AU2007215066A1 - Production of foreign nucleic acids and polypeptides in plant systems - Google Patents

Description

WO 2007/095304 PCT/US2007/003942 1 PRODUCTION OF FOREIGN NUCLEIC ACIDS AND POLYPEPTIDES IN PLANT SYSTEMS Related Applications [00011 This application is a continuation in part of and claims the benefit of co pending U.S. Patent Application No. 11/353,905, filed February 13, 2006 and entitled "Production of Foreign Nucleic Acids and Polypeptides in Sprout Systems". The entire contents of this application are hereby incorporated by reference. 100021 This application also claims the benefit of each of co-pending U.S. Provisional Patent Applications Numbered 60/773,255 (entitled "Bacillus Anthracis Antigens, Vaccine Compositions, and Related Methods"); 60/773,374 (entitled "HPV Antigens, Vaccine Compositions, and Related Methods"); and 60/773,378 (entitled "Influenza Antigen, Vaccine Compositions, and Related Methods"); each of which was filed on February 13, 2006. The entire contents of each of these applications is hereby incorporated by reference. 100031 This application further claims the benefit of co-pending U.S. Provisional Patent Application number 60/813,955, filed June 15, 2006 and entitled "Influenza Antigens, Vaccine Compositions, and Related Methods". The entire contents of this application are hereby incorporated by reference. [00041 This application further claims the benefit of co-pending U.S. Provisional Patent Application number 60/944,770, filed September 15, 2006 and entitled "Influenza Antibodies, Vaccine Compositions, and Related Methods". The entire contents of this application are hereby incorporated by reference. [0005] This application further claims the benefit of co-pending U.S. Provisional Patent Application number 60,879,450, filed January 9, 2007 and entitled "Launch Vector for the Production of Vaccine Antigens in Plants". The entire contents of each of these applications is hereby incorporated by reference. Background of the Invention [0006] The cost of pharmaceuticals is exorbitantly high and continues to rise. Some pharmaceuticals, in addition to their high cost, are also limited in supply, making it impossible for them to be available to every patient that needs them. This is particularly WO 2007/095304 PCT/US2007/003942 2 problematic in developing countries, where both cost and availability hinder the distribution of pharmaceuticals to needy populations. [0007] Several factors contribute to the high costs of producing pharmaceuticals, and result in the high price of the pharmaceuticals for the consumer. A major contributing factor is the lack of economical means of producing the product. This is particularly true for protein and peptide-based medications. Another contributing factor for some medications'is the inability to administer therapeutically effective amounts of the pharmaceutical agent orally. Many pharmaceuticals can only be administrated by injection into a particular site in the body. For example, many immunization medications for the treatment of allergies or infectious diseases require administration by injection. Protein and peptide pharmaceuticals, such as human growth hormone and insulin, can often only be administered by injection. Another factor that contributes to the cost of many pharmaceutical medications is their delivery to the hospital or distribution site. Particularly in hot climates, delivery and storage of pharmaceutical medications requires expensive refrigeration equipment. This is a major challenge in developing countries, where such equipment is often unavailable. [0008] Pharmaceutical proteins and peptides have been produced in a wide variety of hosts. Many therapeutic proteins have been produced in heterologous expression systems including prokaryotes such as Escherichia coli and Bacillus subtilis, and eukaryotes such as yeast, fungi, insect cells, animal cells, and transgenic animals. Bacterial expression systems are relatively easy to manipulate and the yield of the product is high. However, mammalian proteins often require extensive posttranslational modification for functional activity, which can be a limiting factor in bacterial expression systems. Cell culture systems such as mammalian, human, and insect cell culture systems are more convenient for the production of complex proteins. However, long lead times, low recovery of the product, possible pathogen transfer, and high capital and production costs present serious concerns. Transgenic animals may provide an unlimited supply of complex proteins. Unfortunately, this system is limited by the long period of time it takes to generate new and improved products and the risk of pathogen transfer to human subjects. 100091 The economic and biochemical limitations to producing pharmaceutical proteins and peptides in prokaryotic and eukaryotic cells, including high production costs, low yields, secretion problems, inappropriate modifications in protein processing, difficulties scaling up to larger volumes, and contamination have led researchers to examine plants as new hosts for the large-scale production of proteins and peptides with the WO 2007/095304 PCT/US2007/003942 3 expectation of reduced cost. Production of proteins in transgenic plants is described, for example, in U.S. Patent Nos. 5,750,871; 5,565,347; 5,464,763; 5,750,871; and 5,565,347. Although plants are less expensive to grow and harvest in bulk than prokaryotic and eukaryotic cells, expression of the foreign gene in plant cells is typically low. In addition, harvesting the plant typically requires breaking the plants, for example, by removing the leaves, separating the stems from the roots, or removing the roots. Such breakage usually results in a process that initiates wilting of the plant part and apoptosis of the plant. A plant undergoing apoptosis generates proteases that contribute to the degradation of the transgenically expressed protein before purification of the protein is even begun. Even if the plant is to be directly consumed, the activity of the expressed pharmaceutical protein may be reduced by harvest-induced intercellular degradation machinery. [00101 Another major concern associated with producing foreign proteins in transgenic plants that are grown in open fields is the possibility of cross-pollination with plants in the wild, making it possible for the foreign protein to enter the food chain. The complexity of governmental regulations surrounding agricultural practices for transgenic plants makes it difficult to get new transgenic plants approved for agricultural use. Furthermore, the outdoor environment is impossible to control, making proper growth, development, and regulation of foreign gene expression difficult to guarantee. For example, the induction of a heat inducible, light inducible, hormone inducible, or chemically inducible promoter would be practically impossible in an outdoor environment. Of course, the outdoor temperature and light levels cannot be controlled. Additionally, hormones or chemicals sprayed on a plant are likely to be dispersed not onto the plant, but into the environment by wind and rain. Spaying crop fields is also quite costly. 100111 There exists a need for improved systems for the production of proteins or polypeptides. There is a particular need for improved systems for the production of proteins or polypeptides in plants. For example, there is a need for a controlled regulatable system for producing pharmaceutical proteins in plants that decreases the amount of intercellular degradation of the expressed protein upon harvest. Summary of the Invention [00121 The present invention provides systems for the production of proteins or polypeptides (and/or of nucleic acids), particularly pharmaceutical proteins or polypeptides, in plants.

WO 2007/095304 PCT/US2007/003942 4 [00131 In one aspect, the present invention provides systems for rapid expression of proteins or polypeptides in plants. In some embodiments, therefore, the present invention provides for expression of proteins or polypeptides in young plants. In some embodiments, such young plants are sprouted seedlings. In some embodiments, the young plants (e.g., sprouted seedlings) can be consumed or harvested live. In some embodiments, the plants are grown (e.g., from a seed) in a contained, regulatable environment, e.g., indoors. [00141 In some embodiments, a protein or polypeptide to be produced in accordance with the present invention is expressed in plant cells from a nucleic acid construct that is introduced into the plant by the hand of man. In some embodiments, a protein or polypeptide to be produced in accordance with the present invention is translated in plant cells from an RNA with characteristics of a plant virus. In some such embodiments, these characteristics include or are selected from the group consisting of self-replication, cell-to cell movement, systemic movement, and combinations thereof. In some embodiments, the RNA is self-replicating and capable of cell-to-cell movement, but is not capable of systemic movement in the plant. [0015] In some embodiments, a protein or polypeptide to be produced in accordance with the present invention is expressed in plant cells from a nucleic acid construct that replicates in Agrobacterium. In some embodiments, the present invention utilizes a construct that replicates in Agrobacterium and also contains a promoter directing expression of an RNA with characteristics of a plant virus. In some embodiments, this RNA includes sequences encoding the protein or polypeptide of interest. Thus, in some embodiments of the present invention, a protein or polypeptide of interest is produced in plants by a process involving introducing into cells of a plant a vector that replicates in Agrobacterium and also contains a promoter directing expression of an RNA with characteristics of a plant virus, which RNA is not capable of systemic movement in a plant, but is capable of self replication and which RNA further encodes the protein or polypeptide of interest. 10016] In some embodiments of the present invention, where a construct is utilized that replicates in Agrobacterium, the construct is introduced into plant cells by agroinfiltration. [0017] While the invention is described herein primarily in reference to its use for producing pharmaceutical proteins, the invention generally finds use for producing essentially any nucleic acid (DNA and/or RNA) and/or protein of interest, without limitation as to the particular use(s) of the nucleic acid or protein. For example, enzymes of use in any WO 2007/095304 PCT/US2007/003942 5 of a wide variety of industrial processes or bioremediation processes (e.g., enzymes that degrade pollutants) can be produced. Thus the description of the invention, and the claims, are to be considered as applying to any nucleic acid or protein of interest even if not explicitly indicated, including those with therapeutic applications and those without. In certain embodiments the protein is not a nutritionally important protein. Any particular protein may be excluded from the present invention without being named herein. [00181 In certain embodiments of the invention in any of its aspects, the nucleic acid or protein of interest is post-transcriptionally and/or post-translationally processed in the cell in which it is expressed. In certain embodiments of the invention a protein of interest is secreted from the cell in which it is expressed. For example, the protein may naturally comprise a secretion signal sequence, or the coding region of a nucleic acid that encodes the protein may be modified to include a portion that encodes a secretion signal sequence. Secretion signal sequences are well known in the art. 100191 In certain embodiments of the invention in any of its aspects a heterologous sequence that encodes a protein of interest may be altered to employ different codons from those present in the naturally occurring sequence, in order to improve expression in plants generally and/or in plants of a particular species. For example, the sequence may be codon optimized for expression in a particular species. Methods for performing codon optimization are known in the art. [0020] The present invention also provides, among other things, plants containing expression constructs as described herein, compositions containing such plants, preparations of proteins/polypeptides isolated from such plants, compositions containing such proteins/polypeptides isolated from such plants, methods of performing such isolations, and methods of using such isolated proteins/polypeptides (or compositions containing them), including methods of treating a mammal with a pharmaceutically active protein expressed in plants. Definitions [0021] "Administration" of a pharmaceutically active protein or polypeptide to a subject in need thereof is intended as providing the pharmaceutically active protein to such subject in a manner that retains the therapeutic effectiveness of such protein for a length of time sufficient to provide a desired beneficial effect to such host.

WO 2007/095304 PCT/US2007/003942 6 [0022] The term "animal" covers all vertebrates, life forms, humans, bovines, ovines, porcines, canines, felines, ferrets, rodents, primates, fish, birds, e.g., poultry and the like. In some embodiments, the animals are mammals. In some embodiments, the animals are humans. [0023] According to the present invention, a "characteristic portion" of a polypeptide or protein is of a protein or polypeptide is one that contains a continuous stretch of amino acids, or a collection of continuous stretches of amino acids, that together are characteristic of a protein or polypeptide. In some embodiments, each such continuous stretch generally will contain at least 2, 5, 10, 15, 20 or more amino acids. In general, a characteristic portion is one that, in addition to the sequence identity specified above, shares at least one functional characteristic with the relevant intact protein. In some embodiments, the characteristic portion may be biologically active. [00241 A "domain" of a protein or polypeptide, as that term is used herein, generally refers to a segment of protein or polypeptide sequence that, when produced apart from the rest of the protein or polypeptide sequence, maintains a degree of three-dimensional integrity and/or structure. As is known in the art, many proteins and polypeptides have domain structures. In some embodiments the domain has activity (e.g., binding, catalytic, etc.). In some embodiments, a domain is immunogenic. An immunogenic domain is at least as large as a single epitope, and is typically larger; in some embodiments, an immunogenic domain contains sufficient sequence in addition to the epitope to ensure proper presentation of the epitope. [0025] "Expression" refers to transcription and/or translation of an endogenous gene or a transgene in a plant, e.g., a sprout. The transgene may or may not be integrated into the genomic DNA of the plant. For example, "expression" refers to transcription and/or translation in a plant of a gene present in a bacterial, plasmid, or viral nucleic acid, regardless of whether the bacterial, plasmid, or viral nucleic acid is integrated into the genomic DNA of the plant. The gene may be a gene that is heterologous to the bacterium, plasmid, or virus. [0026] "Expression cassette" or "expression vector" refers to a DNA sequence (or an RNA sequence in the case of RNA viruses or RNA plasmids), capable of directing expression of a particular nucleotide sequence in an appropriate host cell. For example, an expression cassette may include a promoter operably linked to a nucleotide sequence of interest, which is optionally operably linked to 3' sequences, such as 3' regulatory sequences WO 2007/095304 PCT/US2007/003942 7 or termination signals. An expression cassette may also typically include sequences required for proper translation of the nucleotide sequence if any such sequences are needed. The coding region usually codes for a protein of interest but may also code for a functional RNA of interest, for example, an antisense RNA or a non-translated RNA that inhibits expression of a particular gene. The expression cassette including the nucleotide sequence of interest may be chimeric, meaning that the nucleotide sequence includes more than one DNA sequence of distinct origin that are fused together by recombinant DNA techniques, resulting in a nucleotide sequence that does not occur naturally and that particularly does not occur in the plant in which it is to be expressed. An expression cassette may also be one that is naturally occurring but has been obtained in a recombination form useful for heterologous expression. Typically, however, the expression cassette is heterologous with respect to the host, i.e., the particular DNA sequence of the expression cassette does not occur naturally in the host cell and must have been introduced into the host cell or an ancestor of the host cell by a transformation event. The expression of the nucleotide sequence in the expression cassette may be under the control of a constitutive promoter or of an inducible promoter that initiates transcription only when the host cell is exposed to some particular external stimulus. In the case of a multicellular organism, such as a plant, the promoter can also be specific to a particular tissue, organ, or stage of development. A nuclear expression cassette is usually inserted into the nuclear genome of a plant and is capable of directing the expression of a particular nucleotide sequence from the nuclear genome of the plant. A plastid expression cassette is usually inserted into the plastid genome of a plant and is capable of directing the expression of a particularly nucleotide sequence from the plastid genome of the plant. In the case of a plastid expression cassette, for expression of nucleotide sequence from a plastid genome, additional elements, e.g., ribosome binding sites, or 3' stem-loop structures that impede plastid RNA polyadenylation and subsequent degradation may be required. In certain embodiments of the invention an expression cassette is utilized that comprises a promoter that is a minimal promoter such as a TATA element, and presence of a trans-activating factor may be necessary to direct expression of the nucleotide sequence, particularly to direct high level expression. For example, the expression cassette may comprise a DNA region for binding of a transcriptional activator. Such expression cassettes, and the promoters therein, are referred to as being "activatable". [00271 A "food" or "food product" is a liquid or solid preparation that can be ingested by humans or other animals. Preferably, the terms include preparations of the raw WO 2007/095304 PCT/US2007/003942 8 or live plants (e.g., sprouted seedlings) that may be fed live directly to humans and/or other animals. Materials obtained from a plant are intended to include a whole edible plant that can be ingested by a human or other animal. The term may also include any processed plant (e.g., sprouted seedling) together with a nutritional carrier that is fed to humans and other animals. Processing steps may include steps commonly used in the food or feed industry. Such steps include, but are not limited to concentration or condensation of the solid matter of the plant to form, for example, a pellet, production of a paste, drying, or lyophilization, or may be produced by cutting, mashing, or grinding of the plant to various extents, or by extraction of the liquid part of the plant to produce a soup, a syrup, or a juice. A processing step can also include cooking, e.g., steaming, the plant (e.g., sprouted seedling). [0028] A "gene" is a sequence that encodes a protein or polypeptide (or RNA) of interest. A gene may include associated regulatory sequences. A gene's coding sequence may be transcribed into RNA, such as mRNA, rRNA, tRNA, snRNA, sense RNA or antisense RNA. As will be appreciated by those of ordinary skill in the art, however, a "gene" may also be an RNA (e.g., a gene in a viral RNA vector). Examples of "regulatory sequences" are promoter sequences, 5' and 3' untranslated sequences, and termination sequences. In addition, introns and exons may also be included. In certain embodiments, the gene is the coding sequence and the associated regulatory sequences are heterologous sequences. [0029] "Heterologous sequences," as used herein, means of different natural origin or of synthetic origin. For example, if a nucleic acid is introduced into a host cell and the host cell does not naturally contain some or all of the sequences present in the nucleic acid, then those sequences (and/or the nucleic acid) are said to be heterologous with respect to the host cell. The introduced nucleic acid may include a heterologous promoter, heterologous coding sequence, or heterologous termination sequence. Alternatively, the transforming nucleic acid may be completely heterologous or may include any possible combination of heterologous and endogenous nucleic acid sequences. Similarly, heterologous refers to a nucleotide sequence derived from and inserted into the same natural, original cell type, but which is present in a non-natural state, e.g., a different copy number, or under the control of different regulatory elements. The term "heterologous" applies to cells, including plant and bacterial cells, and also to plasmids, plastids, and viruses. [0030] A "host cell" is a cell into which a nucleic acid is introduced for expression. Typically, such introduction requires the hand of man.

WO 2007/095304 PCT/US2007/003942 9 [0031] An "inactive expression cassette" or "inactive expression vector" is a DNA or RNA sequence that comprises an inactive or silenced foreign nucleic acid sequence, which is capable of directing expression of a nucleic acid or polypeptide of interest upon its activation. Generally, an inactive expression cassette has the properties of an expression cassette as described above, except that the sequence that codes for a nucleic acid or polypeptide of interest may not be operatively linked to a promoter, e.g., it may be separated from the promoter (or from another regulatory element) by an intervening nucleic acid region. Operative linkage occurs following a recombination event, so that expression then occurs. Such as expression cassette is referred to as being "activatable". [00321 The term "inducible promoter," means a promoter that is turned on by the presence or absence of a particular stimulus that increases promoter activity directly or indirectly. Some non-limiting examples of such stimuli include heat, light, developmental regulatory factors, wounding, hormones, and chemicals, e.g., small molecules. One example of a light-inducible promoter is the ribulose-5-phosphate carboxylase promoter. Chemically-inducible promoters also include receptor-mediated systems, e.g., those derived from other organisms, such as steroid-dependent gene expression, the Lac repressor system and the expression system utilizing the USP receptor from Drosophila mediated by juvenile growth hormone and its agonists, described in WO 97/13864, incorporated herein by reference, as well as systems utilizing combinations of receptors, e.g., as described in WO 96/27673, also incorporated herein by reference. Additional chemically inducible promoters include elicitor-induced promoters, safener-induced promoters as well as the alcA/alcR gene activation system that is inducible by certain alcohols and ketones (WO 93/21334; Caddick et al. (1998) Nat. Biotechnol. 16:177-180, the contents of which are incorporated herein by reference). Wond inducible promoters include promoters for proteinase inhibitors, e.g., proteinase inhibitor 11 promoter from potato, and other plant-derived promoters involved in the wound response pathway, such as promoters for polyphenyl oxidases, LAP, and TD. See, e.g., Gatz "Chemical Control of Gene Expression," Ann. Rev. Plant Physiol. Plant Mol. Biol. (1997) 48:89-108, incorporated herein by reference. Other inducible promoters include plant-derived promoters, such as the promoters in the systemic acquired resistance pathway, for example, PR promoters. It is noted that where inducible promoters are discussed herein, activatable promoters and expression cassettes can be used in a similar fashion in certain embodiments of the invention. [00331 A "marker gene" is a gene encoding a selectable or screenable trait.

WO 2007/095304 PCT/US2007/003942 10 [00341 A "medical food" includes a composition that is eaten or drunk by a subject and has a therapeutic effect on the subject. A medical food includes, for example, a plant (e.g., sprouted seedling) in which a pharmaceutical protein or polypeptide has been produced, or plant matter derived therefrom. A medical food may be ingested alone or may be administered in combination with a pharmaceutical composition well known in the medical arts. A medical food also includes the equivalent feedstuff for non-human animals. [00351 "Operably linked" refers to the association of a nucleic acid elements. For example, a promoter operably linked to a heterologous DNA, which encodes a protein, promotes the production of functional mRNA corresponding to the heterologous DNA. A regulatory DNA sequence is said to be "operably linked to" or "associated with" a DNA sequence that codes for an RNA or a protein if the two sequences are situated such that the regulatory DNA sequence affects expression of the coding DNA sequence. [00361 "Oral administration" of a pharmaceutically active peptide or protein means primarily administration by way of the mouth, preferably by eating, but also intends to include any administration that provides such peptides or proteins to the host's stomach or digestive track. In a preferred embodiment, oral administration results in contact of the pharmaceutically active protein with the gut mucosa. 100371 A "pharmaceutically active nucleic acid" is a nucleic acid that encodes a pharmaceutically active protein or is pharmaceutically active in its own right, e.g., it has one or more pharmaceutical activities such as those described for pharmaceutically active proteins. For example, the nucleic acid may be one or more strands of an RNA interference (RNAi) agent. Such agents include short interfering RNAs (siRNAs), or short hairpin RNAs (shRNAs), or precursor of an siRNA or microRNA-like RNA, targeted to a target transcript, e.g., a transcript of an infectious agent or an endogenous disease-related transcript of a subject. [0038] A "pharmaceutically active protein or polypeptide" aids or contributes to the condition of a host in a positive manner when administered to the host in a therapeutically effective amount. A pharmaceutically active protein or polypeptide has healing curative or palliative properties against a disease and may be administered to ameliorate relieve, alleviate, reverse, delay onset of or lessen the severity of one or more symptoms of a disease or disorder. A pharmaceutically active protein or polypeptide may have prophylactic properties and may be used to delay the onset of a disease or to lessen the severity of such disease or pathological condition when it does emerge. The term "pharmaceutically active WO 2007/095304 PCT/US2007/003942 11 proteins or polypeptides" includes entire proteins or polypeptides, and can also refer to pharma-ceutically active fragments thereof. It can also include pharmaceutically active analogs of the protein or peptide or analogs of fragments of the protein or peptide. The term "pharmaceutically active protein or polypeptide" can also refers to a plurality of proteins or peptides that act cooperatively or synergistically to provide a therapeutic benefit. It is noted that the term "pharmaceutically active protein or polypeptide" specifically includes proteins that comprise vaccine antigens, i.e., administration of the protein to a subject elicits a partially or fully protective immune response in the host. In certain embodiments of the invention the immune response protects the subject against an infectious agent, e.g., a virus, bacterial, fungal, or protozoal pathogen. Examples of vaccine antigens include hepatitis B surface antigen (HBsAg), E. coli heat-labile enterotoxin, rabies virus glycoprotein, and Norwalk virus capsid protein. In other embodiments of the invention the immune response protects the subject against a non-infectious condition or disease or lessens the severity of at least one sign or symptom of the condition or disease. Diseases of interest in this regard include, but are not limited to, cancer and auto-immune diseases. The term "pharmaceutically active protein or polypeptide" includes proteins that partially or fully tolerize a subject to exposure to an allergen that would otherwise elicit an allergic or anaphylactic response. [0039] A "promoter," as used herein, is a DNA sequence that initiates transcription of an associated DNA sequence. The promoter region may also include elements that act as regulators of gene expression such as activators, enhancers, and/or repressors. [00401 "Regulatory elements" refer to sequences involved in conferring the expression of a nucleotide sequence. Regulatory elements include 5' regulatory sequences such as promoters that can be linked to the nucleotide sequence of interest, 3' sequences such as 3' regulatory sequences or termination signals. Regulatory elements also typically encompass sequences required for proper translation of the nucleotide sequence. 100411 "Small molecules" are typically less than about one kilodalton and are biological, organic, or even inorganic compounds (e.g., cisplatin). Examples of such small molecules include nutrients such as sugars and sugar-derivatives (including phosphate derivatives), hormones (such as the phytohormones gibberellic or absisic acid), and synthetic small molecules.

WO 2007/095304 PCT/US2007/003942 12 [0042] "Specifically regulatable" refers to the ability of a small molecule to - preferentially affect transcription from one promoter or group of promoters, as opposed to non-specific effects, such as enhancement or reduction of global transcription within a cell. [00431 A "sprouted seedling" or "sprout" is a young shoot from a seed or a root, preferably a recently germinated seed. In some embodiments, the sprouted seedlings of the invention are edible sprouted seedlings or sprouts (e.g., alfalfa sprouts, mung bean sprouts, radish sprouts, wheat sprouts, mustard sprouts, spinach sprouts, carrot sprouts, beet sprouts, onion sprouts, garlic sprouts, celery sprouts, rhubarb sprouts, a leaf such as cabbage sprouts, or lettuce sprouts, watercress or cress sprouts, herb sprouts such as parsley or clover sprouts, cauliflower sprouts, broccoli sprouts, soybean sprouts, lentil sprouts, edible flower sprouts such as sunflower sprouts, etc.). According to the present invention, the sprouted seedling may have developed to the two-leaf stage. Generally, the sprouts of the invention are two to fourteen days old. [0044] "Substantially isolated" is used in several contexts and typically refers to the at least partial purification of a protein or polypeptide away from unrelated or contaminating components (for example, plant structural and metabolic proteins). Methods for isolating and purifying proteins or polypeptides are well known in the art. [0045] "Transformation" refers to introduction of a nucleic acid into a cell, particularly the stable integration of a DNA molecule into the genome of an organism of interest. Description of the Drawing [0046] Figure 1 is a schematic representation of different strategies for foreign gene expression using plant virus-based vectors. [0047] Figure 2 is a schematic representation of AIMV and TMV genomes. [0048] Figure 3 is a picture of a Western blot of expression of recombinant GFP in Nicotiana benthamiana plants inoculated with Av/A4 and Av/GFP. [0049] Figure 4 is a picture of a Western blot of human growth hormone (hGH) production in N. benthamiana plants infected with in vitro transcripts of GH. [0050] Figure 5 is a schematic representation of transformation constructs for expression of recombinant proteins in Brassicajuncea. 100511 Figure 6 is a picture of an immunoblot of transgenic Brassicajuncea expressing human growth hormone under control of the HSP 18.2 promoter.

WO 2007/095304 PCT/US2007/003942 13 [00521 Figure 7 depicts a schematic representation of various agrobacterial constructs containing target genes. Figure 7A: Vector pBIV, in which a target gene is integrated between a plant promoted (IV = any plant promoter, artificial promoter, or other promoter that functions in plant cells, e.g., a promoter of a plant virus such as cauliflower mosaic virus) and the nos terminator; Figure 7B: Vector pBIV-GUS, in which the GUS gene is inserted in pBIV. Figure 7C: pBIV-Virus Vector + Target, in which a viral vector or replicon (e.g., a viral genome or genome portion) carrying a target gene is inserted in to pBIV; Figure 7D: Vector pBIV-Virus Vector + GFP, in which GFP is the target gene carried by a viral vector or replicon inserted into pBIV. The vectors depicted in Figures 7C and 7D are considered "launch" vectors because, after introduction into plant cells, they "launch" production of the viral sequences (which may be self replicating, at least in the context of the particular plant cell into which they are launched). [0053] Figure 8 demonstrates GUS staining after agroinfiltration of sprouts with pBIV-GUS. Figure 8A demonstrates staining of Mung bean sprout; Figure 8B demonstrates staining of Fenugreek sprouts. [0054] Figure 9 demonstrates GUS staining after agroinfiltration of Brassica sprouts with pBIV-GUS. Figure 9A demonstrates staining results; Figure 9B is a table listing different types of sprouts tested for their ability to express protein or polypeptide delivered by means of an agrobacterial construct that includes a promoter directing expression of viral sequences carrying a gene that encodes the protein or polypeptide of interest. [00551 Figure 10 demonstrates GFP expression in N. benthamiana over time after infiltration with pBI121/D4-GFPC3. [00561 Figure 11 demonstrates western blot analysis of hGH expression in plants as a result of infiltration with Agrobacterium containing a virus vector containing a sequence encoding hGH. Lanes: Lane 1: ladder; Lane 2: 50ng hGH; Lane 3: Plant sample infiltrated with pB1121/D4-HGH 6dpi 1:2 dilution; Lane 4: Plant sample infiltrated with pBI121/D4 HGH 6dpi 1:10 dilution; Lane 5: Plant sample infiltrated with pBI121/D4-HGH 6dpi 1:50 dilution; Lane 6: Plant sample infiltrated with pBI121/D4-HGH 6dpi 1:100 dilution; Lane 7: Plant sample from Healthy plant; Lane 8: Plant sample from pBIl21-infiltrate leaves; Lane 9: Plant sample from D4-HGH infected plant 13dpi; Lane 10: Sample from D4-HGH infected clonal root line. For plant samples: one leaf disc (-5mg tissue) is ground in 1OuL Bradley buffer with Laemmli loading buffer. 1Oul is loaded per lane. Therefore, for lanes 3-6, this primary sample was diluted.

WO 2007/095304 PCT/US2007/003942 14 [00571 Figure 12 demonstrates expression of IA-2ic protein in in Nicotiana benthamiana plants grown in hydroponics: Lanes: 1. IA-2ic standard; 2. Magic Marker; 3. Soil-grown plants injected with agrobacteria.; 4, 5. Hydroponics-grown plants 4 days after infiltration.; 6, 7.. Hydroponics-grown plants 6 days after infiltration. [0058] Figure 13 depicts one emodiment of an agroinfiltration system utilized in accordance with the present invention to delivery an agrobacterial vector that launches viral sequences carrying a target protein of interest into young plants. [0059] Figure 14 illustrates activity of lichenase detected in various pea varieties subjected to agroinfiltration using the system of Figure 13. [00601 Figure 15 shows GFP expression and plant growth for speckled peas subjected to agroinfiltration using the system of Figure 13. [00611 Figure 16 shows tissue specificity and optimal days post infiltration for certain speckled peas subjected to agroinfiltration using the system of Figure 13. [00621 Figure 17 depicts a lichenase carrier molecule that may be used in fusions with proteins or polypeptides of interest in accordance with certain embodiments of the invention. Panel A presents a schematic representation of b-1,3-1,4-glucanase (lichenase) from Clostribium thermocellum. Panel B prsents a schematic representation of the circularly permuted LicKM carrier, In each panel, the vertical hatch corresponds to the N-terminal region of the catalytic doman, and the dotted box corresponds to the C-terminal region of the catalytic domain. [0063] Figure 18 presents a schematic diagram of the launch vector pBID4. [00641 Figure 19 is a schematic representation of each step involved in the process from target gene optimization to purification of a final product that is ready for storage according to one specific embodiment of the invention. [0065] Figure 20 depicts an equipment design useful for automation of steps from plant seeding to tissue harvest. As depicted, the module is estimated to occupy a floor area of about 40 feet by about 70 feet and to be about 32 feet high. The system shown includes the following components connected by conveyors: central shelving units where plants are maintained between steps, a seeding unit, a vacuum infiltration and rinsing unit, and a tissue harvesting unit. Description of Certain Preferred Embodiments Proteins or Polypeptides WO 2007/095304 PCT/US2007/003942 15 [0066] The present invention is applicable to the production of any protein or polypeptide (or any functional DNA or RNA molecule), in plant systems. As indicated above, in certain embodiments, the invention is directed to production of pharmaceutical proteins, but the invention generally is not limited by the particular use(s) of the nucleic acid or protein. For example, enzymes of use in any of a wide variety of industrial processes or bioremediation processes (e.g., enzymes that degrade pollutants) can be produced. Thus the description of the invention, and the claims, are to be considered as applying to any nucleic acid or protein of interest even if not explicitly indicated, including those with therapeutic applications and those without. In certain embodiments the protein is not a nutritionally important protein. Any particular protein may be excluded from the present invention without being named herein. [00671 Typically, the expressed protein or polypeptide is not one that is expressed in the plant in nature. Even if the protein or polypeptide is one that is expressed in the plant in nature, according to the present invention, it is typically expressed in young plant tissue at concentrations above that which would be present in comparable tissue in nature. [0068] To give but a few specific examples, the present invention may be utilized to produce pharmaceutical proteins of interest including, but not limited to, hormones (insulin, thyroid hormone, catecholamines, gonadotrophines, trophic hormones, prolactin, oxytocin, dopamine, bovine somatotropin, leptins and the like), growth hormones (e.g., human grown hormone), growth factors (e.g., epidermal growth factor, nerve growth factor, insulin-like growth factor and the like), growth factor receptors, cytokines and immune system proteins (e.g., interleukins, colony stimulating factor (CSF), granulocyte colony stimulating factor (G-CSF), granulocyte-macrophage colony stimulating factor (GM-CSF), erythropoietin, tumor necrosis factor (TNF), interferons, integrins, addressins, seletins, homing receptors, T cell receptors, immunoglobulins, soluble major histocompatibility complex antigens, immunologically active antigens such as bacterial, parasitic, or viral antigens or allergens), autoantigens, antibodies), enzymes (tissue plasminogen activator, streptokinase, cholesterol biosynthestic or degradative, steriodogenic enzymes, kinases, phosphodiesterases, methylases, de-methylases, dehydrogenases, cellulases, proteases, lipases, phospholipases, aromatases, cytochromes, adenylate or guanylaste cyclases, neuramidases and the like), receptors (steroid hormone receptors, peptide receptors), binding proteins (sterpod binding proteins, growth hormone or growth factor binding proteins and the like), transcription and translation factors, oncoprotiens or proto-oncoprotiens (e.g., cell cycle proteins), muscle WO 2007/095304 PCT/US2007/003942 16 proteins (myosin or tropomyosin and the like), myeloproteins, neuroactive proteins, tumor -growth suppressing proteins (angiostatin or-endostatin, both which inhibit angiogenesis), anti-sepsis proteins (bectericidal permeability-increasing protein), structural proteins (such as collagen, fibroin, fibrinogen, elastin, tubulin, actin, and myosin), blood proteins (thrombin, serum albumin, Factor VII, Factor VIII, insulin, Factor IX, Factor X, tissue plasminogen activator, Protein C, von Wilebrand factor, antithrombin III, glucocerebrosidase, erythropoietin granulocyte colony stimulating factor (GCSF) or modified Factor VIII, anticoagulants such as huridin) and the like. [0069] In some particular embodiments, the present invention is utilized to produce antigenic proteins or polypeptides. For example, the present invention may be utilized to produce proteins (or portions thereof) of infectious organisms that are recognized by the immune system of an infected subject. Such proteins or polypeptides may have particular use in the development of vaccines for protection against infection by the relevant organisms. To give but a few specific examples, useful antigenic proteins from anthrax (Bacillus anthracis ; e.g., LF, PA), cholera (Vibrio cholerae), cytomegalovirus, enterotoxigenic strains of E. coli , foot-and-mouth disease virus, hepatitis B (e.g. hepatitis B surface antigen, HBsAg), hepatitis C (e.g., HCV core protein), human immunodeficiency virus (e.g., Tat, Rev, Nef, gpl60, gpl20, etc.), human papilloma virus (e.g., E7, E6), influenza (e.g., HA, NA), malaria (Plasmodiumfalciparum; e.g. Pfs25, Pfs28, Pfs48/45, Pfs230), measles virus, norwalk virus, plague (Yersiniapestis; e.g., Fl, LcrV), Pseudomonas aeruginosa, rabies virus, respiratory syncytial virus (e.g., F protein, G protein), rhinovirus, rotavirus, Staphylococcus aureus, transmissible gastroenteritis virus, trypanosomes ( Trypanosoma brucei; e.g., alpha-tubulin, beta-tubulin), tuberculosis, SARS, etc. can be produced in accordance with the present inventive system. [0070] In some particular embodiments, the present invention is utilized to produce multimeric protein complexes, including, for example, immunoglobulin proteins such as antibodies (i.e., monoclonal antibodies). To give but a few specific examples, anti-PA, anti LF, anti-NA, anti-TNFa, anti-interleukin-12, etc. can be produced in accordance with the present inventive system. More generally, monoclonal antibodies to antigens associated with diseases such as cancer (e.g., acute myeloid leukemia (AML), breast cancer, colorectal cancer, chronic lymphocytic leukemia (CLL), non-Hodgkin's lymphoma, renal cell carcinoma, solid tumors), inflammatory and autoimmune disorders (e.g., Asthma, Crohn's disease, Diabetes, Graft versus host disease (organ rejection), Inflammatory bowel disease, WO 2007/095304 PCT/US2007/003942 17 Lupus, Multiple sclerosis, Psoriasis, Psoriatic arthritis, Rheumatoid arthritis, Thrombosis, Vasculitis, etc), infectious diseases (e.g., anthrax (Bacillus anthracis), cholera (Vibrio cholerae), cytomegalovirus, enterotoxigenic strains of E. coli, foot-and-mouth disease virus, hepatitis B virus, hepatitis C virus, human immunodeficiency virus, human papilloma virus, influenza, malaria (Plasmodiumfalciparum;), measles virus, norwalk virus, plague (Yersinia pestis), Pseudomonas aeruginosa, rabies virus, respiratory syncytial virus, rhinovirus, rotavirus, Staphylococcus aureus, transmissible gastroenteritis virus, trypanosomes (Trypanosoma brucei), tuberculosis, SARS), etc can be prepared according to the present invention. [00711 In some particular embodiments, the present invention is utilized to produce hGH, auto-antigens for autoimmune diseases (e.g., IA-2ic for diabetes), influenza antigens, anthrax antigens, HPV antigens, influenza antibodies, etc. (see Examples). [00721 In some embodiments of the present invention, full-length heterologous proteins are produced. That is, a protein that occurs in nature or that has been prepared or designed in another context is produced in its entirety in young plants. In some such embodiments, the produced protein is free of any other sequences. In other embodiments, only a portion of the protein is produced, typically a portion that has a known desirable activity (e.g., an epitope of an antigenic protein; an active domain of an enzymatic protein, etc.). In some embodiments, the produced portion is a characteristic portion of the protein or polypeptide. In some embodiments, the produced portion comprises an epitope. In some embodiments, the produced portion comprises an immunogenic domain. In some embodiments, the produced portion comprises a protein domain. [00731 In some embodiments of the present invention, proteins or polypeptides are produced as fusions with other protein or polypeptide sequences. As is known in the art, fusions can be used for any of a variety of reasons. For example, proteins or polypeptides to be produced in young plants (e.g., sprouted seedlings) according to the present invention may be fused with one or more moieties to facilitate detection and/or isolation. For example, proteins or polypeptides of interest might be fused with a known antigenic epitope for which an antibody or other specific ligand is available and can be used to facilitate isolation or purification. Alternatively or additionally, proteins or polypeptides of interest may be fused with another polypeptide of defined three-dimensional structure, for example to impart a desired three-dimensional arrangement to the protein or polypeptide of interest. As yet another example, proteins or polypeptides of interest may be fused with one or more WO 2007/095304 PCT/US2007/003942 18 moieties that will direct their sub-cellular localization (or secretion) in plant cells. Particularly when the protein or polypeptide of interest is a protein antigen (e.g., for use in preparation of a subunit vaccine), it will often be desirable to produce the protein as a fusion with a carrier molecule, for example to enhance expression, stability, and/or immunogenicity, and/or to aid in isolation or purification. Certain exemplary fusion partners known in the art include, for example, antibody epitopes (e.g., His tag, etc.), immunogenic carrier prteins, cholera toxin, heat labile enterotoxin, etc. (see, for example, Vella et al., Biotechnology 20:1, 1992; Kelly et al., Immuology 113:163, 2004; Buttery et al., JR Coll Phuysicians Lond 34:163, 2000; Jacobson et al., Minerva Peditr. 54:295, 2002; Dertzbaugh et al., Infect Immunol. 61:48, 1993; Nashar et al., Vaccine 11:235, 1993; Liljeqvist et al., J Immunol. Methods 210:125, 1997; Stahl et al., Proc. NatL. Acad. Sci. USA 86:6283, 1989; Ulrich et al., Adv. Virus Res. 50:141, 1998; Smith et al., Virology 348:475, 2006; Turpen et al., Biotechnology 13:53, 1995). [00741 One particular fusion partner contemplated in accordance with the present invention is a thermostable protein such as lichenase B from Clostridium thermocellum (see, for example, United States Provisional Patent Application 60/472,495 filed May 22, 2003 and PCT Application USO4/016452 filed May 24, 2004 and published as WO 2005/026375 March 24, 2005. Full-length lichenase (about 35 kDa) consists of a signal peptide, a catalytic domain, a Pro-Thr-rich box, and a docking domain (see Figure 17). According to the present invention, both the Pro-Thr rich box and the docking domain can be deleted in fusion proteins. Also, the native signal peptide can be replaced with one that operates in plants. [0075] The catalytic domain of this lichenase has a loop structure dividing it into two regions, the N-terminal region (N: animo acids 32-84) and the C-terminal region (C:amino acids 85-246). These two regions can be split at the loop structure and circularly permuted to make the molecule more receptive to insertions without affecting enzymatic activity. A multiple cloning site (MCS) was introduced at the junction between these two regions, and a 6xHis tag and the sequence KDEL were places at the 3'-end of the permuted carrier to facilitate purification and retention in the endoplasmic reticulum, respectively. Figure 17) shows a schematic diagram of the modified lichenase (LicKM; GenBank accession number DQ776900) that has a molecular weight of about 27 kDa. Target protein or polypeptide sequences can be expressed as N or C terminal fusions and/or as internal fusions into the MCS, a feature that allows for the simultaneous expression of multiple targets.

WO 2007/095304 PCT/US2007/003942 19 [00761 LicKM allows for fusions to molecules ranging in size from small peptides to full-length proteins of up to about 100 kDa or more. LicKM maintains its enzymatic activity at high temperatures (65 *C), a property that also generally applies to fusions. This feature allows for easy and cost-effective recovery of target proteins because a 10-minute heat treatment at 65 *C removes up to 50% of contaminating plant proteins. LicKM fusion proteins can be tracked during purification by monitoring lichenase activity. The use of LicKM as a carrier molecule contributes additional advantages, including the potential for. enhanced expression, and incorporation of multiple polypeptides of interest (e.g., multiple vaccine determinants). Plants [0077] The teachings of the present invention are applicable to a wide variety of different plants. In general, any plants that are amendable to expression of introduced constructs as described herein are useful in accordance with the present invention. In many embodiments, it will be desirable to use young plants in order to improve the speed of protein/polypeptide production. As indicated here, in many embodiments, sprouted seedlings are utilized. As is known in the art, most sprouts are quick growing, edible plants produced from storage seeds. However, those of ordinary skill in the art will appreciate that the term "sprouted seedling" has been used herein in a more general context, to refer to young plants whether or not of a variety typically classified as "sprouts". Any plant that is grown long enough to have sufficient green biomass to allow introduction and/or expression of an expression construct as provided for herein (recognizing that the relevant time may vary depending on the mode of delivery and/or expression of the expression construct) can be considered a "sprouted seedling" herein. [00781 In many embodiments of the invention, edible plants are utilized (i.e., plants that are edible by - not toxic to - the subject to whom the protein or polypeptide is to be administered). [0079] In certain preferred embodiments, the plants of the invention may be plants of the Brassica or Arabidopsis species. Some suitable plants that are amendable to transformation and are edible as sprouted seedlings include alfalfa, mung bean, radish, wheat, mustard, spinach, carrot, beet, onion, garlic, celery, rhubarb, a leafy plant such as cabbage or lettuce, watercress or cress, herbs such as parsley, mint, or clovers, cauliflower, broccoli, soybean, lentils, edible flowers such as the sunflower etc.

WO 2007/095304 PCT/US2007/003942 20 [00801 A wide variety of plant species have been tested for their suitability in the practice of the present invention: A variety of different bean and other species including, for example, adzuki bean, alfalfa, barley, broccoli, bill jump pea, buckwheat, cabbage, cauliflower, clover, collard greens, fenugreek, flax, garbanzo bean, green pea, Japanese spinach, kale, kamut, kohlrabi, marrowfat pea, mung bean, mustard greens, pinto bean, radish, red clover, soy bean, speckled pea, sunflower, turnip, yellow trapper pea, and others were tested for their amenability to the production of heterologous proteins from viral vectors launched from an agrobacterial construct (introduced by agroinfiltration as described herein)(see, for example, Examples 5 and 8, Figure 9, etc.). The present invention provides the surprising result that certain pea varieties are particularly amenable to such manipulation. For example, according to the present invention, bill jump pea, green pea, marrowfat pea, speckled pea, and/or yellow trapper pea are particularly useful in accordance with this aspect of the invention. In certain embodiments, therefore, the present invention provides production of proteins or polypeptides (e.g., antigens, antibodies, and/or other proteins) in one or more of these plants using an agrobacterial vector that launches a viral construct (i.e., an RNA with characteristics of a plant virus) encoding the relevant protein or polypeptide of interest. In some embodiments, the RNA has characteristics of (and/or includes sequences of ) AlMV. In some embodiments, the RNA has characteristics of (and/or includes sequences of) TMV. [00811 It will be appreciated that, in one aspect, the present invention provides young plants (e.g., sprouted seedlings) that express a target protein or polypeptide of interest. In some embodiments, the young plants were grown from transgenic seeds; the present invention also provides seeds which can be generated and/or utilized for the methods described herein. Seeds transgenic for any gene of interest can be sprouted and optionally induced for production of a protein or polypeptide of interest. For example, seeds capable of expressing any gene of interest can be sprouted and induced through: i) virus infection, ii) agroinfiltration, or iii) bacteria that contain virus genome. Seeds capable of expressing a transgene for heavy or light chain of any monoclonal antibody can be sprouted and induced for production of full-length molecule through: i) virus infection, ii) agroinfiltration, or iii) inoculation with bacteria that contain virus genome. Seeds capable of expressing a transgene for one or more components of a complex molecule comprising multiple components such as sIgA can be sprouted and used for producing a fully functional molecule through: i) virus infection, ii) agroinfiltration, or iii) inoculation with bacteria that WO 2007/095304 PCT/US2007/003942 21 contain virus genome. Seeds from healthy non-transgenic plants can be sprouted and used for producing target sequences through: i) virus infection, ii) agroinfiltration, or iii) inoculation with bacteria that contain a virus genome. {00821 In some embodiments, the young plants were grown from seeds that were not transgenic. Typically, such young plants will harbor viral sequences that direct expression of the protein or polypeptide of interest. In some embodiments, the plants may also harbor agrobacterial sequences, optionally including sequences that "launched" the viral sequences. Systems for Expressing Proteins or Polypeptides in Plants [0083] According to the present invention, any of a variety of different systems can be used to express proteins or polypeptides in young plants (e.g., sprouted seedlings). In some embodiments, transgenic cell lines or seeds are generated, which are then sprouted and grown for a period of time so that a protein or polypeptide included in the transgenic sequences is produced in young plant tissues (e.g., in sprouted seedlings). Typical technologies for the production of transgenic plant cells and/or seeds include Agrobacterium tumefaciens mediated gene transfer and microprojectile bombardment or electroporation. [0084] In some embodiments, transient expression systems are utilized. Typical technologies for producing transient expression of proteins or polypeptides in plant tissues utilize plant viruses. Viral transformation is a more rapid and less costly methods of transforming embryos and sprouted seedlings that can be harvested without an experimental or generational lag prior to obtaining the desired product. On the other hand, viruses that are not attenuated can infect other plants, potentially causing environmental concerns. [0085] The present invention provides expression systems having advantages of viral expression systems (e.g., rapid expression, high levels of production) and of Agrobacterium transformation (e.g., controlled administration). In particular, as discussed in detail below, the present invention provides systems in which an agrobacterial construct (i.e., a construct that replicates in Agrobacterium and therefore can be delivered to plant cells by delivery of Agrobacterium) includes a plant promoter that, after being introduced into a plant, directs expression of viral sequences (e.g., including viral replication sequences) carrying a gene for a protein or polypeptide of interest. This system allows controlled, high level transient expression of proteins or polypeptides in plants.

WO 2007/095304 PCT/US2007/003942 22 [00861 A variety of different embodiments of expression systems, some of which produce transgenic plants and others of which provide for transient expression, are discussed in further detail individually below. For any of these techniques, the skilled artisan reading the present specification would appreciate how to adjust and optimize protocols for expression of proteins or polypeptides in young plant tissues (e.g., sprouted seedlings). Agrobacterium Transformation 10087] Agrobacterium is a representative genus of the gram-negative family Rhizobiaceae. This species is responsible for plant tumors such as crown gall and hairy root disease. In dedifferentiated plant tissue, which is characteristic of tumors, amino acid derivatives known as opines are produced by the Agrobacterium and catabolized by the plant The bacterial genes responsible for expression of opines are a convenient source of control elements for chimeric expression cassettes. According to the present invention, the Agrobacterium transformation system may be used to generate young plants (e.g., sprouted seedlings, including edible sprouted seedlings), which are merely harvested earlier than the mature plants. Agrobacterium transformation methods can easily be applied to regenerate young plants (e.g., sprouted seedlings) expressing pharmaceutical proteins. [0088] In general, transforming plants with Agrobacterium involves the transformation of plant cells grown in tissue culture by co-cultivation with an Agrobacterium tumefaciens carrying a plant/bacterial vector. The vector contains a gene encoding a pharmaceutical protein. The Agrobacterium transfers the vector to the plant host cell and is then eliminated using antibiotic treatment. Transformed plant cells expressing the pharmaceutical protein are selected, differentiated, and finally regenerated into complete plantlets (Hellens et al., Plant Molecular Biology (2000) 42(819-832); Pilon-Smits et al, Plant Physiolog. (Jan 1999) 119(l):123-132; Barfield and Pua Plant Cell Reports (1991)10(6/7):308-314); Riva et al., Journal ofBiotechnology (Dec 15, 1998) 1(3), each incorporated by reference herein. [0089] Agrobacterial expression vectors for use in the present invention include a gene (or expression cassette) encoding a pharmaceutical protein designed for operation in plants, with companion sequences upstream and downstream of the expression cassette. The companion sequences are generally of plasmid or viral origin and provide necessary characteristics to the vector to transfer DNA from bacteria to the desired plant host.

WO 2007/095304 PCT/US2007/003942 23 [00901 The basic bacterial/plant vector construct preferably provides a broad host range prokaryote replication origin; a prokaryote selectable marker. Suitable prokaryotic selectable markers include resistance toward antibiotics such as ampicillin or tetracycline. Other DNA sequences encoding additional functions that are well known in the art may also be present in the vector. [00911 Agrobacterium T-DNA sequences are required for Agrobacterium mediated transfer of DNA to the plant chromosome. The tumor-inducing genes of the T-DNA are typically removed during construction of an agrobacterial expression construct, and are replaced with sequences encoding the pharmaceutical protein or polypeptide. The T-DNA border sequences are retained because they initiate integration of the T-DNA region into the plant genome. If expression of the pharmaceutical protein is not readily amenable to detection, the bacterial/plant vector construct will also include a selectable marker gene suitable for determining if a plant cell has been transformed, e.g., the nptll kanamycin resistance gene. [0092] On the same or different bacterial/plant vector (Ti plasmid) are Ti sequences. Ti sequences include the virulence genes, which encode a set of proteins responsible for the excision, transfer and integration of the T-DNA into the plant genome (Schell, Science (1987) 237:1176-1183). Other sequences suitable for permitting integration of the heterologous sequence into the plant genome may also include transposon sequences, and the like, for homologous recombination. [00931 Certain constructs will include the expression cassette encoding the protein of interest. One, two, or more expression cassettes may be used in a given transformation. The recombinant expression cassette contains, in addition to the pharmaceutical protein encoding sequence, at least the following elements: a promoter region, plant 5' untranslated sequences, initiation codon (depending upon whether or not the expressed gene has its own), and transcription and translation termination sequences. In addition, transcription and translation terminators may be included in the expression cassettes or chimeric genes of the present invention. Signal secretion sequences that allow processing and translocation of the protein, as appropriate, may also be included in the expression cassette. [00941 A variety of promoters, signal sequences, and transcription and translation terminators are described, for example, in Lawton et al., Plant Mol. Biol (1987) 9:315-324 or U.S. Patent No. 5,888,789, incorporated herein by reference. In addition, structural genes for antibiotic resistance are commonly utilized as a selection factor (Fraley et al. Proc. Natl.

WO 2007/095304 PCT/US2007/003942 24 Acad. Sci., USA (1983) 80:4803-4807), incorporated herein by reference. Unique restriction enzyme sites at the 5'- and 3' ends of the cassette allow for easy insertion into a pre-existing vector. [0095] Other binary vector systems for Agrobacterium-mediated transformation, carrying at least one T-DNA border sequence are described in PCT/EP99/07414, incorporated herein by reference. Further discussion of Agrobacterium-mediated transformation is found in Gelvin, S.B., "Agrobacterium-Mediated Plant Transformation: the Biology behind the "Gene-Jockeying" Tool", Microbiology and Molecular Biology Reviews, 67(1): 16-37 (2003), incorporated herein by reference, and references therein, all of which are incorporated herein by reference; Lorence A, Verpoorte R., Gene transfer and expression in plants. Methods Mol Biol. (2004) 267:329-50, incorporated herein by reference. [00961 In certain embodiments of the invention bacteria other than Agrobacteria are used to introduce a nucleic acid sequence into a plant. See, e.g., Broothaerts W, et al., Gene transfer to plants by diverse species of bacteria, Nature (2005), 433(7026):629-633, which is incorporated herein by reference. [00971 Seeds are prepared from plants that have been infected with Agrobacteria (or other bacteria) such that the desired heterologous gene encoding a protein or polypeptide of interest is introduced. Such seeds are harvested, dried, cleaned, and tested for viability and for the presence and expression of a desired gene product. Once this has been determined, seed stock is stored under appropriate conditions of temperature, humidity, sanitation, and security to be used when necessary. Whole plants are then regenerated from cultured protoplasts, e.g., as described in Evans et al., Handbook ofPlant Cell Cultures, Vol. 1:MacMillan Publishing Co. New York, 1983); and Vasil I.R. (ed.), Cell Culture and Somatic Cell Genetics ofPlants, Acad. Press, Orlando, Vol. I, 1984, and Vol. III, 1986, incorporated herein by reference. 10098] In certain embodiments, the plants are not regenerated into adult plants. For example, in some embodiments, plants are regenerated only to the sprouted seedling stage. In other embodiments, whole plants are regenerated to produce seed stocks and young plants (e.g., sprouted seedlings) for use in accordance with the present invention are generated from the seeds of the seed stock. [0099] All plants from which protoplasts can be isolated and cultured to give whole, regenerated plants can be transformed by Agrobacteria according to the present invention so WO 2007/095304 PCT/US2007/003942 25 that whole plants are recovered that contain a transferred gene encoding a protein or polypeptide of interest. It is known that practically all plants can be regenerated from cultured cells or tissues, including, but not limited to, all major species of plants that produce edible sprouts. Some suitable plants include alfalfa, mung bean, radish, wheat, mustard, spinach, carrot, beet, onion, garlic, celery, rhubarb, a leafy plant such as cabbage or lettuce, watercress or cress, herbs such as parsley, mint, or clovers, cauliflower, broccoli, soybean, lentils, edible flowers such as the sunflower etc. [001001 Means for regeneration of plants from transformed cells may vary from one species of plants to the next. However, those skilled in the art will appreciate that generally a suspension of transformed protoplants containing copies of the heterologous gene is first provided. Callus tissue is formed and shoots may be induced from callus and subsequently rooted. Alternatively, embryo formation can be induced from the protoplast suspension. These embryos germinate as natural embryos to form plants. Steeping the seed in water or spraying the seed with water to increase the moisture content of the seed to between 35-45% initiates germination. For germination to proceed, the seeds are typically maintained in air saturated with water under controlled temperature and airflow conditions. The culture media will generally contain various amino acids and hormones, such as auxin and cytokinins. It is also advantageous to add glutamic acid and proline to the medium, especially for such species as alfalfa. Shoots and roots normally develop simultaneously. Efficient regeneration will depend on the medium, the genotype, and the history of the culture. If these three variables are controlled, then regeneration is fuly reproducible and repeatable. [00101] Mature plants, grown from the transformed plant cells, are selfed, and non segregating, homozygous transgenic plants are identified. The inbred plant produces seeds containing the transferred gene encoding a protein or polypeptide of interest. These seeds can be germinated and grown to the young plant (e.g., sprouted seedling) stage to produce the protein or polypeptide of interest. [001021 In related embodiments, transgenic seeds (carrying the transferred gene encoding a protein or polypeptide of interest, typically integrated into the genome) may be formed into seed products and sold with instructions on how to grow young plants to an appropriate stage (e.g., to the sprouted seedling stage) for harvesting and/or or administration or formulation as described herein. In other related embodiments, hybrids or WO 2007/095304 PCT/US2007/003942 26 novel varieties embodying the desired traits (i.e., the transferred gene encoding a protein or polypeptide of interest) are developed from inbred transgenic plants. Direct Integration [001031 Direct integration of DNA fragments into the genome of plant cells by microprojectile bombardment or electroporation may also be used to introduce expression constructs encoding proteins or polypeptides of interest into plant tissues according to the present invention (see, e.g., Kikkert, J.R. Humiston et al., In Vitro Cellular & Developmental Biology. Plant: Journal of the Tissue Culture Association. (Jan/Feb 1999) 35 (1):43-50; Bates, G.W. Florida State University, Tallahassee, FL. Molecular Biotechnology (Oct 1994) 2(2):135-145). More particularly, vectors containing a gene encoding a protein or polypeptide of interest can be introduced into plant cells by a variety of techniques. As described above, the vectors may include selectable markers for use in plant cells. The vectors may also include sequences that allow their selection and propagation in a secondary host, such as sequences containing an origin of replication and selectable marker. Typically, secondary hosts include bacteria and yeast. In one preferred embodiment, the secondary host is Escherichia coli, the origin of replication is a colE 1-type origin of replication, and the selectable marker is a gene encoding ampicillin resistance. Such sequences are well known in the art and are commercially available (e.g., Clontech, Palo Alto, CA or Stratagene, La Jolla, CA). [00104] The vectors of the present invention may also be modified to intermediate plant transformation plasmids that contain a region of homology to an Agrobacterium tumefaciens vector, a T-DNA border region from Agrobacterium tumefaciens, and chimeric genes or expression cassettes described above. Further vectors may include a disarmed plant tumor inducing plasmid of Agrobacterium tumefaciens. [00105] According to the present embodiment, direct transformation of the vectors invention involves microinjecting the vectors directly into plant cells by the use of micropipettes to mechanically transfer the recombinant DNA (see, e.g., Crossway, Mol. Gen. Genet., 202:179-185, 1985, incorporated herein by reference). The genetic material may also be transferred into the plant cell by using polyethylene glycols (see, e.g., Krens et al., Nature (1982) 296:72-74). Another method of introducing nucleic acid segments is high velocity ballistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surface (see, e.g., Klein et al., Nature (1987) 3 27:70- WO 2007/095304 PCT/US2007/003942 27 73; Knudsen and Muller Planta (1991) 185:330-336)). Yet another method of introduction is fusion of protoplasts with other entities, either minicells; cells, lysosomes, or other fusible lipid-surfaced bodies (see, e.g., Fraley et al., Proc. Nati. Acad Sci. USA (1982) 79:1859 1863). Vectors of the invention may also be introduced into plant cells by electroporation (see, e.g., Fromm et al. Proc. Natl. Acad. Sci. USA (1985) 82:5824). According to this technique, plant protoplasts are electroporated in the presence of plasmids containing the gene construct. Electrical impulses of high field strength reversibly permeabilize biomembranes allowing the introduction of the pasmids. Electroporated plant protoplasts reform the cell wall divide and form plant callus, which can be regenerated to form the sprouted seedlings of the invention. Those skilled in the art would appreciate how to utilize these methods to transform plants cells that can be used to generate edible sprouted seedlings. Viral Transformation [00106] According to the present invention, plant virus vectors are used to infect and produce foreign protein in seeds, embryos, sprouted seedlings. In this regard infection includes any method of introducing a viral genome, or portion thereof, into a cell, including, but not limited to, the natural infectious process of a virus, abrasion, inoculation, etc. The term includes introducing a genomic RNA transcript, or a cDNA copy thereof, into a cell. The viral genome need not be a complete genome but will typically contain sufficient sequences to allow replication. The genome may encode a viral replicase and may contain any cis-acting nucleic acid elements necessary for replication. Expression of high levels of foreign genes encoding short peptides as well as large complex proteins (e.g., by tobamoviral vectors) is described, for example, by McCormick et al. (Proc. Nal. Acad Sci. USA (1999) 96:703-708; Kumagai et al. (Gene (2000) 245:169-174 and Verch et al. (J Immunol. Methods (1998) 220, 69-75, each incorporated herein by reference). Thus, plant virus vectors have a demonstrated ability to express short peptides as well as large complex proteins. [00107] In certain embodiments, young plants (e.g., sprouts) which express pharmaceutical proteins such as insulin, GAD, and IA-2 associated with type 1 diabetes, are generated utilizing a host/virus system. Young plants produced by viral infection provide a source of protein or polypeptide of interest that has already been demonstrated to be safe. For example, sprouts are free of contamination with animal pathogens. Unlike, for example, WO 2007/095304 PCT/US2007/003942 28 tobacco, proteins from an edible sprout could at least in theory be used in oral applications -withoutpurification, thus significantly reducing costs. [00108] In addition, a virus/young plant (e.g., sprout) system also offers a much simpler, less expensive route for scale-up and manufacturing, since the relevant genes (encoding the protein or polypeptide of interest) are introduced into the virus, which can be grown up to a commercial scale within a few days. In contrast, transgenic plants can require up to 5-7 years before sufficient seeds or plant material are available for large-scale trials or commercialization. [001091 According to the present invention, plant RNA viruses have certain advantages, which make them attractive as vectors for foreign protein expression. The molecular biology and pathology of a number of plant RNA viruses are well characterized and there is considerable knowledge of virus biology, genetics, and regulatory sequences. Most plant RNA viruses have small genomes and infectious cDNA clones are available to facilitate genetic manipulation. Once the infectious virus material enters the susceptible host cell, it replicates to high levels and spreads rapidly throughout the entire plant (one to ten days post inoculation). Virus particles are easily and economically recovered from infected tissue. Viruses have a wide host range, enabling the use of a single construct for infection of several susceptible species. These characteristics are easily transferable to sprouts. [001101 Figure 1 illustrates several different strategies for expressing foreign genes using plant viruses. Foreign sequences can be expressed by replacing one of the viral genes with desired sequence, by inserting foreign sequences into the virus genome at an appropriate position, or by fusing foreign peptides to the structural proteins of a virus. Moreover, any of these approaches can be combined to express foreign sequences by trans complementation of vital functions of a virus. A number of different strategies exist as tools to express foreign sequences in virus-infected plants using tobacco mosaic virus (TMV), alfalfa mosaic virus (AlMV), and chimeras thereof. [00111] The genome of AlMV is a representative of the Bromoviridae family of viruses and consists of three genomic RNAs (RNAsl-3) and subgenomic RNA (RNA4) (Figure 2). Genomic RNAsl and 2 encode virus replicase proteins P1 and 2, respectively. Genomic RNA3 encodes the cell-to-cell movement protein P3 and the coat protein (CP). The CP is translated from subgenomic RNA4, which is synthesized from genomic RNA3, and is required to start the infection. Studies have demonstrated the involvement of the CP in multiple functions, including genome activation, replication, RNA stability, symptom WO 2007/095304 PCT/US2007/003942 29 formation, and RNA encapsidation (see e.g., Bol et al., Virology (1971) 46: 73-85; Van Der Vossen et al., Virology (1994) 202: 891-903; Yusibov et al., Virology 208: 405-407; Yusibov et al., Virology (1998) 242: 1-5; Bol et al., (Review, 100 refs.). J. Gen. Virol. (1999) 80: 1089-1102; De Graaff, Virology (1995) 208: 583-589; Jaspars et al., Adv. Virus Res (1974). 19, 37-149; Loesch-Fries, Virology (1985)146: 177-187; Neeleman et al., Virology (1991) 181: 687-693; Neeleman et al., Virology (1993) 196: 883-887; Van Der Kuyl et al., Virology (1991) 183: 731-738; Van Der Kuyl et al., Virology (1991) 185: 496 499). [001121 Encapsidation of viral particles is essential for long distance movement of virus from inoculated to un-inoculated parts of the seed, embryo, or young plant (e.g., sprouted seedling) and for systemic infection. According to the present invention, inoculation can occur at any stage of plant development. In embryos and sprouts, spread of the inoculated virus should be very rapid. Virions of AIMV are encapsidated by a unique CP (24 kD), forming more than one type of particle. The size (30- to 60-nm in length and 18 nm in diameter) and shape (spherical, ellipsoidal, or bacilliform) of the particle depends on the size of the encapsidated RNA. Upon assembly, the N-terminus of the AIMV CP is thought to be located on the surface of the virus particles and does not appear to interfere with virus assembly (Bol et al., Virology (1971) 6: 73-85). Additionally, the AIMV CP with an additional 38-amino acid peptide at its N-terminus forms particles in vitro and retains biological activity (Yusibov et al., J. Gen. Virol. (1995) 77: 567-573). [00113] AlMV has a wide host range, which includes a number of agriculturally valuable crop plants, including plant seeds, embryos, and sprouts. Together, these characteristics make the AIMV CP an excellent candidate as a carrier molecule and A1MV an attractive candidate vector for the expression of foreign sequences in the plant at the sprout stage of development. Moreover, upon expression from a heterologous vector such as TMV, the AIMV CP encapsidates TMV genome without interfering with virus infectivity (Yusibov et al., Proc. Natl. Acad. Sci. USA (1997) 94: 5784-5788, incorporated herein by reference). This allows the use of TMV as a carrier virus for A1MV CP fused to foreign sequences. [00114] TMV, the prototype of the tobamoviruses, has a genome consisting of a single plus-sense RNA encapsidated with a 17.0 kD CP, which results in rod-shaped particles (300 nm in length) (Figure 2). The CP is the only structural protein of TMV and is required for encapsidation and long distance movement of the virus in an infected host (Saito WO 2007/095304 PCT/US2007/003942 30 et al., Virology (1990) 176: 329-336). The 183 and 126 kD proteins are translated from genomic RNA and are required- for virus replication (Ishikawa et al., Nucleic Acids Res. (1986) 14: 8291-8308). The 30 kD protein is the cell-to-cell movement protein of virus (Meshi et al., EMBO J (1987) 6: 2557-2563). Movement and coat proteins are translated from subgenomic mRNAs (Hunter et al., Nature (1976) 260: 759-760; Bruening et al., Virology (1976) 71: 498-517; Beachy et al., Virology (1976) 73: 498-507, each incorporated herein by reference). [00115] Schematic representation of AlMV and TMV genomes are shown in Figure2. RNAsi and 2 of A1MV encode replicase proteins P1 and P2, respectively; genomic RNA3 encodes cell-to-cell movement protein P3 and the viral coat protein (CP). The CP is translated from subgenomic RNA4 synthesized from genomic RNA3. The 126 kD and 183 kD proteins of TMV are required for replication; the 30 kD protein is the viral cell-to-cell movement protein; and the 17 kD protein is the CP of virus. The CP and the 30 kD protein are translated from subgenomic RNAs. Arrows indicate position of subgenomic promoters. Flower Transformation [00116] Other methods that may be utilized to introduce a gene encoding a protein or polypeptide of interest into plant cells include transforming the flower of the plant. Transformation of Arabidopsis thaliana can be achieved by dipping the plant flowers into a solution of Agrobacterium tumefaciens (Curtis and Nam, Transgenic Research (Aug 2001) 10 4:363-371; Qing et al., Molecular Breeding: New Strategies in Plant Improvement (Feb 2000). (1):67-72). Transformed plants are formed in the population of seeds generated by the "dipped" plants. At a specific point during flower development, a pore exists in the ovary wall through which Agrobacterium lumefaciens gains access to the interior of the ovary. Once inside the ovary, the Agrobacterium tumefaciens proliferates and transforms individual ovules (Desfeux et al., Plant Physiology (July 2000) 123(3):895-904). The transformed ovules follow the typical pathway of seed formation within the ovary. Agrobacterium-Mediated Transient Expression [00117] As indicated herein, in many embodiments of the present invention, systems for rapid (e.g., transient) expression of proteins or polypeptides in plants are desirable. Among other things, the present invention provides a powerful system for achieving such rapid expression in plants (particularly in young plants, e.g., sprouted seedlings) that utilizes WO 2007/095304 PCT/US2007/003942 31 an agrobacterial construct to deliver a viral expression system encoding the protein or polypeptide of interest. 1001181 Specifically, according to the present invention, a "launch vector" is prepared that contains agrobacterial sequences including replication sequences and also contains plant viral sequences (including self-replication sequences) that carry a gene encoding the protein or polypeptide of interest The launch vector is introduced into plant tissue, preferably by agroinfiltration, which allows substantially systemic delivery. For transient transformation, non-integrated T-DNA copies of the launch vector remain transiently present in the nucleous and are transcribed leading to the expression of the carrying genes (Kapila et al., 1997). Agrobacterium-mediated transient expression, differently from viral vectors, cannot lead to the systemic spreading of the expression of the gene of interest. One advantage of this system is the possibility to clone genes larger than 2kb to generate constructs that would be impossible to obtain with viral vectors (Voinnet et al., 2003). Furthermore, using such technique, it is possible to transform the plant with more than one transgene, such that multimeric proteins (e.g., antibodies subunits of complexed proteins) can be expressed and assembled. Furthermore, the possibility of co-expression of multiple transgenes by means of co-infiltration with different Agrobacterium can be taken advantage of, either by separate infiltration or using mixed cultures. [00119] In certain embodiments, the launch vector includes sequences that allow for selection (or at least detection) in Agrobacteria and also for selection/detection in infiltrated tissues. Furthermore, the launch vector typically includes sequences that are transcribed in the plant to yield viral RNA production, followed by generation of viral proteins. Furthermore, production of viral proteins and viral RNA yields rapid production of multiple copies of RNA encoding the pharmaceutically active protein of interest. Such production results in rapid protein production of the target of interest in a relatively short period of time. Thus, a highly efficient system for protein production can be generated. [001201 The agroinfiltration technique utilizing viral expression vectors can be used to produce limited quantity of protein of interest in order to verify the expression levels before deciding if it is worth generating transgenic plants. Alternatively or additionally, the agroinfiltration technique utilizing viral expression vectors is useful for rapid generation of plants capable of producing huge amounts of protein as a primary production platform. Thus, this transient expression system can be used on industrial scale.

WO 2007/095304 PCT/US2007/003942 32 [00121] Further provided are any of a variety of different Agrobacterial plasmids, binary plasmids; or derivatives thereof such as pBIV, pBI1221, pGreen, etc., which can be used in these and other aspects of the invention. Numerous suitable vectors are known in the art and can be directed and/or modified according to methods known in the art, or those described herein so as to utilize in the methods described provided herein. [00122] Figure 18 presents a schematic diagram of a particular exemplary launch vector, pBID4. This vector contains the 35S promoter of cauliflower mosaic virus (a DNA plant virus) that drives initial transcription of the recombinant viral genome following introduction into plants, and the nos terminator, the transcriptional terminator of Agrobacterium nopaline sunthase. The vector further contains sequences of the tobacco mosaic virus genome including genes for virus replication (126/183K) and cell-t-cell movement (MP). The vector further contains a gene encoding a polypeptide of interest, inserted into a unique cloning site within the tobacco mosaic virus genome sequences and under the transcriptional control of the coat protein subgenomic mRNA promoter. Because this "target gene" (i.e., gene encoding a protein or polypeptide of interest) replaces coding sequences for the TMV coat protein, the resultant viral vector is naked self-replicating RNA that is less subject to recombination than CP-contaiing vectors, and that cannot effectively spread and survive in the environment. Left and right border sequences (LB and RB) delimit the region of the launch vector that is transferred into plant cells following infiltration of plants with recombinant Agrobacterium carrying the vector. Upon introduction of agrobacteria carrying this vector into plant tissue (typically by agroinfiltration but alternatively by injection or other means), multiple single-stranded DNA (ssDNA) copies of sequence between LB and RB are generated and released in a matter of minutes. These introduced sequences are then amplified by viral replication. Translation of the target gene results in accumulation of large amounts of target protein or polypeptide in a short period of time. [00123] In some embodiments of the invention, Agrobacterium-mediated transient expression produces up to about 5 g or more of target protein per kg of plant tissue. For example, in some embodiments, up to about 4, 3, 2, 1, or 0.5 g of target protein is produced per kg of plant tissue. In some embodiments, at least about 20-500 mg, or about 50-500 of target protein, or about 50-200, or about 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, or about 200, 250, 300, 350, 400, 450, 500, 550, 600, 650 700, 750, 800, WO 2007/095304 PCT/US2007/003942 33 850, 900, 950, 1000, 1500, 1750, 2000, 2500, 3000 mg or more of protein per kg of plant tissue is produced. [00124] In some embodiments of the invention, these expression levels are achieved within about 6, 5, 4, 3, or 2 weeks from infiltration. In some embodiments, these expression levels are achieved within about 10, 7, 5, 4, 3, 2 days, or even I day, from introduction of the expression construct. Thus, the time from introduction (e.g., infiltration) to harvest is typically less than about 2 weeks, 10 days, I week or less. Furthermore, one very attractive aspect of this embodiment of the invention is that it allows production of protein within about 8 weeks or less from the selection of amino acid sequence (even including time for "preliminary" expression studies). Also, each batch of protein can typically be produced within about 8 weeks, 6, weeks, 5 weeks, or less. Those of ordinary skill in the art will appreciate that these numbers may vary somewhat depending on the type of plant used. Most sprouts, including peas, will fall within the numbers given. Nicotiana benthamiana, however, may be grown longer, particularly prior to infiltration, as they are slower growing (from a much smaller seed). Other expected adjustments will be clear to those of ordinary skill in the art based on biology of the particular plants utilized. [00125] The present inventors have used a launch vector system to produce a variety of target proteins and polypeptides in a variety of different young plants. The inventors have surprisingly found that certain pea varieties including for example, marrowfat pea, bill jump pea, yellow trapper pea, speckled pea, and green pea are particularly useful in the practice of this aspect of the invention (see, for example, Example 7). [00126] The inventors have also found that various Nicotiana plants are particularly useful in the practice of this aspect of the invention, including in particular Nicotiana benthamiana. It will be understood by those of ordinary skill in the art that Nicotiana plants are generally not considered to be "sprouts". Nonetheless, the present invention teaches that young Nicotiana plants (particularly young Nicotiana benthamiana plants) are useful in the practice of the invention. In general, in the practice of this embodiment of the invention, Nicotiana benthamiana plants are grown for a time sufficient to allow development of an appropriate amount of biomass prior to infiltration (i.e., to delivery of agrobacteria containing the launch vector). Typically, the plants are grown for a period of more than about 3 weeks, more typically more than about 4 weeks, or between about 5-6 weeks to accumulate biomass prior to infiltration.

WO 2007/095304 PCT/US2007/003942 34 [00127] The present inventors have further surprisingly found that, although both TMV and AlMV sequences can prove effective in such launch vector constructs, in some embodiments, AlMV sequences are particularly efficient at ensuring high level production of delivered protein or polypeptides. [00128] Thus, in certain particular embodiments of the present invention, proteins or polypeptides of interest are produced in young pea plants or young Nicotania plants (e.g., Nicotiana benthamiana) from a launch vector that directs production of AlMV sequences carrying the gene of interest. Expression Constructs [001291 Many features of expression constructs useful in accordance with the present invention will be specific to the particular expression system used, as discussed above. However, certain aspects that may be applicable across different expression systems are discussed in further detail here. [001301 To give but one example, in many embodiments of the present invention, it will be desirable that expression of the protein or polypeptide (or nucleic acid) of interest be inducible. In many such embodiments, production of an RNA encoding the protein or polypeptide of interest (and/or production of an antisense RNA) is under the control of an inducible (e.g. exogenously inducible) promoter. Exogenously inducible promoters are caused to increase or decrease expression of a transcript in response to an external, rather than an internal stimulus. A number of environmental factors can act as such an external stimulus. In certain embodiments of the invention,.transcription is controlled by a heat inducible promoter, such as a heat-shock promoter. [00131] Externally inducible promoters may be particularly useful in the context of controlled, regulatable growth settings. For example, using a heat-shock promoter the temperature of a contained environment may simply be raised to induce expression of the relevant transcript. In will be appreciated, of course, that a heat inducible promoter could never be used in the outdoors because the outdoor temperature cannot be controlled. The promoter would be turned on any time the outdoor temperature rose above a certain level. Similarly, the promoter would be turned off every time the outdoor temperature dropped. Such temperature shifts could occur in a single day, for example, turning expression on in the daytime and off at night. A heat inducible promoter, such as those described herein, would likely not even be practical for use in a greenhouse, which is susceptible to climatic WO 2007/095304 PCT/US2007/003942 35 shifts to almost the same degree as the outdoors. Growth of genetically engineered plants in a greenhouse is quite costly. In contrast, in the present system, every variable can be controlled so that the maximum amount of expression can be achieved with every harvest. [001321 Other externally-inducible promoters than can be utilized in accordance with the present invention include light inducible promoters. Light-inducible promoters can be maintained as constitutive promoters if the light in the contained regulatable environment is always on. Alternatively, expression of the relevant transcript can be turned on at a particular time during development by simply turning on the light. [001331 In yet other embodiments, a chemically inducible promoter is used to induce expression of the relevant transcript. According to these embodiments, the chemical could simply be misted or sprayed onto a seed, embryo, or young plant (e.g., seedling) to induce expression of the relevant transcript. Spraying and misting can be precisely controlled and directed onto a paricular seed, embryo, or young plant (e.g., seedling) as desired. A contained environment is devoid of wind or air currents, which could disperse the chemical away from the intended recipient, so that the chemical stays on the recipient for which it was intended. Growth Environments [00134] One aspect of the present invention is the production of proteins or polypeptides (and/or nucleic acids) in plants under controlled, regulated growth conditions. According to the present invention, one attractive feature associated with producing proteins or polypeptides in young plants (e.g., sprouted seedlings) is that reduced growth times are required than would be utilized if the same plant type were grown to adulthood. Furthermore, in many instances, smaller spaces can be utilized than would be required if plants were grown to their full adult size. In general, growing plants that express pharmaceutical proteins or polypeptides in a controlled, regulatable environment provides a pharmaceutical product faster (because the plants are harvested younger) and with less effort, risk, and regulatory considerations than growing genetically engineered plants. A contained, regulatable environment used in the present invention reduces or eliminates the risk of cross-pollinating plants in the nature. [00135] In many embodiments of the invention, proteins or polypeptides are expressed in plants grown in an enclosed system. Such a system avoids risk of environmental contamination and also provides a regulatable, reproducible environment WO 2007/095304 PCT/US2007/003942 36 capable of achieving repeated comparable results. Furthermore, such a system allows controlled induction of proteinor polypeptide expression where desired, for example through the use of an inducible promoter or other regulatable feature as described herein. [00136] In certain embodiments of the present invention, plants are grown in a contained, regulatable environment. In some embodiments, the contained, regulatable environment is a housing unit or room in which the seeds can be grown indoors. All environmental factors of the contained, regulatable environment may be controlled. Since sprouts do not require light to grow, and lighting can be expensive, in one particular embodiment, plants are grown (e.g., to the sprouted seedling stage) indoors in the absence of light. [001371 Other environmental factors that can be regulated in a contained, regulatable environment of the present invention include temperature, humidity, water, nutrients, gas (e.g., 02 or CO 2 content or air circulation), chemicals (small molecules such as sugars and sugar derivatives or hormones such as such as the phytohormones gibberellic or absisic acid, etc.) and the like. [00138] In many embodiments of the invention, plants are grown hydroponically. Hydroponic growth systems offer a number of advantages. For example, hydroponic growth systems often require less space than soil-based systems to grow the same number of plants. Nutrients and other agents can typically be flowed through a hydroponic system, making controlled growth easier to accomplish than in soil-based systems. Many aspects of hydroponic growth may be automated. Furthermore, harvesting of hydroponically grown plants is trivial. Plants can be harvested simply by being lifted from their growth solution. No cleansing is required at the time of harvest. Being able to harvest young plants (e.g., sprouted seedlings) directly from a hydroponic environment without washing or scrubbing minimizes breakage of the harvested material. Breakage and wilting of plants induces apoptosis. During apoptosis, certain proteolytic enzymes become active, which can degrade a pharmaceutical protein or polypeptide expressed in the sprouted seedling, resulting in decreased therapeutic activity of the protein. Apoptosis-induced proteolysis can significantly decrease the yield of protein from mature plants. Using the methods of the present invention, apoptosis is preferably never induced (i.e., apoptosis is avoided), for example because no harvesting takes place until the moment the proteins are extracted from the plant.

WO 2007/095304 PCT/US2007/003942 37 [001391 In certain embodiments of the present invention, plants (e.g., sprouted seedlings) are grown in trays that can be watered, sprayed, or misted at any time -during development. For example, the tray may be fitted with one or more watering, spraying, misting, and draining apparatus that can deliver and/or remove water, nutrients, chemicals etc. at specific time and at precise quantities during development of the sprouted seedling. For example, seeds require sufficient moisture to keep them damp. Excess moisture drains through holes in the trays into drains in the floor of the room. Preferably, drainage water is treated as appropriate for removal of harmful chemicals before discharge back into the environment. [001401 Another advantage of trays is that they can be contained within a very small space. Since often no light is required for young plants (e.g., sprouted seedlings) to grow, the trays containing seeds, embryos, or young plants (e.g., sprouted seedlings) may be tightly stacked vertically on top of one another, providing a large quantity of biomass per unit floor space in a housing facility constructed specifically for these purposes. In addition, the stacks of trays can be arranged in horizontal rows within the housing unit. Once the seedlings have grown to a stage appropriate for harvest (e.g., about two to fourteen days or longer depending on the type of plant, the protein or polypeptide being produced, etc) individual trays are moved into a processing facility, either manually or by automatic means, such as a conveyor belt. [001411 A variety of aspects of growth conditions and techniques applicable to the practice of the present invention will readily be apparent to those of ordinary skill in the art. For example, when an inducible expression system is utilized, the time at which expression is induced may desirably be selected to maximize expression of the protein or polypeptide or interest in the young plant by the time of harvest. Inducing expression in an embryo at a particular stage of growth (e.g., at a particular number of days after germination), may result in maximum production of the protein or polypeptide of interest at the time of harvest. For example, inducing expression from the promoter 4 days after germination may result in more protein synthesis than inducing expression from the promoter after 3 days or after 5 days. Those skilled in the art will appreciate that maximizing expression can be achieved by routine experimentation. In preferred embodiments, young plants, particularly sprouted seedlings, are harvested at about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 days after germination. In other embodiments, young plants, particularly Nicotania plants, are grown for several weeks after germination.

WO 2007/095304 PCT/US2007/003942 38 [00142] When a constitutive rather than an inducible expression system is utilized, young plants may be harvested at a certain time after introduction of encoding sequences. For example, if a sprouted seedling were virally transformed at an early stage of development (e.g., at the embryo stage), the sprouted seedlings may be harvested at a time when expression is at its maximum post-transformation, e.g., at about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 days post-transformation. It could also be that young plants (e.g., sprouts) develop one, two, three or more months post-transformation, depending on the germination of the seed. [001431 Generally, once expression of the pharmaceutical protein begins, the seeds, embryos, or young plants (e.g., sprouted seedlings) are allowed to grow until sufficient levels of the pharmaceutical protein or polypeptide of interest are expressed. In certain embodiments, sufficient levels are levels that would provide a therapeutic benefit to a patient if the harvested biomass were eaten raw. Alternatively, sufficient levels are levels from which the pharmaceutical protein or polypeptide can be concentrated or purified from the biomass and formulated into a pharmaceutical composition that provides a therapeutic benefit to a subject upon administration. [00144] In certain embodiments, once expression of the pharmaceutical protein is induced, growth is allowed to continue until the sprouted seedling stage, at which time the sprouted seedlings are harvested. In a particularly preferred embodiment, the sprouted seedlings are harvested live. Harvesting live sprouted seedlings has several advantages including minimal effort and breakage. [001451 Among other things, the present invention provides a unique system that in turns provides young plant biomass containing high levels of expressed protein or polypeptide (and/or nucleic acid) of interest. Whether consumed directly or processed into the form of a pharmaceutical composition, when young plants (e.g., sprouted seedlings) are grown in a contained, regulatable environment, the plant biomass and/or pharmaceutical composition derived from the biomass can be provided to a consumer at low cost. In addition, the fact that the conditions for growth of the young plants can be controlled makes the quality and purity of the product consistent. The contained, regulatable environment of the invention also obviates many safety regulations of the EPA that can prevent scientists from growing genetically engineered agricultural products out of doors. Protein/Polypeptide Preparations WO 2007/095304 PCT/US2007/003942 39 [001461 The present invention provides various preparations and formulations of proteins or polypeptides (and/or active nucleic acids) produced in young plants: [001471 In some embodiments of the invention, produced proteins or polypeptides are not isolated from plant tissue but rather are provided in the context of live young plants (e.g., sprouted seedlings). In some embodiments, where the plant is edible, plant tissue containing expressed protein or polypeptide is provided directly for consumption. Thus, the present invention provides edible young plant biomass (e.g., edible sprouted seedlings) containing expressed protein or polypeptide. [00148] Where edible young plants (e.g., sprouted seedlings) express sufficient levels of pharmaceutical proteins or polypeptides and are consumed live, in some embodiments absolutely no harvesting occurs before the sprouted seedlings are consumed. In this way, it is guaranteed that there is no harvest-induced proteolytic breakdown of the pharmaceutical protein before administration of the pharmaceutical protein to a patient in need of treatment. For example, young plants (e.g., sprouted seedlings) that are ready to be consumed can be delivered directly to a patient. Alternatively, genetically engineered seeds or embryos are delivered to a patient in need of treatment and grown to the sprouted seedling stage by the patient. In one preferred embodiment, a supply of genetically engineered sprouted seedlings is provided to a patient, or to a doctor who will be treating patients, so that a continual stock of sprouted seedlings expressing certain desirable pharmaceutical proteins may be cultivated. This may be particularly valuable for populations in developing countries, where expensive pharmaceuticals are not affordable or deliverable. The ease with which the sprouted seedlings of the invention can be grown makes the sprouted seedlings of the present invention particularly desirable for such developing populations. [001491 In some embodiments, plant biomass is processed prior to consumption or formulation, for example, by homogenizing, crushing, drying, or extracting. In some embodiments, the expressed protein or polypeptide is isolated or purified from the biomass and formulated into a pharmaceutical composition. [00150] For example, live young plants (e.g., sprouts) may be ground, crushed, or blended to produce a slurry of biomass, in a buffer containing protease inhibitors. Preferably the buffer is at about 4 "C. In certain embodiments, the biomass is air-dried, spray dried, frozen, or freeze-dried. As in mature plants, some of these methods, such as air drying, may result in a loss of activity of the pharmaceutical protein or polypeptide. However, because the plants utilized (e.g., sprouted seedlings) are very small and typically WO 2007/095304 PCT/US2007/003942 40 have a large surface area to volume ratio, this is much less likely to occur. Those skilled in the art will appreciate that many techniques for harvesting the biomass that minimize proteolysis of the pharmaceutical protein or polypeptide are available and could be applied to the present invention. Administration and Pharmaceutical Compositions [00151] The present invention provides young plants expressing a pharmaceutically active protein or polypeptide that maintains its pharmaceutical activity when administered to a host in need thereof. Preferred hosts include vertebrates, preferably mammals, more preferably humans. According to the present invention, the hosts include veterinary subjects such as bovines, ovines, canines, felines, etc. In preferred embodiments, an edible sprout is administered orally to a subject in a therapeutically effective amount. In other preferred embodiments, the pharmaceutically active protein is provided in a pharmaceutical preparation, as described herein. [001521 Pharmaceutical preparations of the present invention can be administered in a wide variety of ways to the host, such as, for example, orally enterally, nasally, parenterally, intramuscularly or intravenously, rectally, vaginally, topically, ocularly, pulmonarily, or by contact application. In a preferred embodiment, a pharmaceutical protein expressed in a young plant (e.g., a sprout) is administered to a host orally. In another preferred embodiment a pharmaceutically active protein expressed in a young plant (e.g., in a sprout) is extracted and/or purified, and used for the preparation of a pharmaceutical composition. Proteins are isolated and purified in accordance with conventional conditions and techniques known in the art. These include methods such as extraction, precipitation, chromatography, affinity chromatography, electrophoresis, and the like. [00153] Compositions of the present invention typically include an effective amount of a pharmaceutically active protein or polypeptide together with one or more organic or inorganic, liquid or solid, pharmaceutically suitable carrier materials. [00154] A pharmaceutically active protein produced according to the present invention may be employed in dosage forms such as tablets, capsules, troches, dispersions, suspensions, solutions, capsules, creams, ointments, aerosols, powder packets, liquid solutions, solvents, diluents, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid bindings as long as the biological activity of the protein is not destroyed by such dosage form).

WO 2007/095304 PCT/US2007/003942 41 [00155] Examples of materials that can serve as pharmaceutically acceptable carriers - - include, but are not limited to sugars such -as lactose, glucose and sucrose; starches such as corn starch and potato starch; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil; safflower oil; sesame oil; olive oil; corn oil and soybean oil; glycols; such a propylene glycol; esters such as ethyl oleate and ethyl laurate; agar; buffering agents such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol, and phosphate buffer solutions, as well as other non toxic compatible lubricants such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, coating agents, sweetening agents, flavoring agents, and perfuming agents, preservatives, and antioxidants can also be present in the composition, according to the judgment of the formulator (see also Remington 's Pharmaceutical Sciences, Fifteenth Edition, E.W. martin (Mack Publishing Co., Easton PA, 1975). For example, the protein may be provided as a pharmaceutical composition by means of conventional mixing granulating dragee-making, dissolving, lyophilizing, or similar processes. [00156] In certain embodiments it may be desirable to prolong the effect of a pharmaceutical preparation by slowing the absorption of the pharmaceutical protein or polypeptide that is subcutaneously or intramuscularly injected. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the protein or polypeptide then depends upon its rate of dissolution, which in turn, may depend upon size and form. [001571 Alternatively, delayed absorption of a parenterally administered protein is accomplished by dissolving or suspending the protein in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the protein in biodegradable polymers such as polylactide-polyglycolide. Depending upon the ratio of protein to polymer and the nature of the particular polymer employed, the rate of release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the protein in liposomes or microemulsions, which are compatible with body tissues. [00158] . Enterally administered protein or polypeptide preparations may be introduced in solid, semi-solid, suspension or emulsion form and may be compounded with any pharmaceutically acceptable carriers, such as water, suspending agents, and emulsifying WO 2007/095304 PCT/US2007/003942 42 agents. The proteins or polypeptides of the invention may also be administered by means of pumps or sustained-release forms, especially when administered as a preventive measure; so as to prevent the development of disease in a subject or to ameliorate or delay an already established disease. [001591 Proteins or polypeptides produced according to the present invention are particularly well suited for oral administration as pharmaceutical compositions. Harvested young plants (e.g., seedlings) may be administered live or may be processed in a variety of ways, e.g., air drying, freeze drying, extraction etc., depending on the properties of the desired protein or polypeptide product and the desired form of the final product. [001601 In certain embodiments, such compositions as described above are ingested orally alone or ingested together with food or feed or a beverage. Compositions for oral administration include sprouted seedlings; extractions of the young plants (e.g., sprouted seedlings), and proteins or polypeptides purified from young plants provided as dry powders, foodstuffs, aqueous or non-aqueous solvents, suspensions, or emulsions. [00161] Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oil, fish oil, and injectable organic esters. Aqueous carriers include water, water alcohol solutions, emulsions or suspensions, including saline and buffered medial parenteral vehicles including sodium chloride solution, Ringer's dextrose solution, dextrose plus sodium chloride solution, Ringer's solution containing lactose or fixed oils. [00162] Examples of dry powders include any young plant (e.g., sprouted seedling) biomass that has been dried, for example, freeze dried, air dried, or spray dried. For example, young plants may be air dried by placing them in a commercial air dryer at about 120 degrees Fahrenheit until the biomass contains less than 5% moisture by weight. The dried plants are stored for further processing as bulk solids or further processed by grinding to a desired mesh sized powder. Alternatively, freeze-drying may be used for products that are sensitive to air-drying. Products may be freeze'dried by placing them into a vacuum drier and dried frozen under a vacuum until the biomass contains less than about 5% moisture by weight. The dried material can be further processed as described herein. [00163] Herbal preparations are well known in the art. Herbal preparations that may be used to administer young plants of the present invention include liquid and solid herbal preparations. Some examples of herbal preparations include tinctures, extracts (e.g., aqueous extracts, alcohol extracts), decoctions, dried preparations (e.g., air-dried, spray dried, frozen, or freeze-dried), powders (e.g., lyophilized powder), and liquid. Herbal WO 2007/095304 PCT/US2007/003942 43 preparations can be provided in any standard delivery vehicle, such as a capsule, tablet, suppository, liquid dosage, etc. Those skilled in the art will appreciate the various formulations and modalities of delivery of herbal preparations that may be applied to the present invention. [001641 Those skilled in the art will appreciate that a particularly preferred method of obtaining the desired pharmaceutically active protein or polypeptide is by extraction. Fresh young plants (e.g., seedlings) may be extracted to remove the desired protein products from the residual biomass, thereby increasing the concentration and purity of the product. Young plants may also be extracted in a buffered solution. For example, the fresh harvested plants may be transferred into an amount of ice-cold water at a ratio of one to one by weight that has been buffered with, e.g., phosphate buffer. Protease inhibitors can also be added as required. Plant tissue can be disrupted by vigorous blending or grinding while suspended in the buffer solution and the extracted biomass removed by filtration or centrifugation. The protein product carried in solution can be further purified by additional steps or converted to a dry powder by freeze-drying or precipitation. [00165] Extraction can also be carried out by pressing. Live plants can be extracted by pressing in a press or by being crushed as they are passed through closely spaced rollers. The fluids expressed from the crushed plants are collected and processed according to methods well known in the art. Extraction by pressing allows the release of the products in a more concentrated form. However, the overall yield of the product may be lower than if the product were extracted in solution. [00166] The young plants (e.g., sprouted seedlings), extractions, powders, dried preparations and purified protein products, etc., can also be in encapsulated form with or without one or more excipients as noted above. Solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active pharmaceutical protein may be admixed with at least one inert diluent such as sucrose, lactose or starch. Such dosage forms may also comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may also comprise buffering agents. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a WO 2007/095304 PCT/US2007/003942 44 certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric-substances and waxes. [00167] In other embodiments, a young plant expressing a pharmaceutically active protein of the present invention or biomass of such a young plant is administered orally as medicinal food. Such edible compositions are consumed by eating raw, if in a solid form, or by drinking, if in liquid form. In a preferred embodiment, the plant material is directly ingested without a prior processing step or after minimal culinary preparation. For example, the pharmaceutically active protein or polypeptide is expressed in a sprout of which can be eaten directly. For example, the protein is expressed in an alfalfa sprout, mung bean sprout, or spinach or lettuce leaf sprout, a young pea plant, etc. In an alternative embodiment, the sprouted seedling biomass is processed and the material recovered after the processing step is ingested. [00168] Processing methods preferably used in the present invention are methods commonly used in the food or feed industry. The final products of such methods still include a substantial amount of the expressed pharmaceutically active protein or polypeptide and are preferably conveniently eaten or drunk. The final product may also be mixed with other food or feed forms, such as salts, carriers, favor enhancers, antibiotics, and the like, and consumed in solid, semi-solid, suspension, emulsion, or liquid form. In another preferred embodiment, such methods include a conservation step, such as, e.g., pasteurization, cooking, or addition of conservation and preservation agents. [00169] Any plant is used and processed in the present invention to produce edible or drinkable plant matter. The amount of pharmaceutically active protein in an edible or drinkable sprout preparation may be tested by methods standard in the art, e.g., gel electrophoresis, Elisa, or Western blot analysis, using an antibody specific for the protein. This determination can be used to standardize the amount of protein ingested. For example, the amount of therapeutically active protein in a sprout juice determined and regulated, for example, by mixing batches of product having different levels of protein so that the quantity of juice to be drunk to ingest a single dose can be standardized. Use of a contained, regulatable environment in accordance with the present invention, however, should minimize the need to carry out such standardization procedures. [001701 A pharmaceutically active protein or polypeptide produced in a young plant (e.g., in a sprouted seedling) and eaten by a host is absorbed by the digestive system. One advantage of the ingestion of a sprouted seedling or sprouted seedling preparation, WO 2007/095304 PCT/US2007/003942 45 particularly intact sprouts or sprout biomass that has been only minimally processed, is to provide encapsulation or sequestration of the protein in cells of the plant. Thus, the protein may receive at least some protection from digestion in the upper digestive tract before reaching the gut or intestine and a higher proportion of active would be available for uptake. [001711 Pharmaceutical compositions of the present invention can be administered therapeutically or prophylactically. In certain preferred embodiments, the compositions may be used to treat or prevent (e.g., to delay onset of) a disease. For example, any individual who suffers from a disease or who is at risk of developing a disease may be treated. It will be appreciated that an individual can be considered at risk for developing a disease without having been diagnosed with any symptoms of the disease. For example, if the individual has a particular genetic marker identified as being associated with increased risk for developing a particular disease, that individual will be considered at risk for developing the disease. Similarly, if members of an individual's family have been diagnosed with a particular disease, e.g., cancer, the individual may be considered to be at risk for developing that disease. [00172] Liquid dosage forms for oral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups, and elixirs. In addition to the proteins or polypeptides of interest, the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents. [00173] Compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compositions of this invention with suitable non irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active protein. [001741 Dosage forms for topical or transdermal administration of a pharmaceutical composition of this invention include ointments, pastes, creams, lotions, gels, powders, WO 2007/095304 PCT/US2007/003942 46 solutions, sprays, inhalants or patches. The active protein, or preparation thereof, is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required. Ophthalmic formulation, eardrops, and eye drops are also contemplated as being within the scope of this invention. Additionally, the present invention contemplates the use of transdermal patches, which have the added advantage of providing controlled delivery of a pharmaceutically active protein to the body. Such dosage forms can be made by suspending or dispensing the pharmaceutically active protein in the proper medium. Absorption enhancers can also be used to increase the flux of the pharmaceutically active protein across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the pharmaceutically active protein in a polymer matrix or gel. [00175] Compositions are administered in such amounts and for such time as is necessary to achieve the desired result. As described above, in certain embodiments of the present invention a "therapeutically effective amount" of a pharmaceutical composition is that amount effective for treating, attenuating, or preventing a disease in a host. Thus, the "amount effective to treat, attenuate, or prevent disease", as used herein, refers to a nontoxic but sufficient amount of the pharmaceutical composition to treat, attenuate, or prevent disease in any host. As but one example, the "therapeutically effective amount" can be an amount to treat, attenuate, or prevent diabetes. [00176] The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the stage of the disease, the particular pharmaceutical mixture, its mode of administration, and the like. Young plants (e.g., sprouted seedlings) of the invention and/or protein preparations thereof are preferably formulated in dosage unit form for ease of administration and uniformity of dosage. The expression "dosage unit form," as used herein, refers to a physically discrete unit of pharmaceutically active protein appropriate for the patient to be treated. It will be understood, however, that the total daily usage of the compositions of the present invention are preferably decided by an attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular patient or organism will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex of the patient, diet of the patient, pharmacokinetic condition of the patient, the time of administration, route of WO 2007/095304 PCT/US2007/003942 47 administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combinationor coincidental- with the specific compound employed; and like factors well known in the medical arts. [001771 It will also be appreciated that pharmaceutical compositions of the present invention can be employed in combination therapies, that is, the pharmaceutical compositions can be administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures. The particular combination of therapies (therapeutics or procedures) to employ in a combination regimen will take into account compatibility of the desired therapeutics and/or procedures and the desired therapeutic effect to be achieved. It will also be appreciated that the therapies employed may achieve a desired effect for the same disorder (for example, an inventive compound may be administered concurrently with another anti-cancer agent), or they may achieve different effects. Kits [00178] In still another aspect, the present invention also provides a pharmaceutical pack or kit including live young plants (e.g., sprouted seedlings) of the present invention or preparations, extracts, or pharmaceutical compositions containing the pharmaceutically active protein or polypeptide expressed by the young plants in one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of the invention. In certain embodiments, the pharmaceutical pack or kit includes an additional approved therapeutic agent for use as a combination therapy. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceutical products, which notice reflects approval by the agency of manufacture, use, or sale for human administration. [001791 The present invention involves the purification and affordable scaling up of the production of pharmaceutical proteins from young plants (e.g., sprouted seedlings) using any of a variety of plant expression systems, most preferably viral plant expression systems (that is, systems including a viral component). Kits are provided that include each protein in a diagnostic kit for genetic and immunologic diseases. In one preferred embodiment, the present invention provides kits having test samples of biological proteins and reagents for testing for the presence of antibodies in a patient's serum to those biological proteins. For example, the kit may provide IA-2 and GAD and reagents to test for the presence of excess WO 2007/095304 PCT/US2007/003942 48 amounts of antibodies to these proteins in a patient's serum, a clear indication of the presence or development of type 1 diabetes. [001801 The present invention can be extended to provide diagnostic reagents in the form of a kit. As but one non-limiting example, the proteins insulin, GAD, and IA-2, associated with the autoimmune reaction in diabetes, can be provided as oral formulations and administered to induce oral tolerance to these proteins. Alternatively, one or more therapeutic protein can be provided in an injectable formulation or vaccine for administration. According to preferred embodiments, pharmaceutical doses or instructions therefor are provided in the kit for administration to an individual diagnosed with a disease, e.g., a diabetic individual, or an individual at risk for developing a disease, e.g., type 1 diabetes. Equivalents [00181] The representative examples that follow are intended to help illustrate the invention, and are not intended to, nor should they be construed to, limit the scope of the invention. Indeed, various modifications of the invention and many further embodiments thereof, in addition to those shown and described herein, will become apparent to those skilled in the art from the full contents of this document, including the examples which follow and the references to the scientific and patent literature cited herein. It should further be appreciated that the contents of those cited references are incorporated herein by reference to help illustrate the state of the art. The following examples contain important additional information, exemplification and guidance, which can be adapted to the practice of this invention in its various embodiments and the equivalents thereof. Examples Example 1: Production of Pharmaceutical Proteins or Polypeptides in Transgenic Sprouts Prepared by Agrobacterium Transformation [001821 Seeds of plants are transformed by Agrobacterium are harvested, dried, cleaned, and tested for viability and presence of desired genetic material. Seed stock is stored under appropriate conditions until use. At the time of use, appropriate amounts of seeds are soaked in water containing an amount of surface sterilizing agent (e.g., Clorox) for 20 minutes to 4 hours. Seeds are spread onto a flat of trays, which contain provisions for WO 2007/095304 PCT/US2007/003942 49 sustenance of growth and drainage of water. Trays containing the seeds are put on racks in the contained, regulatable environment under-controlled temperature, lighting, access, air circulation, water supply, and drainage. Trays are misted with water from misters equipped with automatic timers for one to 30 minutes at intervals of 30 minutes to four hours, sufficient to keep seeds damp. Excess moisture drains through holes in the trays into drains in the floor of the room. [00183] Seeds are allowed to germinate and develop under controlled conditions. Seeds are incubated for about two to fourteen days before harvest and processing. At some point during the incubation process, from four hours to seven days prior to harvest, seeds are exposed to environmental conditions that cause the induction of an introduced or indigenous DNA promoter sequence that causes an increase in the synthesis of one or more desired proteins in the tissues of the sprouting seedling. A transient increase in the incubation temperature from about 30 *C to about 37 C to cause induction of a heat shock promoter. [001841 After incubation of the seedlings for two to fourteen days, the seedlings are harvested by moving the individual trays into a processing facility on a conveyor belt. The harvested seedlings are processed by extraction in phosphate buffered solution containing protease inhibitors. The seedlings are disrupted by vigorous blending or grinding while suspended in the buffer solution and the extracted biomass removed by centrifugation. Example 2: Production of Pharmaceutical Proteins or Polypeptides in Sprouted Seedlings Transiently Infected by a Plants Virus [00185] Seeds of desired plants are obtained from a contract of commercial grower as wild-type seeds. The seed stock is stored under appropriate conditions of temperature, humidity, sanitation, and security until use. At the time of use, appropriate amounts of seeds are soaked in water and incubated on trays as described above under controlled conditions. [001861 After incubation for two to fourteen days, the germinated seedlings are sprayed with a solution containing a virus harboring a transgene, and further or simultaneously treated with a material that causes mechanical abrasion of the plant leaf tissue. In this example, the leaves are abraded with a spray of air containing abrasive particles. The virus is allowed to systemically infect the plants for an appropriate period; from about one to about ten days and expression of the desired heterologous protein is monitored.

WO 2007/095304 PCT/US2007/003942 50 [001871 After infection of the seedlings for one to ten days, the seedlings are harvested as described in Example 1 above. Example 3: Expression of Diabetes Associated Proteins and Human Growth Hormone from Viral vectors (AvA4) in Nicotiana Benthamiana Plants [00188] Early onset Type 1 or juvenile diabetes is a disease that affects children, adolescents, and young adults. Beta islet cells of the pancreatic endocrine system produce insulin in response to the metabolic signal of high blood glucose. The underlying etiology of the disease is the attack and destruction of the beta islet cells by the body's own immune system. [001891 Individuals with type 1 diabetes produce antibodies against at least three proteins that are normally found in all individuals, i.e., insulin, glutamic acid decarboxylase (GAD), and the tyrosine-phosphatase-like protein IA-2 (Leslie et al., Diabetologia (1999) 42:30-14). Autoantibodies to the IA-2 and GAD proteins are found in 50 to 75% of type I diabetes patients prior to onset of the disease. In addition, the appearance of autoantibodies against these seemingly normal proteins occurs 7 to 8 years ahead of onset of the classical symptoms associated with type I diabetes. [00190] Autoantigens such as insulin, GAD and IA-2 are useful in inducing at-least a degree of oral tolerance to these proteins in susceptible individuals and prevent or reduce the damage to islet cells that results in the development of diabetes. Non-obese diabetic mice (NOD) spontaneously develop an autoimmune form of diabetes (Zahang, et al., Proc. Natl. Acad. Sci. USA (1991) 88:10252-10256). The gene encoding human insulin has been fused with the cholera toxin B subunit gene and the resulting construct expressed in transgenic potato plants. When these plants were fed to NOD mice, the animals showed a substantial reduction in pancreatic islet inflammation and a delay in the progression of diabetes (Arakawa et al., Nat. Biotechnol. (1998) 16:934-936). The GAD protein has also been expressed in potato plants. These transgenic potatoes, when fed to NOD mice, also either prevented or significantly delayed the onset of diabetes after 40 weeks (Ma et al., Nature Medicine (1997) 3:793-796). [001911 In this example, certain non-limiting conditions for expression and recovery of GAD and IA-2 from plants are described. The GAD and IA-2 proteins are purified using the His-tag method. Production of raw material and proteins takes place in two stages: 1) WO 2007/095304 PCT/US2007/003942 51 small scale (mg quantities) for preliminary studies in animals; and 2) medium scale (gram quantities for clinical trials. 100192] Testing stability and movement To conduct viral stability and movement tests, small quantities of each construct are synthesized. Each construct contains a T7 or SP6 RNA polymerase promoter fused to the exact 5' terminus of viral genomic RNA and a unique restriction site at the 3' end that is used to linearize the plasmid prior to in vitro transcription. The T7 or SP6 RNA polymerase then generates run-off transcripts, which are used to inoculate plants. Plants are inoculated mechanically at two-leaf stage, by gently rubbing the inoculum onto the leaf surface in the presence of an abrasive agent, such as carborundum powder (320-grit; Fisher, Pittsburgh, PA). Five to ten plants are inoculated per construct and 1-2 4g of each RNA transcript is used per inoculation. The plants are monitored for severity of symptoms, spread of virus throughout entire plant, and product recovery. At 10-15 days post infection (dpi) leaf samples from infected leaf samples are harvested to assess the presence of full-size recombinant IA-2 and GAD. A portion of the harvested material (10 leaves) is frozen in _80-C and retained as a seed inoculum for the subsequent production scale-up of selected constructs. The rest of the tissue is processed immediately. 1001931 At 15-20 days post infection (dpi) recombinant IA-2 and GAD are recovered. The procedure is optimized to recover optimum quantities of high purity product (90-95% purity). Once products with the expected sizes are recovered and serological identity (recognized by specific antibodies using Western blot and ELISA) determined, the stability of the constructs is tested by three passages on healthy plants. Problems with assembly, recovery or stability of recombinant virus with proteins in the size range employed are manage at the level of nucleotide sequence or amino acid sequence by changing the conditions of infection or by using an alternative host plant. [00194] Establishing seed-lot and procedures for medium scale production. When stage I is completed, a small quantity (100 ul) of in vitro synthesized transcripts of the recombinant constructs is prepared and used to inoculate 10 plants. Within 10-12 days after inoculation the leaves are harvested, tested for the presence of GAD or IA-2 by Western blot, and stored at _70*C as seed material. A portion of this material (3-4) is used to inoculate 150-200 plants (1-2 kg of fresh tissue). Fifteen to twenty days after inoculation, WO 2007/095304 PCT/US2007/003942 52 recombinant protein is recovered and used for functional studies. An average of 60 mg of product per batch is-expected. [001951 Plant inoculation and product recovery. In vitro transcripts of recombinant virus containing GAD and IA-2 are synthesized using T7 RNA polymerase and purified plasmid DNA. Transcripts are capped using the RNA cap structure analog m7G(5)ppp(5)G. For inoculation, a mixture of in vitro transcription products is applied to the leaves of the target host plants after abrading the leaf surface with carborundum and gently rubbing on the leaf surface to spread the inoculum and further abrade the surface. The purity and activity of the plant produced IA-I and GAD are tested. The antibody binding capacity of the plant produced antigens is tested by ELISA during and after purification of the proteins. [001961 Protein expression in Nicotiana benthamiana: To express full-length proteins in virus-infected plants, we used a functional complementation approach to express green fluorescent protein (GFP) from jellyfish in N. benthamiana plants (Fig. 4). During plant-to plant passages, the amount of Alfalfa mosaic virus (Av)/GFP in the infected tissue gradually decreased and after the third transfer, only Av/A4 was detectable. (This is an advantage from an environmental safety point of view.) Using this approach, we could express an average of 100 pg of GFP per gram fresh tissue. An important component of this system, Alfalfa mosaic virus CP, is unique in its ability to encapsidate the genomic RNAs of unrelated viruses into infectious particles in the infected host. This unique ability of Alfalfa mosaic virus CP is exploited to engineer hybrid vectors that specifically target selected crop species. [00197] Expression of recombinant GFP in Nicotiana benthamiana plants inoculated with Av/A4 and Av/A4GFP was analyzed by Western Blot (see Figure 3). Protein extracts from leaves infected systematically as described herein were separated by electrophoresis on a 12% SDS-polyacrylamide gel, transferred to a nitrocellulose membrane and reacted with protein-specific antibodies. Alfalfa mosaic virus CP-specific antibodies recognized the expected size protein (24.0 kD) in plants inoculated with Av/A4 or with the mixture of Av/A4 and Av/A4GFP. GFP-specific antibodies recognized protein only in extracts from plants inoculated with the mixture of Av/A4 and Av/A4GFP. GFP-specific antibodies did not react with any proteins in plants inoculated with only Av/A4. Neither Alfalfa mosaic virus CP- nor GFP-specific antibodies reacted with any protein in extracts from plants inoculated with Av/GFP only, suggesting the lack of systemic movement.

WO 2007/095304 PCT/US2007/003942 53 [00198] We have also engineered and expressed human growth hormone using this Av/A4 vector system. Nicotiana benthamiana plants were inoculated with in vitro transcripts and the plants monitored for production of hGH. No signal specific to the protein could be detected at 5 dpi (days post inoculation), although at 11 dpi we could detect a signal for hGH in the inoculated plants. Figure 4 is a Western Blot of hGH produced in N. benthamiana plants infected with in vitro transcripts of 125C/hGH. Samples were analyzed 24 hours post inoculation. I pg of purified hGH was loaded as standard. MWM is molecular weight marker. The arrow in Figure 4 points toward the hGH band on the blot detected by hGH-specific antibodies. Example 4: Expression ofAnthrax Associated Proteins and Human Growth Hormone in Transgenic Brassica Juncea Plants [001991 The virulence of anthrax is due to at least two major virulence factors. These factors are a polyglutamate capsule that helps protect the bacterium in the host and a three part circulating toxin. Anthrax toxin is encoded by a 184 kb plasmid named pXOI and consists of a receptor-binding protein named protective antigen (PA), and two enzymatically active proteins named edema factor and lethal factor (Bhatnagar and Batra. Crit. Rev. Mirobiol. (2001) 27(3):167-200). [00200] In this example, two inactivated anthrax toxin components, protective antigen (PA) and lethal factor (LF) are produced in the leaves of Brassica juncea at concentration of at least 0.1 mg/gm dry weight. We have optimized the codon usage of these genes for plants and changed the amino acid sequences to minimize toxicity for both toxin molecules. We propose to insert the synthesized DNA into vectors capable of regulated gene expression in Brassicajuncea. The PA gene was altered to delete phenylalanine residues at positions 314 and 315. The LF gene has an alanine substituted for a histidine at position 686 or position 690 (see, e.g., Singh et al., J. Biol. Chem. (1994) 269:29039-29046; Klimpel et al., Mol. Microbiol. (1994) 13: 1093-1097). [00201] -Transformation vector: The binary vector pGREENII 0229 (Hellens et al., Plant Molecular Biology (Apr 2000) 42(6):819-832) is used for plant transformation (see Figure 5). This plasmid includes the following components. 1) The pGREENII plasmid backbone includes sequences necessary for replication in Escherichia coli and Agrobacterium tumefaciens. 2) The Agrobacterium tumefaciens T-DNA left and right border (LB and RB) sequences are necessary for integration of all sequences between LB WO 2007/095304 PCT/US2007/003942 54 and RB into the plant genome. 3) The npt gene encoding kanamycin resistance for selection of Escherichia coli and Agrobacterium tumefacients tranformants. 4) The nos-bar gene, which encodes resistance to the herbicide Bialaphos (resistance to Bialophos is used to select transgenic plants. The nos-bar gene is transcribed from the Cauliflower mosaic virus (CAMV) 35S promoter with constitutive activity in plants, and transcription of the gene is terminated using the CaMV terminator. 5) Expression of vir genes PA and LF are driven either by the CAMV 35S promoter as shown in Figure 5, or by the HSP18.2 promoter (GenBank accession # X1 7295, locus At5g59720) for the Arabidopsis thaliana low molecular weight heat shock protein (Matsuhara et al., The Plant Journal:for Cell & Molecular Biolog (Apr 2000) 22(l):79-86). Transcriptional termination is mediated by the terminator of the nopaline synthase gene (nos). The 35S and HSP18.2 promoters where chosen for their differing activities. The 35S promoter is constitutively active in most plant tissues. In many cases the 35S promoter drives high-level expression of the protein of interest. By contrast the HSP18.2 promoter is nearly inactive unless the plants are challenged by heat shock. High-level expression of some proteins can only be achieved using an inducible promoter system. 1002021 Vector construction and plant transformation The vectors are constructed using DH5, a laboratory strain of Escherichia coli. The construction is analyzed by restriction endonuclease mapping and sequencing. After construction is confirmed the vector is used to transform Agrobacterium tumefaciens strain GV3 101, lacking a native Ti plasmid and suitable for transfer of the TDNA of binary vectors into plants. Brassicajuncea plants are transformed by introduction of GV3101 carrying the transformation vector into flowers by any available transformation method. [002031 Modifications introduced into PA and LF genes. The nucleotide sequences of both PA and LF are modified for expression in plants. The coding sequence of native PA is 2295 bp and native LF is 2430 bp. These sequences are modified as follows: 1) Mutations are introduced that render PA and LF inactive as toxins. Phe314 and Phe315 are deleted from PA and His686 and His690 are mutated to Ala. 2) Codon usage is optimized for expression in Brassicajuncea. Since the codon usage and GC/AT ratio of Brassicajuncea is neutral the changes introduced into PA and LF are not extensive. Four codons are changed in PA and seven in LF. 3) Unique restriction sites are added to the 5' and 3' ends of the genes for cloning into the plant expression vector. [4] A consensus sequence for translation initiation will be added (Joshi et al., Plant Molecular Biology. (Dec 1997) WO 2007/095304 PCT/US2007/003942 55 35(6):993-100 1). The restriction sites and optimized translation initiation site are illustrated --in-Figure 5. The 5' end shows the added XbaI-restriction site and'the consensus translation initiation site for plant genes, which includes the initiation codon followed by an Ala codon. The 3' end shows the added SacI restriction site. The modified PA and LF genes are chemically synthesized by Entelechon, Inc. (Regensburg, Germany). 100204] A second construction is also produced for PA and LF. The intention of the second construct is to optimize the accumulation for PA and LF by targeting and retaining the proteins in the endoplasmic reticulum 40 . Targeting and retention in the ER has the potential to produce high-level accumulation of a recombinant protein (Haseloff, et al., Proceedings ofthe National Academy ofSciences USA. (Mar 18, 1997) 94(6):2122-2127). To achieve this, an amino-terminal signal sequence and a carboxyl terminal ER retention sequence is added. The signal sequence includes 22 codons derived from the Arabidopsis thaliana chitinase gene (Haseloff, et al., supra). The ER retention sequence is the tetrapeptide HisAspGluLeu (Gomord et al, The Plant Journal: for Cell & Molecular Biology. (Feb 1997) 11(2):313-325). The signal sequence is added by PCR stitching using the synthetic genes produced by Entelechon as templates (Tomme et al., JBacteriol. (1995) 177:4356-4363). The ER retention sequence is added by PCR amplification of the PA and LF genes using a 3' primer into which the HisAspGluLeu coding sequence has been incorporated. Modified PA and LF sequences are cloned into 35S and HSP 18.2 expression vectors. Two modified version of each PA and LF (a total of 4) are cloned. In total, 8 different constructions are tested. [00205] Selection and analysis of plants expressing transgenes. After transformation of Brassicajuncea with Agrobacterium tumefaciens strain GV3 101 carrying the transformation construct the plants are allowed to progress through their normal developmental program. Within 25 days, mature seeds are produced, dried, and harvested. The seeds are sown in potting soil and seedling plants are grown for 15 days. The leaves of each plant are then sprayed with a 0.0058% (w/v) solution of Bialophos (FINALE, Famam, Inc., Phoenix, AZ). Sensitive, non-transgenic plants are typically killed within 5 to 7 days. Bialophos-resistant plants are evident by their green and healthy appearance. The putative transgenic plants are confirmed and analyzed using a series of protocols. Polymerase chain reaction using oligonucleotide primers specific for the construct are used to confirm the presence of the TDNA in putative transgenic plants. The presence of the TDNA is then be examined by blotting of genomic DNA using a specific DNA probe, the modified PA or LF WO 2007/095304 PCT/US2007/003942 56 genes. Finally, expression of the protein of interest is examined by SDS-PAGE followed by staining with Coomassie Blue or immunoblotting. The protocol for analysis of protein expression differs depending upon the construct used to produce the transgenic plant. Plants carrying 35S promoter constructions are analyzed directly since expression from this promoter is constitutive. Plants carrying the HSP1 8.2 promoter are heat shocked before analysis. The kinetics of recombinant protein expression might differ in different transgenic plants. Ultimately, the induction conditions are optimized for each using standard methods. However, for initial analysis it is possible to carry out a standardized heat shock protocol that is established for expression of other recombinant proteins in Brassicajuncea. [002061 Figure 6 shows an immunoblot of transgenic Brassicajuncea expressing human growth hormone (hGH) under control of the HSPI8.,2 promoter. Transgenic Brassicajuncea were grown in potting mix. As shown in Figure 6, a leaf weighing I to 3 grams fresh weight was detached from the plant and placed in a petri dish containing a filter paper moistened with water. The petri dish is covered and placed in a high humidity, 37 *C incubator for 1.5 hours. The petri dish containing the leaf was then removed from the incubator and placed for 5 hours in a 24 *C growth chamber under fluorescent lights at an intensity of 100 pmol photons m- 2 s1. The plant material was then harvested and analyzed by immunoblotting using a monoclonal antibody against hGH (Sigma Chemical Co., Product #G-8523). The lower band is the 16 kDa recombinant hGH. This band is not observed before heat shock. Lane 8 shows the results from a transgenic plant transformed with the vector alone. The higher molecular weight band is a non-specific reaction with the horseradish peroxidase-linked secondary antibody used to detect immune-complexes. PA is predicted to be approximately 88 kDa and LF 93 kDa. [002071 After an initial screen for anthrax toxin expression a more detailed analysis of expression is carried out. An ELISA method is used to quantitate the level of expression. Further analysis is carried out on subsequent plant generation. In order to avoid the need to select for transgenic plants in subsequent generations it is ultimately necessary to isolate transgenic lines that are non-segregating for the TDNA construct. This is accomplished by self-pollinating the primary transgenic plants, raising the secondary generation plants to maturity, and testing the tertiary generation for segregation of Bialophos resistance. Secondary generation individuals are identified that are non-segregating. Thereafter, progeny of non-segregating plants are bulked and used for analysis of production scale conditions (e.g., 1,600 Kg per month of dried biomass). For production scale the growth WO 2007/095304 PCT/US2007/003942 57 and induction conditions are optimized for plants grown as seedlings. At this point it is also desirable to characterize the insertion site and TDNA -copy number of elite lines and to characterize expression at the level of mRNA expression. Example 5: Expression of a GUS Reporter in Sprouts From an Agrobacterial Construct Containing Viral Sequences [00208] pBIl21 containing a GUS reporter gene was transformed into Agrobacterium tumefaciens LBA 4404. Bacterial cultures were grown overnight in YEB medium containing 50 gg/ml kanamycin, 20 sM acetosyringone and 10 mM MES pH 5.6. Overnight cultures were centrifuged, resuspended in MMA medium (MS salts,10 mM MES pH 5.6, 200 pM acetosyringone and 2% sucrose) at ODoo 2.0 and used for vacuum infiltration of sprouts. [00209] Seeds of various plants were imbibed in water for 24 hr at room temperature on a rocking platform, transferred into plastic containers with wet filter paper and incubated for 4 to 6 days (depending on plant species) under 12 hr daylight at 21 "C. 100210] After vacuum infiltration, sprouts were incubated for additional 48-60 hr under 12 hr daylight at 21 *C and the GUS activity was detected in situ using X-gluc histochernical substrate. The staining was performed overnight at 37 0 C and the plant samples were de-stained in ethanol. [002111 The system was tested using a wide variety of sprouts. See Figure 8A and 8B and Figure 9. Example 6: Expression of Diabetes Associated Proteins and Human Growth Hormone from an Agrobacterial Construct Containing Viral Sequences [00212] We created a TMV-based vector in agrobacterial vector: D4-hGH or D4 GFP. For this, we first had to create multiple cloning sites in pBI121. pBI121-Xbal BamHl- Sall -Pacl-BsiWI-Stul-Xhol-Spel- Kpnl-Sac1-pBI121. Using appropriate primers and PCR, we created pB1121 with these sites. After confirming the sequence, we then proceeded to introduce TMV genomic sequence into this plasmid. See also U.S.S.N. 10/770,600 filed February 3, 2004 and U.S. Provisional application no. 60/444,615, filed February 3, 2003, incorporated herein by reference and U.S.S.N. 10/832,603 and U.S. provisional application 60/546,339, incorporated herein by reference, for further discussion of D4-hGH and D4-GFP. The parental vector, D4, and vectors derived therefrom, are WO 2007/095304 PCT/US2007/003942 58 described in Shivprasad et al., Virology, 255(2):312-23, 1999. The resultant plasmid is referred to as pBID4. [002131 The 35S promoter of cauliflower mosaic virus was fused to TMV sequence. Thus the 35S promoter directs transcription of the TMV sequence. Upon successful incorporation into a cell, viral transcripts are produced. In certain embodiments of the invention, components needed for viral replication and spread throughout the plant are also produced. These components include, e.g., replicase, movement protein, and coat protein, which may be from TMV or from another virus such as alfalfa mosaic virus in various embodiments. These components may be encoded within the TMV sequence, the plasmid sequence, provided in a separate viral vector or plasmid, or the plant may be a transgenic plant comprising a transgene that encodes the components. See, for example USSN 10/770,600 filed February 3, 2004, which is incorporated herein by reference. [00214] A subgenomic TMV promoter within the TMV sequence directs transcription of the hGH sequence. A hammerhead ribozyme was introduced 3' of the TMV sequence. The ribozyme is not required for the present invention. The nos terminator (well known in the art) is 3' of the ribozyme sequence. [002151 The final vector contained D4-hGH or D4-GFP. These constructs in pBI121 were then used to transform A. tumefaciens and plants infiltrated with transformed Agrobacterium. Since a replicating virus is present we incubated the plants for 2 weeks. Leaf discs were analysed for hGH production by Western blots. GFP expression was monitored by illuminating the plants with long wave ultraviolet light and photographed. The results shown in Figure 10 demonstrates GFP expression throughout the infiltrated leaves. Western blot analysis shown in Figure 11 using antibody directed to hGH confirmed that the construct was functional in plants, and hGH could be detected at high levels. [00216] Similarly, IA-2ic was engineered into pBID4 plasmid to generate pBID4-IA 2ic. Additionally, AMV viral based vector carrying GFP was generated. Resulting plasmids was used to transform Agrobacterium and hydroponically grown Nicotiana benthamiana was infiltrated with transformed Agrobacterium. Briefly, Nicotiana benthamiana seeds were sown on a Rockwool slab (18 X 8 X1) pre-wetted in %/ strength Hoagland solution as a nutrient in hydroponic conditions. The hydroponics plants were kept in the same solution for four weeks. Four week-old plants were then vacuum infiltrated in Agrobacterium suspension (0D 6 00 0.1) carrying pBID4-IA-2ic or AMV viral based vector carrying GFP.

WO 2007/095304 PCT/US2007/003942 59 [00217] Bacterial cultures were grown and induced over night, then cells were re suspended in MMA medium (MS salts,10 mM MES pH 5.6, 20 g/l sucrose, 200 sM acetosyringone) to an OD 600 of 0.1. Re-suspended culture was incubated at room temperature for 2-3 h with gentle shaking, and hydroponics Nicotiana benthamiana plants were placed in the bacterial suspension, then vacuum was applied for 30-60 second at room temperature. Vacuum was quickly released to facilitate efficient infusion of the bacteria into the tissue, and infiltrated plants were kept in 2 strength Hoagland solution nutrient for 5-7 days Alternatively, the bacterial suspension was forced under the epidermis of fully expanded leaves, using a 10 cm 2 syringe with no needle. Leaves were harvested between 3 6 days post-infiltration and stored at -80 *C or analyzed for expression analysis. Figure 12 demonstrates western blot analysis of plants expressing IA-2ic. Analysis of plants infiltrated with AMV based GFP constructs under light demonstrated expression of GFP throughout leaves of infiltrated plants. Example 7: Expression ofProteins (Green Fluorescence Protein; Lichenase) in Pea Varieties from a an Agrobacterial Construct Containing Viral Sequences [002181 The present Example describes agroinfiltration of certain pea varieties with agrobacterial constructs that carry a viral expression vector. [00219] Figure 13 depicts the overall strategy utilized for agrobacterial constructs carrying A1MV sequences. Given that AlMV has a segmented genome (as discussed above), three different constructs were used: one (pMOG-R1&2) that carried AlMV sequences encoding replicases 1 and 2; one (pBI-RNA3) that carried AIMV RNA3 sequences (optionally including a gene of interest to be expressed, which typically replaces the natural AIMV coat protein sequences in RNA3); and one (pBI-CP) that carried AlMV sequences encoding the A1MV coat protein. Those of ordinary skill in the art will appreciate that inclusion of the construct encoding the AlMV coat protein is not, strictly speaking required. However, it can be useful to include such a construct, as coat protein can facilitate replication and/or systemic spread of viral sequences (and therefore of the gene of interest they carry). 100220] Even where it is desirable to ensure expression of the A1MV coat protein, it is not essential that three constructs be utilized. For example, one alternative might be to utilize plants that are already transgenic for the AlMV coat protein so that it need not be WO 2007/095304 PCT/US2007/003942 60 separately supplied. Alternatively or additionally, plants could be utilized that are transgenic for one or both of the AlMV-replicase proteins: In such plants (optionally further transgenic for the AIMV coat protein), a single construct could be utilized, carrying just the RNA3 and gene of interest sequences, to achieve similar results. [002211 As indicated in Figure 13, in these particular experiments, constructs expressing three different proteins, green fluorescence protein (GFP), lichenase (Lich), and a lichenase-anthrax protective antigen fusion (Li-PA) were utilized. [00222] In the particular experiments addressed in Figure 13, at least a liter of each agrobacterial strain (i.e., each strain carrying one of the three constructs pMOG-Rl&R2, pBI-RNA3/Protein of Interest; pBI-CP) was grown up, pelleted, and resuspended in MMA to an O.D. of 1.0. Those of ordinary skill in the art will appreciate that different O.D.s may be desirable for different plants. For peas, higher O.D.s, for example in the range of 1.5, are often desirable if technically achievable. [00223] In the particular experiments addressed in Figure 13, agrobacterial strains carrying the replicase (pMOG-RI&R2), coat protein (pMOG-CP), and RNA3/Target Protein (pBI-RNA3/GFP, Lich, or Li-PA) were combined in a ratio of 1:1:2 to a total volume of 1.5 L. Those of ordinary skill in the art will appreciate that these ratios and volumes are not critical; the particular ratio utilized was selected to reflect that the ALMV life cycle typically involves higher levels of RNA3 than of other genome components. Also, there was a desire for higher levels of the RNA that carried the gene of interest (i.e., the GFP, Lichenase, or Lichanse-Protective Antigen gene). [00224] In the particular experiments addressed in Figure 13, bean sprouts were grown hydroponically with a non-soil support (in this case cheesecloth) as is known in the art. Sprouts were submerged in the combined agrobacterium mixture, and vacuum was applied for 90 sec at -28 psi ot achieve agroinfiltration. In some cases, vaccum was applied more than once. [00225] In the particular experiments addressed in Figure 13, sprouts were rinsed once in tap water after agroinfiltration, and then were returned to the growth space and watered. Sprouts were later harvested, pooled, and extracted. [00226] Figures 14-16 present the results of various experiments performed according to the strategy illustrated in Figure 13. For example, as shown in Figure 14, Lichenase producing constructs were agroinfiltrated into speckled pea (SP), yellow pea (YP), or bill WO 2007/095304 PCT/US2007/003942 61 jump pea (BP) srpouts. Prior to agroinfiltration, the sprouts were grown for 2 days in the dark (to allow germination) and 8 days in the light (as -indicated by the "2(8)" notation). These 10 days were then agroinfiltrated as described above, and were grown for 5 days post inoculation (dpi) prior to detection of produced protein. As can be seen in Figure 14, lichenase protein was produced by all three pea varieties, with yellow pea having somewhat higher production levels than speckled pea, and bill jump pea having somewhat lower production levels. Such variability is well within the realm of experience of those of ordinary skill in expressing proteins in plants; in light of these results, no more than routine experimentation would be required to select a preferred plant variety for production of any particular protein. In general, expression levels observed in these pea sprout systems were approximately 1/3 of those observed when expressing the relevant proteins (e.g., Lich-PA) in Nicotiana benthamiana (not shown). These sprouts have the advantage over Nicotiana benthamiana that they are edible, which should simplify any required isolation of produced pharmaceutically active protein(s) as all components of the plants are known to be unhanful at least to humans. Furthermore, they grow rapidly and are inexpensive. On the other hand, seed storage is easier for Nicotiana benthamiana, as the seeds are much smaller than those of sprouts generally and peas in particular. [00227] As can also be seen with reference to Figure 14, in these particular experiments, the above-described AlMV production system was more successful at producing the protein of interest than was an analogous TMV system (as described herein). Those of ordinary skill in the art will appreciate that a TMV system will be preferable for production of certain particular proteins in certain particular plant species, whereas A1MV is preferable in other circumstances including these. [002281 Figure 15 shows successful production of GFP in speckled pea and yellow pea grown for different periods of time prior to agorinfiltration. In the particular experiments presented in Figure 15, vaccuum was applied three times for 90 seconds each. Also, the particular resuspension medium utilized was "full MMA". Those of ordinary skill in the art will appreciate that any of a variety of other infiltration media, including minimal MMA, AB, etc., could alternatively be used and might increase or decrease the ultimate efficiency of agroinfiltration and therefore of protein or polypeptide production. [002291 Figure 16 shows expression of lichenase in speckled pea leaves (L), whole sprouts (W), roots (R), or hypocotyl (H) at different periods of time post-infiltration. As can be seen, most expression is in the leaves. Moreover, expression is best in this particular WO 2007/095304 PCT/US2007/003942 62 system approximately 5-7 days after infiltration. Some variation should be expected based on the age and variety of plant being utilized, as-well as the protein(s) being expressed. [00230] Other similar experiments demonstrated, for example, that use of a pBl-CP construct lacking the 5/3' UTR structure increased production of the protein of interest, presumably by increasing production of coat protein (CP). Also, in this system, 9-12 day old plants were optimal for expression. In general, higher levels of protein were expressed in younger tissue, but older tissue had more biomass. [00231] Still other similar experiments generated that exposing plants to 24 hr of light rather than a 12/12 light/dark cycle materially decreased levels of the protein of interest. [00232] Still other similar experiments demonstrated that exposure of pea sprouts to weak detergent during agroinfiltration may increase levels of production of protein of interest, presumably by increasing efficiency and/or extent of successful agroinfiltration. Example 8: Modular Systemfor Large Scale Production of Proteins or Polypeptides in Plants [00233] The present Example describes a technology platform that will revolutionize the manufacture of biopharmaceuticals, reducing lot production time, in some cases to five weeks. The particular production system described in this Example utilizes an agrobacterial vector to deliver very large copy numbers of plant viral RNAs that carry the coding sequence of the protein or polypeptide of interest into young plants within a few minutes. High levels of transient expression of the protein or polypeptide of interest can thus be achieved in bulk plant biomass within a week of introducing the agrobacterial vector into the plant. [00234] The technology platform described in this Example is applicable for a broad range of monomeric or multimeric proteins, including vaccine antigens, monoclonal antibodies and other therapeutics (among other things), and can be performed in a variety of plant species. Expression in plants is more likely to provide correct folding and solubility than some altearnative systems and has the added advantage of being free from animal pathogens. In this particular Example, we focus on engineering and producing vaccine antigens and monoclonal antibodies in seedlings.

WO 2007/095304 PCT/US2007/003942 63 [002351 As described in this Example, genes encoding the proteins or polypeptides of interest are cloned into a launch vector that combines elements of agrobacterial and plant RNA virus sequences. Agrobacterium is then used to introduce millions of copies of the launch vector into plants by vacuum infiltration. In plant tissues the vector sequences are further massively amplified through viral replication. Target proteins are then produced from these viral transcripts in less than a week following introduction of the vector. It will be appreciated that it is not required (though it is also not prohibited) for the agrobacterial vector to integrate in the plant cells. Rather, the agrobacterial elements of the vector merely facilitate rapid systemic delivery (via agroinfiltration) of the viral RNA from which protein is ultimately produced. [00236] This system can be used to produce very large amounts (e.g., hundred milligram quantities) of target protein per kg of fresh plant tissue. Furthermore, very high capacity can be achieved as large quantities of seeds (which, as noted, need not be transgenic) can be readily made available. [00237] As described herein, in some instances, target protein or polypeptide is produced as a fusion with a carrier molecule, for example to stabilize the protein and/or to facilitate downstream processing. Such carriers may be particularly useful in the production of antigen proteins. Carriers of particular interest include, for example, thermostable proteins such as those described in, for example, USSN 60/472,495 filed May 22, 2003 and PCT/USO4/016452, filed May 24, 2004 and published as WO 05/0263 75 on March 24, 2005). We note that In this One such thermostable carrier molecule is an engineered version of p-1,2-1,4-gucanase (LicKM) from Clostridium thermocellum. Target sequences can be rapidly engineered as N-terminal, C-terminal or internal fusions to LicKM. The presence of foreign sequences in LicKM does not result in loss of the molecule's thermostability. This property facilitates easy and cost efficient recovery of target proteins. A simple heat treatment step (e.g., up to 10 minutes at 65 *C) results in removal of most of the host proteins. Furthermore, more than one target protein can be fused to each molecule of LicKM but using multiple insertion sites simultaneously. [002381 Specifically, seeds from non-genetically modified plants are germinated in hydroponic conditions and maintained for a period of time (e.g., typically up to about 10 days for sprouts; sometimes 2-6 weeks for Nicotiana benthamania) in contained indoor plant facilities prior to vacuum infiltration. Under these conditions, the yield of plant WO 2007/095304 PCT/US2007/003942 64 biomass per square foot is typically 4-5 fold higher than that achieved with plants grown in soil. By using young plants (e.g., sprouted seedlings), we can generate a dense- canopy with a large amount (e.g., about 100 - 1000 kg) of green tissue per square foot. To give but a few examples, we can typically generate a canopy with about 700 g green tissue/square foot with sprouts such as peas; a canopy with about 200 g green tissue/square foot is typically generated with Nicotiana benthamania. Those of ordinary skill in the art will appreciate that other plants will likely be between these amounts. [00239] Very high capacity can be achieved by stacking racks of young plants (e.g., seedlings) above one another on shelving with fitted light units (a 1000 sq. ft. growth room will provide up to four metric tons of biomass in less than two weeks). All aerial parts of plants are infiltrated with agrobacteria harboring the launch vector by applying, and then quickly releasing, a vacuum. This forces agrobacteria into the whole canopy of plant tissue with near complete leaf coverage. Target protein then accumulates over a period of a few days (e.g., about 2 to about 14 days, in some embodiments about 2 to 10, 3 to 7, 4 to 6, etc. days). [002401 The whole process from seed to harvested tissue typically takes a few weeks (e.g., less than 6, 5, 4, 3, or two weeks; often about 2 weeks for sprouts). Since the seed material is non-transgenic, seed generation and storage are inexpensive and straightforward and there is effectively no limitation of scale-up. Thus, very large quantities of recombinant protein can potentially be generated in a matter of weeks. [002411 Produced target proteins can be isolated, if desired. A heat step can be useful in the isolation of targets fused to a thermostable carrier. Other purifications can involve various separation and/or chromatography steps. For example, steps such as ammonium sulfate precipitation, pH-dependent separation, size exclusion chromatorgraphy, ion exchange chromatography, and affinity chromatography may be employed. [002421 The entire process contemplated in this Example involves 1) gene optimization and synthesis; 2) cloning in to the launch vector; 3) preparation of plant material and agrobacterial cultures; 4) vacuum infiltration of sprouted seedlings; 5) target expression; 6) tissue harvest; 7) and target recovery. To allow for high throughput production, we will automate much of this process. Specifically, all steps from seeding non transgenic seed and fermentation of agrobacterial cultures, through to homogenization, clarification and volume reduction of homogenized plant material (see Figure 19) will be WO 2007/095304 PCT/US2007/003942 65 automated. We will design and build a module with capacity to produce 1.5 metric tons of plant biomass in one batch. Specifically, we will construct the equipment conceptually shown in Figure 20. [00243] The equipment design depicted in Figure 20 uses a tower concept such that the entire module will fit within an approximately 5000 sq. ft. space. The central shelving unit provides the necessary space, light and water supply to grow 1.5 metic tons of plant biomass. Humidity, temperature and light are automatically monitored and controlled. In the design depicted in Figure 20, plants will be grown hydroponically in trays that are 1' x 2' in size. Thus, approximately 6000 trays will be used. The module can be constructed from 36 individual storage unis that are stackable. Each storage unit will hold 6 x 7 x 4 trays. The modularity of the design allows for scalable production. There are two robots, one on each side of the shelves, that get the trays in and out of the shelves. Automated seeding is done on a material suitable for hydroponic growth. Once the plants have reached an appropriate maturity, a conveyor transports them to the infiltration unit, which has a vacuum chamber that has the capacity to infiltrate 1.5 metric tons of plant biomass in about 8 hours. A rinsing unit removes excess agrobacterial culture. Once the plants are rinsed they are conveyed back to the central shelving unit for target accumulation for several days. Subsequently, the trays are conveyed to the harvesting unit where the plants are harvested and homogenized. The homogenized plant extract is then transported to a downstream processing unit. Example 9: Expression of HPVAntigenfrom a an Agrobacterial Construct Containing Viral Sequences [00244] Agrobacterium-mediated transient expression system achieved by Agrobacterium infiltration can be utilized (Turpen et al., 1993, J Virol. Methods, 42:227). Healthy leaves of N. benthamiana were infiltrated with A. rhizogenes containing viral vectors engineered to express LicKM-E7 or LicKM-E7GGG. [00245] The A. rhizogenes strain A4 (ATCC 43057) or A. tumefaciens (GV3103) was transformed with the constructs pBI-D4- PRACS-LicKM-E7-KDEL, pBI-D4-PRACS LicKM-E7VAC, pBI-D4-PRACS-LicKM-E7GGG-KDEL and pBI-D4-PRACS-LicKM E7GGG-VAC. Agrobacterium cultures were grown and induced as described (Kapila et al., 1997, Plant Sci., 122:101). A 2 ml starter-culture (picked from a fresh colony) was grown WO 2007/095304 PCT/US2007/003942 66 overnight in YEB (5 g/l beef extract, 1 g/1 yeast extract, 5 g/l peptone, 5 g/l sucrose, 2 mM -MgSO4) with 25 pg/ml kanamycin at 28 *C. The starter culture- was diluted -1:500 into 500 ml of YEB with 25 pg/ml kanamycin, 10 mM 2-4(-morpholino)ethanesulfonic acid (MES) pH 5.6, 2 mM additional MgSO4 and 20 pM acetosyringone. The diluted culture was then grown overnight to an O.D.600 of-1.7 at 28 *C. The cells were centrifuged at 3,000 x g for 15 minutes and re-suspended in MiMA medium (MS salts, 10 mM MES pH 5.6, 20 g/l sucrose, 200 pM acetosyringone) to an O.D.600 of 2.4, kept for 1 hour at room temperature, and used for Agrobacterium-infiltration. N. benthamiana leaves were injected with the Agrobacterium-suspension using a disposable syringe without a needle. Infiltrated leaves were harvested 6 days post-infiltration. Example 10: Expression ofAnthrax Antigenfrom a an Agrobacterial Construct Containing Viral Sequences [002461 An Agrobacterium-mediated transient expression system achieved by Agrobacterium infiltration can be utilized to produce anthrax antigen(s). Healthy leaves of N. benthamiana were infiltrated with A. rhizogenes containing viral vectors engineered to express LicKM or LicKM-PAD4. The vector used was pBI-D4, a version of the viral expression vector D4 introduced into the Agrobacterium vector pBI121. (Chen et al., 2003, Mol. Breed., 11:287). The 35S promoter is fused at the 5' end of the viral sequence. The vector sequence is positioned between the BamHIL and SacI sites of pBI121. The hammerhead ribozyme is placed 3' of the viral sequence (Turpen et al., 1993, J. Virol. Methods, 42:227). These constructs include fusions of sequences encoding LicKM-PAD4 or LicKM, to sequences encoding the signal peptide from tobacco PR-i a protein, a 6x His tag and the ER-retention anchor sequence KDEL (see SEQ ID NO.: 10). [00247] The A. rhizogenes strain A4 (ATCC 43057) was transformed with the constructs pBI-D4-PRLicKM-PAD4K and pBI-D4-PRLicKMK. Agrobacterium cultures were grown and induced as described (Kapila et al., 1997, Plant Sci., 122:101). A 2 ml starter-culture (picked from a fresh colony) was grown overnight in YEB (5 g/l beef extract, 1 g/l yeast extract, 5 g/l peptone, 5 g/l sucrose, 2 mM MgSO 4 ) with 25 pg/ml kanamycin at 28 *C. The starter culture was diluted 1:500 into 500 ml of YEB with 25 gg/ml kanamycin, 10 mM 2-4(-morpholino)ethanesulfonic acid (MES) pH 5.6,2 mM additional MgSO 4 and 20 jiM acetosyringone. The diluted culture was then grown overnight to an O.D.

600 of-i.7 at 28 *C. The cells were centrifuged at 3,000 x g for 15 minutes and re-suspended in MMA WO 2007/095304 PCT/US2007/003942 67 medium (MS salts, 10 mM MES pH 5.6, 20 g/l sucrose, 200 pM acetosyringone) to an

-O.D.-

6 6 of 2.4, kept for 1 hour at room temperature, and used for Agrobacterium-infiltration. N. benthamiana leaves were injected with the Agrobacterium-suspension using a disposable syringe without a needle. Infiltrated leaves were harvested 6 days post-infiltration. Example 11: Expression of Influenza Antigen from a an Agrobacterial Construct Containing Viral Sequences [002481 Agrobacterium-mediated transient expression system achieved by Agrobacterium infiltration can be utilized to express influenza antigen(s). (Turpen et al., (1993) Transfection of whole plants from wounds inoculated with Agrobacterium tumefaciens containing cDNA of tobacco mosaic virus (J. Virol. Methods, 42:227) Healthy leaves of N. benthamiana were infiltrated with A. rhizogenes containing viral vectors engineered to express LicKM-HA or LicKM-NA. [00249] The A. rhizogenes strain A4 (ATCC 43057) was transformed with the constructs pBI-D4- PRACS-LicKM-HA-KDEL, pBI-D4-PRACS-LicKM-HA-VAC, pBI D4-PRACS-LicKM-NA-KDEL and pBI-D4-PRACS-LicKM-NA-VAC. Agrobacterium cultures were grown and induced as described by Kapila et al. (Kapila J., De Rycke R., Van Montagu M. and Angenon G. (1997) An Agrobacterium-mediated transient gene expression system for intact leaves. Plant Sci. 122, 101-108.). A 2 ml starter-culture (picked from a fresh colony) was grown overnight in YEB (5 g/l beef extract, 1 g/l yeast extract, 5 g/l peptone, 5 g/l sucrose, 2 mM MgSO 4 ) with 25 gg/ml kanamycin at 28 *C. The starter culture was diluted 1:500 into 500 ml of YEB with 25 pg/ml kanamycin, 10 mM 2-4( morpholino)ethanesulfonic acid (MES) pH 5.6, 2 mM additional MgSO 4 and 20 gM acetosyringone. The diluted culture was then grown overnight to an O.D.

600 of-1.7 at 28 *C. The cells were centrifuged at 3,000 x g for 15 minutes and re-suspended in MMA medium (MS salts, 10 mM MES pH 5.6, 20 g/l sucrose, 200 pM acetosyringone) to an

O.D.

6 o of 2.4, kept for 1-3 hour at room temperature, and used for Agrobacterium infiltration. N. benthamiana leaves were injected with the Agrobacterium-suspension using a disposable syringe without a needle. Infiltrated leaves were harvested 6 days post infiltration. Plants can be screened for the presence of target antigen expression by assessment of lichenase activity assay and immunoblot analysis.

WO 2007/095304 PCT/US2007/003942 68 [002501 Zymogram analysis revealed the expression of both HA and NA chimeric - -proteins in the Nicotiana benthamiana transgenic roots tested: The expression is associated with lichenase activity. The activity band related to the fusion proteins show a higher molecular weight than the lichenase control and the same molecular weight of the product expressed by plants after agro-infection, confirming the presence of whole fusion product. Example 12: Expression of Influenza Antibody from a an Agrobacterial Construct Containing Viral Sequences Other Embodiments [002511 Those of ordinary skill in the art will appreciate that the foregoing represents certain preferred embodiments of the present invention and should not be construed to limit the spirit or scope of the invention as defined by the following claims:

Claims (45)

1. A method for producing pharmaceutically active protein or polypeptide in young plants, comprising steps of: infusing a young pea plant with an agrobacterial construct that includes a promoter controlling transcription of viral sequences, which viral sequences carry coding sequences encoding a protein or polypeptide of interest; incubating the infused young pea plant under conditions and for a time sufficient to allow transcription from the promoter such that a viral transcript is produced, which viral transcript includes sequences encoding a protein or polypeptide of interest; incubating the infused young pea plant under conditions and for a time sufficient to allow production of the protein or polypeptide.

2. The method of claim 1, wherein the agrobacterial construct comprises viral sequences of tobacco mosaic virus, alfalfa mosaic virus, cauliflower mosaic virus, or any combination of the foregoing.

3. The method of claim 1, wherein the agrobacterial construct comprises viral sequences of tobacco mosaic virus.

4. The method of claim 1, wherein the agrobacterial construct comprises viral sequences of alfalfa mosaic virus.

5. The method of claim 1, wherein the agrobacterial construct comprises viral sequences of cauliflower mosaic virus.

6. The method of claim 1, wherein the viral sequences are under control of the 35S promoter of cauliflower mosaic virus.

7. The method of claim 6, wherein the 35S promoter of cauliflower mosaic virus drives initial transcription of a recombinant viral genome following infusion into the young pea plant.

8. The method of claim 1, wherein the promoter controlling transcription of viral sequences is a constitutive promoter. WO 2007/095304 PCT/US2007/003942 70

9. The method of claim 1, wherein the promoter controlling transcription of viral sequences is an inducible promoter.

10. The method of claim 9, wherein the inducible promoter is a heat shock promoter.

11. The method of claim 9, wherein the inducible promoter is a light-inducible promoter.

12. The method of claim 9, wherein the inducible promoter is a chemically-inducible promoter.

13. The method of claim 1, wherein the agrobacterial construct comprises a transcriptional terminator.

14. The method of claim 13, wherein the transcriptional terminator is the transcriptional terminator of Agrobacterium nopaline synthase.

15. The method of claim 1, wherein the agrobacterial construct comprises one or more genes for virus replication.

16. The method of claim 1, wherein the agrobacterial construct comprises one or more genes for cell-to-cell movement.

17. The method of claim 1, wherein the protein or polypeptide of interest is under the transcriptional control of a viral mRNA promoter.

18. The method of claim 17, wherein the viral mRNA promoter is the coat protein subgenomic mRNA promoter.

19. The method of claim 1, wherein the agrobacterial construct comprises left and right border sequences.

20. The method of claim 19, wherein the left and right border sequences delimit the region of the agrobacterial construct that is transferred into young pea plant cells following infusion of the young pea plant the agrobacterial construct.

21. The method of claim 1, wherein the young pea plant is infused with multiple constructs. WO 2007/095304 PCT/US2007/003942 71

22. The method of claim 1, wherein the young pea plant is selected from the group consisting of marrowfat pea, bill jump pea, yellow trapper pea, speckled pea, and green pea.

23. The method of claim 1, wherein the protein or polypeptide of interest is insulin.

24. The method of claim 1, wherein the protein or polypeptide of interest is glutamic acid decarboxylase.

25. The method of claim 1, wherein the protein or polypeptide of interest is tyrosine phosphatase-like protein IA-2.

26. The method of claim 1, wherein the protein or polypeptide of interest is green fluorescent protein.

27. The method of claim 1, wherein the protein or polypeptide of interest is human growth hormone.

28. The method of claim 1, wherein the protein or polypeptide of interest is one or more components of anthrax toxin.

29. The method of claim 28, wherein the component of anthrax toxin is protective antigen.

30. The method of claim 29, wherein a mutation has been introduced that renders the protective antigen inactive as a toxin.

31. The method of claim 28, wherein the component of anthrax toxin is lethal factor.

32. The method of claim 31, wherein a mutation has been introduced that renders the lethal factor inactive as a toxin.

33. The method of claim 1, wherein the protein or polypeptide of interest comprises lichenase sequences.

34. The method of claim 1, wherein the infused young pea plant is incubated under conditions of hydroponic growth. WO 2007/095304 PCT/US2007/003942 72

35. The method of claim 1, wherein at least 5 grams of the protein or polypeptide is produced per kilogram of plant tissue.

36. The method of claim 1, wherein at least about 1 gram of the protein or polypeptide is produced per kilogram of plant tissue.

37. The method of claim 1, wherein at least about 0.5 grams of the protein or polypeptide is produced per kilogram of plant tissue.

38. The method of claim 1, wherein at least about 20-500 mg of the protein or polypeptide is produced per kilogram of plant tissue.

39. The method of claim 1, wherein the time sufficient to allow production of the protein or polypeptide is at least about 6 weeks from infusion of the agrobacterial construct.

40. The method of claim 1, wherein the time sufficient to allow production of the protein or polypeptide is at least about 3 weeks from infusion of the agrobacterial construct.

41. The method of claim 1, wherein the time sufficient to allow production of the protein or polypeptide is at least about 2 weeks from infusion of the agrobacterial construct. 41. The method of claim 1, wherein the time sufficient to allow production of the protein or polypeptide is at least about I week from infusion of the agrobacterial construct.

42. The method of claim 1, wherein the time sufficient to allow production of the protein or polypeptide is at least about 3 days from infusion of the agrobacterial construct.

43. The method of claim 1, wherein the time sufficient to allow production of the protein or polypeptide is at least about 1 day from infusion of the agrobacterial construct.

44. The method of claim 1 wherein the young plants are young pea plants.

45. A method for producing pharmaceutically active protein or polypeptide in Nicotiana plants, comprising steps of: infusing a young Nicotiana plant with an agrobacterial construct that includes a promoter controlling transcription of viral sequences, which viral sequences carry coding sequences encoding a protein or polypeptide of interest; incubating the infused young Nicotiana plant under conditions and for a time WO 2007/095304 PCT/US2007/003942 73 sufficient to allow transcription from the promoter such that a viral transcript is produced, which viral transcript includes the coding sequences encoding a protein or polypeptide of interest; incubating the infused young Nicotiana plant under conditions and for a time sufficient to allow production of the protein or polypeptide.