillus subtilis
gabT	P22256.1	16130576	Escherichia coli K12
puuE	NP_415818.1	16129263	Escherichia coli K12
lat	BAB13756.1	10336502	Flavobacterium lutescens
lat	AAA26777.1	153343	Streptomyces clavuligenus
dat	P56744.1	6685373	Acinetobacter baumanii
ygjG	NP_417544	145698310	Escherichia coli
spuC	AAG03688	9946143	Pseudomonas aeruginosa

In FIG. 1, Step C, 2,4-dioxopentanoate is decarboxylated to form 3-oxobutyraldehyde by 2,4-dioxopentanoate decarboxylase. 2,4-dioxopentanoate is similar to the native substrates of pyruvate decarboxylase (EC 4.1.1.1) and benzoylformate decarboxylase (EC 4.1.1.7). Pyruvate decarboxylase (PDC), also termed keto-acid decarboxylase, is a key enzyme in alcoholic fermentation, catalyzing the decarboxylation of pyruvate to acetaldehyde. The enzyme from Saccharomyces cerevisiae has a broad substrate range for aliphatic 2-keto acids including 2-ketobutyrate, 2-ketovalerate, 3-hydroxypyruvate and 2-phenylpyruvate (Li et al., Biochemistry, 38:10004-10012 (1999)). This enzyme has been extensively studied, engineered for altered activity, and functionally expressed in E. coli (Killenberg-Jabs et al., Eur. J. Biochem., 268:1698-1704 (2001); Li et al., supra; Schure et al., Appl. Environ. Microbiol., 64:1303-1307 (1998)). The PDC from Zymomonas mobilus, encoded by pdc, also has a broad substrate range and has been a subject of directed engineering studies to alter the affinity for different substrates (Siegert et al., Protein Eng. Des. Sel., 18:345-357 (2005)). The crystal structure of this enzyme is available (Killenberg-Jabs, supra). Other well-characterized PDC enzymes include the enzymes from Acetobacter pasteurians (Chandra et al., Arch. Microbiol. 176:443-451 (2001)) and Kluyveromyces lactis (Krieger et al., Eur. J. Biochem., 269:3256-3263 (2002)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 20.

TABLE 20

Protein	GenBank ID	GI Number	Organism

pdc	P06672.1	118391	Zymomonas mobilis
pdc1	P06169	30923172	Saccharomyces cerevisiae
pdc	Q8L388	20385191	Acetobacter pasteurians
pdc1	Q12629	52788279	Kluyveromyces lactis

Like PDC, benzoylformate decarboxylase (EC 4.1.1.7) has a broad substrate range and has been the target of enzyme engineering studies. The enzyme from Pseudomonas putida has been extensively studied and crystal structures of this enzyme are available (Polovnikova et al., Biochemistry 42:1820-1830 (2003); Hasson et al., Biochemistry, 37:9918-9930 (1998)). Site-directed mutagenesis of two residues in the active site of the Pseudomonas putida enzyme altered the affinity (Km) of naturally and non-naturally occurring substrates (Siegert et al., supra). The properties of this enzyme have been further modified by directed engineering (Lingen et al., Chembiochem, 4:721-726 (2003); Lingen et al., Protein Eng., 15:585-593 (2002)). The enzyme from Pseudomonas aeruginosa, encoded by mdlC, has also been characterized experimentally (Barrowman et al., FEMS Microbiology Letters, 34:57-60 (1986)). Additional genes from Pseudomonas stutzeri, Pseudomonas fluorescens and other organisms can be inferred by sequence homology or identified using a growth selection system developed in Pseudomonas putida (Henning et al., Appl. Environ. Microbiol., 72:7510-7517 (2006)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 21.

TABLE 21

Protein	GenBank ID	GI Number	Organism

mdlC	P20906.2	3915757	Pseudomonas putida
mdlC	Q9HUR2.1	81539678	Pseudomonas aeruginosa
dpgB	ABN80423.1	126202187	Pseudomonas stutzeri
ilvB-1	YP_260581.1	70730840	Pseudomonas fluorescens

A third enzyme capable of decarboxylating 2-oxoacids is alpha-ketoglutarate decarboxylase (KGD). The substrate range of this class of enzymes has not been studied to date. The KDC from Mycobacterium tuberculosis (Tian et al., Proc. Natl. Acad. Sci. USA, 102:10670-10675 (2005)) has been cloned and has been functionally expressed in E. coli at Genomatica. KDC enzyme activity has been detected in several species of Rhizobia including Bradyrhizobium japonicum and Mesorhizobium loti (Green et al., J. Bacteriol., 182:2838-2844 (2000)). Although the KDC-encoding gene(s) have not been isolated in these organisms, the genome sequences are available and several genes in each genome are annotated as putative KDCs. A KDC from Euglena gracilis has also been characterized but the gene associated with this activity has not been identified to date (Shigeoka et al., Arch. Biochem. Biophys., 288:22-28 (1991)). The first twenty amino acids starting from the N-terminus were sequenced MTYKAPVKDVKFLLDKVFKV (Shigeoka et al., supra). The gene can be identified by testing genes containing this N-terminal sequence for KDC activity. Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 22.

TABLE 22

Protein	GenBank ID	GI Number	Organism

kgd	O50463.4	160395583	Mycobacterium tuberculosis
kgd	NP_767092.1	27375563	Bradyrhizobium japonicum
			USDA110
kgd	NP_105204.1	13473636	Mesorhizobium loti

A fourth enzyme for catalyzing this step is the branched chain alpha-ketoacid decarboxylase (BCKA). This class of enzymes has been shown to act on a variety of compounds varying in chain length from 3 to 6 carbons (Oku et al., J. Biol. Chem., 263:18386-18396 (1988); Smit et al., Appl. Environ. Microbiol., 71:303-311 (2005)). The enzyme in Lactococcus lactis has been characterized on a variety of branched and linear substrates including 2-oxobutanoate, 2-oxohexanoate, 2-oxopentanoate, 3-methyl-2-oxobutanoate, 4-methyl-2-oxobutanoate and isocaproate (Smit et al., supra). The enzyme has been structurally characterized (Berthold et al., D. Biol. Crystallogr., 63:1217-1224 (2007)). Sequence alignments between the Lactococcus lactis enzyme and the pyruvate decarboxylase of Zymomonas mobilus indicate that the catalytic and substrate recognition residues are nearly identical (Siegert et al., supra), so this enzyme is readily amenable to directed engineering. Additional BCKA genes can be identified by homology to the Lactococcus lactis protein sequence (kdcA, AAS49166.1, 44921617, Lactococcus lactis). Many of the high-scoring BLASTp hits to this enzyme are annotated as indolepyruvate decarboxylases (EC 4.1.1.74). Indolepyruvate decarboxylase (IPDA) is an enzyme that catalyzes the decarboxylation of indolepyruvate to indoleacetaldehyde in plants and plant bacteria.
2-amino-4-ketopentanoate is decarboxylated to form 4-aminobutan-2-one by AKP decarboxylase in Step E of FIG. 1. This transformation can be catalyzed by an amino acid decarboxylase. Selection of an appropriate decarboxylase depends on the stereochemical configuration of 4-amino-4-oxopentanoate. When this compound is in a D-configuration, a D-amino acid decarboxylase can be utilized. One such D-amino acid decarboxylase is diaminopimelate decarboxylase (DDC, EC 4.1.1.20). This enzyme decarboxylates the D-stereocenter of meso-diaminopimelate, catalyzing the final step of lysine biosynthesis. DDC has been studied in many organisms including E. coli (Momany et al., D. Biol. Crystallogr., 58:549-552 (2002)), Mycobacterium tuberculosis (Kefala et al., Acta. Crystallogr. Sect. F. Struct. Biol. Cryst. Commun., 61:782-784 (2005); Gokulan et al., J. Biol. Chem., 278:18588-18596 (2003); Andersen et al., Gene, 124:105-109 (1993)), Methylophilus methylotrophus (Tsujimoto et al., J. Biotechnol, 124:327-337 (2006)), and Helicobacter pylori (Hu et al., J. Biol. Chem., 283:21284-21293 (2008)). Alternately, the ornithine decarboxylase (EC 4.1.1.17) from Homo sapiens has a weak activity on the D-isomer of ornithine (Qu et al., Biochem. J., 375:465-470 (2003); Fitzgerald et al., DNA, 8:623-634 (1989)) and can be used for the decarboxylation in step E. Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 23.

TABLE 23

Protein	GenBank ID	GI Number	Organism

lysA	NP_417315.1	16130742	Escherichia coli
lysA	AAA25361.1	149964	Mycobacterium tuberculosis
lysA	BAC92756.1	37196770	Methylophilus methylotrophus
lysA	ABW70801.1	158523325	Helicobacter pylori
odc1	AA59969.1	386989	Homo sapiens

When 2-amino-4-ketopentanoate exhibits L-stereochemistry, an amino acid decarboxylase such as aspartate decarboxylase (EC 4.1.1.11), ornithine decarboxylase (EC 4.1.1.17) or lysine decarboxylase (EC 4.1.1.18) can be utilized. An exemplary enzyme is aspartate decarboxylase (EC 4.1.1.11). 2-Amino-4-ketopentanoate bears structural similarity to aspartate, the native substrate of this enzyme. Aspartate decarboxylase participates in pantothenate biosynthesis and is encoded by panD in Escherichia coli (Dusch et al., Appl. Environ. Microbiol., 65:1530-1539 (1999); Ramjee et al., Biochem. J., 323:661-669 (1997); Merkel et al., FEMS Microbiol. Lett., 143:247-252 (1996); Schmitzberger et al., EMBO J., 22:6193-6204 (2003)). The enzymes from Mycobacterium tuberculosis (Chopra et al., Protein Expr. Purif., 25:533-540 (2002)) and Corynebacterium glutamicum (Dusch et al., supra) have been expressed and characterized in E. coli. Lysine decarboxylase enzymes are encoded in the E. coli genome by genes cadA and ldcC. A lysine decarboxylase analogous to CadA was recently identified in Vibrio parahaemolyticus (Tanaka et al., J. Appl. Microbiol. 104:1283-1293 (2008)). The lysine decarboxylase from Selenomonas ruminantium, encoded by ldc, bears sequence similarity to eukaryotic ornithine decarboxylases, and accepts both L-lysine and L-ornithine as substrates (Takatsuka et al., Biosci. Biotechnol Biochem. 63:1843-1846 (1999)). Ornithine decarboxylase enzyme candidates are found in Nicotiana glutinosa (Lee et al., Biochem. J. 360:657-665 (2001)), Lactobacillus sp. 30a (Guirard et al., J Biol. Chem. 255:5960-5964 (1980)) and Vibrio vulnificus (Lee et al., J Biol. Chem. 282:27115-27125 (2007)). The residues involved in substrate specificity Vibrio vulnificus have been elucidated (Lee et al., supra).
Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 24.

TABLE 24

Protein	GenBank ID	GI Number	Organism

panD	P0A790	67470411	Escherichia coli
panD	Q9X4N0	18203593	Corynebacterium
			glutanicum
panD	P65660.1	54041701	Mycobacterium
			tuberculosis
cadA	AAA23536.	145458	Escherichia coli
ldcC	AAC73297.1	1786384	Escherichia coli
ldc	O50657.1	13124043	Selenomonas
			ruminantium
cadA	AB124819.1	44886078	Vibrio
			parahaemolyticus
AF323910.1:1..1299	AAG45222.1	12007488	Nicotiana glutinosa
odc1	P43099.2	1169251	Lactobacillus sp.
			30a
VV2_1235	NP_763142.1	27367615	Vibrio vulnificus

In reaction J (FIG. 1), acetylacrylate is decarboxylated to 2-oxobutene by acetoacrylate decarboxylase. An enzyme catalyzing this transformation has not been identified to date, but similar reactions are catalyzed by the enzymes aconitate decarboxylase, 4-oxalocrotonate decarboxylase and cinnamate decarboxylase.
Aconitate decarboxylase catalyzes the final step in itaconate biosynthesis in a strain of Candida and also in the filamentous fungus Aspergillus terreus (Bonnarme et al., J. Bacteriol., 177:3573-3578 (1995); Willke et al., Appl. Microbiol. Biotechnol., 56:289-295 (2001)). A cis-aconitate decarboxylase (CAD) (EC 4.1.16), encoded by ATEG_—09971, has been identified and extensively studied in Aspergillus terreus and other related fungi. Recently, the gene has been cloned and functionally characterized (Kanamasa et al., Appl. Biotechnol., 80:223-229 (2008)) and (WO/2009/014437).
4-oxalocronate decarboxylase has been isolated from numerous organisms and characterized. Genes encoding this enzyme include dmpH and dmpE in Pseudomonas sp. (strain 600) (Shingler et al., J. Bacteriol., 174:711-724 (1992)), xylII and xylIII from Pseudomonas putida (Kato et al., Arch. Microbiol., 168:457-463 (1997); Stanley et al., Biochemistry, 39:3514 (2000); Lian et al., J. Am. Chem. Soc., 116:10403-10411 (1994)) and Reut_B5691 and Reut_B5692 from Ralstonia eutropha JMP134 (Hughes et al., J. Bacteriol., 158:79-83 (1984)). The genes encoding the enzyme from Pseudomonas sp. (strain 600) have been cloned and expressed in E. coli (Shingler et al., supra). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 25.

TABLE 25

Protein	GenBank ID	GI Number	Organism

dmpH	CAA43228.1	45685	Pseudomonas sp. CF600
dmpE	CAA43225.1	45682	Pseudomonas sp. CF600
xylII	YP_709328.1	111116444	Pseudomonas putida
xylIII	YP_709353.1	111116469	Pseudomonas putida
Reut_B5691	YP_299880.1	73539513	Ralstonia eutropha
			JMP134
Reut_B5692	YP_299881.1	73539514	Ralstonia eutropha
			JMP134
ATEG_09971	EAU29420.1	114187720	Aspergillus terreus

An additional class of decarboxylases has been characterized that catalyze the conversion of cinnamate (phenylacrylate) and substituted cinnamate derivatives to the corresponding styrene derivatives. These enzymes are common in a variety of organisms and specific genes encoding these enzymes that have been cloned and expressed in E. coli are: pad 1 from Saccharomyces cerevisae (Clausen et al., Gene, 142:107-112 (1994)), pdc from Lactobacillus plantarum (Barthelmebs et al., Appl. Environ. Microbiol., 67:1063-1069 (2001); Rodriguez et al., J. Agric. Food Chem., 56:3068-3072 (2008); Qi et al., Biochem. J., 375:465-470 (2007)), pofK (pad) from Klebsiella oxytoca (Uchiyama et al., Biosci. Biotechnol. Biochem., 72:116-123 (2008); Hashidoko et al., Biosci. Biotech. Biochem., 58:217-218 (1994)), Pedicoccus pentosaceus (Barthelmebs et al., supra) and padC from Bacillus subtilis and Bacillus pumilus (Cavin et al., Appl. Environ. Microbiol., 64:1466-1471 (1998)). A ferulic acid decarboxylase from Pseudomonas fluorescens also has been purified and characterized (Huang et al., J. Bacteriol., 176:5912-5918 (1994)). Importantly, this class of enzymes has been shown to be stable and does not require either exogenous or internally bound co-factors, thus making these enzymes ideally suitable for biotransformations (Sariaslani, F. S., Annu. Rev. Microbiol., 61:51-69 (2007)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 26.

TABLE 26

Protein	GenBank ID	GI Number	Organism

pad1	AAB64980.1	1165293	Saccharomyces cerevisae
pdc	AAC45282.1	1762616	Lactobacillus plantarum
pad	BAF65031.1	149941608	Klebsiella oxytoca
padC	NP_391320.1	16080493	Bacillus subtilis
pad	YP_804027.1	116492292	Pedicoccus pentosaceus
pad	CAC18719.1	11691810	Bacillus pumilus

An additional enzyme for decarboxylation is acetoacetate decarboxylase (EC 4.1.1.4), an enzyme that decarboxylates acetoacetate to acetone and has therefore been studied for its role in bacterial solventogenesis. Exemplary bacterial enzymes have been characterized from Clostridium acetobutylicum (Benner et al., J. Am. Chem. So. 103:993-994 (1981); Hlghbarger et al., Biochemistry 35:41-46 (1996); Petersen et al., Appl. Environ. Microbiol. 56:3491-3498 (1990); Rozzel et al. J. Am. Chem. Soc. 106:4937-4941 (1984)) Clostridium saccharoperbutylacetonicum (Kosaka, et al., Biosci. Biotechnol Biochem. 71:58-68 (2007)) and Clostridium beijerinckii (Ravagnani et al. Mol. Microbiol. 37:1172-1185 (2000)). Acetoacetate decarboxylase activity has also been demonstrated in Pseudomonas putida and Bacillus polymyxa but genes are not associated with this activity to date (Matiasek et al., Curr. Microbiol. 42: 276-281 (2001)). Bacterial genes in other organisms such as Clostridium botulinum and Bacillus amyloliquefaciens can be identified by sequence homology. In humans and other mammals, acetoacetate decarboxylase catalyzes the final step of the ketone-body pathway (Kalapos, Biochim. Biophys. Acta 1621:122-139 (2003)), but genes associated with this activity have not been identified to date. Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 27.

TABLE 27

Protein	GenBank ID	GI Number	Organism

adc	NP_149328.1	15004868	Clostridium
			acetobutylicum
adc	AAP42566.1	31075386	Clostridium
			saccharoperbutyl-
			acetonicum
cbei_3835	YP_001310906.1	150018652	Clostridium
			beijerinckii
CLL_A2135	YP_001886324.1	187933144	Clostridium
			botulinum
RBAM_030030	YP_001422565.1	154687404	Bacillus
			amyloliquefaciens

All the aforementioned gene candidates can also be used to catalyze the decarboxylation of 2-oxo-4-hydroxypentanoate to 3-hydroxybutyraldehyde in Step N of FIG. 1.
Butenone hydratase (Step G, FIG. 1), 4-hydroxybutyryl-CoA dehydratase (Step A, FIG. 3) and crotonase (Step A, FIG. 3) are hydrolyase-type transformations. Specifically, the hydration of butenone to 4-hydroxy-2-butanone (Step G, FIG. 1) can be accomplished by an enzyme in the hydratase family of enzymes. Enzymes that can carry out this transformation include fumarate hydratase (EC 4.2.1.2), 2-(hydroxymethyl)glutarate dehydratase (EC 4.2.1.-), dimethylmaleate hydratase (EC 4.2.1.85) and citramalate hydrolyase (EC 4.2.1.34).
Fumarate hydratase enzymes naturally catalyze the reversible hydration of fumarate to malate. Although the ability of fumarate hydratase to react with butanone as a substrate has not been described in the literature, a wealth of structural information is available for this enzyme and other researchers have successfully engineered the enzyme to alter activity, inhibition and localization (Weaver, T., B. Biol. Crystallogr., 61:1395-1401 (2005)). E. coli has three fumarases: FumA, FumB, and FumC that are regulated by growth conditions. FumB is oxygen sensitive and only active under anaerobic conditions. FumA is active under microanaerobic conditions, and FumC is the only active enzyme in aerobic growth (Tseng et al., J. Bacteriol., 183:461-467 (2001); Woods et al., Biochem. Biophys. Acta., 954:14-26 (1988); Guest et al., J. Gen. Microbiol., 131:2971-2984 (1985)). Additional enzymes are found in Campylobacter jejuni (Smith et al., Int. J. Biochem. Cell Biol., 31:961-975 (1999)), Thermus thermophilus (Mizobata et al., Arch. Biochem. Biophys., 355:49-55 (1998)) and Rattus norvegicus (Kobayashi et al., J. Biochem., 89:1923-1931 (1981)). Similar enzymes with high sequence homology include fum1 from Arabidopsis thaliana and fumC from Corynebacterium glutamicum. The MmcBC fumarase from Pelotomaculum thermopropionicum is another class of fumarase with two subunits (Shimoyama et al., FEMS Microbiol. Lett., 270:207-213 (2007)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 28.

TABLE 28

Protein	GenBank ID	GI Number	Organism

fumA	NP_416129.1	16129570	Escherichia coli
fumB	NP_418546.1	16131948	Escherichia coli
fumC	NP_416128.1	16129569	Escherichia coli
fumC	O69294	9789756	Campylobacter jejuni
fumC	P84127	75427690	Thermus thermophilus
fumH	P14408	120605	Rattus norvegicus
fum1	P93033	39931311	Arabidopsis thaliana
fumC	Q8NRN8	39931596	Corynebacterium glutamicum
MmcB	YP_001211906	147677691	Pelotomaculum
			thermopropionicum
MmcC	YP_001211907	147677692	Pelotomaculum
			thermopropionicum

Two additional hydratase enzymes are 2-(hydroxymethyl)glutarate dehydratase and dimethylmaleate hydratase, enzymes studied for their role in nicontinate catabolism in Eubacterium barkeri (formerly Clostridium barkeri) (Alhapel et al., Proc. Natl. Acad. Sci. USA, 103:12341-12346 (2006)). 2-(Hydroxymethyl)glutarate dehydratase is a [4Fe-4S]-containing enzyme that dehydrates 2-(hydroxymethyl)glutarate to 2-methylene-glutarate. This enzyme is encoded by hmd in Eubacterium barkeri (Alhapel et al., supra). Similar enzymes with high sequence homology are found in Bacteroides capillosus, Anaerotruncus colihominis, and Natranaerobius thermophilius. These enzymes are homologous to the alpha and beta subunits of [4Fe-4S]-containing bacterial serine dehydratases (e.g., E. coli enzymes encoded by tdcG, sdhB, and sdaA). Dimethylmaleate hydratase (EC 4.2.1.85) is a reversible Fe²⁺-dependent and oxygen-sensitive enzyme in the aconitase family that hydrates dimethylmaeate to form (2R,3S)-2,3-dimethylmalate. This enzyme is encoded by dmdAB in Eubacterium barkeri (Alhapel, et al., supra; Kollmann-Koch et al., Physiol. Chem., 365:847-857 (1984)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 29.

TABLE 29

Protein	GenBank ID	GI Number	Organism

hmd	ABC88407.1	86278275	Eubacterium
			barkeri
BACCAP_02294	ZP_02036683.1	154498305	Bacteroides
			capillosus ATCC
			29799
ANACOL_02527	ZP_02443222.1	167771169	Anaerotruncus
			colihominis DSM
			17241
NtherDRAFT_2368	ZP_02852366.1	169192667	Natranaerobius
			thermophilus
			JW/NM-WN-LF
dmdA	ABC88408	86278276	Eubacterium
			barkeri
dmdB	ABC88409.1	86278277	Eubacterium
			barkeri

An additional enzyme is 2-methylmalate dehydratase, also called citramalate hydrolyase, a reversible hydrolyase that catalyzes the alpha, beta elimination of water from citramalate to form mesaconate. This enzyme has been purified and characterized in Clostridium tetanomorphum (Wang et al., J. Biol. Chem., 244:2516-2526 (1969)). The activity of this enzyme has also been detected in several bacteria in the genera Citrobacter and Morganella in the context of the glutamate degradation VI pathway (Kato et al., supra). Genes encoding this enzyme have not been identified in any organism to date.
Hydration of crotonyl-CoA to form 3-hydroxybutyryl-CoA (Step B, FIG. 3) is catalyzed by a crotonase (EC 4.2.1.55). These enzymes are required for n-butanol formation in some organisms, particularly Clostridial species, and also comprise one step of the 3-hydroxypropionate/4-hydroxybutyrate cycle in thermoacidophilic Archaea of the genera Sulfolobus, Acidianus, and Metallosphaera. Exemplary genes encoding crotonase enzymes can be found in C. acetobutylicum (Boynton et al., J. Bacteriol., 178:3015-3024 (1996)), C. kluyveri (Hillmer et al., FEBS Lett., 21:351-354 (1972)), and Metallosphaera sedula (Berg et al., supra). Enoyl-CoA hydratases, which are involved in fatty acid beta-oxidation and/or the metabolism of various amino acids, can also catalyze the hydration of crotonyl-CoA to form 3-hydroxybutyryl-CoA (Roberts et al., Arch. Microbiol., 117:99-108 (1978); Agnihotri et al., Bioorg. Med. Chem., 11:9-20 (2003); Conrad et al., J. Bacteriol., 118:103-111 (1974)). An exemplary enoyl-CoA hydratase is the gene product of ech from Pseudomonas putida (Roberts et al., supra). The enoyl-CoA hydratases, phaA and phaB, of P. putida have been indicated to carry out the hydroxylation of double bonds during phenylacetate catabolism (Olivera et al., Proc. Natl. Acad. Sci USA, 95:6419-6424 (1998)). The paaA and paaB from P. fluorescens catalyze analogous transformations (Olivera et al., supra). Lastly, a number of Escherichia coli genes have been shown to demonstrate enoyl-CoA hydratase functionality including maoC (Park et al., J. Bacteriol., 185:5391-5397 (2003)), paaF (Ismail et al., Eur. J. Biochem., 270:3047-3054 (2003); Park et al., Appl. Biochem. Biotechnol., 113-116:335-346 (2004); Park et al., Biotechnol Bioeng., 86:681-686 (2004)) and paaG (Ismail et al., supra; Park et al., supra; Park et al., supra). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 30.

TABLE 30

Protein	GenBank ID	GI Number	Organism

crt	NP_349318.1	15895969	Clostridium acetobutylicum
crt1	YP_001393856	153953091	Clostridium kluyveri DSM
			555
ech	NP_745498.1	26990073	Pseudomonas putida
phaA	ABF82233.1	26990002	Pseudomonas putida
phaB	ABF82234.1	26990001	Pseudomonas putida
paaA	NP_745427.1	106636093	Pseudomonas fluorescens
paaB	NP_745426.1	106636094	Pseudomonas fluorescens
maoC	NP_415905.1	16129348	Escherichia coli
paaF	NP_415911.1	16129354	Escherichia coli
paaG	NP_415912.1	16129355	Escherichia coli

Alternatively, the E. coli gene products of fadA and fadB encode a multienzyme complex involved in fatty acid oxidation that exhibits enoyl-CoA hydratase activity (Haller et al., Biochemistry 39:4622-4629 (2000); Martinez-Carrion et al., J. Biol. Chem. 240:3538-3546 (1965); Matthies et al., Appl. Environ. Micriobiol. 58:1435-1439 (1992)). Knocking out a negative regulator encoded by fadR can be utilized to activate the fadB gene product (Jeng et al., A. Biochemistry 13:2898-2903 (1974)). The fadI and fadJ genes encode similar functions and are naturally expressed under anaerobic conditions (Atsumi et al., Nature 451:86-89 (2008)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 31.

TABLE 31

Protein	GenBank ID	GI Number	Organism

fadA	YP_026272.1	49176430	Escherichia coli
fadB	NP_418288.1	16131692	Escherichia coli
fadI	NP_416844.1	16130275	Escherichia coli
fadJ	NP_416843.1	16130274	Escherichia coli
fadR	NP_415705.1	16129150	Escherichia coli

The reversible condensation of 4-hydroxybutyryl-CoA to crotonyl-CoA (Step A, FIG. 3) is catalyzed by the bifunctional enzyme 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA Δ-isomerase. This enzyme first dehydrates 4-hydroxybutyryl-CoA to vinylacetyl-CoA, which subsequently rearranges to form crotonoyl-CoA. The enzymes from Clostridium kluyveri and C. aminobutyrium have been purified, characterized, and sequenced at the N-terminal domain (Scherf et al., Eur. J. Biochem., 215:421-429 (1993); Scherf et al., Arch. Microbiol., 161:239-245 (1994)). The abfD genes from C. aminobutyrium and C. kluyveri match exactly with these N-terminal amino acid sequences, and have been indicated to encode the 4-hydroxybutyrul-CoA dehydratases/vinylacetyl-CoA A-isomerase activities. Similar genes are identified through homology from genome projects, including abfD from Porphyromonas gingivalis and Msed_—1220 from Metallosphaera sedula. Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 32.

TABLE 32

Protein	GenBank ID	GI Number	Organism

abfD	YP_001396399.1	153955634	Clostridium kluyveri
abfD	P55792	84028213	Clostridium
			aminobutyricum
abfD	YP_001928843	188994591	Porphyromonas
			gingivalis
Msed_1220	YP_001191305.1	146303989	Metallosphaera sedula

Deamination of 2-amino-4-ketopentanoate (FIG. 1, Reaction I) and of 4-aminobutan-2-one (Step F, FIG. 1) can be accomplished by AKP ammonia-lyase and 4-aminobutan-2-one ammonia-lyase respectively. These deaminations are very similar to the deamination of aspartate to fumarate by aspartase. The enzyme has been extensively studied and several crystal structures are available. The E. coli enzyme has been shown to react with alternate substrates such as aspartatephenylmethylester, asparagine, benzyl-aspartate and malate (Ma et al., Ann. N.Y. Acad. Sci., 672:60-65 (1992). In a separate study, directed evolution has been implemented on this enzyme to alter substrate specificity (Asano et al., Biomol. Eng., 22:95-101 (2005)). Enzymes with aspartase functionality have also been characterized in Haemophilus influenzae (Sjostrom et al., Biochem. Biophys. Acta., 1324:182-190 (1997)), Pseudomonas fluorescens (Takagi et al., J. Biochem., 96:545-552 (1984)), Bacillus subtilus (Sjostrom et al., supra) and Serratia marcescens (Takagi et al., J. Bacteriol., 161:1-6 (1985)). Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 33.

TABLE 33

Protein	GenBank ID	GI Number	Organism

aspA	NP_418562	90111690	Escherichia coli
aspA	P44324.1	1168534	Haemophilus influenzae
aspA	P07346.1	114273	Pseudomonas fluorescens
ansB	P26899.1	251757243	Bacillus subtilus
aspA	P33109.1	416661	Serratia marcescens

A similar ammonia lyase reaction is catalyzed by methylaspartase (EC 4.3.1.2), an enzyme participating in the glutamate fermentation route via mesaconate (Kato et al., supra). This enzyme, also known as beta-methylaspartase and 3-methylaspartate ammonia-lyase, naturally catalyzes the deamination of threo-3-methylasparatate to mesaconate. The 3-methylaspartase from Clostridium tetanomorphum has been cloned, functionally expressed in E. coli, and crystallized (Asuncion et al., 57:731-733 (2001); Asuncion et al., J Biol Chem. 277:8306-8311 (2002); Botting et al., 27:2953-2955 (1988); Goda et al., 31:10747-10756 (1992)). In Citrobacter amalonaticus, this enzyme is encoded by BAA28709 (Kato et al., Arch. Microbiol 168:457-463 (1997)). 3-Methylaspartase has also been crystallized from E. coli YG1002 (Asano et al., FEMS Microbiol Lett. 118:255-258 (1994)) although the protein sequence is not listed in public databases such as GenBank. Data related to the sequences for each of these exemplary gene products can be found using the following GenBank accession numbers shown in Table 34.

TABLE 34

Protein	GenBank ID	GI Number	Organism

mal	AAB24070.1	259429	Clostridium tetanomorphum
BAA28709	BAA28709.1	3184397	Citrobacter amalonaticus

Referring now to FIG. 8B, gene candidates for alanine dehydrogenase alanine aminotransferase are shown below which convert pyruvate to alanine.

TABLE 35

glutamate-pyruvate	Escherichia coli	Accession: AAC76384.1
aminotransferase (alaB)	K-12 substr.	GI: 1789759
	MG1655
glutamate-pyruvate	Escherichia coli	Accession: AAC75350.1
aminotransferase (alaA)	K-12 substr.	GI: 1788627
	MG1655
glutamate-pyruvate	Escherichia coli	Accession: AAC75438.1
aminotransferase (alaC)	K-12 substr.	GI: 1788722
	MG1655
alanine transaminase	Arabidopsis	Accession: AEE30370.1
(AOAT1)	thaliana col	GI: 332192249
alanine transaminase	Arabidopsis	Accession: AEE35084.1
(AOAT2)	thaliana col	GI: 332196963
tryptophan	Arabidopsis	Accession:
aminotransferase (TAA1)	thaliana col	NP_177213.1 GI:
		15223183
alanine aminotransferase	Homo sapiens	Accession:
(GPT2)		NP_597700.1 GI:
		19263340
alanine aminotransferase	Homo sapiens	Accession: AAB20194.1
(GPT)		GI: 238134
alanine aminotransferase	Clostridium
	propionicum
alanine dehydrogenase	Phormidium	Accession: BAA24455.1
(ald)	lapideum	GI: 2804515
alanine dehydrogenase	Enterobacter	Accession: BAA77513.1
(aladh)	aerogenes	GI: 4803749
L-alanine dehydrogenase	Bacillus cereus
L-alanine dehydrogenase	Bacillus subtilis	Accession:
(ald)		NP_391071.1 GI:
		16080244
alanine dehydrogenase	Bilophila	Accession: AF269148.1
	wadsworthia	GI: 13661832
	RZATAU

Five requisite pathways to achieve the biosynthesis of 4-HB are exemplified herein and shown for purposes of illustration in FIG. 9B. One requisite 4-HB biosynthetic pathway includes the biosynthesis of 4-HB from succinate (the succinate pathway). The enzymes participating in this 4-HB pathway include succinate reductase, 4-hydroxybutanoate dehydrogenase (Steps F and C, FIG. 9B). Another requisite 4-HB biosynthetic pathway includes the biosynthesis from succinate through succinyl-CoA (the succinyl-CoA pathway). The enzymes participating in this 4-HB pathway include succinyl-CoA synthetase, CoA-dependent succinic semialdehyde dehydrogenase, and 4-hydroxybutanoate dehydrogenase (Steps A, I and K, FIG. 9B). Three other requisite 4-HB biosynthetic pathways include the biosynthesis of 4-HB from α-ketoglutarate (the α-ketoglutarate pathways). Hence, a third requisite 4-HB biosynthetic pathway is the biosynthesis of succinic semialdehyde through succinyl-CoA (Steps V, B, and C, FIG. 9B). AKG can be converted into succinyl-CoA by alpha-ketoglutarate dehydrogenase. This is then transformed into succinate semialdehyde and 4-HB as described earlier. Yet another pathway (Steps Q, R, S, T, U, FIG. 9B) for synthesizing 4-HB entails conversion of AKG into glutamate via glutamate dehydrogenase or glutamate transaminase. Glutamate is decarboxylated to form 4-aminobutyrate by glutamate decarboxylase and then 4-aminobutyrate dehydrogenase or 4-aminobutyrate transaminase can convert it into succinate semialdehyde. The final 4-HB biosynthetic pathway described here also includes the biosynthesis of 4-HB from α-ketoglutarate (Steps I and C, FIG. 9B), but utilizes α-ketoglutarate decarboxylase to catalyze succinic semialdehyde synthesis. 4-hydroxybutanoate dehydrogenase catalyzes the conversion of succinic semialdehyde to 4-HB. 4-hydroxybutanoate dehydrogenase catalyzes the conversion of succinic semialdehyde to 4-HB. 4HB can further be converted into 4-HB-CoA by 4-HB-CoA ligase, 4-HB-CoA synthetase or 4-HB-CoA transferase. Alternatively, the conversion of 4-HB to 4-HB CoA can be carried out by 4-Hydroxybutyrate kinase and Phosphotrans-4-hydroxybutyrylase (Steps D and E, FIG. 9B). Each of these 4-HB and 4HB-CoA biosynthetic pathways, their substrates, reactants and products are described further below in the Examples.
The non-naturally occurring microbial organisms of the invention can be produced by introducing expressible nucleic acids encoding one or more of the enzymes participating in one or more 4-HB biosynthetic pathways. Depending on the host microbial organism chosen for biosynthesis, nucleic acids for some or all of a particular 4-HB biosynthetic pathway can be expressed. For example, if a chosen host is deficient in both enzymes in the succinate to 4-HB pathway and this pathway is selected for 4-HB biosynthesis, then expressible nucleic acids for both succinate reductase and 4-hydroxybutanoate dehydrogenase are introduced into the host for subsequent exogenous expression. Alternatively, if the chosen host exhibits endogenous succinate reductase, but is deficient in 4-hydroxybutanoate dehydrogenase then an encoding nucleic acid is needed for this enzyme to achieve 4-HB biosynthesis.
In like fashion, where 4-HB biosynthesis is selected to occur through the succinate to succinyl-CoA pathway (the succinyl-CoA pathway), encoding nucleic acids for host deficiencies in the enzymes succinyl-CoA synthetase, CoA-dependent succinic semialdehyde dehydrogenase and/or 4-hydroxybutanoate dehydrogenase are to be exogenously expressed in the recipient host. Selection of 4-HB biosynthesis through the α-ketoglutarate to succinic semialdehyde pathway (the α-ketoglutarate pathway) can utilize exogenous expression for host deficiencies in one or more of the enzymes for glutamate dehydrogenase, glutamate transaminase, glutamate decarboxylase, 4-aminobutyrate dehydrogenase, 4-aminobutyrate transaminase, and/or 4-hydroxybutanoate dehydrogenase.
Depending on the 4-HB biosynthetic pathway constituents of a selected host microbial organism, the non-naturally occurring microbial 4-HB biocatalysts of the invention will include at least one exogenously expressed 4-HB pathway-encoding nucleic acid and up to all encoding nucleic acids for one or more 4-HB biosynthetic pathways. For example, 4-HB-CoA biosynthesis can be established from all five pathways in a host deficient in 4-hydroxybutanoate dehydrogenase through exogenous expression of a 4-hydroxybutanoate dehydrogenase encoding nucleic acid. In contrast, 4-HB biosynthesis can be established from all five pathways in a host deficient in all eleven enzymes through exogenous expression of all eight of CoA-independent succinic semialdehyde dehydrogenase, succinyl-CoA synthetase, CoA-dependent succinic semialdehyde dehydrogenase, glutamate: succinic semialdehyde transaminase, glutamate decarboxylase, α-ketoglutarate decarboxylase and 4-hydroxybutanoate dehydrogenase.
Given the teachings and guidance provided herein, those skilled in the art will understand that the number of encoding nucleic acids to introduce in an expressible form will, at least, parallel the 4-HB pathway deficiencies of the selected host microbial organism. Therefore, a non-naturally occurring microbial organism of the invention can have one, two, three, four, five, six or seven or up to eleven nucleic acids encoding the above enzymes constituting one or more 4-HB biosynthetic pathways. In some embodiments, the non-naturally occurring microbial organisms also can include other genetic modifications that facilitate or optimize 4-HB-CoA biosynthesis or that confer other useful functions onto the host microbial organism. One such other functionality can include, for example, augmentation of the synthesis of one or more of the 4-HB-CoA pathway precursors such as succinate, succinyl-CoA and/or α-ketoglutarate.
In some embodiments, a non-naturally occurring microbial organism of the invention is generated from a host that contains the enzymatic capability to synthesize 4-HB. In this specific embodiment it can be useful to increase the synthesis or accumulation of a 4-HB pathway product to, for example, drive 4-HB pathway reactions toward 4-HB production. Increased synthesis or accumulation can be accomplished by, for example, overexpression of nucleic acids encoding one or more of the above-described 4-HB pathway enzymes. Over expression of the 4-HB pathway enzyme or enzymes can occur, for example, through exogenous expression of the endogenous gene or genes, or through exogenous expression of the heterologous gene or genes. Therefore, naturally occurring organisms can be readily generated to be non-naturally 4-HB producing microbial organisms of the invention through overexpression of one, two, three, four, five, six or seven nucleic or all eleven acids encoding 4-HB biosynthetic pathway enzymes. In addition, a non-naturally occurring organism can be generated by mutagenesis of an endogenous gene that results in an increase in activity of an enzyme in the 4-HB biosynthetic pathway.
Non-naturally occurring microbial organisms also can be generated which biosynthesize 1,3-BDO. As with the 4-HB producing microbial organisms of the invention, the 1,3-BDO producing microbial organisms also can produce intracellularly or secret the 1,3-BDO into the culture medium. Following the teachings and guidance provided previously for the construction of microbial organisms that synthesize 4-HB, additional 1,3-BDO pathways can be incorporated into the 4-HB producing microbial organisms to generate organisms that also synthesize 1,3-BDO and other 1,3-BDO family compounds. The non-naturally occurring microbial organisms of the invention capable of 1,3-BDO biosynthesis circumvent these chemical synthesis using 4-HB as an entry point as illustrated in FIG. 9B.
The additional 1,3-BDO pathways to introduce into 4-HB producers include, for example, the exogenous expression in a host deficient background or the overexpression of one or more of the enzymes exemplified in FIG. 9B. An initial step in the entry pathway to 1,3-BDO is the conversion of 4-hydroxybutyrate to 4-hydroxybutyryl-CoA using 4-hydroxybutyrate:CoA transferase or 4-hydroxybutyryl-CoA synthetase (or ligase) the combination of butyrate kinase and phosphotransbutyrylase. Accordingly, the additional initial 1,3-BDO pathways to introduce into 4-HB producers to produce 4-hydroxybutyryl-CoA include, for example, the exogenous expression in a host deficient background or the overexpression of one or more of a 4-hydroxybutyrate:CoA transferase, 4-hydroxybutyryl-CoA synthetase (or ligase), butyrate kinase or phosphotransbutyrylase. In the absence of endogenous acyl-CoA synthetase capable of modifying 4-HB, the non-naturally occurring 1,3-BDO producing microbial organisms can further include an exogenous acyl-CoA synthetase selective for 4-HB, or the combination of multiple enzymes that have as a net reaction conversion of 4-HB into 4-HB-CoA. As exemplified further below in the Examples, butyrate kinase and phosphotransbutyrylase exhibit 1,3-BDO pathway activity and catalyze the conversions illustrated in FIG. 9B with a 4-HB substrate. Therefore, these enzymes also can be referred to herein as 4-hydroxybutyrate kinase and phosphotranshydroxybutyrylase respectively. Once 4-hydroxybutyryl-CoA is generated it can then be utilized for the biosynthesis of 1,3-BDO following the subsequent steps shown FIG. 9B.
Step A of FIG. 9B involves CoA synthetase or ligase reactions for succinate as the substrate. Exemplary genes encoding enzymes likely to carry out these transformations include the sucCD genes of E. coli which naturally form a succinyl-CoA synthetase complex. This enzyme complex naturally catalyzes the formation of succinyl-CoA from succinate with the contaminant consumption of one ATP, a reaction which is reversible in vivo (Buck et al., Biochem. 24:6245-6252 (1985)).

TABLE 36

Gene	Accession No.	GI No.	Organism

sucC	NP_415256.1	16128703	Escherichia coli
sucD	AAC73823.1	1786949	Escherichia coli

Additional exemplary CoA-ligases include the rat dicarboxylate-CoA ligase for which the sequence is yet uncharacterized (Vamecq et al., Biochemical Journal 230:683-693 (1985)), either of the two characterized phenylacetate-CoA ligases from P. chrysogenum (Lamas-Maceiras et al., Biochem. J. 395:147-155 (2005); Wang et al., Biochem Biophy Res Commun 360(2):453-458 (2007)), the phenylacetate-CoA ligase from Pseudomonas putida (Martinez-Blanco et al., J. Biol. Chem. 265:7084-7090 (1990)), and the 6-carboxyhexanoate-CoA ligase from Bacillus subtilis (Bower et al., J. Bacteriol. 178(14):4122-4130 (1996)). Additional candidate enzymes are acetoacetyl-CoA synthetases from Mus musculus (Hasegawa et al., Biochim Biophys Acta 1779:414-419 (2008)) and Homo sapiens (Ohgami et al., Biochem Pharmacol 65:989-994 (2003)) which naturally catalyze the ATP-dependant conversion of acetoacetate into acetoacetyl-CoA. 4-hydroxybutyryl-CoA synthetase activity has been demonstrated in Metallosphaera sedula (Berg et al., Science 318:1782-1786 (2007)). This function has been tentatively assigned to the Msed_—1422 gene.

TABLE 37

Gene	Accession No.	GI No.	Organism

phl	CAJ15517.1	77019264	Penicillium chrysogenum
phlB	ABS19624.1	152002983	Penicillium chrysogenum
paaF	AAC24333.2	22711873	Pseudomonas putida
bioW	NP_390902.2	50812281	Bacillus subtilis
AACS	NP_084486.1	21313520	Mus musculus
AACS	NP_076417.2	31982927	Homo sapiens
Msed_1422	YP_001191504	146304188	Metallosphaera sedula

ADP-forming acetyl-CoA synthetase (ACD, EC 6.2.1.13) is another candidate enzyme that couples the conversion of acyl-CoA esters to their corresponding acids with the concurrent synthesis of ATP. Several enzymes with broad substrate specificities have been described in the literature. ACD I from Archaeoglobus fulgidus, encoded by AF1211, was shown to operate on a variety of linear and branched-chain substrates including acetyl-CoA, propionyl-CoA, butyryl-CoA, acetate, propionate, butyrate, isobutyrate, isovalerate, succinate, fumarate, phenylacetate, indoleacetate (Musfeldt et al., J Bacteriol 184:636-644 (2002)). The enzyme from Haloarcula marismortui (annotated as a succinyl-CoA synthetase) accepts propionate, butyrate, and branched-chain acids (isovalerate and isobutyrate) as substrates, and was shown to operate in the forward and reverse directions (Brasen et al., Arch Microbiol 182:277-287 (2004)). The ACD encoded by PAE3250 from hyperthermophilic crenarchaeon Pyrobaculum aerophilum showed the broadest substrate range of all characterized ACDs, reacting with acetyl-CoA, isobutyryl-CoA (preferred substrate) and phenylacetyl-CoA (Brasen et al., supra). The enzymes from A. fulgidus, H. marismortui and P. aerophilum have all been cloned, functionally expressed, and characterized in E. coli (Musfeldt et al., supra; Brasen et al., supra).

TABLE 38

Gene	Accession No.	GI No.	Organism

AF1211	NP_070039.1	11498810	Archaeoglobus fulgidus DSM
			4304
scs	YP_135572.1	55377722	Haloarcula marismortui ATCC
			43049
PAE3250	NP_560604.1	18313937	Pyrobaculum aerophilum str.
			IM2

The conversion of succinate to succinate semialdehyde (Step F) can be catalyzed by a carboxylic acid reductase. One notable carboxylic acid reductase can be found in Nocardia iowensis which catalyzes the magnesium, ATP and NADPH-dependent reduction of carboxylic acids to their corresponding aldehydes (Venkitasubramanian et al., J Biol. Chem. 282:478-485 (2007)). This enzyme is encoded by the car gene and was cloned and functionally expressed in E. coli (Venkitasubramanian et al., J Biol. Chem. 282:478-485 (2007)). Expression of the npt gene product improved activity of the enzyme via post-transcriptional modification. The npt gene encodes a specific phosphopantetheine transferase (PPTase) that converts the inactive apo-enzyme to the active holo-enzyme. The natural substrate of this enzyme is vanillic acid and the enzyme exhibits broad acceptance of aromatic and aliphatic substrates (Venkitasubramanian et al. “Biocatalytic Reduction of Carboxylic Acids: Mechanism and Applications” Chapter 15 in Biocatalysis in the Pharmaceutical and Biotechnology Industires, ed. R. N. Patel, CRC Press LLC, Boca Raton, Fla. (2006)). Additional car and npt genes can be identified based on sequence homology.

TABLE 39A

Gene	Accession No.	GI No.	Organism

car	AAR91681.1	40796035	Nocardia iowensis (sp. NRRL
			5646)
npt	ABI83656.1	114848891	Nocardia iowensis (sp. NRRL
			5646)

TABLE 39B

Gene	Accession No.	GI No.	Organism

fadD9	YP_978699.1	121638475	Mycobacterium bovis
			BCG
BCG_2812c	YP_978898.1	121638674	Mycobacterium bovis
			BCG
nfa20150	YP_118225.1	54023983	Nocardia farcinica
			IFM 10152
nfa40540	YP_120266.1	54026024	Nocardia farcinica
			IFM 10152
SGR_6790	YP_001828302.1	182440583	Streptomyces griseus
			subsp. griseus NBRC
			13350
SGR_665	YP_001822177.1	182434458	Streptomyces griseus
			subsp. griseus NBRC
			13350

An additional enzyme candidate found in Streptomyces griseus is encoded by the griC and griD genes. This enzyme is believed to convert 3-amino-4-hydroxybenzoic acid to 3-amino-4-hydroxybenzaldehyde as deletion of either griC or griD led to accumulation of extracellular 3-acetylamino-4-hydroxybenzoic acid, a shunt product of 3-amino-4-hydroxybenzoic acid metabolism (Suzuki, et al., J. Antibiot. 60(6):380-387 (2007)). Co-expression of griC and griD with SGR_—665, an enzyme similar in sequence to the Nocardia iowensis npt, may be beneficial.

TABLE 40

Gene	Accession No.	GI No.	Organism

griC	182438036	YP_001825755.1	Streptomyces griseus subsp.
			griseus NBRC 13350
griD	182438037	YP_001825756.1	Streptomyces griseus subsp.
			griseus NBRC 13350

An enzyme with similar characteristics, alpha-aminoadipate reductase (AAR, EC 1.2.1.31), participates in lysine biosynthesis pathways in some fungal species. This enzyme naturally reduces alpha-aminoadipate to alpha-aminoadipate semialdehyde. The carboxyl group is first activated through the ATP-dependent formation of an adenylate that is then reduced by NAD(P)H to yield the aldehyde and AMP. Like CAR, this enzyme utilizes magnesium and requires activation by a PPTase. Enzyme candidates for AAR and its corresponding PPTase are found in Saccharomyces cerevisiae (Morris et al., Gene 98:141-145 (1991)), Candida albicans (Guo et al., Mol. Genet. Genomics 269:271-279 (2003)), and Schizosaccharomyces pombe (Ford et al., Curr. Genet. 28:131-137 (1995)). The AAR from S. pombe exhibited significant activity when expressed in E. coli (Guo et al., Yeast 21:1279-1288 (2004)). The AAR from Penicillium chrysogenum accepts S-carboxymethyl-L-cysteine as an alternate substrate, but did not react with adipate, L-glutamate or diaminopimelate (Hijarrubia et al., J Biol. Chem 278:8250-8256 (2003)). The gene encoding the P. chrysogenum PPTase has not been identified to date and no high-confidence hits were identified by sequence comparison homology searching.

TABLE 41

Gene	Accession No.	GI No.	Organism

LYS2	AAA34747.1	171867	Saccharomyces cerevisiae
LYS5	P50113.1	1708896	Saccharomyces cerevisiae
LYS2	AAC02241.1	2853226	Candida albicans
LYS5	AAO26020.1	28136195	Candida albicans
Lys1p	P40976.3	13124791	Schizosaccharomyces pombe
Lys7p	Q10474.1	1723561	Schizosaccharomyces pombe
Lys2	CAA74300.1	3282044	Penicillium chrysogenum

The conversion of succinyl-CoA to succinate semialdehyde (Step B, FIG. 9B) is catalyzed by an aldehyde forming succinyl-CoA reductase. Several acyl-CoA dehydrogenases are capable of reducing an acyl-CoA to its corresponding aldehyde. Exemplary genes that encode such enzymes include the Acinetobacter calcoaceticus acr1 encoding a fatty acyl-CoA reductase (Reiser and Somerville, J. Bacteriology 179:2969-2975 (1997)), the Acinetobacter sp. M-1 fatty acyl-CoA reductase (Ishige et al. Appl. Environ. Microbiol. 68:1192-1195 (2002)), and a CoA- and NADP-dependent succinate semialdehyde dehydrogenase encoded by the sucD gene in Clostridium kluyveri (Sohling and Gottschalk J Bacteriol 178:871-80 (1996); Sohling and Gottschalk J Bacteriol. 178:871-880 (1996)). SucD of P. gingivalis is another aldehyde-forming succinyl-CoA reductase (Takahashi et al. J. Bacteriol. 182:4704-4710 (2000)). The enzyme acylating acetaldehyde dehydrogenase in Pseudomonas sp, encoded by bphG, is yet another as it has been demonstrated to oxidize and acylate acetaldehyde, propionaldehyde, butyraldehyde, isobutyraldehyde and formaldehyde (Powlowski et al. J Bacteriol. 175:377-385 (1993)). In addition to reducing acetyl-CoA to ethanol, the enzyme encoded by adhE in Leuconostoc mesenteroides has been shown to oxidize the branched chain compound isobutyraldehyde to isobutyryl-CoA (Koo et al., Biotechnol Lett. 27:505-510 (2005)). Butyraldehyde dehydrogenase catalyzes a similar reaction, conversion of butyryl-CoA to butyraldehyde, in solventogenic organisms such as Clostridium saccharoperbutylacetonicum (Kosaka et al., Biosci. Biotechnol Biochem. 71:58-68 (2007)).

TABLE 42

Gene	Accession No.	GI No.	Organism

acr1	YP_047869.1	50086359	Acinetobacter calcoaceticus
acr1	AAC45217	1684886	Acinetobacter baylyi
acr1	BAB85476.1	18857901	Acinetobacter sp. Strain M-1
sucD	P38947.1	730847	Clostridium kluyveri
sucD	NP_904963.1	34540484	Porphyromonas gingivalis
bphG	BAA03892.1	425213	Pseudomonas sp
adhE	AAV66076.1	55818563	Leuconostoc mesenteroides
bld	AAP42563.1	31075383	Clostridium
			saccharoperbutylacetonicum

An additional enzyme type that converts an acyl-CoA to its corresponding aldehyde is malonyl-CoA reductase which transforms malonyl-CoA to malonic semialdehyde. Malonyl-CoA reductase is a key enzyme in autotrophic carbon fixation via the 3-hydroxypropionate cycle in thermoacidophilic archael bacteria (Berg et al. Science 318:1782-1786 (2007); Thauer, R. K. Science 318:1732-1733 (2007)). The enzyme utilizes NADPH as a cofactor and has been characterized in Metallosphaera and Sulfolobus spp (Alber et al. J. Bacteriol. 188:8551-8559 (2006); Hugler et al. J. Bacteriol. 184:2404-2410 (2002)). The enzyme is encoded by Msed_—0709 in Metallosphaera sedula (Alber et al. J. Bacteriol. 188:8551-8559 (2006); Berg et al. Science 318:1782-1786 (2007)). A gene encoding a malonyl-CoA reductase from Sulfolobus tokodaii was cloned and heterologously expressed in E. coli (Alber et al. J. Bacteriol. 188:8551-8559 (2006)). Although the aldehyde dehydrogenase functionality of these enzymes is similar to the bifunctional dehydrogenase from Chloroflexus aurantiacus, there is little sequence similarity. Both malonyl-CoA reductase enzyme candidates have high sequence similarity to aspartate-semialdehyde dehydrogenase, an enzyme catalyzing the reduction and concurrent dephosphorylation of aspartyl-4-phosphate to aspartate semialdehyde. Additional gene candidates can be found by sequence homology to proteins in other organisms including Sulfolobus solfataricus and Sulfolobus acidocaldarius. Yet another candidate for CoA-acylating aldehyde dehydrogenase is the ald gene from Clostridium beijerinckii (Toth et al., Appl Environ. Microbiol 65:4973-4980 (1999)). This enzyme has been reported to reduce acetyl-CoA and butyryl-CoA to their corresponding aldehydes. This gene is very similar to eutE that encodes acetaldehyde dehydrogenase of Salmonella typhimurium and E. coli (Toth et al., Appl Environ. Microbiol 65:4973-4980 (1999)).

TABLE 43

Gene	Accession No.	GI No.	Organism

Msed_0709	YP_001190808.1	146303492	Metallosphaera sedula
mcr	NP_378167.1	15922498	Sulfolobus tokodaii
asd-2	NP_343563.1	15898958	Sulfolobus solfataricus
Saci_2370	YP_256941.1	70608071	Sulfolobus
			acidocaldarius
Ald	AAT66436	49473535	Clostridium beijerinckii
eutE	AAA80209	687645	Salmonella typhimurium
eutE	P77445	2498347	Escherichia coli

Glutamate dehydrogenase (Step Q, FIG. 9B) and 4-aminobutyrate dehydrogenase (Step T, FIG. 9B) can be catalyzed by aminating oxidoreductases. Enzymes in this EC class (1.4.1.a) catalyze the oxidative deamination of alpha-amino acids with NAD⁺ or NADP⁺ as acceptor, and the reactions are typically reversible. Exemplary oxidoreductases operating on amino acids include glutamate dehydrogenase (deaminating), encoded by gdhA, leucine dehydrogenase (deaminating), encoded by ldh, and aspartate dehydrogenase (deaminating), encoded by nadX. The gdhA gene product from Escherichia coli (Korber et al. J. Mol. Biol. 234:1270-1273 (1993); McPherson and Wootton Nucleic. Acids Res. 11:5257-5266 (1983)), gdh from Thermotoga maritima (Kort et al. Extremophiles 1:52-60 (1997); Lebbink, et al. J. Mol. Biol. 280:287-296 (1998)); Lebbink et al. J. Mol. Biol. 289:357-369 (1999)), and gdhA1 from Halobacterium salinarum (Ingoldsby et al. Gene 349:237-244 (2005)) catalyze the reversible interconversion of glutamate to 2-oxoglutarate and ammonia, while favoring NADP(H), NAD(H), or both, respectively. The ldh gene of Bacillus cereus encodes the LeuDH protein that has a wide of range of substrates including leucine, isoleucine, valine, and 2-aminobutanoate (Ansorge and Kula Biotechnol Bioeng. 68:557-562 (2000); Stoyan et al. J. Biotechnol 54:77-80 (1997)). The nadX gene from Thermotoga maritime encoding for the aspartate dehydrogenase is involved in the biosynthesis of NAD (Yang et al. J. Biol. Chem. 278:8804-8808 (2003)).

TABLE 44

Gene	Accession No.	GI No.	Organism

gdhA	P00370	118547	Escherichia coli
gdh	P96110.4	6226595	Thermotoga maritima
gdhA1	NP_279651.1	15789827	Halobacterium salinarum
ldh	P0A393	61222614	Bacillus cereus
nadX	NP_229443.1	15644391	Thermotoga maritima

Additional glutamate dehydrogenase gene candidates are found in Bacillus subtilis (Khan et al., Biosci. Biotechnol Biochem. 69:1861-1870 (2005)), Nicotiana tabacum (Purnell et al., Planta 222:167-180 (2005)), Oryza sativa (Abiko et al., Plant Cell Physiol 46:1724-1734 (2005)), Haloferax mediterranei (Diaz et al., Extremophiles. 10:105-115 (2006)) and Halobactreium salinarum (Hayden et al., FEMS Microbiol Lett. 211:37-41 (2002)). The Nicotiana tabacum enzyme is composed of alpha and beta subunits encoded by gdh1 and gdh2 (Purnell et al., Planta 222:167-180 (2005)). Overexpression of the NADH-dependent glutamate dehydrogenase was found to improve ethanol production in engineered strains of S. cerevisiae (Roca et al., Appl Environ. Microbiol 69:4732-4736 (2003)).

TABLE 45

Gene	Accession No.	GI No.	Organism

rocG	NP_391659.1	16080831	Bacillus subtilis
gdh1	AAR11534.1	38146335	Nicotiana tabacum
gdh2	AAR11535.1	38146337	Nicotiana tabacum
GDH	Q852M0	75243660	Oryza sativa
GDH	Q977U6	74499858	Haloferax mediterranei
GDH	P29051	118549	Halobactreium salinarum
GDH2	NP_010066.1	6319986	Saccharomyces cerevisiae

An exemplary enzyme for catalyzing the conversion of aldehydes to their corresponding primary amines is lysine 6-dehydrogenase (EC 1.4.1.18), encoded by the lysDH genes. The lysine 6-dehydrogenase (deaminating), encoded by lysDH gene, catalyze the oxidative deamination of the ε-amino group of L-lysine to form 2-aminoadipate-6-semialdehyde, which in turn nonenzymatically cyclizes to form Δ1-piperideine-6-carboxylate (Misono and Nagasaki J. Bacteriol. 150:398-401 (1982)). The lysDH gene from Geobacillus stearothermophilus encodes a thermophilic NAD-dependent lysine 6-dehydrogenase (Heydari et al. Appl Environ. Microbiol 70:937-942 (2004)). The lysDH gene from Aeropyrum pernix K1 is identified through homology from genome projects. Additional enzymes can be found in Agrobacterium tumefaciens (Hashimoto et al., J Biochem. 106:76-80 (1989); Misono et al., J Bacteriol. 150:398-401 (1982)) and Achromobacter denitrificans (Ruldeekulthamrong et al., BMB. Rep. 41:790-795 (2008)).

TABLE 46

Gene	Accession No.	GI No.	Organism

lysDH	BAB39707	13429872	Geobacillus stearothermophilus
lysDH	NP_147035.1	14602185	Aeropyrum pernix K1
lysDH	NP_353966	15888285	Agrobacterium tumefaciens
lysDH	AAZ94428	74026644	Achromobacter denitrificans

An enzyme that converts 3-oxoacids to 3-amino acids is 3,5-diaminohexanoate dehydrogenase (EC 1.4.1.11), an enzyme found in organisms that ferment lysine. The gene encoding this enzyme, kdd, was recently identified in Fusobacterium nucleatum (Kreimeyer et al., 282:7191-7197 (2007)). The enzyme has been purified and characterized in other organisms (Baker et al., 247:7724-7734 (1972); Baker et al., 13:292-299 (1974)) but the genes associated with these enzymes are not known. Candidates in Myxococcus xanthus, Porphyromonas gingivalis W83 and other sequenced organisms can be inferred by sequence homology.

TABLE 47

Gene	Accession No.	GI No.	Organism

kdd	AAL93966.1	19713113	Fusobacterium nucleatum
mxan_439	ABF87267.1	108462082	Myxococcus xanthus
pg_1069	AAQ66183.1	34397119	Porphyromonas gingivalis

Steps R and U in FIG. 9B can be catalyzed by aminotransferases that reversibly convert an aldehyde or ketone to an amino group. Common amino donor/acceptor combinations include glutamate/alpha-ketoglutarate, alanine/pyruvate, and aspartate/oxaloacetate. Several enzymes have been shown to convert aldehydes to primary amines, and vice versa. Lysine-6-aminotransferase (EC 2.6.1.36) is one exemplary enzyme capable of forming a primary amine. This enzyme function, converting lysine to alpha-aminoadipate semialdehyde, has been demonstrated in yeast and bacteria. Candidates from Candida utilis (Hammer et al., J Basic Microbiol 32:21-27 (1992)), Flavobacterium lutescens (Fujii et al., J Biochem. 128:391-397 (2000)) and Streptomyces clavuligenus (Romero et al., J Ind. Microbiol Biotechnol 18:241-246 (1997)) have been characterized. A recombinant lysine-6-aminotransferase from S. clavuligenus was functionally expressed in E. coli (Tobin et al., J Bacteriol. 173:6223-6229 (1991)). The F. lutescens enzyme is specific to alpha-ketoglutarate as the amino acceptor (Soda et al., 7:4110-4119 (1968)). Other enzymes which convert aldehydes to terminal amines include the dat gene product in Acinetobacter baumanii encoding 2,4-diaminobutanoate:2-ketoglutarate 4-transaminase (Ikai et al., J Bacteriol. 179:5118-5125 (1997)). In addition to its natural substrate, 2,4-diaminobutyrate, DAT transaminates the terminal amines of lysine, 4-aminobutyrate and ornithine.

TABLE 48

Gene	Accession No.	GI No.	Organism

lat	BAB13756.1	10336502	Flavobacterium lutescens
lat	AAA26777.1	153343	Streptomyces clavuligenus
dat	P56744.1	6685373	Acinetobacter baumanii

The conversion of an aldehyde to a terminal amine can also be catalyzed by gamma-aminobutyrate transaminase (GABA transaminase or 4-aminobutyrate transaminase). This enzyme naturally interconverts succinic semialdehyde and glutamate to 4-aminobutyrate and alpha-ketoglutarate and is known to have a broad substrate range (Schulz et al., 56:1-6 (1990); Liu et al., 43:10896-10905 (2004)). The two GABA transaminases in E. coli are encoded by gabT (Bartsch et al., J Bacteriol. 172:7035-7042 (1990)) and puuE (Kurihara et al., J. Biol. Chem. 280:4602-4608 (2005)). GABA transaminases in Mus musculus, Pseudomonas fluorescens, and Sus scrofa have been shown to react with a range of alternate substrates including 6-aminocaproic acid (Cooper, 113:80-82 (1985); SCOTT et al., 234:932-936 (1959)).

TABLE 49

Gene	Accession No.	GI No.	Organism

gabT	NP_417148.1	16130576	Escherichia coli
puuE	NP_415818.1	16129263	Escherichia coli
Abat	NP_766549.2	37202121	Mus musculus
gabT	YP_257332.1	70733692	Pseudomonas fluorescens
abat	NP_999428.1	47523600	Sus scrofa

Additional enzyme candidates for interconverting aldehydes and primary amines are putrescine transminases or other diamine aminotransferases. The E. coli putrescine aminotransferase is encoded by the ygjG gene and the purified enzyme also was able to transaminate cadaverine and spermidine (Samsonova et al., BMC. Microbiol 3:2 (2003)). In addition, activity of this enzyme on 1,7-diaminoheptane and with amino acceptors other than 2-oxoglutarate (e.g., pyruvate, 2-oxobutanoate) has been reported (Samsonova et al., BMC. Microbiol 3:2 (2003); KIM, 239:783-786 (1964)). A putrescine aminotransferase with higher activity with pyruvate as the amino acceptor than alpha-ketoglutarate is the spuC gene of Pseudomonas aeruginosa (Lu et al., J Bacteriol. 184:3765-3773 (2002)).

TABLE 50

Gene	Accession No.	GI No.	Organism

ygjG	NP_417544	145698310	Escherichia coli
spuC	AAG03688	9946143	Pseudomonas aeruginosa

Enzymes that transaminate 3-oxoacids include GABA aminotransferase (described above), beta-alanine/alpha-ketoglutarate aminotransferase and 3-amino-2-methylpropionate aminotransferase. Beta-alanine/alpha-ketoglutarate aminotransferase (WO08027742) reacts with beta-alanine to form malonic semialdehyde, a 3-oxoacid. The gene product of SkPYD4 in Saccharomyces kluyveri was shown to preferentially use beta-alanine as the amino group donor (Andersen et al., Gene 124:105-109 (1993)). SkUGA1 encodes a homologue of Saccharomyces cerevisiae GABA aminotransferase, UGA1 (Ramos et al., Eur. J. Biochem. 149:401-404 (1985)), whereas SkPYD4 encodes an enzyme involved in both beta-alanine and GABA transamination (Andersen and Hansen, Gene 124:105-109 (1993)). 3-Amino-2-methylpropionate transaminase catalyzes the transformation from methylmalonate semialdehyde to 3-amino-2-methylpropionate. The enzyme has been characterized in Rattus norvegicus and Sus scrofa and is encoded by Abat (Tamaki et al., 324:376-389 (2000); Kakimoto et al., 156:374-380 (1968)).

TABLE 51

Gene	Accession No.	GI No.	Organism

SkyPYD4	ABF58893.1	98626772	Lachancea kluyveri
SkUGA1	ABF58894.1	98626792	Lachancea kluyveri
UGA1	NP_011533.1	6321456	Saccharomyces cerevisiae
Abat	P50554.3	122065191	Rattus norvegicus
Abat	P80147.2	120968	Sus scrofa

Several aminotransferases transaminate the amino groups of amino acids to form 2-oxoacids. Aspartate aminotransferase is an enzyme that naturally transfers an oxo group from oxaloacetate to glutamate, forming alpha-ketoglutarate and aspartate. Aspartate is similar in structure to OHED and 2-AHD. Aspartate aminotransferase activity is catalyzed by, for example, the gene products of aspC from Escherichia coli (Yagi et al., 100:81-84 (1979): Yagi et al., 113:83-89 (1985)), AAT2 from Saccharomyces cerevisiae (Yagi et al., 92:35-43 (1982)) and ASP5 from Arabidopsis thaliana (Kwok et al., 55:595-604 (2004); de la et al., 46:414-425 (2006); Wilkie et al., Protein Expr. Purif. 12:381-389 (1998)). The enzyme from Rattus norvegicus has been shown to transaminate alternate substrates such as 2-aminohexanedioic acid and 2,4-diaminobutyric acid (Recasens et al., 19:4583-4589 (1980)). Aminotransferases that work on other amino-acid substrates may also be able to catalyze this transformation. Valine aminotransferase catalyzes the conversion of valine and pyruvate to 2-ketoisovalerate and alanine. The E. coli gene, avtA, encodes one such enzyme (Whalen et al., J. Bacteriol. 150:739-746 (1982)). This gene product also catalyzes the transamination of alpha-ketobutyrate to generate α-aminobutyrate, although the amine donor in this reaction has not been identified (Whalen et al., J. Bacteriol. 158:571-574 (1984)). The gene product of the E. coli serC catalyzes two reactions, phosphoserine aminotransferase and phosphohydroxythreonine aminotransferase (Lam et al., J. Bacteriol. 172:6518-6528 (1990)), and activity on nonphosphorylated substrates could not be detected (Drewke et al., FEBS. Lett. 390:179-182 (1996)).

TABLE 52

Gene	Accession No.	GI No.	Organism

aspC	NP_415448.1	16128895	Escherichia coli
AAT2	P23542.3	1703040	Saccharomyces cerevisiae
ASP5	P46248.2	20532373	Arabidopsis thaliana
Got2	P00507	112987	Rattus norvegicus
avtA	YP_026231.1	49176374	Escherichia coli
serC	NP_415427.1	16128874	Escherichia coli

Another enzyme candidate is alpha-aminoadipate aminotransferase (EC 2.6.1.39), an enzyme that participates in lysine biosynthesis and degradation in some organisms. This enzyme interconverts 2-aminoadipate and 2-oxoadipate, using alpha-ketoglutarate as the amino acceptor. Gene candidates are found in Homo sapiens (Okuno et al., Enzyme Protein 47:136-148 (1993)) and Thermus thermophilus (Miyazaki et al., 150:2327-2334 (2004)). The Thermus thermophilus enzyme, encoded by lysN, is active with several alternate substrates including oxaloacetate, 2-oxoisocaproate, 2-oxoisovalerate, and 2-oxo-3-methylvalerate.

TABLE 53

Gene	Accession No.	GI No.	Organism

lysN	BAC76939.1	31096548	Thermus thermophilus
AadAT-II	Q8N5Z0.2	46395904	Homo sapiens

Alpha-ketoglutarate decarboxylase (Step I, FIG. 9B) and glutamate decarboxylase (Step S, FIG. 9B) all involve the decarboxylation of an alpha-ketoacid. The decarboxylation of keto-acids is catalyzed by a variety of enzymes with varied substrate specificities, including pyruvate decarboxylase (EC 4.1.1.1), benzoylformate decarboxylase (EC 4.1.1.7), alpha-ketoglutarate decarboxylase and branched-chain alpha-ketoacid decarboxylase.
Pyruvate decarboxylase (PDC), also termed keto-acid decarboxylase, is a key enzyme in alcoholic fermentation, catalyzing the decarboxylation of pyruvate to acetaldehyde. The enzyme from Saccharomyces cerevisiae has a broad substrate range for aliphatic 2-keto acids including 2-ketobutyrate, 2-ketovalerate, 3-hydroxypyruvate and 2-phenylpyruvate. This enzyme has been extensively studied, engineered for altered activity, and functionally expressed in E. coli (Killenberg-Jabs et al., 268:1698-1704 (2001); Li et al., Biochemistry. 38:10004-10012 (1999); ter Schure et al., Appl. Environ. Microbiol. 64:1303-1307 (1998)). The PDC from Zymomonas mobilus, encoded by pdc, also has a broad substrate range and has been a subject of directed engineering studies to alter the affinity for different substrates (Siegert et al., 18:345-357 (2005)). The crystal structure of this enzyme is available (Killenberg-Jabs et al., 268:1698-1704 (2001)). Other well-characterized PDC candidates include the enzymes from Acetobacter pasteurians (Chandra et al., 176:443-451 (2001)) and Kluyveromyces lactis (Krieger et al., 269:3256-3263 (2002)).

TABLE 54

Gene	Accession No.	GI No.	Organism

pdc	P06672.1	118391	Zymomonas mobilus
pdc1	P06169	30923172	Saccharomyces cerevisiae
pdc	AM21208	20385191	Acetobacter pasteurians
pdc1	Q12629	52788279	Kluyveromyces lactis

Like PDC, benzoylformate decarboxylase (EC 4.1.1.7) has a broad substrate range and has been the target of enzyme engineering studies. The enzyme from Pseudomonas putida has been extensively studied and crystal structures of this enzyme are available (Polovnikova et al., 42:1820-1830 (2003); Hasson et al., 37:9918-9930 (1998)). Site-directed mutagenesis of two residues in the active site of the Pseudomonas putida enzyme altered the affinity (Km) of naturally and non-naturally occurring substrates (Siegert et al., 18:345-357 (2005)). The properties of this enzyme have been further modified by directed engineering (Lingen et al., Chembiochem. 4:721-726 (2003); Lingen et al., Protein Eng 15:585-593 (2002)). The enzyme from Pseudomonas aeruginosa, encoded by mdlC, has also been characterized experimentally (Barrowman et al., 34:57-60 (1986)). Additional gene candidates from Pseudomonas stutzeri, Pseudomonas fluorescens and other organisms can be inferred by sequence homology or identified using a growth selection system developed in Pseudomonas putida (Henning et al., Appl. Environ. Microbiol. 72:7510-7517 (2006)).

TABLE 55

Gene	Accession No.	GI No.	Organism

A third enzyme capable of decarboxylating 2-oxoacids is alpha-ketoglutarate decarboxylase (KGD). The substrate range of this class of enzymes has not been studied to date. The KDC from Mycobacterium tuberculosis (Tian et al., 102:10670-10675 (2005)) has been cloned and functionally expressed in other internal projects at Genomatica. However, it is not an ideal candidate for strain engineering because it is large (˜130 kDa) and GC-rich. KDC enzyme activity has been detected in several species of rhizobia including Bradyrhizobium japonicum and Mesorhizobium loti (Green et al., 182:2838-2844 (2000)). Although the KDC-encoding gene(s) have not been isolated in these organisms, the genome sequences are available and several genes in each genome are annotated as putative KDCs. A KDC from Euglena gracilis has also been characterized but the gene associated with this activity has not been identified to date (Shigeoka et al., 288:22-28 (1991)). The first twenty amino acids starting from the N-terminus were sequenced MTYKAPVKDVKFLLDKVFKV (Shigeoka and Nakano, 288:22-28 (1991)). The gene could be identified by testing candidate genes containing this N-terminal sequence for KDC activity.

TABLE 56

Gene	Accession No.	GI No.	Organism

kgd	O50463.4	160395583	Mycobacterium tuberculosis
kgd	NP_767092.1	27375563	Bradyrhizobium japonicum
kgd	NP_105204.1	13473636	Mesorhizobium loti

A fourth candidate enzyme for catalyzing this reaction is branched chain alpha-ketoacid decarboxylase (BCKA). This class of enzyme has been shown to act on a variety of compounds varying in chain length from 3 to 6 carbons (Oku et al., 263:18386-18396 (1988); Smit et al., 71:303-311 (2005)). The enzyme in Lactococcus lactis has been characterized on a variety of branched and linear substrates including 2-oxobutanoate, 2-oxohexanoate, 2-oxopentanoate, 3-methyl-2-oxobutanoate, 4-methyl-2-oxobutanoate and isocaproate (Smit et al., 71:303-311 (2005)). The enzyme has been structurally characterized (Berg et al., 318:1782-1786 (2007)). Sequence alignments between the Lactococcus lactis enzyme and the pyruvate decarboxylase of Zymomonas mobilus indicate that the catalytic and substrate recognition residues are nearly identical (Siegert et al., 18:345-357 (2005)), so this enzyme would be a promising candidate for directed engineering. Decarboxylation of alpha-ketoglutarate by a BCKA was detected in Bacillus subtilis; however, this activity was low (5%) relative to activity on other branched-chain substrates (Oku and Kaneda, 263:18386-18396 (1988)) and the gene encoding this enzyme has not been identified to date. Additional BCKA gene candidates can be identified by homology to the Lactococcus lactis protein sequence. Many of the high-scoring BLASTp hits to this enzyme are annotated as indolepyruvate decarboxylases (EC 4.1.1.74). Indolepyruvate decarboxylase (IPDA) is an enzyme that catalyzes the decarboxylation of indolepyruvate to indoleacetaldehyde in plants and plant bacteria.


Gene	Accession No.	GI No.	Organism

kdcA	AAS49166.1	44921617	Lactococcus lactis

Recombinant branched chain alpha-keto acid decarboxylase enzymes derived from the E1 subunits of the mitochondrial branched-chain keto acid dehydrogenase complex from Homo sapiens and Bos taurus have been cloned and functionally expressed in E. coli (Davie et al., 267:16601-16606 (1992); Wynn et al., 267:12400-12403 (1992); Wynn et al., 267:1881-1887 (1992)). In these studies, the authors found that co-expression of chaperonins GroEL and GroES enhanced the specific activity of the decarboxylase by 500-fold (Wynn et al., 267:12400-12403 (1992)). These enzymes are composed of two alpha and two beta subunits.

TABLE 57

Gene	Accession No.	GI No.	Organism

BCKDHB	NP_898871.1	34101272	Homo sapiens
BCKDHA	NP_000700.1	11386135	Homo sapiens
BCKDHB	P21839	115502434	Bos taurus
BCKDHA	P11178	129030	Bos taurus

Conversion of succinate semialdehyde to 4-hydroxybutyrate (Step C, FIG. 9B) can be catalyzed by an oxidoreducatse that converts an aldehyde to alcohol. Exemplary genes encoding enzymes that catalyze the conversion of an aldehyde to alcohol, that is, alcohol dehydrogenase or equivalently aldehyde reductase, include alrA encoding a medium-chain alcohol dehydrogenase for C2-C14 (Tani et al. Appl. Environ. Microbiol. 66:5231-5235 (2000)), ADH2 from Saccharomyces cerevisiae (Atsumi et al. Nature 451:86-89 (2008)), yqhD from E. coli which has preference for molecules longer than C3 (Sulzenbacher et al. Journal of Molecular Biology 342:489-502 (2004)), and bdh I and bdh II from C. acetobutylicum which converts butyrylaldehyde into butanol (Walter et al. Journal of Bacteriology 174:7149-7158 (1992)). The protein sequences for each of these exemplary gene products, if available, can be found using the following GenBank accession numbers:

TABLE 58

Gene	Accession No.	GI No.	Organism

alrA	BAB12273.1	9967138	Acinetobacter sp. Strain M-1
ADH2	NP_014032.1	6323961	Saccharomyces cerevisiae
yqhD	NP_417484.1	16130909	Escherichia coli
bdh I	NP_349892.1	15896543	Clostridium acetobutylicum
bdh II	NP_349891.1	15896542	Clostridium acetobutylicum

Enzymes exhibiting 4-hydroxybutyrate dehydrogenase activity (EC 1.1.1.61) have been characterized in Ralstonia eutropha (Bravo et al. J. Forensic Sci. 49:379-387 (2004), Clostridium kluyveri (Wolff et al. Protein Expr. Purif. 6:206-212 (1995)) and Arabidopsis thaliana (Breitkreuz et al. J. Biol. Chem. 278:41552-41556 (2003)).

TABLE 59

Gene	Accession No.	GI No.	Organism

4-HBd	YP_726053.1	113867564	Ralstonia eutropha H16
4-HBd	EDK35022.1	146348486	Clostridium kluyveri DSM 555
4-HBd	Q94B07	75249805	Arabidopsis thaliana

The adhl gene from Geobacillus thermoglucosidasius M10EXG (Jeon et al., J Biotechnol 135:127-133 (2008)) has been indicated to exhibit high activity on both 4-hydroxybutanal and butanal. Thus this enzyme exhibits 1,4-butanediol dehydrogenase activity.

TABLE 60

Gene	Accession No.	GI No.	Organism

adh1	AAR91477.1	40795502	Geobacillus
			thermoglucosidasius M10EXG

Another exemplary enzyme is 3-hydroxyisobutyrate dehydrogenase which catalyzes the reversible oxidation of 3-hydroxyisobutyrate to methylmalonate semialdehyde. This enzyme participates in valine, leucine and isoleucine degradation and has been identified in bacteria, eukaryotes, and mammals. The enzyme encoded by P84067 from Thermus thermophilus HB8 has been structurally characterized (Lokanath et al. J Mol Biol 352:905-17 (2005)). The reversibility of the human 3-hydroxyisobutyrate dehydrogenase was demonstrated using isotopically-labeled substrate (Manning et al. Biochem J 231:481-484 (1985)). Additional genes encoding this enzyme include 3hidh in Homo sapiens (Hawes et al. Methods Enzymol. 324:218-228 (2000)) and Oryctolagus cuniculus (Chowdhury et al. Biosci. Biotechnol Biochem. 60:2043-2047 (1996); Hawes et al. Methods Enzymol. 324:218-228 (2000)), mmsb in Pseudomonas aeruginosa, and dhat in Pseudomonas putida (Aberhart et al. J Chem. Soc. [Perkin 1] 6:1404-1406 (1979); Chowdhury et al. Biosci. Biotechnol Biochem. 67:438-441 (2003); Chowdhury et al. Biosci. Biotechnol Biochem. 60:2043-2047 (1996)).

TABLE 61

Gene	Accession No.	GI No.	Organism

P84067	P84067	75345323	Thermus thermophilus
mmsb	P28811.1	127211	Pseudomonas aeruginosa
dhat	Q59477.1	2842618	Pseudomonas putida
3hidh	P31937.2	12643395	Homo sapiens
3hidh	P32185.1	416872	Oryctolagus cuniculus

Several 3-hydroxyisobutyrate dehydrogenase enzymes have also been shown to convert malonic semialdehyde to 3-hydroxyproprionic acid (3-HP). Three gene candidates exhibiting this activity are mmsB from Pseudomonas aeruginosa PAO1(62), mmsB from Pseudomonas putida KT2440 (Liao et al., US Publication 2005/0221466) and mmsB from Pseudomonas putida E23 (Chowdhury et al., Biosci. Biotechnol. Biochem. 60:2043-2047 (1996)). An enzyme with 3-hydroxybutyrate dehydrogenase activity in Alcaligenes faecalis M3A has also been identified (Gokam et al., U.S. Pat. No. 7,393,676; Liao et al., US Publication No. 2005/0221466). Additional gene candidates from other organisms including Rhodobacter spaeroides can be inferred by sequence similarity.

TABLE 62

Gene	Accession No.	GI No.	Organism

mmsB	AAA25892.1	151363	Pseudomonas aeruginosa
mmsB	NP_252259.1	15598765	Pseudomonas aeruginosa PAO1
mmsB	NP_746775.1	26991350	Pseudomonas putida KT2440
mmsB	JC7926	60729613	Pseudomonas putida E23
orfB1	AAL26884	16588720	Rhodobacter spaeroides

The conversion of malonic semialdehyde to 3-HP can also be accomplished by two other enzymes: NADH-dependent 3-hydroxypropionate dehydrogenase and NADPH-dependent malonate semialdehyde reductase. An NADH-dependent 3-hydroxypropionate dehydrogenase is thought to participate in beta-alanine biosynthesis pathways from propionate in bacteria and plants (Rathinasabapathi, B. Journal of Plant Pathology 159:671-674 (2002); Stadtman, E. R. J. Am. Chem. Soc. 77:5765-5766 (1955)). This enzyme has not been associated with a gene in any organism to date. NADPH-dependent malonate semialdehyde reductase catalyzes the reverse reaction in autotrophic CO₂-fixing bacteria. Although the enzyme activity has been detected in Metallosphaera sedula, the identity of the gene is not known (Alber et al. J. Bacteriol. 188:8551-8559 (2006)).
Step V in FIG. 9B depicts the conversion of alpha-ketoglutarate to succinyl-CoA. This reaction is catalyzed by alpha-ketoglutarate dehydrogenase, These enzymes are multi-enzyme complexes that catalyze a series of partial reactions which result in acylating oxidative decarboxylation of 2-keto-acids. This 2-keto-acid dehydrogenase complex occupies key positions in intermediary metabolism, and enzyme activity is typically tightly regulated (Fries et al. Biochemistry 42:6996-7002 (2003)). The enzyme shares a complex but common structure composed of multiple copies of three catalytic components: alpha-ketoacid decarboxylase (E1), dihydrolipoamide acyltransferase (E2) and dihydrolipoamide dehydrogenase (E3). The E3 component is shared among all 2-keto-acid dehydrogenase complexes in an organism, while the E1 and E2 components are encoded by different genes. The enzyme components are present in numerous copies in the complex and utilize multiple cofactors to catalyze a directed sequence of reactions via substrate channeling. The overall size of these dehydrogenase complexes is very large, with molecular masses between 4 and 10 million Da (that is, larger than a ribosome).
Activity of enzymes in the 2-keto-acid dehydrogenase family is normally low or limited under anaerobic conditions in E. coli. Increased production of NADH (or NADPH) could lead to a redox-imbalance, and NADH itself serves as an inhibitor to enzyme function. Engineering efforts have increased the anaerobic activity of the E. coli pyruvate dehydrogenase complex (Kim et al. Appl. Environ. Microbiol. 73:1766-1771 (2007); Kim et al. J. Bacteriol. 190:3851-3858) 2008); Zhou et al. Biotechnol. Lett. 30:335-342 (2008)). For example, the inhibitory effect of NADH can be overcome by engineering an H322Y mutation in the E3 component (Kim et al. J. Bacteriol. 190:3851-3858 (2008)). Structural studies of individual components and how they work together in complex provide insight into the catalytic mechanisms and architecture of enzymes in this family (Aevarsson et al. Nat. Struct. Biol. 6:785-792 (1999); Zhou et al. Proc. Natl. Acad. Sci. U.S.A. 98:14802-14807 (2001)). The substrate specificity of the dehydrogenase complexes varies in different organisms, but generally branched-chain ketoacid dehydrogenases have the broadest substrate range.
Alpha-ketoglutarate dehydrogenase (AKGD) converts alpha-ketoglutarate to succinyl-CoA and is the primary site of control of metabolic flux through the TCA cycle (Hansford, R. G. Curr. Top. Bioenerg. 10:217-278 (1980)). Encoded by genes sucA, sucB and lpd in E. coli, AKGD gene expression is downregulated under anaerobic conditions and during growth on glucose (Park et al. Mol. Microbiol. 15:473-482 (1995)). Structural studies of the catalytic core of the E2 component pinpoint specific residues responsible for substrate specificity (Knapp et al. J. Mol. Biol. 280:655-668 (1998)). The Bacillus subtilis AKGD, encoded by odhAB (E1 and E2) and pdhD (E3, shared domain), is regulated at the transcriptional level and is dependent on the carbon source and growth phase of the organism (Resnekov et al. Mol. Gen. Genet. 234:285-296 (1992)). In yeast, the LPD1 gene encoding the E3 component is regulated at the transcriptional level by glucose (Roy and Dawes J. Gen. Microbiol. 133:925-933 (1987)). The E1 component, encoded by KGD1, is also regulated by glucose and activated by the products of HAP2 and HAP3 (Repetto and Tzagoloff Mol. Cell Biol. 9:2695-2705 (1989)). The AKGD enzyme complex, inhibited by products NADH and succinyl-CoA, is well-studied in mammalian systems, as impaired function of has been linked to several neurological diseases (Tretter and dam-Vizi Philos. Trans. R. Soc. Lond B Biol. Sci. 360:2335-2345 (2005)).

TABLE 63

Gene	Accession No.	GI No.	Organism

sucA	NP_415254.1	16128701	Escherichia coli str. K12
sucB	NP_415255.1	16128702	Escherichia coli str. K12
lpd	NP_414658.1	16128109	Escherichia coli str. K12
odhA	P23129.2	51704265	Bacillus subtilis
odhB	P16263.1	129041	Bacillus subtilis
pdhD	P21880.1	118672	Bacillus subtilis
KGD1	NP_012141.1	6322066	Saccharomyces cerevisiae
KGD2	NP_010432.1	6320352	Saccharomyces cerevisiae
LPD1	NP_116635.1	14318501	Saccharomyces cerevisiae

Steps A and H in FIG. 9B involve CoA transferase activities. The gene products of cat1, cat2, and cat3 of Clostridium kluyveri have been shown to exhibit succinyl-CoA, 4-hydroxybutyryl-CoA, and butyryl-CoA acetyltransferase activities (Seedorf et al. Proc Natl Acad Sci U.S.A. 105(6):2128-2133 (2008); Sohling and Gottschalk J Bacteriol 178(3):871-880 (1996)). Similar CoA transferase activities are also present in Trichomonas vaginalis (van Grinsven et al., J. Biol. Chem. 283:1411-1418 (2008)) and Trypanosoma brucei (Riviere et al., J. Biol. Chem. 279:45337-45346 (2004)).

TABLE 64

Gene	Accession No.	GI No.	Organism

cat1	P38946.1	729048	Clostridium kluyveri
cat2	P38942.2	1705614	Clostridium kluyveri
cat3	EDK35586.1	146349050	Clostridium kluyveri
TVAG_395550	XP_001330176	123975034	Trichomonas
			vaginalis G3
Tb11.02.0290	XP_828352	71754875	Trypanosoma brucei

An additionally useful enzyme for this type of transformation is acyl-CoA:acetate-CoA transferase, also known as acetate-CoA transferase (EC 2.8.3.8), which has been shown to transfer the CoA moiety to acetate from a variety of branched and linear acyl-CoA substrates, including isobutyrate (Matthies and Schink Appl Environ Microbiol 58:1435-1439 (1992)), valerate (Vanderwinkel et al. Biochem. Biophys. Res Commun. 33:902-908 (1968)) and butanoate (Vanderwinkel, supra (1968)). This enzyme is encoded by atoA (alpha subunit) and atoD (beta subunit) in E. coli sp. K12 (Korolev et al. Acta Crystallogr. D Biol Crystallogr. 58:2116-2121 (2002); Vanderwinkel, supra (1968)). Similar enzymes exist in Corynebacterium glutamicum ATCC 13032 (Duncan et al., 68:5186-5190 (2002)), Clostridium saccharoperbutylacetonicum (Kosaka et al., Biosci. Biotechnol Biochem. 71:58-68 (2007)), and Clostridium acetobutylicum (Cary et al., 56:1576-1583 (1990); Wiesenbom et al., 55:323-329 (1989)).

TABLE 65

Gene	Accession No.	GI No.	Organism

atoA	P76459.1	2492994	Escherichia coli K12
atoD	P76458.1	2492990	Escherichia coli K12
actA	YP_226809.1	62391407	Corynebacterium glutamicum
cg0592	YP_224801.1	62389399	Corynebacterium glutamicum
ctfA	NP_149326.1	15004866	Clostridium acetobutylicum
ctfB	NP_149327.1	15004867	Clostridium acetobutylicum
ctfA	AAP42564.1	31075384	Clostridium
			saccharoperbutylacetonicum
ctfB	AAP42565.1	31075385	Clostridium
			saccharoperbutylacetonicum

The glutaconate-CoA-transferase (EC 2.8.3.12) enzyme from anaerobic bacterium Acidaminococcus fermentans reacts with diacid glutaconyl-CoA and 3-butenoyl-CoA (Mack and Buckel FEBS Lett. 405:209-212 (1997)). The genes encoding this enzyme are gctA and gctB. This enzyme has reduced but detectable activity with other CoA derivatives including glutaryl-CoA, 2-hydroxyglutaryl-CoA, adipyl-CoA and acrylyl-CoA (Buckel et al. Eur. J. Biochem. 118:315-321 (1981)). The enzyme has been cloned and expressed in E. coli (Mac et al. Eur. J. Biochem. 226:41-51 (1994)).

TABLE 66

Gene	Accession No.	GI No.	Organism

gctA	CAA57199.1	559392	Acidaminococcus fermentans
gctB	CAA57200.1	559393	Acidaminococcus fermentans

Step H of FIG. 9B involves CoA synthetase or ligase reactions for 4-HB as the substrate. Exemplary CoA-ligases include the rat dicarboxylate-CoA ligase for which the sequence is yet uncharacterized (Vamecq et al., Biochemical Journal 230:683-693 (1985)), either of the two characterized phenylacetate-CoA ligases from P. chrysogenum (Lamas-Maceiras et al., Biochem. J. 395:147-155 (2005); Wang et al., Biochem Biophy Res Commun 360(2):453-458 (2007)), the phenylacetate-CoA ligase from Pseudomonas putida (Martinez-Blanco et al., J. Biol. Chem. 265:7084-7090 (1990)), and the 6-carboxyhexanoate-CoA ligase from Bacillus subtilis (Bower et al., J. Bacteriol. 178(14):4122-4130 (1996)). Additional candidate enzymes are acetoacetyl-CoA synthetases from Mus musculus (Hasegawa et al., Biochim Biophys Acta 1779:414-419 (2008)) and Homo sapiens (Ohgami et al., Biochem Pharmacol 65:989-994 (2003)) which naturally catalyze the ATP-dependant conversion of acetoacetate into acetoacetyl-CoA. 4-hydroxybutyryl-CoA synthetase activity has been demonstrated in Metallosphaera sedula (Berg et al., Science 318:1782-1786 (2007)). This function has been tentatively assigned to the Msed_—1422 gene.

TABLE 67

Gene	Accession No.	GI No.	Organism

TABLE 68

Gene	Accession No.	GI No.	Organism

AF1211	NP_070039.1	11498810	Archaeoglobus fulgidus DSM
			4304
scs	YP_135572.1	55377722	Haloarcula marismortui ATCC
			43049
PAE3250	NP_560604.1	18313937	Pyrobaculum aerophilum str.
			IM2

Exemplary phosphate transferring acyltransferases that transform 4-hydroxybutyryl-CoA to 4-hydroxybutyryl-phosphate include phosphotransacetylase, encoded by pta, and phosphotransbutyrylase, encoded by ptb. The pta gene from E. coli encodes an enzyme that can convert acetyl-CoA into acetyl-phosphate, and vice versa (Suzuki, T. Biochim. Biophys. Acta 191:559-569 (1969)). This enzyme can also utilize propionyl-CoA instead of acetyl-CoA forming propionate in the process (Hesslinger et al. Mol. Microbiol 27:477-492 (1998)). Similarly, the ptb gene from C. acetobutylicum encodes an enzyme that can convert butyryl-CoA into butyryl-phosphate (Walter et al. Gene 134(1): p. 107-11 (1993)); Huang et al. J Mol Microbiol Biotechnol 2(1): p. 33-38 (2000). Additional ptb genes can be found in butyrate-producing bacterium L2-50 (Louis et al. J. Bacteriol. 186:2099-2106 (2004)) and Bacillus megaterium (Vazquez et al. Curr. Microbiol 42:345-349 (2001)).

TABLE 69

Gene	Accession No.	GI No.	Organism

pta	NP_416800.1	16130232	Escherichia coli
ptb	NP_349676	15896327	Clostridium acetobutylicum
ptb	AAR19757.1	38425288	butyrate-producing bacterium
			L2-50
ptb	CAC07932.1	10046659	Bacillus megaterium

The conversion of 4-hydroxybutyryl-phosphate to 4-hydroxybutanal can be catalyzed by an oxidoreductase in the EC class 1.2.1. Aspartate semialdehyde dehydrogenase (ASD, EC 1.2.1.11) catalyzes the NADPH-dependent reduction of 4-aspartyl phosphate to aspartate-4-semialdehyde. ASD participates in amino acid biosynthesis and recently has been studied as an antimicrobial target (Hadfield et al., 40:14475-14483 (2001)). The E. coli ASD structure has been solved (Hadfield et al., 289:991-1002 (1999)) and the enzyme has been shown to accept the alternate substrate beta-3-methylaspartyl phosphate (Shames et al., 259:15331-15339 (1984)). The Haemophilus influenzae enzyme has been the subject of enzyme engineering studies to alter substrate binding affinities at the active site (Blanco et al., Acta Crystallogr. D. Biol. Crystallogr. 60:1388-1395 (2004); Blanco et al., Acta Crystallogr. D. Biol. Crystallogr. 60:1808-1815 (2004)). Other ASD candidates are found in Mycobacterium tuberculosis (Shafiani et al., J Appl Microbiol 98:832-838 (2005)), Methanococcus jannaschii (Faehnle et al., 353:1055-1068 (2005)), and the infectious microorganisms Vibrio cholera and Heliobacter pylori (Moore et al., Protein Expr. Purif. 25:189-194 (2002)). A related enzyme candidate is acetylglutamylphosphate reductase (EC 1.2.1.38), an enzyme that naturally reduces acetylglutamylphosphate to acetylglutamate-5-semialdehyde, found in S. cerevisiae (Pauwels et al., Eur. J Biochem. 270:1014-1024 (2003)), B. subtilis (O'Reilly et al., 140 (Pt 5):1023-1025 (1994)) and other organisms.

TABLE 70

Gene	Accession No.	GI No.	Organism

asd	NP_417891.1	16131307	Escherichia coli
asd	YP_248335.1	68249223	Haemophilus influenzae
asd	AAB49996	1899206	Mycobacterium tuberculosis
VC2036	NP_231670	15642038	Vibrio cholera
asd	YP_002301787.1	210135348	Heliobacter pylori
ARG5,6	NP_010992.1	6320913	Saccharomyces cerevisiae
argC	NP_389001.1	16078184	Bacillus subtilis

Other exemplary enzymes in this class include glyceraldehyde 3-phosphate dehydrogenase which converts glyceraldehyde-3-phosphate into D-glycerate 1,3-bisphosphate (e.g., E. coli gapA (Branlant et al., Eur. J. Biochem. 150:61-66 (1985))), N-acetyl-gamma-glutamyl-phosphate reductase which converts N-acetyl-L-glutamate-5-semialdehyde into N-acetyl-L-glutamyl-5-phosphate (e.g., E. coli argC (Parsot et al., Gene. 68:275-283 (1988))), and glutamate-5-semialdehyde dehydrogenase which converts L-glutamate-5-semialdehyde into L-glutamyl-5-phospate (e.g., E. coli proA (Smith et al., J. Bacteriol. 157:545-551 (1984a))). Genes encoding glutamate-5-semialdehyde dehydrogenase enzymes from Salmonella typhimurium (Mahan et al., J Bacteriol. 156:1249-1262 (1983)) and Campylobacter jejuni (Louie et al., 240:29-35 (1993)) were cloned and expressed in E. coli.

TABLE 71

Gene	Accession No.	GI No.	Organism

gapA	P0A9B2.2	71159358	Escherichia coli
argC	NP_418393.1	16131796	Escherichia coli
proA	NP_414778.1	16128229	Escherichia coli
proA	NP_459319.1	16763704	Salmonella typhimurium
proA	P53000.2	9087222	Campylobacter jejuni

In some embodiments, the 2-amino-4-ketopentanoate (AKP) thiolase encoded by one or more genes selected from the group consisting of ortA (α), ortB (β), Amet_—2368 (α), Amet_—2369 (β), Teth514_—1478 (α), Teth514_—1479 (β), TTE1235 (α), and thrC (β).
In some embodiments, the AKP dehydrogenase is encoded by one or more genes selected from the group consisting of thrA, akthr2, hom6, hom1, hom2, fadB, fadJ, Hbd2, Hbd1, hbd, HSD17B10, phbB, phaB, Msed_—1423, Msed_—0399, Msed_—0389, Msed_—1993, adh, adhA, adh-A, mdh, ldhA, ldh, and bdh.
In some embodiments, the 2-amino-4-hydroxypentanoate aminotransferase is encoded by one or more genes selected from the group consisting of aspC, AAT2, ASP5, got2, avtA, lysN, AadAT-II, dat, lat, ygjG, spuC, SkyPYD4, SkUGA1, UGA1, Abat, Abat, Gta-1, gabT, and puuE.
In some embodiments, the 2-amino-4-hydroxypentanoate oxidoreductase (deaminating) is encoded by one or more genes selected from the group consisting of gdhA, gdh, gdhA1, rocG, gdh1, gdh2, GDH, GDH2, ldh and nadX.
In some embodiments, the 2-oxo-4-hydroxypentanoate decarboxylase is encoded by one or more genes selected from the group consisting of pdc, pdc1, mdlC, dpgB, ilvB-1, kgd, kdcA, lysA, panD, cadA, ldc, ldcC, AF323910.1:1 . . . 1299, odc1, VV2_—1235, dmpH, dmpE, xylII, xylIII, Reut_B5691, Reut_B5692, CAD, pad1, pofK (pad), padC, pad, adc, cbei_—3835, CLL_A2135, RBAM_—030030,
In some embodiments, the 3-hydroxybutyraldehdye reductase is encoded by one or more genes selected from the group consisting of alrA, ADH2, yqhD, bdh I, bdh II, adhA, 4hbd, adhI, P84067, mmsb, dhat, and 3hidh.
In some embodiments, the AKP aminotransferase is encoded by one or more genes selected from the group consisting of aspC, AAT2, ASP5, got2, avtA, lysN, AadAT-II, dat, lat, ygjG, spuC, SkyPYD4, SkUGA1, UGA1, Abat, Gta-1, gabT, and puuE.
In some embodiments, the AKP oxidoreductase (deaminating) is encoded by one or more genes selected from the group consisting of gdhA, gdh, gdhA1, rocG, gdh1, gdh2, GDH, GDH2, ldh and nadX. In some embodiments, the 2,4-dioxopentanoate decarboxylase is encoded by one or more genes selected from the group consisting of pdc, pdc1, mdlC, dpgB, ilvB-1, kgd, kdcA, lysA, panD, cadA, ldc, ldcC, AF323910.1:1 . . . 1299, odc1, VV2_—1235, dmpH, dmpE, xylII, xylIII, Reut_B5691, Reut_B5692, CAD, pad1, padC, and pad, adc, cbei_—3835, CLL_A2135, RBAM_—030030.
In some embodiments, the 3-oxobutyraldehyde reductase (ketone reducing) is encoded by one or more genes selected from the group consisting of thrA, akthr2, hom6, hom1, hom2, fadB, fadJ, Hbd2, Hbd1, hbd, HSD17B10, phbB, phaB, Msed_—1423, Msed_—0399, Msed_—0389, Msed_—1993, adh, adhA, adh-A, mdh, ldhA, ldh, and bdh.
In some embodiments, the 3-oxobutyraldehyde reductase (aldehyde reducing) is encoded by one or more genes selected from the group consisting of alrA, ADH2, yqhD, bdh I, bdh II, adhA, 4hbd, adhI, P84067, mmsb, dhat, and 3hidh.
In some embodiments, the 4-hydroxy-2-butanone reductase is encoded by one or more genes selected from the group consisting of thrA, akthr2, hom6, hom1, hom2, fadB, fadJ, Hbd2, Hbd1, hbd, HSD17B10, phbB, phaB, Msed_—1423, Msed_—0399, Msed_—0389, Msed_—1993, adh, adhA, adh-A, mdh, ldhA, ldh, and bdh.
In some embodiments, the AKP decarboxylase is encoded by one or more genes selected from the group consisting of pdc, pdc1, mdlC, dpgB, ilvB-1, kgd, kdcA, lysA, panD, cadA, ldc, ldcC, AF323910.1:1 . . . 1299, odc1, VV2_—1235, dmpH, dmpE, xylII, xylIII, Reut_B5691, Reut_B5692, CAD, pad1, pofK(pad), padC, pad.
In some embodiments, the 4-aminobutan-2-one aminotransferase is encoded by one or more genes selected from the group consisting of aspC, AAT2, ASP5, got2, avtA, lysN, AadAT-II, dat, lat, ygjG, spuC, SkyPYD4, SkUGA1, UGA1, Abat, Gta-1, gabT, and puuE.
In some embodiments, the 4-aminobutan-2-one oxidoreductase (deaminating) is encoded by one or more genes selected from the group consisting of gdhA, gdh, gdhA1, rocG, gdh1, gdh2, GDH, GDH2, ldh, nadX, kdd and lysDH.
In some embodiments, the 4-aminobutan-2-one ammonia-lyase is encoded by one or more genes selected from the group consisting of aspA, ansB, mal and BAA28709.
In some embodiments, the butenone hydratase is encoded by one or more genes selected from the group consisting of fumA, fumB, fumC, fumH, fum1, MmcB, MmcC, hmd, BACCAP_—02294, ANACOL_—02527, NtherDRAFT_—2368, dmdA, dmdB, crt, crt1, ech paaA, paaB, phaA, phaB, maoC, paaF, paaG, abfD, Msed_—1220, fadA, fadB, fadI, fadJ, and fadR.
In some embodiments, the AKP ammonia-lyase is encoded by one or more genes selected from the group consisting of aspA, ansB, mal and BAA28709.
In some embodiments, the acetylacrylate decarboxylase is encoded by one or more genes selected from the group consisting of pdc, pdc1, mdlC, dpgB, ilvB-1, kgd, kdcA, lysA, panD, cadA, ldc, ldcC, AF323910.1:1 . . . 1299, odc1, VV2_—1235, dmpH, dmpE, xylII, xylIII, Reut_B5691, Reut_B5692, CAD, pad1, pofK (pad), padC, pad, adc, cbei_—3835, CLL_A2135, RBAM_—030030)
In some embodiments, the acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming) is encoded by one or more genes selected from the group consisting of acr1, sucD, bphG, bld, adhE, Msed_—0709, mcr, asd-2, Saci_—2370, Ald, and eutE.
In some embodiments, the acetoacetyl-CoA reductase (CoA-dependent, alcohol forming) is encoded by one or more genes selected from the group consisting of adhE, adhE2, mcr, Rcas_—2929, NAP1_—02720, MGP2080_—00535, and FAR.
In some embodiments, the acetoacetyl-CoA reductase (ketone reducing) is encoded by one or more genes selected from the group consisting of thrA, akthr2, hom6, hom1, hom2, fadB, fadJ, Hbd2, Hbd1, hbd, HSD17B10, phbB, phaB, Msed_—1423, Msed_—0399, Msed_—0389, Msed_—1993, adh, adhA, adh-A, mdh, ldhA, ldh, and bdh.
In some embodiments, the 3-hydroxybutyryl-CoA reductase (aldehyde forming) is encoded by one or more genes selected from the group consisting of acr1, sucD, bphG, bld, adhE, Msed_—0709, mcr, asd-2, SacI_—2370, Ald, and eutE.
In some embodiments, the 3-hydroxybutyryl-CoA reductase (alcohol forming) is encoded by one or more genes selected from the group consisting of adhE, adhE2, mcr, Rcas_—2929, NAP1_—02720, MGP2080_—00535, and FAR.
In some embodiments, the 4-hydroxybutyryl-CoA dehydratase is encoded by one or more genes selected from the group consisting of fumA, fumB, fumC, fumH, fum1, MmcB, MmcC, hmd, BACCAP_—02294, ANACOL_—02527, NtherDRAFT_—2368, dmdA, dmdB, crt, crt1, ech, paaA, paaB, phaA, phaB, maoC, paaF, paaG, abfD, Msed_—1220, fadA, fadB, fadI, fadJ, and fadR.
In some embodiments, the crotonase is encoded by one or more genes selected from the group consisting of fumA, fumB, fumC, fumH, fumI, MmcB, MmcC, hmd, BACCAP_—02294, ANACOL_—02527, NtherDRAFT_—2368, dmdA, dmdB, crt, crt1, ech paaA, paaB, phaA, phaB, maoC, paaF, paaG, abfD, Msed_—1220, fadA, fadB, fadI, fadJ, and fadR.
In some embodiments, the 3-hydroxybutyryl-CoA hydrolase, transferase, or synthetase is encoded by one or more genes selected from a group consisting of acot12, ACH1, acot8, tesB, acot8, teas, ybgC, paaI, pbdB, gctA, gctB, and hibCH.
In some embodiments, 3-hydroxybutyrate reductase is encoded by one or more genes selected from a group consisting of car, npt, fadD9, BCG_—2812c, nfa20150, nfa40540, SGR_—6790, SGR_—665, griC, griD.
The non-naturally occurring microbial organisms of the invention can be produced by introducing expressible nucleic acids encoding one or more of the enzymes or proteins participating in one or more 1,3-butanediol biosynthetic pathways. Depending on the host microbial organism chosen for biosynthesis, nucleic acids for some or all of a particular 1,3-butanediol biosynthetic pathway can be expressed. For example, if a chosen host is deficient in one or more enzymes or proteins for a desired biosynthetic pathway, then expressible nucleic acids for the deficient enzyme(s) or protein(s) are introduced into the host for subsequent exogenous expression. Alternatively, if the chosen host exhibits endogenous expression of some pathway genes, but is deficient in others, then an encoding nucleic acid is needed for the deficient enzyme(s) or protein(s) to achieve 1,3-butanediol biosynthesis. Thus, a non-naturally occurring microbial organism of the invention can be produced by introducing exogenous enzyme or protein activities to obtain a desired biosynthetic pathway or a desired biosynthetic pathway can be obtained by introducing one or more exogenous enzyme or protein activities that, together with one or more endogenous enzymes or proteins, produces a desired product such as 1,3-butanediol.
Host microbial organisms can be selected from, and the non-naturally occurring microbial organisms generated in, for example, bacteria, yeast, fungus or any of a variety of other microorganisms applicable to fermentation processes. Exemplary bacteria include species selected from Escherichia coli, Klebsiella oxytoca, Anaerobiospirillum succiniciproducens, Actinobacillus succinogenes, Mannheimia succiniciproducens, Rhizobium etli, Bacillus subtilis, Corynebacterium glutamicum, Gluconobacter oxydans, Zymomonas mobilis, Lactococcus lactis, Lactobacillus plantarum, Streptomyces coelicolor, Clostridium acetobutylicum, Pseudomonas fluorescens, and Pseudomonas putida. Exemplary yeasts or fungi include species selected from Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, Kluyveromyces marxianus, Aspergillus terreus, Aspergillus niger, Pichia pastoris, Rhizopus arrhizus, Rhizobus oryzae, Yarrowia lipolytica, and the like. E. coli is a particularly useful host organism since it is a well characterized microbial organism suitable for genetic engineering. Other particularly useful host organisms include yeast such as Saccharomyces cerevisiae. It is understood that any suitable microbial host organism can be used to introduce metabolic and/or genetic modifications to produce a desired product.
Depending on the 1,3-butanediol biosynthetic pathway constituents of a selected host microbial organism, the non-naturally occurring microbial organisms of the invention will include at least one exogenously expressed 1,3-butanediol pathway-encoding nucleic acid and up to all encoding nucleic acids for one or more 1,3-butanediol biosynthetic pathways. For example, 1,3-butanediol biosynthesis can be established in a host deficient in a pathway enzyme or protein through exogenous expression of the corresponding encoding nucleic acid. In a host deficient in all enzymes or proteins of a 1,3-butanediol pathway, exogenous expression of all enzyme or proteins in the pathway can be included, although it is understood that all enzymes or proteins of a pathway can be expressed even if the host contains at least one of the pathway enzymes or proteins. For example, exogenous expression of all enzymes or proteins in a pathway for production of 1,3-butanediol can be included.
Given the teachings and guidance provided herein, those skilled in the art will understand that the number of encoding nucleic acids to introduce in an expressible form will, at least, parallel the 1,3-butanediol pathway deficiencies of the selected host microbial organism. Therefore, a non-naturally occurring microbial organism of the invention can have one, two, three, four, five, up to all nucleic acids encoding the enzymes or proteins constituting a 1,3-butanediol biosynthetic pathway disclosed herein. In some embodiments, the non-naturally occurring microbial organisms also can include other genetic modifications that facilitate or optimize 1,3-butanediol biosynthesis or that confer other useful functions onto the host microbial organism. One such other functionality can include, for example, augmentation of the synthesis of one or more of the 1,3-butanediol pathway precursors such as acetyl-CoA.
Generally, a host microbial organism is selected such that it produces the precursor of a 1,3-butanediol pathway, either as a naturally produced molecule or as an engineered product that either provides de novo production of a desired precursor or increased production of a precursor naturally produced by the host microbial organism. For example, acetyl-CoA is produced naturally in a host organism such as E. coli. A host organism can be engineered to increase production of a precursor, as disclosed herein. In addition, a microbial organism that has been engineered to produce a desired precursor can be used as a host organism and further engineered to express enzymes or proteins of a 1,3-butanediol pathway.
In some embodiments, a non-naturally occurring microbial organism of the invention is generated from a host that contains the enzymatic capability to synthesize 1,3-butanediol. In this specific embodiment it can be useful to increase the synthesis or accumulation of a 1,3-butanediol pathway product to, for example, drive 1,3-butanediol pathway reactions toward 1,3-butanediol production. Increased synthesis or accumulation can be accomplished by, for example, overexpression of nucleic acids encoding one or more of the above-described 1,3-butanediol pathway enzymes or proteins. Overexpression of the enzyme or enzymes and/or protein or proteins of the 1,3-butanediol pathway can occur, for example, through exogenous expression of the endogenous gene or genes, or through exogenous expression of the heterologous gene or genes. Therefore, naturally occurring organisms can be readily generated to be non-naturally occurring microbial organisms of the invention, for example, producing 1,3-butanediol, through overexpression of one, two, three, four, five, that is, up to all nucleic acids encoding 1,3-butanediol biosynthetic pathway enzymes or proteins. In addition, a non-naturally occurring organism can be generated by mutagenesis of an endogenous gene that results in an increase in activity of an enzyme in the 1,3-butanediol biosynthetic pathway.
In particularly useful embodiments, exogenous expression of the encoding nucleic acids is employed. Exogenous expression confers the ability to custom tailor the expression and/or regulatory elements to the host and application to achieve a desired expression level that is controlled by the user. However, endogenous expression also can be utilized in other embodiments such as by removing a negative regulatory effector or induction of the gene's promoter when linked to an inducible promoter or other regulatory element. Thus, an endogenous gene having a naturally occurring inducible promoter can be up-regulated by providing the appropriate inducing agent, or the regulatory region of an endogenous gene can be engineered to incorporate an inducible regulatory element, thereby allowing the regulation of increased expression of an endogenous gene at a desired time. Similarly, an inducible promoter can be included as a regulatory element for an exogenous gene introduced into a non-naturally occurring microbial organism.
It is understood that, in methods of the invention, any of the one or more exogenous nucleic acids can be introduced into a microbial organism to produce a non-naturally occurring microbial organism of the invention. The nucleic acids can be introduced so as to confer, for example, 1,3-butanediol biosynthetic pathway onto the microbial organism. Alternatively, encoding nucleic acids can be introduced to produce an intermediate microbial organism having the biosynthetic capability to catalyze some of the required reactions to confer 1,3-butanediol biosynthetic capability. For example, a non-naturally occurring microbial organism having 1,3-butanediol biosynthetic pathway can comprise at least two exogenous nucleic acids encoding desired enzymes or proteins. For example, the non-naturally occurring microbial organism can comprise at least two exogenous nucleic acids encoding an acetoacetyl-CoA reductase (CoA-dependent, alcohol forming) and a 4-hydroxy,2-butanone reductase (FIG. 2, steps D and F). Thus, it is understood that any combination of two or more enzymes or proteins of a biosynthetic pathway can be included in a non-naturally occurring microbial organism of the invention. Similarly, it is understood that any combination of three or more enzymes or proteins of a biosynthetic pathway can be included in a non-naturally occurring microbial organism of the invention and so forth, as desired, so long as the combination of enzymes and/or proteins of the desired biosynthetic pathway results in production of the corresponding desired product. For example, the non-naturally occurring microbial organism can comprise at least three exogenous nucleic acids encoding an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming), a 3-oxobutyraldehyde reductase (ketone reducing), and a 3-hydroxybutyraldehyde reductase (FIG. 2, steps A, B and C). Similarly, any combination of four, or more enzymes or proteins of a biosynthetic pathway as disclosed herein can be included in a non-naturally occurring microbial organism of the invention, as desired, so long as the combination of enzymes and/or proteins of the desired biosynthetic pathway results in production of the corresponding desired product. For example, the non-naturally occurring microbial organism can comprise at least five exogenous nucleic acids encoding an AKP thiolase, an AKP decarboxylase, a 4-aminobutan-2-one ammonia-lyase, a butenone hydratase, and a 4-hydroxy,2-butanone reductase, (FIG. 8B, steps A, E, F, G and H). Other individual pathways depicted in the figures are also contemplated embodiments of the compositions and methods provided herein.
In addition to the biosynthesis of 1,3-butanediol as described herein, the non-naturally occurring microbial organisms and methods of the invention also can be utilized in various combinations with each other and with other microbial organisms and methods well known in the art to achieve product biosynthesis by other routes. For example, one alternative to produce 1,3-butanediol other than use of the 1,3-butanediol producers is through addition of another microbial organism capable of converting 1,3-butanediol pathway intermediate to 1,3-butanediol. One such procedure includes, for example, the fermentation of a microbial organism that produces 1,3-butanediol pathway intermediate. The 1,3-butanediol pathway intermediate can then be used as a substrate for a second microbial organism that converts the 1,3-butanediol pathway intermediate to 1,3-butanediol. The 1,3-butanediol pathway intermediate can be added directly to another culture of the second organism or the original culture of the 1,3-butanediol pathway intermediate producers can be depleted of these microbial organisms by, for example, cell separation, and then subsequent addition of the second organism to the fermentation broth can be utilized to produce the final product without intermediate purification steps.
In other embodiments, the non-naturally occurring microbial organisms and methods of the invention can be assembled in a wide variety of subpathways to achieve biosynthesis of, for example, 1,3-butanediol. In these embodiments, biosynthetic pathways for a desired product of the invention can be segregated into different microbial organisms, and the different microbial organisms can be co-cultured to produce the final product. In such a biosynthetic scheme, the product of one microbial organism is the substrate for a second microbial organism until the final product is synthesized. For example, the biosynthesis of 1,3-butanediol can be accomplished by constructing a microbial organism that contains biosynthetic pathways for conversion of one pathway intermediate to another pathway intermediate or the product. Alternatively, 1,3-butanediol also can be biosynthetically produced from microbial organisms through co-culture or co-fermentation using two organisms in the same vessel, where the first microbial organism produces 1,3-butanediol intermediate and the second microbial organism converts the intermediate to 1,3-butanediol.
Given the teachings and guidance provided herein, those skilled in the art will understand that a wide variety of combinations and permutations exist for the non-naturally occurring microbial organisms and methods of the invention together with other microbial organisms, with the co-culture of other non-naturally occurring microbial organisms having subpathways and with combinations of other chemical and/or biochemical procedures well known in the art to produce 1,3-butanediol.
Sources of encoding nucleic acids for 1,3-butanediol pathway enzyme or protein can include, for example, any species where the encoded gene product is capable of catalyzing the referenced reaction. Such species include both prokaryotic and eukaryotic organisms including, but not limited to, bacteria, including archaea and eubacteria, and eukaryotes, including yeast, plant, insect, animal, and mammal, including human. Exemplary species for such sources include, for example, Escherichia coli, as well as other exemplary species disclosed herein or available as source organisms for corresponding genes. However, with the complete genome sequence available for now more than 550 species (with more than half of these available on public databases such as the NCBI), including 395 microorganism genomes and a variety of yeast, fungi, plant, and mammalian genomes, the identification of genes encoding the requisite 1,3-butanediol biosynthetic activity for one or more genes in related or distant species, including for example, homologues, orthologs, paralogs and nonorthologous gene displacements of known genes, and the interchange of genetic alterations between organisms is routine and well known in the art. Accordingly, the metabolic alterations allowing biosynthesis of 1,3-butanediol described herein with reference to a particular organism such as E. coli can be readily applied to other microorganisms, including prokaryotic and eukaryotic organisms alike. Given the teachings and guidance provided herein, those skilled in the art will know that a metabolic alteration exemplified in one organism can be applied equally to other organisms.
In some instances, such as when an alternative 1,3-butanediol biosynthetic pathway exists in an unrelated species, 1,3-butanediol biosynthesis can be conferred onto the host species by, for example, exogenous expression of a paralog or paralogs from the unrelated species that catalyzes a similar, yet non-identical metabolic reaction to replace the referenced reaction. Because certain differences among metabolic networks exist between different organisms, those skilled in the art will understand that the actual gene usage between different organisms can differ. However, given the teachings and guidance provided herein, those skilled in the art also will understand that the teachings and methods of the invention can be applied to all microbial organisms using the cognate metabolic alterations to those exemplified herein to construct a microbial organism in a species of interest that will synthesize 1,3-butanediol.
Host microbial organisms can be selected from, and the non-naturally occurring microbial organisms generated in, for example, bacteria, yeast, fungus or any of a variety of other microorganisms applicable to fermentation processes. Exemplary bacteria include species selected from Escherichia coli, Klebsiella oxytoca, Anaerobiospirillum succiniciproducens, Actinobacillus succinogenes, Mannheimia succiniciproducens, Rhizobium etli, Bacillus subtilis, Corynebacterium glutamicum, Gluconobacter oxydans, Zymomonas mobilis, Lactococcus lactis, Lactobacillus plantarum, Streptomyces coelicolor, Clostridium acetobutylicum, Pseudomonas fluorescens, and Pseudomonas putida. Exemplary yeasts or fungi include species selected from Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, Kluyveromyces marxianus, Aspergillus terreus, Aspergillus niger and Pichia pastoris. E. coli is a particularly useful host organism since it is a well characterized microbial organism suitable for genetic engineering. Other particularly useful host organisms include yeast such as Saccharomyces cerevisiae.
Methods for constructing and testing the expression levels of a non-naturally occurring 1,3-butanediol-producing host can be performed, for example, by recombinant and detection methods well known in the art. Such methods can be found described in, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual, Third Ed., Cold Spring Harbor Laboratory, New York (2001); and Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1999).
Exogenous nucleic acid sequences involved in a pathway for production of 1,3-butanediol can be introduced stably or transiently into a host cell using techniques well known in the art including, but not limited to, conjugation, electroporation, chemical transformation, transduction, transfection, and ultrasound transformation. For exogenous expression in E. coli or other prokaryotic cells, some nucleic acid sequences in the genes or cDNAs of eukaryotic nucleic acids can encode targeting signals such as an N-terminal mitochondrial or other targeting signal, which can be removed before transformation into prokaryotic host cells, if desired. For example, removal of a mitochondrial leader sequence led to increased expression in E. coli (Hoffmeister et al., J. Biol. Chem. 280:4329-4338 (2005)). For exogenous expression in yeast or other eukaryotic cells, genes can be expressed in the cytosol without the addition of leader sequence, or can be targeted to mitochondrion or other organelles, or targeted for secretion, by the addition of a suitable targeting sequence such as a mitochondrial targeting or secretion signal suitable for the host cells. Thus, it is understood that appropriate modifications to a nucleic acid sequence to remove or include a targeting sequence can be incorporated into an exogenous nucleic acid sequence to impart desirable properties. Furthermore, genes can be subjected to codon optimization with techniques well known in the art to achieve optimized expression of the proteins.
An expression vector or vectors can be constructed to include one or more 1,3-butanediol biosynthetic pathway encoding nucleic acids as exemplified herein operably linked to expression control sequences functional in the host organism. Expression vectors applicable for use in the microbial host organisms of the invention include, for example, plasmids, phage vectors, viral vectors, episomes and artificial chromosomes, including vectors and selection sequences or markers operable for stable integration into a host chromosome. Additionally, the expression vectors can include one or more selectable marker genes and appropriate expression control sequences. Selectable marker genes also can be included that, for example, provide resistance to antibiotics or toxins, complement auxotrophic deficiencies, or supply critical nutrients not in the culture media. Expression control sequences can include constitutive and inducible promoters, transcription enhancers, transcription terminators, and the like which are well known in the art. When two or more exogenous encoding nucleic acids are to be co-expressed, both nucleic acids can be inserted, for example, into a single expression vector or in separate expression vectors. For single vector expression, the encoding nucleic acids can be operationally linked to one common expression control sequence or linked to different expression control sequences, such as one inducible promoter and one constitutive promoter. The transformation of exogenous nucleic acid sequences involved in a metabolic or synthetic pathway can be confirmed using methods well known in the art. Such methods include, for example, nucleic acid analysis such as Northern blots or polymerase chain reaction (PCR) amplification of mRNA, or immunoblotting for expression of gene products, or other suitable analytical methods to test the expression of an introduced nucleic acid sequence or its corresponding gene product. It is understood by those skilled in the art that the exogenous nucleic acid is expressed in a sufficient amount to produce the desired product, and it is further understood that expression levels can be optimized to obtain sufficient expression using methods well known in the art and as disclosed herein.
The invention provides a method for producing 1,3-BDO that includes culturing the non-naturally occurring microbial organism disclosed herein, under conditions and for a sufficient period of time to produce 1,3-BDO, including organisms that incorporate one, two, three, four, five, up to all exogenous nucleic acids encoding enzymes that complete a 1,3-BDO pathway. The 1,3-BDO pathways include a set of 1,3-BDO pathway enzymes, where the set of 1,3-BDO pathway enzymes are identified as above, namely: (a) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP dehydrogenase; (3) a 2-amino-4-hydroxypentanoate aminotransferase or oxidoreductase (deaminating); (4) a 2-oxo-4-hydroxypentanoate decarboxylase; and (5) a 3-hydroxybutyraldehyde reductase; (b) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP aminotransferase or oxidoreductase (deaminating); (3) a 2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase; (c) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP aminotransferase or oxidoreductase (deaminating); (3) a 2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase; (d) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase; (e) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase; (f) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one ammonia-lyase; (4) a butanone hydratase; and (5) a 4-hydroxy-2-butanone reductase; (g) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP ammonia-lyase; (3) an acetylacrylate decarboxylase; (4) a butanone hydratase; and (5) a 4-hydroxy-2-butanone reductase; (h) (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde reductase (ketone reducing); and (3) a 3-hydroxybutyraldehyde reductase; (i) (1) an acetoacetyl-CoA reductase (CoA dependent, alcohol faulting) and (2) a 4-hydroxy-2-butanone reductase; (j) (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (3) a 4-hydroxy-2-butanone reductase; (k) (1) an acetoacetyl-CoA reductase (ketone reducing) and (2) a 3-hydroxybutyryl-CoA reductase (alcohol forming); (l) (1) an acetoacetyl-CoA reductase (ketone reducing); (2) a 3-hydroxybutyryl-CoA reductase (aldehyde forming); and (3) a 3-hydroxybutyraldehyde reductase; (m) (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; and (3) a 3-hydroxybutyryl-CoA reductase (alcohol forming); and (n) (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; (3) a 3-hydroxybutyryl-CoA reductase (aldehyde forming); and (4) a 3-hydroxybutyraldehyde reductase.
In some embodiments, a method for producing 1,3-BDO includes culturing a non-naturally occurring microbial organism provided herein under conditions and for a sufficient period of time to produce 1,3-BDO. In some embodiments, the non-naturally occurring microbial organism has a 1,3-butanediol pathway, wherein said microbial organism comprises at least one exogenous nucleic acid encoding a 1,3-butanediol pathway enzyme expressed in a sufficient amount to produce 1,3-butanediol. In some embodiments, the non-naturally occurring microbial organism includes at least one of
(i) a reductive TCA pathway, wherein said microbial organism comprises at least one exogenous nucleic acid encoding a reductive TCA pathway enzyme selected from the group consisting of an ATP-citrate lyase, citrate lyase, a fumarate reductase, and an alpha-ketoglutarate:ferredoxin oxidoreductase;
(ii) a reductive TCA pathway, wherein said microbial organism comprises at least one exogenous nucleic acid encoding a reductive TCA pathway enzyme selected from the group consisting of a pyruvate:ferredoxin oxidoreductase, a phosphoenolpyruvate carboxylase, a phosphoenolpyruvate carboxykinase, a CO dehydrogenase, and an H₂hydrogenase; or
(iii) at least one exogenous nucleic acid encodes an enzyme selected from the group consisting of a CO dehydrogenase, an H₂hydrogenase, and combinations thereof;
wherein said 1,3-butanediol pathway comprises a pathway selected from the group consisting of:
(a) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP dehydrogenase; (3) a 2-amino-4-hydroxypentanoate aminotransferase or oxidoreductase (deaminating); (4) a 2-oxo-4-hydroxypentanoate decarboxylase; and (5) a 3-hydroxybutyraldehyde reductase;
(b) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP aminotransferase or oxidoreductase (deaminating); (3) a 2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase;
(c) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP aminotransferase or oxidoreductase (deaminating); (3) a 2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase;
(d) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase;
(e) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase;
(f) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one ammonia-lyase; (4) a butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase;
(g) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP ammonia-lyase; (3) an acetylacrylate decarboxylase; (4) a butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase;
(h) (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde reductase (ketone reducing); and (3) a 3-hydroxybutyraldehyde reductase;
(i) (1) an acetoacetyl-CoA reductase (CoA dependent, alcohol forming) and (2) a 4-hydroxy-2-butanone reductase;
(j) (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (3) a 4-hydroxy-2-butanone reductase;
(k) (1) an acetoacetyl-CoA reductase (ketone reducing) and (2) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(l) (1) an acetoacetyl-CoA reductase (ketone reducing); (2) a 3-hydroxybutyryl-CoA reductase (aldehyde forming); and (3) a 3-hydroxybutyraldehyde reductase;
(m) (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; and (3) a 3-hydroxybutyryl-CoA reductase (alcohol forming); and
(n) (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; (3) a 3-hydroxybutyryl-CoA reductase (aldehyde forming); and (4) a 3-hydroxybutyraldehyde reductase;
(o) (1) a succinyl-CoA transferase, a succinyl-CoA synthetase or a succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyrate kinase, (5) a phosphotrans-4-hydroxybutyrylase, (6) a 4-hydroxybutyryl-CoA dehydratase, (7) a crotonase, (8) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (9) a 3-hydroxybutanal reductase;
(p) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase; (6) a crotonase, (7) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (8) a 3-hydroxybutanal reductase;
(q) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (7) a 3-hydroxybutanal reductase;
(r) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, and (7) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(s) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, and (6) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(t) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (8) a 3-hydroxybutyrate reductase;
(u) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (7) a 3-hydroxybutyrate reductase.
(v) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (8) a 3-hydroxybutanal reductase;
(w) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), (7) a 3-hydroxybutanal reductase;
(x) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, and (7) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(y) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, and (6) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(z) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (8) a 3-hydroxybutyrate reductase;
(aa) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (7) a 3-hydroxybutyrate reductase;
(bb) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (5) a 4-hydroxybutyrate kinase, (6) a pPhosphotrans-4-hydroxybutyrylase, (7) a 4-hydroxybutyryl-CoA dehydratase, (8) a crotonase, and (9) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(cc) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyrate kinase, (5) a phosphotrans-4-hydroxybutyrylase, (6) a 4-hydroxybutyryl-CoA dehydratase, (7) a crotonase, (8) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (9) a 3-hydroxybutyrate reductase;
(dd) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (8) a 3-hydroxybutanal reductase;
(ee) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, and (7) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(ff) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (8) a 3-hydroxybutyrate reductase;
(gg) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyryl-CoA transferase, or 4-hydroxybutyryl-CoA synthetase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (8) a 3-hydroxybutanal reductase;
(hh) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, and (7) a 3-hydroxybutyryl-CoA reductase (alcohol forming);
(ii) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, (8) a 3-hydroxybutyrate reductase;
(jj) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (7) a 3-hydroxybutanal reductase;
(kk) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, and (6) a 3-hydroxybutyryl-CoA reductase (alcohol forming); and
(ll) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (8) a 3-hydroxybutyrate reductase.
In some embodiments, the method includes a non-naturally occurring microbial organism (e.g., having pathway (i)) that further includes an exogenous nucleic acid encoding an enzyme selected from a pyruvate:ferredoxin oxidoreductase, an aconitase, an isocitrate dehydrogenase, a succinyl-CoA synthetase, a succinyl-CoA transferase, a fumarase, a malate dehydrogenase, an acetate kinase, a phosphotransacetylase, an acetyl-CoA synthetase, an NAD(P)H:ferredoxin oxidoreductase, ferredoxin, and combinations thereof.
In some embodiments, the method includes a non-naturally occurring microbial organism (e.g., having pathway (ii)) that further includes an exogenous nucleic acid encoding an enzyme selected from an aconitase, an isocitrate dehydrogenase, a succinyl-CoA synthetase, a succinyl-CoA transferase, a fumarase, a malate dehydrogenase, and combinations thereof.
In some embodiments, the method includes a microbial organism that includes two, three, four, five, six, seven, eight or nine exogenous nucleic acids, each encoding a 1,3-BDO pathway enzyme.
In some embodiments, the method includes a microbial organism that comprises exogenous nucleic acids encoding each of the enzymes of at least one of the 1,3-butanediol pathways selected from the group consisting of (a)-(ll).
In some embodiments, the method includes at least one exogenous nucleic acid that is a heterologous nucleic acid.
In some embodiments, the method includes the non-naturally occurring microbial organism in a substantially anaerobic culture medium.
Suitable purification and/or assays to test for the production of 1,3-butanediol can be performed using well known methods. Suitable replicates such as triplicate cultures can be grown for each engineered strain to be tested. For example, product and byproduct formation in the engineered production host can be monitored. The final product and intermediates, and other organic compounds, can be analyzed by methods such as HPLC (High Performance Liquid Chromatography), GC-MS (Gas Chromatography-Mass Spectroscopy) and LC-MS (Liquid Chromatography-Mass Spectroscopy) or other suitable analytical methods using routine procedures well known in the art. The release of product in the fermentation broth can also be tested with the culture supernatant. Byproducts and residual glucose can be quantified by HPLC using, for example, a refractive index detector for glucose and alcohols, and a UV detector for organic acids (Lin et al., Biotechnol. Bioeng. 90:775-779 (2005)), or other suitable assay and detection methods well known in the art. The individual enzyme or protein activities from the exogenous DNA sequences can also be assayed using methods well known in the art (see, for example, WO/2008/115840 and Hanai et al., Appl. Environ. Microbiol. 73:7814-7818 (2007)).
The 1,3-butanediol can be separated from other components in the culture using a variety of methods well known in the art. Such separation methods include, for example, extraction procedures as well as methods that include continuous liquid-liquid extraction, pervaporation, membrane filtration, membrane separation, reverse osmosis, electrodialysis, distillation, crystallization, centrifugation, extractive filtration, ion exchange chromatography, size exclusion chromatography, adsorption chromatography, and ultrafiltration. All of the above methods are well known in the art.
Any of the non-naturally occurring microbial organisms described herein can be cultured to produce and/or secrete the biosynthetic products of the invention. For example, the 1,3-butanediol producers can be cultured for the biosynthetic production of 1,3-butanediol.
For the production of 1,3-butanediol, the recombinant strains are cultured in a medium with carbon source and other essential nutrients. It is sometimes desirable and can be highly desirable to maintain anaerobic conditions in the fermenter to reduce the cost of the overall process. Such conditions can be obtained, for example, by first sparging the medium with nitrogen and then sealing the flasks with a septum and crimp-cap. For strains where growth is not observed anaerobically, microaerobic conditions can be applied by perforating the septum with a small hole for limited aeration. Exemplary anaerobic conditions have been described previously and are well-known in the art. Exemplary aerobic and anaerobic conditions are described, for example, in United States Publication No. US-2009-0047719, filed Aug. 10, 2007. Fermentations can be performed in a batch, fed-batch or continuous manner, as disclosed herein.
If desired, the pH of the medium can be maintained at a desired pH, in particular neutral pH, such as a pH of around 7 by addition of a base, such as NaOH or other bases, or acid, as needed to maintain the culture medium at a desirable pH. The growth rate can be determined by measuring optical density using a spectrophotometer (600 nm), and the glucose uptake rate by monitoring carbon source depletion over time.
In addition to renewable feedstocks such as those exemplified above, the 1,3-butanediol microbial organisms of the invention also can be modified for growth on syngas as its source of carbon. In this specific embodiment, one or more proteins or enzymes are expressed in the 1,3-butanediol producing organisms to provide a metabolic pathway for utilization of syngas or other gaseous carbon source.
Organisms of the present invention can utilize, and the growth medium can include, for example, any carbohydrate source which can supply a source of carbon to the non-naturally occurring microorganism. Such sources include, for example, sugars such as glucose, xylose, arabinose, galactose, mannose, fructose and starch. Other sources of carbohydrate include, for example, renewable feedstocks and biomass. Exemplary types of biomasses that can be used as feedstocks in the methods of the invention include cellulosic biomass, hemicellulosic biomass and lignin feedstocks or portions of feedstocks. Such biomass feedstocks contain, for example, carbohydrate substrates useful as carbon sources such as glucose, xylose, arabinose, galactose, mannose, fructose and starch. Given the teachings and guidance provided herein, those skilled in the art will understand that renewable feedstocks and biomass other than those exemplified above also can be used for culturing the microbial organisms of the invention for the production of 1,3-butanediol.
In addition to renewable feedstocks such as those exemplified above, the 1,3-butanediol microbial organisms of the invention also can be modified for growth on syngas as its source of carbon. In this specific embodiment, one or more proteins or enzymes are expressed in the 1,3-butanediol producing organisms to provide a metabolic pathway for utilization of syngas or other gaseous carbon source.
Synthesis gas, also known as syngas or producer gas, is the major product of gasification of coal and of carbonaceous materials such as biomass materials, including agricultural crops and residues. Syngas is a mixture primarily of H₂and CO and can be obtained from the gasification of any organic feedstock, including but not limited to coal, coal oil, natural gas, biomass, and waste organic matter. Gasification is generally carried out under a high fuel to oxygen ratio. Although largely H₂and CO, syngas can also include CO₂and other gases in smaller quantities. Thus, synthesis gas provides a cost effective source of gaseous carbon such as CO and, additionally, CO₂.
The Wood-Ljungdahl pathway catalyzes the conversion of CO and H₂to acetyl-CoA and other products such as acetate. Organisms capable of utilizing CO and syngas also generally have the capability of utilizing CO₂and CO₂/H₂mixtures through the same basic set of enzymes and transformations encompassed by the Wood-Ljungdahl pathway. H₂-dependent conversion of CO₂to acetate by microorganisms was recognized long before it was revealed that CO also could be used by the same organisms and that the same pathways were involved. Many acetogens have been shown to grow in the presence of CO₂and produce compounds such as acetate as long as hydrogen is present to supply the necessary reducing equivalents (see for example, Drake, Acetogenesis, pp. 3-60 Chapman and Hall, New York, (1994)). This can be summarized by the following equation:
2CO₂+4H₂ +nADP+nPi→CH₃COOH+2H₂O+nATP
Hence, non-naturally occurring microorganisms possessing the Wood-Ljungdahl pathway can utilize CO₂and H₂mixtures as well for the production of acetyl-CoA and other desired products.
The Wood-Ljungdahl pathway is well known in the art and consists of 12 reactions which can be separated into two branches: (1) methyl branch and (2) carbonyl branch. The methyl branch converts syngas to methyl-tetrahydrofolate (methyl-THF) whereas the carbonyl branch converts methyl-THF to acetyl-CoA. The reactions in the methyl branch are catalyzed in order by the following enzymes or proteins: ferredoxin oxidoreductase, formate dehydrogenase, formyltetrahydrofolate synthetase, methenyltetrahydrofolate cyclodehydratase, methylenetetrahydrofolate dehydrogenase and methylenetetrahydrofolate reductase. The reactions in the carbonyl branch are catalyzed in order by the following enzymes or proteins: methyltetrahydrofolate:corrinoid protein methyltransferase (for example, AcsE), corrinoid iron-sulfur protein, nickel-protein assembly protein (for example, AcsF), ferredoxin, acetyl-CoA synthase, carbon monoxide dehydrogenase and nickel-protein assembly protein (for example, CooC). Following the teachings and guidance provided herein for introducing a sufficient number of encoding nucleic acids to generate a 1,3-butanediol pathway, those skilled in the art will understand that the same engineering design also can be performed with respect to introducing at least the nucleic acids encoding the Wood-Ljungdahl enzymes or proteins absent in the host organism. Therefore, introduction of one or more encoding nucleic acids into the microbial organisms of the invention such that the modified organism contains the complete Wood-Ljungdahl pathway will confer syngas utilization ability.
Additionally, the reductive (reverse) tricarboxylic acid cycle coupled with carbon monoxide dehydrogenase and/or hydrogenase activities can also be used for the conversion of CO, CO₂and/or H₂to acetyl-CoA and other products such as acetate. Organisms capable of fixing carbon via the reductive TCA pathway can utilize one or more of the following enzymes: ATP citrate-lyase, citrate lyase, aconitase, isocitrate dehydrogenase, alpha-ketoglutarate:ferredoxin oxidoreductase, succinyl-CoA synthetase, succinyl-CoA transferase, fumarate reductase, fumarase, malate dehydrogenase, NAD(P)H:ferredoxin oxidoreductase, carbon monoxide dehydrogenase, and hydrogenase. Specifically, the reducing equivalents extracted from CO and/or H₂by carbon monoxide dehydrogenase and hydrogenase are utilized to fix CO₂via the reductive TCA cycle into acetyl-CoA or acetate. Acetate can be converted to acetyl-CoA by enzymes such as acetyl-CoA transferase, acetate kinase/phosphotransacetylase, and acetyl-CoA synthetase. Acetyl-CoA can be converted to the 1,3-butanediol precursors, glyceraldehyde-3-phosphate, phosphoenolpyruvate, and pyruvate, by pyruvate:ferredoxin oxidoreductase and the enzymes of gluconeogenesis. Following the teachings and guidance provided herein for introducing a sufficient number of encoding nucleic acids to generate a 1,3-butanediol pathway, those skilled in the art will understand that the same engineering design also can be performed with respect to introducing at least the nucleic acids encoding the reductive TCA pathway enzymes or proteins absent in the host organism. Therefore, introduction of one or more encoding nucleic acids into the microbial organisms of the invention such that the modified organism contains a reductive TCA pathway can confer syngas utilization ability.
Accordingly, given the teachings and guidance provided herein, those skilled in the art will understand that a non-naturally occurring microbial organism can be produced that secretes the biosynthesized compounds of the invention when grown on a carbon source such as a carbohydrate, syngas, CO and/or CO2. Such compounds include, for example, 1,3-butanediol and any of the intermediate metabolites in the 1,3-butanediol pathway. All that is required is to engineer in one or more of the required enzyme or protein activities to achieve biosynthesis of the desired compound or intermediate including, for example, inclusion of some or all of the 1,3-butanediol biosynthetic pathways. Accordingly, the invention provides a non-naturally occurring microbial organism that produces and/or secretes 1,3-butanediol when grown on a carbohydrate or other carbon source and produces and/or secretes any of the intermediate metabolites shown in the 1,3-butanediol pathway when grown on a carbohydrate or other carbon source. The 1,3-butanediol producing microbial organisms of the invention can initiate synthesis from an intermediate, for example, acetyl-CoA.
The non-naturally occurring microbial organisms of the invention are constructed using methods well known in the art as exemplified herein to exogenously express at least one nucleic acid encoding a 1,3-butanediol pathway enzyme or protein in sufficient amounts to produce 1,3-butanediol. It is understood that the microbial organisms of the invention are cultured under conditions sufficient to produce 1,3-butanediol. Following the teachings and guidance provided herein, the non-naturally occurring microbial organisms of the invention can achieve biosynthesis of 1,3-butanediol resulting in intracellular concentrations between about 0.1-200 mM or more. Generally, the intracellular concentration of 1,3-butanediol is between about 3-150 mM, particularly between about 5-125 mM and more particularly between about 8-100 mM, including about 10 mM, 20 mM, 50 mM, 80 mM, or more. Intracellular concentrations between and above each of these exemplary ranges also can be achieved from the non-naturally occurring microbial organisms of the invention.
In some embodiments, culture conditions include anaerobic or substantially anaerobic growth or maintenance conditions. Exemplary anaerobic conditions have been described previously and are well known in the art. Exemplary anaerobic conditions for fermentation processes are described herein and are described, for example, in U.S. publication 2009/0047719, filed Aug. 10, 2007. Any of these conditions can be employed with the non-naturally occurring microbial organisms as well as other anaerobic conditions well known in the art. Under such anaerobic or substantially anaerobic conditions, the 1,3-butanediol producers can synthesize 1,3-butanediol at intracellular concentrations of 5-10 mM or more as well as all other concentrations exemplified herein. It is understood that, even though the above description refers to intracellular concentrations, 1,3-butanediol producing microbial organisms can produce 1,3-butanediol intracellularly and/or secrete the product into the culture medium.
In addition to the culturing and fermentation conditions disclosed herein, growth condition for achieving biosynthesis of 1,3-butanediol can include the addition of an osmoprotectant to the culturing conditions. In certain embodiments, the non-naturally occurring microbial organisms of the invention can be sustained, cultured or fermented as described herein in the presence of an osmoprotectant. Briefly, an osmoprotectant refers to a compound that acts as an osmolyte and helps a microbial organism as described herein survive osmotic stress. Osmoprotectants include, but are not limited to, betaines, amino acids, and the sugar trehalose. Non-limiting examples of such are glycine betaine, praline betaine, dimethylthetin, dimethylsulfonioproprionate, 3-dimethylsulfonio-2-methylproprionate, pipecolic acid, dimethylsulfonioacetate, choline, L-carnitine and ectoine. In one aspect, the osmoprotectant is glycine betaine. It is understood to one of ordinary skill in the art that the amount and type of osmoprotectant suitable for protecting a microbial organism described herein from osmotic stress will depend on the microbial organism used. The amount of osmoprotectant in the culturing conditions can be, for example, no more than about 0.1 mM, no more than about 0.5 mM, no more than about 1.0 mM, no more than about 1.5 mM, no more than about 2.0 mM, no more than about 2.5 mM, no more than about 3.0 mM, no more than about 5.0 mM, no more than about 7.0 mM, no more than about 10 mM, no more than about 50 mM, no more than about 100 mM or no more than about 500 mM.
In some embodiments, the carbon feedstock and other cellular uptake sources such as phosphate, ammonia, sulfate, chloride and other halogens can be chosen to alter the isotopic distribution of the atoms present in 1,3-butanediol or any 1,3-butanediol pathway intermediate. The various carbon feedstock and other uptake sources enumerated above will be referred to herein, collectively, as “uptake sources.” Uptake sources can provide isotopic enrichment for any atom present in the product 1,3-butanediol or 1,3-butanediol pathway intermediate including any 1,3-butanediol impurities, or for side products generated in reactions diverging away from a 1,3-butanediol pathway. Isotopic enrichment can be achieved for any target atom including, for example, carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus, chloride or other halogens.
In some embodiments, the uptake sources can be selected to alter the carbon-12, carbon-13, and carbon-14 ratios. In some embodiments, the uptake sources can be selected to alter the oxygen-16, oxygen-17, and oxygen-18 ratios. In some embodiments, the uptake sources can be selected to alter the hydrogen, deuterium, and tritium ratios. In some embodiments, the uptake sources can be selected to alter the nitrogen-14 and nitrogen-15 ratios. In some embodiments, the uptake sources can be selected to alter the sulfur-32, sulfur-33, sulfur-34, and sulfur-35 ratios. In some embodiments, the uptake sources can be selected to alter the phosphorus-31, phosphorus-32, and phosphorus-33 ratios. In some embodiments, the uptake sources can be selected to alter the chlorine-35, chlorine-36, and chlorine-37 ratios.
In some embodiments, a target isotopic ratio of an uptake source can be obtained via synthetic chemical enrichment of the uptake source. Such isotopically enriched uptake sources can be purchased commercially or prepared in the laboratory. In some embodiments, a target isotopic ratio of an uptake source can be obtained by choice of origin of the uptake source in nature. In some embodiments, the isotopic ratio of a target atom can be varied to a desired ratio by selecting one or more uptake sources. An uptake source can be derived from a natural source, as found in nature, or from a man-made source, and one skilled in the art can select a natural source, a man-made source, or a combination thereof, to achieve a desired isotopic ratio of a target atom. An example of a man-made uptake source includes, for example, an uptake source that is at least partially derived from a chemical synthetic reaction. Such isotopically enriched uptake sources can be purchased commercially or prepared in the laboratory and/or optionally mixed with a natural source of the uptake source to achieve a desired isotopic ratio. In some embodiments, a target atom isotopic ratio of an uptake source can be achieved by selecting a desired origin of the uptake source as found in nature. For example, as discussed herein, a natural source can be a biobased derived from or synthesized by a biological organism or a source such as petroleum-based products or the atmosphere. In some such embodiments, a source of carbon, for example, can be selected from a fossil fuel-derived carbon source, which can be relatively depleted of carbon-14, or an environmental or atmospheric carbon source, such as CO2, which can possess a larger amount of carbon-14 than its petroleum-derived counterpart.
The unstable carbon isotope carbon-14 or radiocarbon makes up for roughly 1 in 10¹²carbon atoms in the earth's atmosphere and has a half-life of about 5700 years. The stock of carbon is replenished in the upper atmosphere by a nuclear reaction involving cosmic rays and ordinary nitrogen (¹⁴N). Fossil fuels contain no carbon-14, as it decayed long ago. Burning of fossil fuels lowers the atmospheric carbon-14 fraction, the so-called “Suess effect”.
Methods of determining the isotopic ratios of atoms in a compound are well known to those skilled in the art. Isotopic enrichment is readily assessed by mass spectrometry using techniques known in the art such as accelerated mass spectrometry (AMS), Stable Isotope Ratio Mass Spectrometry (SIRMS) and Site-Specific Natural Isotopic Fractionation by Nuclear Magnetic Resonance (SNIF-NMR). Such mass spectral techniques can be integrated with separation techniques such as liquid chromatography (LC), high performance liquid chromatography (HPLC) and/or gas chromatography, and the like.
In the case of carbon, ASTM D6866 was developed in the United States as a standardized analytical method for determining the biobased content of solid, liquid, and gaseous samples using radiocarbon dating by the American Society for Testing and Materials (ASTM) International. The standard is based on the use of radiocarbon dating for the determination of a product's biobased content. ASTM D6866 was first published in 2004, and the current active version of the standard is ASTM D6866-11 (effective Apr. 1, 2011). Radiocarbon dating techniques are well known to those skilled in the art, including those described herein.
The biobased content of a compound is estimated by the ratio of carbon-14 (¹⁴C) to carbon-12 (¹²C). Specifically, the Fraction Modern (Fm) is computed from the expression: Fm=(S−B)/(M−B), where B, S and M represent the ¹⁴C/¹²C ratios of the blank, the sample and the modern reference, respectively. Fraction Modern is a measurement of the deviation of the ¹⁴C/¹²C ratio of a sample from “Modern.” Modern is defined as 95% of the radiocarbon concentration (in AD 1950) of National Bureau of Standards (NBS) Oxalic Acid I (i.e., standard reference materials (SRM) 4990b) normalized to δ¹³C_VPDB=−19 per mil. (Olsson, The use of Oxalic acid as a Standard. in, Radiocarbon Variations and Absolute Chronology, Nobel Symposium, 12th Proc., John Wiley & Sons, New York (1970)). Mass spectrometry results, for example, measured by ASM, are calculated using the internationally agreed upon definition of 0.95 times the specific activity of NBS Oxalic Acid I (SRM 4990b) normalized to δ¹³C_VPDB=−19 per mil. This is equivalent to an absolute (AD 1950) ¹⁴C/¹²C ratio of 1.176±0.010×10⁻¹²(Karlen et al., Arkiv Geofysik, 4:465-471 (1968)). The standard calculations take into account the differential uptake of one isotope with respect to another, for example, the preferential uptake in biological systems of C¹²over C¹³over C¹⁴, and these corrections are reflected as a Fm corrected for δ¹³.
An oxalic acid standard (SRM 4990b or HOx 1) was made from a crop of 1955 sugar beet. Although there were 1000 lbs made, this oxalic acid standard is no longer commercially available. The Oxalic Acid II standard (HOx 2; N.I.S.T designation SRM 4990 C) was made from a crop of 1977 French beet molasses. In the early 1980's, a group of 12 laboratories measured the ratios of the two standards. The ratio of the activity of Oxalic acid II to 1 is 1.2933±0.001 (the weighted mean). The isotopic ratio of HOx II is −17.8 per mille. ASTM D6866-11 suggests use of the available Oxalic Acid II standard SRM 4990 C (Hox2) for the modern standard (see discussion of original vs. currently available oxalic acid standards in Mann, Radiocarbon, 25(2):519-527 (1983)). A Fm=0% represents the entire lack of carbon-14 atoms in a material, thus indicating a fossil (for example, petroleum based) carbon source. A Fm=100%, after correction for the post-1950 injection of carbon-14 into the atmosphere from nuclear bomb testing, indicates an entirely modern carbon source. As described herein, such a “modern” source includes biobased sources.
As described in ASTM D6866, the percent modern carbon (pMC) can be greater than 100% because of the continuing but diminishing effects of the 1950s nuclear testing programs, which resulted in a considerable enrichment of carbon-14 in the atmosphere as described in ASTM D6866-11. Because all sample carbon-14 activities are referenced to a “pre-bomb” standard, and because nearly all new biobased products are produced in a post-bomb environment, all pMC values (after correction for isotopic fraction) must be multiplied by 0.95 (as of 2010) to better reflect the true biobased content of the sample. A biobased content that is greater than 103% suggests that either an analytical error has occurred, or that the source of biobased carbon is more than several years old.
ASTM D6866 quantifies the biobased content relative to the material's total organic content and does not consider the inorganic carbon and other non-carbon containing substances present. For example, a product that is 50% starch-based material and 50% water would be considered to have a Biobased Content=100% (50% organic content that is 100% biobased) based on ASTM D6866. In another example, a product that is 50% starch-based material, 25% petroleum-based, and 25% water would have a Biobased Content=66.7% (75% organic content but only 50% of the product is biobased). In another example, a product that is 50% organic carbon and is a petroleum-based product would be considered to have a Biobased Content=0% (50% organic carbon but from fossil sources). Thus, based on the well known methods and known standards for determining the biobased content of a compound or material, one skilled in the art can readily determine the biobased content and/or prepared downstream products that utilize of the invention having a desired biobased content.
Applications of carbon-14 dating techniques to quantify bio-based content of materials are known in the art (Currie et al., Nuclear Instruments and Methods in Physics Research B, 172:281-287 (2000)). For example, carbon-14 dating has been used to quantify bio-based content in terephthalate-containing materials (Colonna et al., Green Chemistry, 13:2543-2548 (2011)). Notably, polypropylene terephthalate (PPT) polymers derived from renewable 1,3-propanediol and petroleum-derived terephthalic acid resulted in Fm values near 30% (i.e., since 3/11 of the polymeric carbon derives from renewable 1,3-propanediol and 8/11 from the fossil end member terephthalic acid) (Currie et al., supra, 2000). In contrast, polybutylene terephthalate polymer derived from both renewable 1,4-butanediol and renewable terephthalic acid resulted in bio-based content exceeding 90% (Colonna et al., supra, 2011).
Accordingly, in some embodiments, the present invention provides 1,3-butanediol or a 1,3-butanediol intermediate that has a carbon-12, carbon-13, and carbon-14 ratio that reflects an atmospheric carbon, also referred to as environmental carbon, uptake source. For example, in some aspects the 1,3-butanediol or a 1,3-butanediol intermediate can have an Fm value of at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or as much as 100%. In some such embodiments, the uptake source is CO₂. In some embodiments, the present invention provides 1,3-butanediol or a 1,3-butanediol intermediate that has a carbon-12, carbon-13, and carbon-14 ratio that reflects petroleum-based carbon uptake source. In this aspect, the 1,3-butanediol or a 1,3-butanediol intermediate can have an Fm value of less than 95%, less than 90%, less than 85%, less than 80%, less than 75%, less than 70%, less than 65%, less than 60%, less than 55%, less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, less than 5%, less than 2% or less than 1%. In some embodiments, the present invention provides 1,3-butanediol or a 1,3-butanediol intermediate that has a carbon-12, carbon-13, and carbon-14 ratio that is obtained by a combination of an atmospheric carbon uptake source with a petroleum-based uptake source. Using such a combination of uptake sources is one way by which the carbon-12, carbon-13, and carbon-14 ratio can be varied, and the respective ratios would reflect the proportions of the uptake sources.
Further, the present invention relates to the biologically produced 1,3-butanediol or 1,3-butanediol intermediate as disclosed herein, and to the products derived therefrom, wherein the 1,3-butanediol or a 1,3-butanediol intermediate has a carbon-12, carbon-13, and carbon-14 isotope ratio of about the same value as the CO₂that occurs in the environment. For example, in some aspects the invention provides: bioderived 1,3-butanediol or a bioderived 1,3-butanediol intermediate having a carbon-12 versus carbon-13 versus carbon-14 isotope ratio of about the same value as the CO₂that occurs in the environment, or any of the other ratios disclosed herein. It is understood, as disclosed herein, that a product can have a carbon-12 versus carbon-13 versus carbon-14 isotope ratio of about the same value as the CO₂that occurs in the environment, or any of the ratios disclosed herein, wherein the product is generated from bioderived 1,3-butanediol or a bioderived 1,3-butanediol intermediate as disclosed herein, wherein the bioderived product is chemically modified to generate a final product. Methods of chemically modifying a bioderived product of 1,3-butanediol, or an intermediate thereof, to generate a desired product are well known to those skilled in the art, as described herein. The invention further provides organic solvents, polyurethane resins, polyester resins, hypoglycaemic agents, butadiene and/or butadiene-based products having a carbon-12 versus carbon-13 versus carbon-14 isotope ratio of about the same value as the CO₂that occurs in the environment, wherein the organic solvents, polyurethane resins, polyester resins, hypoglycaemic agents, butadiene and/or butadiene-based products are generated directly from or in combination with bioderived 1,3-butanediol or a bioderived 1,3-butanediol intermediate as disclosed herein.
1,3-butanediol is a chemical used in commercial and industrial applications and is also used as a raw material in the production of a wide range of products. Non-limiting examples of such applications and products include organic solvents, polyurethane resins, polyester resins, hypoglycaemic agents, butadiene and/or butadiene-based products organic solvents, polyurethane resins, polyester resins, hypoglycaemic agents, butadiene and/or butadiene-based products. Accordingly, in some embodiments, the invention provides biobased used as a raw material in the production of a wide range of products comprising one or more bioderived 1,3-butanediol or bioderived 1,3-butanediol intermediate produced by a non-naturally occurring microorganism of the invention or produced using a method disclosed herein.
As used herein, the term “bioderived” means derived from or synthesized by a biological organism and can be considered a renewable resource since it can be generated by a biological organism. Such a biological organism, in particular the microbial organisms of the invention disclosed herein, can utilize feedstock or biomass, such as, sugars or carbohydrates obtained from an agricultural, plant, bacterial, or animal source. Alternatively, the biological organism can utilize atmospheric carbon. As used herein, the term “biobased” means a product as described above that is composed, in whole or in part, of a bioderived compound of the invention. A biobased or bioderived product is in contrast to a petroleum derived product, wherein such a product is derived from or synthesized from petroleum or a petrochemical feedstock.
In some embodiments, the invention provides organic solvents, polyurethane resins, polyester resins, hypoglycaemic agents, butadiene and/or butadiene-based products comprising bioderived 1,3-butanediol or bioderived 1,3-butanediol intermediate, wherein the bioderived 1,3-butanediol or bioderived 1,3-butanediol intermediate includes all or part of the 1,3-butanediol or 1,3-butanediol intermediate used in the production of organic solvents, polyurethane resins, polyester resins, hypoglycaemic agents, butadiene and/or butadiene-based products. Thus, in some aspects, the invention provides biobased organic solvents, polyurethane resins, polyester resins, hypoglycaemic agents, butadiene and/or butadiene-based products comprising at least 2%, at least 3%, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or 100% bioderived 1,3-butanediol or bioderived 1,3-butanediol intermediate as disclosed herein. Additionally, in some aspects, the invention provides biobased organic solvents, polyurethane resins, polyester resins, hypoglycaemic agents, butadiene and/or butadiene-based products wherein the 1,3-butanediol or 1,3-butanediol intermediate used in its production is a combination of bioderived and petroleum derived 1,3-butanediol or 1,3-butanediol intermediate. For example, biobased organic solvents, polyurethane resins, polyester resins, hypoglycaemic agents, butadiene and/or butadiene-based products can be produced using 50% bioderived 1,3-butanediol and 50% petroleum derived 1,3-butanediol or other desired ratios such as 60%/40%, 70%/30%, 80%/20%, 90%/10%, 95%/5%, 100%/0%, 40%/60%, 30%/70%, 20%/80%, 10%/90% of bioderived/petroleum derived precursors, so long as at least a portion of the product comprises a bioderived product produced by the microbial organisms disclosed herein. It is understood that methods for producing organic solvents, polyurethane resins, polyester resins, hypoglycaemic agents, butadiene and/or butadiene-based products using the bioderived 1,3-butanediol or bioderived 1,3-butanediol intermediate of the invention are well known in the art.
The non-naturally occurring microbial organisms of the invention are constructed using methods well known in the art as exemplified herein to exogenously express at least one nucleic acid encoding a 1,3-butanediol pathway enzyme or protein in sufficient amounts to produce 1,3-butanediol. It is understood that the microbial organisms of the invention are cultured under conditions sufficient to produce 1,3-butanediol. Following the teachings and guidance provided herein, the non-naturally occurring microbial organisms of the invention can achieve biosynthesis of 1,3-butanediol resulting in intracellular concentrations between about 0.1-2000 mM or more. Generally, the intracellular concentration of 1,3-butanediol is between about 3-1800 mM, particularly between about 5-1700 mM and more particularly between about 8-1600 mM, including about 100 mM, 200 mM, 500 mM, 800 mM, or more. Intracellular concentrations between and above each of these exemplary ranges also can be achieved from the non-naturally occurring microbial organisms of the invention.
In some embodiments, culture conditions include anaerobic or substantially anaerobic growth or maintenance conditions. Exemplary anaerobic conditions have been described previously and are well known in the art. Exemplary anaerobic conditions for fermentation processes are described herein and are described, for example, in U.S. patent application No. US 2009/0047719, filed Aug. 10, 2007. Any of these conditions can be employed with the non-naturally occurring microbial organisms as well as other anaerobic conditions well known in the art. Under such anaerobic conditions, the 1,3-butanediol producers can synthesize 1,3-butanediol at intracellular concentrations of 5-10 mM or more as well as all other concentrations exemplified herein. It is understood that, even though the above description refers to intracellular concentrations, 1,3-butanediol producing microbial organisms can produce 1,3-butanediol intracellularly and/or secrete the product into the culture medium.
In addition to the culturing and fermentation conditions disclosed herein, growth condition for achieving biosynthesis of 1,3-butanediol can include the addition of an osmoprotectant to the culturing conditions. In certain embodiments, the non-naturally occurring microbial organisms of the invention can be sustained, cultured or fermented as described herein in the presence of an osmoprotectant. Briefly, an osmoprotectant refers to a compound that acts as an osmolyte and helps a microbial organism as described herein survive osmotic stress. Osmoprotectants include, but are not limited to, betaines, amino acids, and the sugar trehalose. Non-limiting examples of such are glycine betaine, praline betaine, dimethylthetin, dimethylsulfonioproprionate, 3-dimethylsulfonio-2-methylproprionate, pipecolic acid, dimethylsulfonioacetate, choline, L-carnitine and ectoine. In one aspect, the osmoprotectant is glycine betaine. It is understood to one of ordinary skill in the art that the amount and type of osmoprotectant suitable for protecting a microbial organism described herein from osmotic stress will depend on the microbial organism used. The amount of osmoprotectant in the culturing conditions can be, for example, no more than about 0.1 mM, no more than about 0.5 mM, no more than about 1.0 mM, no more than about 1.5 mM, no more than about 2.0 mM, no more than about 2.5 mM, no more than about 3.0 mM, no more than about 5.0 mM, no more than about 7.0 mM, no more than about 10 mM, no more than about 50 mM, no more than about 100 mM or no more than about 500 mM.
The culture conditions can include, for example, liquid culture procedures as well as fermentation and other large scale culture procedures. As described herein, particularly useful yields of the biosynthetic products of the invention can be obtained under anaerobic or substantially anaerobic culture conditions.
As described herein, one exemplary growth condition for achieving biosynthesis of 1,3-butanediol includes anaerobic culture or fermentation conditions. In certain embodiments, the non-naturally occurring microbial organisms of the invention can be sustained, cultured or fermented under anaerobic or substantially anaerobic conditions. Briefly, anaerobic conditions refers to an environment devoid of oxygen. Substantially anaerobic conditions include, for example, a culture, batch fermentation or continuous fermentation such that the dissolved oxygen concentration in the medium remains between 0 and 10% of saturation. Substantially anaerobic conditions also includes growing or resting cells in liquid medium or on solid agar inside a sealed chamber maintained with an atmosphere of less than 1% oxygen. The percent of oxygen can be maintained by, for example, sparging the culture with an N2/CO2 mixture or other suitable non-oxygen gas or gases.
The culture conditions described herein can be scaled up and grown continuously for manufacturing of 1,3-butanediol. Exemplary growth procedures include, for example, fed-batch fermentation and batch separation; fed-batch fermentation and continuous separation, or continuous fermentation and continuous separation. All of these processes are well known in the art. Fermentation procedures are particularly useful for the biosynthetic production of commercial quantities of 1,3-butanediol. Generally, and as with non-continuous culture procedures, the continuous and/or near-continuous production of 1,3-butanediol will include culturing a non-naturally occurring 1,3-butanediol producing organism of the invention in sufficient nutrients and medium to sustain and/or nearly sustain growth in an exponential phase. Continuous culture under such conditions can include, for example, growth for 1 day, 2, 3, 4, 5, 6 or 7 days or more. Additionally, continuous culture can include longer time period of 1 week, 2, 3, 4 or 5 or more weeks and up to several months. Alternatively, organisms of the invention can be cultured for hours, if suitable for a particular application. It is to be understood that the continuous and/or near-continuous culture conditions also can include all time intervals in between these exemplary periods. It is further understood that the time of culturing the microbial organism of the invention is for a sufficient period of time to produce a sufficient amount of product for a desired purpose.
Fermentation procedures are well known in the art. Briefly, fermentation for the biosynthetic production of 1,3-butanediol can be utilized in, for example, fed-batch fermentation and batch separation; fed-batch fermentation and continuous separation, or continuous fermentation and continuous separation. Examples of batch and continuous fermentation procedures are well known in the art.
In addition to the above fermentation procedures using the 1,3-butanediol producers of the invention for continuous production of substantial quantities of 1,3-butanediol, the 1,3-butanediol producers also can be, for example, simultaneously subjected to chemical synthesis procedures to convert the product to other compounds or the product can be separated from the fermentation culture and sequentially subjected to chemical or enzymatic conversion to convert the product to other compounds, if desired. For example, 1,3-butanediol can be dehydrated to provide 1,3-butadiene.
To generate better producers, metabolic modeling can be utilized to optimize growth conditions. Modeling can also be used to design gene knockouts that additionally optimize utilization of the pathway (see, for example, U.S. patent publications US 2002/0012939, US 2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US 2002/0168654 and US 2004/0009466, and U.S. Pat. No. 7,127,379). Modeling analysis allows reliable predictions of the effects on cell growth of shifting the metabolism towards more efficient production of 1,3-butadiene.
In some embodiments, syngas can be used as a carbon feedstock. Important process considerations for a syngas fermentation are high biomass concentration and good gas-liquid mass transfer (Bredwell et al., Biotechnol Prog., 15:834-844 (1999). The solubility of CO in water is somewhat less than that of oxygen. Continuously gas-sparged fermentations can be performed in controlled fermenters with constant off-gas analysis by mass spectrometry and periodic liquid sampling and analysis by GC and HPLC. The liquid phase can function in batch mode. Fermentation products such as alcohols, organic acids, and residual glucose along with residual methanol are quantified by HPLC (Shimadzu, Columbia Md.), for example, using an Aminex® series of HPLC columns (for example, HPX-87 series) (BioRad, Hercules Calif.), using a refractive index detector for glucose and alcohols, and a UV detector for organic acids. The growth rate is determined by measuring optical density using a spectrophotometer (600 nm). All piping in these systems is glass or metal to maintain anaerobic conditions. The gas sparging is performed with glass fits to decrease bubble size and improve mass transfer. Various sparging rates are tested, ranging from about 0.1 to 1 vvm (vapor volumes per minute). To obtain accurate measurements of gas uptake rates, periodic challenges are performed in which the gas flow is temporarily stopped, and the gas phase composition is monitored as a function of time.
In order to achieve the overall target productivity, methods of cell retention or recycle are employed. One method to increase the microbial concentration is to recycle cells via a tangential flow membrane from a sidestream. Repeated batch culture can also be used, as previously described for production of acetate by Moorella (Sakai et al., J Biosci. Bioeng, 99:252-258 (2005)). Various other methods can also be used (Bredwell et al., Biotechnol Prog., 15:834-844 (1999); Datar et al., Biotechnol Bioeng, 86:587-594 (2004)). Additional optimization can be tested such as overpressure at 1.5 atm to improve mass transfer (Najafpour et al., Enzyme and Microbial Technology, 38[1-2], 223-228 (2006)).
Once satisfactory performance is achieved using pure H2/CO as the feed, synthetic gas mixtures are generated containing inhibitors likely to be present in commercial syngas. For example, a typical impurity profile is 4.5% CH4, 0.1% C2H2, 0.35% C2H6, 1.4% C2H4, and 150 ppm nitric oxide (Datar et al., Biotechnol Bioeng, 86:587-594 (2004)). Tars, represented by compounds such as benzene, toluene, ethylbenzene, p-xylene, o-xylene, and naphthalene, are added at ppm levels to test for any effect on production. For example, it has been shown that 40 ppm NO is inhibitory to C. carboxidivorans (Ahmed et al., Biotechnol Bioeng, 97:1080-1086 (2007)). Cultures are tested in shake-flask cultures before moving to a fermentor. Also, different levels of these potential inhibitory compounds are tested to quantify the effect they have on cell growth. This knowledge is used to develop specifications for syngas purity, which is utilized for scale up studies and production. If any particular component is found to be difficult to decrease or remove from syngas used for scale up, an adaptive evolution procedure is utilized to adapt cells to tolerate one or more impurities.
Advances in the field of protein engineering make it feasible to alter any of the enzymes disclosed herein to act efficiently on substrates not known to be natural to them. Below are several examples of broad-specificity enzymes from diverse classes of interest and methods that have been used for evolving such enzymes to act on non-natural substrates.
One class of enzymes in the pathways disclosed herein is the oxidoreductases that interconvert ketones or aldehydes to alcohols (1.1.1). Enzymes in this class that can operate on a wide range of substrates. An alcohol dehydrogenase (1.1.1.1) purified from the soil bacterium Brevibacterium sp KU 1309 (Hirano et al., J. Biosci. Bioeng. 100:318-322 (2005)) was shown to operate on a plethora of aliphatic as well as aromatic alcohols with high activities. Table 72 shows the activity of the enzyme and its Km on different alcohols. The enzyme is reversible and has very high activity on several aldehydes also as shown in Table 73.

TABLE 72

	RELATIVE ACTIVITY	K_M
SUBSTRATE	(%)	(MM)

2-Phenylethanol	100	0.025
(S)-2-Phenylpropanol	156	0.157
(R)-2-Phenylpropanol	63	0.020
Benzyl alcohol	199	0.012
3-Phenylpropanol	135	0.033
Ethanol	76
1-Butanol	111
1-Octanol	101
1-Dodecanol	68
1-Phenylethanol	46
2-Propanol	54

In this Table, the activity of 2-phenylethanol, corresponding to 19.2 U/mg, was taken as 100%.

TABLE 73

	RELATIVE ACTIVITY	κ_M
SUBSTRATE	(%)	(MM)

Phenylacetaldehyde	100	0.261
2-Phenylpropionaldehyde	188	0.864
1-Octylaldehyde	87
Acetophenone	0

Lactate dehydrogenase (1.1.1.27) from Ralstonia eutropha is another enzyme that has been demonstrated to have high activities on several 2-oxoacids such as 2-oxobutyrate, 2-oxopentanoate and 2-oxoglutarate (a C5 compound analogous to 2-oxoadipate) (Steinbuchel et al., supra). Column 2 in Table 74 demonstrates the activities of ldhA from R. eutropha (formerly A. eutrophus) on different substrates (Steinbuchel et al., supra).

	TABLE 74

	Activity of

	L(+)-	L(+)-	D(−)-
	lactate	lactate dehydro-	lactate
	dehydro-genase	genase from	dehydro-genase
	from	rabbit	from
Substrate	A. eustrophus %	muscle	L. leischmanii

Glyoxylate	8.7	23.9	5.0
Pyruvate	100.0	100.0	100.0
2-Oxobutyrate	107.0	18.6	1.1
2-Oxovalerate	125.0	0.7	0.0
3-Methyl-2-	28.5	0.0	0.0
oxobutyrate
3-Methyl-2-	5.3	0.0	0.0
oxovalerate
4-Methyl-2-	39.0	1.4	1.1
oxopentanoate
Oxaloacetate	0.0	33.1	23.1
2-Oxoglutarate	79.6	0.0	0.0
3-Fluoropyruvate	33.6	74.3	40.0

Oxidoreductases that can convert 2-oxoacids to their acyl-CoA counterparts (1.2.1) have been shown to accept multiple substrates as well. For example, branched-chain 2-keto-acid dehydrogenase complex (BCKAD), also known as 2-oxoisovalerate dehydrogenase (1.2.1.25), participates in branched-chain amino acid degradation pathways, converting 2-keto acids derivatives of valine, leucine and isoleucine to their acyl-CoA derivatives and CO₂. In some organisms including Rattus norvegicus (Paxton et al., Biochem. J. 234:295-303 (1986)) and Saccharomyces cerevisiae (Sinclair et al., Biochem. Mol. Biol. Int. 31:911-922 (1993)), this complex has been shown to have a broad substrate range that includes linear oxo-acids such as 2-oxobutanoate and alpha-ketoglutarate, in addition to the branched-chain amino acid precursors.
Members of yet another class of enzymes, namely aminotransferases (2.6.1), have been reported to act on multiple substrates. Aspartate aminotransferase (aspAT) from Pyrococcus fursious has been identified, expressed in E. coli and the recombinant protein characterized to demonstrate that the enzyme has the highest activities towards aspartate and alpha-ketoglutarate but lower, yet significant activities towards alanine, glutamate and the aromatic amino acids (Ward et al., Archaea. 1:133-141 (2002)). In another instance, an aminotransferase identified from Leishmania mexicana and expressed in E. coli Vernal et al., FEMS Microbiol. Lett. 229:217-222 (2003)) was reported to have a broad substrate specificity towards tyrosine (activity considered 100% on tyrosine), phenylalanine (90%), tryptophan (85%), aspartate (30%), leucine (25%) and methionine (25%) respectively (Vernal et al., Mol. Biochem. Parasitoi. 96:83-92 (1998)). Similar broad specificity has been reported for a tyrosine aminotransferase from Trypanosoma cruzi, even though both of these enzymes have a sequence homology of only 6%. Note that the latter enzyme can accept leucine, methionine as well as tyrosine, phenylalanine, tryptophan and alanine as efficient amino donors (Nowicki et al., Biochim. Biophys. Acta 1546: 268-281 (2001)).
In contrast to these examples where the enzymes naturally have broad substrate specificities, numerous enzymes have been modified using directed evolution to broaden their specificity towards their non-natural substrates. Alternatively, the substrate preference of an enzyme has also been changed using directed evolution. For example, it has been reported that the enantioselectivity of a lipase from Pseudomonas aeruginosa was improved significantly. This enzyme hydrolyzed p-nitrophenyl 2-methyldecanoate with only 2% enantiomeric excess (ee) in favor of the (S)-acid. However, after four successive rounds of error-prone mutagenesis and screening, a variant was produced that catalyzed the requisite reaction with 81% ee Reetz et al., Angew. Chem. Int. Ed Engl. 36:2830-2832 (1997)).
Directed evolution methods have made possible the modification of an enzyme to function on an array of unnatural substrates. The substrate specificity of the lipase in P. aeruginosa was broadened by randomization of amino acid residues near the active site. This allowed for the acceptance of alpha-substituted carboxylic acid esters by this enzyme Reetz et al., Angew. Chem. Int. Ed Engl. 44:4192-4196 (2005)). In another successful attempt, DNA shuffling was employed to create an Escherichia coli aminotransferase that accepted β-branched substrates, which were poorly accepted by the wild-type enzyme (Yano et al., Proc. Natl. Acad. Sci. U.S.A 95:5511-5515 (1998)). Specifically, at the end of four rounds of shuffling, the activity of aspartate aminotransferase for valine and 2-oxovaline increased by up to five orders of magnitude, while decreasing the activity towards the natural substrate, aspartate, by up to 30-fold. Recently, an algorithm was used to design a retro-aldolase that could be used to catalyze the carbon-carbon bond cleavage in a non-natural and non-biological substrate, 4-hydroxy-4-(6-methoxy-2-naphthyl)-2-butanone. These algorithms used different combinations of four different catalytic motifs to design new enzymes and 20 of the selected designs for experimental characterization had four-fold improved rates over the uncatalyzed reaction (Jiang et al., Science 319:1387-1391 (2008)). Thus, not only are these engineering approaches capable of expanding the array of substrates on which an enzyme can act, but allow the design and construction of very efficient enzymes. For example, a method of DNA shuffling (random chimeragenesis on transient templates or RACHITT) was reported to lead to an engineered monooxygenase that had an improved rate of desulfurization on complex substrates as well as 20-fold faster conversion of a non-natural substrate (Coco et al. Nat. Biotechnol. 19:354-359 (2001)). Similarly, the specific activity of a sluggish mutant triosephosphate isomerase enzyme was improved up to 19-fold from 1.3 fold (Hermes et al., Proc. Natl. Acad. Sci. U.S.A 87:696-700 (1990)). This enhancement in specific activity was accomplished by using random mutagenesis over the whole length of the protein and the improvement could be traced back to mutations in six amino acid residues.
The effectiveness of protein engineering approaches to alter the substrate specificity of an enzyme for a desired substrate has also been demonstrated. Isopropylmalate dehydrogenase from Thermus thermophilus was modified by changing residues close to the active site so that it could now act on malate and D-lactate as substrates (Fujita et al., Biosci. Biotechnol Biochem. 65:2695-2700 (2001)). In this study as well as in others, it was pointed out that one or a few residues could be modified to alter the substrate specificity. A case in point is the dihydroflavonol 4-reductase for which a single amino acid was changed in the presumed substrate-binding region that could preferentially reduce dihydrokaempferol Johnson et al., Plant J. 25:325-333 (2001)). The substrate specificity of a very specific isocitrate dehydrogenase from Escherichia coli was changed from isocitrate to isopropylmalate by changing one residue in the active site (Doyle et al., Biochemistry 40:4234-4241 (2001)). In a similar vein, the cofactor specificity of a NAD+-dependent 1,5-hydroxyprostaglandin dehydrogenase was altered to NADP+ by changing a few residues near the N-terminal end Cho et al., Arch. Biochem. Biophys. 419:139-146 (2003)). Sequence analysis and molecular modeling analysis were used to identify the key residues for modification, which were further studied by site-directed mutagenesis.
A fucosidase was evolved from a galactosidase in E. coli by DNA shuffling and screening (Zhang et al., Proc Natl Acad Sci US.A 94:4504-4509 (1997)). Similarly, aspartate aminotransferase from E. coli was converted into a tyrosine aminotransferase using homology modeling and site-directed mutagenesis (Onuffer et al., Protein Sci. 4:1750-1757 (1995)). Site-directed mutagenesis of two residues in the active site of benzoylformate decarboxylase from P. putida reportedly altered the affinity (Km) towards natural and non-natural substrates Siegert et al., Protein Eng Des Sel 18:345-357 (2005)). Cytochrome c peroxidase (CCP) from Saccharomyces cerevisiae was subjected to directed molecular evolution to generate mutants with increased activity against the classical peroxidase substrate guaiacol, thus changing the substrate specificity of CCP from the protein cytochrome c to a small organic molecule. After three rounds of DNA shuffling and screening, mutants were isolated which possessed a 300-fold increased activity against guaiacol and up to 1000-fold increased specificity for this substrate relative to that for the natural substrate (Iffland et al., Biochemistry 39:10790-10798 (2000)).
In some cases, enzymes with different substrate preferences than both the parent enzymes have been obtained. For example, biphenyl-dioxygenase-mediated degradation of polychlorinated biphenyls was improved by shuffling genes from two bacteria, Pseudomonas pseudoalcaligens and Burkholderia cepacia (Kumamaru et al., Nat. Biotechnol 16, 663-666 (1998)). The resulting chimeric biphenyl oxygenases showed different substrate preferences than both the parental enzymes and enhanced the degradation activity towards related biphenyl compounds and single aromatic ring hydrocarbons such as toluene and benzene which were originally poor substrates for the enzyme.
It is not only possible to change the enzyme specificity but also to enhance the activities on those substrates on which the enzymes naturally have low activities. One study demonstrated that amino acid racemase from P. putida that had broad substrate specificity (on lysine, arginine, alanine, serine, methionine, cysteine, leucine and histidine among others) but low activity towards tryptophan could be improved significantly by random mutagenesis Kino et al., Appl. Microbiol. Biotechnol. 73:1299-1305 (2007)). Similarly, the active site of the bovine BCKAD was engineered to favor alternate substrate acetyl-CoA (Meng et al. Biochemistry 33:12879-12885 (1994)). An interesting aspect of these approaches is that even when random methods have been applied to generate these mutated enzymes with efficacious activities, the exact mutations or structural changes that confer the improvement in activity can be identified. For example, in the aforementioned study, the mutations that facilitated improved activity on tryptophan could be traced back to two different positions.
Directed evolution has also been used to express proteins that are difficult to express. For example, by subjecting the horseradish peroxidase to random mutagenesis and gene recombination, mutants could be extracted that had more than 14-fold activity than the wild type (Lin et al., Biotechnol. Frog. 15:467-471 (1999)).
A final example of directed evolution shows the extensive modifications to which an enzyme can be subjected to achieve a range of desired functions. The enzyme, lactate dehydrogenase from Bacillus stearothermophilus was subjected to site-directed mutagenesis, and three amino acid substitutions were made at sites that were indicated to determine the specificity towards different hydroxyacids (Clarke et al., Biochem. Biophys. Res. Commun. 148:15-23 (1987)). After these mutations, the specificity for oxaloacetate over pyruvate was increased to 500 in contrast to the wild type enzyme that had a catalytic specificity for pyruvate over oxaloacetate of 1000. This enzyme was further engineered using site-directed mutagenesis to have activity towards branched-chain substituted pyruvates (Wilks et al., Biochemistry 29:8587-8591 (1990)). Specifically, the enzyme had a 55-fold improvement in Kcat for alpha-ketoisocaproate. Three structural modifications were made in the same enzyme to change its substrate specificity from lactate to malate. The enzyme was highly active and specific towards malate (Wilks et al., Science 242:1541-1544 (1988)). The same enzyme from B. stearothermophilus was subsequently engineered to have high catalytic activity towards alpha-keto acids with positively charged side chains, such as those containing ammonium groups (Hogan et al., Biochemistry 34:4225-4230 (1995)). Mutants with acidic amino acids introduced at position 102 of the enzyme favored binding of such side chain ammonium groups. The results obtained proved that the mutants showed up to 25-fold improvements in kcat/Km values for omega-amino-alpha-keto acid substrates. This enzyme was also structurally modified to function as a phenyllactate dehydrogenase instead of a lactate dehydrogenase (Wilks et al., Biochemistry 31:7802-7806 (1992)). Restriction sites were introduced into the gene for the enzyme which allowed a region of the gene to be excised. This region coded for a mobile surface loop of polypeptide (residues 98-110) which normally seals the active site vacuole from bulk solvent and is a major determinant of substrate specificity. The variable length and sequence loops were inserted into the cut gene and used to synthesize hydroxyacid dehydrogenases with altered substrate specificities. With one longer loop construction, activity with pyruvate was reduced one-million-fold but activity with phenylpyruvate was largely unaltered. A switch in specificity (kcat/Km) of 390,000-fold was achieved. The 1700:1 selectivity of this enzyme for phenylpyruvate over pyruvate is that required in a phenyllactate dehydrogenase.
As indicated above, directed evolution is a powerful approach that involves the introduction of mutations targeted to a specific gene in order to improve and/or alter the properties of an enzyme. Improved and/or altered enzymes can be identified through the development and implementation of sensitive high-throughput screening assays that allow the automated screening of many enzyme variants (e.g., >104). Iterative rounds of mutagenesis and screening typically are performed to afford an enzyme with optimized properties. Computational algorithms that can help to identify areas of the gene for mutagenesis also have been developed and can significantly reduce the number of enzyme variants that need to be generated and screened.
Numerous directed evolution technologies have been developed (for reviews, see Hibbert, E. G., F. Baganz, H. C. Hailes, J. M. Ward, G. J. Lye, J. M. Woodley, and P. A. Dalby, 2005, Directed evolution of biocatalytic processes. Biomol. Eng 22:11-19; Huisman, G. W. and J. J. Lalonde, 2007, Enzyme evolution for chemical process applications, p. 717-742. In R. N. Patel (ed.), Biocatalysis in the pharmaceutical and biotechnology industries. CRC Press; Otten, L. G. and W. J. Quax. 2005. Directed evolution: selecting today's biocatalysts. Biomol. Eng 22:1-9; and Sen, S., D. Venkata, V, and B. Mandal, 2007, Developments in directed evolution for improving enzyme functions. Appl Biochem. Biotechnol 143:212-223) to be effective at creating diverse variant libraries and these methods have been successfully applied to the improvement of a wide range of properties across many enzyme classes.
Enzyme characteristics that have been improved and/or altered by directed evolution technologies include, for example, selectivity/specificity—for conversion of non-natural substrates; temperature stability—for robust high temperature processing; pH stability—for bioprocessing under lower or higher pH conditions; substrate or product tolerance—so that high product titers can be achieved; binding (Km)—broadens substrate binding to include non-natural substrates; inhibition (Ki)—to remove inhibition by products, substrates, or key intermediates; activity (kcat)—increases enzymatic reaction rates to achieve desired flux; expression levels—increases protein yields and overall pathway flux; oxygen stability—for operation of air sensitive enzymes under aerobic conditions; and anaerobic activity—for operation of an aerobic enzyme in the absence of oxygen.
The following exemplary methods have been developed for the mutagenesis and diversification of genes to target desired properties of specific enzymes. Any of these can be used to alter/optimize activity of a decarboxylase enzyme.
EpPCR (Pritchard, L., D. Come, D. Kell, J. Rowland, and M. Winson, 2005, A general model of error-prone PCR. J Theor. Biol 234:497-509) introduces random point mutations by reducing the fidelity of DNA polymerase in PCR reactions by the addition of Mn2+ ions, by biasing dNTP concentrations, or by other conditional variations. The five step cloning process to confine the mutagenesis to the target gene of interest involves: 1) error-prone PCR amplification of the gene of interest; 2) restriction enzyme digestion; 3) gel purification of the desired DNA fragment; 4) ligation into a vector; 5) transformation of the gene variants into a suitable host and screening of the library for improved performance. This method can generate multiple mutations in a single gene simultaneously, which can be useful. A high number of mutants can be generated by EpPCR, so a high-throughput screening assay or a selection method (especially using robotics) is useful to identify those with desirable characteristics.
Error-prone Rolling Circle Amplification (epRCA) (Fujii, R., M. Kitaoka, and K. Hayashi, 2004, One-step random mutagenesis by error-prone rolling circle amplification. Nucleic Acids Res 32:e145; and Fujii, R., M. Kitaoka, and K. Hayashi, 2006, Error-prone rolling circle amplification: the simplest random mutagenesis protocol. Nat. Protoc. 1:2493-2497) has many of the same elements as epPCR except a whole circular plasmid is used as the template and random 6-mers with exonuclease resistant thiophosphate linkages on the last 2 nucleotides are used to amplify the plasmid followed by transformation into cells in which the plasmid is re-circularized at tandem repeats. Adjusting the Mn2+ concentration can vary the mutation rate somewhat. This technique uses a simple error-prone, single-step method to create a full copy of the plasmid with 3-4 mutations/kbp. No restriction enzyme digestion or specific primers are required. Additionally, this method is typically available as a kit.
DNA or Family Shuffling (Stemmer, W. P. 1994, DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci US.A 91:10747-10751; and Stemmer, W. P. 1994. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370:389-391) typically involves digestion of 2 or more variant genes with nucleases such as Dnase I or EndoV to generate a pool of random fragments that are reassembled by cycles of annealing and extension in the presence of DNA polymerase to create a library of chimeric genes. Fragments prime each other and recombination occurs when one copy primes another copy (template switch). This method can be used with >1 kbp DNA sequences. In addition to mutational recombinants created by fragment reassembly, this method introduces point mutations in the extension steps at a rate similar to error-prone PCR. The method can be used to remove deleterious random neutral mutations that might confer antigenicity.
Staggered Extension (StEP) (Zhao, H., L. Giver, Z. Shao, J. A. Affholter, and F. H. Arnold, 1998, Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat. Biotechnol 16:258-261) entails template priming followed by repeated cycles of 2 step PCR with denaturation and very short duration of annealing/extension (as short as 5 sec). Growing fragments anneal to different templates and extend further, which is repeated until full-length sequences are made. Template switching means most resulting fragments have multiple parents. Combinations of low-fidelity polymerases (Taq and Mutazyme) reduce error-prone biases because of opposite mutational spectra.
In Random Priming Recombination (RPR) random sequence primers are used to generate many short DNA fragments complementary to different segments of the template. (Shao, Z., H. Zhao, L. Giver, and F. H. Arnold, 1998, Random-priming in vitro recombination: an effective tool for directed evolution. Nucleic Acids Res 26:681-683.) Base misincorporation and mispriming via epPCR give point mutations. Short DNA fragments prime one another based on homology and are recombined and reassembled into full-length by repeated thermocycling. Removal of templates prior to this step assures low parental recombinants. This method, like most others, can be performed over multiple iterations to evolve distinct properties. This technology avoids sequence bias, is independent of gene length, and requires very little parent DNA for the application.
In Heteroduplex Recombination linearized plasmid DNA is used to form heteroduplexes that are repaired by mismatch repair. (Volkov, A. A., Z. Shao, and F. H. Arnold. 1999. Recombination and chimeragenesis by in vitro heteroduplex formation and in vivo repair. Nucleic Acids Res 27:e18; and Volkov, A. A., Z. Shao, and F. H. Arnold. 2000. Random chimeragenesis by heteroduplex recombination. Methods Enzymol. 328:456-463.) The mismatch repair step is at least somewhat mutagenic. Heteroduplexes transform more efficiently than linear homoduplexes. This method is suitable for large genes and whole operons.
Random Chimeragenesis on Transient Templates (RACHITT) (Coco, W. M., W. E. Levinson, M. J. Crist, H. J. Hektor, A. Darzins, P. T. Pienkos, C. H. Squires, and D. J. Monticello, 2001, DNA shuffling method for generating highly recombined genes and evolved enzymes. Nat. Biotechnol 19:354-359) employs Dnase I fragmentation and size fractionation of ssDNA. Homologous fragments are hybridized in the absence of polymerase to a complementary ssDNA scaffold. Any overlapping unhybridized fragment ends are trimmed down by an exonuclease. Gaps between fragments are filled in, and then ligated to give a pool of full-length diverse strands hybridized to the scaffold (that contains U to preclude amplification). The scaffold then is destroyed and is replaced by a new strand complementary to the diverse strand by PCR amplification. The method involves one strand (scaffold) that is from only one parent while the priming fragments derive from other genes; the parent scaffold is selected against. Thus, no reannealing with parental fragments occurs. Overlapping fragments are trimmed with an exonuclease. Otherwise, this is conceptually similar to DNA shuffling and StEP. Therefore, there should be no siblings, few inactives, and no unshuffled parentals. This technique has advantages in that few or no parental genes are created and many more crossovers can result relative to standard DNA shuffling.
Recombined Extension on Truncated templates (RETT) entails template switching of unidirectionally growing strands from primers in the presence of unidirectional ssDNA fragments used as a pool of templates. (Lee, S. H., E. J. Ryu, M. J. Kang, E.-S. Wang, Z. C. Y. Piao, K. J. J. Jung, and Y. Shin, 2003, A new approach to directed gene evolution by recombined extension on truncated templates (RETT). J. Molec. Catalysis 26:119-129.) No DNA endonucleases are used. Unidirectional ssDNA is made by DNA polymerase with random primers or serial deletion with exonuclease. Unidirectional ssDNA are only templates and not primers. Random priming and exonucleases don't introduce sequence bias as true of enzymatic cleavage of DNA shuffling/RACHITT. RETT can be easier to optimize than StEP because it uses normal PCR conditions instead of very short extensions. Recombination occurs as a component of the PCR steps—no direct shuffling. This method can also be more random than StEP due to the absence of pauses.
In Degenerate Oligonucleotide Gene Shuffling (DOGS) degenerate primers are used to control recombination between molecules; (Bergquist, P. L. and M. D. Gibbs, 2007, Degenerate oligonucleotide gene shuffling. Methods Mol. Biol. 352:191-204; Bergquist, P. L., R. A. Reeves, and M. D. Gibbs, 2005, Degenerate oligonucleotide gene shuffling (DOGS) and random drift mutagenesis (RNDM): two complementary techniques for enzyme evolution. Biomol. Eng 22:63-72; Gibbs, M. D., K. M. Nevalainen, and P. L. Bergquist, 2001, Degenerate oligonucleotide gene shuffling (DOGS): a method for enhancing the frequency of recombination with family shuffling. Gene 271:13-20) this can be used to control the tendency of other methods such as DNA shuffling to regenerate parental genes. This method can be combined with random mutagenesis (epPCR) of selected gene segments. This can be a good method to block the reformation of parental sequences. No endonucleases are needed. By adjusting input concentrations of segments made, one can bias towards a desired backbone. This method allows DNA shuffling from unrelated parents without restriction enzyme digests and allows a choice of random mutagenesis methods.
Incremental Truncation for the Creation of Hybrid Enzymes (ITCHY) creates a combinatorial library with 1 base pair deletions of a gene or gene fragment of interest. (Ostermeier et al., Proc Natl Acad Sci US.A. 96:3562-3567 (1999); Ostermeier et al., 1999 Nat. Biotechnol. 17:1205-1209 (1999)) Truncations are introduced in opposite direction on pieces of 2 different genes. These are ligated together and the fusions are cloned. This technique does not require homology between the 2 parental genes. When ITCHY is combined with DNA shuffling, the system is called SCRATCHY (see below). A major advantage of both is no need for homology between parental genes; for example, functional fusions between an E. coli and a human gene were created via ITCHY. When ITCHY libraries are made, all possible crossovers are captured.
Thio-Incremental Truncation for the Creation of Hybrid Enzymes (THIO-ITCHY) is almost the same as ITCHY except that phosphothioate dNTPs are used to generate truncations. (Lutz, S., M. Ostermeier, and S. J. Benkovic, 2001, Rapid generation of incremental truncation libraries for protein engineering using alpha-phosphothioate nucleotides. Nucleic Acids Res 29:E16) Relative to ITCHY, THIO-ITCHY can be easier to optimize, provide more reproducibility, and adjustability.
SCRATCHY—ITCHY combined with DNA shuffling is a combination of DNA shuffling and ITCHY; therefore, allowing multiple crossovers. (Lutz et al., Proc Natl Acad Sci US.A. 98:11248-11253 (2001).) SCRATCHY combines the best features of ITCHY and DNA shuffling. Computational predictions can be used in optimization. SCRATCHY is more effective than DNA shuffling when sequence identity is below 80%.
In Random Drift Mutagenesis (RNDM) mutations made via epPCR followed by screening/selection for those retaining usable activity. (Bergquist et al., Biomol. Eng. 22:63-72 (2005).) Then, these are used in DOGS to generate recombinants with fusions between multiple active mutants or between active mutants and some other desirable parent. Designed to promote isolation of neutral mutations; its purpose is to screen for retained catalytic activity whether or not this activity is higher or lower than in the original gene. RNDM is usable in high throughput assays when screening is capable of detecting activity above background. RNDM has been used as a front end to DOGS in generating diversity. The technique imposes a requirement for activity prior to shuffling or other subsequent steps; neutral drift libraries are indicated to result in higher/quicker improvements in activity from smaller libraries. Though published using epPCR, this could be applied to other large-scale mutagenesis methods.
Sequence Saturation Mutagenesis (SeSaM) is a random mutagenesis method that: 1) generates pool of random length fragments using random incorporation of a phosphothioate nucleotide and cleavage; this pool is used as a template to 2) extend in the presence of “universal” bases such as inosine; 3) replication of a inosine-containing complement gives random base incorporation and, consequently, mutagenesis. (Wong et al., Biotechnol J. 3:74-82 (2008); Wong Nucleic Acids Res 32:e26; Wong et al. Anal. Biochem. 341:187-189 (2005).) Using this technique it can be possible to generate a large library of mutants within 2-3 days using simple methods. This is very non-directed compared to mutational bias of DNA polymerases. Differences in this approach makes this technique complementary (or alternative) to epPCR.
In Synthetic Shuffling, overlapping oligonucleotides are designed to encode “all genetic diversity in targets” and allow a very high diversity for the shuffled progeny. (Ness, et al., Nat. Biotechnol 20:1251-1255 (2002).) In this technique, one can design the fragments to be shuffled. This aids in increasing the resulting diversity of the progeny. One can design sequence/codon biases to make more distantly related sequences recombine at rates approaching more closely related sequences and it doesn't require possessing the template genes physically.
Nucleotide Exchange and Excision Technology NexT exploits a combination of dUTP incorporation followed by treatment with uracil DNA glycosylase and then piperidine to perform endpoint DNA fragmentation. (Muller et al., Nucleic Acids Res 33:e117 (2005)) The gene is reassembled using internal PCR primer extension with proofreading polymerase. The sizes for shuffling are directly controllable using varying dUPT::dTTP ratios. This is an end point reaction using simple methods for uracil incorporation and cleavage. One can use other nucleotide analogs such as 8-oxo-guanine with this method. Additionally, the technique works well with very short fragments (86 bp) and has a low error rate. Chemical cleavage of DNA means very few unshuffled clones.
In Sequence Homology-Independent Protein Recombination (SHIPREC) a linker is used to facilitate fusion between 2 distantly/unrelated genes; nuclease treatment is used to generate a range of chimeras between the two. Result is a single crossover library of these fusions. (Sieber, V., C. A. Martinez, and F. H. Arnold. 2001. Libraries of hybrid proteins from distantly related sequences. Nat. Biotechnol 19:456-460.) This produces a limited type of shuffling; mutagenesis is a separate process. This technique can create a library of chimeras with varying fractions of each of 2 unrelated parent genes. No homology is needed. SHIPREC was tested with a heme-binding domain of a bacterial CP450 fused to N-terminal regions of a mammalian CP450; this produced mammalian activity in a more soluble enzyme.
In Gene Site Saturation Mutagenesis (GSSM) the starting materials are a supercoiled dsDNA plasmid with insert and 2 primers degenerate at the desired site for mutations. (Kretz, K. A., T. H. Richardson, K. A. Gray, D. E. Robertson, X. Tan, and J. M. Short, 2004, Gene site saturation mutagenesis: a comprehensive mutagenesis approach. Methods Enzymol. 388:3-11.) Primers carry the mutation of interest and anneal to the same sequence on opposite strands of DNA; mutation in the middle of the primer and ˜20 nucleotides of correct sequence flanking on each side. The sequence in the primer is NNN or NNK (coding) and MNN (noncoding) (N=all 4, K=G, T, M=A, C). After extension, DpnI is used to digest dam-methylated DNA to eliminate the wild-type template. This technique explores all possible amino acid substitutions at a given locus (i.e., one codon). The technique facilitates the generation of all possible replacements at one site with no nonsense codons and equal or near-equal representation of most possible alleles. It does not require prior knowledge of structure, mechanism, or domains of the target enzyme. If followed by shuffling or Gene Reassembly, this technology creates a diverse library of recombinants containing all possible combinations of single-site up-mutations. The utility of this technology combination has been demonstrated for the successful evolution of over 50 different enzymes, and also for more than one property in a given enzyme.
Combinatorial Cassette Mutagenesis (CCM) involves the use of short oligonucleotide cassettes to replace limited regions with a large number of possible amino acid sequence alterations. (Reidhaar-Olson, J. F., J. U. Bowie, R. M. Breyer, J. C. Hu, K. L. Knight, W. A. Lim, M. C. Mossing, D. A. Parsell, K. R. Shoemaker, and R. T. Sauer, 1991, Random mutagenesis of protein sequences using oligonucleotide cassettes. Methods Enzymol. 208:564-586; and Reidhaar-Olson, J. F. and R. T. Sauer, 1988, Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. Science 241:53-57.) Simultaneous substitutions at 2 or 3 sites are possible using this technique. Additionally, the method tests a large multiplicity of possible sequence changes at a limited range of sites. It has been used to explore the information content of lambda repressor DNA-binding domain.
Combinatorial Multiple Cassette Mutagenesis (CMCM) is essentially similar to CCM except it is employed as part of a larger program: 1) Use of epPCR at high mutation rate to 2) ID hot spots and hot regions and then 3) extension by CMCM to cover a defined region of protein sequence space. (Reetz, M. T., S. Wilensek, D. Zha, and K. E. Jaeger, 2001, Directed Evolution of an Enantioselective Enzyme through Combinatorial Multiple-Cassette Mutagenesis. Angew. Chem. Int. Ed Engl. 40:3589-3591.) As with CCM, this method can test virtually all possible alterations over a target region. If used along with methods to create random mutations and shuffled genes, it provides an excellent means of generating diverse, shuffled proteins. This approach was successful in increasing, by 51-fold, the enantioselectivity of an enzyme.
In the Mutator Strains technique conditional is mutator plasmids allow increases of 20- to 4000-X in random and natural mutation frequency during selection and to block accumulation of deleterious mutations when selection is not required. (Selifonova, 0., F. Valle, and V. Schellenberger, 2001, Rapid evolution of novel traits in microorganisms. Appl Environ Microbiol 67:3645-3649.) This technology is based on a plasmid-derived mutD5 gene, which encodes a mutant subunit of DNA polymerase III. This subunit binds to endogenous DNA polymerase III and compromises the proofreading ability of polymerase III in any of the strain that harbors the plasmid. A broad-spectrum of base substitutions and frameshift mutations occur. In order for effective use, the mutator plasmid should be removed once the desired phenotype is achieved; this is accomplished through a temperature sensitive origin of replication, which allows plasmid curing at 41° C. It should be noted that mutator strains have been explored for quite some time (e.g., see Winter and coworkers, 1996, J. Mol. Biol. 260, 359-3680. In this technique very high spontaneous mutation rates are observed. The conditional property minimizes non-desired background mutations. This technology could be combined with adaptive evolution to enhance mutagenesis rates and more rapidly achieve desired phenotypes.
“Look-Through Mutagenesis (LTM) is a multidimensional mutagenesis method that assesses and optimizes combinatorial mutations of selected amino acids.” (Rajpal, A., N. Beyaz, L. Haber, G. Cappuccilli, H. Yee, R. R. Bhatt, T. Takeuchi, R. A. Lerner, and R. Crea, 2005, A general method for greatly improving the affinity of antibodies by using combinatorial libraries. Proc Natl Acad Sci US.A 102:8466-8471.) Rather than saturating each site with all possible amino acid changes, a set of 9 is chosen to cover the range of amino acid R-group chemistry. Fewer changes per site allows multiple sites to be subjected to this type of mutagenesis. A >800-fold increase in binding affinity for an antibody from low nanomolar to picomolar has been achieved through this method. This is a rational approach to minimize the number of random combinations and should increase the ability to find improved traits by greatly decreasing the numbers of clones to be screened. This has been applied to antibody engineering, specifically to increase the binding affinity and/or reduce dissociation. The technique can be combined with either screens or selections.
Gene Reassembly is a DNA shuffling method that can be applied to multiple genes at one time or to creating a large library of chimeras (multiple mutations) of a single gene. (on the world-wide web at www.verenium.com/Pages/Technology/EnzymeTech/TechEnzyTGR.html) Typically this technology is used in combination with ultra-high-throughput screening to query the represented sequence space for desired improvements. This technique allows multiple gene recombination independent of homology. The exact number and position of cross-over events can be pre-determined using fragments designed via bioinformatic analysis. This technology leads to a very high level of diversity with virtually no parental gene reformation and a low level of inactive genes. Combined with GSSM, a large range of mutations can be tested for improved activity. The method allows “blending” and “fine tuning” of DNA shuffling, e.g. codon usage can be optimized.
In Silico Protein Design Automation PDA is an optimization algorithm that anchors the structurally defined protein backbone possessing a particular fold, and searches sequence space for amino acid substitutions that can stabilize the fold and overall protein energetics. (Hayes, R. J., J. Bentzien, M. L. Ary, M. Y. Hwang, J. M. Jacinto, J. Vielmetter, A. Kundu, and B. I. Dahiyat, 2002, Combining computational and experimental screening for rapid optimization of protein properties. Proc Natl Acad Sci US.A 99:15926-15931.) This technology allows in silico structure-based entropy predictions in order to search for structural tolerance toward protein amino acid variations. Statistical mechanics is applied to calculate coupling interactions at each position—structural tolerance toward amino acid substitution is a measure of coupling. Ultimately, this technology is designed to yield desired modifications of protein properties while maintaining the integrity of structural characteristics. The method computationally assesses and allows filtering of a very large number of possible sequence variants (1050). Choice of sequence variants to test is related to predictions based on most favorable thermodynamics and ostensibly only stability or properties that are linked to stability can be effectively addressed with this technology. The method has been successfully used in some therapeutic proteins, especially in engineering immunoglobulins. In silico predictions avoid testing extraordinarily large numbers of potential variants. Predictions based on existing three-dimensional structures are more likely to succeed than predictions based on hypothetical structures. This technology can readily predict and allow targeted screening of multiple simultaneous mutations, something not possible with purely experimental technologies due to exponential increases in numbers.
Iterative Saturation Mutagenesis (ISM) involves 1) Use knowledge of structure/function to choose a likely site for enzyme improvement. 2) Saturation mutagenesis at chosen site using Stratagene QuikChange (or other suitable means). 3) Screen/select for desired properties. 4) With improved clone(s), start over at another site and continue repeating. (Reetz, M. T. and J. D. Carballeira, 2007, Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat. Protoc. 2:891-903; and Reetz, M. T., J. D. Carballeira, and A. Vogel, 2006, Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angew. Chem. Int. Ed Engl. 45:7745-7751.) This is a proven methodology assures all possible replacements at a given position are made for screening/selection.
Any of the aforementioned methods for mutagenesis can be used alone or in any combination. Additionally, any one or combination of the directed evolution methods can be used in conjunction with adaptive evolution techniques.
To generate better producers, metabolic modeling can be utilized to optimize growth conditions. Modeling can also be used to design gene knockouts that additionally optimize utilization of the pathway (see, for example, U.S. patent publications US 2002/0012939, US 2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US 2002/0168654 and US 2004/0009466, and U.S. Pat. No. 7,127,379). Modeling analysis allows reliable predictions of the effects on cell growth of shifting the metabolism towards more efficient production of 1,3-butanediol.
One computational method for identifying and designing metabolic alterations favoring biosynthesis of a desired product is the OptKnock computational framework (Burgard et al., Biotechnol. Bioeng. 84:647-657 (2003)). OptKnock is a metabolic modeling and simulation program that suggests gene deletion strategies that result in genetically stable microorganisms which overproduce the target product. Specifically, the framework examines the complete metabolic and/or biochemical network of a microorganism in order to suggest genetic manipulations that force the desired biochemical to become an obligatory byproduct of cell growth. By coupling biochemical production with cell growth through strategically placed gene deletions or other functional gene disruption, the growth selection pressures imposed on the engineered strains after long periods of time in a bioreactor lead to improvements in performance as a result of the compulsory growth-coupled biochemical production. Lastly, when gene deletions are constructed there is a negligible possibility of the designed strains reverting to their wild-type states because the genes selected by OptKnock are to be completely removed from the genome. Therefore, this computational methodology can be used to either identify alternative pathways that lead to biosynthesis of a desired product or used in connection with the non-naturally occurring microbial organisms for further optimization of biosynthesis of a desired product.
Briefly, OptKnock is a term used herein to refer to a computational method and system for modeling cellular metabolism. The OptKnock program relates to a framework of models and methods that incorporate particular constraints into flux balance analysis (FBA) models. These constraints include, for example, qualitative kinetic information, qualitative regulatory information, and/or DNA microarray experimental data. OptKnock also computes solutions to various metabolic problems by, for example, tightening the flux boundaries derived through flux balance models and subsequently probing the performance limits of metabolic networks in the presence of gene additions or deletions. OptKnock computational framework allows the construction of model formulations that enable an effective query of the performance limits of metabolic networks and provides methods for solving the resulting mixed-integer linear programming problems. The metabolic modeling and simulation methods referred to herein as OptKnock are described in, for example, U.S. 2002/0168654, WO 2002/055995, and U.S. 2009/0047719.
Another computational method for identifying and designing metabolic alterations favoring biosynthetic production of a product is a metabolic modeling and simulation system termed SimPheny®. This computational method and system is described in, for example, U.S. 2003/0233218, filed Jun. 14, 2002, and in WO/2003/106998. SimPheny® is a computational system that can be used to produce a network model in silico and to simulate the flux of mass, energy or charge through the chemical reactions of a biological system to define a solution space that contains any and all possible functionalities of the chemical reactions in the system, thereby determining a range of allowed activities for the biological system. This approach is referred to as constraints-based modeling because the solution space is defined by constraints such as the known stoichiometry of the included reactions as well as reaction thermodynamic and capacity constraints associated with maximum fluxes through reactions. The space defined by these constraints can be interrogated to determine the phenotypic capabilities and behavior of the biological system or of its biochemical components.
These computational approaches are consistent with biological realities because biological systems are flexible and can reach the same result in many different ways. Biological systems are designed through evolutionary mechanisms that have been restricted by fundamental constraints that all living systems must face. Therefore, constraints-based modeling strategy embraces these general realities. Further, the ability to continuously impose further restrictions on a network model via the tightening of constraints results in a reduction in the size of the solution space, thereby enhancing the precision with which physiological performance or phenotype can be predicted.
Given the teachings and guidance provided herein, those skilled in the art will be able to apply various computational frameworks for metabolic modeling and simulation to design and implement biosynthesis of a desired compound in host microbial organisms. Such metabolic modeling and simulation methods include, for example, the computational systems exemplified above as SimPheny® and OptKnock. For illustration of the invention, some methods are described herein with reference to the OptKnock computation framework for modeling and simulation. Those skilled in the art will know how to apply the identification, design and implementation of the metabolic alterations using OptKnock to any of such other metabolic modeling and simulation computational frameworks and methods well known in the art.
The methods described above will provide one set of metabolic reactions to disrupt. Elimination of each reaction within the set or metabolic modification can result in a desired product as an obligatory product during the growth phase of the organism. Because the reactions are known, a solution to the bilevel OptKnock problem also will provide the associated gene or genes encoding one or more enzymes that catalyze each reaction within the set of reactions. Identification of a set of reactions and their corresponding genes encoding the enzymes participating in each reaction is generally an automated process, accomplished through correlation of the reactions with a reaction database having a relationship between enzymes and encoding genes.
Once identified, the set of reactions that are to be disrupted in order to achieve production of a desired product are implemented in the target cell or organism by functional disruption of at least one gene encoding each metabolic reaction within the set. One particularly useful means to achieve functional disruption of the reaction set is by deletion of each encoding gene. However, in some instances, it can be beneficial to disrupt the reaction by other genetic aberrations including, for example, mutation, deletion of regulatory regions such as promoters or cis binding sites for regulatory factors, or by truncation of the coding sequence at any of a number of locations. These latter aberrations, resulting in less than total deletion of the gene set can be useful, for example, when rapid assessments of the coupling of a product are desired or when genetic reversion is less likely to occur.
To identify additional productive solutions to the above described bilevel OptKnock problem which lead to further sets of reactions to disrupt or metabolic modifications that can result in the biosynthesis, including growth-coupled biosynthesis of a desired product, an optimization method, termed integer cuts, can be implemented. This method proceeds by iteratively solving the OptKnock problem exemplified above with the incorporation of an additional constraint referred to as an integer cut at each iteration. Integer cut constraints effectively prevent the solution procedure from choosing the exact same set of reactions identified in any previous iteration that obligatorily couples product biosynthesis to growth. For example, if a previously identified growth-coupled metabolic modification specifies reactions 1, 2, and 3 for disruption, then the following constraint prevents the same reactions from being simultaneously considered in subsequent solutions. The integer cut method is well known in the art and can be found described in, for example, Burgard et al., Biotechnol. Prog. 17:791-797 (2001). As with all methods described herein with reference to their use in combination with the OptKnock computational framework for metabolic modeling and simulation, the integer cut method of reducing redundancy in iterative computational analysis also can be applied with other computational frameworks well known in the art including, for example, SimPheny®.
The methods exemplified herein allow the construction of cells and organisms that biosynthetically produce a desired product, including the obligatory coupling of production of a target biochemical product to growth of the cell or organism engineered to harbor the identified genetic alterations. Therefore, the computational methods described herein allow the identification and implementation of metabolic modifications that are identified by an in silico method selected from OptKnock or SimPheny®. The set of metabolic modifications can include, for example, addition of one or more biosynthetic pathway enzymes and/or functional disruption of one or more metabolic reactions including, for example, disruption by gene deletion.
As discussed above, the OptKnock methodology was developed on the premise that mutant microbial networks can be evolved towards their computationally predicted maximum-growth phenotypes when subjected to long periods of growth selection. In other words, the approach leverages an organism's ability to self-optimize under selective pressures. The OptKnock framework allows for the exhaustive enumeration of gene deletion combinations that force a coupling between biochemical production and cell growth based on network stoichiometry. The identification of optimal gene/reaction knockouts requires the solution of a bilevel optimization problem that chooses the set of active reactions such that an optimal growth solution for the resulting network overproduces the biochemical of interest (Burgard et al., Biotechnol. Bioeng. 84:647-657 (2003)).
An in silico stoichiometric model of E. coli metabolism can be employed to identify essential genes for metabolic pathways as exemplified previously and described in, for example, U.S. patent publications US 2002/0012939, US 2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US 2002/0168654 and US 2004/0009466, and in U.S. Pat. No. 7,127,379. As disclosed herein, the OptKnock mathematical framework can be applied to pinpoint gene deletions leading to the growth-coupled production of a desired product. Further, the solution of the bilevel OptKnock problem provides only one set of deletions. To enumerate all meaningful solutions, that is, all sets of knockouts leading to growth-coupled production formation, an optimization technique, termed integer cuts, can be implemented. This entails iteratively solving the OptKnock problem with the incorporation of an additional constraint referred to as an integer cut at each iteration, as discussed above.
As disclosed herein, a nucleic acid encoding a desired activity of a 1,3-butanediol pathway can be introduced into a host organism. In some cases, it can be desirable to modify an activity of a 1,3-butanediol pathway enzyme or protein to increase production of 1,3-butanediol. For example, known mutations that increase the activity of a protein or enzyme can be introduced into an encoding nucleic acid molecule. Additionally, optimization methods can be applied to increase the activity of an enzyme or protein and/or decrease an inhibitory activity, for example, decrease the activity of a negative regulator.
One such optimization method is directed evolution. Directed evolution is a powerful approach that involves the introduction of mutations targeted to a specific gene in order to improve and/or alter the properties of an enzyme. Improved and/or altered enzymes can be identified through the development and implementation of sensitive high-throughput screening assays that allow the automated screening of many enzyme variants (for example, >10⁴). Iterative rounds of mutagenesis and screening typically are performed to afford an enzyme with optimized properties. Computational algorithms that can help to identify areas of the gene for mutagenesis also have been developed and can significantly reduce the number of enzyme variants that need to be generated and screened. Numerous directed evolution technologies have been developed (for reviews, see Hibbert et al., Biomol. Eng 22:11-19 (2005); Huisman and Lalonde, In Biocatalysis in the pharmaceutical and biotechnology industries pgs. 717-742 (2007), Patel (ed.), CRC Press; Otten and Quax. Biomol. Eng 22:1-9 (2005); and Sen et al., Appl Biochem. Biotechnol 143:212-223 (2007)) to be effective at creating diverse variant libraries, and these methods have been successfully applied to the improvement of a wide range of properties across many enzyme classes. Enzyme characteristics that have been improved and/or altered by directed evolution technologies include, for example: selectivity/specificity, for conversion of non-natural substrates; temperature stability, for robust high temperature processing; pH stability, for bioprocessing under lower or higher pH conditions; substrate or product tolerance, so that high product titers can be achieved; binding (K_m), including broadening substrate binding to include non-natural substrates; inhibition (K_i), to remove inhibition by products, substrates, or key intermediates; activity (kcat), to increases enzymatic reaction rates to achieve desired flux; expression levels, to increase protein yields and overall pathway flux; oxygen stability, for operation of air sensitive enzymes under aerobic conditions; and anaerobic activity, for operation of an aerobic enzyme in the absence of oxygen.
A number of exemplary methods have been developed for the mutagenesis and diversification of genes to target desired properties of specific enzymes. Such methods are well known to those skilled in the art. Any of these can be used to alter and/or optimize the activity of a 1,3-butanediol pathway enzyme or protein. Such methods include, but are not limited to EpPCR, which introduces random point mutations by reducing the fidelity of DNA polymerase in PCR reactions (Pritchard et al., J Theor. Biol. 234:497-509 (2005)); Error-prone Rolling Circle Amplification (epRCA), which is similar to epPCR except a whole circular plasmid is used as the template and random 6-mers with exonuclease resistant thiophosphate linkages on the last 2 nucleotides are used to amplify the plasmid followed by transformation into cells in which the plasmid is re-circularized at tandem repeats (Fujii et al., Nucleic Acids Res. 32:e145 (2004); and Fujii et al., Nat. Protoc. 1:2493-2497 (2006)); DNA or Family Shuffling, which typically involves digestion of two or more variant genes with nucleases such as Dnase I or EndoV to generate a pool of random fragments that are reassembled by cycles of annealing and extension in the presence of DNA polymerase to create a library of chimeric genes (Stemmer, Proc Natl Acad Sci USA 91:10747-10751 (1994); and Stemmer, Nature 370:389-391 (1994)); Staggered Extension (StEP), which entails template priming followed by repeated cycles of 2 step PCR with denaturation and very short duration of annealing/extension (as short as 5 sec) (Zhao et al., Nat. Biotechnol. 16:258-261 (1998)); Random Priming Recombination (RPR), in which random sequence primers are used to generate many short DNA fragments complementary to different segments of the template (Shao et al., Nucleic Acids Res 26:681-683 (1998)).
Additional methods include Heteroduplex Recombination, in which linearized plasmid DNA is used to form heteroduplexes that are repaired by mismatch repair (Volkov et al, Nucleic Acids Res. 27:e18 (1999); and Volkov et al., Methods Enzymol. 328:456-463 (2000)); Random Chimeragenesis on Transient Templates (RACHITT), which employs Dnase I fragmentation and size fractionation of single stranded DNA (ssDNA) (Coco et al., Nat. Biotechnol. 19:354-359 (2001)); Recombined Extension on Truncated templates (RETT), which entails template switching of unidirectionally growing strands from primers in the presence of unidirectional ssDNA fragments used as a pool of templates (Lee et al., J. Molec. Catalysis 26:119-129 (2003)); Degenerate Oligonucleotide Gene Shuffling (DOGS), in which degenerate primers are used to control recombination between molecules; (Bergquist and Gibbs, Methods Mol. Biol 352:191-204 (2007); Bergquist et al., Biomol. Eng 22:63-72 (2005); Gibbs et al., Gene 271:13-20 (2001)); Incremental Truncation for the Creation of Hybrid Enzymes (ITCHY), which creates a combinatorial library with 1 base pair deletions of a gene or gene fragment of interest (Ostermeier et al., Proc. Natl. Acad. Sci. USA 96:3562-3567 (1999); and Ostermeier et al., Nat. Biotechnol. 17:1205-1209 (1999)); Thio-Incremental Truncation for the Creation of Hybrid Enzymes (THIO-ITCHY), which is similar to ITCHY except that phosphothioate dNTPs are used to generate truncations (Lutz et al., Nucleic Acids Res 29:E16 (2001)); SCRATCHY, which combines two methods for recombining genes, ITCHY and DNA shuffling (Lutz et al., Proc. Natl. Acad. Sci. USA 98:11248-11253 (2001)); Random Drift Mutagenesis (RNDM), in which mutations made via epPCR are followed by screening/selection for those retaining usable activity (Bergquist et al., Biomol. Eng. 22:63-72 (2005)); Sequence Saturation Mutagenesis (SeSaM), a random mutagenesis method that generates a pool of random length fragments using random incorporation of a phosphothioate nucleotide and cleavage, which is used as a template to extend in the presence of “universal” bases such as inosine, and replication of an inosine-containing complement gives random base incorporation and, consequently, mutagenesis (Wong et al., Biotechnol. J. 3:74-82 (2008); Wong et al., Nucleic Acids Res. 32:e26 (2004); and Wong et al., Anal. Biochem. 341:187-189 (2005)); Synthetic Shuffling, which uses overlapping oligonucleotides designed to encode “all genetic diversity in targets” and allows a very high diversity for the shuffled progeny (Ness et al., Nat. Biotechnol. 20:1251-1255 (2002)); Nucleotide Exchange and Excision Technology NexT, which exploits a combination of dUTP incorporation followed by treatment with uracil DNA glycosylase and then piperidine to perform endpoint DNA fragmentation (Muller et al., Nucleic Acids Res. 33:e117 (2005)).
Further methods include Sequence Homology-Independent Protein Recombination (SHIPREC), in which a linker is used to facilitate fusion between two distantly related or unrelated genes, and a range of chimeras is generated between the two genes, resulting in libraries of single-crossover hybrids (Sieber et al., Nat. Biotechnol. 19:456-460 (2001)); Gene Site Saturation Mutagenesis™ (GSSM™), in which the starting materials include a supercoiled double stranded DNA (dsDNA) plasmid containing an insert and two primers which are degenerate at the desired site of mutations (Kretz et al., Methods Enzymol. 388:3-11 (2004)); Combinatorial Cassette Mutagenesis (CCM), which involves the use of short oligonucleotide cassettes to replace limited regions with a large number of possible amino acid sequence alterations (Reidhaar-Olson et al. Methods Enzymol. 208:564-586 (1991); and Reidhaar-Olson et al. Science 241:53-57 (1988)); Combinatorial Multiple Cassette Mutagenesis (CMCM), which is essentially similar to CCM and uses epPCR at high mutation rate to identify hot spots and hot regions and then extension by CMCM to cover a defined region of protein sequence space (Reetz et al., Angew. Chem. Int. Ed Engl. 40:3589-3591 (2001)); the Mutator Strains technique, in which conditional is mutator plasmids, utilizing the mutD5 gene, which encodes a mutant subunit of DNA polymerase III, to allow increases of 20 to 4000-X in random and natural mutation frequency during selection and block accumulation of deleterious mutations when selection is not required (Selifonova et al., Appl. Environ. Microbiol. 67:3645-3649 (2001)); Low et al., J. Mol. Biol. 260:359-3680 (1996)).
Additional exemplary methods include Look-Through Mutagenesis (LTM), which is a multidimensional mutagenesis method that assesses and optimizes combinatorial mutations of selected amino acids (Rajpal et al., Proc. Natl. Acad. Sci. USA 102:8466-8471 (2005)); Gene Reassembly, which is a DNA shuffling method that can be applied to multiple genes at one time or to create a large library of chimeras (multiple mutations) of a single gene (Tunable GeneReassembly™ (TGR™) Technology supplied by Verenium Corporation), in Silico Protein Design Automation (PDA), which is an optimization algorithm that anchors the structurally defined protein backbone possessing a particular fold, and searches sequence space for amino acid substitutions that can stabilize the fold and overall protein energetics, and generally works most effectively on proteins with known three-dimensional structures (Hayes et al., Proc. Natl. Acad. Sci. USA 99:15926-15931 (2002)); and Iterative Saturation Mutagenesis (ISM), which involves using knowledge of structure/function to choose a likely site for enzyme improvement, performing saturation mutagenesis at chosen site using a mutagenesis method such as Stratagene QuikChange (Stratagene; San Diego Calif.), screening/selecting for desired properties, and, using improved clone(s), starting over at another site and continue repeating until a desired activity is achieved (Reetz et al., Nat. Protoc. 2:891-903 (2007); and Reetz et al., Angew. Chem. Int. Ed Engl. 45:7745-7751 (2006)).
Any of the aforementioned methods for mutagenesis can be used alone or in any combination. Additionally, any one or combination of the directed evolution methods can be used in conjunction with adaptive evolution techniques, as described herein.
It is understood that modifications which do not substantially affect the activity of the various embodiments of this invention are also included within the definition of the invention provided herein. Accordingly, the following examples are intended to illustrate but not limit the present invention.

Example I

1,3-Butanediol Synthesis Via Alanine

This example describes the generation of a microbial organism capable of producing 1,3-butanediol using the alanine pathway in FIG. 1 via Steps A, B, C, D and H.
Escherichia coli is used as a target organism to engineer a 1,3-butanediol-producing pathway as shown in FIG. 1. E. coli provides a good host for generating a non-naturally occurring microorganism capable of producing 1,3-butanediol. E. coli is amenable to genetic manipulation and is known to be capable of producing various products, like ethanol, acetic acid, formic acid, lactic acid, and succinic acid, effectively under anaerobic or microaerobic conditions.
To generate an E. coli strain engineered to produce 1,3-butanediol, nucleic acids encoding the enzymes utilized in the alanine pathway as described previously, are expressed in E. coli using well known molecular biology techniques (see, for example, Sambrook, supra, 2001; Ausubel supra, 1999; Roberts et al., supra, 1989).
In particular, the ortA (YP_—001086914.1), ortB (YP_—001086915.1), dat (P19938), and pdc (P06672) genes encoding the AKP thiolase, AKP aminotransferase and 2,4-dioxopentanoate decarboxylase activities, respectively, are cloned into the pZE13 vector (Expressys, Ruelzheim, Germany) under the PA1/lacO promoter. In addition, the yqhD (NP_—417484.1) and adh (AAA23199.2) genes encoding 3-oxobutyraldehdye reductase (aldehyde reducing) and 4-hydroxy,2-butanone reductase, respectively are cloned into the pZA33 vector (Expressys, Ruelzheim, Germany) under the PA1/lacO promoter. The two sets of plasmids are transformed into E. coli strain MG1655 to express the proteins and enzymes required for 1,3-butanediol synthesis via the alanine pathway. Note that E. coli possesses the ability to form D-alanine.
The resulting genetically engineered organism is cultured in glucose containing medium following procedures well known in the art (see, for example, Sambrook et al., supra, 2001). The expression of alanine pathway genes is corroborated using methods well known in the art for determining polypeptide expression or enzymatic activity, including for example, Northern blots, PCR amplification of mRNA, immunoblotting. Enzymatic activities of the expressed enzymes are confirmed using assays specific for the individually activities. The ability of the engineered E. coli strain to produce 1,3-butanediol is confirmed using HPLC, gas chromatography-mass spectrometry (GCMS) or liquid chromatography-mass spectrometry (LCMS).
Microbial strains engineered to have a functional 1,3-butanediol synthesis pathway are further augmented by optimization for efficient utilization of the pathway. Briefly, the engineered strain is assessed to determine whether any of the exogenous genes are expressed at a rate limiting level. Expression is increased for any enzymes expressed at low levels that can limit the flux through the pathway by, for example, introduction of additional gene copy numbers.
To generate better producers, metabolic modeling is utilized to optimize growth conditions. Modeling is also used to design gene knockouts that additionally optimize utilization of the pathway (see, for example, U.S. patent publications US 2002/0012939, US 2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US 2002/0168654 and US 2004/0009466, and in U.S. Pat. No. 7,127,379). Modeling analysis allows reliable predictions of the effects on cell growth of shifting the metabolism towards more efficient production of 1,3-butanediol. One modeling method is the bilevel optimization approach, OptKnock (Burgard et al., Biotechnol. Bioengineer. 84:647-657 (2003)), which is applied to select gene knockouts that collectively result in better production of 1,3-butanediol. Adaptive evolution also can be used to generate better producers of, for example, alanine or 2-amino-4-oxopentanoate intermediates or the 1,3-butanediol product. Adaptive evolution is performed to improve both growth and production characteristics (Fong and Palsson, Nat. Genet. 36:1056-1058 (2004); Alper et al., Science 314:1565-1568 (2006)). Based on the results, subsequent rounds of modeling, genetic engineering and adaptive evolution can be applied to the 1,3-butanediol producer to further increase production.
For large-scale production of 1,3-butanediol, the above alanine pathway-containing organism is cultured in a fermenter using a medium known in the art to support growth of the organism under anaerobic conditions. Fermentations are performed in either a batch, fed-batch or continuous manner. Anaerobic conditions are maintained by first sparging the medium with nitrogen and then sealing culture vessel (e.g., flasks can be sealed with a septum and crimp-cap). Microaerobic conditions also can be utilized by providing a small hole for limited aeration. The pH of the medium is maintained at a pH of 7 by addition of an acid, such as H2SO4. The growth rate is determined by measuring optical density using a spectrophotometer (600 nm), and the glucose uptake rate by monitoring carbon source depletion over time. Byproducts such as undesirable alcohols, organic acids, and residual glucose can be quantified by HPLC (Shimadzu) with an HPX-087 column (BioRad), using a refractive index detector for glucose and alcohols, and a UV detector for organic acids, Lin et al., Biotechnol. Bioeng., 775-779 (2005).

Example II

1,3-BDO Synthesis Using Acetoacetyl-CoA as the Intermediate

This Example describes the generation of a microbial organism capable of producing 1,3-butanediol using acetoacetyl-CoA as the precursor (Steps G, H and I in FIG. 2).
Escherichia coli is used as a target organism to engineer the pathway through Steps G (conversion of acetoacetyl-CoA into 3-hydroxybutyryl-CoA), H (conversion of 3-hydroxybutyryl-CoA into 3-hydroxybutyraldehyde) and I (conversion of 3-hydroxybutyraldehyde into 1,3-butanediol) in FIG. 2. E. coli provides a good host for generating a non-naturally occurring microorganism capable of producing 1,3-butanediol. E. coli is amenable to genetic manipulation and is known to be capable of producing various products, like ethanol, acetic acid, formic acid, lactic acid, and succinic acid, effectively under anaerobic or microaerobic conditions.
To generate an E. coli strain engineered to produce 1,3-butanediol, nucleic acids encoding the enzymes utilized in the disclosed pathway (Steps G, H and I) as described previously, are expressed in E. coli using well known molecular biology techniques (see, for example, Sambrook, supra, 2001; Ausubel supra, 1999; Roberts et al., supra, 1989). Note that E. coli has a native thiolase encoded by atop (Accession number: NP_—416728.1) that condenses two molecules of acetyl-CoA to form acetoacetyl-CoA.
Further, hbd (NP_—349314.1) encoding acetoacetyl-CoA reductase (ketone reducing), is cloned into the pZE 13 vector (Expressys, Ruelzheim, Germany) under the PA1/lacO promoter. The plasmid is transformed into E. coli strain MG1655 to express the enzyme required for the formation of 3-hydroxybutyryl-CoA via acetoacetyl-CoA. An aldehyde dehydrogenase (selected from Table 75 below) that converts 3-hydroxybutyryl-CoA into 3-hydroxybutyraldehyde, and an alcohol dehydrogenase (selected from Table 76 below) that further reduces 3-hydroxybutyraldehyde into 1,3-BDO are also cloned into the pZE13 vector under the PA1/lacO promoter.
The resulting genetically engineered organism is cultured in glucose containing medium following procedures well known in the art (see, for example, Sambrook et al., supra, 2001). The expression of the pathway genes is corroborated using methods well known in the art for determining polypeptide expression or enzymatic activity, including, for example, Northern blots, PCR amplification of mRNA, immunoblotting. Enzymatic activities of the expressed enzymes are confirmed using assays specific for the individually activities. The ability of the engineered E. coli strain to produce 1,3-butanediol is confirmed using HPLC, gas chromatography-mass spectrometry (GCMS) or liquid chromatography-mass spectrometry (LCMS).
Microbial strains engineered to have a functional 1,3-butanediol synthesis pathway are further augmented by optimization for efficient utilization of the pathway. Briefly, the engineered strain is assessed to determine whether any of the exogenous genes are expressed at a rate limiting level. Expression is increased for any enzymes expressed at low levels that can limit the flux through the pathway by, for example, introduction of additional gene copy numbers.
To generate better producers, metabolic modeling is utilized to optimize growth conditions. Modeling is also used to design gene knockouts that additionally optimize utilization of the pathway (see, for example, U.S. patent publications US 2002/0012939, US 2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US 2002/0168654 and US 2004/0009466, and in U.S. Pat. No. 7,127,379). Modeling analysis allows reliable predictions of the effects on cell growth of shifting the metabolism towards more efficient production of 1,3-butanediol. One modeling method is the bilevel optimization approach, OptKnock (Burgard et al., Biotechnol. Bioengineer. 84:647-657 (2003)), which is applied to select gene knockouts that collectively result in better production of 1,3-butanediol. Adaptive evolution also can be used to generate better producers of, for example, the acetyl-CoA intermediate or the 1,3-butanediol product. Adaptive evolution is performed to improve both growth and production characteristics (Fong and Palsson, Nat. Genet. 36:1056-1058 (2004); Alper et al., Science 314:1565-1568 (2006)). Based on the results, subsequent rounds of modeling, genetic engineering and adaptive evolution can be applied to the 1,3-butanediol producer to further increase production.
For large-scale production of 1,3-butanediol, the recombinant organism is cultured in a fermenter using a medium known in the art to support growth of the organism under anaerobic conditions. Fermentations are performed in either a batch, fed-batch or continuous manner. Anaerobic conditions are maintained by first sparging the medium with nitrogen and then sealing culture vessel (e.g., flasks can be sealed with a septum and crimp-cap). Microaerobic conditions also can be utilized by providing a small hole for limited aeration. The pH of the medium is maintained at a pH of 7 by addition of an acid, such as H2SO4. The growth rate is determined by measuring optical density using a spectrophotometer (600 nm), and the glucose uptake rate by monitoring carbon source depletion over time. Byproducts such as undesirable alcohols, organic acids, and residual glucose can be quantified by HPLC (Shimadzu) with an HPX-087 column (BioRad), using a refractive index detector for glucose and alcohols, and a UV detector for organic acids (Lin et al., Biotechnol. Bioeng., 90:775-779 (2005)).
Several aldehyde dehydrogenases were tested for activity on 3-hydroxybutyryl-CoA. Crude lysates of bacteria, each strain carrying one out of six genes listed in Table 75 below encoding for an aldehyde dehydrogenase was tested for activity on 3-hydroxybutyryl-CoA by measuring the release of CoA moiety. The genes that were tested and were found to have significant activity on 3-HBCoA encode the proteins with the following accession and GI numbers:

TABLE 75

Protein	GenBank ID	GI Number	Organism

bld	AAP42563.1	31075383	Clostridium
			saccharoperbutyl-
			acetonicum
ald	ACL06658.1	218764192	Desulfatibacillum
			alkenivorans
			AK-01
ald	YP_001452373	157145054	Citrobacter
			koseri
			ATCC BAA-895
pduP	NP_460996.1	16765381	Salmonella
			enterica
			Typhimurium
pduP	ABJ64680.1	116099531	Lactobacillus
			brevis
			ATCC 367
BselDRAFT_1651	ZP_02169447
	163762382	Bacillus
			selenitireducens
			MLS10

To correct for background activity in the lysate, measured activities were compared to a negative control without ALD gene (vector only, “Vo”). FIG. 4 shows the specific activity of each of the tested genes on 3-hydroxybutyryl-CoA. The gene ids are shown on the x-axis.
Further, bld (GenBank ID: AAP42563.1, GI number: 31075383) was also tested for activity on 3-HBCoA. The following FIG. 5 shows the activity of the gene on 3-hydroxybutyryl-CoA before and after dialysis.
Alcohol dehydrogenases that were tested for activity on 3-hydroxybutyraldehyde and demonstrated to have significant activity are listed below.

TABLE 76

Protein	GenBank ID	GI Number	Organism

Bdh (Cbei_2181)	YP_001309304	150017050	Clostridium
			beijerinckii
Bdh (Cbei_1722)	YP_001309535.1	150016596	Clostridium
			beijerinckii
Bdh (Cbei_2421)	YP_001309535.1	150017281	Clostridium
			beijerinckii

The following protocol was used to demonstrate alcohol dehydrogenase activity (i.e., conversion of 3-hydroxybutyraldehyde to 1,3-BDO) and combined aldehyde and alcohol dehydrogenase activities (i.e., conversion of 3-hydroxybutyryl-CoA into 1,3-BDO).
Chemically competent cells were transformed with plasmids containing either an aldehyde dehydrogenase or an alcohol dehydrogenase (listed in Tables 75 and 76 above). Colonies from the plates were picked and grown in LB plus 100 ug/ml carbenecillin overnight, then 0.6 mL was used to inoculate 60 mL culture of each alcohol dehydrogenase, or 1.5 mL was used to inoculate a 500 mL culture of each aldehyde dehydrogenase. Cells were grown at 37° C. to an O.D. of ˜0.7 and induced with IPTG. The cultures were incubated at 30° C. during protein expression for 4 hours. The cell cultures were divided into 30 ml aliquots, centrifuged and the cell pellets were stored at −80° C. A sample of the cell culture was used to estimate final cell density.
Combinations of alcohol dehydrogenases and aldehyde dehydrogenases were screened in a 96-well plate format with 3-hydroxybutyryl-CoA as a substrate plus a control (no substrate). Alternatively, for testing the alcohol dehydrogenases activity, only the alcohol dehydrogenases were added with and without the substrate, 3-hydroxybutyraldehyde. Preparation of cell lysates was performed on ice in the coldroom (4° C.). Final cell density was used to calculate the quantity of Bug Buster cell lysis reagent for each cell pellet. Lysozyme (10 uL) and benzonase (10 uL) were added to 35 ml bugbuster and gently inverted to mix. First, 50 tun of dithiothreitol (100 mM stock) was added to the pellet, then 0.5 ml per O.D. of 1.0 (at 600 nm) of the Bug Buster plus enzyme mixture was added to the cell pellet and gently mixed to resuspend.
To each well, 50 ul of 1 M MOPS (pH=7.5), and 25 ul of cofactor mixture (4 mM NADH and 4 mM NADPH), both 100 uL aldehyde dehydrogenase cell lysate, 150 uL alcohol dehydrogenase cell lysate or only 150 uL alcohol dehydrogenase cell lysate was added and gently mixed. Then, the relevant substrate was added to the wells. 25 mg of 3-hydroxybutyryl CoA was resuspended in 250 uL water and 5 ul was added to each well testing for both alcohol and aldehyde dehydrogenase activities for a final concentration of 1.8 mM. For testing only the alcohol dehydrogenase activity, 50 uL of 3-hydroxybutyraldehyde (prepared by mixing 0.6 ml acetaldehyde in 5 ml water plus catalytic base (one pellet of NaOH) Guthrie, J. P. (reference attached) was added to each well. The final concentration of 3-hydroxybutyraldehyde in each well was approximately 50 mM. The 96-deepwell plate was sealed with a plastic PCR seal and incubated at 30° C. shaking overnight (18 hours total). Because protein and cell debris form precipitates during the incubation period, the plates were centrifuged for 10 min at 4500×g, and the supernate was filtered through a Whatman 96-well filter plate (0.45 μm) prior to LC-MS analysis. Samples were analyzed for 1,3-butanediol formation.
FIG. 6 shows 1,3-BDO concentrations when 3-hydroxybutyraldehyde was added as a substrate and in the control samples with no substrate. The GI numbers for the alcohol dehydrogenases are shown.
FIG. 7 shows 1,3-BDO concentrations when 3-hydroxybutyryl-CoA was added as a substrate and in the control samples with no substrate. The GI numbers for the alcohol dehydrogenases are shown. The GI number for the aldehyde dehydrogenase tested in conjunction is 163762382.

Example III

1,3-BDO Synthesis Using 4-Hydroxybutyryl-CoA as the Intermediate

This Example describes the generation of a microbial organism capable of producing 1,3-butanediol using 4-hydroxybutyryl-CoA as the precursor (Steps A, B and E in FIG. 3).
Escherichia coli is used as a target organism to engineer the pathway through Steps A, B and E in FIG. 3. E. coli provides a good host for generating a non-naturally occurring microorganism capable of producing 1,3-butanediol. E. coli is amenable to genetic manipulation and is known to be capable of producing various products, like ethanol, acetic acid, formic acid, lactic acid, and succinic acid, effectively under anaerobic or microaerobic conditions.
To generate an E. coli strain engineered to produce 1,3-butanediol, nucleic acids encoding the enzymes utilized in the disclosed pathway (Steps A, B and E) as described previously, are expressed in E. coli using well known molecular biology techniques (see, for example, Sambrook, supra, 2001; Ausubel supra, 1999; Roberts et al., supra, 1989). A recombinant strain that has ben engineered to produce significant quantities of 4-hydroxybutyryl-CoA has been described by the applicants previously (Burk et al. (US 20090075351) and will be used for inserting the proposed pathway to 1,3-butanediol.
Further, abfD (YP_—3001396399.1), crt (NP_—349318.1) and adhE2 (AAK09379.1) genes encoding 4-hydroxybutyryl-CoA dehydratase, crotonase and 3-hydroxybutyryl-CoA reductase (alcohol forming) activities respectively, are cloned into the pZE 13 vector (Expressys, Ruelzheim, Germany) under the PA1/lacO promoter. The plasmid is transformed into the recombinant E. coli strain producing 4-hydroxybutyryl-CoA to express the proteins and enzymes required for 1,3-butanediol synthesis from this metabolite.
The resulting genetically engineered organism is cultured in glucose containing medium following procedures well known in the art (see, for example, Sambrook et al., supra, 2001). The expression of the pathway genes is corroborated using methods well known in the art for determining polypeptide expression or enzymatic activity, including, for example, Northern blots, PCR amplification of mRNA, immunoblotting. Enzymatic activities of the expressed enzymes are confirmed using assays specific for the individually activities. The ability of the engineered E. coli strain to produce 1,3-butanediol is confirmed using HPLC, gas chromatography-mass spectrometry (GCMS) or liquid chromatography-mass spectrometry (LCMS).
Microbial strains engineered to have a functional 1,3-butanediol synthesis pathway are further augmented by optimization for efficient utilization of the pathway. Briefly, the engineered strain is assessed to determine whether any of the exogenous genes are expressed at a rate limiting level. Expression is increased for any enzymes expressed at low levels that can limit the flux through the pathway by, for example, introduction of additional gene copy numbers.
To generate better producers, metabolic modeling is utilized to optimize growth conditions. Modeling is also used to design gene knockouts that additionally optimize utilization of the pathway (see, for example, U.S. patent publications US 2002/0012939, US 2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US 2002/0168654 and US 2004/0009466, and in U.S. Pat. No. 7,127,379). Modeling analysis allows reliable predictions of the effects on cell growth of shifting the metabolism towards more efficient production of 1,3-butanediol. One modeling method is the bilevel optimization approach, OptKnock (Burgard et al., Biotechnol. Bioengineer. 84:647-657 (2003)), which is applied to select gene knockouts that collectively result in better production of 1,3-butanediol. Adaptive evolution also can be used to generate better producers of, for example, the acetyl-CoA intermediate or the 1,3-butanediol product. Adaptive evolution is performed to improve both growth and production characteristics (Fong and Palsson, Nat. Genet. 36:1056-1058 (2004); Alper et al., Science 314:1565-1568 (2006)). Based on the results, subsequent rounds of modeling, genetic engineering and adaptive evolution can be applied to the 1,3-butanediol producer to further increase production.
For large-scale production of 1,3-butanediol, the recombinant organism is cultured in a fermenter using a medium known in the art to support growth of the organism under anaerobic conditions. Fermentations are performed in either a batch, fed-batch or continuous manner. Anaerobic conditions are maintained by first sparging the medium with nitrogen and then sealing culture vessel (e.g., flasks can be sealed with a septum and crimp-cap). Microaerobic conditions also can be utilized by providing a small hole for limited aeration. The pH of the medium is maintained at a pH of 7 by addition of an acid, such as H2SO4. The growth rate is determined by measuring optical density using a spectrophotometer (600 nm), and the glucose uptake rate by monitoring carbon source depletion over time. Byproducts such as undesirable alcohols, organic acids, and residual glucose can be quantified by HPLC (Shimadzu) with an HPX-087 column (BioRad), using a refractive index detector for glucose and alcohols, and a UV detector for organic acids (Lin et al., Biotechnol Bioeng. 90:775-779 (2005)).

Example IV

Exemplary Hydrogenase and CO Dehydrogenase Enzymes for Extracting Reducing Equivalents from Syngas and Exemplary Reductive TCA Cycle Enzymes

Enzymes of the reductive TCA cycle useful in the non-naturally occurring microbial organisms of the present invention include one or more of ATP-citrate lyase and three CO₂-fixing enzymes: isocitrate dehydrogenase, alpha-ketoglutarate:ferredoxin oxidoreductase, pyruvate:ferredoxin oxidoreductase. The presence of ATP-citrate lyase or citrate lyase and alpha-ketoglutarate:ferredoxin oxidoreductase indicates the presence of an active reductive TCA cycle in an organism. Enzymes for each step of the reductive TCA cycle are shown below.
ATP-citrate lyase (ACL, EC 2.3.3.8), also called ATP citrate synthase, catalyzes the ATP-dependent cleavage of citrate to oxaloacetate and acetyl-CoA. ACL is an enzyme of the RTCA cycle that has been studied in green sulfur bacteria Chlorobium limicola and Chlorobium tepidum. The alpha(4)beta(4) heteromeric enzyme from Chlorobium limicola was cloned and characterized in E. coli (Kanao et al., Eur. J. Biochem. 269:3409-3416 (2002). The C. limicola enzyme, encoded by aclAB, is irreversible and activity of the enzyme is regulated by the ratio of ADP/ATP. A recombinant ACL from Chlorobium tepidum was also expressed in E. coli and the holoenzyme was reconstituted in vitro, in a study elucidating the role of the alpha and beta subunits in the catalytic mechanism (Kim and Tabita, J. Bacteriol. 188:6544-6552 (2006). ACL enzymes have also been identified in Balnearium lithotrophicum, Sulfurihydrogenibium subterraneum and other members of the bacterial phylum Aquificae (Hugler et al., Environ. Microbiol. 9:81-92 (2007)). This activity has been reported in some fungi as well. Exemplary organisms include Sordaria macrospora (Nowrousian et al., Curr. Genet. 37:189-93 (2000), Aspergillus nidulans, Yarrowia lipolytica (Hynes and Murray, Eukaryotic Cell, July: 1039-1048, (2010) and Aspergillus niger (Meijer et al. J. Ind. Microbiol. Biotechnol. 36:1275-1280 (2009). Other candidates can be found based on sequence homology. Information related to these enzymes is tabulated below:

TABLE 77

Protein	GenBank ID	GI Number	Organism

aclA	BAB21376.1	12407237	Chlorobium limicola
aclB	BAB21375.1	12407235	Chlorobium limicola
aclA	AAM72321.1	21647054	Chlorobium tepidum
aclB	AAM72322.1	21647055	Chlorobium tepidum
aclA	ABI50076.1	114054981	Balnearium lithotrophicum
aclB	ABI50075.1	114054980	Balnearium lithotrophicum
aclA	ABI50085.1	114055040	Sulfurihydrogenibium subterraneum
aclB	ABI50084.1	114055039	Sulfurihydrogenibium subterraneum
aclA	AAX76834.1	62199504	Sulfurimonas denitrificans
aclB	AAX76835.1	62199506	Sulfurimonas denitrificans
acl1	XP_504787.1	50554757	Yarrowia lipolytica
acl2	XP_503231.1	50551515	Yarrowia lipolytica
SPBC1703.07	NP_596202.1	19112994	Schizosaccharomyces pombe
SPAC22A12.16	NP_593246.1	19114158	Schizosaccharomyces pombe
acl1	CAB76165.1	7160185	Sordaria macrospora
acl2	CAB76164.1	7160184	Sordaria macrospora
aclA	CBF86850.1	259487849	Aspergillus nidulans
aclB	CBF86848	259487848	Aspergillus nidulans

In some organisms the conversion of citrate to oxaloacetate and acetyl-CoA proceeds through a citryl-CoA intermediate and is catalyzed by two separate enzymes, citryl-CoA synthetase (EC 6.2.1.18) and citryl-CoA lyase (EC 4.1.3.34) (Aoshima, M., Appl. Microbiol. Biotechnol. 75:249-255 (2007). Citryl-CoA synthetase catalyzes the activation of citrate to citryl-CoA. The Hydrogenobacter thermophilus enzyme is composed of large and small subunits encoded by ccsA and ccsB, respectively (Aoshima et al., Mol. Micrbiol. 52:751-761 (2004)). The citryl-CoA synthetase of Aquifex aeolicus is composed of alpha and beta subunits encoded by sucC1 and sucD1 (Hugler et al., Environ. Microbiol. 9:81-92 (2007)). Citryl-CoA lyase splits citryl-CoA into oxaloacetate and acetyl-CoA. This enzyme is a homotrimer encoded by ccl in Hydrogenobacter thermophilus (Aoshima et al., Mol. Microbiol. 52:763-770 (2004)) and aq_—150 in Aquifex aeolicus (Hugler et al., supra (2007)). The genes for this mechanism of converting citrate to oxaloacetate and citryl-CoA have also been reported recently in Chlorobium tepidum (Eisen et al., PNAS 99(14): 9509-14 (2002).

TABLE 78

Protein	GenBank ID	GI Number	Organism

ccsA	BAD17844.1	46849514	Hydrogenobacter thermophilus
ccsB	BAD17846.1	46849517	Hydrogenobacter thermophilus
sucC1	AAC07285	2983723	Aquifex aeolicus
sucD1	AAC07686	2984152	Aquifex aeolicus
ccl	BAD17841.1	46849510	Hydrogenobacter thermophilus
aq_150	AAC06486	2982866	Aquifex aeolicus
CT0380	NP_661284	21673219	Chlorobium tepidum
CT0269	NP_661173.1	21673108	Chlorobium tepidum
CT1834	AAM73055.1	21647851	Chlorobium tepidum

Oxaloacetate is converted into malate by malate dehydrogenase (EC 1.1.1.37), an enzyme which functions in both the forward and reverse direction. S. cerevisiae possesses three copies of malate dehydrogenase, MDH1 (McAlister-Henn and Thompson, J. Bacteriol. 169:5157-5166 (1987), MDH2 (Minard and McAlister-Henn, Mol. Cell. Biol. 11:370-380 (1991); Gibson and McAlister-Henn, J. Biol. Chem. 278:25628-25636 (2003)), and MDH3 (Steffan and McAlister-Henn, J. Biol. Chem. 267:24708-24715 (1992)), which localize to the mitochondrion, cytosol, and peroxisome, respectively. E. coli is known to have an active malate dehydrogenase encoded by mdh.

TABLE 79

Protein	GenBank ID	GI Number	Organism

MDH1	NP_012838	6322765	Saccharomyces cerevisiae
MDH2	NP_014515	116006499	Saccharomyces cerevisiae
MDH3	NP_010205	6320125	Saccharomyces cerevisiae
Mdh	NP_417703.1	16131126	Escherichia coli

Fumarate hydratase (EC 4.2.1.2) catalyzes the reversible hydration of fumarate to malate. The three fumarases of E. coli, encoded by fumA, fumB and fumC, are regulated under different conditions of oxygen availability. FumB is oxygen sensitive and is active under anaerobic conditions. FumA is active under microanaerobic conditions, and FumC is active under aerobic growth conditions (Tseng et al., J. Bacteriol. 183:461-467 (2001); Woods et al., Biochim. Biophys. Acta 954:14-26 (1988); Guest et al., J. Gen. Microbiol. 131:2971-2984 (1985)). S. cerevisiae contains one copy of a fumarase-encoding gene, FUM1, whose product localizes to both the cytosol and mitochondrion (Sass et al., J. Biol. Chem. 278:45109-45116 (2003)). Additional fumarase enzymes are found in Campylobacter jejuni (Smith et al., Int. J. Biochem. Cell. Biol. 31:961-975 (1999)), Thermus thermophilus (Mizobata et al., Arch. Biochem. Biophys. 355:49-55 (1998)) and Rattus norvegicus (Kobayashi et al., J. Biochem. 89:1923-1931 (1981)). Similar enzymes with high sequence homology include fum1 from Arabidopsis thaliana and fumC from Corynebacterium glutamicum. The MmcBC fumarase from Pelotomaculum thermopropionicum is another class of fumarase with two subunits (Shimoyama et al., FEMS Microbiol. Lett. 270:207-213 (2007)).

TABLE 80

Protein	GenBank ID	GI Number	Organism

fumA	NP_416129.1	16129570	Escherichia coli
fumB	NP_418546.1	16131948	Escherichia coli
fumC	NP_416128.1	16129569	Escherichia coli
FUM1	NP_015061	6324993	Saccharomyces cerevisiae
fumC	Q8NRN8.1	39931596	Corynebacterium glutamicum
fumC	O69294.1	9789756	Campylobacter jejuni
fumC	P84127	75427690	Thermus thermophilus
fumH	P14408.1	120605	Rattus norvegicus
MmcB	YP_001211906	147677691	Pelotomaculum
			thermopropionicum
MmcC	YP_001211907	147677692	Pelotomaculum
			thermopropionicum

Fumarate reductase catalyzes the reduction of fumarate to succinate. The fumarate reductase of E. coli, composed of four subunits encoded by frdABCD, is membrane-bound and active under anaerobic conditions. The electron donor for this reaction is menaquinone and the two protons produced in this reaction do not contribute to the proton gradient (Iverson et al., Science 284:1961-1966 (1999)). The yeast genome encodes two soluble fumarate reductase isozymes encoded by FRDS1 (Enomoto et al., DNA Res. 3:263-267 (1996)) and FRDS2 (Muratsubaki et al., Arch. Biochem. Biophys. 352:175-181 (1998)), which localize to the cytosol and promitochondrion, respectively, and are used during anaerobic growth on glucose (Arikawa et al., FEMS Microbiol. Lett. 165:111-116 (1998)).

TABLE 81

Protein	GenBank ID	GI Number	Organism

FRDS1	P32614	418423	Saccharomyces cerevisiae
FRDS2	NP_012585	6322511	Saccharomyces cerevisiae
frdA	NP_418578.1	16131979	Escherichia coli
frdB	NP_418577.1	16131978	Escherichia coli
frdC	NP_418576.1	16131977	Escherichia coli
frdD	NP_418475.1	16131877	Escherichia coli

The ATP-dependent acylation of succinate to succinyl-CoA is catalyzed by succinyl-CoA synthetase (EC 6.2.1.5). The product of the LSC1 and LSC2 genes of S. cerevisiae and the sucC and sucD genes of E. coli naturally form a succinyl-CoA synthetase complex that catalyzes the formation of succinyl-CoA from succinate with the concomitant consumption of one ATP, a reaction which is reversible in vivo (Buck et al., Biochemistry 24:6245-6252 (1985)). These proteins are identified below:

TABLE 82

Protein	GenBank ID	GI Number	Organism

LSC1	NP_014785	6324716	Saccharomyces cerevisiae
LSC2	NP_011760	6321683	Saccharomyces cerevisiae
sucC	NP_415256.1	16128703	Escherichia coli
sucD	AAC73823.1	1786949	Escherichia coli

Alpha-ketoglutarate:ferredoxin oxidoreductase (EC 1.2.7.3), also known as 2-oxoglutarate synthase or 2-oxoglutarate:ferredoxin oxidoreductase (OFOR), forms alpha-ketoglutarate from CO2 and succinyl-CoA with concurrent consumption of two reduced ferredoxin equivalents. OFOR and pyruvate:ferredoxin oxidoreductase (PFOR) are members of a diverse family of 2-oxoacid:ferredoxin (flavodoxin) oxidoreductases which utilize thiamine pyrophosphate, CoA and iron-sulfur clusters as cofactors and ferredoxin, flavodoxin and FAD as electron carriers (Adams et al., Archaea. Adv. Protein Chem. 48:101-180 (1996)). Enzymes in this class are reversible and function in the carboxylation direction in organisms that fix carbon by the RTCA cycle such as Hydrogenobacter thermophilus, Desulfobacter hydrogenophilus and Chlorobium species (Shiba et al. 1985; Evans et al., Proc. Natl. Acad. ScI. U.S.A. 55:92934 (1966); Buchanan, 1971). The two-subunit enzyme from H. thermophilus, encoded by korAB, has been cloned and expressed in E. coli (Yun et al., Biochem. Biophys. Res. Commun. 282:589-594 (2001)). A five subunit OFOR from the same organism with strict substrate specificity for succinyl-CoA, encoded by forDABGE, was recently identified and expressed in E. coli (Yun et al. 2002). The kinetics of CO₂fixation of both H. thermophilus OFOR enzymes have been characterized (Yamamoto et al., Extremophiles 14:79-85 (2010)). A CO2-fixing OFOR from Chlorobium thiosulfatophilum has been purified and characterized but the genes encoding this enzyme have not been identified to date. Enzyme candidates in Chlorobium species can be inferred by sequence similarity to the H. thermophilus genes. For example, the Chlorobium limicola genome encodes two similar proteins. Acetogenic bacteria such as Moorella thermoacetica are predicted to encode two OFOR enzymes. The enzyme encoded by Moth_—0034 is predicted to function in the CO2-assimilating direction. The genes associated with this enzyme, Moth_—0034 have not been experimentally validated to date but can be inferred by sequence similarity to known OFOR enzymes.
OFOR enzymes that function in the decarboxylation direction under physiological conditions can also catalyze the reverse reaction. The OFOR from the thermoacidophilic archaeon Sulfolobus sp. strain 7, encoded by ST2300, has been extensively studied (Zhang et al. 1996. A plasmid-based expression system has been developed for efficiently expressing this protein in E. coli (Fukuda et al., Eur. J. Biochem. 268:5639-5646 (2001)) and residues involved in substrate specificity were determined (Fukuda and Wakagi, Biochim. Biophys. Acta 1597:74-80 (2002)). The OFOR encoded by Ape1472/Ape1473 from Aeropyrum pernix str. K1 was recently cloned into E. coli, characterized, and found to react with 2-oxoglutarate and a broad range of 2-oxoacids (Nishizawa et al., FEBS Lett. 579:2319-2322 (2005)). Another exemplary OFOR is encoded by oorDABC in Helicobacter pylori (Hughes et al. 1998). An enzyme specific to alpha-ketoglutarate has been reported in Thauera aromatica (Dorner and Boll, J, Bacteriol. 184 (14), 3975-83 (2002). A similar enzyme can be found in Rhodospirillum rubrum by sequence homology. A two subunit enzyme has also been identified in Chlorobium tepidum (Eisen et al., PNAS 99(14): 9509-14 (2002)).

TABLE 83

Protein	GenBank ID	GI Number	Organism

korA	BAB21494	12583691	Hydrogenobacter
			thermophilus
korB	BAB21495	12583692	Hydrogenobacter
			thermophilus
forD	BAB62132.1	14970994	Hydrogenobacter
			thermophilus
forA	BAB62133.1	14970995	Hydrogenobacter
			thermophilus
forB	BAB62134.1	14970996	Hydrogenobacter
			thermophilus
forG	BAB62135.1	14970997	Hydrogenobacter
			thermophilus
forE	BAB62136.1	14970998	Hydrogenobacter
			thermophilus
Clim_0204	ACD89303.1	189339900	Chlorobium limicola
Clim_0205	ACD89302.1	189339899	Chlorobium limicola
Clim_1123	ACD90192.1	189340789	Chlorobium limicola
Clim_1124	ACD90193.1	189340790	Chlorobium limicola
Moth_1984	YP_430825.1	83590816	Moorella thermoacetica
Moth_1985	YP_430826.1	83590817	Moorella thermoacetica
Moth_0034	YP_428917.1	83588908	Moorella thermoacetica
ST2300	NP_378302.1	15922633	Sulfolobus sp. strain 7
Ape1472	BAA80470.1	5105156	Aeropyrum pernix
Ape1473	BAA80471.2	116062794	Aeropyrum pernix
oorD	NP_207383.1	15645213	Helicobacter pylori
oorA	NP_207384.1	15645214	Helicobacter pylori
oorB	NP_207385.1	15645215	Helicobacter pylori
oorC	NP_207386.1	15645216	Helicobacter pylori
CT0163	NP_661069.1	21673004	Chlorobium tepidum
CT0162	NP_661068.1	21673003	Chlorobium tepidum
korA	CAA12243.2	19571179	Thauera aromatica
korB	CAD27440.1	19571178	Thauera aromatica
Rru_A2721	YP_427805.1	83594053	Rhodospirillum rubrum
Rru_A2722	YP_427806.1	83594054	Rhodospirillum rubrum

Isocitrate dehydrogenase catalyzes the reversible decarboxylation of isocitrate to 2-oxoglutarate coupled to the reduction of NAD(P)⁺. IDH enzymes in Saccharomyces cerevisiae and Escherichia coli are encoded by IDP1 and icd, respectively (Haselbeck and McAlister-Henn, J. Biol. Chem. 266:2339-2345 (1991); Nimmo, H. G., Biochem. J. 234:317-2332 (1986)). The reverse reaction in the reductive TCA cycle, the reductive carboxylation of 2-oxoglutarate to isocitrate, is favored by the NADPH-dependent CO₂-fixing IDH from Chlorobium limicola and was functionally expressed in E. coli (Kanao et al., Eur. J. Biochem. 269:1926-1931 (2002)). A similar enzyme with 95% sequence identity is found in the C. tepidum genome in addition to some other candidates listed below.

TABLE 84

Protein	GenBank ID	GI Number	Organism

Icd	ACI84720.1	209772816	Escherichia coli
IDP1	AAA34703.1	171749	Saccharomyces cerevisiae
Idh	BAC00856.1	21396513	Chlorobium limicola
Icd	AAM71597.1	21646271	Chlorobium tepidum
icd	NP_952516.1	39996565	Geobacter sulfurreducens
icd	YP_393560.	78777245	Sulfurimonas denitrificans

In H. thermophilus the reductive carboxylation of 2-oxoglutarate to isocitrate is catalyzed by two enzymes: 2-oxoglutarate carboxylase and oxalosuccinate reductase. 2-Oxoglutarate carboxylase (EC 6.4.1.7) catalyzes the ATP-dependent carboxylation of alpha-ketoglutarate to oxalosuccinate (Aoshima and Igarashi, Mol. Microbiol. 62:748-759 (2006)). This enzyme is a large complex composed of two subunits. Biotinylation of the large (A) subunit is required for enzyme function (Aoshima et al., Mol. Microbiol. 51:791-798 (2004)). Oxalosuccinate reductase (EC 1.1.1.-) catalyzes the NAD-dependent conversion of oxalosuccinate to D-threo-isocitrate. The enzyme is a homodimer encoded by icd in H. thermophilus. The kinetic parameters of this enzyme indicate that the enzyme only operates in the reductive carboxylation direction in vivo, in contrast to isocitrate dehydrogenase enzymes in other organisms (Aoshima and Igarashi, J. Bacteriol. 190:2050-2055 (2008)). Based on sequence homology, gene candidates have also been found in Thiobacillus denitrilicans and Thermocrinis albus.

TABLE 85

Protein	GenBank ID	GI Number	Organism

cfiA	BAF34932.1	116234991	Hydrogenobacter
			thermophilus
cifB	BAF34931.1	116234990	Hydrogenobacter
			thermophilus
Icd	BAD02487.1	38602676	Hydrogenobacter
			thermophilus
Tbd_1556	YP_315314	74317574	Thiobacillus denitrificans
Tbd_1555	YP_315313	74317573	Thiobacillus denitrificans
Tbd_0854	YP_314612	74316872	Thiobacillus denitrificans
Thal_0268	YP_003473030	289548042	Thermocrinis albus
Thal_0267	YP_003473029	289548041	Thermocrinis albus
Thal_0646	YP_003473406	289548418	Thermocrinis albus

Aconitase (EC 4.2.1.3) is an iron-sulfur-containing protein catalyzing the reversible isomerization of citrate and iso-citrate via the intermediate cis-aconitate. Two aconitase enzymes are encoded in the E. coli genome by acnA and acnB. AcnB is the main catabolic enzyme, while AcnA is more stable and appears to be active under conditions of oxidative or acid stress (Cunningham et al., Microbiology 143 (Pt 12):3795-3805 (1997)). Two isozymes of aconitase in Salmonella typhimurium are encoded by acnA and acnB (Horswill and Escalante-Semerena, Biochemistry 40:4703-4713 (2001)). The S. cerevisiae aconitase, encoded by ACO1, is localized to the mitochondria where it participates in the TCA cycle (Gangloff et al., Mol. Cell. Biol. 10:3551-3561 (1990)) and the cytosol where it participates in the glyoxylate shunt (Regev-Rudzki et al., Mol. Biol. Cell. 16:4163-4171 (2005)).

TABLE 86

Protein	GenBank ID	GI Number	Organism

acnA	AAC7438.1	1787531	Escherichia coli
acnB	AAC73229.1	2367097	Escherichia coli
HP0779	NP_207572.1	15645398	Helicobacter pylori 26695
H16_B0568	CAJ95365.1	113529018	Ralstonia eutropha
DesfrDRAFT_3783	ZP_07335307.1	303249064	Desulfovibrio fructosovorans JJ
Suden_1040	ABB44318.1	78497778	Sulfurimonas denitrificans
(acnB)
Hydth_0755	ADO45152.1	308751669	Hydrogenobacter thermophilus
CT0543 (acn)	AAM71785.1	21646475	Chlorobium tepidum
Clim_2436	YP_001944436.1	189347907	Chlorobium limicola
Clim_0515	ACD89607.1	189340204	Chlorobium limicola
acnA	NP_460671.1	16765056	Salmonella typhimurium
acnB	NP_459163.1	16763548	Salmonella typhimurium
ACO1	AAA34389.1	170982	Saccharomyces cerevisiae

Pyruvate:ferredoxin oxidoreductase (PFOR) catalyzes the reversible oxidation of pyruvate to form acetyl-CoA. The PFOR from Desulfovibrio africanus has been cloned and expressed in E. coli resulting in an active recombinant enzyme that was stable for several days in the presence of oxygen (Pieulle et al., J. Bacteriol. 179:5684-5692 (1997)). Oxygen stability is relatively uncommon in PFORs and is believed to be conferred by a 60 residue extension in the polypeptide chain of the D. africanus enzyme. Two cysteine residues in this enzyme form a disulfide bond that protects it against inactivation in the form of oxygen. This disulfide bond and the stability in the presence of oxygen has been found in other Desulfovibrio species also (Vita et al., Biochemistry, 47: 957-64 (2008)). The M. thermoacetica PFOR is also well characterized (Menon and Ragsdale, Biochemistry 36:8484-8494 (1997)) and was shown to have high activity in the direction of pyruvate synthesis during autotrophic growth (Furdui and Ragsdale, J. Biol. Chem. 275:28494-28499 (2000)). Further, E. coli possesses an uncharacterized open reading frame, ydbK, encoding a protein that is 51% identical to the M. thermoacetica PFOR. Evidence for pyruvate oxidoreductase activity in E. coli has been described (Blaschkowski et al., Eur. J. Biochem. 123:563-569 (1982)). PFORs have also been described in other organisms, including Rhodobacter capsulatas (Yakunin and Hallenbeck, Biochimica et Biophysica Acta 1409 (1998) 39-49 (1998)) and Choloboum tepidum (Eisen et al., PNAS 99(14): 9509-14 (2002)). The five subunit PFOR from H. thermophilus, encoded by porEDABG, was cloned into E. coli and shown to function in both the decarboxylating and CO₂-assimilating directions (Ikeda et al. 2006; Yamamoto et al., Extremophiles 14:79-85 (2010)). Homologs also exist in C. carboxidivorans P7. Several additional PFOR enzymes are described in the following review (Ragsdale, S. W., Chem. Rev. 103:2333-2346 (2003)). Finally, flavodoxin reductases (e.g., fgrB from Helicobacter pylori or Campylobacter jejuni) (St Maurice et al., J. Bacteriol. 189:4764-4773 (2007)) or Rnf-type proteins (Seedorf et al., Proc. Natl. Acad. Sci. U.S.A. 105:2128-2133 (2008); and Herrmann, J. Bacteriol 190:784-791 (2008)) provide a means to generate NADH or NADPH from the reduced ferredoxin generated by PFOR. These proteins are identified below.

TABLE 87

Protein	GenBank ID	GI Number	Organism

DesfrDRAFT_0121	ZP_07331646.1	303245362	Desulfovibrio fructosovorans JJ
Por	CAA70873.1	1770208	Desulfovibrio africanus
por	YP_012236.1	46581428	Desulfovibrio vulgaris str.
			Hildenborough
Dde_3237	ABB40031.1	78220682	DesulfoVibrio desulfuricans G20
Ddes_0298	YP_002478891.1	220903579	Desulfovibrio desulfuricans subsp.
			desulfuricans str. ATCC 27774
Por	YP_428946.1	83588937	Moorella thermoacetica
YdbK	NP_415896.1	16129339	Escherichia coli
nifJ (CT1628)	NP_662511.1	21674446	Chlorobium tepidum
CJE1649	YP_179630.1	57238499	Campylobacter jejuni
nifJ	ADE85473.1	294476085	Rhodobacter capsulatus
porE	BAA95603.1	7768912	Hydrogenobacter thermophilus
porD	BAA95604.1	7768913	Hydrogenobacter thermophilus
porA	BAA95605.1	7768914	Hydrogenobacter thermophilus
porB	BAA95606.1	776891	Hydrogenobacter thermophilus
porG	BAA95607.1	7768916	Hydrogenobacter thermophilus
FqrB	YP_001482096.1	157414840	Campylobacter jejuni
HP1164	NP_207955.1	15645778	Helicobacter pylori
RnfC	EDK33306.1	146346770	Clostridium kluyveri
RnfD	EDK33307.1	146346771	Clostridium kluyveri
RnfG	EDK33308.1	146346772	Clostridium kluyveri
RnfE	EDK33309.1	146346773	Clostridium kluyveri
RnfA	EDK33310.1	146346774	Clostridium kluyveri
RnfB	EDK33311.1	146346775	Clostridium kluyveri

The conversion of pyruvate into acetyl-CoA can be catalyzed by several other enzymes or their combinations thereof. For example, pyruvate dehydrogenase can transform pyruvate into acetyl-CoA with the concomitant reduction of a molecule of NAD into NADH. It is a multi-enzyme complex that catalyzes a series of partial reactions which results in acylating oxidative decarboxylation of pyruvate. The enzyme comprises of three subunits: the pyruvate decarboxylase (E1), dihydrolipoamide acyltransferase (E2) and dihydrolipoamide dehydrogenase (E3). This enzyme is naturally present in several organisms, including E. coli and S. cerevisiae. In the E. coli enzyme, specific residues in the E1 component are responsible for substrate specificity (Bisswanger, H., J. Biol. Chem. 256:815-82 (1981); Bremer, J., Eur. J. Biochem. 8:535-540 (1969); Gong et al., J. Biol. Chem. 275:13645-13653 (2000)). Enzyme engineering efforts have improved the E. coli PDH enzyme activity under anaerobic conditions (Kim et al., J. Bacteriol. 190:3851-3858 (2008); Kim et al., Appl. Environ. Microbiol. 73:1766-1771 (2007); Zhou et al., Biotechnol. Lett. 30:335-342 (2008)). In contrast to the E. coli PDH, the B. subtilis complex is active and required for growth under anaerobic conditions (Nakano et al., J. Bacteriol. 179:6749-6755 (1997)). The Klebsiella pneumoniae PDH, characterized during growth on glycerol, is also active under anaerobic conditions (5). Crystal structures of the enzyme complex from bovine kidney (18) and the E2 catalytic domain from Azotobacter vinelandii are available (4). Yet another enzyme that can catalyze this conversion is pyruvate formate lyase. This enzyme catalyzes the conversion of pyruvate and CoA into acetyl-CoA and formate. Pyruvate formate lyase is a common enzyme in prokaryotic organisms that is used to help modulate anaerobic redox balance. Exemplary enzymes can be found in Escherichia coli encoded by pf1/3 (Knappe and Sawers, FEMS. Microbiol Rev. 6:383-398 (1990)), Lactococcus lactis (Melchiorsen et al., Appl Microbiol Biotechnol 58:338-344 (2002)), and Streptococcus mutans (Takahashi-Abbe et al., Oral. Microbiol Immunol. 18:293-297 (2003)). E. coli possesses an additional pyruvate formate lyase, encoded by tdcE, that catalyzes the conversion of pyruvate or 2-oxobutanoate to acetyl-CoA or propionyl-CoA, respectively (Hesslinger et al., Mol. Microbiol 27:477-492 (1998)). Both pflB and tdcE from E. coli require the presence of pyruvate formate lyase activating enzyme, encoded by pflA. Further, a short protein encoded by yfiD in E. coli can associate with and restore activity to oxygen-cleaved pyruvate formate lyase (Vey et al., Proc. Natl. Acad. Sci. U.S.A. 105:16137-16141 (2008). Note that pflA and pflB from E. coli were expressed in S. cerevisiae as a means to increase cytosolic acetyl-CoA for butanol production as described in WO/2008/080124]. Additional pyruvate formate lyase and activating enzyme candidates, encoded by pfl and act, respectively, are found in Clostridium pasteurianum (Weidner et al., J. Bacteriol. 178:2440-2444 (1996)).
Further, different enzymes can be used in combination to convert pyruvate into acetyl-CoA. For example, in S. cerevisiae, acetyl-CoA is obtained in the cytosol by first decarboxylating pyruvate to form acetaldehyde; the latter is oxidized to acetate by acetaldehyde dehydrogenase and subsequently activated to form acetyl-CoA by acetyl-CoA synthetase. Acetyl-CoA synthetase is a native enzyme in several other organisms including E. coli (Kumari et al., J. Bacteriol. 177:2878-2886 (1995)), Salmonella enterica (Starai et al., Microbiology 151:3793-3801 (2005); Starai et al., J. Biol. Chem. 280:26200-26205 (2005)), and Moorella thermoacetica (described already). Alternatively, acetate can be activated to form acetyl-CoA by acetate kinase and phosphotransacetylase. Acetate kinase first converts acetate into acetyl-phosphate with the accompanying use of an ATP molecule. Acetyl-phosphate and CoA are next converted into acetyl-CoA with the release of one phosphate by phosphotransacetylase. Both acetate kinase and phosphotransacetylyase are well-studied enzymes in several Clostridia and Methanosarcina thermophila.
Yet another way of converting pyruvate to acetyl-CoA is via pyruvate oxidase. Pyruvate oxidase converts pyruvate into acetate, using ubiquione as the electron acceptor. In E. coli, this activity is encoded by poxB. PoxB has similarity to pyruvate decarboxylase of S. cerevisiae and Zymomonas mobilis. The enzyme has a thiamin pyrophosphate cofactor (Koland and Gennis, Biochemistry 21:4438-4442 (1982)); O'Brien et al., Biochemistry 16:3105-3109 (1977); O'Brien and Gennis, J. Biol. Chem. 255:3302-3307 (1980)) and a flavin adenine dinucleotide (FAD) cofactor. Acetate can then be converted into acetyl-CoA by either acetyl-CoA synthetase or by acetate kinase and phosphotransacetylase, as described earlier. Some of these enzymes can also catalyze the reverse reaction from acetyl-CoA to pyruvate.
For enzymes that use reducing equivalents in the form of NADH or NADPH, these reduced carriers can be generated by transferring electrons from reduced ferredoxin. Two enzymes catalyze the reversible transfer of electrons from reduced ferredoxins to NAD(P)⁺, ferredoxin:NAD+ oxidoreductase (EC 1.18.1.3) and ferredoxin:NADP+ oxidoreductase (FNR, EC 1.18.1.2). Ferredoxin:NADP+ oxidoreductase (FNR, EC 1.18.1.2) has a noncovalently bound FAD cofactor that facilitates the reversible transfer of electrons from NADPH to low-potential acceptors such as ferredoxins or flavodoxins (Blaschkowski et al., Eur. J. Biochem. 123:563-569 (1982); Fujii et al., 1977). The Helicobacter pylori FNR, encoded by HP1164 (fqrB), is coupled to the activity of pyruvate:ferredoxin oxidoreductase (PFOR) resulting in the pyruvate-dependent production of NADPH (St et al. 2007). An analogous enzyme is found in Campylobacter jejuni (St et al. 2007). A ferredoxin:NADP+ oxidoreductase enzyme is encoded in the E. coli genome by fpr (Bianchi et al. 1993). Ferredoxin:NAD+ oxidoreductase utilizes reduced ferredoxin to generate NADH from NAD+. In several organisms, including E. coli, this enzyme is a component of multifunctional dioxygenase enzyme complexes. The ferredoxin:NAD+ oxidoreductase of E. coli, encoded by hcaD, is a component of the 3-phenylproppionate dioxygenase system involved in involved in aromatic acid utilization (Diaz et al. 1998). NADH:ferredoxin reductase activity was detected in cell extracts of Hydrogenobacter thermophilus strain TK-6, although a gene with this activity has not yet been indicated (Yoon et al. 2006). NADP oxidoreductase of C. kluyveri, encoded by nfnAB, catalyzes the concomitant reduction of ferredoxin and NAD+ with two equivalents of NADPH (Wang et al, J Bacteriol 192: 5115-5123 (2010)). Finally, the energy-conserving membrane-associated Rnf-type proteins (Seedorf et al., Proc. Natl. Acad. Sci. U.S.A. 105:2128-2133 (2008); Herrmann et al., J. Bacteriol. 190:784-791 (2008)) provide a means to generate NADH or NADPH from reduced ferredoxin. Additional ferredoxin:NAD(P)+ oxidoreductases have been annotated in Clostridium carboxydivorans P7 and Clostridium ljungdahli.

TABLE 88

Protein	GenBank ID	GI Number	Organism

HP1164	NP_207955.1	15645778	Helicobacter pylori
RPA3954	CAE29395.1	39650872	Rhodopseudomonas palustris
fpr	BAH29712.1	225320633	Hydrogenobacter
			thermophilus
yumC	NP_391091.2	255767736	Bacillus subtilis
CJE0663	AAW35824.1	57167045	Campylobacter jejuni
fpr	P28861.4	399486	Escherichia coli
hcaD	AAC75595.1	1788892	Escherichia coli
LOC100282643	NP_001149023.1	226497434	Zea mays
NfnA	YP_001393861.1	153953096	Clostridium kluyveri
NfnB	YP_001393862.1	153953097	Clostridium kluyveri
RnfC	EDK33306.1	146346770	Clostridium kluyveri
RnfD	EDK33307.1	146346771	Clostridium kluyveri
RnfG	EDK33308.1	146346772	Clostridium kluyveri
RnfE	EDK33309.1	146346773	Clostridium kluyveri
RnfA	EDK33310.1	146346774	Clostridium kluyveri
RnfB	EDK33311.1	146346775	Clostridium kluyveri
CcarbDRAFT_2639	ZP_05392639.1	255525707	Clostridium carboxidivorans
			P7
CcarbDRAFT_2638	ZP_05392638.1	255525706	Clostridium carboxidivorans
			P7
CcarbDRAFT_2636	ZP_05392636.1	255525704	Clostridium carboxidivorans
			P7
CcarbDRAFT_5060	ZP_05395060.1	255528241	Clostridium carboxidivorans
			P7
CcarbDRAFT_2450	ZP_05392450.1	255525514	Clostridium carboxidivorans
			P7
CcarbDRAFT_1084	ZP_05391084.1	255524124	Clostridium carboxidivorans
			P7
CLJU_c11410	ADK14209.1	300434442	Clostridium ljungdahli
(RnfB)
CLJU_c11400	ADK14208.1	300434441	Clostridium ljungdahli
(RnfA)
CLJU_c11390	ADK14207.1	300434440	Clostridium ljungdahli
(RnfE)
CLJU_c11380	ADK14206.1	300434439	Clostridium ljungdahli
(RnfG)
CLJU_c11370	ADK14205.1	300434438	Clostridium ljungdahli
(RnfD)
CLJU_c11360	ADK14204.1	300434437	Clostridium ljungdahli
(RnfC)

Ferredoxins are small acidic proteins containing one or more iron-sulfur clusters that function as intracellular electron carriers with a low reduction potential. Reduced ferredoxins donate electrons to Fe-dependent enzymes such as ferredoxin-NADP+ oxidoreductase, pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OFOR). The H. thermophilus gene fdx1 encodes a [4Fe-4S]-type ferredoxin that is required for the reversible carboxylation of 2-oxoglutarate and pyruvate by OFOR and PFOR, respectively (Yamamoto et al., Extremophiles 14:79-85 (2010)). The ferredoxin associated with the Sulfolobus solfataricus 2-oxoacid:ferredoxin reductase is a monomeric dicluster [3Fe-4S][4Fe-4S] type ferredoxin (Park et al. 2006). While the gene associated with this protein has not been fully sequenced, the N-terminal domain shares 93% homology with the zfx ferredoxin from S. acidocaldarius. The E. coli genome encodes a soluble ferredoxin of unknown physiological function, fdx. Some evidence indicates that this protein can function in iron-sulfur cluster assembly (Takahashi and Nakamura, 1999). Additional ferredoxin proteins have been characterized in Helicobacter pylori (Mukhopadhyay et al. 2003) and Campylobacter jejuni (van Vliet et al. 2001). A 2Fe-2S ferredoxin from Clostridium pasteurianum has been cloned and expressed in E. coli (Fujinaga and Meyer, Biochemical and Biophysical Research Communications, 192(3): (1993)). Acetogenic bacteria such as Moorella thermoacetica, Clostridium carboxidivorans P7, Clostridium ljungdahli and Rhodospirillum rubrum are predicted to encode several ferredoxins, listed in the table below.

TABLE 89

Protein	GenBank ID	GI Number	Organism

fdx1	BAE02673.1	68163284	Hydrogenobacter thermophilus
M11214.1	AAA83524.1	144806	Clostridium pasteurianum
Zfx	AAY79867.1	68566938	Sulfolobus acidocalarius
Fdx	AAC75578.1	1788874	Escherichia coli
hp_0277	AAD07340.1	2313367	Helicobacter pylori
fdxA	CAL34484.1	112359698	Campylobacter jejuni
Moth_0061	ABC18400.1	83571848	Moorella thermoacetica
Moth_1200	ABC19514.1	83572962	Moorella thermoacetica
Moth_1888	ABC20188.1	83573636	Moorella thermoacetica
Moth_2112	ABC20404.1	83573852	Moorella thermoacetica
Moth_1037	ABC19351.1	83572799	Moorella thermoacetica
CcarbDRAFT_4383	ZP_05394383.1	255527515	Clostridium carboxidivorans P7
CcarbDRAFT_2958	ZP_05392958.1	255526034	Clostridium carboxidivorans P7
CcarbDRAFT_2281	ZP_05392281.1	255525342	Clostridium carboxidivorans P7
CcarbDRAFT_5296	ZP_05395295.1	255528511	Clostridium carboxidivorans P7
CcarbDRAFT_1615	ZP_05391615.1	255524662	Clostridium carboxidivorans P7
CcarbDRAFT_1304	ZP_05391304.1	255524347	Clostridium carboxidivorans P7
cooF	AAG29808.1	11095245	Carboxydothermus
			hydrogenoformans
fdxN	CAA35699.1	46143	Rhodobacter capsulatus
Rru_A2264	ABC23064.1	83576513	Rhodospirillum rubrum
Rru_A1916	ABC22716.1	83576165	Rhodospirillum rubrum
Rru_A2026	ABC22826.1	83576275	Rhodospirillum rubrum
cooF	AAC45122.1	1498747	Rhodospirillum rubrum
fdxN	AAA26460.1	152605	Rhodospirillum rubrum
Alvin_2884	ADC63789.1	288897953	Allochromatium vinosum DSM
			180
fdx	YP_002801146.1	226946073	Azotobacter vinelandii DJ
CKL_3790	YP_001397146.1	153956381	Clostridium kluyveri DSM 555
fer1	NP_949965.1	39937689	Rhodopseudomonas palustris
			CGA009
fdx	CAA12251.1	3724172	Thauera aromatica
CHY_2405	YP_361202.1	78044690	Carboxydothermus
			hydrogenoformans
fer	YP_359966.1	78045103	Carboxydothermus
			hydrogenoformans
fer	AAC83945.1	1146198	Bacillus subtilis
fdx1	NP_249053.1	15595559	Pseudomonas aeruginosa PA01
yfhL	AP_003148.1	89109368	Escherichia coli K-12
CLJU_c00930	ADK13195.1	300433428	Clostridium ljungdahli
CLJU_c00010	ADK13115.1	300433348	Clostridium ljungdahli
CLJU_c01820	ADK13272.1	300433505	Clostridium ljungdahli
CLJU_c17980	ADK14861.1	300435094	Clostridium ljungdahli
CLJU_c17970	ADK14860.1	300435093	Clostridium ljungdahli
CLJU_c22510	ADK15311.1	300435544	Clostridium ljungdahli
CLJU_c26680	ADK15726.1	300435959	Clostridium ljungdahli
CLJU_c29400	ADK15988.1	300436221	Clostridium ljungdahli

Succinyl-CoA transferase catalyzes the conversion of succinyl-CoA to succinate while transferring the CoA moiety to a CoA acceptor molecule. Many transferases have broad specificity and can utilize CoA acceptors as diverse as acetate, succinate, propionate, butyrate, 2-methylacetoacetate, 3-ketohexanoate, 3-ketopentanoate, valerate, crotonate, 3-mercaptopropionate, propionate, vinylacetate, and butyrate, among others.
The conversion of succinate to succinyl-CoA can be carried by a transferase which does not require the direct consumption of an ATP or GTP. This type of reaction is common in a number of organisms. The conversion of succinate to succinyl-CoA can also be catalyzed by succinyl-CoA:Acetyl-CoA transferase. The gene product of cat1 of Clostridium kluyveri has been shown to exhibit succinyl-CoA: acetyl-CoA transferase activity (Sohling and Gottschalk, J. Bacteriol. 178:871-880 (1996)). In addition, the activity is present in Trichomonas vaginalis (van Grinsven et al. 2008) and Trypanosoma brucei (Riviere et al. 2004). The succinyl-CoA:acetate CoA-transferase from Acetobacter aceti, encoded by aarC, replaces succinyl-CoA synthetase in a variant TCA cycle (Mullins et al. 2008). Similar succinyl-CoA transferase activities are also present in Trichomonas vaginalis (van Grinsven et al. 2008), Trypanosoma brucei (Riviere et al. 2004) and Clostridium kluyveri (Sohling and Gottschalk, 1996c). The beta-ketoadipate:succinyl-CoA transferase encoded by pcaI and pcaJ in Pseudomonas putida is yet another candidate (Kaschabek et al. 2002). The aforementioned proteins are identified below.

TABLE 90

Protein	GenBank ID	GI Number	Organism

cat1	P38946.1	729048	Clostridium kluyveri
TVAG_395550	XP_001330176	123975034	Trichomonas
			vaginalis G3
Tb11.02.0290	XP_828352	71754875	Trypanosoma brucei
pcaI	AAN69545.1	24985644	Pseudomonas putida
pcaJ	NP_746082.1	26990657	Pseudomonas putida
aarC	ACD85596.1	189233555	Acetobacter aceti

An additional exemplary transferase that converts succinate to succinyl-CoA while converting a 3-ketoacyl-CoA to a 3-ketoacid is succinyl-CoA:3:ketoacid-CoA transferase (EC 2.8.3.5). Exemplary succinyl-CoA:3:ketoacid-CoA transferases are present in Helicobacter pylori (Corthesy-Theulaz et al. 1997), Bacillus subtilis, and Homo sapiens (Fukao et al. 2000; Tanaka et al. 2002). The aforementioned proteins are identified below.

TABLE 91

Protein	GenBank ID	GI Number	Organism

HPAG1_0676	YP_627417	108563101	Helicobacter pylori
HPAG1_0677	YP_627418	108563102	Helicobacter pylori
ScoA	NP_391778	16080950	Bacillus subtilis
ScoB	NP_391777	16080949	Bacillus subtilis
OXCT1	NP_000427	4557817	Homo sapiens
OXCT2	NP_071403	11545841	Homo sapiens

Converting succinate to succinyl-CoA by succinyl-CoA:3:ketoacid-CoA transferase requires the simultaneous conversion of a 3-ketoacyl-CoA such as acetoacetyl-CoA to a 3-ketoacid such as acetoacetate. Conversion of a 3-ketoacid back to a 3-ketoacyl-CoA can be catalyzed by an acetoacetyl-CoA:acetate:CoA transferase. Acetoacetyl-CoA:acetate:CoA transferase converts acetoacetyl-CoA and acetate to acetoacetate and acetyl-CoA, or vice versa. Exemplary enzymes include the gene products of atoAD from E. coli (Hanai et al., Appl Environ Microbiol 73:7814-7818 (2007), ctfAB from C. acetobutylicum (Jojima et al., Appl Microbiol Biotechnol 77:1219-1224 (2008), and ctfAB from Clostridium saccharoperhutylacetonicum (Kosaka et al., Biosci. Biotechnol Biochem. 71:58-68 (2007)) are shown below.

TABLE 92

Protein	GenBank ID	GI Number	Organism

AtoA	NP_416726.1	2492994	Escherichia coli
AtoD	NP_416725.1	2492990	Escherichia coli
CtfA	NP_149326.1	15004866	Clostridium acetobutylicum
CtfB	NP_149327.1	15004867	Clostridium acetobutylicum
CtfA	AAP42564.1	31075384	Clostridium
			saccharoperbutylacetonicum
CtfB	AAP42565.1	31075385	Clostridium
			saccharoperbutylacetonicum

Yet another possible CoA acceptor is benzylsuccinate. Succinyl-CoA:(R)-Benzylsuccinate CoA-Transferase functions as part of an anaerobic degradation pathway for toluene in organisms such as Thauera aromatica (Leutwein and Heider, J. Bact. 183(14) 4288-4295 (2001)). Homologs can be found in Azoarcus sp. T, Aromatoleum aromaticum EbN1, and Geobacter metallireducens GS-15. The aforementioned proteins are identified below.

TABLE 93

Protein	GenBank ID	GI Number	Organism

bbsE	AAF89840	9622535	Thauera aromatica
Bbsf	AAF89841	9622536	Thauera aromatica
bbsE	AAU45405.1	52421824	Azoarcus sp. T
bbsF	AAU45406.1	52421825	Azoarcus sp. T
bbsE	YP_158075.1	56476486	Aromatoleum aromaticum
			EbN1
bbsF	YP_158074.1	56476485	Aromatoleum aromaticum
			EbN1
Gmet_1521	YP_384480.1	78222733	Geobacter metallireducens
			GS-15
Gmet_1522	YP_384481.1	78222734	Geobacter metallireducens
			GS-15

Additionally, ygfH encodes a propionyl CoA:succinate CoA transferase in E. coli (Haller et al., Biochemistry, 39(16) 4622-4629). Close homologs can be found in, for example, Citrobacter youngae ATCC 29220, Salmonella enterica subsp. arizonae serovar, and Yersinia intermedia ATCC 29909. The aforementioned proteins are identified below.

TABLE 94

Protein	GenBank ID	GI Number	Organism

ygfH	NP_417395.1	16130821	Escherichia coli str.
			K-12 substr.
			MG1655
CIT292_04485	ZP_03838384.1	227334728	Citrobacter youngae
			ATCC 29220
SARI_04582	YP_001573497.1	161506385	Salmonella enterica
			subsp. arizonae
			serovar
yinte0001_14430	ZP_04635364.1	238791727	Yersinia intermedia
			ATCC 29909

Citrate lyase (EC 4.1.3.6) catalyzes a series of reactions resulting in the cleavage of citrate to acetate and oxaloacetate. The enzyme is active under anaerobic conditions and is composed of three subunits: an acyl-carrier protein (ACP, gamma), an ACP transferase (alpha), and a acyl lyase (beta). Enzyme activation uses covalent binding and acetylation of an unusual prosthetic group, 2′-(5″-phosphoribosyl)-3-′-dephospho-CoA, which is similar in structure to acetyl-CoA. Acylation is catalyzed by CitC, a citrate lyase synthetase. Two additional proteins, CitG and CitX, are used to convert the apo enzyme into the active holo enzyme (Schneider et al., Biochemistry 39:9438-9450 (2000)). Wild type E. coli does not have citrate lyase activity; however, mutants deficient in molybdenum cofactor synthesis have an active citrate lyase (Clark, FEMS Microbiol. Lett. 55:245-249 (1990)). The E. coli enzyme is encoded by citEFD and the citrate lyase synthetase is encoded by citC (Nilekani and SivaRaman, Biochemistry 22:4657-4663 (1983)). The Leuconostoc mesenteroides citrate lyase has been cloned, characterized and expressed in E. coli (Bekal et al., J. Bacteriol. 180:647-654 (1998)). Citrate lyase enzymes have also been identified in enterobacteria that utilize citrate as a carbon and energy source, including Salmonella typhimurium and Klebsiella pneumoniae (Bott, Arch. Microbiol. 167: 78-88 (1997); Bott and Dimroth, Mol. Microbiol. 14:347-356 (1994)). The aforementioned proteins are tabulated below.

TABLE 95

Protein	GenBank ID	GI Number	Organism

citF	AAC73716.1	1786832	Escherichia coli
Cite	AAC73717.2	87081764	Escherichia coli
citD	AAC73718.1	1786834	Escherichia coli
citC	AAC73719.2	87081765	Escherichia coli
citG	AAC73714.1	1786830	Escherichia coli
citX	AAC73715.1	1786831	Escherichia coli
citF	CAA71633.1	2842397	Leuconostoc mesenteroides
Cite	CAA71632.1	2842396	Leuconostoc mesenteroides
citD	CAA71635.1	2842395	Leuconostoc mesenteroides
citC	CAA71636.1	3413797	Leuconostoc mesenteroides
citG	CAA71634.1	2842398	Leuconostoc mesenteroides
citX	CAA71634.1	2842398	Leuconostoc mesenteroides
citF	NP_459613.1	16763998	Salmonella typhimurium
cite	AAL19573.1	16419133	Salmonella typhimurium
citD	NP_459064.1	16763449	Salmonella typhimurium
citC	NP_459616.1	16764001	Salmonella typhimurium
citG	NP_459611.1	16763996	Salmonella typhimurium
citX	NP_459612.1	16763997	Salmonella typhimurium
citF	CAA56217.1	565619	Klebsiella pneumoniae
cite	CAA56216.1	565618	Klebsiella pneumoniae
citD	CAA56215.1	565617	Klebsiella pneumoniae
citC	BAH66541.1	238774045	Klebsiella pneumoniae
citG	CAA56218.1	565620	Klebsiella pneumoniae
citX	AAL60463.1	18140907	Klebsiella pneumoniae

Acetate kinase (EC 2.7.2.1) catalyzes the reversible ATP-dependent phosphorylation of acetate to acetylphosphate. Exemplary acetate kinase enzymes have been characterized in many organisms including E. coli, Clostridium acetobutylicum and Methanosarcina thermophila (Ingram-Smith et al., J. Bacteriol. 187:2386-2394 (2005); Fox and Roseman, J. Biol. Chem. 261:13487-13497 (1986); Winzer et al., Microbioloy 143 (Pt 10):3279-3286 (1997)). Acetate kinase activity has also been demonstrated in the gene product of E. coli purT (Marolewski et al., Biochemistry 33:2531-2537 (1994). Some butyrate kinase enzymes (EC 2.7.2.7), for example buk1 and buk2 from Clostridium acetobutylicum, also accept acetate as a substrate (Hartmanis, M. G., J. Biol. Chem. 262:617-621 (1987)).

TABLE 96

Protein	GenBank ID	GI Number	Organism

ackA	NP_416799.1	16130231	Escherichia coli
Ack	AAB18301.1	1491790	Clostridium acetobutylicum
Ack	AAA72042.1	349834	Methanosarcina thermophila
purT	AAC74919.1	1788155	Escherichia coli
buk1	NP_349675	15896326	Clostridium acetobutylicum
buk2	Q97II1	20137415	Clostridium acetobutylicum

The formation of acetyl-CoA from acetylphosphate is catalyzed by phosphotransacetylase (EC 2.3.1.8). The pta gene from E. coli encodes an enzyme that reversibly converts acetyl-CoA into acetyl-phosphate (Suzuki, T., Biochim. Biophys. Acta 191:559-569 (969)). Additional acetyltransferase enzymes have been characterized in Bacillus subtilis (Rado and Hoch, Biochim. Biophys. Acta 321:114-125 (1973), Clostridium kluyveri (Stadtman, E., Methods Enzymol. 1:5896-599 (1955), and Thermotoga maritima (Bock et al., J. Bacteriol. 181:1861-1867 (1999)). This reaction is also catalyzed by some phosphotranbutyrylase enzymes (EC 2.3.1.19) including the ptb gene products from Clostridium acetobutylicum (Wiesenborn et al., App. Environ. Microbiol. 55:317-322 (1989); Walter et al., Gene 134:107-111 (1993)). Additional ptb genes are found in butyrate-producing bacterium L2-50 (Louis et al., J. Bacteriol. 186:2099-2106 (2004) and Bacillus megaterium (Vazquez et al., Curr. Microbiol. 42:345-349 (2001).

TABLE 97

Protein	GenBank ID	GI Number	Organism

Pta	NP_416800.1	71152910	Escherichia coli
Pta	P39646	730415	Bacillus subtilis
Pta	A5N801	146346896	Clostridium kluyveri
Pta	Q9X0L4	6685776	Thermotoga maritima
Ptb	NP_349676	34540484	Clostridium acetobutylicum
Ptb	AAR19757.1	38425288	butyrate-producing bacterium
			L2-50
Ptb	CAC07932.1	10046659	Bacillus megaterium

The acylation of acetate to acetyl-CoA is catalyzed by enzymes with acetyl-CoA synthetase activity. Two enzymes that catalyze this reaction are AMP-forming acetyl-CoA synthetase (EC 6.2.1.1) and ADP-forming acetyl-CoA synthetase (EC 6.2.1.13). AMP-forming acetyl-CoA synthetase (ACS) is the predominant enzyme for activation of acetate to acetyl-CoA. Exemplary ACS enzymes are found in E. coli (Brown et al., J. Gen. Microbiol. 102:327-336 (1977)), Ralstonia eutropha (Priefert and Steinbuchel, J. Bacteriol. 174:6590-6599 (1992)), Methanothermobacter thermautotrophicus (Ingram-Smith and Smith, Archaea 2:95-107 (2007)), Salmonella enterica (Gulick et al., Biochemistry 42:2866-2873 (2003)) and Saccharomyces cerevisiae (Jogl and Tong, Biochemistry 43:1425-1431 (2004)). ADP-forming acetyl-CoA synthetases are reversible enzymes with a generally broad substrate range (Musfeldt and Schonheit, J. Bacteriol. 184:636-644 (2002)). Two isozymes of ADP-forming acetyl-CoA synthetases are encoded in the Archaeoglobus fulgidus genome by are encoded by AF1211 and AF1983 (Musfeldt and Schonheit, supra (2002)). The enzyme from Haloarcula marismortui (annotated as a succinyl-CoA synthetase) also accepts acetate as a substrate and reversibility of the enzyme was demonstrated (Brasen and Schonheit, Arch. Microbiol. 182:277-287 (2004)). The ACD encoded by PAE3250 from hyperthermophilic crenarchaeon Pyrobaculum aerophilum showed the broadest substrate range of all characterized ACDs, reacting with acetate, isobutyryl-CoA (preferred substrate) and phenylacetyl-CoA (Brasen and Schonheit, supra (2004)). Directed evolution or engineering can be used to modify this enzyme to operate at the physiological temperature of the host organism. The enzymes from A. fulgidus, H. marismortui and P. aerophilum have all been cloned, functionally expressed, and characterized in E. coli (Brasen and Schonheit, supra (2004); Musfeldt and Schonheit, supra (2002)). Additional candidates include the succinyl-CoA synthetase encoded by sucCD in E. coli (Buck et al., Biochemistry 24:6245-6252 (1985)) and the acyl-CoA ligase from Pseudomonas putida (Fernandez-Valverde et al., Appl. Environ. Microbiol. 59:1149-1154 (1993)). The aforementioned proteins are tabulated below.

TABLE 98

Protein	GenBank ID	GI Number	Organism

acs	AAC77039.1	1790505	Escherichia coli
acoE	AAA21945.1	141890	Ralstonia eutropha
acs1	ABC87079.1	86169671	Methanothermobacter
			thermautotrophicus
acs1	AAL23099.1	16422835	Salmonella enterica
ACS1	Q01574.2	257050994	Saccharomyces cerevisiae
AF1211	NP_070039.1	11498810	Archaeoglobus fulgidus
AF1983	NP_070807.1	11499565	Archaeoglobus fulgidus
scs	YP_135572.1	55377722	Haloarcula marismortui
PAE3250	NP_560604.1	18313937	Pyrobaculum aerophilum str.
			IM2
sucC	NP_415256.1	16128703	Escherichia coli
sucD	AAC73823.1	1786949	Escherichia coli
paaF	AAC24333.2	22711873	Pseudomonas putida

The product yields per C-mol of substrate of microbial cells synthesizing reduced fermentation products such as 1,3-butanediol, are limited by insufficient reducing equivalents in the carbohydrate feedstock. Reducing equivalents, or electrons, can be extracted from synthesis gas components such as CO and H2 using carbon monoxide dehydrogenase (CODH) and hydrogenase enzymes, respectively. The reducing equivalents are then passed to acceptors such as oxidized ferredoxins, oxidized quinones, oxidized cytochromes, NAD(P)+, water, or hydrogen peroxide to form reduced ferredoxin, reduced quinones, reduced cytochromes, NAD(P)H, H2, or water, respectively. Reduced ferredoxin and NAD(P)H are particularly useful as they can serve as redox carriers for various Wood-Ljungdahl pathway and reductive TCA cycle enzymes.
Here, we show specific examples of how additional redox availability from CO and/or H2 can improve the yields of reduced products such as 1,3-butanediol. The maximum theoretical yield to produce 1,3-butanediol from glucose is 1.09 mole 1,3-butanediol per mole of glucose under aerobic conditions via the pathways shown in FIG. 8B or 1.09 mole 1,3-butanediol per mole of glucose under aerobic conditions via the pathways shown in FIG. 9B. Gasification of glucose to form syngas will result in the maximum theoretical yield of 1.09 moles of 1,3-BDO per mole of glucose consumed, assuming that 6 moles of CO and 6 moles of H2 are obtained from glucose.
6CO+6H₂→1.091C₄H₁₀O₂+1.636CO₂+0.545H₂
When additional reducing equivalents are provided, the yield can be improved to 2 mol/mol glucose.
1C₆H₁₂O₆+2CO+8H₂→2C₄H₁₀O₂+4H₂O
When both feedstocks of sugar and syngas are available, the syngas components CO and H₂can be utilized together or separately (from any source) to generate reducing equivalents by employing the hydrogenase and/or CO dehydrogenase. The reducing equivalents generated from CO and/or hydrogen will be utilized to power the glucose to 1,3-butanediol production pathways. Theoretically, all carbons in glucose will be conserved, thus resulting in a maximal theoretical yield to produce 1,3-butanediol from glucose.
As shown in above example, a combined feedstock strategy where syngas is combined with a sugar-based feedstock or other carbon substrate can greatly improve the theoretical yields. In this co-feeding approach, syngas components H2 and/or CO can be utilized by the hydrogenase and CO dehydrogenase to generate reducing equivalents, that can be used to power chemical production pathways in which the carbons from sugar or other carbon substrates will be maximally conserved and the theoretical yields improved. Such improvements provide environmental and economic benefits and greatly enhance sustainable chemical production.
As shown in above example, a combined feedstock strategy where syngas is combined with a sugar-based feedstock or other carbon substrate can greatly improve the theoretical yields. In this co-feeding approach, syngas components H2 and CO can be utilized by the hydrogenase and CO dehydrogenase to generate reducing equivalents, that can be used to power chemical production pathways in which the carbons from sugar or other carbon substrates will be maximally conserved and the theoretical yields improved. In case of 1,3-butanediol production from glucose or sugar, the theoretical yields improve from 1.09 mol 1,3-butanediol per mol of glucose to 2 mol 1,3-butanediol per mol of glucose. Such improvements provide environmental and economic benefits and greatly enhance sustainable chemical production.
Herein below the enzymes and the corresponding genes used for extracting redox from syngas components are described. CODH is a reversible enzyme that interconverts CO and CO2 at the expense or gain of electrons. The natural physiological role of the CODH in ACS/CODH complexes is to convert CO2 to CO for incorporation into acetyl-CoA by acetyl-CoA synthase. Nevertheless, such CODH enzymes are suitable for the extraction of reducing equivalents from CO due to the reversible nature of such enzymes. Expressing such CODH enzymes in the absence of ACS allows them to operate in the direction opposite to their natural physiological role (i.e., CO oxidation).
In M. thermoacetica, C. hydrogenoformans, C. carboxidivorans P7, and several other organisms, additional CODH encoding genes are located outside of the ACS/CODH operons. These enzymes provide a means for extracting electrons (or reducing equivalents) from the conversion of carbon monoxide to carbon dioxide. The M. thermoacetica gene (GenBank Accession Number: YP_—430813) is expressed by itself in an operon and is believed to transfer electrons from CO to an external mediator like ferredoxin in a “Ping-pong” reaction. The reduced mediator then couples to other reduced nicolinamide adenine dinucleotide phosphate (NAD(P)H) carriers or ferredoxin-dependent cellular processes (Ragsdale, Annals of the New York Academy of Sciences 1125: 129-136 (2008)). The genes encoding the C. hydrogenoformans CODH-II and CooF, a neighboring protein, were cloned and sequenced (Gonzalez and Robb, FEMS Microbiol Lett. 191:243-247 (2000)). The resulting complex was membrane-bound, although cytoplasmic fractions of CODH-II were shown to catalyze the formation of NADPH suggesting an anabolic role (Svetlitchnyi et al., J Bacteriol. 183:5134-5144 (2001)). The crystal structure of the CODH-II is also available (Dobbek et al., Science 293:1281-1285 (2001)). Similar ACS-free CODH enzymes can be found in a diverse array of organisms including Geobacter metallireducens GS-15, Chlorobium phaeobacteroides DSM 266, Clostridium cellulolyticum H10, Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774, Pelobacter carbinolicus DSM 2380, and Campylobacter curvus 525.92.

TABLE 99

Protein	GenBank ID	GI Number	Organism

CODH (putative)	YP_430813	83590804	Moorella thermoacetica
CODH-II (CooS-II)	YP_358957	78044574	Carboxydothermus
			hydrogenoformans
CooF	YP_358958	78045112	Carboxydothermus
			hydrogenoformans
CODH (putative)	ZP_05390164.1	255523193	Clostridium carboxidivorans P7
CcarbDRAFT_0341	ZP_05390341.1	255523371	Clostridium carboxidivorans P7
CcarbDRAFT_1756	ZP_05391756.1	255524806	Clostridium carboxidivorans P7
CcarbDRAFT_2944	ZP_05392944.1	255526020	Clostridium carboxidivorans P7
CODH	YP_384856.1	78223109	Geobacter metallireducens GS-15
Cpha266_0148	YP_910642.1	119355998	Chlorobium
(cytochrome c)			phaeobacteroides DSM 266
Cpha266_0149	YP_910643.1	119355999	Chlorobium
(CODH)			phaeobacteroides DSM 266
Ccel_0438	YP_002504800.1	220927891	Clostridium cellulolyticum H10
Ddes_0382	YP_002478973.1	220903661	Desulfovibrio desulfuricans subsp.
(CODH)			desulfuricans str. ATCC 27774
Ddes_0381	YP_002478972.1	220903660	Desulfovibrio desulfuricans subsp.
(CooC)			desulfuricans str. ATCC 27774
Pcar_0057	YP_355490.1	7791767	Pelobacter carbinolicus DSM
(CODH)			2380
Pcar_0058	YP_355491.1	7791766	Pelobacter carbinolicus DSM
(CooC)			2380
Pcar_0058	YP_355492.1	7791765	Pelobacter carbinolicus DSM
(HypA)			2380
CooS (CODH)	YP_001407343.1	154175407	Campylobacter curvus 525.92
CLJU_c09110	ADK13979.1	300434212	Clostridium ljungdahli
CLJU_c09100	ADK13978.1	300434211	Clostridium ljungdahli
CLJU_c09090	ADK13977.1	300434210	Clostridium ljungdahli

In some cases, hydrogenase encoding genes are located adjacent to a CODH. In Rhodospirillum rubrum, the encoded CODH/hydrogenase proteins form a membrane-bound enzyme complex that has been indicated to be a site where energy, in the form of a proton gradient, is generated from the conversion of CO and H₂O to CO₂and H₂(Fox et al., J Bacteriol. 178:6200-6208 (1996)). The CODH-I of C. hydrogenoformans and its adjacent genes have been proposed to catalyze a similar functional role based on their similarity to the R. rubrum CODH/hydrogenase gene cluster (Wu et al., PLoS Genet. 1:e65 (2005)). The C. hydrogenoformans CODH-I was also shown to exhibit intense CO oxidation and CO₂reduction activities when linked to an electrode (Parkin et al., J Am. Chem. Soc. 129:10328-10329 (2007)). The protein sequences of exemplary CODH and hydrogenase genes can be identified by the following GenBank accession numbers.

TABLE 100

		GI
Protein	GenBank ID	Number	Organism

CODH-I (CooS-I)	YP_360644	78043418	Carboxydothermus
			hydrogenoformans
CooF	YP_360645	78044791	Carboxydothermus
			hydrogenoformans
HypA	YP_360646	78044340	Carboxydothermus
			hydrogenoformans
CooH	YP_360647	78043871	Carboxydothermus
			hydrogenoformans
CooU	YP_360648	78044023	Carboxydothermus
			hydrogenoformans
CooX	YP_360649	78043124	Carboxydothermus
			hydrogenoformans
CooL	YP_360650	78043938	Carboxydothermus
			hydrogenoformans
CooK	YP_360651	78044700	Carboxydothermus
			hydrogenoformans
CooM	YP_360652	78043942	Carboxydothermus
			hydrogenoformans
CooC	YP_360654.1	78043296	Carboxydothermus
			hydrogenoformans
CooA-1	YP_360655.1	78044021	Carboxydothermus
			hydrogenoformans
CooL	AAC45118	1515468	Rhodospirillum rubrum
CooX	AAC45119	1515469	Rhodospirillum rubrum
CooU	AAC45120	1515470	Rhodospirillum rubrum
CooH	AAC45121	1498746	Rhodospirillum rubrum
CooF	AAC45122	1498747	Rhodospirillum rubrum
CODH (CooS)	AAC45123	1498748	Rhodospirillum rubrum
CooC	AAC45124	1498749	Rhodospirillum rubrum
CooT	AAC45125	1498750	Rhodospirillum rubrum
CooJ	AAC45126	1498751	Rhodospirillum rubrum

Native to E. coli and other enteric bacteria are multiple genes encoding up to four hydrogenases (Sawers, G., Antonie Van Leeuwenhoek 66:57-88 (1994); Sawers et al., J Bacteriol. 164:1324-1331 (1985); Sawers and Boxer, Eur. J Biochem. 156:265-275 (1986); Sawers et al., J Bacteriol. 168:398-404 (1986)). Given the multiplicity of enzyme activities, E. coli or another host organism can provide sufficient hydrogenase activity to split incoming molecular hydrogen and reduce the corresponding acceptor. E. coli possesses two uptake hydrogenases, Hyd-1 and Hyd-2, encoded by the hyaABCDEF and hybOABCDEFG gene clusters, respectively (Lukey et al., How E. coli is equipped to oxidize hydrogen under different redox conditions, J Biol Chem published online Nov. 16, 2009). Hyd-1 is oxygen-tolerant, irreversible, and is coupled to quinone reduction via the hyaC cytochrome. Hyd-2 is sensitive to O₂, reversible, and transfers electrons to the periplasmic ferredoxin hybA which, in turn, reduces a quinone via the hybB integral membrane protein. Reduced quinones can serve as the source of electrons for fumarate reductase in the reductive branch of the TCA cycle. Reduced ferredoxins can be used by enzymes such as NAD(P)H:ferredoxin oxidoreductases to generate NADPH or NADH. They can alternatively be used as the electron donor for reactions such as pyruvate ferredoxin oxidoreductase, AKG ferredoxin oxidoreductase, and 5,10-methylene-H4folate reductase.

TABLE 101

Protein	GenBank ID	GI Number	Organism

HyaA	AAC74057.1	1787206	Escherichia coli
HyaB	AAC74058.1	1787207	Escherichia coli
HyaC	AAC74059.1	1787208	Escherichia coli
HyaD	AAC74060.1	1787209	Escherichia coli
HyaE	AAC74061.1	1787210	Escherichia coli
HyaF	AAC74062.1	1787211	Escherichia coli

TABLE 102

Protein	GenBank ID	GI Number	Organism

HybO	AAC76033.1	1789371	Escherichia coli
HybA	AAC76032.1	1789370	Escherichia coli
HybB	AAC76031.1	2367183	Escherichia coli
HybC	AAC76030.1	1789368	Escherichia coli
HybD	AAC76029.1	1789367	Escherichia coli
HybE	AAC76028.1	1789366	Escherichia coli
HybF	AAC76027.1	1789365	Escherichia coli
HybG	AAC76026.1	1789364	Escherichia coli

The hydrogen-lyase systems of E. coli include hydrogenase 3, a membrane-bound enzyme complex using ferredoxin as an acceptor, and hydrogenase 4 that also uses a ferredoxin acceptor. Hydrogenase 3 and 4 are encoded by the hyc and hyf gene clusters, respectively. Hydrogenase 3 has been shown to be a reversible enzyme (Maeda et al., Appl Microbiol Biotechnol 76(5):1035-42 (2007)). Hydrogenase activity in E. coli is also dependent upon the expression of the hyp genes whose corresponding proteins are involved in the assembly of the hydrogenase complexes (Jacobi et al., Arch. Microbiol 158:444-451 (1992); Rangarajan et al., J. Bacteriol. 190:1447-1458 (2008)).

TABLE 103

Protein	GenBank ID	GI Number	Organism

HycA	NP_417205	16130632	Escherichia coli
HycB	NP_417204	16130631	Escherichia coli
HycC	NP_417203	16130630	Escherichia coli
HycD	NP_417202	16130629	Escherichia coli
HycE	NP_417201	16130628	Escherichia coli
HycF	NP_417200	16130627	Escherichia coli
HycG	NP_417199	16130626	Escherichia coli
HycH	NP_417198	16130625	Escherichia coli
HycI	NP_417197	16130624	Escherichia coli

TABLE 104

Protein	GenBank ID	GI Number	Organism

HyfA	NP_416976	90111444	Escherichia coli
HyfB	NP_416977	16130407	Escherichia coli
HyfC	NP_416978	90111445	Escherichia coli
HyfD	NP_416979	16130409	Escherichia coli
HyfE	NP_416980	16130410	Escherichia coli
HyfF	NP_416981	16130411	Escherichia coli
HyfG	NP_416982	16130412	Escherichia coli
HyfH	NP_416983	16130413	Escherichia coli
HyfI	NP_416984	16130414	Escherichia coli
HyfJ	NP_416985	90111446	Escherichia coli
HyfR	NP_416986	90111447	Escherichia coli

TABLE 105

Protein	GenBank ID	GI Number	Organism

HypA	NP_417206	16130633	Escherichia coli
HypB	NP_417207	16130634	Escherichia coli
HypC	NP_417208	16130635	Escherichia coli
HypD	NP_417209	16130636	Escherichia coli
HypE	NP_417210	226524740	Escherichia coli
HypF	NP_417192	16130619	Escherichia coli

The M. thermoacetica hydrogenases are suitable for a host that lacks sufficient endogenous hydrogenase activity. M. thermoacetica can grow with CO2 as the exclusive carbon source indicating that reducing equivalents are extracted from H2 to enable acetyl-CoA synthesis via the Wood-Ljungdahl pathway (Drake, H. L., J. Bacteriol. 150:702-709 (1982); Drake and Daniel, Res. Microbiol. 155:869-883 (2004); Kellum and Drake, J. Bacteriol. 160:466-469 (1984)). M. thermoacetica has homologs to several hyp, hyc, and hyf genes from E. coli. The protein sequences encoded for by these genes are identified by the following GenBank accession numbers.
Proteins in M. thermoacetica whose genes are homologous to the E. coli hyp genes are shown below.

TABLE 106

Protein	GenBank ID	GI Number	Organism

Moth_2175	YP_431007	83590998	Moorella thermoacetica
Moth_2176	YP_431008	83590999	Moorella thermoacetica
Moth_2177	YP_431009	83591000	Moorella thermoacetica
Moth_2178	YP_431010	83591001	Moorella thermoacetica
Moth_2179	YP_431011	83591002	Moorella thermoacetica
Moth_2180	YP_431012	83591003	Moorella thermoacetica
Moth_2181	YP_431013	83591004	Moorella thermoacetica

Proteins in M. thermoacetica that are homologous to the E. coli Hydrogenase 3 and/or 4 proteins are listed in the following table.

TABLE 107

Protein	GenBank ID	GI Number	Organism

Moth_2182	YP_431014	83591005	Moorella thermoacetica
Moth_2183	YP_431015	83591006	Moorella thermoacetica
Moth_2184	YP_431016	83591007	Moorella thermoacetica
Moth_2185	YP_431017	83591008	Moorella thermoacetica
Moth_2186	YP_431018	83591009	Moorella thermoacetica
Moth_2187	YP_431019	83591010	Moorella thermoacetica
Moth_2188	YP_431020	83591011	Moorella thermoacetica
Moth_2189	YP_431021	83591012	Moorella thermoacetica
Moth_2190	YP_431022	83591013	Moorella thermoacetica
Moth_2191	YP_431023	83591014	Moorella thermoacetica
Moth_2192	YP_431024	83591015	Moorella thermoacetica

In addition, several gene clusters encoding hydrogenase functionality are present in M. thermoacetica and their corresponding protein sequences are provided below.

TABLE 108A

Protein	GenBank ID	GI Number	Organism

Moth_0439	YP_429313	83589304	Moorella thermoacetica
Moth_0440	YP_429314	83589305	Moorella thermoacetica
Moth_0441	YP_429315	83589306	Moorella thermoacetica
Moth_0442	YP_429316	83589307	Moorella thermoacetica
Moth_0809	YP_429670	83589661	Moorella thermoacetica
Moth_0810	YP_429671	83589662	Moorella thermoacetica
Moth_0811	YP_429672	83589663	Moorella thermoacetica
Moth_0812	YP_429673	83589664	Moorella thermoacetica
Moth_0814	YP_429674	83589665	Moorella thermoacetica
Moth_0815	YP_429675	83589666	Moorella thermoacetica
Moth_0816	YP_429676	83589667	Moorella thermoacetica
Moth_1193	YP_430050	83590041	Moorella thermoacetica
Moth_1194	YP_430051	83590042	Moorella thermoacetica
Moth_1195	YP_430052	83590043	Moorella thermoacetica
Moth_1196	YP_430053	83590044	Moorella thermoacetica
Moth_1717	YP_430562	83590553	Moorella thermoacetica
Moth_1718	YP_430563	83590554	Moorella thermoacetica
Moth_1719	YP_430564	83590555	Moorella thermoacetica
Moth_1883	YP_430726	83590717	Moorella thermoacetica
Moth_1884	YP_430727	83590718	Moorella thermoacetica
Moth_1885	YP_430728	83590719	Moorella thermoacetica
Moth_1886	YP_430729	83590720	Moorella thermoacetica
Moth_1887	YP_430730	83590721	Moorella thermoacetica
Moth_1888	YP_430731	83590722	Moorella thermoacetica
Moth_1452	YP_430305	83590296	Moorella thermoacetica
Moth_1453	YP_430306	83590297	Moorella thermoacetica
Moth_1454	YP_430307	83590298	Moorella thermoacetica

Genes encoding hydrogenase enzymes from C. ljungdahli are shown below.

TABLE 108B

Protein	GenBank ID	GI Number	Organism

CLJU_c20290	ADK15091.1	300435324	Clostridium ljungdahli
CLJU_c07030	ADK13773.1	300434006	Clostridium ljungdahli
CLJU_c07040	ADK13774.1	300434007	Clostridium ljungdahli
CLJU_c07050	ADK13775.1	300434008	Clostridium ljungdahli
CLJU_c07060	ADK13776.1	300434009	Clostridium ljungdahli
CLJU_c07070	ADK13777.1	300434010	Clostridium ljungdahli
CLJU_c07080	ADK13778.1	300434011	Clostridium ljungdahli
CLJU_c14730	ADK14541.1	300434774	Clostridium ljungdahli
CLJU_c14720	ADK14540.1	300434773	Clostridium ljungdahli
CLJU_c14710	ADK14539.1	300434772	Clostridium ljungdahli
CLJU_c14700	ADK14538.1	300434771	Clostridium ljungdahli
CLJU_c28670	ADK15915.1	300436148	Clostridium ljungdahli
CLJU_c28660	ADK15914.1	300436147	Clostridium ljungdahli
CLJU_c28650	ADK15913.1	300436146	Clostridium ljungdahli
CLJU_c28640	ADK15912.1	300436145	Clostridium ljungdahli

Ralstonia eutropha H16 uses hydrogen as an energy source with oxygen as a terminal electron acceptor. Its membrane-bound uptake [NiFe]-hydrogenase is an “O2-tolerant” hydrogenase (Cracknell, et al. Proc Nat Acad Sci, 106(49) 20681-20686 (2009)) that is periplasmically-oriented and connected to the respiratory chain via a b-type cytochrome (Schink and Schlegel, Biochim. Biophys. Acta, 567, 315-324 (1979); Bernhard et al., Eur. J. Biochem. 248, 179-186 (1997)). R. eutropha also contains an O₂-tolerant soluble hydrogenase encoded by the Hox operon which is cytoplasmic and directly reduces NAD+ at the expense of hydrogen (Schneider and Schlegel, Biochim. Biophys. Acta 452, 66-80 (1976); Burgdorf, J. Bact. 187(9) 3122-3132 (2005)). Soluble hydrogenase enzymes are additionally present in several other organisms including Geobacter sulfurreducens (Coppi, Microbiology 151, 1239-1254 (2005)), Synechocystis str. PCC 6803 (Germer, J. Biol. Chem., 284(52), 36462-36472 (2009)), and Thiocapsa roseopersicina (Rakhely, Appl. Environ. Microbiol. 70(2) 722-728 (2004)). The Synechocystis enzyme is capable of generating NADPH from hydrogen. Overexpression of both the Hox operon from Synechocystis str. PCC 6803 and the accessory genes encoded by the Hyp operon from Nostoc sp. PCC 7120 led to increased hydrogenase activity compared to expression of the Hox genes alone (Germer, J. Biol. Chem. 284(52), 36462-36472 (2009)).

TABLE 109

Protein	GenBank ID	GI Number	Organism

HoxF	NP_942727.1	38637753	Ralstonia eutropha H16
HoxU	NP_942728.1	38637754	Ralstonia eutropha H16
HoxY	NP_942729.1	38637755	Ralstonia eutropha H16
HoxH	NP_942730.1	38637756	Ralstonia eutropha H16
HoxW	NP_942731.1	38637757	Ralstonia eutropha H16
HoxI	NP_942732.1	38637758	Ralstonia eutropha H16
HoxE	NP_953767.1	39997816	Geobacter sulfurreducens
HoxF	NP_953766.1	39997815	Geobacter sulfurreducens
HoxU	NP_953765.1	39997814	Geobacter sulfurreducens
HoxY	NP_953764.1	39997813	Geobacter sulfurreducens
HoxH	NP_953763.1	39997812	Geobacter sulfurreducens
GSU2717	NP_953762.1	39997811	Geobacter sulfurreducens
HoxE	NP_441418.1	16330690	Synechocystis str. PCC
			6803
HoxF	NP_441417.1	16330689	Synechocystis str. PCC
			6803
Unknown	NP_441416.1	16330688	Synechocystis str. PCC
function			6803
HoxU	NP_441415.1	16330687	Synechocystis str. PCC
			6803
HoxY	NP_441414.1	16330686	Synechocystis str. PCC
			6803
Unknown	NP_441413.1	16330685	Synechocystis str. PCC
function			6803
Unknown	NP_441412.1	16330684	Synechocystis str. PCC
function			6803
HoxH	NP_441411.1	16330683	Synechocystis str. PCC
			6803
HypF	NP_484737.1	17228189	Nostoc sp. PCC 7120
HypC	NP_484738.1	17228190	Nostoc sp. PCC 7120
HypD	NP_484739.1	17228191	Nostoc sp. PCC 7120
Unknown	NP_484740.1	17228192	Nostoc sp. PCC 7120
function
HypE	NP_484741.1	17228193	Nostoc sp. PCC 7120
HypA	NP_484742.1	17228194	Nostoc sp. PCC 7120
HypB	NP_484743.1	17228195	Nostoc sp. PCC 7120
Hox1E	AAP50519.1	37787351	Thiocapsa roseopersicina
Hox1F	AAP50520.1	37787352	Thiocapsa roseopersicina
Hox1U	AAP50521.1	37787353	Thiocapsa roseopersicina
Hox1Y	AAP50522.1	37787354	Thiocapsa roseopersicina
Hox1H	AAP50523.1	37787355	Thiocapsa roseopersicina

Several enzymes and the corresponding genes used for fixing carbon dioxide to either pyruvate or phosphoenolpyruvate to form the TCA cycle intermediates, oxaloacetate or malate are described below.
Carboxylation of phosphoenolpyruvate to oxaloacetate is catalyzed by phosphoenolpyruvate carboxylase. Exemplary PEP carboxylase enzymes are encoded by ppc in E. coli (Kai et al., Arch. Biochem. Biophys. 414:170-179 (2003), ppcA in Methylobacterium extorquens AM1 (Arps et al., J. Bacteriol. 175:3776-3783 (1993), and ppc in Corynebacterium glutamicum (Eikmanns et al., Mol. Gen. Genet. 218:330-339 (1989).

TABLE 110

Protein	GenBank ID	GI Number	Organism

Ppc	NP_418391	16131794	Escherichia coli
ppcA	AAB58883	28572162	Methylobacterium extorquens
Ppc	ABB53270	80973080	Corynebacterium glutamicum

An alternative enzyme for converting phosphoenolpyruvate to oxaloacetate is PEP carboxykinase, which simultaneously forms an ATP while carboxylating PEP. In most organisms PEP carboxykinase serves a gluconeogenic function and converts oxaloacetate to PEP at the expense of one ATP. S. cerevisiae is one such organism whose native PEP carboxykinase, PCK1, serves a gluconeogenic role (Valdes-Hevia et al., FEBS Lett. 258:313-316 (1989). E. coli is another such organism, as the role of PEP carboxykinase in producing oxaloacetate is believed to be minor when compared to PEP carboxylase, which does not form ATP, possibly due to the higher K_mfor bicarbonate of PEP carboxykinase (Kim et al., Appl. Environ. Microbiol. 70:1238-1241 (2004)). Nevertheless, activity of the native E. coli PEP carboxykinase from PEP towards oxaloacetate has been recently demonstrated in ppc mutants of E. coli K-12 (Kwon et al., J. Microbiol. Biotechnol. 16:1448-1452 (2006)). These strains exhibited no growth defects and had increased succinate production at high NaHCO₃concentrations. Mutant strains of E. coli can adopt Pck as the dominant CO2-fixing enzyme following adaptive evolution (Zhang et al. 2009). In some organisms, particularly rumen bacteria, PEP carboxykinase is quite efficient in producing oxaloacetate from PEP and generating ATP. Examples of PEP carboxykinase genes that have been cloned into E. coli include those from Mannheimia succiniciproducens (Lee et al., Biotechnol. Bioprocess Eng. 7:95-99 (2002)), Anaerobiospirillum succiniciproducens (Laivenieks et al., Appl. Environ. Microbiol. 63:2273-2280 (1997), and Actinobacillus succinogenes (Kim et al. supra). The PEP carboxykinase enzyme encoded by Haemophilus influenza is effective at forming oxaloacetate from PEP.

TABLE 111

Protein	GenBank ID	GI Number	Organism

PCK1	NP_013023	6322950	Saccharomyces cerevisiae
pck	NP_417862.1	16131280	Escherichia coli
pckA	YP_089485.1	52426348	Mannheimia succiniciproducens
pckA	O09460.1	3122621	Anaerobiospirillum
			succiniciproducens
pckA	Q6W6X5	75440571	Actinobacillus succinogenes
pckA	P43923.1	1172573	Haemophilus influenza

Pyruvate carboxylase (EC 6.4.1.1) directly converts pyruvate to oxaloacetate at the cost of one ATP. Pyruvate carboxylase enzymes are encoded by PYC1 (Walker et al., Biochem. Biophys. Res. Commun. 176:1210-1217 (1991) and PYC2 (Walker et al., supra) in Saccharomyces cerevisiae, and pyc in Mycobacterium smegmatis (Mukhopadhyay and Purwantini, Biochim. Biophys. Acta 1475:191-206 (2000)).

TABLE 112

Protein	GenBank ID	GI Number	Organism

PYC1	NP_011453	6321376	Saccharomyces cerevisiae
PYC2	NP_009777	6319695	Saccharomyces cerevisiae
Pyc	YP_890857.1	118470447	Mycobacterium smegmatis

Malic enzyme can be applied to convert CO₂and pyruvate to malate at the expense of one reducing equivalent. Malic enzymes for this purpose can include, without limitation, malic enzyme (NAD-dependent) and malic enzyme (NADP-dependent). For example, one of the E. coli malic enzymes (Takeo, J. Biochem. 66:379-387 (1969)) or a similar enzyme with higher activity can be expressed to enable the conversion of pyruvate and CO₂to malate. By fixing carbon to pyruvate as opposed to PEP, malic enzyme allows the high-energy phosphate bond from PEP to be conserved by pyruvate kinase whereby ATP is generated in the formation of pyruvate or by the phosphotransferase system for glucose transport. Although malic enzyme is typically assumed to operate in the direction of pyruvate formation from malate, overexpression of the NAD-dependent enzyme, encoded by maeA, has been demonstrated to increase succinate production in E. coli while restoring the lethal Δpfl-ΔldhA phenotype under anaerobic conditions by operating in the carbon-fixing direction (Stols and Donnelly, Appl. Environ. Microbiol. 63(7) 2695-2701 (1997)). A similar observation was made upon overexpressing the malic enzyme from Ascaris suum in E. coli (Stols et al., Appl. Biochem. Biotechnol. 63-65(1), 153-158 (1997)). The second E. coli malic enzyme, encoded by maeB, is NADP-dependent and also decarboxylates oxaloacetate and other alpha-keto acids (Iwakura et al., J. Biochem. 85(5):1355-65 (1979)).

TABLE 113

Protein	GenBank ID	GI Number	Organism

maeA	NP_415996	90111281	Escherichia coli
maeB	NP_416958	16130388	Escherichia coli
NAD-ME	P27443	126732	Ascaris suum

The enzymes used for converting oxaloacetate (formed from, for example, PEP carboxylase, PEP carboxykinase, or pyruvate carboxylase) or malate (formed from, for example, malic enzyme or malate dehydrogenase) to succinyl-CoA via the reductive branch of the TCA cycle are malate dehydrogenase, fumarate dehydratase (fumarase), fumarate reductase, and succinyl-CoA transferase. The genes for each of the enzymes are described herein above.
Enzymes, genes and methods for engineering pathways from succinyl-CoA to various products into a microorganism are now known in the art. The additional reducing equivalents obtained from CO and/or H2, as disclosed herein, improve the yields of 1,3-butanediol when utilizing carbohydrate-based feedstock. For example, 1,3-butanediol can be produced from succinyl-CoA via succinate semialdehyde, 4-hydroxybutyrate, 4-hydroxybutyryl-phosphate, 4-hydroxybutyrl-CoA, crotonyl-CoA, 3-hydroxybutyryl-CoA, 3-hydroxybutanal, and/or 3-hydroxybutryate. Exemplary enzymes for the conversion succinyl-CoA to 1,3-butanediol include: A. Succinyl-CoA transferase, or Succinyl-CoA synthetase (or succinyl-CoA ligase), B. Succinyl-CoA reductase (aldehyde forming), C. 4-Hydroxybutyrate dehydrogenase, D. 4-Hydroxybutyrate kinase, E. Phosphotrans-4-hydroxybutyrylase, F. Succinate reductase, G. Succinyl-CoA reductase (alcohol forming), H. 4-Hydroxybutyryl-CoA transferase, or 4-Hydroxybutyryl-CoA synthetase, I. Alpha-ketoglutarate decarboxylase or (Q. Glutamate dehydrogenase and/or R. Glutamate transaminase; S. Glutamate decarboxylase; T. 4-aminobutyrate dehydrogenase and/or U. 4-aminobutyrate transaminase), J. 4-hydroxybutyryl-CoA dehydratase, K. crotonase, L. 3-hydroxybutyryl-CoA reductase (aldehyde forming), M. 3-hydroxybutanal reductase, N. 3-hydroxybutyryl-CoA reductase (alcohol forming), O. 3-hydroxybutyryl-CoA hydrolase, transferase, or synthetase, P. 3-hydroxybutyrate reductase.
Enzymes, genes and methods for engineering pathways from glycolysis intermediates to various products into a microorganism are known in the art. The additional reducing equivalents obtained from CO and H2, as described herein, improve the yields of all these products on carbohydrates. For example, 1,3-butanediol can be produced from the glycolysis intermediate, pyruvate. Exemplary enzymes for the conversion of pyruvate to 1,3-butanediol include alanine dehydrogenase alanine aminotransferase; the remaining enzymatic transformations shown are carried out by the following enzymes: A) AKP thiolase, B) AKP aminotransferase or AKP oxidoreductase (deaminating), C) 2,4-dioxopentanoate decarboxylase, D) 3-oxobutyraldehyde reductase (aldehyde reducing), E) AKP decarboxylase, F) 4-aminobutan-2-one ammonia-lyase, G) Butenone hydratase, H) 4-hydroxy,2-butanone reductase, I) AKP ammonia-lyase, J) acetylacrylate decarboxylase, K) 4-aminobutan-2-one aminotransferase or 4-aminobutan-2-one oxidoreductase (deaminating), L) AKP dehydrogenase, M) 2-amino-4-hydroxypentanoate aminotransferase or 2-amino-4-hydroxypentanoate oxidoreductase (deaminating), N) 2-oxo-4-hydroxypentanoate decarboxylase, O) 3-oxobutyraldehyde reductase (ketone reducing), and P) 3-hydroxybutyraldehdye reductase.

Example V

Methods for Handling CO and Anaerobic Cultures

This example describes methods used in handling CO and anaerobic cultures.
A. Handling of CO in small quantities for assays and small cultures. CO is an odorless, colorless and tasteless gas that is a poison. Therefore, cultures and assays that utilized CO required special handling. Several assays, including CO oxidation, acetyl-CoA synthesis, CO concentration using myoglobin, and CO tolerance/utilization in small batch cultures, called for small quantities of the CO gas that were dispensed and handled within a fume hood. Biochemical assays called for saturating very small quantities (<2 mL) of the biochemical assay medium or buffer with CO and then performing the assay. All of the CO handling steps were performed in a fume hood with the sash set at the proper height and blower turned on; CO was dispensed from a compressed gas cylinder and the regulator connected to a Schlenk line. The latter ensures that equal concentrations of CO were dispensed to each of several possible cuvettes or vials. The Schlenk line was set up containing an oxygen scrubber on the input side and an oil pressure release bubbler and vent on the other side. Assay cuvettes were both anaerobic and CO-containing. Therefore, the assay cuvettes were tightly sealed with a rubber stopper and reagents were added or removed using gas-tight needles and syringes. Secondly, small (˜50 mL) cultures were grown with saturating CO in tightly stoppered serum bottles. As with the biochemical assays, the CO-saturated microbial cultures were equilibrated in the fume hood using the Schlenk line setup. Both the biochemical assays and microbial cultures were in portable, sealed containers and in small volumes making for safe handling outside of the fume hood. The compressed CO tank was adjacent to the fume hood.
Typically, a Schlenk line was used to dispense CO to cuvettes, each vented. Rubber stoppers on the cuvettes were pierced with 19 or 20 gage disposable syringe needles and were vented with the same. An oil bubbler was used with a CO tank and oxygen scrubber. The glass or quartz spectrophotometer cuvettes have a circular hole on top into which a Kontes stopper sleeve, Sz7 774250-0007 was fitted. The CO detector unit was positioned proximal to the fume hood.
B. Handling of CO in larger quantities fed to large-scale cultures. Fermentation cultures are fed either CO or a mixture of CO and H2 to simulate syngas as a feedstock in fermentative production. Therefore, quantities of cells ranging from 1 liter to several liters can include the addition of CO gas to increase the dissolved concentration of CO in the medium. In these circumstances, fairly large and continuously administered quantities of CO gas are added to the cultures. At different points, the cultures are harvested or samples removed. Alternatively, cells are harvested with an integrated continuous flow centrifuge that is part of the fermenter.
The fermentative processes are carried out under anaerobic conditions. In some cases, it is uneconomical to pump oxygen or air into fermenters to ensure adequate oxygen saturation to provide a respiratory environment. In addition, the reducing power generated during anaerobic fermentation may be needed in product formation rather than respiration. Furthermore, many of the enzymes for various pathways are oxygen-sensitive to varying degrees. Classic acetogens such as M. thermoacetica are obligate anaerobes and the enzymes in the Wood-Ljungdahl pathway are highly sensitive to irreversible inactivation by molecular oxygen. While there are oxygen-tolerant acetogens, the repertoire of enzymes in the Wood-Ljungdahl pathway might be incompatible in the presence of oxygen because most are metallo-enzymes, key components are ferredoxins, and regulation can divert metabolism away from the Wood-Ljungdahl pathway to maximize energy acquisition. At the same time, cells in culture act as oxygen scavengers that moderate the need for extreme measures in the presence of large cell growth.
C. Anaerobic chamber and conditions. Exemplary anaerobic chambers are available commercially (see, for example, Vacuum Atmospheres Company, Hawthorne Calif.; MBraun, Newburyport Mass.). Conditions included an O2 concentration of 1 ppm or less and 1 atm pure N2. In one example, 3 oxygen scrubbers/catalyst regenerators were used, and the chamber included an O2 electrode (such as Teledyne; City of Industry Calif.). Nearly all items and reagents were cycled four times in the airlock of the chamber prior to opening the inner chamber door. Reagents with a volume >5 mL were sparged with pure N2 prior to introduction into the chamber. Gloves are changed twice/yr and the catalyst containers were regenerated periodically when the chamber displays increasingly sluggish response to changes in oxygen levels. The chamber's pressure was controlled through one-way valves activated by solenoids. This feature allowed setting the chamber pressure at a level higher than the surroundings to allow transfer of very small tubes through the purge valve.
The anaerobic chambers achieved levels of O2 that were consistently very low and were needed for highly oxygen sensitive anaerobic conditions. However, growth and handling of cells does not usually require such precautions. In an alternative anaerobic chamber configuration, platinum or palladium can be used as a catalyst that requires some hydrogen gas in the mix. Instead of using solenoid valves, pressure release can be controlled by a bubbler. Instead of using instrument-based O2 monitoring, test strips can be used instead.
D. Anaerobic microbiology. Small cultures were handled as described above for CO handling. In particular, serum or media bottles are fitted with thick rubber stoppers and aluminum crimps are employed to seal the bottle. Medium, such as Terrific Broth, is made in a conventional manner and dispensed to an appropriately sized serum bottle. The bottles are sparged with nitrogen for ˜30 min of moderate bubbling. This removes most of the oxygen from the medium and, after this step, each bottle is capped with a rubber stopper (such as Bellco 20 mm septum stoppers; Bellco, Vineland, N.J.) and crimp-sealed (Bellco 20 mm). Then the bottles of medium are autoclaved using a slow (liquid) exhaust cycle. At least sometimes a needle can be poked through the stopper to provide exhaust during autoclaving; the needle needs to be removed immediately upon removal from the autoclave. The sterile medium has the remaining medium components, for example buffer or antibiotics, added via syringe and needle. Prior to addition of reducing agents, the bottles are equilibrated for 30-60 minutes with nitrogen (or CO depending upon use). A reducing agent such as a 100×150 mM sodium sulfide, 200 mM cysteine-HCl is added. This is made by weighing the sodium sulfide into a dry beaker and the cysteine into a serum bottle, bringing both into the anaerobic chamber, dissolving the sodium sulfide into anaerobic water, then adding this to the cysteine in the serum bottle. The bottle is stoppered immediately as the sodium sulfide solution generates hydrogen sulfide gas upon contact with the cysteine. When injecting into the culture, a syringe filter is used to sterilize the solution. Other components are added through syringe needles, such as B 12 (10 □M cyanocobalamin), nickel chloride (NiCl2, 20 microM final concentration from a 40 mM stock made in anaerobic water in the chamber and sterilized by autoclaving or by using a syringe filter upon injection into the culture), and ferrous ammonium sulfate (final concentration needed is 100 □M—made as 100-1000× stock solution in anaerobic water in the chamber and sterilized by autoclaving or by using a syringe filter upon injection into the culture). To facilitate faster growth under anaerobic conditions, the 1 liter bottles were inoculated with 50 mL of a preculture grown anaerobically. Induction of the pA1-lacO1 promoter in the vectors was performed by addition of isopropyl β-D-1-thiogalactopyranoside (IPTG) to a final concentration of 0.2 mM and was carried out for about 3 hrs.
Large cultures can be grown in larger bottles using continuous gas addition while bubbling. A rubber stopper with a metal bubbler is placed in the bottle after medium addition and sparged with nitrogen for 30 minutes or more prior to setting up the rest of the bottle. Each bottle is put together such that a sterile filter will sterilize the gas bubbled in and the hoses on the bottles are compressible with small C clamps. Medium and cells are stirred with magnetic stir bars. Once all medium components and cells are added, the bottles are incubated in an incubator in room air but with continuous nitrogen sparging into the bottles.

Example VI

CO Oxidation (CODH) Assay

This example describes assay methods for measuring CO oxidation (CO dehydrogenase; CODH).
The 7 gene CODH/ACS operon of Moorella thermoacetica was cloned into E. coli expression vectors. The intact ˜10 kbp DNA fragment was cloned, and it is likely that some of the genes in this region are expressed from their own endogenous promoters and all contain endogenous ribosomal binding sites. These clones were assayed for CO oxidation, using an assay that quantitatively measures CODH activity. Antisera to the M. thermoacetica gene products was used for Western blots to estimate specific activity. M. thermoacetica is Gram positive, and ribosome binding site elements are expected to work well in E. coli. This activity, described below in more detail, was estimated to be ˜ 1/50th of the M. thermoacetica specific activity. It is possible that CODH activity of recombinant E. coli cells could be limited by the fact that M. thermoacetica enzymes have temperature optima around 55° C. Therefore, a mesophilic CODH/ACS pathway could be advantageous such as the close relative of Moorella that is mesophilic and does have an apparently intact CODH/ACS operon and a Wood-Ljungdahl pathway, Desulfitobacterium hafniense. Acetogens as potential host organisms include, but are not limited to, Rhodospirillum rubrum, Moorella thermoacetica and Desulfitobacterium hafniense.
CO oxidation is both the most sensitive and most robust of the CODH/ACS assays. It is likely that an E. coli-based syngas using system will ultimately need to be about as anaerobic as Clostridial (i.e., Moorella) systems, especially for maximal activity. Improvement in CODH should be possible but will ultimately be limited by the solubility of CO gas in water.
Initially, each of the genes was cloned individually into expression vectors. Combined expression units for multiple subunits/1 complex were generated. Expression in E. coli at the protein level was determined. Both combined M. thermoacetica CODH/ACS operons and individual expression clones were made.
CO oxidation assay. This assay is one of the simpler, reliable, and more versatile assays of enzymatic activities within the Wood-Ljungdahl pathway and tests CODH (Seravalli et al., Biochemistry 43:3944-3955 (2004)). A typical activity of M. thermoacetica CODH specific activity is 500 U at 55° C. or ˜60 U at 25° C. This assay employs reduction of methyl viologen in the presence of CO. This is measured at 578 nm in stoppered, anaerobic, glass cuvettes.
In more detail, glass rubber stoppered cuvettes were prepared after first washing the cuvette four times in deionized water and one time with acetone. A small amount of vacuum grease was smeared on the top of the rubber gasket. The cuvette was gassed with CO, dried 10 mM with a 22 Ga. needle plus an exhaust needle. A volume of 0.98 mL of reaction buffer (50 mM Hepes, pH 8.5, 2 mM dithiothreitol (DTT) was added using a 22 Ga. needle, with exhaust needled, and 100% CO. Methyl viologen (CH3 viologen) stock was 1 M in water. Each assay used 20 microliters for 20 mM final concentration. When methyl viologen was added, an 18 Ga needle (partial) was used as a jacket to facilitate use of a Hamilton syringe to withdraw the CH3 viologen. 4-5 aliquots were drawn up and discarded to wash and gas equilibrate the syringe. A small amount of sodium dithionite (0.1 M stock) was added when making up the CH3 viologen stock to slightly reduce the CH3 viologen. The temperature was equilibrated to 55° C. in a heated Olis spectrophotometer (Bogart GA). A blank reaction (CH3 viologen+buffer) was run first to measure the base rate of CH3 viologen reduction. Crude E. coli cell extracts of ACS90 and ACS91 (CODH-ACS operon of M. thermoacetica with and without, respectively, the first cooC). 10 microliters of extract were added at a time, mixed and assayed. Reduced CH3 viologen turns purple. The results of an assay are shown in Table 114.

TABLE 114

Crude extract CO Oxidation Activities.

ACS90	7.7 mg/ml	ACS91	11.8 mg/ml
Mta98	9.8 mg/ml	Mta99	11.2 mg/ml

Extract	Vol	OD/	U/ml	U/mg

ACS90	10 microliters	0.073	0.376	0.049
ACS91	10 microliters	0.096	0.494	0.042
Mta99	10 microliters	0.0031	0.016	0.0014
ACS90	10 microliters	0.099	0.51	0.066
Mta99	25 microliters	0.012	0.025	0.0022
ACS91	25 microliters	0.215	0.443	0.037
Mta98	25 microliters	0.019	0.039	0.004
ACS91	10 microliters	0.129	0.66	0.056
Averages
ACS90	0.057 U/mg
ACS91	0.045 U/mg
Mta99	0.0018 U/mg

Mta98/Mta99 are E. coli MG1655 strains that express methanol methyltransferase genes from M. thermoacetia and, therefore, are negative controls for the ACS90 ACS91 E. coli strains that contain M. thermoacetica CODH operons.
If ˜1% of the cellular protein is CODH, then these figures would be approximately 100× less than the 500 U/mg activity of pure M. thermoacetica CODH. Actual estimates based on Western blots are 0.5% of the cellular protein, so the activity is about 50× less than for M. thermoacetica CODH. Nevertheless, this experiment demonstrates CO oxidation activity in recombinant E. coli with a much smaller amount in the negative controls. The small amount of CO oxidation (CH3 viologen reduction) seen in the negative controls indicates that E. coli may have a limited ability to reduce CH3 viologen.
To estimate the final concentrations of CODH and Mtr proteins, SDS-PAGE followed by Western blot analyses were performed on the same cell extracts used in the CO oxidation, ACS, methyltransferase, and corrinoid Fe—S assays. The antisera used were polyclonal to purified M. thermoacetica CODH-ACS and Mtr proteins and were visualized using an alkaline phosphatase-linked goat-anti-rabbit secondary antibody. The Westerns were performed and results are shown in FIG. 9. The amounts of CODH in ACS90 and ACS91 were estimated at 50 ng by comparison to the control lanes. Expression of CODH-ACS operon genes including 2 CODH subunits and the methyltransferase were confirmed via Western blot analysis. Therefore, the recombinant E. coli cells express multiple components of a 7 gene operon. In addition, both the methyltransferase and corrinoid iron sulfur protein were active in the same recombinant E. coli cells. These proteins are part of the same operon cloned into the same cells.
The CO oxidation assays were repeated using extracts of Moorella thermoacetica cells for the positive controls. Though CODH activity in E. coli ACS90 and ACS91 was measurable, it was at about 130-150× lower than the M. thermoacetica control. The results of the assay are shown in FIG. 11. Briefly, cells (M. thermoacetica or E. coli with the CODH/ACS operon; ACS90 or ACS91 or empty vector: pZA33S) were grown and extracts prepared as described above. Assays were performed as described above at 55° C. at various times on the day the extracts were prepared. Reduction of methylviologen was followed at 578 nm over a 120 sec time course.
These results describe the CO oxidation (CODH) assay and results. Recombinant E. coli cells expressed CO oxidation activity as measured by the methyl viologen reduction assay.

Example VII

E. coli CO Tolerance Experiment and CO Concentration Assay (Myoglobin Assay)

This example describes the tolerance of E. coli for high concentrations of CO.
To test whether or not E. coli can grow anaerobically in the presence of saturating amounts of CO, cultures were set up in 120 ml serum bottles with 50 ml of Terrific Broth medium (plus reducing solution, NiCl2, Fe(II)NH4SO4, cyanocobalamin, IPTG, and chloramphenicol) as described above for anaerobic microbiology in small volumes. One half of these bottles were equilibrated with nitrogen gas for 30 min. and one half was equilibrated with CO gas for 30 min. An empty vector (pZA33) was used as a control, and cultures containing the pZA33 empty vector as well as both ACS90 and ACS91 were tested with both N2 and CO. All were inoculated and grown for 36 hrs with shaking (250 rpm) at 37° C. At the end of the 36 hour period, examination of the flasks showed high amounts of growth in all. The bulk of the observed growth occurred overnight with a long lag.
Given that all cultures appeared to grow well in the presence of CO, the final CO concentrations were confirmed. This was performed using an assay of the spectral shift of myoglobin upon exposure to CO. Myoglobin reduced with sodium dithionite has an absorbance peak at 435 nm; this peak is shifted to 423 nm with CO. Due to the low wavelength and need to record a whole spectrum from 300 nm on upwards, quartz cuvettes must be used. CO concentration is measured against a standard curve and depends upon the Henry's Law constant for CO of maximum water solubility=970 micromolar at 20° C. and 1 atm.
For the myoglobin test of CO concentration, cuvettes were washed 10× with water, 1× with acetone, and then stoppered as with the CODH assay. N2 was blown into the cuvettes for ˜10 min. A volume of 1 ml of anaerobic buffer (HEPES, pH 8.0, 2 mM DTT) was added to the blank (not equilibrated with CO) with a Hamilton syringe. A volume of 10 microliter myoglobin (˜1 mM—can be varied, just need a fairly large amount) and 1 microliter dithionite (20 mM stock) were added. A CO standard curve was made using CO saturated buffer added at 1 microliter increments. Peak height and shift was recorded for each increment. The cultures tested were pZA33/CO, ACS90/CO, and ACS91/CO. Each of these was added in 1 microliter increments to the same cuvette. Midway through the experiment a second cuvette was set up and used. The results are shown in Table 115.

TABLE 115

Carbon Monoxide Concentrations, 36 hrs.

Strain and Growth Conditions	Final CO concentration (micromolar)

pZA33-CO	930
ACS90-CO	638
	494
	734
	883
ave	687
SD	164
ACS91-CO	728
	812
	760
	611
ave.	728
SD	85

The results shown in Table 115 indicate that the cultures grew whether or not a strain was cultured in the presence of CO or not. These results indicate that E. coli can tolerate exposure to CO under anaerobic conditions and that E. coli cells expressing the CODH-ACS operon can metabolize some of the CO.
These results demonstrate that E. coli cells, whether expressing CODH/ACS or not, were able to grow in the presence of saturating amounts of CO. Furthermore, these grew equally well as the controls in nitrogen in place of CO. This experiment demonstrated that laboratory strains of E. coli are insensitive to CO at the levels achievable in a syngas project performed at normal atmospheric pressure. In addition, preliminary experiments indicated that the recombinant E. coli cells expressing CODH/ACS actually consumed some CO, probably by oxidation to carbon dioxide.

Example VIII

Exemplary Carboxylic Acid Reductases

This example describes the use of carboxylic acid reductases (CAR) to carry out the conversion of a carboxylic acid to an aldehyde.
Any intermediate carboxylic acid in a 1,3-butanediol pathway (or accessible carboxylic acid via its CoA derivative) can be converted to an aldehyde, if so desired. The conversion of unactivated acids to aldehydes can be carried out by an acid reductase. Examples of such conversions include, but are not limited, the conversion of 4-hydroxybutyrate, succinate, alpha-ketoglutarate, and 4-aminobutyrate to 4-hydroxybutanal, succinate semialdehyde, 2,5-dioxopentanoate, and 4-aminobutanal, respectively. One notable carboxylic acid reductase can be found in Nocardia iowensis which catalyzes the magnesium, ATP and NADPH-dependent reduction of carboxylic acids to their corresponding aldehydes (Venkitasubramanian et al., J. Biol. Chem. 282:478-485 (2007)). This enzyme is encoded by the car gene and was cloned and functionally expressed in E. coli (Venkitasubramanian et al., J. Biol. Chem. 282:478-485 (2007)). Expression of the npt gene product improved activity of the enzyme via post-transcriptional modification. The npt gene encodes a specific phosphopantetheine transferase (PPTase) that converts the inactive apo-enzyme to the active holo-enzyme. The natural substrate of this enzyme is vanillic acid, and the enzyme exhibits broad acceptance of aromatic and aliphatic substrates (Venkitasubramanian et al., in Biocatalysis in the Pharmaceutical and Biotechnology Industires, ed. R. N. Patel, Chapter 15, pp. 425-440, CRC Press LLC, Boca Raton, Fla. (2006)).

TABLE 116

Gene	Accession No.	GI No.	Organism

Additional car and npt genes can be identified based on sequence homology.

TABLE 117

Gene	Accession No.	GI No.	Organism

An additional enzyme candidate found in Streptomyces griseus is encoded by the griC and griD genes. This enzyme is believed to convert 3-amino-4-hydroxybenzoic acid to 3-amino-4-hydroxybenzaldehyde as deletion of either griC or griD led to accumulation of extracellular 3-acetylamino-4-hydroxybenzoic acid, a shunt product of 3-amino-4-hydroxybenzoic acid metabolism (Suzuki, et al., J. Antibiot. 60(6):380-387 (2007)). Co-expression of griC and griD with SGR_—665, an enzyme similar in sequence to the Nocardia iowensis npt, can be beneficial.

TABLE 118

Gene	Accession No.	GI No.	Organism

griC	182438036	YP_001825755.1	Streptomyces griseus subsp.
			griseus NBRC 13350
griD	182438037	YP_001825756.1	Streptomyces griseus subsp.
			griseus NBRC 13350
MSMEG_2956	YP_887275.1	YP_887275.1	Mycobacterium smegmatis
			MC2 155
MSMEG_5739	YP_889972.1	118469671	Mycobacterium smegmatis
			MC2 155
MSMEG_2648	YP_886985.1	118471293	Mycobacterium smegmatis
			MC2 155
MAP1040c	NP_959974.1	41407138	Mycobacterium avium
			subsp. paratuberculosis K-
			10
MAP2899c	NP_961833.1	41408997	Mycobacterium avium
			subsp. paratuberculosis K-
			10
MMAR_2117	YP_001850422.1	183982131	Mycobacterium marinum M
MMAR_2936	YP_001851230.1	183982939	Mycobacterium marinum M
MMAR_1916	YP_001850220.1	183981929	Mycobacterium marinum M
TpauDRAFT_33060	ZP_04027864.1	227980601	Tsukamurella
			paurometabola DSM
			20162
TpauDRAFT_20920	ZP_04026660.1	227979396	Tsukamurella
			paurometabola DSM
			20162
CPCC7001_1320	ZP_05045132.1	254431429	Cyanobium PCC7001
DDBDRAFT_0187729	XP_636931.1	66806417	Dictyostelium discoideum
			AX4

An enzyme with similar characteristics, alpha-aminoadipate reductase (AAR, EC 1.2.1.31), participates in lysine biosynthesis pathways in some fungal species. This enzyme naturally reduces alpha-aminoadipate to alpha-aminoadipate semialdehyde. The carboxyl group is first activated through the ATP-dependent formation of an adenylate that is then reduced by NAD(P)H to yield the aldehyde and AMP. Like CAR, this enzyme utilizes magnesium and requires activation by a PPTase. Enzyme candidates for AAR and its corresponding PPTase are found in Saccharomyces cerevisiae (Morris et al., Gene 98:141-145 (1991)), Candida albicans (Guo et al., Mol. Genet. Genomics 269:271-279 (2003)), and Schizosaccharomyces pombe (Ford et al., Curr. Genet. 28:131-137 (1995)). The AAR from S. pombe exhibited significant activity when expressed in E. coli (Guo et al., Yeast 21:1279-1288 (2004)). The AAR from Penicillium chrysogenum accepts S-carboxymethyl-L-cysteine as an alternate substrate, but did not react with adipate, L-glutamate or diaminopimelate (Hijarrubia et al., J. Biol. Chem. 278:8250-8256 (2003)). The gene encoding the P. chrysogenum PPTase has not been identified to date.

TABLE 119

Gene	Accession No.	GI No.	Organism

Cloning and Expression of Carboxylic Acid Reductase.
Escherichia coli is used as a target organism to engineer the pathway for 1,3-butanediol. E. coli provides a good host for generating a non-naturally occurring microorganism capable of producing 1,3-butanedial. E. coli is amenable to genetic manipulation and is known to be capable of producing various intermediates and products effectively under various oxygenation conditions.
To generate a microbial organism strain such as an E. coli strain engineered to produce 1,3-butanedial, nucleic acids encoding a carboxylic acid reductase and phosphopantetheine transferase are expressed in E. coli using well known molecular biology techniques (see, for example, Sambrook, supra, 2001; Ausubel supra, 1999). In particular, car genes from Nocardia iowensis (designated 720), Mycobacterium smegmatis mc(2)155 (designated 890), Mycobacterium avium subspecies paratuberculosis K-10 (designated 891) and Mycobacterium marinum M (designated 892) were cloned into pZS*13 vectors (Expressys, Ruelzheim, Germany) under control of PA1/lacO promoters. The npt (ABI83656.1) gene (i.e., 721) was cloned into the pKJL33S vector, a derivative of the original mini-F plasmid vector PML31 under control of promoters and ribosomal binding sites similar to those used in pZS*13.
The car gene (GNM_—720) was cloned by PCR from Nocardia genomic DNA. Its nucleic acid and protein sequences are shown in FIGS. 12A and 12B, respectively. A codon-optimized version of the npt gene (GNM_—721) was synthesized by GeneArt (Regensburg, Germany). Its nucleic acid and protein sequences are shown in FIGS. 13A and 13B, respectively. The nucleic acid and protein sequences for the Mycobacterium smegmatis mc(2)155 (designated 890), Mycobacterium avium subspecies paratuberculosis K-10 (designated 891) and Mycobacterium marinum M (designated 892) genes and enzymes can be found in FIGS. 14, 15, and 16, respectively. The plasmids are transformed into a host cell to express the proteins and enzymes required for 1,3-butanedial production.
Additional CAR variants were generated. A codon optimized version of CAR 891 was generated and designated 891GA. The nucleic acid and amino acid sequences of CAR 891 GA are shown in FIGS. 17A and 17B, respectively. Over 2000 CAR variants were generated. In particular, all 20 amino acid combinations were made at positions V295, M296, G297, G391, G421, D413, G414, Y415, G416, and S417, and additional variants were tested as well. Exemplary CAR variants include: E16K; Q95L; L100M; A1011T; K823E; T941S; H15Q; D198E; G446C; S392N; F699L; V8831; F467S; T987S; R12H; V295G; V295A; V295S; V295T; V295C; V295V; V295L; V2951; V295M; V295P; V295F; V295Y; V295W; V295D; V295E; V295N; V295Q; V295H; V295K; V295R; M296G; M296A; M296S; M296T; M296C; M296V; M296L; M296I; M296M; M296P; M296F; M296Y; M296W; M296D; M296E; M296N; M296Q; M296H; M296K; M296R; G297G; G297A; G297S; G297T; G297C; G297V; G297L; G297I; G297M; G297P; G297F; G297Y; G297W; G297D; G297E; G297N; G297Q; G297H; G297K; G297R; G391G; G391A; G391S; G391T; G391C; G391V; G391L; G391I; G391M; G391P; G391F; G391Y; G391W; G391D; G391E; G391N; G391Q; G391H; G391K; G391R; G421G; G421A; G421S; G421T; G421C; G421V; G421L; G421I G421M; G421P; G421F; G421Y; G421W; G421D; G421E; G421N; G421Q; G421H; G421K; G421R; D413G; D413A; D413S; D413T; D413C; D413V; D413L; D413I; D413M; D413P; D413F; D413Y; D413W; D413D; D413E; D413N; D413Q; D413H; D413K; D413R; G414G; G414A; G414S; G414T; G414C; G414V; G414L; G414I; G414M; G414P; G414F; G414Y; G414W; G414D; G414E; G414N; G414Q; G414H; G414K; G414R; Y415G; Y415A; Y415S; Y415T; Y415C; Y415V; Y415L; Y415I; Y415M; Y415P; Y415F; Y415Y; Y415W; Y415D; Y415E; Y415N; Y415Q; Y415H; Y415K; Y415R; G416G; G416A; G416S; G416T; G416C; G416V; G416L; G416I; G416M; G416P; G416F; G416Y; G416W; G416D; G416E; G416N; G416Q; G416H; G416K; G416R; S417G; S417A; S417S; S417T; S417C; S417V S417L; S417I; S417M; S417P; S417F; S417Y; S417W; S417D; S417E; S417N; S417Q; S417H; S417K; and S417R.
The CAR variants were screened for activity, and numerous CAR variants were found to exhibit CAR activity. This example describes the use of CAR for converting carboxylic acids to aldehydes.

TABLE 120

(Ref: FIG. 1)

Step	EC class	Desired substrate	Desired product	Enzyme name	Gene name

A	2.3.1.b	D-alanine	2-amino-4-	AKP Thiolase	ortA
			oxopentanoate
					ortB
					Amet_2368
					Amet_2369
					Teth514_1478
					Teth514_1479
B	2.6.1.a	2-amino-4-	2,4-	2-amino-4-	aspC
		oxopentanoate	dioxopentanoate	oxopentanoate
				aminotransferase or
				oxidoreductase
				(deaminating)
					avtA
					AAT2
					dat
					dat
					ldh
					nadX
C	4.1.1.a	2,4-dioxopentanoate	3-oxobutyr-	2,4-dioxopentanoate	pdc
			aldehyde	decarboxylase
			(3-oxobutanal)		pdc1
					mdlC
					kgd
D	1.1.1.a	3-oxobutyraldehyde	4-hydroxy,2-	3-oxobutyraldehyde	alrA
			butanone	reductase (aldehyde
				reducing)
					ADH2
					yqhD
					bdh I
					bdh II
					4hbd
					ADHI
					mmsb
					P84067
E	4.1.1.a	2-amino-4-	4-aminobutan-2-	2-amino-4-	lysA
		oxopentanoate	one	oxopentanoate
				decarboxylase
					lysA
					lysA
					odc1
					panD
					panD
					panD
F	4.3.1.a	4-aminobutan-2-one	butenone	4-aminobutan-2-one	aspA
				ammonia lyase
					aspA
					aspA
					ansB
					aspA
G	4.2.1.a	butenone	4-hydroxy,2-	butenone hydratase	fumA
			butanone
					fumC
					fumC
					fumC
					fumH
					hmd
					dmdA
					dmdB
H	1.1.1.a	4-hydroxy,2-	1,3-butanediol	4-hydroxy,2-	bdh
		butanone		butanone reductase
					adh
					adhA
					ldh
					adh
I	4.3.1.a	2-amino-4-	acetylacrylate	2-amino-4-	aspA
		oxopentanoate		oxopentanoate
				ammonia lyase
					aspA
					aspA
					ansB
					aspA
J	4.1.1.a	acetylacrylate	butenone	acetylacrylate	xylII
				decarboxylase
					xylIII
					dmpH
					dmpE
					pdc
					pad
K	2.6.1.a	4-aminobutan-2-one	3-oxobutyr-	4-aminobutan-2-one	SkyPYD4
			aldehyde	aminotransferase or
			(3-oxobutanal)	oxidoreductase
				(deaminating)
					gabT
					Abat
					UGA1
					kdd
					lysDH
L	1.1.1.a	2-amino-4-	2-amino-4-	2-amino-4-	thrA
		oxopentanoate	hydroxypentanoate	oxopentanoate
				dehydrogenase
					hom6
					hom2
					akthr2
					hom1
M	2.6.1.a	2-amino-4-	2-oxo-4-	2-amino-4-	aspC
		hydroxypentanoate	hydroxypentanoate	hydroxypentanoate
				aminotransferase or
				oxidoreductase
				(deaminating)
					avtA
					AAT2
					dat
					dat
					ldh
					nadX
N	4.1.1.a	2-oxo-4-	3-hydroxybutyr-	2-oxo-4-	pdc
		hydroxypentanoate	aldehyde	hydroxypentanoate
			(3-hydroxybutanal)		pdc1
					mdlC
					kgd
O	1.1.1.a	3-oxobutyraldehyde	3-hydroxybutyr-	3-oxobutyraldehyde	bdh
			aldehyde	reductase (ketone
				reducing)
					adh
					adhA
					ldh
					adh
P	1.1.1.a	3-hydroxybutyr-	1,3-butanediol	3-hydroxybutyr-	alrA
		aldehyde		aldehyde reductase
					ADH2
					yqhD
					bdh I
					bdh II
					4hbd
					ADHI
					mmsb
					P84067

	GenBank ID
Step	(if available)	Organism	Known Substrates

A	YP_001086914.1	Clostridium	D-alanine
		difficile 630
	YP_001086915.1	Clostridium	D-alanine
		difficile 630
	YP_001320181.1	Alkaliphilus	D-alanine
		metalliredigenes
		QYF
	YP_001320182.1	Alkaliphilus	D-alanine
		metalliredigenes
		QYF
	YP_001663101.1	Thermoanaero-	D-alanine
		bacter sp. X514
	YP_001663102.1	Thermoanaero-	D-alanine
		bacter sp. X514
B	NP_415448.1	Escherichia coli	L-aspartate
	YP_026231.1	Escherichia coli	L-alanine, L-valine
	P23542.3	Saccharomyces	L-aspartate
		cerevisae
	P19938	Bacillus sp. YM-1	D-alanine, D-2-
			minobutanoate, D-
			aspartate
	O07597	Bacillus subtilis	D-alanine, D-2-
			aminobutanoate,
			D-aspartate
	P0A393	Bacillus cereus	L-leucine, L-valine,
			2-aminobutanoate,
			L-isoleucine
	NP_229443.1	Thermotoga	L-aspartate
		maritima
C	P06672.1	Zymomonas	2-ketobutyrate
		mobilus
	P06169	Saccharomyces	2-ketobutyrate, 3-
		cerevisae	hydroxypyruvate
	P20906.2	Pseudomonas	2-ketobutyrate
		putdia
	O50463.4	Mycobacterium	alpha-ketoglutarate
		tuberculosis
D	BAB12273.1	Acinetobacter sp.	C2-C14 aldehydes
		Strain M-1
	NP_014032.1	Saccharymyces	propionaldehyde,
		cerevisiae	isobutyraldehyde,
			butyraldehyde, 2-
			methylbutyraldehyde,
			3-
			methylbutyraldehyde,
			2-phenylacetaldehyde
	NP_417484.1	Escherichia coli	acetaldehyde,
			malondialdehyde,
			propanaldehyde,
			butanaldehyde,
			and acrolein
	NP_349892.1	Clostridium	butyraldehyde
		acetobutylicum
	NP_349891.1	Clostridium	butyraldehyde
		acetobutylicum
	YP_726053.1	Ralstonia eutropha	succinate
		H16	semialdehyde
	AAR91477.1	Geobacillus	ethanol, 1-butanol, 1-
		thermo-	pentanol, 1-heptanol,
		glucosidasius	1-hexanol, 1-octanol,
		M10EXG	2-propanol
	P28811.1	Pseudomonas	3-
		aeruginosa	hydroxybutyraldehyde,
			malonic semialdehyde,
			methylmalonate
			semialdehyde
	P84067	Thermus	methylmalonate
		thermophilus	semialdehyde
E	NP_417315.1	Escherichia coli	meso-
			diaminopimelate
	AAA25361.1	Mycobacterium	meso-
		tuberculosis	diaminopimelate
	BAC92756.1	Methylophilus	meso-
		methylotrophus	diaminopimelate
	AA59967.1	Homo sapiens	D-ornithine
	P0A790	Escherichia coli	L-aspartate
	Q9X4N0	Corynebacterium	L-aspartate
		glutanicum
	P65660	Mycobacterium	L-aspartate
		tuberculosis
F	NP_418562	Escherichia coli	L-aspartate
		K12 subsp.
		MG1655
	P44324.1	Haemophilus	L-aspartate
		influenzae
	P07346.1	Pseudomonas	L-aspartate
		fluorescens
	P26899.1	Bacillus subtilus	L-aspartate
	P33109.1	Serratia	L-aspartate
		marcescens
G	P0AC33	Escherichia coli	fumarate
		K12
	P05042	Escherichia coli	fumarate
		K12
	O69294	Campylobacter	fumarate
		jejuni
	P84127	Thermus	fumarate
		thermophilus
	P14408	Rattus norvegicus	fumarate
	ABC88407.1	Eubacterium	2-methylene-
		barkeri	glutarate
	ABC88408	Eubacterium	dimethylmaleate
		barkeri
	ABC88409.1	Eubacterium	dimethylmaleate
		barkeri
H	AAA58352.1	Homo sapiens	3-oxobutyrate
	AAA23199.2	Clostridium	acetone
		beijerinckii NRRL
		B593
	AAC25556	Pyrococuus	2-pentanaol,
		furiosus	pyruvaldehyde
	YP_725182.1	Ralstonia eutropha	lactate, 2-
			oxobutyrate,
			2-oxopentaonotae,
			2-oxoglutarate
	P14941.1	Thermoanaero-	acetone
		bacter brockii
		HTD4
I	NP_418562	Escherichia coli	L-aspartate
		K12 subsp.
		MG1655
	P44324.1	Haemophilus	L-aspartate
		influenzae
	P07346.1	Pseudomonas	L-aspartate
		fluorescens
	P26899.1	Bacillus subtilus	L-aspartate
	P33109.1	Serratia	L-aspartate
		marcescens
J	YP_709328.1	Pseudomonas	4-oxalocrotonate
		putida
	YP_709353.1	Pseudomonas	4-oxalocrotonate
		putida
	CAA43228.1	Pseudomonas sp.	4-oxalocrotonate
		CF600
	CAA43225.1	Pseudomonas sp.	4-oxalocrotonate
		CF600
	U63827	Lactobacillus	cinnamate and
		plantarum	derivatives
	AB330293	Klebsiella oxytoca	cinnamate and
			derivatives
K	ABF58893	Saccharomyces	beta-alanine
		kluyveri
	P22256	Escherichia coli	4-aminobutyrate
	P50554	Rattus norvegicus	3-amino-2-
			methylpropionate
	NP_011533	Saccharomyces	4-aminobutyrate
		cerevisae
	AAL93966.1	Fusobacterium	3,5-
		nucleatum	diaminohexanoate
	BAB39707	Geobacillus	L-lysine
		stearothermophilus
L	AAC73113	Escherichia coli	aspartate
			semialdehyde
	CAA89671	Saccharomyces	aspartate
		cerevisae	semialdehyde
	CAD63186	Lactobacillus	aspartate
		plantarum	semialdehyde
	O81852	Arabidopsis	aspartate
		thaliana	semialdehyde
	CAD64819	Lactobacillus	aspartate
		plantarum	semialdehyde
M	NP_415448.1	Escherichia coli	L-aspartate
	YP_026231.1	Escherichia coli	L-alanine, L-valine
	P23542.3	Saccharomyces	L-aspartate
		cerevisae
	Bacillus sp. YM-1	P19938	D-alanine, D-2-
			aminobutanoate,
			D-aspartate
	Bacillus subtilis	O07597	D-alanine,
			D-2-aminobutanoate,
			D-aspartate
	P0A393	Bacillus cereus	L-leucine, L-valine,
			2-aminobutanoate, L-
			isoleucine
	NP_229443.1	Thermotoga	L-aspartate
		maritima
N	P06672.1	Zymomonas	2-ketobutyrate
		mobilus
	P06169	Saccharomyces	2-ketobutyrate,
		cerevisae	3-hydroxypyruvate
	P20906.2	Pseudomonas	2-ketobutyrate
		putdia
	O50463.4	Mycobacterium	alpha-ketoglutarate
		tuberculosis
O	AAA58352.1	Homo sapiens	3-oxobutyrate
	AAA23199.2	Clostridium	acetone
		beijerinckii NRRL
		B593
	AAC25556	Pyrococuus	2-pentanaol,
		furiosus	pyruvaldehyde
	YP_725182.1	Ralstonia eutropha	lactate,
			2-oxobutyrate,
			2-oxopentaonotae,
			2-oxoglutarate
	P14941.1	Thermoanaero-	acetone
		bacter brockii
		HTD4
P	BAB12273.1	Acinetobacter sp.	C2-C14 aldehydes
		Strain M-1
	NP_014032.1	Saccharymyces	propionaldehyde,
		cerevisiae	isobutyraldehyde,
			butyraldehyde,
			2-methylbutyr-
			aldehyde,
			3-methylbutyr-
			aldehyde, 2-
			phenylacetaldehyde
	NP_417484.1	Escherichia coli	acetaldehyde,
			malondialdehyde,
			propanaldehyde,
			butanaldehyde,
			and acrolein
	NP_349892.1	Clostridium	butyraldehyde
		acetobutylicum
	NP_349891.1	Clostridium	butyraldehyde
		acetobutylicum
	YP_726053.1	Ralstonia eutropha	succinate
		H16	semialdehyde
	AAR91477.1	Geobacillus	ethanol, 1-butanol,
		thermoglucosidasius	1-pentanol,
		M10EXG	1-heptanol,
			1-hexanol, 1-octanol,
			2-propanol
	P28811.1	Pseudomonas	3-hydroxy-
		aeruginosa	butyraldehyde,
			malonic
			semialdehyde,
			methylmalonate
			semialdehyde
	P84067	Thermus	methylmalonate
		thermophilus	semialdehyde

TABLE 121

(Ref: FIG. 2)

	EC					GenBank ID (if
Step	class	Desired substrate	Desired product	Enzyme name	Gene name	available)	Organism	Known Substrates

A	1.2.1.b	acetoacetyl-CoA	3-oxobutyraldehyde	acetoacetyl-	Ald	AAT66436	Clostridium	butyryl-CoA
				CoA reductase			beijerinckii
				(aldehdye
				forming)
					sucD	NP_904963.1	Porphyromonas	succinyl-CoA
							gingivalis
					bphG	BAA03892.1	Pseudomonas sp	acetaldehyde,
								propionaldehyde,
								butyraldehyde,
								isobutyraldehyde
								and formaldehyde
					Msed_0709	YP_001190808.1	Metallosphaera	malonyl-CoA
							sedula
					mcr	NP_378167	Sulfolobus	malonyl-CoA,
							tokodaii	methylmalonyl-
								CoA
B	1.1.1.a	3-oxobutyr-	3-	3-oxobutyr-	bdh	AAA58352.1	Homo sapiens	3-oxobutyrate
		aldehyde	hydroxybutyraldehyde	aldehyde
				reductase
				(ketone-
				reducing)
					adh	AAA23199.2	Clostridium	acetone
							beijerinckii
							NRRL B593
					adhA	AAC25556	Pyrococuus	2-pentanaol,
							furiosus	pyruvaldehyde
					ldh	YP_725182.1	Ralstonia	lactate, 2-
							eutropha	oxobutyrate, 2-
								oxopentaonotae,
								2-oxoglutarate
					adh	P14941.1	Thermoanaero-	acetone
							bacter brockii
							HTD4
C	1.1.1.a	3-hydroxybutyr-	1,3-butanediol	3-hydroxy-	alrA	BAB12273.1	Acinetobacter sp.	C2-C14
		aldehyde		butyraldehyde			Strain M-1	aldehydes
				reductase
					ADH2	NP_014032.1	Saccharymyces	propionaldehyde,
							cerevisiae	isobutyraldehyde,
								butyraldehyde,
								2-methylbutyr-
								aldehyde,
								3-methylbutyr-
								aldehyde,
								2-phenylacet-
								aldehyde
					yqhD	NP_417484.1	Escherichia coli	acetaldehyde,
								malondialdehyde,
								propanaldehyde,
								butanaldehyde,
								and acrolein
					bdh I	NP_349892.1	Clostridium	butyraldehyde
							acetobutylicum
					bdh II	NP_349891.1	Clostridium	butyraldehyde
							acetobutylicum
					4hbd	YP_726053.1	Ralstonia	succinate
							eutropha H16	semialdehyde
					ADHI	AAR91477.1	Geobacillus	ethanol,
							thermoglucosidasius	1-butanol,
							M10EXG	1-pentanol,
								1-heptanol,
								1-hexanol,
								1-octanol,
								2-propanol
					mmsb	P28811.1	Pseudomonas	3-hydroxybutyr-
							aeruginosa	aldehyde, malonic
								semialdehyde,
								methylmalonate
								semialdehyde
					P84067	P84067	Thermus	methylmalonate
							thermophilus	semialdehyde
D	1.1.1.c	acetoacetyl-CoA	4-hydroxy,2-butanone	acetoacetyl-	adhE2	AAK09379.1	Clostridium	butanoyl-CoA
				CoA reductase			acetobutylicum
				(alcohol-
				forming)
					mcr	AAS20429.1	Chloroflexus	malonyl-CoA
							aurantiacus
					FAR	AAD38039.1	Simmondsia	long chain acyl-
							chinensis	CoA
E	1.1.1.a	3-oxobutyr-	4-hydroxy,2-butanone	3-	alrA	BAB12273.1	Acinetobacter sp.	C2-C14
		aldehyde		oxobutyraldeh			Strain M-1	aldehydes
				dye reductase
				(aldehyde
				reducing)
					ADH2	NP_014032.1	Saccharymyces	propionaldehyde,
							cerevisiae	isobutyraldehyde,
								butyraldehyde, 2-
								methyl-
								butyraldehyde,
								3-methylbutyr-
								aldehyde, 2-
								phenyl-
								acetaldehyde
					yqhD	NP_417484.1	Escherichia coli	acetaldehyde,
								malondialdehyde,
								propanaldehyde,
								butanaldehyde,
								and acrolein
					bdh I	NP_349892.1	Clostridium	butyraldehyde
							acetobutylicum
					bdh II	NP_349891.1	Clostridium	butyraldehyde
							acetobutylicum
					4hbd	YP_726053.1	Ralstonia	succinate
							eutropha H16	semialdehyde
					ADHI	AAR91477.1	Geobacillus	ethanol,
							thermoglucosidasius	1-butanol,
							M10EXG	1-pentanol,
								1-heptanol,
								1-hexanol,
								1-octanol,
								2-propanol
					mmsb	P28811.1	Pseudomonas	3-
							aeruginosa	hydroxy-
								butyraldehyde,
								malonic
								semialdehyde,
								methylmalonate
								semialdehyde
					P84067	P84067	Thermus	methylmalonate
							thermophilus	semialdehyde
F	1.1.1.a	4-hydroxy,	1,3-butanediol	4-hydroxy,2-	bdh	AAA58352.1	Homo sapiens	3-oxobutyrate
		2-butanone		butanone
				reductase
					adh	AAA23199.2	Clostridium	acetone
							beijerinckii
							NRRL B593
					adhA	AAC25556	Pyrococuus	2-pentanaol,
							furiosus	pyruvaldehyde
					ldh	YP_725182.1	Ralstonia	lactate, 2-
							eutropha	oxobutyrate,
								2-
								oxopentaonotae,
								2-oxoglutarate
					adh	P14941.1	Thermoanaero-	acetone
							bacter brockii
							HTD4
G	1.1.1.a	acetoacetyl-CoA	3-hydroxybutyryl-CoA	acetaocetyl	hbd	NP_349314.1	Clostridium	acetoacetyl-CoA
				CoA reductase			acetobutylicum
				(ketone
				reducing)
					hbd	AAM14586.1	Clostridium	acetoacetyl-CoA
							beijerinckii
					Hbd2	EDK34807.1	Clostridium	acetoacetyl-CoA
							kluyveri
					Hbd1	EDK32512.1	Clostridium	acetoacetyl-CoA
							kluyveri
					Msed_1423	YP_001191505	Metallosphaera	3-hydroxybutyryl-
							sedula	CoA (suspected)
					Msed_0399	YP_001190500	Metallosphaera	3-hydroxybutyryl-
							sedula	CoA (suspected)
					Msed_0389	YP_001190490	Metallosphaera	3-hydroxybutyryl-
							sedula	CoA (suspected)
					Msed_1993	YP_001192057	Metallosphaera	3-hydroxybutyryl-
							sedula	CoA (suspected)
					fadB	P21177.2	Escherichia coli	3-oxoacyl-CoA
					fadJ	P77399.1	Escherichia coli	3-oxoacyl-CoA
H	1.2.1.b	3-hydroxybutyryl-	3-hydroxybutyr-	3-hydroxy-	Ald	AAT66436	Clostridium	butyryl-CoA
		CoA	aldehyde	butyryl-CoA			beijerinckii
				redcutase
				(aldehyde
				forming)
					sucD	NP_904963.1	Porphyromonas	succinyl-CoA
							gingivalis
					bphG	BAA03892.1	Pseudomonas sp	acetaldehyde,
								propionaldehyde,
								butyraldehyde,
								isobutyraldehyde
								and formaldehyde
					Msed_0709	YP_001190808.1	Metallosphaera	malonyl-CoA
							sedula
					mcr	NP_378167	Sulfolobus	malonyl-CoA,
							tokodaii	methylmalonyl-
								CoA
I	1.1.1.c	3-hydroxybutyryl-	1,3-butanediol	3-hydroxy-	adhE2	AAK09379.1	Clostridium	butanoyl-CoA
		CoA		butyryl-CoA			acetobutylicum
				reductase
				(alcohol
				forming)
					mcr	AAS20429.1	Chloroflexus	malonyl-CoA
							aurantiacus
					FAR	AAD38039.1	Simmondsia	long chain acyl-
							chinensis	CoA

TABLE 122

(Ref: FIG. 3)

	EC				Gene	GenBank ID (if
Step	class	Desired substrate	Desired product	Enzyme name	name	available)	Organism	Known Substrates

A	4.2.1.a	4-hydroxybutyryl-	crotonyl-CoA	4-hydroxy-	abfD	YP_001396399.1	Clostridium	4-hydroxybutyryl-
		CoA		butyryl-CoA			kluyveri DSM 555	CoA
				dehydratase
					abfD	P55792	Clostridium	4-hydroxybutyryl-
							aminobutyricum	CoA
					abfD	YP_001928843	Porphyromonas	4-hydroxybutyryl-
							gingivalis ATCC	CoA
							33277
B	4.2.1.a	crotonyl-CoA	3-hydroxybutyryl-	crotonase	crt	NP_349318.1	Clostridium	3-hydroxybutyryl-
			CoA				acetobutylicum	CoA
					crt1	YP_001393856	Clostridium	3-hydroxybutyryl-
							kluyveri DSM 555	CoA
					crt	YP_001929291.1	Porphyromonas	example based on
							gingivalis ATCC	sequence similarity
							33277
					paaA	NP_745427.1	Pseudomonas	enoyl-CoA, cis-
							putida	dihydrodiol
								derivative of
								phenylacetyl-CoA
					paaB	NP_745426.1	Pseudomonas	enoyl-CoA, cis-
							putida	dihydrodiol
								derivative of
								phenylacetyl-CoA
					phaA	ABF82233.1	Pseudomonas	enoyl-CoA, cis-
							fluorescens	dihydrodiol
								derivative of
								phenylacetyl-CoA
					phaB	ABF82234.1	Pseudomonas	enoyl-CoA, cis-
							fluorescens	dihydrodiol
								derivative of
								phenylacetyl-CoA
					maoC	NP_415905.1	Escherichia coli	enoyl-CoA, cis-
								dihydrodiol
								derivative of
								phenylacetyl-CoA
					paaF	NP_415911.1	Escherichia coli	enoyl-CoA, cis-
								dihydrodiol
								derivative of
								phenylacetyl-CoA
					paaG	NP_415912.1	Escherichia coli	enoyl-CoA,
								cis-dihydrodiol
								derivative of
								phenylacetyl-CoA
C	1.2.1.b	3-hydroxybutyryl-	3-hydroxy-	3-hydroxy-	Ald	AAT66436	Clostridium	butyryl-CoA
		CoA	butyraldehyde	butyryl-CoA			beijerinckii
				reductase
				(aldehyde
				forming)
					sucD	NP_904963.1	Porphyromonas	succinyl-CoA
							gingivalis
					bphG	BAA03892.1	Pseudomonas sp	acetaldehyde,
								propionaldehyde,
								butyraldehyde,
								isobutyraldehyde
								and formaldehyde
					Msed_0709	YP_001190808.1	Metallosphaera	malonyl-CoA
							sedula
					mcr	NP_378167	Sulfolobus tokodaii	malonyl-CoA,
								methylmalonyl-
								CoA
D	1.1.1.a	3-hydroxy-	1,3-butanediol	3-hydroxy-	alrA	BAB12273.1	Acinetobacter sp.	C2-C14 aldehydes
		butyraldehyde		butyraldehyde			Strain M-1
				reductase
					ADH2	NP_014032.1	Saccharymyces	propionaldehyde,
							cerevisiae	isobutyraldehyde,
								butyraldehyde,
								2-methylbutyr-
								aldehyde,
								3-methylbutyr-
								aldehyde,
								2-phenylacet-
								aldehyde
					yqhD	NP_417484.1	Escherichia coli	acetaldehyde,
								malondialdehyde,
								propanaldehyde,
								butanaldehyde, and
								acrolein
					bdh I	NP_349892.1	Clostridium	butyraldehyde
							acetobutylicum
					bdh II	NP_349891.1	Clostridium	butyraldehyde
							acetobutylicum
					4hbd	YP_726053.1	Ralstonia eutropha	succinate
							H16	semialdehyde
					ADHI	AAR91477.1	Geobacillus	ethanol, 1-butanol,
							thermoglucosidasius	1-pentanol,
							M10EXG	1-heptanol, 1-hexanol,
								1-octanol, 2-propanol
					mmsb	P28811.1	Pseudomonas	3-hydroxy-
							aeruginosa	butyraldehyde,
								malonic
								semialdehyde,
								methylmalonate
								semialdehyde
					P84067	P84067	Thermus	methylmalonate
							thermophilus	semialdehyde
E	1.1.1.c	3-hydroxybutyryl-	1,3-butanediol	3-hydroxy-	adhE2	AAK09379.1	Clostridium	butanoyl-CoA
		CoA		butyryl-CoA			acetobutylicum
				reductase
				(alcohol
				forming)
					mcr	AAS20429.1	Chloroflexus	malonyl-CoA
							aurantiacus
					FAR	AAD38039.1	Simmondsia	long chain acyl-
							chinensis	CoA

Sequence Listing

The present specification is being filed with a computer readable form (CRF) copy of the Sequence Listing. The CRF entitled 12956-143_SEQLIST.txt, which was created on Jun. 15, 2012 and is 77,805 bytes in size, is identical to the paper copy of the Sequence Listing and is incorporated herein by reference in its entirety.
Throughout this application various publications have been referenced. The disclosures of these publications in their entireties, including GenBank and GI number publications, are hereby incorporated by reference in this application in order to more fully describe the state of the art to which this invention pertains. Although the invention has been described with reference to the examples and embodiments provided above, it should be understood that various modifications can be made without departing from the spirit of the invention.

Claims

1. A non-naturally occurring microbial organism having a 1,3-butanediol pathway, wherein said microbial organism comprises at least one exogenous nucleic acid encoding a 1,3-butanediol pathway enzyme expressed in a sufficient amount to produce 1,3-butanediol; said non-naturally occurring microbial organism further comprising:

(i) a reductive TCA pathway, wherein said microbial organism comprises at least one exogenous nucleic acid encoding a reductive TCA pathway enzyme selected from the group consisting of an ATP-citrate lyase, citrate lyase, a fumarate reductase, and an alpha-ketoglutarate:ferredoxin oxidoreductase;

(ii) a reductive TCA pathway, wherein said microbial organism comprises at least one exogenous nucleic acid encoding a reductive TCA pathway enzyme selected from the group consisting of a pyruvate:ferredoxin oxidoreductase, a phosphoenolpyruvate carboxylase, a phosphoenolpyruvate carboxykinase, a CO dehydrogenase, and an H₂hydrogenase; or

(iii) at least one exogenous nucleic acid encoding an enzyme selected from the group consisting of a CO dehydrogenase, an H₂hydrogenase, and combinations thereof;

wherein said 1,3-butanediol pathway comprises a pathway selected from the group consisting of:

(a) (1) a 2-amino-4-ketopentanoate (AKP) thiolase; (2) an AKP dehydrogenase; (3) a 2-amino-4-hydroxypentanoate aminotransferase or oxidoreductase (deaminating); (4) a 2-oxo-4-hydroxypentanoate decarboxylase; and (5) a 3-hydroxybutyraldehyde reductase;

(b) (1) an AKP thiolase; (2) an AKP aminotransferase or oxidoreductase

(deaminating); (3) a 2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase;

(c) (1) an AKP thiolase; (2) an AKP aminotransferase or oxidoreductase

(deaminating); (3) a 2,4-dioxopentanoate decarboxylase; (4) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase;

(d) (1) an AKP thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase (ketone reducing); and (5) a 3-hydroxybutyraldehyde reductase;

(e) (1) an AKP thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one aminotransferase or oxidoreductase (deaminating); (4) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (5) a 4-hydroxy-2-butanone reductase;

(f) (1) an AKP thiolase; (2) an AKP decarboxylase; (3) a 4-aminobutan-2-one ammonia-lyase; (4) a butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase;

(g) (1) an AKP thiolase; (2) an AKP ammonia-lyase; (3) an acetylacrylate decarboxylase; (4) a butenone hydratase; and (5) a 4-hydroxy-2-butanone reductase;

(h) (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde reductase (ketone reducing); and (3) a 3-hydroxybutyraldehyde reductase;

(i) an acetoacetyl-CoA reductase (CoA dependent, alcohol forming) and (2) a 4-hydroxy-2-butanone reductase;

(j) (1) an acetoacetyl-CoA reductase (CoA-dependent, aldehyde forming); (2) a 3-oxobutyraldehyde reductase (aldehyde reducing); and (3) a 4-hydroxy-2-butanone reductase;

(k) (1) an acetoacetyl-CoA reductase (ketone reducing) and (2) a 3-hydroxybutyryl-CoA reductase (alcohol forming);

(l) (1) an acetoacetyl-CoA reductase (ketone reducing); (2) a 3-hydroxybutyryl-CoA reductase (aldehyde forming); and (3) a 3-hydroxybutyraldehyde reductase;

(m) (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; and (3) a 3-hydroxybutyryl-CoA reductase (alcohol forming); and

(n) (1) a 4-hydroxybutyryl-CoA dehydratase; (2) a crotonase; (3) a 3-hydroxybutyryl-CoA reductase (aldehyde forming); and (4) a 3-hydroxybutyraldehyde reductase;

(o) (1) a succinyl-CoA transferase, a succinyl-CoA synthetase or a succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyrate kinase, (5) a phosphotrans-4-hydroxybutyrylase, (6) a 4-hydroxybutyryl-CoA dehydratase, (7) a crotonase, (8) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (9) a 3-hydroxybutanal reductase;

(p) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase; (6) a crotonase, (7) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (8) a 3-hydroxybutanal reductase;

(q) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (7) a 3-hydroxybutanal reductase;

(r) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, and (7) a 3-hydroxybutyryl-CoA reductase (alcohol forming);

(s) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, and (6) a 3-hydroxybutyryl-CoA reductase (alcohol forming);

(t) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (8) a 3-hydroxybutyrate reductase;

(u) (1) (i) an alpha-ketoglutarate decarboxylase, or (ii) (a) a glutamate dehydrogenase and/or a glutamate transaminase, (b) a glutamate decarboxylase, and (c) a 4-aminobutyrate dehydrogenase and/or a 4-aminobutyrate transaminase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (7) a 3-hydroxybutyrate reductase.

(v) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (8) a 3-hydroxybutanal reductase;

(w) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), (7) a 3-hydroxybutanal reductase;

(x) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, and (7) a 3-hydroxybutyryl-CoA reductase (alcohol forming);

(y) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, and (6) a 3-hydroxybutyryl-CoA reductase (alcohol forming);

(z) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (8) a 3-hydroxybutyrate reductase;

(aa) (1) a succinate reductase, (2) a 4-hydroxybutyrate dehydrogenase, (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (7) a 3-hydroxybutyrate reductase;

(bb) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (5) a 4-hydroxybutyrate kinase, (6) a pPhosphotrans-4-hydroxybutyrylase, (7) a 4-hydroxybutyryl-CoA dehydratase, (8) a crotonase, and (9) a 3-hydroxybutyryl-CoA reductase (alcohol forming);

(cc) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyrate kinase, (5) a phosphotrans-4-hydroxybutyrylase, (6) a 4-hydroxybutyryl-CoA dehydratase, (7) a crotonase, (8) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (9) a 3-hydroxybutyrate reductase;

(dd) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (8) a 3-hydroxybutanal reductase;

(ee) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, and (7) a 3-hydroxybutyryl-CoA reductase (alcohol forming);

(ff) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyrate kinase, (4) a phosphotrans-4-hydroxybutyrylase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (8) a 3-hydroxybutyrate reductase;

(gg) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyryl-CoA transferase, or 4-hydroxybutyryl-CoA synthetase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA reductase (aldehyde forming), and (8) a 3-hydroxybutanal reductase;

(hh) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, and (7) a 3-hydroxybutyryl-CoA reductase (alcohol forming);

(ii) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (aldehyde forming), (3) a 4-hydroxybutyrate dehydrogenase, (4) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, (8) a 3-hydroxybutyrate reductase;

(jj) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, (6) a 3-hydroxybutyryl-CoA reductase (aldehyde faulting), and (7) a 3-hydroxybutanal reductase;

(kk) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (4) a 4-hydroxybutyryl-CoA dehydratase, (5) a crotonase, and (6) a 3-hydroxybutyryl-CoA reductase (alcohol forming); and

(ll) (1) a succinyl-CoA transferase, succinyl-CoA synthetase or succinyl-CoA ligase, (2) a succinyl-CoA reductase (alcohol forming), (3) a 4-hydroxybutyryl-CoA transferase or 4-hydroxybutyryl-CoA synthetase, (5) a 4-hydroxybutyryl-CoA dehydratase, (6) a crotonase, (7) a 3-hydroxybutyryl-CoA hydrolase, transferase or synthetase, and (8) a 3-hydroxybutyrate reductase.

2. The non-naturally occurring microbial organism of claim 1, wherein said microbial organism further comprises an exogenous nucleic acid encoding an enzyme selected from the group consisting of a pyruvate:ferredoxin oxidoreductase, an aconitase, an isocitrate dehydrogenase, a succinyl-CoA synthetase, a succinyl-CoA transferase, a fumarase, a malate dehydrogenase, an acetate kinase, a phosphotransacetylase, an acetyl-CoA synthetase, an NAD(P)H:ferredoxin oxidoreductase, a ferredoxin, and combinations thereof.

3. The non-naturally occurring microbial organism of claim 1, wherein said microbial organism further comprises an exogenous nucleic acid encoding an enzyme selected from the group consisting of a succinyl-CoA synthetase, a succinyl-CoA transferase, a fumarase, a malate dehydrogenase, and combinations thereof.

4. The non-naturally occurring microbial organism of claim 1, wherein said microbial organism comprises two, three, four, five, six, seven, eight or nine exogenous nucleic acids, each encoding a 1,3-BDO pathway enzyme.

5. The non-naturally occurring microbial organism of claim 1, wherein said microbial organism comprises exogenous nucleic acids encoding each of the enzymes of at least one of the 1,3-butanediol pathways selected from the group consisting of (a)-(ll).

6. The non-naturally occurring microbial organism of claim 1, wherein said at least one exogenous nucleic acid is a heterologous nucleic acid.

7. The non-naturally occurring microbial organism of claim 1, wherein said non-naturally occurring microbial organism is in a substantially anaerobic culture medium.

8. A method for producing 1,3-BDO, comprising culturing a non-naturally occurring microbial organism according to claim 1, under conditions and for a sufficient period of time to produce 1,3-BDO.

9. The method of claim 8, wherein said microbial organism further comprises an exogenous nucleic acid encoding an enzyme selected from the group consisting of a pyruvate:ferredoxin oxidoreductase, an aconitase, an isocitrate dehydrogenase, a succinyl-CoA synthetase, a succinyl-CoA transferase, a fumarase, a malate dehydrogenase, an acetate kinase, a phosphotransacetylase, an acetyl-CoA synthetase, an NAD(P)H:ferredoxin oxidoreductase, ferredoxin, and combinations thereof.

10. The method of claim 8, wherein said microbial organism further comprises an exogenous nucleic acid encoding an enzyme selected from the group consisting of an aconitase, an isocitrate dehydrogenase, a succinyl-CoA synthetase, a succinyl-CoA transferase, a fumarase, a malate dehydrogenase, and combinations thereof.

11. The method of claim 8, wherein said microbial organism comprises two, three, four, five, six, seven, eight or nine exogenous nucleic acids, each encoding a 1,3-BDO pathway enzyme.

12. The method of claim 8, wherein said microbial organism comprises exogenous nucleic acids encoding each of the enzymes of at least one of the 1,3-butanediol pathways selected from the group consisting of (a)-(ll).

13. The method of claim 8, wherein said at least one exogenous nucleic acid is a heterologous nucleic acid.

14. The method of claim 8, wherein said non-naturally occurring microbial organism is in a substantially anaerobic culture medium.