| PATENT ASSIGNEE'S COUNTRY | USA |
| UPDATE | 04.00 |
| PATENT NUMBER | This data is not available for free |
| PATENT GRANT DATE | 25.04.00 |
| PATENT TITLE |
Isoflavone biosynthetic enzymes |
| PATENT ABSTRACT |
This invention relates to an isolated nucleic acid fragment encoding soybean enzymes that catalyze steps in biosynthesis of isoflavones, the enzyme a member selected from the group consisting of chalcone isomerase, isoflavone reductase and vestitone reductase. The invention also relates to the construction of chimeric genes encoding all or a substantial portion of the enzymes, in sense or antisense orientation, wherein expression of the chimeric gene results in production of altered levels of the enzyme in a transformed host cell. |
| PATENT INVENTORS | This data is not available for free |
| PATENT ASSIGNEE | This data is not available for free |
| PATENT FILE DATE | 17.09.98 |
| PATENT REFERENCES CITED |
McKhann et al, Plant Mol. Biol., vol. 24, pp. 767-777, 1994. Fromm et al, Biotechnology, vol. 8, pp. 833-839, 1990. Dixon et al, Plant Cell, vol. 7, pp. 1085-1097, 1995. van der Krol et al., Nature, pp. 866-869, 1988. Terai, Y. et al., "Cloning And Overexpression of the Chalcone-Flavanone Isomerase Cdna From Pueraria Lobata and Its Overexpression In Escherichia Cloli," EMBL Sequence Data Library, 15, Aug. 15, 1995, XP002090217. Scolnik, P.A. and Bartley, G.E., Two Members of an Arabidopsis Geranylgeranyl Pyrophosphate Synthase Gene Family, EMBL Sequence Data Library, 23, Mar. 1996, XP002090218. Guo, L. and Paiva, N.L., "Molecular Cloning and Expression of Alfalfa (Medicago sativa L.) Vestitone Reductase, the Penultimate Enzyme in Medicarpin Biosynthesis," Archives of Biochemistry and Biophysics, 320 No. 2, Jul. 1995, 353-360, XP002090219. Paiva, N.L. et al., "Stress Responses in Alfalfa (Medicago Sativa L) 11 Molecular Cloning and Expression of Alfalfa Isoflavone Reductase, Akey Enzyme of Isoflavonoid Phytoalexin Biosynthesis," Plant Molecular Biology, 17 No. 4, Oct. 1, 1991, 653-667, XP000570444. Paiva, N.L, "Biotransformation of Isoflavenoids by Transgenic Tobacco Cell Cultures," Abstract of Papers, ACS National Meeting, No. 1/02, Apr. 2, 1995, XP000571305. Seehaus, K. and Tenhaken, R., "Cloning of Genes by mRNA Differential Display Associated with the Hypersensitive Reaction of Soybean After Inoculation with Pseudomonas Syringae pv. Glycinea," EMBL Sequence Data Library, 25, Aug. 1998, XP002090220. Schopper, C.R., "Unpublished" EMBL Sequence Data Library, Dec. 11, 1997, XP002090221. Chu et al., Sci. Sin. Peking, 18, 659-668, 1975. Deblaere et al., Meth. Enzymol., 153, 277-292, 1987. Hoheisel, J.D. et al., in Nonmammalian Genomic Analysis: A Practical Guide, Academic Press, 319-346, 1996. Altschul, S.F. et al., J. Mol. Biol., 215, 403-410, 1990. Jones et al., EMBO J., 4, 2411-2418, 1985. Keegstra, K., Cell, 56, 247-253, 1989. Biochemical Journal, 219(2), 345-373, 1984. Kitamura et al., J. Breed, 41, 651-654, 1991. Mathur et al., J. Nutrition, 84, 201-204, 1964. Adams et al., Science, 252, 1651, 1991. Laan et al., Genome Research, 5, 13-20, 1995. Lander et al., Genomics, 1, 174-181, 1987. Botstein, D. et al., Am. J. Hum. Genet., 32, 314-331, 1980. Bernatzky, R. and Tanksley, S.D., Plant Mol. Biol. Reporter, 4(1), 37-41, 1986. Cornish-Bowden, A. Nucleic Acids Research, 13, 3021-3030, 1985. ODell et al., Nature, 313, 810-812, 1985. De Almeida et al., Mol. Gen. Genetics, 218, 78-86, 1989. Loh et al., Science, 243, 217, 1989. Dixon, R. A. and Paiva, N. L., The Plant Cell, 7, 1085-1097, 1995. R. D. Sharma, Lipids, 14(6), 535-540, 1978. Studier et al., J. Mol. Biol., 189, 113-130, 1986. Kazazian et al., J. Lab. Clin. Med., 114, 95-96, 1989. Okamuro and Goldberg, Biochemistry of Plants, 15, 1-82, 1989. Ingelbrecht et al., Plant Cell, 1, 671-680, 1989. Gish, W. and States, D.J., Nature Genetics, 3, 266-272, 1993. Klein et al., Nature (London), 327, 70-73, 1987. Ohara et al., PNAS USA, 86, 5673, 1989. Frohman, M.A. and Martin, G. R., Techniques, 1, 165, 1989. Rosenberg et al., Gene, 56, 125-135, 1987. Tsukamoto et al., J. Agric. Food Chem., 43, 1184-1192, 1995. Messina, M. and Barnes, S., Commentary, 83(8), 541-546, 1991. Dear and Cook, Nucleic Acids Research, 17, 6795-6807, 1989. Walter et al., Nature Genetics, 7, 22-28, 1987. Raikel, Plant Phys., 100, 1627-1632, 1992. Turner, R. and Foster, G.D., Molecular Biotechnology, 3, 225, 1995. Fromm et al., Bio/Technology, 8, 833-839, 1990. Trask et al., Trends Genet., 7, 149-154, 1991. Ballinger et al., Proc. Natl. Acad. Sci., 86, 9402-9406, 1989. Landengren et al., Science, 241, 1077-1080, 1988. Koes et al., Proc. Natl. Acad. Sci., 92, 8149, 1995. Peterson, G. and Barnes, S., Biochem. and Biophys. Res. Com., 179(1), 661-667, 1991. Naim et al., J. Agr. Food Chem., 22(5), 806-810, 1974. Sokolov B. P., Nucl. Acids Res., 18(12), 3671, 1989. Bensen et al., The Plant Cell, 7, 75-84, 1995. Lerner, R.A., Adv. Immunol., 36, 1 Maniatis, 1984. Frohman et al., PNAS USA, 85, 8998, 1988. Chrispeels, J.J., Ann. Rev. Plant Phys. Plant Mol. Biol., 42, 21-53, 1991. Doyle et al., J. Biol. Chem., 261, 9228-9238, 1986. Gritz, L. et al., Gene, 25, 179-188, 1985. Scheffield et al., Genomics, 16, 325-332, 1993. Price, K. R. and Fenwick, G. R., Food Additives and Contaminates, 2, 73, 106, 1985. Naim et al., J. Agric. Food Chem., 24(6), 1174-1177, 1976. Wang et al., J. Agric. Food Chem., 42, 1674-1677, 1994. |
| PATENT PARENT CASE TEXT | This data is not available for free |
| PATENT CLAIMS |
What is claimed is: 1. An isolated nucleic acid fragment comprising a member selected from the group comprising of: (a) an isolated nucleic acid fragment encoding the chalcone isomerase polypeptide set forth in SEQ ID NO:2; (b) an isolated nucleic acid fragment that is at least 95% identical to an isolated nucleic acid fragment encoding the chalcone isomerase polypeptide set forth in SEQ ID NO:2; and (c) an isolated nucleic acid fragment that is complementary to (a) or (b). 2. The isolated nucleic acid fragment of claim 1 wherein the nucleotide sequence of the fragment is set forth in SEQ ID NO:1. 3. A chimeric gene comprising the nucleic acid fragment of claim 1 operably linked to suitable regulatory sequences. 4. A transformed host cell comprising the chimeric gene of claim 3. 5. A method of altering the level of expression of a plant isoflavone biosynthetic enzyme in a host cell comprising: (a) transforming a host cell with the chimeric gene of claim 3; and (b) growing the transformed host cell produced in step (a) under conditions that are suitable for expression of the chimeric gene wherein expression of the chimeric gene results in production of altered levels of a plant isoflavone biosynthetic enzyme in the transformed host cell. -------------------------------------------------------------------------------- |
| PATENT DESCRIPTION |
FIELD OF THE INVENTION This invention is in the field of plant molecular biology. More specifically, this invention pertains to nucleic acid fragments encoding enzymes involved in isoflavone biosynthesis in plants and seeds. BACKGROUND OF THE INVENTION Isoflavones represent a class of secondary metabolites produced in legumes by the phenylpropanoid metabolic pathway. The biosynthetic pathway for free isoflavones and their relationship with several other classes of phenylpropanoids is presented in FIG. 1. Many of the enzymes involved in the synthesis of isoflavones in soybean have been identified and the genes in the pathway from phenylalanine ammonia lyase to chalcone synthase and chalcone reductase have been cloned. However, remaining soybean genes involved in synthesis (chalcone isomerase and isoflavone synthase), further metabolism (isoflavone reductase and vestitone reductase), and branch points of the isoflavone pathway that could compete for substrates (flavanone hydroxylase and flavonol synthase) heretofore have not been available. Free isoflavones rarely accumulate to high levels in soybeans. Instead they are usually conjugated to carbohydrates or organic acids. Soybean seeds contain three types of isoflavones in four different forms: the aglycones daidzein, genistein, and glycitein; the glucosides diadzin, genistin, and glycitin; the acetylgucosides 6"-O-acetyldaidzin, 6"-O-acetylgenistin, and 6"-O-acetylglycitin; and the malonylglucosides 6"-O-malonyldaidzin, 6"-O-malonylgenistin, and 6"-O-malonylglycitin. It has been reported that the isoflavones found in soybean seeds possess antihemolytic (Naim, M. et al. (1976) J.Agric. Food Chem. 24:1174-1177), antifungal (Naim, M. et al. (1974) J Agr. Food Chem. 22:806-810), oestrogenic (Price, K. R. and Fenwick, G. R. (1985) Food Addit. Contam. 2:73-106), tumor suppressing (Messina, M. and Barnes, S. (1991) J. Natl. Cancer Inst. 83:541-546; Peterson, G. et al. (1991) Biochem. Biophys. Res. Commun. 179:661-667), hypolipidemic (Mathur, K. et al. (1964) J. Nutr. 84:201-204), and serum cholesterol lowering (Sharma, R. D. (1979) Lipids 14:535-540) effects. These epidemiological studies indicate that when isoflavone levels are high in soybean seeds and in the subsequent commercial protein products made from the seeds, the dietary intake of these products provide many health benefits. The content of isoflavones in soybean seeds, however, is quite variable and is affected by both genetics and environmental conditions such as growing location and temperature during seed fill (Tsukamoto, C. et al. (1995) J. Agric. Food Chem. 43:1184-1192; Wang, H. and Murphy, P. A. (1994) J. Agric. Food Chem. 42:1674-1677). In addition, isoflavone content in legumes can be stress-induced by pathogenic attack, wounding, high UV light exposure, and pollution (Dixon, R. A. and Paiva, N. L. (1995) The Plant Cell 7:1085-1097). To date, it has proven difficult to develop soybean lines with consistantly high levels of isoflavones; moreover, lines reported to be low in isoflavone content produced normal levels of isoflavones when grown under standard cultural conditions (Kitamura, K. et al. (1991) Jap. J. Breed. 41:651-654). The isolation and cloning of genes associated with synthesis and metabolism of isoflavones in soybean will afford the application of molecular techniques to achieve stable, high level accumulation of isoflavones. SUMMARY OF THE INVENTION The instant invention relates to isolated nucleic acid fragments encoding plant enzymes involved in isoflavone biosynthesis. Specifically, this invention concerns isolated nucleic acid fragments encoding the following soybean enzymes that catalyze steps in the biosynthesis of isoflavones from phenylalanine: chalcone isomerase, isoflavone reductase and vestitone reductase. In addition, this invention relates to nucleic acid fragments that are complementary to nucleic acid fragments encoding the listed soybean biosynthetic enzymes. In another embodiment, the instant invention relates to chimeric genes encoding the isoflavone biosynthetic acid enzymes listed above or to chimeric genes that comprise nucleic acid fragments that are complementary to the nucleic acid fragments encoding the enzymes, operably linked to suitable regulatory sequences, wherein expression of the chimeric genes results in production of levels of isoflavone biosynthetic enzymes in transformed host cells that are altered (i.e., increased or decreased) from the levels produced in untransformed host cells. In a further embodiment, the instant invention concerns a transformed host cell comprising in its genome a chimeric gene encoding an isoflavone biosynthetic enzyme operably linked to suitable regulatory sequences, the enzyme selected from the group consisting of chalcone isomerase, isoflavone reductase and vestitone reductase. Expression of the chimeric gene results in production of altered levels of the biosynthetic enzyme in the transformed host cell. The transformed host cell can be of eukaryotic or prokaryotic origin, and include cells derived from higher plants and microorganisms. The invention also includes transformed plants that arise from transformed host cells of higher plants, and seeds derived from such transformed plants. An additional embodiment of the instant invention concerns a method of altering the level of expression of a plant isoflavone biosynthetic enzyme in a transformed host cell comprising: a) transforming a host cell with a chimeric gene comprising a nucleic acid fragment encoding a soybean isoflavone biosynthetic enzyme selected from the group consisting of chalcone isomerase, isoflavone reductase and vestitone reductase, operably linked to suitable regulatory sequences; and b) growing the transformed host cell under conditions that are suitable for expression of the chimeric gene wherein expression of the chimeric gene results in production of altered levels of an isoflavone biosynthetic enzyme in the transformed host cell. An additional embodiment of the instant invention concerns a method for obtaining a nucleic acid fragment encoding all or substantially all of an amino acid sequence encoding a plant chalcone isomerase, isoflavone reductase and vestitone reductase. BRIEF DESCRIPTION OF THE DRAWINGS AND SEQUENCE DESCRIPTIONS The invention can be more fully understood from the following detailed description and the accompanying drawings and sequence descriptions which form a part of this application. FIG. 1 depicts the phenylpropanoid metabolic pathway illustrating the biosynthesis of isoflavones. FIG. 2 shows a comparison of the amino acid sequences of the Pueraria lobata chalcone flavanone isomerase (D63577) and the instant soybean chalcone isomerase (ssm.pk0013.e3). FIG. 3 shows a comparison of the amino acid sequences of the isoflavone reductase homolog from Lupinus albus (P52581) and the instant soybean isoflavone reductase (se3.pk0034.g5). FIG. 4 shows a comparison of the amino acid sequences of the Medicago sativa vestitone reductase (U28213) and the instant soybean vestitone reductase (sre.pk0016.c8). The following sequence descriptions and sequences listings attached hereto comply with the rules governing nucleotide and/or amino acid sequence disclosures in patent applications as set forth in 37 C.F.R. .sctn.1.821-1.825. SEQ ID NO:1 is the nucleotide sequence comprising part of the cDNA insert in clone ssm.pk0013.e3 encoding a soybean chalcone isomerase. SEQ ID NO:2 is the deduced amino acid sequence of a soybean chalcone isomerase derived from the nucleotide sequence of SEQ ID NO:1. SEQ ID NO:3 is the amino acid sequence encoding the Pueraria lobata chalcone flavanone isomerase having DDJB Accession No. D63577. SEQ ID NO:4 is the nucleotide sequence comprising part of the cDNA insert in clone se3.pk0034.g5 encoding a soybean isoflavone reductase. SEQ ID NO:5 is the deduced amino acid sequence of a soybean isoflavone reductase derived from the nucleotide sequence of SEQ ID NO:4. SEQ ID NO:6 is the amino acid sequence encoding the isoflavone reductase homolog from Lupinus albus having SWISS-PROT Accession No. P52581. SEQ ID NO:7 is the nucleotide sequence comprising part of the cDNA insert in clone sre.pk0016.c8 encoding a soybean vestitone reductase. SEQ ID NO:8 is the deduced amino acid sequence of a soybean vestitone reductase derived from the nucleotide sequence of SEQ ID NO:7. SEQ ID NO:9 is the amino acid sequence encoding the Medicago sativa vestitone reductase having GenBank Accession No. U28213. The Sequence Descriptions contain the one letter code for nucleotide sequence characters and the three letter codes for amino acids as defined in conformity with the IUPAC-IUB standards described in Nucleic Acids Research 13:3021-3030 (1985) and in the Biochemical Journal 219 (No. 2):345-373 (1984) which are herein incorporated by reference. The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. .sctn.1.822. DETAILED DESCRIPTION OF THE INVENTION The instant invention discloses the amino acid sequence for three enzymes involved in the synthesis and metabolism of isoflavones in soybeans: chalcone isomerase, isoflavone reductase and vestitone reductase. As these genes code for enzymes nearer to the desired isoflavones in the phenylpropanoid pathway (see FIG. 1), they may be more useful in manipulating isoflavone content without affecting other portions of the phenylpropanoid pathway associated with lignin, anthocyanin or flavonol biosynthesis. In the context of this disclosure, a number of terms shall be utilized. As used herein, an "isolated nucleic acid fragment" is a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases. An isolated nucleic acid fragment in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA or synthetic DNA. As used herein, "substantially similar" refers to nucleic acid fragments wherein changes in one or more nucleotide bases results in substitution of one or more amino acids, but do not affect the functional properties of the protein encoded by the DNA sequence. "Substantially similar" also refers to nucleic acid fragments wherein changes in one or more nucleotide bases does not affect the ability of the nucleic acid fragment to mediate alteration of gene expression by antisense or co-suppression technology. "Substantially similar" also refers to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of one or more nucleotides that do not substantially affect the functional properties of the resulting transcript vis-a-vis the ability to mediate alteration of gene expression by antisense or co-suppression technology or alteration of the functional properties of the resulting protein molecule. It is therefore understood that the invention encompasses more than the specific exemplary sequences. For example, it is well known in the art that antisense suppression and co-suppression of gene expression may be accomplished using nucleic acid fragments representing less that the entire coding region of a gene, and by nucleic acid fragments that do not share 100% identity with the gene to be suppressed. Moreover, alterations in a gene which result in the production of a chemically equivalent amino acid at a given site, but do not effect the functional properties of the encoded protein, are well known in the art. For example, a codon for the amino acid alanine, a hydrophobic amino acid, may be substituted by a codon encoding another less hydrophobic residue, such as glycine, or a more hydrophobic residue, such as valine, leucine, or isoleucine. Similarly, changes which result in substitution of one negatively charged residue for another, such as aspartic acid for glutamic acid, or one positively charged residue for another, such as lysine for arginine, can also be expected to produce a functionally equivalent product. Nucleotide changes which result in alteration of the N-terminal and C-terminal portions of the protein molecule would also not be expected to alter the activity of the protein. Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products. Moreover, the skilled artisan recognizes that substantially similar sequences encompassed by this invention are also defined by their ability to remain hybridized under conditions of moderate stringency (washes in 1.times.SSC, 0.1% SDS, at 55.degree. C.), with the sequences exemplified herein. Preferred substantially similar nucleic acid fragments of the instant invention are those nucleic acid fragments whose DNA sequences are 80% identical to the DNA sequence of the nucleic acid fragments reported herein. More preferred nucleic acid fragments are 90% identical to the identical to the DNA sequence of the nucleic acid fragments reported herein. Most preferred are nucleic acid fragments that are 95% identical to the DNA sequence of the nucleic acid fragments reported herein. Determination of percent identity of any DNA or protein sequences is performed by application of the comparison algorithm of Hein (Methods in Enzymology 183:626-645 (1990)), and using the following values for the variable parameters: GAP PENALTY=11, GAP LENGTH PENALTY=3, and for the case of pairwise alignments KTUPLE 6. A "substantial portion" of an amino acid or nucleotide sequence comprises enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to afford putative identification of that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., (1993) J. Mol. Biol. 215:403-410; see also www.ncbi.nlm.nih.gov/BLAST/). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a "substantial portion" of a nucleotide sequence comprises enough of the sequence to afford specific identification and/or isolation of a nucleic acid fragment comprising the sequence. The instant specification teaches partial or complete amino acid and nucleotide sequences encoding one or more particular plant proteins. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above. "Codon degeneracy" refers to divergence in the genetic code permitting variation of the nucleotide sequence without effecting the amino acid sequence of an encoded polypeptide. Accordingly, the instant invention relates to any nucleic acid fragment that encodes all or a substantial portion of the amino acid sequence encoding the isoflavone biosynthetic enzymes as set forth in SEQ ID NOs:2, 5 and 8. The skilled artisan is well aware of the "codon-bias" exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell. "Synthetic genes" can be assembled from oligonucleotide building blocks that are chemically synthesized using procedures known to those skilled in the art. These building blocks are ligated and annealed to form gene segments which are then enzymatically assembled to construct the entire gene. "Chemically synthesized", as related to a sequence of DNA, means that the component nucleotides were assembled in vitro. Manual chemical synthesis of DNA may be accomplished using well established procedures, or automated chemical synthesis can be performed using one of a number of commercially available machines. Accordingly, the genes can be tailored for optimal gene expression based on optimization of nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful gene expression if codon usage is biased towards those codons favored by the host. Determination of preferred codons can be based on a survey of genes derived from the host cell where sequence information is available. "Gene" refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5' non-coding sequences) and following (3' non-coding sequences) the coding sequence. "Native gene" refers to a gene as found in nature with its own regulatory sequences. "Chimeric gene" refers any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. "Endogenous gene" refers to a native gene in its natural location in the genome of an organism. A "foreign" gene refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. A "transgene" is a gene that has been introduced into the genome by a transformation procedure. "Coding sequence" refers to a DNA sequence that codes for a specific amino acid sequence. "Regulatory sequences" refer to nucleotide sequences located upstream (5' non-coding sequences), within, or downstream (3' non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, and polyadenylation recognition sequences. "Promoter" refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3' to a promoter sequence. The promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. Accordingly, an "enhancer" is a DNA sequence which can stimulate promoter activity and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue-specificity of a promoter. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. Promoters which cause a gene to be expressed in most cell types at most times are commonly referred to as "constitutive promoters". New promoters of various types useful in plant cells are constantly being discovered; numerous examples may be found in the compilation by Okamuro and Goldberg, (1989) Biochemistry of Plants 15:1-82. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths may have identical promoter activity. The "translation leader sequence" refers to a DNA sequence located between the promoter sequence of a gene and the coding sequence. The translation leader sequence is present in the fully processed mRNA upstream of the translation start sequence. The translation leader sequence may affect processing of the primary transcript to mRNA, mRNA stability or translation efficiency. Examples of translation leader sequences have been described (Turner, R. and Foster, G. D. (1995) Molecular Biotechnology 3:225). The "3' non-coding sequences" refer to DNA sequences located downstream of a coding sequence and include polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3' end of the mRNA precursor. The use of different 3' non-coding sequences is exemplified by Ingelbrecht et al., (1989) Plant Cell 1:671-680. "RNA transcript" refers to the product resulting from RNA polymerase-catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is referred to as the primary transcript or it may be a RNA sequence derived from posttranscriptional processing of the primary transcript and is referred to as the mature RNA. "Messenger RNA (mRNA)" refers to the RNA that is without introns and that can be translated into protein by the cell. "cDNA" refers to a double-stranded DNA that is complementary to and derived from mRNA. "Sense" RNA refers to RNA transcript that includes the mRNA and so can be translated into protein by the cell. "Antisense RNA" refers to a RNA transcript that is complementary to all or part of a target primary transcript or mRNA and that blocks the expression of a target gene (U.S. Pat. No. 5,107,065). The complementarity of an antisense RNA may be with any part of the specific gene transcript, i.e., at the 5' non-coding sequence, 3' non-coding sequence, introns, or the coding sequence. "Functional RNA" refers to antisense RNA, ribozyme RNA, or other RNA that is not translated yet has an effect on cellular processes. The term "operably linked" refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation. The term "expression", as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid fragment of the invention. Expression may also refer to translation of mRNA into a polypeptide. "Antisense inhibition" refers to the production of antisense RNA transcripts capable of suppressing the expression of the target protein. "Overexpression" refers to the production of a gene product in transgenic organisms that exceeds levels of production in normal or non-transformed organisms. "Co-suppression" refers to the production of sense RNA transcripts capable of suppressing the expression of identical or substantially similar foreign or endogenous genes (U.S. Pat. No. 5,231,020). "Altered levels" refers to the production of gene product(s) in transgenic organisms in amounts or proportions that differ from that of normal or non-transformed organisms. "Mature" protein refers to a post-translationally processed polypeptide; i.e., one from which any pre- or propeptides present in the primary translation product have been removed. "Precursor" protein refers to the primary product of translation of mRNA; i.e., with pre- and propeptides still present. Pre- and propeptides may be but are not limited to intracellular localization signals. A "chloroplast transit peptide" is an amino acid sequence which is translated in conjunction with a protein and directs the protein to the chloroplast or other plastid types present in the cell in which the protein is made. "Chloroplast transit sequence" refers to a nucleotide sequence that encodes a chloroplast transit peptide. A "signal peptide" is an amino acid sequence which is translated in conjunction with a protein and directs the protein to the secretory system (Chrispeels, J. J., (1991) Ann. Rev. Plant Phys. Plant Mol. Biol. 42:21-53). If the protein is to be directed to a vacuole, a vacuolar targeting signal (supra) can further be added, or if to the endoplasmic reticulum, an endoplasmic reticulum retention signal (supra) may be added. If the protein is to be directed to the nucleus, any signal peptide present should be removed and instead a nuclear localization signal included (Raikhel (1992) Plant Phys. 100:1627-1632). "Transformation" refers to the transfer of a nucleic acid fragment into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as "transgenic" organisms. Examples of methods of plant transformation include Agrobacterium-mediated transformation (De Blaere et al. (1987) Meth. Enzymol. 153:277) and particle-accelerated or "gene gun" transformation technology (Klein et al. (1987) Nature (London) 327:70-73; U.S. Pat. No. 4,945,050). Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described more fully in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1989 (hereinafter "Maniatis"). Nucleic acid fragments encoding several soybean isoflavone biosynthetic enzymes have been isolated and identified by comparison of random plant cDNA sequences to public databases containing nucleotide and protein sequences using the BLAST algorithms well known to those skilled in the art. Table 1 lists the isoflavone biosynthetic enzymes that are described herein, and the designation of the cDNA clones that comprise the nucleic acid fragments encoding these enzymes. TABLE 1 ______________________________________ Isoflavone Biosynthetic Enzymes Enzyme Clone ______________________________________ chalcone isomerase ssm.pk0013.e3 isoflavone reductase se3.pk0034.g5 vestitone reductase sre.pk0016.c8 ______________________________________ The nucleic acid fragments of the instant invention may be used to isolate cDNAs and genes encoding homologous enzymes from the same or other plant species. Isolation of homologous genes using sequence-dependent protocols is well known in the art. Examples of sequence-dependent protocols include, but are not limited to, methods of nucleic acid hybridization, and methods of DNA and RNA amplification as exemplified by various uses of nucleic acid amplification technologies (e.g., polymerase chain reaction, ligase chain reaction). For example, genes encoding other isoflavone biosynthetic enzymes, either as cDNAs or genomic DNAs, could be isolated directly by using all or a portion of the instant nucleic acid fragments as DNA hybridization probes to screen libraries from any desired plant employing methodology well known to those skilled in the art. Specific oligonucleotide probes based upon the instant nucleic acid sequences can be designed and synthesized by methods known in the art (Maniatis). Moreover, the entire sequences can be used directly to synthesize DNA probes by methods known to the skilled artisan such as random primers DNA labeling, nick translation, or end-labeling techniques, or RNA probes using available in vitro transcription systems. In addition, specific primers can be designed and used to amplify a part of or full-length of the instant sequences. The resulting amplification products can be labeled directly during amplification reactions or labeled after amplification reactions, and used as probes to isolate full length cDNA or genomic fragments under conditions of appropriate stringency. In addition, two short segments of the instant nucleic acid fragments may be used in polymerase chain reaction protocols to amplify longer nucleic acid fragments encoding homologous genes from DNA or RNA. The polymerase chain reaction may also be performed on a library of cloned nucleic acid fragments wherein the sequence of one primer is derived from the instant nucleic acid fragments, and the sequence of the other primer takes advantage of the presence of the polyadenylic acid tracts to the 3' end of the mRNA precursor encoding plant genes. Alternatively, the second primer sequence may be based upon sequences derived from the cloning vector. For example, the skilled artisan can follow the RACE protocol (Frohman et al., (1988) PNAS USA 85:8998) to generate cDNAs by using PCR to amplify copies of the region between a single point in the transcript and the 3' or 5' end. Primers oriented in the 3' and 5' directions can be designed from the instant sequences. Using commercially available 3' RACE or 5' RACE systems (BRL), specific 3' or 5' cDNA fragments can be isolated (Ohara et al., (1989) PNAS USA 86:5673; Loh et al., (1989) Science 243:217). Products generated by the 3' and 5' RACE procedures can be combined to generate full-length cDNAs (Frohman, M. A. and Martin, G. R., (1989) BioTechniques 1:165). Availability of the instant nucleotide and deduced amino acid sequences facilitates immunological screening cDNA expression libraries. Synthetic peptides representing portions of the instant amino acid sequences may be synthesized. These peptides can be used to immunize animals to produce polyclonal or monoclonal antibodies with specificity for peptides or proteins comprising the amino acid sequences. These antibodies can be then be used to screen cDNA expression libraries to isolate full-length cDNA clones of interest (Lerner, R. A. (1984) Adv. Immunol. 36:1; Maniatis). The nucleic acid fragments of the instant invention may be used to create transgenic plants in which expression of nucleic acid sequences (or their complements) encoding the disclosed biosynthetic enzymes result in levels of the corresponding endogenous enzymes that are higher or lower than normal. Alternatively, expression of the instant nucleic acid sequences may result in the production of the encoded enzymes in cell types or developmental stages in which they are not normally found. Either strategy would have the effect of altering the level of isoflavones. For example, overexpression of chalcone isomerase may result in an increase in isoflavone content in legumes, and anthocyanin, flavone and flavanols in other plant species. Chalcone isomerase overexpression may result in an increase in levels of 7,4'-dihydroxyflavone and 5,7,4'-trihydroxyflavone, precursors in the biosynthetic pathways leading to isoflavone, flavone and dihydroflavanol (which upon continuation leads to anthocyanin and flavanols) synthesis (see FIG. 1). Increased isoflavone content in legumes has been shown to be associated with beneficial health effects in humans. In contrast, certain soy food products would benefit from lower levels of isoflavone, flavone, anthocyanins and flavanols due to adverse effects on flavor. Accordingly, in some applications, decreased chalcone isomerase activity, induced by antisense suppression or co-suppression of gene expression, may be desireable. Likewise, overexpression of isoflavone reductase and vestitone reductase could lead to increased metabolism of isoflavones in legumes, resulting in lower levels of isoflavones. Conversly, inhibition of expression of genes encoding isoflavone reductase and vestitone reductase may result in increased isoflavone content by reducing isoflavone metabolism by these enzymes. Overexpression of the biosynthetic enzymes of the instant invention may be accomplished by first constructing chimeric genes in which the coding regions are operably linked to promoters capable of directing expression of a gene in the desired tissues at the desired stage of development. For reasons of convenience, the chimeric genes may comprise promoter sequences and translation leader sequences derived from the same genes. 3' Non-coding sequences encoding transcription termination signals may also be provided. The instant chimeric genes may also comprise one or more introns in order to facilitate gene expression. Plasmid vectors comprising the instant chimeric genes can then constructed. The choice of plasmid vector is dependent upon the method that will be used to transform host plants. The skilled artisan is well aware of the genetic elements that must be present on the plasmid vector in order to successfully transform, select and propagate host cells containing the chimeric gene. The skilled artisan will also recognize that different independent transformation events will result in different levels and patterns of expression (Jones et al., (1985) EMBO J. 4:2411-2418; De Almeida et al., (1989) Mol. Gen. Genetics 218:78-86), and thus that multiple events must be screened in order to obtain lines displaying the desired expression level and pattern. Such screening may be accomplished by Southern analysis of DNA, Northern analysis of mRNA expression, Western analysis of protein expression, or phenotypic analysis. For some applications it may be useful to direct the instant biosynthetic enzymes to different cellular compartments, or to facilitate their secretion from the cell. It is thus envisioned that the chimeric genes described above may be further supplemented by altering the coding sequences to encode enzymes with appropriate intracellular targeting sequences such as transit sequences (Keegstra, K. (1989) Cell 56:247-253), signal sequences or sequences encoding endoplasmic reticulum localization (Chrispeels, J. J., (1991) Ann. Rev. Plant Phys. Plant Mol. Biol. 42:21-53), or nuclear localization signals (Raikhel, N. (1992) Plant Phys. 100:1627-1632) added and/or with targeting sequences that are already present removed. While the references cited give examples of each of these, the list is not exhaustive and more targeting signals of utility may be discovered in the future. It may also be desirable to reduce or eliminate expression of the genes encoding isoflavone biosynthetic enzymes in plants for some applications. In order to accomplish this, chimeric genes designed for co-suppression of the instant biosynthetic enzymes can be constructed by linking the genes or gene fragments encoding the enzymes to plant promoter sequences. Alternatively, chimeric genes designed to express antisense RNA for all or part of the instant nucleic acid fragments can be constructed by linking the genes or gene fragment in reverse orientation to plant promoter sequences. Either the co-suppression or antisense chimeric genes could be introduced into plants via transformation wherein expression of the corresponding endogenous genes are reduced or eliminated. The instant isoflavone biosynthetic enzymes (or portions of the enzymes) may be produced in heterologous host cells, particularly in the cells of microbial hosts, and can be used to prepare antibodies to the enzymes by methods well known to those skilled in the art. The antibodies are useful for detecting the enzymes in situ in cells or in vitro in cell extracts. Preferred heterologous host cells for production of the instant isoflavone biosynthetic enzymes are microbial hosts. Microbial expression systems and expression vectors containing regulatory sequences that direct high level expression of foreign proteins are well known to those skilled in the art. Any of these could be used to construct chimeric genes for production of the instant isoflavone biosynthetic enzymes. These chimeric genes could then be introduced into appropriate microorganisms via transformation to provide high level expression of the enzymes. An example of a vector for high level expression of the instant isoflavone biosynthetic enzymes in a bacterial host is provided (Example 5). All or a portion of the nucleic acid fragments of the instant invention may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. For example, the instant nucleic acid fragments may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Maniatis) of restriction-digested plant genomic DNA may be probed with the nucleic acid fragments of the instant invention. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et at., (1987) Genomics 1:174-181) in order to construct a genetic map. In addition, the nucleic acid fragments of the instant invention may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the instant nucleic acid sequence in the genetic map previously obtained using this population (Botstein, D. et al., (1980) Am. J. Hum. Genet. 32:314-331). For example, the instant nucleic acid fragments may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Maniatis) of restriction-digested plant genomic DNA may be probed with the nucleic acid fragments of the instant invention. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et at., (1987) Genomics 1:174-181) in order to construct a genetic map. In addition, the nucleic acid fragments of the instant invention may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the instant nucleic acid sequence in the genetic map previously obtained using this population (Botstein, D. et al., (1980) Am. J. Hum. Genet.32:314-331). The production and use of plant gene-derived probes for use in genetic mapping is described in R. Bernatzky, R. and Tanksley, S. D. (1986) Plant Mol. Biol. Reporter 4(1):37-41. Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art. Nucleic acid probes derived from the instant nucleic acid sequences may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel, J. D., et al., In: Nonmammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein). In another embodiment, nucleic acid probes derived from the instant nucleic acid sequences may be used in direct fluorescence in situ hybridization (FISH) mapping (Trask, B. J. (1991) Trends Genet. 7:149-154). Although current methods of FISH mapping favor use of large clones (several to several hundred KB; see Laan, M. et al. (1995) Genome Research 5:13-20), improvements in sensitivity may allow performance of FISH mapping using shorter probes. A variety of nucleic acid amplification-based methods of genetic and physical mapping may be carried out using the instant nucleic acid sequences. Examples include allele-specific amplification (Kazazian, H. H. (1989) J. Lab. Clin. Med. 114(2):95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield, V. C. et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren, U. et al. (1988) Science 241:1077-1080), nucleotide extension reactions (Sokolov, B. P. (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid Mapping (Walter, M. A. et al. (1997) Nature Genetics 7:22-28) and Happy Mapping (Dear, P. H. and Cook, P. R. (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid fragment is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods. Loss of function mutant phenotypes may be identified for the instant cDNA clone encoding chalcone isomerase either by targeted gene disruption protocols or by identifying specific mutants for these genes contained in a maize population carrying mutations in all possible genes (Ballinger and Benzer, (1989) Proc. Natl. Acad. Sci USA 86:9402; Koes et al., (1995) Proc. Natl. Acad. Sci USA 92:8149; Bensen et al., (1995) Plant Cell 7:75). The latter approach may be accomplished in two ways. First, short segments of the instant nucleic acid fragments may be used in polymerase chain reaction protocols in conjunction with a mutation tag sequence primer on DNAs prepared from a population of plants in which Mutator transposons or some other mutation-causing DNA element has been introduced (see Bensen, supra). The amplification of a specific DNA fragment with these primers indicates the insertion of the mutation tag element in or near the genes encoding the plant chalcone isomerase. Alternatively, the instant nucleic acid fragments may be used as hybridization probes against PCR amplification products generated from the mutation population using the mutation tag sequence primer in conjunction with an arbitrary genomic site primer, such as that for a restriction enzyme site-anchored synthetic adaptor. With either method, a plant containing a mutation in the chalcone isomerase gene can be identified and obtained. This mutant plant can then be used to determine or confirm the natural function of the plant gene product. |
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