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Bioengineering
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Synthetic Biology and Bioprocess Engineering for High-Value Compounds
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Synthetic Biology and Bioprocess Engineering for High-Value Compounds

A special issue of Bioengineering (ISSN 2306-5354). This special issue belongs to the section "Biochemical Engineering".

Deadline for manuscript submissions: closed (31 January 2025) | Viewed by 3804

Special Issue Editor

Dr. M. Ahsanul Islam

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Guest Editor
Department of Chemical Engineering, Loughborough University, Loughborough LE11 3TU, Leicestershire, UK
Interests: biochemical engineering; biotechnology; systems biology; synthetic biology; metabolic engineering; computational biology; bioinformatics; bioremediation; electro-fermentation; environmental biotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

High-value compounds such as fuels, chemicals, and materials are the backbone of our modern industry and economy. Ironically, as these compounds are primarily sourced from fossil fuels, their manufacturing, transportation, and consumption have mainly contributed to the unprecedented rise in the global greenhouse gas (GHG) emissions, resulting in the current climate crisis of global warming and climate change. Thus, decarbonizing the commodity chemical sector is the key to tackling the menacing climate emergency in order to achieve a sustainable, carbon-neutral, or carbon-negative Net-Zero future. The versatility and ingenuity of bioprocesses can play a pivotal role in decarbonizing and transforming the unsustainable commodity chemical sector into a sustainable one. Engineered microbial cell factories or chassis strains can be the main vectors of this transformation, with the potential to produce petro-commodities at scale. In addition, cell-free synthesis systems have gained considerable attention from bioprocess engineers recently due to their relative ease of use without requiring extensive and complicated genetic manipulation of cell-based systems. With the advent of state-of-the-art synthetic biology and metabolic engineering technologies, as well as computational cheminformatics and machine learning tools, it is now possible to produce virtually any commodity using engineered cell factories or cell-free synthesis systems. These systems can use GHGs and other renewable resources, including lignocellulosic biomass, industrial waste gases, and municipal solid waste as raw materials to produce high-value compounds.

This Special Issue aims to assemble and publish a collection of high-quality research articles and review papers on synthetic biology and bioprocess engineering efforts to produce bio-based commodities and healthcare products using both engineered microbial cell factories and cell-free synthesis systems. For review papers, it is advisable to contact the Editor to discuss topic relevance before submitting the manuscript.

Dr. M. Ahsanul Islam
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Bioengineering is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • high-value compounds
  • microbial cell factories
  • bioprocess engineering
  • synthetic biology
  • metabolic engineering
  • cell-free synthesis systems
  • bio-based commodities

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Published Papers (3 papers)

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Research

Jump to: Review

13 pages, 2737 KiB  
Article
Genomic Comparisons Revealed the Key Genotypes of Streptomyces sp. CB03234-GS26 to Optimize Its Growth and Relevant Production of Tiancimycins
by Huiming Liu, Jing Lin, Yong Huang, Yanwen Duan and Xiangcheng Zhu
Bioengineering 2024, 11(11), 1128; https://doi.org/10.3390/bioengineering11111128 - 8 Nov 2024
Viewed by 753
Abstract
Strain robustness and titer improvement are major challenges faced in the industrial development of natural products from Streptomyces. Tiancimycins (TNMs) produced by Streptomyces sp. CB03234 are promising anticancer payloads for antibody-drug conjugates, but further development is severely limited by the low titer [...] Read more.
Strain robustness and titer improvement are major challenges faced in the industrial development of natural products from Streptomyces. Tiancimycins (TNMs) produced by Streptomyces sp. CB03234 are promising anticancer payloads for antibody-drug conjugates, but further development is severely limited by the low titer of TNMs. Despite many efforts to generate various TNMs overproducers, the mechanisms underlying high TNMs production remain to be explored. Herein, genome resequencing and genomic comparisons of different TNMs overproducers were conducted to explore the unique genotypes in CB03234-GS26. Four target genes were selected for further bioinformatic analyses and genetic validations. The results indicated that the inactivation of histidine ammonia-lyase (HAL) showed the most significant effect by blocking the intracellular degradation of histidine to facilitate relevant enzymatic catalysis and thus improve the production of TNMs. Additionally, the potassium/proton antiporter (P/PA) was crucial for intracellular pH homeostasis, and its deficiency severely impaired the alkaline tolerance of the cells. Subsequent pan-genomic analysis suggested that HAL and P/PA are core enzymes that are highly conserved in Streptomyces. Therefore, HAL and P/PA represented novel targets to regulate secondary metabolism and enhance strain robustness and could become potential synthetic biological modules to facilitate development of natural products and strain improvement in Streptomyces. Full article
(This article belongs to the Special Issue Synthetic Biology and Bioprocess Engineering for High-Value Compounds)
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Graphical abstract

Graphical abstract
Full article ">Figure 1
<p>The structures of anthraquinone-fused ten-membered enediynes.</p> Full article ">Figure 2
<p>Genome resequencing results of CB03234-G, CB03234-S, and CB03234-GS26. (<b>a</b>) The number of mutations in each mutant. (<b>b</b>) COG functional classification of 22 mutated CDSs.</p> Full article ">Figure 3
<p>Proposed metabolic or physiological functions of the screened target proteins in CB03234-GS26.</p> Full article ">Figure 4
<p>Fermentation characterization of various strains and mutants. (<b>a</b>) Growth curves of CB03234-S, CB03234-GS26, and their related mutants cultured in OP medium. (<b>b</b>) The TNMs titers of the CB03234-S related gene knockout mutants in OP medium. (<b>c</b>) The TNMs titers of the CB03234-GS26 related overexpression mutants in OP and 4FP media, respectively.</p> Full article ">Figure 5
<p>SSN analysis of P/PA homologues and <span class="html-italic">Streptomyces</span>-based pan-genomic analyses of target genes. (<b>a</b>) the taxonomic distribution and (<b>b</b>) the SSN analysis (E value = 1 × 10<sup>−250</sup>) of 4784 P/PA homologues. (<b>c</b>) Pan-genomic analyses of four target genes under different IC values.</p> Full article ">
19 pages, 2302 KiB  
Article
Heterologous Production of Isopropanol Using Metabolically Engineered Acetobacterium woodii Strains
by Franziska Höfele, Teresa Schoch, Catarina Oberlies and Peter Dürre
Bioengineering 2023, 10(12), 1381; https://doi.org/10.3390/bioengineering10121381 - 30 Nov 2023
Cited by 6 | Viewed by 1443
Abstract
The depletion of fossil fuel resources and the CO2 emissions coupled with petroleum-based industrial processes present a relevant issue for the whole of society. An alternative to the fossil-based production of chemicals is microbial fermentation using acetogens. Acetogenic bacteria are able to [...] Read more.
The depletion of fossil fuel resources and the CO2 emissions coupled with petroleum-based industrial processes present a relevant issue for the whole of society. An alternative to the fossil-based production of chemicals is microbial fermentation using acetogens. Acetogenic bacteria are able to metabolize CO or CO2 (+H2) via the Wood–Ljungdahl pathway. As isopropanol is widely used in a variety of industrial branches, it is advantageous to find a fossil-independent production process. In this study, Acetobacterium woodii was employed to produce isopropanol via plasmid-based expression of the enzymes thiolase A, CoA-transferase, acetoacetate decarboxylase and secondary alcohol dehydrogenase. An examination of the enzymes originating from different organisms led to a maximum isopropanol production of 5.64 ± 1.08 mM using CO2 + H2 as the carbon and energy source. To this end, the genes thlA (encoding thiolase A) and ctfA/ctfB (encoding CoA-transferase) of Clostridium scatologenes, adc (encoding acetoacetate decarboxylase) originating from C. acetobutylicum and sadH (encoding secondary alcohol dehydrogenase) of C. beijerinckii DSM 6423 were employed. Since bottlenecks in the isopropanol production pathway are known, optimization of the strain was investigated, resulting in a 2.5-fold increase in isopropanol concentration. Full article
(This article belongs to the Special Issue Synthetic Biology and Bioprocess Engineering for High-Value Compounds)
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Graphical abstract

Graphical abstract
Full article ">Figure 1
<p>Production of isopropanol using recombinant <span class="html-italic">A. woodii</span> strains, harboring the secondary alcohol dehydrogenase (<span class="html-italic">sadH</span>) gene of <span class="html-italic">C. beijerinckii</span> DSM 6423, cultivated with 60 mM fructose (<b>A</b>–<b>C</b>) or CO<sub>2</sub> + H<sub>2</sub> (<b>D</b>–<b>F</b>) as substrate. Growth was performed in biological triplicates with <span class="html-italic">A. woodii</span> wild-type and <span class="html-italic">A. woodii</span> [pJIR750] as control strains (depicted as black line with filled circles or filled black column and dashed black line with empty circles or dashed black column, respectively). During growth, (<b>A</b>,<b>D</b>) the optical density at 600 nm (OD<sub>600</sub>), (<b>B</b>,<b>E</b>) changes in pH and (<b>C</b>,<b>F</b>) product concentrations of acetone and isopropanol were monitored. The recombinant strains <span class="html-italic">A. woodii</span> [pJIR750_ac1t1s1] and <span class="html-italic">A. woodii</span> [pJIR750_ac1t2s1] are depicted as dark blue lines with filled rectangles or filled dark blue column and dashed dark blue lines with empty rectangles or dashed dark blue column, respectively. <span class="html-italic">A. woodii</span> [pJIR750_ac2t1s1] and <span class="html-italic">A. woodii</span> [pJIR750_ac2t2s1] are shown as light blue lines with filled rhombus or light blue column and dashed light blue lines with empty rhombus or dashed light blue column, respectively. The pastel blue lines with filled triangle or pastel blue column depict <span class="html-italic">A. woodii</span> [pJIR750_ac3t3s1].</p> Full article ">Figure 2
<p>Production of isopropanol using recombinant <span class="html-italic">A. woodii</span> strains, harboring the <span class="html-italic">sadH</span> gene of <span class="html-italic">C. beijerinckii</span> DSM 15410, cultivated with 60 mM fructose (<b>A</b>–<b>C</b>) or CO<sub>2</sub> + H<sub>2</sub> (<b>D</b>–<b>F</b>) as substrate. Growth was performed in biological triplicates with <span class="html-italic">A. woodii</span> wild-type and <span class="html-italic">A. woodii</span> [pJIR750] as control strains (depicted as black line with filled circles or filled black column and dashed black line with empty circles or dashed black column, respectively). During growth, (<b>A</b>,<b>D</b>) OD<sub>600</sub>, (<b>B</b>,<b>E</b>) changes in pH and (<b>C</b>,<b>F</b>) product concentrations of acetone and isopropanol were monitored. The recombinant strains <span class="html-italic">A. woodii</span> [pJIR750_ac1t1s2] and <span class="html-italic">A. woodii</span> [pJIR750_ac1t2s2] are depicted as green lines with filled rectangles or filled green column and dashed green lines with empty rectangles or dashed green column, respectively. <span class="html-italic">A. woodii</span> [pJIR750_ac2t1s2] and <span class="html-italic">A. woodii</span> [pJIR750_ac2t2s2] are shown as light green lines with filled rhombus or filled light green column and dashed light green lines with empty rhombus or dashed light green column, respectively. The brown-green lines with filled triangle or brown-green column depict <span class="html-italic">A. woodii</span> [pJIR750_ac3t3s2].</p> Full article ">Figure 3
<p>Production of isopropanol using recombinant <span class="html-italic">A. woodii</span> strains, harboring the <span class="html-italic">sadH</span> gene of <span class="html-italic">C. ljungdahlii</span>, cultivated with 60 mM fructose (<b>A</b>–<b>C</b>) or CO<sub>2</sub> + H<sub>2</sub> (<b>D</b>–<b>F</b>) as substrate. Growth was performed in biological triplicates with <span class="html-italic">A. woodii</span> wild-type and <span class="html-italic">A. woodii</span> [pJIR750] as control strains (depicted as black line with filled circles or filled black column and dashed black line with empty circles or dashed black column, respectively). During growth, (<b>A</b>,<b>D</b>) OD<sub>600</sub>, (<b>B</b>,<b>E</b>) changes in pH and (<b>C</b>,<b>F</b>) product concentrations of acetone and isopropanol were monitored. The recombinant strains <span class="html-italic">A. woodii</span> [pJIR750_ac1t1s3] and <span class="html-italic">A. woodii</span> [pJIR750_ac1t2s3] are depicted as pink lines with filled rectangles or filled pink column and dashed pink lines with empty rectangles or dashed pink column, respectively. <span class="html-italic">A. woodii</span> [pJIR750_ac2t1s3] and <span class="html-italic">A. woodii</span> [pJIR750_ac2t2s3] are shown as purple lines with filled rhombus or filled purple column and dashed purple lines with empty rhombus or dashed purple column, respectively. The rosa lines with filled triangle or rosa column depict <span class="html-italic">A. woodii</span> [pJIR750_ac3t3s3].</p> Full article ">Figure 4
<p>Production of isopropanol using recombinant <span class="html-italic">A. woodii</span> strains, harboring the <span class="html-italic">hydG</span> gene of <span class="html-italic">C. beijerinckii</span> DSM 6423, cultivated with 60 mM fructose as substrate. Growth was performed in biological triplicates with <span class="html-italic">A. woodii</span> wild-type, <span class="html-italic">A. woodii</span> [pJIR750] and <span class="html-italic">A. woodii</span> [pJIR750] [pMTL83251] as control strains (depicted as black line with filled circles or filled black column, dashed black line or column and dotted black line or column with empty circles, respectively). During growth, (<b>A</b>) OD<sub>600</sub>, (<b>B</b>) changes in pH and (<b>C</b>) maximum product concentrations of acetone and isopropanol were monitored. The recombinant strains <span class="html-italic">A. woodii</span> [pJIR750_ac3t3s1] and <span class="html-italic">A. woodii</span> [pJIR750_ac3t3s1] [pMTL83251_PthlA_h1] are depicted as pastel blue lines with filled rectangles or filled pastel blue columns and dashed pastel blue lines with empty rectangles or dashed pastel blue columns, respectively. <span class="html-italic">A. woodii</span> [pJIR750_ac3t3s2] and <span class="html-italic">A. woodii</span> [pJIR750_ac3t3s2] [pMTL83251_PthlA_h1] are shown as brown-green lines with filled rhombus or filled brown-green columns and dashed brown-green lines with empty rhombus or dashed brown-green column, respectively. The rosa lines with filled triangle or filled rosa columns and dashed rosa lines with empty rectangles or dashed rosa columns depict <span class="html-italic">A. woodii</span> [pJIR750_ac3t3s3] and <span class="html-italic">A. woodii</span> [pJIR750_ac3t3s3] [pMTL83251_PthlA_h1], respectively.</p> Full article ">Figure 5
<p>Production of isopropanol using recombinant <span class="html-italic">A. woodii</span> strains, harboring the <span class="html-italic">sadH</span>-<span class="html-italic">hydG</span> gene cluster of <span class="html-italic">C. beijerinckii</span> DSM 6423 and an additional copy of <span class="html-italic">ctfA/ctfB</span> originating from <span class="html-italic">C. scatologenes</span>, cultivated with 60 mM fructose (<b>A</b>–<b>C</b>) or CO<sub>2</sub> + H<sub>2</sub> (<b>D</b>–<b>F</b>) as substrate. Growth was performed in biological triplicates with <span class="html-italic">A. woodii</span> wild-type, <span class="html-italic">A. woodii</span> [pJIR750] and <span class="html-italic">A. woodii</span> [pJIR750] [pMTL83251] as control strains (depicted as black line with filled circles or filled black column, dashed black line or column and dotted black line or column with empty circles, respectively). During growth, (<b>A</b>,<b>D</b>) OD<sub>600</sub>, (<b>B</b>,<b>E</b>) changes in pH and (<b>C</b>,<b>F</b>) maximum product concentrations of acetone and isopropanol were monitored. The recombinant strains <span class="html-italic">A. woodii</span> [pJIR750_ac3t3], <span class="html-italic">A. woodii</span> [pJIR750_ac3t3] [pMTL83251_PthlA_sh1] and <span class="html-italic">A. woodii</span> [pJIR750_ac3t3] [pMTL83251_PthlA_sh1c3] are depicted as dark blue lines or column with filled rhombus, dashed dark blue lines or column with empty rhombus and dotted dark blue lines or column with empty rhombus, respectively. <span class="html-italic">A. woodii</span> [pJIR750_ac3t3s1], <span class="html-italic">A. woodii</span> [pJIR750_ac3t3s1] [pMTL83251_PthlA_sh1] and <span class="html-italic">A. woodii</span> [pJIR750_ac3t3s1] [pMTL83251_PthlA_sh1c3] are shown as pastel blue lines or column with filled triangles, dashed pastel blue lines or column with empty triangles and dotted pastel blue lines or column with empty triangles, respectively.</p> Full article ">Figure 6
<p>Recombinant isopropanol production pathway in <span class="html-italic">A. woodii</span>. Abbreviations: CoA, coenzyme A; NADP<sup>+</sup>, nicotinamide adenine dinucleotide phosphate; H<sup>+</sup>, proton; P, phosphate; WLP, Wood–Ljungdahl pathway; ThlA, thiolase A; CtfA/CtfB, CoA-transferase; Adc, acetoacetate decarboxylase; Sadh, secondary alcohol dehydrogenase.</p> Full article ">

Review

Jump to: Research

20 pages, 1270 KiB  
Review
Current Understanding on the Heterogenous Expression of Plastic Depolymerising Enzymes in Pichia pastoris
by Shuyan Wu, David Hooks and Gale Brightwell
Bioengineering 2025, 12(1), 68; https://doi.org/10.3390/bioengineering12010068 - 14 Jan 2025
Viewed by 585
Abstract
Enzymatic depolymerisation is increasingly recognised as a reliable and environmentally friendly method. The development of this technology hinges on the availability of high-quality enzymes and associated bioreaction systems for upscaling biodegradation. Microbial heterologous expression systems have been studied for meeting this demand. Among [...] Read more.
Enzymatic depolymerisation is increasingly recognised as a reliable and environmentally friendly method. The development of this technology hinges on the availability of high-quality enzymes and associated bioreaction systems for upscaling biodegradation. Microbial heterologous expression systems have been studied for meeting this demand. Among these systems, the Pichia pastoris expression system has emerged as a widely used platform for producing secreted heterologous proteins. This article provides an overview of studies involving the recombinant expression of polymer-degrading enzymes using the P. pastoris expression system. Research on P. pastoris expression of interested enzymes with depolymerising ability, including cutinase, lipase, and laccase, are highlighted in the review. The key factors influencing the heterologous expression of polymer-degrading enzymes in P. pastoris are discussed, shedding light on the challenges and opportunities in the development of depolymerising biocatalysts through the P. pastoris expression system. Full article
(This article belongs to the Special Issue Synthetic Biology and Bioprocess Engineering for High-Value Compounds)
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Figure 1

Figure 1
<p>Highlighted factors influencing the effective functional overexpression of plastic-depolymerising enzymes in <span class="html-italic">P. pastoris</span>.</p> Full article ">Figure 2
<p>Overview of the heterogenous expression of depolymerising enzymes in the <span class="html-italic">P. pastoris</span> system (generated by BioRender).</p> Full article ">
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