# Patent

## Title
Production of cereal grain with reduced starch granule size and uses thereof

## Abstract

The invention alters the physical characteristics of starch granules in a plant. Methods are provided for reducing starch granule size by stably introducing into the genome of the plant or plant cell a DNA construct comprising a polynucleotide encoding a polypeptide operably linked to a promoter that drives expression in a plant and operably linked to a plastid transit peptide. Compositions of the invention include transgenic plants and seeds having a reduced starch granule size. Compositions also include starch isolated from these plants and seeds. The modified starch granules find use in a wide range of food, feed, and industrial applications.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application Ser. No. 60/533,762, filed Dec. 31, 2003, the contents of which are hereby incorporated in their entirety by reference herein.


FIELD OF THE INVENTION
The invention relates to the production of modified starch granules in plants. Specifically, the starch granules have a reduced size, which may find utility in numerous feed and industrial applications.
BACKGROUND OF THE INVENTION
Starch is a complex polymer of glucosyl residues and is the major storage form for carbohydrates in higher plants. It is used to supply the needs of the plant for energy and biosynthesis when photosynthesis is not occurring. Starch accumulates in the chloroplasts of photosynthetic cells, as well as in amyloplasts present in storage organs such as seeds, fruit and tubers.
Starch is a mixture of two polysaccharides: amylose, which is a linear chain of glucosyl units linked by alpha-1,4-glycosidic bonds; and amylopectin, which is made up of many linear chains of alpha-1,4-polyglucans which are joined together by alpha-1,6 glycosidic bonds. The amylose/amylopectin ratio varies between plants and can affect the physical properties of starch, such as gelatinization temperature, retrogradation and viscosity.
Many plants with altered starch granules have been identified, and particular applications utilizing starch having these alterations have been recognized. Starch with no amylose (all amylopectin) is called “waxy” starch. Waxy starch, once gelatinized, is more rapidly digested than normal starch (70-75% amylopectin, 25-30% amylose). Waxy starches are useful as thickeners or gel-forming agents because they form a clear stable gel with little retrogradation (Morell et al. (1995) Aust. J. Plant Physiol. 22:647-660). High amylose (70%) starch forms insoluble aggregations, is more slowly digested, and therefore is suited for use in formulating adhesives, plastics and as a source of dietary fiber (Whistler R. L. (1984) “Starch” (Eds. R. L. Whistler, J. N. BeMiller and E. F. Paschall) Academic Press: Orlando; Doane (1994) Cereal Foods World 39:556-563). Boyer et al. showed that the increased proportion of larger granules in developing kernels of various genotypes (normal, ae, and ae su) is related to a higher amylose percentage, whereas in late development a decrease in amylose percentage results in a decrease in granule size (Boyer et al. (1976) Cereal Chemistry 53:327-337). The soft starch (h) gene increases starch granule size compared with normal genotypes, and results in a loose packing of starch granules (Gutiérrez et al. (2002) Crop Sci. 42:355-359).
The size and branching patterns of starch molecules also affects physical properties of starch, such as the gelatinization temperature, starch swelling and viscosity. In maize kernels, the sugaryl mutation causes the absence of a debranching enzyme which hydrolyzes alpha-1,6-glycosyl linkages of starch (James et al. (1995) Plant Cell 7:417-429). The mutation results in a decreased concentration of amylopectin and accumulation of the highly branched glucopolysaccharide phytoglycogen, and produces several advantageous physical characteristics of starch. For example, the accumulation of phytoglycogen in sul mutants is associated with smaller and more numerous starch granules (Wang et al. (1993) Cereal Chem. 70:171-179; Brown et al. (1971) Crop Sci. 11:297-302). In addition, starch from sugaryl mutant endosperm containing a high phytoglycogen content has a reduced temperature of gelatinization compared to that of waxy or normal starch (Wang et al. (1992) Cereal Chem. 69:328-334). The reduced gelatinization temperature increases starch solubility after processing (grinding, pelleting, steam flaking) at temperatures below the gelatinization temperature of normal starch. The smaller granule size and reduced temperature of gelatinization may both contribute to the high digestibility of starch from sugaryl mutant corn. See, for example, Fuwa et al. (1979) J. Nutr. Sci. Vitaminol. 25:103-114 and Fuwa et al. (1979) Cereal Chem 54:230-237 and Ninomya et al. (1989) Starch 41:165-167.
Granule size is important in the manufacturing of degradable plastic films, carbonless copy paper, dusting powder, baking powder, laundry-stiffening agents, and utilization of small granules as a fat substitute (Gutiérrez et al. (2002) Crop Sci. 42:355-359). Starch is a major source of carbohydrates for both man and livestock through crops such as wheat, maize, rice and potatoes. Starch is also used industrially in the production of paper, textiles, plastics, adhesives, and provides the raw material for some bioreactors. The type of starch affects the quality of the final product and therefore its profitability. Therefore, methods are needed to modify starch, particularly starch granule size, for use in various industrial applications. One example of an industrial application that may benefit from the use of grain with small starch granules is the corn dry-grind ethanol industry, in which starch of the grain is hydrolyzed to glucose for fermentation into ethanol. Grain with smaller-than-normal starch granules may be hydrolyzed at a lower cost by the α-amylase and glucoamylase enzymes used normally, because smaller starch granules have a larger surface area and would be “attacked” by α-amylase more efficiently (for example, in a quicker fashion, or with reduced amount of enzyme required) than with starch from a normal genetic background.
SUMMARY OF INVENTION
Methods and compositions are provided for modifying properties of starch granules in plants. Specifically, a method is provided for reducing starch granule size in a plant. The method comprises stably introducing into the genome of the plant or plant cell a DNA construct comprising a polynucleotide encoding a polypeptide of interest operably linked to a promoter that drives expression in a plant and operably linked to a plastid transit peptide. Expression of proteins that are natively plastid-associated and proteins that are not natively plastid-associated but which are targeted to a plant plastid with a plastid transit peptide result in the biosynthesis of starch granules with reduced size. The methods of the invention find use in reducing starch granule size, increasing the digestibility of starch, and in altering the physical properties of starch, including thermal stabilization, retrogradation, gelatinization temperature, water affinity, starch pasting, kernel texture, gel hardness, stickiness, and viscosity.
Compositions of the invention include an expression cassette or a DNA construct comprising a polynucleotide operably linked to a promoter that drives expression in a plant and operably linked to a plastid transit peptide, wherein the polynucleotide encodes a polypeptide of interest or fragment thereof. Compositions of the invention further include genetically modified plants having stably incorporated into their genome a heterologous polynucleotide operably linked to a plastid transit peptide, as well as transformed seed from the plant. Compositions further comprise the modified starch, which is useful as a food additive and in industrial applications, such as those previously mentioned.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows an alignment of an oleosin protein sequence from maize (Ole16) (NCBI Accession No. P13436) (SEQ ID NO:16), a cDNA fragment of the L3 lipid body-associated major protein of maize (NCBI Accession No. A29788) (SEQ ID NO:23), a 16 kD oleosin from Oryza sativa (NCBI Accession No.Q42980) (SEQ ID NO:24), oleosin 2 from barley (Hordeum vulgare) (NCBI Accession No.S57779) (SEQ ID NO:25), and a 16 kD oleosin from Bromus secalinus (NCBI Accession No. Q96543) (SEQ ID NO:26).
FIGS. 2A and 2B show an alignment of starch synthase protein sequences from cassava (NCBI Accession No. AAF13168) (SEQ ID NO:27), pea (NCBI Accession No. S61505) (SEQ ID NO:28), rice (NCBI Accession Nos. CAC59826; AAK81729; and AAK64284) (SEQ ID NOS:29, 30, and 31), and Curcuma zedoria (SEQ ID NO:2).
FIGS. 3A and 3B show an alignment of FtsZ2 protein sequences from liverwort (NCBI Accession No. BAC57988) (SEQ ID NO:32), moss (NCBI Accession No. T51090) (SEQ ID NO:33), bread wheat (NCBI Accession No. CAD99148) (SEQ ID NO:34), potato (NCBI Accession No. CAD99146) (SEQ ID NO:35), tobacco (NCBI Accession No. CAB89288) (SEQ ID NO:36), and Arabidopsis thaliana (NCBI Accession Nos. JC7770 and AAK63846) (SEQ ID NOS:37 and 38).
FIG. 4 shows an alignment of Arabidopsis mitochondrial carrier protein family (NCBI Accession No. AAK50084) (SEQ ID NO:21) to Zea mays Brittle-1 protein (ZM-Bt1) (SEQ ID NO:8).
FIG. 5 shows that overexpression of Brittle-1 improves the digestibility of grain. Grain was tested for in vitro digestibility by analyzing within-row segregating ears of maize that were either wild-type or carrying the transgene. Significantly increased Enzyme Digestible Dry Matter (EDDM) was observed after 4 hours of treatment.



DETAILED DESCRIPTION OF THE INVENTION
Compositions and methods are provided for the production of modified starch granules, which are useful in a wide range of food and industrial applications. Specifically, the starch granule size is reduced when compared to unmodified starch granules. By “starch” is intended a complex granular structure composed of polyglucan chains comprising amylopectin and amylose. By “polyglucan” is intended any polyglucan structure comprising glucose molecules connected by α1-4 glycosidic bonds or α1-4 and α1-6 glycosidic bonds. Characteristics of amylopectin include a high molecular weight (107-109 Da) and a polyglucan chain containing approximately 5% α-1,6 branches. Amylose is a smaller linear molecule (molecular weight of 105-106 Da) and contains very few α-1,6 branches (less than 1%) (Ball et al. (1996) Cell 86:349-352). The characteristics of amylose and amylopectin are further described in Nakamura et al. (1996) Plant Science 121:1-18 and in Helt et al. (1997) Plant Biochemistry and Molecular Biology, Oxford University Press, both of which are herein incorporated by reference.
Methods of the present invention comprise stably introducing into the genome of a plant a DNA construct comprising a polynucleotide of interest operably linked to a promoter that drives expression in a plant and operably linked to a plastid transit peptide, wherein the polynucleotide encodes a polypeptide or fragment thereof. The polypeptide of interest is thereby targeted to a plastid. The method of the invention increases the level of a polypeptide, or fragment thereof, in a plastid and thereby reduces starch granule size when compared to an unmodified plant. The polypeptide employed in this method may comprise a protein that is natively associated with a plant plastid or a protein operably linked to a heterologous plastid transit peptide. By “reduced” size of the starch granule is intended at least about 10%, at least about 12%, at least about 15%, at least about 20%, at least about 25%, and at least about 45% decrease in granule size compared to unmodified plants. Methods for measuring granule size are well known in the art (see, for example, Evers (1973) Starch 9:303-304; Evers and Lindley (1977) Journal of the Science of Food and Agriculture 28:98-102; Stark and Lynn (1992) Biochemical Society Transactions 20:7-12; Bechtel et al. (1990) Cereal Chemisty 67:59-63; Stoddard (2003) Aust. J. Agric. Res. 54:637-648).
The plants, plant cells, seeds, and plant tissues are “modified” in that they comprise one or more polynucleotides that, when expressed, lead to alteration of the physical properties of the starch granules. As noted below, various methods are available for creating modified plants, plant cells, and plant tissues including, but not limited to, transformation, transfection and breeding. Such techniques will lead to altered expression and targeting of proteins in the modified plant, plant cell, seed, or tissue.
It is to be understood that as used herein the term “transgenic” includes any cell, cell line, callus, tissue, plant part, or plant the genotype of which has been altered by the presence of heterologous nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic. The term “transgenic” as used herein does not encompass the alteration of the genome (chromosomal or extra-chromosomal) by conventional plant breeding methods or by naturally occurring events such as random cross-fertilization, non-recombinant viral infection, non-recombinant bacterial transformation, non-recombinant transposition, or spontaneous mutation.
As used herein, the term plant includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli, plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruit, kernels, ears, cobs, husks, stalks, roots, root tips, anthers, and the like. Grain is intended to mean the mature seed produced by commercial growers for purposes other than growing or reproducing the species. Progeny, variants, and mutants of the regenerated plants are also included within the scope of the invention, provided that these parts comprise the introduced polynucleotides.
By “plastid transit peptide” is intended an N-terminal sequence of about 30-100 amino acids that targets proteins into plastid organelles. After protein translocation, the transit peptides are removed by proteolytic cleavage. Transit peptides target precursor proteins from the cytosol into plastids, such as chloroplasts and amyloplasts. Proteins targeted to chloroplasts may also contain domains with intraorganellar information, resulting in transport of the protein across the thylakoid membrane and into the lumen (Ko and Cashmore (1989) EMBO J. 8:3187-3194; Meadows et al. (1989) FEBS Lett. 253:244-246; Hageman et al. (1990) Plant Cell 2:479-494). Plastids of different plant tissues are able to import foreign proteins, indicating that plastids may have similar or identical protein import mechanisms (Weisbeek et al. (1989) J. Cell Sci. Suppl. 11:199-223). Many studies have shown that chloroplast transit peptides can effectively target proteins to other plastid types. The amyloplast transit peptide of the waxy protein of maize can direct the import of an artificial preprotein consisting of the waxy transit peptide and the first 34 amino acids of the mature waxy protein fused in-frame to the beta-glucuronidase of E. coli into chloroplasts (Klosgen et al. (1989) Mol. Gen. Genet. 217:155-161; Klosgen and Weil (1991) Mol. Gen. Genet. 225:297-304). Conversely, the chloroplast ribulose-1,5-bisphosphate carboxylase precursor proteins are targeted to leucoplasts (Boyle et al. (1986) Plant Physiol. 81:817-822; Halpin et al. (1989) FEBS Lett. 258:32-34), etioplasts (Schindler and Soll (1986) Arch. Biochem. Biophys. 247:211-220), and amyloplasts (Strzalka et al. (1987) Biochem. Biophys. Res. Commun. 149:799-806). Therefore, the protein import mechanism of plants is able to recognize different types of transit peptides regardless of the protein being transported. This is to be expected, as all plastid types are derived from proplastids (Wan et al. (1996) J. Biol. Chem. 271:31227-31233).
Transit peptides for use in the present invention are known in the art and include, but are not limited to, those from Brittle-1 (SEQ ID NO:10); Curcuma soluble starch synthase (SEQ ID NO:4); chloroplast small subunit of ribulose-1,5-bisphosphate carboxylase (Rubisco) (de Castro Silva Filho et al. (1996) Plant Mol. Biol. 30:769-780; Schnell et al. (1991) J. Biol. Chem. 266(5):3335-3342); 5-(enolpyruvyl)shikimate-3-phosphate synthase (EPSPS) (Archer et al. (1990) J. Bioenerg. Biomemb. 22(6):789-810); tryptophan synthase (Zhao et al. (1995) J. Biol. Chem. 270(11):6081-6087); plastocyanin (Lawrence et al. (1997) J. Biol. Chem. 272(33):20357-20363); chorismate synthase (Schmidt et al. (1993) J. Biol. Chem. 268(36):27447-27457); the light harvesting chlorophyll a/b binding protein (LHBP) (Lamppa et al. (1988) J. Biol. Chem. 263:14996-14999), the transit peptide for the plant plastid acyl carrier protein (ACP), the transit peptide for GBSSI (granule bound starch synthase I) and the native transit peptide of a targeting protein. See also Von Heijne et al. (1991) Plant Mol. Biol. Rep. 9:104-126; Clark et al. (1989) J. Biol. Chem. 264:17544-17550; Della-Cioppa et al. (1987) Plant Physiol. 84:965-968; Romer et al. (1993) Biochem. Biophys. Res. Commun. 196:1414-1421; and Shah et al. (1986) Science 233:478-481. Other examples of transit peptides include the transit peptides described in U.S. Publication No. US 2002/0073443 and U.S. Publication No. US 2002/0178467. Combinations of transit peptides may also be used. Such transit peptides are known in the art. See, for example, U.S. Publication No. US 2002/0178467. Each of these references is hereby incorporated in its entirety by reference herein.
It is recognized that synthetic or variant transit peptides may be utilized. In this regard, three major blocks of amino acid homology have been found in transit peptides of two chloroplast proteins (Karlin-Neumann and Tobin (1986) EMBO J. 5:9-13). Functional domains of the ferredoxin transit peptide have also been identified (Pilon et al. (1995) J. Cell Biol. 270:3882-3893; Rensink et al. (1998) Plant Physiol. 118: 691-699). Conserved cleavage-site motifs in chloroplast or mitochondrial targeting proteins have been identified (Gavel et al. (1990) FEBS Lett. 261:455-458; Gavel et al. (1990) Protein Eng. 4:33-37; Emanuelsson et al. (1999) Protein Science 8:978-984).
The polypeptide of interest may be one that is natively plastid-associated or may be one that is not natively plastid-associated but which is targeted to a plant plastid with a plastid transit peptide. In one embodiment, the polypeptide of interest is one that is involved in plastid division, such as FtsZ. In another embodiment, the polypeptide is involved in lipid storage, such as oleosin. By “lipid storage” or “lipid storage-related” is intended a polypeptide that associates with a lipid storage body in a plant, such as an oil body. In yet another embodiment, the polypeptide is involved in lipid synthesis. In another embodiment, the polypeptide is involved in amino acid metabolism. In still another embodiment, the polypeptide is a chloroplast-associated protein. By “chloroplast-associated” protein is intended a polypeptide that is natively expressed in a chloroplast or is targeted to the chloroplast. Methods for identifying chloroplast-associated proteins are well known in the art. See, for example, Wijk (2000) Trends Plant Sci. 5:420-425; Leister (2003) Trends Genet. 19:47-56), where the identification of coding regions of chloroplast proteins by experimental proteomic analysis is described. In another embodiment, the polypeptide of interest is a starch-related polypeptide. By “starch-related” is intended a polypeptide that is involved in the transport, synthesis, or regulation of starch, including, but not limited to, a plastid-associated polypeptide or an enzyme involved in starch synthesis.
By “plastid-associated polypeptide” is intended a polypeptide that is targeted to or expressed in a plastid, including those targeted to the outer envelope membrane, the inner envelope membrane, the intermembrane space, the stroma, the thylakoid membrane, and the thylakoid lumen of a plastid. By “plastid” is intended any plastidic organelle of a plant, including, but not limited to a proplastid, an etioplast, a chloroplast, a chromoplast, and a leucoplast. All plastids share certain features, including being enclosed by an envelope composed of two concentric membranes. Proplastids are the precursors of all plastid types and are present in the immature cells of plant meristems and cells of developing endosperm (Bechtel and Wilson (2003) Cereal Chem. 80:175-183). Etioplasts are present in plants that are grown in the dark, and contain a yellow chlorophyll precursor instead of chlorophyll. When exposed to the light, etioplasts develop into chloroplasts. Chloroplasts are specialized for photosynthesis and contain an internal thylakoid membrane system. Other plastids have two membranes, but lack the thylakoid membrane and other components of the photosynthetic apparatus. Chromoplasts lack chlorophyll, but contain carotenoids. Leucoplasts are nonpigmented and store a variety of energy sources in nonphotysynthetic tissues. One form of a leucoplast is an amyloplast, which accumulates starch in various tissues. Another form of leucoplast is an elaioplast, which functions in lipid storage. See Lodish et al. (2000) Molecular Cell Biology (4th ed. W. H. Freeman & Co., New York), for more information about plastids.
The coding sequence for any polypeptide may be used. Examples include, but are not limited to, Brittle-1, FtsZ, oleosin, and starch synthase. See the sequences set forth in SEQ ID NOS:2, 6, 8, 12, 14, and 16, or a fragment or variant thereof. In some embodiments, the polypeptide is an enzyme involved in starch synthesis, including, but not limited to, a phosphoglucomutase, an ADP glucose pyrophosphorylase, a soluble or granule-bound starch synthase, or a starch branching enzyme; the polypeptide may be involved in transport into or out of the plastid, or may be a debranching enzyme, such as an isoamylase or a pullulanase.
The maize Brittle-1 (Bt-1) locus was identified in 1926 by mutations that decreased the amount of starch produced in the endosperm (Mangelsdorf (1926) Conn. Agric. Exp. Stn. Bull. 279:509-614; Wentz (1926) J. Hered. 17:327-329). Bt-1 encodes a seed-specific, amyloplast membrane protein thought to transport ADP-glucose, the substrate of starch biosynthesis, into the plastid (Sullivan and Kaneko (1995) Planta 196:477-484; Sullivan et al. (1991) Plant Cell 3:1337-1348). Bt-1-encoded protein shows the greatest sequence similarity to Arabidopsis mitochondrial carrier protein family (i.e. 53% amino acid sequence identity). The NCBI Accession Number for maize Bt-1 is P29518. An alignment of maize Bt-1 (SEQ ID NO:6) with Arabidopsis mitochondrial carrier protein family (NCBI Accession No. AAK50084) (SEQ ID NO:15) is provided in FIG. 4. Bt-1 has a KTGGL (SEQ ID NO:16) motif (amino acid residues 36-40 of SEQ ID NO:6) common to the ADP-glucose-binding site of starch synthases and bacterial glycogen synthases (Shannon et al. (1998) Plant Physiol. 117:1235-1252). A variant of Bt-1, Bt1-m has been identified (NCBI Accession No. M79334) that has a transposable element inserted into it (Sullivan et al., supra). Methods to assay for solute transport into plastids are known in the art (see, for example, Shannon et al., supra.; Keegstra and Froehlich (1999) Curr. Opinion Plant Biol. 2:471-6). Each of these Accession Nos. is herein incorporated by reference.
Oleosin is an amphipathic protein normally found within the membrane of plants' lipid storage bodies called oil bodies. Expression occurs in tissues that produce storage lipids such as triacylglycerols. In maize, expression is typically very strong in scutellar and aleurone cells, while typically extremely low in endosperm cells. Oleosin is divided into three structural portions: an N-terminal amphipathic stretch of undefined secondary structures residing on the organelle surface (20-60 residues); a conserved central hydrophobic domain of beta-strand structure penetrating into the matrix (about 70 residues); and a C-terminal amphipathic-helix locating on the organelle surface, interacting with the phospholipid layer (60-100 residues). The three structural portions enable the protein to interact with other molecules on the surface of an oil body (Ting et al. (1997) J. Biol. Chem. 272:3699-3706). The most conserved region is the 13-amino acid residue turn separating the two anti-parallel beta-strands (Huang (1996) Plant Physiol. 110:1055-1061). Inside this region are three universally conserved proline residues, forming the “proline knot” motif. The loss of the proline knot results in instability of the oleosin during trafficking (Abell et al. (1997) Plant Cell 9:1481-1493).
The function of oleosin has not been fully characterized, but it is known to serve a structural role in stabilizing the lipid body. The long hydrophobic strands act as an anchor and penetrate into the matrix of triacylglycerols, and the cytosol-exposed regions interact with the surface lipids to generate additional stability. Oleosins form a steric barrier between adjacent oil bodies, preventing their coalescence (Huang (1996) Plant Physiol. 110:1055-1061). Oleosin may also act as recognition signals for specific binding of lipase to the lipid bodies, to facilitate lipolysis during germination (Vance and Huang (1987) J. Biol. Chem. 262:11275-11279; Huang (1996) Plant Physiol. 110:1055-1061).
The first oleosin gene, L3, was cloned from maize using in vitro translation and an anti-L3 antibody (Vance et al. (1987) J. Biol. Chem. 262:11275-11279). Numerous isoforms of oleosin genes from such different species as Brassica, soybean, carrot, pine, and Arabidopsis have been cloned (Huang, A. H. C. (1992) Ann. Reviews Plant Phys. and Plant Mol. Biol. 43:177-200; Kirik et al. (1996) Plant Mol. Biol. 31:413-417; Van Rooijen et al. (1992) Plant Mol. Biol. 18:1177-1179; Zou et al. (1996) Plant Mol. Biol. 31:429-433). An alignment of maize Ole16 (NCBI Accession No. P13436) (SEQ ID NO:16), a cDNA fragment of the L3 lipid body-associated major protein of maize (NCBI Accession No. A29788) (SEQ ID NO:23), a 16 kD oleosin from Oryza sativa (NCBI Accession No. Q42980) (SEQ ID NO:24), oleosin 2 from barley (Hordeum vulgare) (NCBI Accession No. S57779) (SEQ ID NO:25), and a 16 kD oleosin from Bromus secalinus (NCBI Accession No. Q96543) (SEQ ID NO:26) is provided in FIG. 1. Oleosin protein sequences predicted from these genes are highly conserved, especially for the central hydrophobic domain. Methods to determine the secondary structure and other protein characteristics of oleosin-like proteins are well known in the art (see, for example, Vance and Huang (1987) J. Biol. Chem. 262:11275-11279; Tzen et al. (1992) J. Biol. Chem. 267:15626-15634; Ting et al. (1997) Journal of Biological Chemistry 272:3699-3706; Ting and Huang (1997) “Oils-to-oleosins ratio determines the size and shape of oil bodies in maize kernels.” Physiology, Biochemistry and Molecular Biology of Plant Lipids. J. P. Williams, M. U. Khan and N. W. Lem. PO Box 17/3300 AA Dordrecht/Netherlands, Kluwer Academic Publ:295-297).
Starch synthase transfers a glucose residue from ADP-glucose or, less commonly, UDP-glucose, to the OH-group in the 4-position of the terminal glucose molecule in the polysaccharide chain. The starch synthases are divided into three classes based on their subcellular location (soluble phase, granule fraction, or both). Several plant starch synthases are known in the art. Examples of granule-bound starch synthases include, but are not limited to, cassava (NCBI Accession No. AAF13168), pea (NCBI Accession No. S61505), potato (NCBI Accession No. Q43847), maize (NCBI Accession No. CAA27574), sorghum (NCBI Accession No. AAC49804), sweet potato (NCBI Accession Nos. AAC19119 and AAD38494), wheat (NCBI Accession Nos. BAB71785 and BAA77351), sugar beet (NCBI Accession No. AF173652), and rice (NCBI Accession Nos. AAD41242, AAD41241, and A1736032). Examples of soluble starch synthases include, but are not limited to, rice (NCBI Accession Nos. CAC59826, AAK64284, and AAK81729), Arabidopsis thaliana (NCBI Accession No. AAF24126), potato (NCBI Accession No. P93568), wheat (NCBI Accession No. Q43654), and sorghum (NCBI Accession No. AAD45815). Each of these Accession Nos. is herein incorporated by reference. Starch synthases are also disclosed in U.S. Pat. No. 6,423,886. An alignment of starch synthase from cassava (SEQ ID NO:27), pea (SEQ ID NO:28), rice (SEQ ID NOS:29, 30, and 31), and Curcuma (SEQ ID NO:2) is provided in FIG. 2. Plant starch synthase consensus regions can be found in Cao et al. (1999) Plant Physiol. 120:205-215.
Variants of plant starch synthases include both loss of function, recessive, and gain of function, dominant, mutant alleles. For example, the major granule-bound starch synthase in maize is encoded by the Wx gene. Recessive mutations in Wx resulting in either the absence or a decrease in the granule-bound starch synthase activity have been identified (Nelson et al. (1968) Genetics 60:507-524, Shure et al. (1983) Cell 35:225-233, Wessler et al. (1985) PNAS 82:4177-4181, and Klosgen et al. (1986) Mol. Gen. Genet. 203:237-244). Other variants of plant granule bound starch synthases include: the amf-1 from potato (Visser et al. (1989) Plant Science 64:185-192), the Wx-D1b null allele from wheat (NCBI Accession No. AF113844), and the Wx-A1 allele from wheat (NCBI Accession No. AF113843). Each of these Accession Nos. is herein incorporated by reference. Variants of soluble starch synthases include mutants of dull1 (Gao et al. (1998) The Plant Cell 10:399-412).
Assays for soluble or granule-bound starch synthases are also known in the art. Such assays include measuring the affinity for ADP glucose and glucan substrates, glucan synthase assays, activation by amylopectin, and the processivity of glucan chain extension. Such assays can be found in, for example, Edwards et al. (1999) European J. Biochem. 266:724-736, Cao et al. (1999) Plant Physiol. 120:205-215, and Cao et al. (2000) Arch. Biochem. Biophys. 373:135-146, herein incorporated by reference.
FtsZ proteins are involved in plastid division and are divided into two families, FtsZ1 and FtsZ2 (Osteryoung and Pyke (1998) Curr. Opin. Plant Biol. 1:475-479; Osteryoung et al. (1998) Plant Cell 10:1991-2004). FtsZ has also been identified in prokaryotes, where it is involved in cell division, and forms a ring at the leading edge of the cell division site. Bacterial and eukaryotic FtsZ proteins are highly conserved in the NH2-terminal region, but more variable in the COOH terminus (Kiessling et al. (2000) J. Cell Biol. 151:945-950). Three FtsZ genes (FtsZ1-1, FtsZ2-1 and FtsZ2-2) have been identified in Arabidopsis. They all contain cleavable chloroplast targeting transit peptide sequences (McAndrew et al. (2001) Plant Physiol. 127:1656-1666). Antisense down-regulation or overexpression of either FtsZ1 or FtsZ2 in transgenic Arabidopsis inhibits chloroplast division (Osteryoung et al. (1998) Plant Cell 10:1991-2004; Stokes et al. (2000) Plant Physiol. 124:1668-1677; McAndrew et al. (2001) Plant Physiol. 127:1656-1666)
Numerous FtsZ2 proteins have been isolated, including liverwort (NCBI Accession No. BAC57988) (SEQ ID NO:32), moss (NCBI Accession No. T51090) (SEQ ID NO:33), bread wheat (NCBI Accession No. CAD99148) (SEQ ID NO:34), potato (NCBI Accession No. CAD99146) (SEQ ID NO:35), tobacco (NCBI Accession No. CAB89288) (SEQ ID NO:36), Arabidopsis thaliana (NCBI Accession No. JC7770 (SEQ ID NO:37) and NCBI Accession No. AAK63846 (SEQ ID NO:38)). The amino acid sequences for these FtsZ2 proteins are aligned in FIG. 3.
The first plant FtsZ cDNA was isolated from a terrestrial seedless plant Physcomitrella patens (Strepp et al. (1998) Proc. Natl. Acad. Sce. U.S.A. 95:4368-4373). Its function was established by knockout plants generated by homologous recombination. Seven out of 51 transgenics contain one huge chloroplast per cell with no effect on mitochondrial division, indicating the chloroplast division in those plants was inhibited. Assays for measuring FtsZ protein activity are known in the art (see, for example, Stokes et al. (2000) Plant Physiol. 124:1668-1677; Vitha et al. (2001) J Cell Biol 153:111-119). Methods to assay for expression, including tissue-preferred expression, of the various polypeptides are known in the art. For example, transcript or protein levels can be assayed using standard molecular biology techniques.
The method of the invention increases the level of a polypeptide in a plastid. In general, the polypeptide level is increased by at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% relative to a native control plant, plant part, or cell which did not have the sequence of interest introduced. The increase in the level of the polypeptide in the plastid may occur during and/or subsequent to growth of the plant to the desired stage of development. In specific embodiments, the polypeptides of the present invention are modulated in monocots, particularly maize.
An increase in the level of the heterologous polypeptide of the invention can be achieved by providing to the plant a heterologous polypeptide. As discussed elsewhere herein, many methods are known the art for providing a polypeptide to a plant including, but not limited to, direct introduction of the polypeptide into the plant, introducing into the plant (transiently or stably) a polynucleotide construct encoding a polypeptide.
The expression level of the heterologous polypeptide may be measured directly, for example, by assaying for the level of the heterologous polypeptide in the plant, or indirectly, for example, by measuring the activity of the heterologous polypeptide in the plant or by assaying for reduced starch granule size. Methods for determining the activity of representative polypeptides of interest are disclosed elsewhere herein.
In specific embodiments, the polypeptide or the polynucleotide of the invention is introduced into the plant cell. Subsequently, a plant cell having the introduced sequence of the invention is selected using methods known to those of skill in the art such as, but not limited to, Southern blot analysis, DNA sequencing, PCR analysis, or phenotypic analysis. A plant or plant part altered or modified by the foregoing embodiments is grown under plant forming conditions for a time sufficient to modulate the concentration and/or activity of polypeptides of the present invention in the plant. Plant forming conditions are well known in the art and discussed briefly elsewhere herein.
Physical Characteristics of Starch
Embodiments of the present invention produce transgenic plants that have reduced starch granule size. This reduced starch granule size increases the effective surface area and further enhances the rate of enzymatic digestion.
Furthermore, it is believed that expression of proteins in plastids such as amyloplasts and chloroplasts may produce starch granules that display a reduced temperature of gelatinization that would increase starch solubility during processing (grinding, pelleting, steam flaking) at temperatures below the gelatinization temperature of normal starch. The reduced gelatinization temperature may elevate the degree of starch gelatinization in processed feed and hence, starch digestibility, and reduce the energy required in feed processing (grinding, pelleting, steam-flanking).
The reduced starch granule size may lead to an increased digestibility of the starch. The modified starch granules with increased digestibility may be useful as silage or forage for feed animals. By “increased digestibility” is intended the rate of starch digestion is about 5% to about 10%, about 10% to about 15%, about 15% to about 25%, about 25% to about 50% or greater, or at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% or greater than that of starch from an unmodified plant. By use of the PHI in vitro digestion test (4 hr. Enzyme Digestible Dry Matter (EDDM)), smaller granules produced by overexpression of Brittle-1 showed up to 13% greater EDDM that the control. Methods for measuring the rate of starch digestion include measuring α-amylase hydrolysis, and are well known in the art (see, for example Knutson et al. (1982) Cereal Chem. 59:512-515; Pell and Schofield (1993) J. Dairy Sci. 76:1063-1073; Schofield and Pell (1995) J. Anim. Sci. 73:3455-3463; Franco et al. (1998) Starch 50:193-198; Kereliuk and Sosulski (1996) Food Science and Technology 29:349-356).
In one embodiment, starch from plants with reduced granule size may be chemically modified more effectively, for use in the production of food and industrial starches. In another embodiment, starch from plants with reduced granule size produces a different “mouth feel” when used as a food ingredient. This is useful in the manufacture of various processed food products, for example, starch-based fat mimetics. Sensory analysis of reduced-fat frozen desert mixes into which small starch granules from wheat and amaranth were incorporated indicated that up to 50% of the fat may be replaced by these starches at the 2% level (Malinski et al. (2003) Cereal Chem. 80:1-4). Methods for formulating deserts using modified starches and for performing sensory analysis of the products are well known in the art (see Malinski et al., supra).
In yet another embodiment, the grinding property of the grain is modified (i.e. the particle size distribution of ground grain), whereby less energy is needed to produce a ground product. This would benefit the feed and dry grind ethanol markets. In yet another embodiment, the grit yield of the grain is improved, leading to an advantage in the corn dry mill industry. Other physical properties of starch granules, such as thermal stabilization, retrogradation, water affinity, starch pasting, kernel texture, gel hardness, and viscosity might be altered as a result of the methods of the current invention. Assays to measure these physical characteristics are well known in the art (see, for example, Gaines et al, (2000) Cereal Chem. 77:163-168 and Chiotelli and Le Meste (2002) Cereal Chem. 79:286-293; Eliasson and Gudmundsson (1996) “Starch: Physicochemical and functional aspects.” Carbohydrates in Food. A. C. Eliasson. 270 Madison Ave/New York/N.Y. 10016, Marcel Dekker: 431-503; Hizukuri (1996) “Starch: Analytical aspects.” Carbohydrates in Food A. C. Eliasson. 270 Madison Ave/New York/N.Y. 10016, Marcel Dekker: 347-429; Morrison and Karkalas (1990) “Starch”. Methods In Plant Biochemistry. P. M. Dey and J. B. Harborne, Academic Press Limited. 2:323-352.)
Variants and Fragments
Fragments and variants of the polynucleotide of interest and proteins encoded thereby can be used in the present invention. By “fragment” is intended a portion of the polynucleotide of interest or a portion of the amino acid sequence and hence protein encoded thereby. Fragments of a polynucleotide may encode protein fragments that retain the biological activity of the native protein and, when expressed in a plant plastid, reduce starch granule size. Thus, fragments of a polynucleotide may range from at least about 20 nucleotides, about 50 nucleotides, about 100 nucleotides, and up to the full-length polynucleotide encoding the proteins used in the methods of the invention.
A fragment of a polynucleotide that encodes a biologically active portion or a non-biologically active portion of a polypeptide of the invention will encode at least 15, 25, 30, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600 or 650 contiguous amino acids, or up to the total number of amino acids present in a full-length protein of the invention (for example, 690 amino acids for SEQ ID NO:2, 436 for SEQ ID NO:8, 467 for SEQ ID NO:14, and 156 for SEQ ID NO:16).
Thus, a fragment of a polynucleotide may encode a biologically active portion of a polypeptide. A biologically active portion of a polypeptide can be prepared by isolating a portion of one of the polynucleotides encoding a polypeptide, expressing the encoded portion of the protein (e.g., by recombinant expression in vitro), and assessing the activity of the encoded portion of the polypeptide. Nucleic acid molecules that are fragments of a polynucleotide that modulate the activity of a polypeptide comprise at least 16, 20, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000 contiguous nucleotides, or up to the number of nucleotides present in a full-length polynucleotide encoding the protein (for example, 2073 nucleotides for SEQ ID NO:1, 1311 for SEQ ID NO:7, 1404 for SEQ ID NO:13, and 471 for SEQ ID NO:15).
By “variants” is intended substantially similar sequences. As used herein, a “native” polynucleotide or polypeptide comprises a naturally occurring polynucleotide or amino acid sequence, respectively. For polynucleotides, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode similar amino acid sequences. Naturally occurring allelic variants such as these can be identified with the use of well-known molecular biology techniques, as, for example, with polymerase chain reaction (PCR) and hybridization techniques as outlined below. Variant polynucleotides also include synthetically derived polynucleotides, such as those generated, for example, by using site-directed mutagenesis but which still encode a polypeptide. Generally, variants of a particular polynucleotide of the invention will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular polynucleotide as determined by sequence alignment programs and parameters as described elsewhere herein.
Variants of a particular polynucleotide used in the methods of the invention (i.e., the reference polynucleotide) can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide. Thus, for example, isolated polynucleotide that encode a polypeptide with a given percent sequence identity to the polypeptide of SEQ ID NOS:2, 6, 8, 12, 14, and 16 are disclosed. Percent sequence identity between any two polypeptides can be calculated using sequence alignment programs described elsewhere herein. Where any given pair of polynucleotides of the invention is evaluated by comparison of the percent sequence identity shared by the two polypeptides they encode, the percent sequence identity between the two encoded polypeptides is at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity.
By “variant” protein is intended a protein derived from the native protein by deletion (so-called truncation) or addition of one or more amino acids to the N-terminal and/or C-terminal end of the native protein; deletion and/or addition of one or more amino acids at one or more sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein. Variant proteins encompassed by the present invention are biologically active, that is they continue to possess the biological activity of the native protein and, when expressed in a plant plastid, such as an amyloplast or a chloroplast, reduce starch granule size. Such variants may result from, for example, genetic polymorphism or from human manipulation. Biologically active variants of a native polypeptide will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the amino acid sequence for the native protein as determined by sequence alignment programs described elsewhere herein. A biologically active variant of a protein of the invention may differ from that protein by as few as 1-15 amino acid residues, as few as 1-10, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue. Peptides that are “substantially similar” share sequences as noted above except that residue positions that are not identical may differ by conservative amino acid changes.
The proteins used in the methods of the invention may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions. Methods for such manipulations are generally known in the art. For example, amino acid sequence variants of the polypeptides can be prepared by mutations in the DNA. Methods for mutagenesis and polynucleotide alterations are well known in the art. See, for example, Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) Methods in Enzymol. 154:367-382; U.S. Pat. No. 4,873,192; Walker and Gaastra, eds. (1983) Techniques in Molecular Biology (MacMillan Publishing Company, New York) and the references cited therein. Guidance as to appropriate amino acid substitutions that do not affect biological activity of the protein of interest may be found in the model of Dayhoff et al. (1978) Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found., Washington, D.C.), herein incorporated by reference. Conservative substitutions, such as exchanging one amino acid with another having similar properties, may be optimal.
Thus, the genes and polynucleotides used in the present invention include both the naturally occurring sequences as well as mutant forms. Likewise, the proteins used in the present invention encompass naturally occurring proteins as well as variations and modified forms thereof. Such variants will continue to possess the desired ability to reduce starch granule size when expressed in a plant plastid such as an amyloplast or a chloroplast. Obviously, the mutations that will be made in the DNA encoding the variant must not place the sequence out of reading frame and optimally will not create complementary regions that could produce secondary mRNA structure. See, EP Patent Application Publication No. 75,444.
The deletions, insertions, and substitutions of the protein sequences used in the methods encompassed herein are not expected to produce radical changes in the characteristics of the protein. However, when it is difficult to predict the exact effect of the substitution, deletion, or insertion in advance of doing so, one skilled in the art will appreciate that the effect will be evaluated by routine screening assays. That is, the activity can be evaluated by assaying the characteristics of the starch granule synthesized. See Experimental section for methods to analyze the physical properties of starch granules. Alternatively, the activity of the protein can be assayed using methods described herein and compared to that of the unmodified protein.
Variant polynucleotides and proteins also encompass sequences and proteins derived from a mutagenic and recombinogenic procedure such as DNA shuffling. With such a procedure, one or more different sequences can be manipulated to create a new sequence possessing the desired properties. In this manner, libraries of recombinant polynucleotides are generated from a population of related sequence polynucleotides comprising sequence regions that have substantial sequence identity and can be homologously recombined in vitro or in vivo. For example, using this approach, sequence motifs encoding a domain of interest may be shuffled between the starch synthase gene of SEQ ID NO:3 and other known starch synthase genes to obtain a new gene coding for a protein with an improved property of interest, such as an increased Km in the case of an enzyme. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) Proc. Natl. Acad. Sci. USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997) Proc. Natl. Acad. Sci. USA 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458.
The following terms are used to describe the sequence relationships between two or more polynucleotides: (a) “reference sequence”, (b) “comparison window”, (c) “sequence identity”, (d) “percentage of sequence identity”, and (e) “substantial identity”.
(a) As used herein, “reference sequence” is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence.
(b) As used herein, “comparison window” makes reference to a contiguous and specified segment of a polynucleotide, wherein the polynucleotide in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Generally, the comparison window is at least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50, 100, or longer. Those of skill in the art understand that to avoid a high similarity to a reference sequence due to inclusion of gaps in the polynucleotide a gap penalty is typically introduced and is subtracted from the number of matches.
Methods of alignment of sequences for comparison are well known in the art. Thus, the determination of percent identity between any two sequences can be accomplished using a mathematical algorithm. Non-limiting examples of such mathematical algorithms are the algorithm of Myers and Miller (1988) CABIOS 4:11-17; the local alignment algorithm of Smith et al. (1981) Adv. Appl. Math. 2:482; the global alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453; the search-for-local alignment method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. 85:2444-2448; the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 872264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877.
Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Version 10 (available from Accelrys Inc., 9685 Scranton Road, San Diego, Calif., USA). Alignments using these programs can be performed using the default parameters. The CLUSTAL program is well described by Higgins et al. (1988) Gene 73:237-244 (1988); Higgins et al. (1989) CABIOS 5:151-153; Corpet et al. (1988) Polynucleotide Res. 16:10881-90; Huang et al. (1992) CABIOS 8:155-65; and Pearson et al. (1994) Meth. Mol. Biol. 24:307-331. The ALIGN program is based on the algorithm of Myers and Miller (1988) supra. A PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used with the ALIGN program when comparing amino acid sequences. The BLAST programs of Altschul et al (1990) J. Mol. Biol. 215:403 are based on the algorithm of Karlin and Altschul (1990) supra. BLAST nucleotide searches can be performed with the BLASTN program, score=100, wordlength=12, to obtain polynucleotides homologous to a polynucleotide encoding a protein of the invention. BLAST protein searches can be performed with the BLASTX program, score=50, wordlength=3, to obtain amino acid sequences homologous to a protein or polypeptide of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al. (1997) Polynucleotide Res. 25:3389. Alternatively, PSI-BLAST (in BLAST 2.0) can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, PSI-BLAST, the default parameters of the respective programs (e.g., BLASTN for polynucleotides, BLASTX for proteins) can be used. See www.ncbi.hlm.nih.gov. Alignment may also be performed manually by inspection.
Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a polynucleotide using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and % similarity for an amino acid sequence using GAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix; or any equivalent program thereof. By “equivalent program” is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.
GAP uses the algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453, to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. GAP considers all possible alignments and gap positions and creates the alignment with the largest number of matched bases and the fewest gaps. It allows for the provision of a gap creation penalty and a gap extension penalty in units of matched bases. GAP must make a profit of gap creation penalty number of matches for each gap it inserts. If a gap extension penalty greater than zero is chosen, GAP must, in addition, make a profit for each gap inserted of the length of the gap times the gap extension penalty. Default gap creation penalty values and gap extension penalty values in Version 10 of the Wisconsin Genetics Software Package for protein sequences are 8 and 2, respectively. For polynucleotides the default gap creation penalty is 50 while the default gap extension penalty is 3. The gap creation and gap extension penalties can be expressed as an integer selected from the group of integers consisting of from 0 to 200. Thus, for example, the gap creation and gap extension penalties can be 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65 or greater.
GAP presents one member of the family of best alignments. There may be many members of this family, but no other member has a better quality. GAP displays four figures of merit for alignments: Quality, Ratio, Identity, and Similarity. The Quality is the metric maximized in order to align the sequences. Ratio is the quality divided by the number of bases in the shorter segment. Percent Identity is the percent of the symbols that actually match. Percent Similarity is the percent of the symbols that are similar. Symbols that are across from gaps are ignored. A similarity is scored when the scoring matrix value for a pair of symbols is greater than or equal to 0.50, the similarity threshold. The scoring matrix used in Version 10 of the Wisconsin Genetics Software Package is BLOSUM62 (see Henikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915).
(c) As used herein, “sequence identity” or “identity” in the context of two polynucleotide or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences that differ by such conservative substitutions are said to have “sequence similarity” or “similarity”. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif.).
(d) As used herein, “percentage of sequence identity” means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.
(e)(i) The term “substantial identity” of polynucleotides means that a polynucleotide comprises a sequence that has at least 70% sequence identity, preferably at least 80%, more preferably at least 90%, and most preferably at least 95%, compared to a reference sequence using one of the alignment programs described using standard parameters. One of skill in the art will recognize that these values can be appropriately adjusted to determine corresponding identity of proteins encoded by two polynucleotides by taking into account codon degeneracy, amino acid similarity, reading frame positioning, and the like. Substantial identity of amino acid sequences for these purposes normally means sequence identity of at least 60%, more preferably at least 70%, 80%, 90%, and most preferably at least 95%.
Another indication that polynucleotides are substantially identical is if two molecules hybridize to each other under stringent conditions. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. However, stringent conditions encompass temperatures in the range of about 1° C. to about 20° C., depending upon the desired degree of stringency as otherwise qualified herein. Polynucleotides that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides they encode are substantially identical. This may occur, e.g., when a copy of a polynucleotide is created using the maximum codon degeneracy permitted by the genetic code. One indication that two polynucleotides are substantially identical is when the polypeptide encoded by the first polynucleotide is immunologically cross reactive with the polypeptide encoded by the second polynucleotide.
(e)(ii) The term “substantial identity” in the context of a peptide indicates that a peptide comprises a sequence with at least 70% sequence identity to a reference sequence, preferably 80%, more preferably 85%, most preferably at least 90% or 95% sequence identity to the reference sequence over a specified comparison window. Preferably, optimal alignment is conducted using the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453. An indication that two peptide sequences are substantially identical is that one peptide is immunologically reactive with antibodies raised against the second peptide. Thus, a peptide is substantially identical to a second peptide, for example, where the two peptides differ only by a conservative substitution. Peptides that are “substantially similar” share sequences as noted above except that residue positions that are not identical may differ by conservative amino acid changes.
In a PCR approach, oligonucleotide primers can be designed for use in PCR reactions to amplify corresponding DNA sequences from cDNA or genomic DNA extracted from any plant of interest. Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York). Known methods of PCR include, but are not limited to, methods using paired primers, nested primers, single specific primers, degenerate primers, gene-specific primers, vector-specific primers, partially-mismatched primers, and the like.
In hybridization techniques, all or part of a known polynucleotide is used as a probe that selectively hybridizes to other corresponding polynucleotides present in a population of cloned genomic DNA fragments or cDNA fragments (i.e., genomic or cDNA libraries) from a chosen organism. The hybridization probes may be genomic DNA fragments, cDNA fragments, RNA fragments, or other oligonucleotides, and may be labeled with a detectable group such as 32P, or any other detectable marker. Thus, for example, probes for hybridization can be made by labeling synthetic oligonucleotides based on the sequence encoding the protein involved in starch granule formation. Methods for preparation of probes for hybridization and for construction of cDNA and genomic libraries are generally known in the art and are disclosed in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
For example, the entire Curcuma soluble starch synthase polynucleotide disclosed herein (SEQ ID NO:1), or one or more portions thereof, may be used as a probe capable of specifically hybridizing to corresponding starch synthase polynucleotide and messenger RNAs. To achieve specific hybridization under a variety of conditions, such probes include sequences that are unique among starch synthase polynucleotides and are optimally at least about 10 nucleotides in length, and most optimally at least about 20 nucleotides in length. Such probes may be used to amplify corresponding starch synthase polynucleotide from a chosen plant by PCR. This technique may be used to isolate additional coding sequences from a desired plant or as a diagnostic assay to determine the presence of coding sequences in a plant. Hybridization techniques include hybridization screening of plated DNA libraries (either plaques or colonies; see, for example, Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
Hybridization of such sequences may be carried out under stringent conditions. By “stringent conditions” or “stringent hybridization conditions” is intended conditions under which a probe will hybridize to its target sequence to a detectably greater degree than to other sequences (e.g., at least 2-fold over background). Stringent conditions are sequence-dependent and will be different in different circumstances. By controlling the stringency of the hybridization and/or washing conditions, target sequences that are 100% complementary to the probe can be identified (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing). Generally, a probe is less than about 1000 nucleotides in length, preferably less than 500 nucleotides in length.
Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C. Duration of hybridization is generally less than about 24 hours, usually about 4 hours to about 12 hours.
Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl (1984) Anal. Biochem. 138:267-284: Tm=81.5° C.+16.6 (log M)+0.41 (% GC)−0.61 (% form)−500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. Tm is reduced by about 1° C. for each 1% of mismatching; thus, Tm, hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with ≧90% identity are sought, the Tm can be decreased 10° C. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermal melting point (Tm); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point (Tm); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point (Tm). Using the equation, hybridization and wash compositions, and desired Tm, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a Tm of less than 45° C. (aqueous solution) or 32° C. (formamide solution), it is preferred to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of polynucleotide is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes, Part I, Chapter 2 (Elsevier, N.Y.); and Ausubel et al., eds. (1995) Current Protocols in Molecular Biology, Chapter 2 (Greene Publishing and Wiley-Interscience, New York). See Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (2d ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.).
Thus, isolated sequences that encode for a protein of interest and which hybridize under stringent conditions to the polynucleotides encoding the protein of interest, or to fragments thereof, may be used in the methods of the present invention.
Vectors and Expression Cassettes
The use of the term “nucleic acid” or “polynucleotide” is not intended to limit the present invention to polynucleotides comprising DNA. Those of ordinary skill in the art will recognize that polynucleotides can comprise ribonucleotides and combinations of ribonucleotides and deoxyribonucleotides. Such deoxyribonucleotides and ribonucleotides include both naturally occurring molecules and synthetic analogues. The polynucleotides for use in the methods of the invention also encompass all forms of sequences including, but not limited to, single-stranded forms, double-stranded forms, hairpins, stem-and-loop structures, and the like.
The polynucleotides used in the methods of the present invention can be provided in expression cassettes for expression in a plant of interest. The expression cassette will include 5′ and 3′ regulatory sequences operably linked to a polynucleotide encoding a polypeptide. The cassette may additionally contain at least one additional gene to be cotransformed into the organism. Alternatively, the additional gene(s) can be provided on another expression cassette. Such an expression cassette is provided with a plurality of restriction sites and/or recombination sites for insertion of the polynucleotide of interest to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes.
“Operably linked” is intended to mean a functional linkage between two or more elements. For example, an operable linkage between a polynucleotide of interest and a regulatory sequence (i.e., a promoter) is functional link that allows for expression of the polynucleotide of interest. Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions, by operably linked is intended that the coding regions are in the same reading frame.
The expression cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (i.e., a promoter), a coding sequence of the protein of interest and a transcriptional and translational termination region (i.e., termination region) functional in plants.
The coding sequence of the protein of interest is operably linked to a transit peptide that is capable of directing the sequence to the plastid. The regulatory regions (i.e., promoters, transcriptional regulatory regions, and translational termination regions) and/or the polynucleotide of interest and/or the transit peptide may be native/analogous to the host cell or to each other. Alternatively, the regulatory regions and/or the polynucleotide of interest and/or the transit peptide may be heterologous to the host cell or to each other. As used herein, “heterologous” in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention. For example, a promoter operably linked to a heterologous transit peptide or heterologous polynucleotide is from a species different from the species from which the transit peptide or polynucleotide was derived, or, if from the same/analogous species, one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked transit peptide or polynucleotide. When the native promoter sequences are used, the expression levels of the proteins in the plant or plant cell will change. Thus, the phenotype of the plant or plant cell is altered.
In one embodiment, the polynucleotide of interest is targeted to the chloroplast for expression. In this manner, where the polynucleotide of interest is not directly introduced into the chloroplast, the expression cassette will additionally contain a nucleic acid encoding a transit peptide to direct the gene product of interest to the chloroplasts.
The termination region may be native with the transcriptional initiation region, may be native with the operably linked DNA sequence of interest, or may be derived from another source (i.e., foreign or heterologous) to the promoter, the sequence of interest, the plant host, or any combination thereof. Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also Guerineau et al. (1991) Mol. Gen. Genet. 262:141-144; Proudfoot (1991) Cell 64:671-674; Sanfacon et al. (1991) Genes Dev. 5:141-149; Mogen et al. (1990) Plant Cell 2:1261-1272; Munroe et al. (1990) Gene 91:151-158; Ballas et al. (1989) Polynucleotide Res. 17:7891-7903; and Joshi et al. (1987) Nucleic Acid Res. 15:9627-9639.
Where appropriate, the polynucleotide may be optimized for increased expression in the transformed plant. That is, the polynucleotide can be synthesized using plant-preferred codons for improved expression. See, for example, Campbell and Gowri (1990) Plant Physiol. 92:1-11 for a discussion of host-preferred codon usage. Methods are available in the art for synthesizing plant-preferred genes. See, for example, U.S. Pat. Nos. 5,380,831, and 5,436,391, and Murray et al. (1989) Polynucleotide Res. 17:477-498, herein incorporated by reference. In one embodiment, the polynucleotide of interest to be targeted to the chloroplast and/or amyloplast may be optimized for expression in the plastid to account for differences in codon usage between the plant nucleus and this organelle. In this manner, the polynucleotide of interest may be synthesized using chloroplast-(or amyloplast)-preferred codons. See, for example, U.S. Pat. No. 5,380,831, herein incorporated by reference.
Additional sequence modifications are known to enhance gene expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well-characterized sequences that may be deleterious to gene expression. The G-C content of the sequence may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. When possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures.
The expression cassettes may additionally contain 5′ non-translated leader sequences or 5′ non-coding sequences. As used herein, “5′ leader sequence,” “translation leader sequence,” or “5′ non-coding sequence” refer to that DNA sequence portion of a gene between the promoter and coding sequence that is transcribed into RNA and is present in the fully processed mRNA upstream (5′) of the translation start codon. A 5′ non-translated leader sequence is usually characterized as that portion of the mRNA molecule that most typically extends from the 5′ CAP site to the AUG protein translation initiation codon. The translation leader sequence may affect processing of the primary transcript to mRNA, mRNA stability or translation efficiency (Turner et al. (1995) Molecular Biotechnology 3:225). Thus, translation leader sequences play an important role in the regulation of gene expression. Translation leaders are known in the art and include: picomavirus leaders, for example, EMCV leader (Encephalomyocarditis 5′ noncoding region) (Elroy-Stein et al. (1989) PNAS USA 86:6126-6130); potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) (Allison et al. (1986); MDMV leader (Maize Dwarf Mosaic Virus); Virology 154:9-20), and human immunoglobulin heavy-chain binding protein (BiP), (Macejak et al. (1991) Nature 353:90-94); untranslated leader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA 4) (Jobling et al. (1987) Nature 325:622-625); tobacco mosaic virus leader (TMV) (Gallie et al. (1989) in Molecular Biology of RNA, ed. Cech (Liss, N.Y.), pp. 237-256); and maize chlorotic mottle virus leader (MCMV) (Lommel et al. (1991) Virology 81:382-385). See also, Della-Cioppa et al. (1987) Plant Physiol. 84:965-968.
The expression cassette may additionally contain a 3′ non-coding sequence. A “3′ non-coding sequence” or “3′ non-translated region” refer to a polynucleotide located 3′ (downstream) of a coding sequence and include polyadenylation signal sequences and other sequences encoding regulatory signals capable of affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor. A 3′ non-translated region comprises a region of the mRNA generally beginning with the translation termination codon and extending at least beyond the polyadenylation site. Non-translated sequences located in the 3′ end of a gene have been found to influence gene expression levels. Ingelbrecht et al. (see, Plant Cell, 1:671-680, 1989) evaluated the importance of these elements and found large differences in expression in stable plants depending on the source of the 3′ non-translated region. Using 3′ non-translated regions associated with octopine synthase, 2S seed protein from Arabidopsis, small subunit of rbcS from Arabidopsis, extension from carrot, and chalcone synthase from Antirrhinium, a 60-fold difference was observed between the best-expressing construct (which contained the rbcS 3′ non-translated region) and the lowest-expressing construct (which contained the chalcone synthase 3′ region).
Transcription levels may also be increased by the utilization of enhancers in combination with the promoter regions of the invention. Enhancers are polynucleotides that act to increase the expression of a promoter region. Enhancers are known in the art and include the SV40 enhancer region, the 35S enhancer element, and the like.
In preparing the expression cassette, the various DNA fragments may be manipulated, so as to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved.
Reporter genes or selectable marker genes may be included in the expression cassettes. Examples of suitable reporter genes known in the art can be found in, for example, Jefferson et al. (1991) in Plant Molecular Biology Manual, ed. Gelvin et al. (Kluwer Academic Publishers), pp. 1-33; DeWet et al. (1987) Mol. Cell. Biol. 7:725-737; Goff et al. (1990) EMBO J. 9:2517-2522; Kain et al. (1995) BioTechniques 19:650-655; and Chiu et al. (1996) Current Biology 6:325-330.
Selectable marker genes are utilized for the selection of transformed cells or tissues. Marker genes include genes encoding antibiotic resistance, such as those encoding neomycin phosphotransferase II (NEO) and hygromycin phosphotransferase (HPT), as well as genes conferring resistance to herbicidal compounds, such as glufosinate ammonium, imidazolinones, and 2,4-dichlorophenoxyacetate (2,4-D). Additional selectable markers include phenotypic markers such as β-galactosidase and fluorescent proteins such as green fluorescent protein (GFP) (Su et al. (2004) Biotechnol Bioeng 85:610-9 and Fetter et al. (2004) Plant Cell 16:215-28), cyan florescent protein (CYP) (Bolte et al. (2004) J. Cell Science 117:943-54 and Kato et al. (2002) Plant Physiol 129:913-42), and yellow florescent protein (PhiYFPTM from Evrogen, see, Bolte et al. (2004) J. Cell Science 117:943-54). Other examples of suitable selectable marker genes include, but are not limited to, genes encoding resistance to chloramphenicol (Herrera Estrella et al. (1983) EMBO J. 2:987-992); methotrexate (Herrera Estrella et al. (1983) Nature 303:209-213 and Meijer et al. (1991) Plant Mol. Biol. 16:807-820); hygromycin (Waldron et al. (1985) Plant Mol. Biol. 5:103-108 and Zhijian et al. (1995) Plant Science 108:219-227); streptomycin (Jones et al. (1987) Mol. Gen. Genet. 210:86-91); spectinomycin (Bretagne-Sagnard et al. (1996) Transgenic Res. 5:131-137); bleomycin (Hille et al. (1990) Plant Mol. Biol. 7:171-176); sulfonamide (Guerineau et al. (1990) Plant Mol. Biol. 15:127-136); bromoxynil (Stalker et al. (1988) Science 242:419-423); glyphosate (Shaw et al. (1986) Science 233:478-481 and U.S. patent application Ser. No. 10/004,357); phosphinothricin (DeBlock et al. (1987) EMBO J. 6:2513-2518). The above list of selectable marker genes is not meant to be limiting. Any selectable marker gene can be used in the present invention.
Other genes that could serve utility in the recovery of transgenic events but might not be required in the final product would include, but are not limited to, examples such as GUS (b-glucoronidase; Jefferson (1987) Plant Mol. Biol. Rep. 5:387), GFP (green florescence protein; Chalfie et al. (1994) Science 263:802), luciferase (Riggs et al. (1987) Polynucleotide Res. 15(19):8115 and Luehrsen et al. (1992) Methods Enzymol. 216:397-414), and the maize genes encoding for anthocyanin production (Ludwig et al. (1990) Science 247:449).
A number of promoters can be used in the practice of the invention. The promoters can be selected based on the desired outcome. The polynucleotide can be combined with constitutive, tissue-preferred, or other promoters for expression in plants. “Tissue-preferred promoters” express the genes under their control in only one or more cell types in specific organs, specific tissues, or specific cell types. Tissue-preferred promoters include promoters that are temporally regulated, such as in early or late embryogenesis, during fruit ripening in developing seeds or fruit, in fully differentiated leaf, or at the onset of senescence. In contrast, “constitutive promoters” refer to promoters that are able to express the genes under their control in all or nearly all of the plant tissues during all or nearly all developmental stages of the plant, thereby generating “constitutive expression” of the genes. Yet another type of promoter known as an “inducible promoter” is a type of regulated promoter that can be turned on in one or more cell types by an external stimulus, such as a chemical, light, hormone, stress, or a pathogen.
Constitutive promoters include, for example, the core promoter of the Rsyn7 promoter and other constitutive promoters disclosed in WO 99/43838 and U.S. Pat. No. 6,072,050; the core CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet. 81:581-588); MAS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026), and the like. Other constitutive promoters include, for example, U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; 5,608,142; and 6,177,611.
Tissue-preferred promoters can be utilized to target the expression of the protein within a particular plant tissue. Such promoters include, but are not limited to, seed-preferred promoters. “Seed-preferred” promoters include both “seed-specific” promoters (those promoters active during seed development such as promoters of seed storage proteins) as well as “seed-germinating” promoters (those promoters active during seed germination). See Thompson et al. (1989) BioEssays 10:108, herein incorporated by reference. Such seed-preferred promoters include, but are not limited to, Cim1 (cytokinin-induced message); cZ19B1 (maize 19 kDa zein); and celA (cellulose synthase) (see WO 00/11177 and U.S. Pat. No. 6,225,529; herein incorporated by reference). Gamma-zein is an endosperm-specific promoter, as are the promoters for the high molecular weight glutenin (HMWG) of wheat, prolamin, ITR1, gliadin, branching enzyme, ADPG pyrophosphorylase, starch synthase, granule-bound starch synthase, and Glob-1. For dicots, seed-specific promoters include, but are not limited to, bean β-phaseolin, napin, β-conglycinin, soybean lectin, cruciferin, and the like. For monocots, seed-specific promoters include, but are not limited to, maize 15 kDa zein, 22 kDa zein, 27 kDa zein, γ-zein, waxy, shrunken 1, shrunken 2, globulin 1, etc. See also WO 00/12733, where seed-preferred promoters from end1 and end2 genes are disclosed; herein incorporated by reference.
As used herein, “vector” refers to a DNA molecule such as a plasmid, cosmid, or bacterial phage for introducing a nucleotide construct, for example, an expression cassette, into a host cell. Cloning vectors typically contain one or a small number of restriction endonuclease recognition sites at which foreign DNA sequences can be inserted in a determinable fashion without loss of essential biological function of the vector, as well as a marker gene that is suitable for use in the identification and selection of cells transformed with the cloning vector.
The methods of the invention involve introducing a polypeptide or polynucleotide into a plant. “Introducing” is intended to mean presenting to the plant the polynucleotide or polypeptide in such a manner that the sequence gains access to the interior of a cell of the plant. The methods of the invention do not depend on a particular method for introducing a sequence into a plant, only that the polynucleotide or polypeptides gains access to the interior of at least one cell of the plant. Methods for introducing polynucleotide or polypeptides into plants are known in the art including, but not limited to, conventional breeding methods, stable transformation methods, transient transformation methods, and virus-mediated methods. “Transient transformation” is intended to mean that a polynucleotide is introduced into the plant and does not integrate into the genome of the plant or a polypeptide is introduced into a plant. By “stable transformation” is intended that the nucleotide construct introduced into a plant integrates into the genome of the plant and is capable of being inherited by progeny thereof. By “primary transformant” and “T0 generation” is intended transgenic plants that are of the same genetic generation as the tissue that was initially transformed (i.e., not having gone through meiosis and fertilization since transformation). “Secondary transformants” and the “T1, T2, T3, etc. generations” refer to transgenic plants derived from primary transformants through one or more meiotic and fertilization cycles. They may be derived by self-fertilization of primary or secondary transformants or crosses of primary or secondary transformants with other transformed or untransformed plants.
The nucleotide constructs of the invention may be introduced into plants by contacting plants with a virus or viral polynucleotide. Generally, such methods involve incorporating a nucleotide construct of the invention within a viral DNA or RNA molecule. Methods for introducing nucleotide constructs into plants and expressing a protein encoded therein, involving viral DNA or RNA molecules, are known in the art. See, for example, U.S. Pat. Nos. 5,889,191, 5,889,190, 5,866,785, 5,589,367, and 5,316,931; herein incorporated by reference.
Transformation protocols as well as protocols for introducing polynucleotides into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation. Suitable methods of introducing polynucleotides into plant cells and subsequent insertion into the plant genome include microinjection (Crossway et al. (1986) Biotechniques 4:320-334), electroporation (Riggs et al. (1986) Proc. Natl. Acad. Sci. USA 83:5602-5606, Agrobacterium-mediated transformation (Townsend et al., U.S. Pat. No. 5,563,055; Zhao et al., U.S. Pat. No. 5,981,840), direct gene transfer (Paszkowski et al. (1984) EMBO J. 3:2717-2722), and ballistic particle acceleration (see, for example, Sanford et al., U.S. Pat. No. 4,945,050; Tomes et al. (1995) “Direct DNA Transfer into Intact Plant Cells via Microprojectile Bombardment,” in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg and Phillips (Springer-Verlag, Berlin); McCabe et al. (1988) Biotechnology 6:923-926); and Lec1 transformation (WO 00/28058). Also see Weissinger et al. (1988) Ann. Rev. Genet. 22:421-477; Sanford et al. (1987) Particulate Science and Technology 5:27-37 (onion); Christou et al. (1988) Plant Physiol. 87:671-674 (soybean); McCabe et al. (1988) Bio/Technology 6:923-926 (soybean); Finer and McMullen (1991) In vitro Cell Dev. Biol. 27P:175-182 (soybean); Singh et al. (1998) Theor. Appl. Genet. 96:319-324 (soybean); Datta et al. (1990) Biotechnology 8:736-740 (rice); Klein et al. (1988) Proc. Natl. Acad. Sci. USA 85:4305-4309 (maize); Klein et al. (1988) Biotechnology 6:559-563 (maize); Tomes, U.S. Pat. No. 5,240,855; Buising et al., U.S. Pat. Nos. 5,322,783 and 5,324,646; Tomes et al. (1995) “Direct DNA Transfer into Intact Plant Cells via Microprojectile Bombardment,” in Plant Cell, Tissue, and Organ Culture: Fundamental Methods, ed. Gamborg (Springer-Verlag, Berlin) (maize); Klein et al. (1988) Plant Physiol. 91:440-444 (maize); Fromm et al. (1990) Biotechnology 8:833-839 (maize); Hooykaas-Van Slogteren et al. (1984) Nature (London) 311:763-764; Bytebier et al. (1987) Proc. Natl. Acad. Sci. USA 84:5345-5349 (Liliaceae); De Wet et al. (1985) in The Experimental Manipulation of Ovule Tissues, ed. Chapman et al. (Longman, N.Y.), pp. 197-209 (pollen); Kaeppler et al. (1990) Plant Cell Reports 9:415-418 and Kaeppler et al. (1992) Theor. Appl. Genet. 84:560-566 (whisker-mediated transformation); D'Halluin et al. (1992) Plant Cell 4:1495-1505 (electroporation); Li et al. (1993) Plant Cell Reports 12:250-255 and Christou and Ford (1995) Annals of Botany 75:407-413 (rice); Osjoda et al. (1996) Nature Biotechnology 14:745-750 (maize via Agrobacterium tumefaciens); all of which are herein incorporated by reference.
Methods for transformation of chloroplasts are known in the art. See, for example, Svab et al. (1990) Proc. Natl. Acad. Sci. USA 87:8526-8530; Svab and Maliga (1993) Proc. Natl. Acad. Sci. USA 90:913-917; Svab and Maliga (1993) EMBO J. 12:601-606. The method relies on particle gun delivery of DNA containing a selectable marker and targeting of the DNA to the plastid genome through homologous recombination. Additionally, plastid transformation can be accomplished by transactivation of a silent plastid-borne transgene by tissue-preferred expression of a nuclear-encoded and plastid-directed RNA polymerase. Such a system has been reported in McBride et al. (1994) Proc. Natl. Acad. Sci. USA 91:7301-7305.
The cells that have been transformed may be grown into plants in accordance with conventional ways. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84. These plants may then be grown, and either pollinated with the same transformed strain or different strains, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that constitutive expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure constitutive expression of the desired phenotypic characteristic has been achieved. Thus as used herein, “transformed seed” or “transgenic seed” refers to seeds that contain the nucleotide construct stably incorporated into the plant genome.
The present invention may be used for transformation of any plant species, including, but not limited to, monocots and dicots. Examples of plants of interest include, but are not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B. juncea), particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatus), cassava (Manihot esculenta), coffee (Coffea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado (Persea americana), fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica), olive (Olea europaea), papaya (Carica papaya), cashew (Anacardium occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, barley, vegetables, ornamentals, and conifers.
Vegetables include tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca saliva), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo). Ornamentals include azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrim), and chrysanthemum. Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata); Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga canadensis); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and balsam fir (Abies balsamea); and cedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis). Preferably, plants of the present invention are crop plants (for example, corn, alfalfa, sunflower, Brassica, soybean, cotton, safflower, peanut, sorghum, wheat, millet, tobacco, etc.), more preferably corn and soybean plants, yet more preferably corn plants.
Other plants of interest include grain plants that provide seeds of interest, oil-seed plants, and leguminous plants. Seeds of interest include grain seeds, such as corn, wheat, barley, rice, sorghum, rye, etc. Oil seed plants include cotton, soybean, safflower, sunflower, Brassica, maize, alfalfa, palm, coconut, etc. Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc.
Gene Stacking
In certain embodiments the polynucleotides used in the methods of the present invention can be stacked with any combination of polynucleotides of interest in order to create plants with a desired trait. A trait, as used herein, refers to the phenotype derived from a particular sequence or groups of sequences. A single expression cassette may contain both a polynucleotide encoding a polypeptide of interest to decrease starch granule size, and at least one additional gene, such as the gamma zein gene, UDP glucose dehydrogenase gene (U.S. Pat. No. 6,399,859), RGP genes (U.S. Pat. No. 6,194,638), or genes employed to increase the oil content and/or quality of the plant. Alternatively, the additional gene(s) can be provided on multiple expression cassettes. In specific embodiments, the additional genes co-transformed into the plant include polynucleotides that, upon expression, modify the cell wall properties and/or starch content and/or oil content and/or oil quality of the seed and further enhance the nutritive and digestive value of the plant material.
The approach could be entirely transgenic (expression of a first polynucleotide encoding a protein of interest to decrease starch granule size, and expression or suppression of a second polynucleotide that modulates expression of a protein affecting rate of feed digestibility) or by transferring the second polynucleotide into a newly obtained transgenic plant that expresses a protein in a plant plastid, such as an amyloplast or a chloroplast. In a specific embodiment, the second polynucleotide results in greatly reduced levels of the 27 kDa γ-zein protein in endosperm cells.
These stacked combinations can be created by any method including, but not limited to, cross-breeding plants by any conventional or TopCross methodology, or genetic transformation. If the sequences are stacked by genetically transforming the plants, the polynucleotides of interest can be combined at any time and in any order. For example, a transgenic plant comprising one or more desired traits can be used as the target to introduce further traits by subsequent transformation. The traits can be introduced simultaneously in a co-transformation protocol with the polynucleotides of interest provided by any combination of transformation cassettes. For example, if two sequences will be introduced, the two sequences can be contained in separate transformation cassettes (trans) or contained on the same transformation cassette (cis). Expression of the sequences can be driven by the same promoter or by different promoters. In certain cases, it may be desirable to introduce a transformation cassette that will suppress the expression of the polynucleotide of interest. This may be combined with any combination of other suppression cassettes or overexpression cassettes to generate the desired combination of traits in the plant. It is further recognized that polynucleotides can be stacked at a desired genomic location using a site-specific recombination system. See, for example, WO99/25821, WO99/25854, WO99/25840, WO99/25855, and WO99/25853, all of which are herein incorporated by reference.
Additional polynucleotides that can be introduced in combination with a polypeptide that reduces granule size include, but are not limited to, insecticidal coding sequences, such as other Bacillus thuringiensis toxic proteins (described in U.S. Pat. Nos. 5,366,892; 5,747,450; 5,737,514; 5,723,756; 5,593,881; and Geiser et al. (1986) Gene 48:109), lectins (Van Damme et al. (1994) Plant Mol. Biol. 24:825, pentin (described in U.S. Pat. No. 5,981,722); nematicidal coding sequences; disease or herbicide resistance genes (e.g., fumonisin detoxification genes (U.S. Pat. No. 5,792,931); avirulence and disease resistance genes (Jones et al. (1994) Science 266:789; Martin et al. (1993) Science 262:1432; Mindrinos et al. (1994) Cell 78:1089); acetolactate synthase (ALS) mutants that lead to herbicide resistance such as the S4 and/or Hra mutations; inhibitors of glutamine synthase such as phosphinothricin or basta (e.g., bar gene); and glyphosate resistance (EPSPS gene)); anti-microbial coding sequences, anti-fungal coding sequences, anti-viral coding sequences, abiotic stress tolerance coding sequences, nutritional quality coding sequences, visible marker coding sequences, selectable marker coding sequences, traits desirable for animal feed such as high oil genes (e.g., U.S. Pat. No. 6,232,529); balanced amino acids (e.g., hordothionins (U.S. Pat. Nos. 5,990,389; 5,885,801; 5,885,802; and 5,703,409); barley high lysine (Williamson et al. (1987) Eur. J. Biochem. 165:99-106; and WO 98/20122) and high methionine proteins (Pedersen et al. (1986) J. Biol. Chem. 261:6279; Kirihara et al. (1988) Gene 71:359; and Musumura et al. (1989) Plant Mol. Biol. 12:123)); increased digestibility (e.g., modified storage proteins (U.S. application Ser. No. 10/053,410, filed Nov. 7, 2001); and thioredoxins (U.S. application Ser. No. 10/005,429, filed Dec. 3, 2001)); the disclosures of which are herein incorporated by reference.
Additional traits of interest include those desirable for processing or process products such as high oil (e.g., U.S. Pat. No. 6,232,529); modified oils (e.g., fatty acid desaturase genes (U.S. Pat. No. 5,952,544; WO 94/11516)); modified starches (e.g., ADPG pyrophosphorylases (AGPase), starch synthases (SS), starch branching enzymes (SBE), and starch debranching enzymes (SDBE)); and polymers or bioplastics (e.g., U.S. Pat. No. 5.602,321; beta-ketothiolase, polyhydroxybutyrate synthase, and acetoacetyl-CoA reductase (Schubert et al. (1988) J. Bacteriol. 170:5837-5847) facilitate expression of polyhydroxyalkanoates (PHAs)); the disclosures of which are herein incorporated by reference. One could also combine the polynucleotides of the present invention with polynucleotides providing agronomic traits such as male sterility (e.g., see U.S. Pat. No. 5.583,210), stalk strength, flowering time, or transformation technology traits such as cell cycle regulation or gene targeting (e.g., WO 99/61619, WO 00/17364, and WO 99/25821); the disclosures of which are herein incorporated by reference.
In specific embodiments of the present invention, the polynucleotide of the additional gene of interest can be used to generate antisense constructions, which are complementary to at least a portion of the messenger RNA (mRNA) encoding these proteins. Antisense nucleotides are constructed to hybridize with the corresponding mRNA. Modifications of the antisense sequences may be made as long as the sequences hybridize to and interfere with expression of the corresponding mRNA. In this manner, antisense constructions having 70%, 80%, 85%, 90% or 95% sequence identity to the corresponding antisense sequences may be used. Furthermore, portions of the antisense nucleotides may be used to disrupt the expression of the target gene. Generally, sequences of at least 50 nucleotides, 100 nucleotides, 200 nucleotides, or greater may be used.
The polynucleotides of the additional gene of interest may also be used in the sense orientation to suppress the expression of endogenous genes in plants. Methods for suppressing gene expression in plants using polynucleotides in the sense orientation are known in the art. The methods generally involve transforming plants with a DNA construct comprising a promoter that drives expression in a plant operably linked to at least a portion of a polynucleotide that corresponds to the transcript of the endogenous gene. Typically, such a polynucleotide has substantial sequence identity to the sequence of the transcript of the endogenous gene, preferably greater than about 65% sequence identity, more preferably greater than about 85% sequence identity, most preferably greater than about 95% sequence identity. See U.S. Pat. Nos. 5,283,184 and 5,034,323; herein incorporated by reference.
The following examples are offered by way of illustration and not by way of limitation.
Experimental
EXAMPLE 1
Overexpression of Brittle-1 in Homozygous T3 Seed Reduces Starch Granule Size
Transformation constructs were made with the Brittle-1 gene (SEQ ID NO:7) including its transit peptide. The construct was operably linked to either the γ-zein or 22-kD zein promoter and delivered into plants via particle bombardment. Regenerated plants were grown in a greenhouse and pollinated with a proprietary inbred (subsequently serving as a recurring backcross inbred) to produce T1 seed. T1 seed of multiple transgenic events was sown in the field and resulting T1 plants were self-pollinated to produce multiple ears of T2 seed for each transgenic event. Seed of these ears were planted in the field on an ear-to-row basis and resulting T2 plants were self-pollinated to produce ears containing T3 seed. Multiple ears of T3 seed, each with robust seed set, were harvested from each row of T2 plants for each event. Twenty kernels from each ear of T3 seed were sown in a flat and grown in the greenhouse. After 10 days of growth, resulting seedlings were sprayed with a solution (1% vol/vol) of glufosinate herbicide. Seedlings were scored seven days later for resistance to the herbicide. Ears of T3 seed were classified as wild-type if all 20 seedlings were killed, hemizygous if only a portion of the seedlings were killed, and homozygous for the transgene if none of the seedlings displayed leaf burn. In total, T3 seed of 1351 ears were evaluated. To confirm the results, another 20 kernels from ears believed to be homozygous were planted, grown to the seedling stage, sprayed with a 2% (vol/vol) solution of glufosinate herbicide, and scored for leaf burn as done previously. Subsequently, endosperm were isolated from multiple wild-type and homozygous ears of T3 seed and compared as within-row segregants. Total protein was extracted from the endosperm, separated on SDS-PAGE gels, and immunologically evaluated via Western blots for the level of Brittle-1 protein. Multiple events overexpressed the Brittle-1 protein (data not shown), in some cases by as much as 32-fold compared to within-row wild-type endosperm, as quantified by serial dilution of protein extracts measured by Western analysis and quantitated with a Bio-Rad GS7000 densitometer. Finally, starch granules were isolated according to White et al. (White et al. (1990) Cereal Chem. 67:70-73) from wild-type and homozygous endosperm of transgenic events overexpressing the Brittle-1 protein. Granule size was measured by digital image analysis using a Leica DMLB microscope with a Diagnostics Instruments, Inc. SPOT camera and employing Media Cybernetics Image-Pro Plus (Ver 4.0) software. Results with the same isolated starch were later confirmed using a Malvern Mastersizer 2000 Low Angle Laser Light Scattering particle size analyzer, using absorption and refractive indexes of 0.1 and 1.53, respectively. Both methods of particle size analysis gave very similar results. As shown in Table 1, transgenic events overexpressing the Brittle-1 protein (SEQ ID NO:8) produced smaller-than-normal starch granules in the endosperm when compared to starch granules isolated from wild-type plants.







TABLE 1







Low Angle Laser Light Scattering (LALLS) determination of the size of


starch granules isolated from T3 wild-type and transgenic homozygous


endosperm overexpressing the Brittle-1 protein.









Starch


SAMPLE NAME
Granule Modal Size (micron)











Bt1-T3 Starch - TC2853 - Homo
13.9


Bt1-T3 Starch - TC2853 - Wild-type
14.5


Bt1-T3 Starch - TC2862a - Homo
10.4


Bt1-T3 Starch - TC2862a - Wild-type
14.7


Bt1-T3 Starch - TC2862b - Homo
9.8


Bt1-T3 Starch - TC2862b - Homo
9.6


Bt1-T3 Starch - TC2862b - Wild-type
14.5


Bt1-T3 Starch - TC2862b - Wild-type
14.0


Bt1-T3 Starch - TC2862c - Homo
10.4


Bt1-T3 Starch - TC2862c - Wild-type
14.4


Bt1-T3 Starch - TC2862c - Homo
10.4


Bt1-T3 Starch - TC2863a - Homo
11.7


Bt1-T3 Starch - TC2863a - Wild-type
14.1


Bt1-T3 Starch - TC2863b - Homo
10.4


Bt1-T3 Starch - TC2863b - Wild-type
15.6


Bt1-T3 Starch - TC2863b - Homo
10.6


Bt1-T3 Starch - TC2863b - Wild-type
14.4


Bt1-T3 Starch - TC2864 - Homo
13.7


Bt1-T3 Starch - TC2864 - Wild-type
14.1









EXAMPLE 2
Overexpression of Brittle-1 Improves In Vitro Digestibility of Grain
T3 maize seed judged to be homozygous for transgenic expression of the Brittle-1 protein (SEQ ID NO:8) and displaying concomitant reduction of starch granule size were propagated in field plots and backcrossed with a recurring elite inbred. The genetic materials were then grown for an additional two generations, with self-pollination occurring in each cycle. This produced BC3S2 seed on ears that segregated for wild-type and homozygous transgenic backgrounds. Homozygotes were identified by segregation analysis of seedling sensitivity to glufosinate herbicide, as already described. Whole grain of wild-type and transgenic homozygous plants was used in an in vitro digestion assay which determines the amount of enzyme digestible dry matter. Enzyme digestible dry matter percent (EDDM %) of the grain was measured using the method of Boisen and Fernandez (Boisen and Fernandez (1997) Animal Feed Sci. Technol. 68:277), with the exceptions that pepsin and cell wall degradative enzymes were not used, pancreatin concentration was 0.5% (wt/vol), and incubation occurred for four hours. In addition to controlling the experiment by utilizing backcrossed genetic materials, replicated comparisons were always made by contrasting wild-type and homozygous transgenic ears that segregated from a common genetic pedigree. A consistent pattern of significantly increased digestibility was observed after four hours of digestion, as shown in FIG. 5. The grain from the Brittle-1 transgenic seed responded positively to pretreatment with dithiothreietol (DTT), indicating that the effect on digestion occurs by a mechanism different than that seen with the γ-zein gene. Furthermore, SDS-PAGE analysis of transgenic seed indicated that normal levels of γ-zein protein were present in the grain.
EXAMPLE 3
Overexpression of Oleosin Produces Smaller Starch Granules
Ole16 (SEQ ID NO:15) was expressed in maize endosperm using the γ-zein promoter and targeted to the amyloplast by linking the coding region of oleosin to the Brittle-1 transit peptide (SEQ ID NO:9). Endosperm were dissected from mature T1 seed and tested by Western blot analysis for overexpression of oleosin protein. Nontransgenic endosperm of the same genotype used for transformation was used as a negative control to determine the native level of oleosin present in mature maize endosperm. A small amount of the protein can be detected in mature wild-type endosperm even after great care is taken to avoid contamination with non-endosperm tissues. Hence, overexpression of oleosin against a low background of native occurring protein was easy to distinguish in transgenic seed (data not shown). Following Western blot analysis of multiple individual endosperm from transgenic events, pools were formed of wild-type and “overexpression” endosperm within the ears of multiple events. Starch was isolated from the pools and granule size determined using low angle laser light scattering for particle size determination. A strong coincidence of significantly smaller-than-normal granules was found in seed that overexpresses 16 kDa oleosin, as shown in Table 2.







TABLE 2







Low Angle Laser Light Scattering (LALLS) determination of the size


of starch granules isolated from T1 wild-type endosperm and T1


transgenic endosperm overexpressing the 16 kDa oleosin protein









Events
Wild-type Mean Starch
Transgenic Mean Starch


(EU IDs)
Granule Size (micron)
Granule Size (micron)





3247998, 3248002,
16.2
13.2


3248010


3248002, 3248003,
14.3
12.2


3248012, 3248400









EXAMPLE 4
Overexpression of Curcuma Starch Synthase Reduces Starch Granule Size
A Curcuma zedoria starch synthase gene (SEQ ID NO:1) including its transit peptide was expressed in maize endosperm using the y-zein promoter. Endosperm were dissected from mature T1 seed and tested by Western blot analysis to demonstrate overexpression of the starch synthase protein. Only weak cross-reaction occurred between the antibody and native maize starch synthase protein (data not shown). Following Western blot analysis of multiple individual endosperm from single transgenic events, pools were formed of wild-type-and overexpression-endosperm within the ears of multiple events. Starch was isolated from the pools and granule size determined using low angle laser light scattering for particle size determination. A strong coincidence of significantly smaller-than-normal granules was found in seed that overexpresses the starch synthase protein, as shown in Table 3.







TABLE 3







Low Angle Laser Light Scattering (LALLS) determination of the size


of starch granules isolated from T1 wild-type endosperm and T1


transgenic endosperm overexpressing the Curcuma zedoria starch


synthase protein










Wild-type Starch Granule
Transgenic Starch granule


Event
Modal Size (micron)
Modal Size (micron)





1869174
13.7
12.2


1869168
12.0
11.2


1865454
13.2
12.3









EXAMPLE 5
Overexpression of Zea mays FtsZ2 Reduces Starch Granule Size
ZM-FtsZ2 (SEQ ID NO:13) was transformed into maize and expressed in the endosperm using the gamma-zein promoter. This gene should have a transit peptide as both Arabidopsis FtsZ2-1 and FtsZ2-2 are targeted to the chloroplast by cleavable transit peptides, imported and localized to the chloroplast stroma (McAndrew et. al. (2001) Plant Physiology 127:1656-1666). T-zero plants were self-pollinated in the greenhouse and for each event endosperm were dissected from two mature T1 seed and pooled into one sample. Starch was isolated according to White et al., 1990, supra, and granule size distribution measured by Low Angle Laser Light Scattering (Malvern Mastersizer 2000). Attention was focused upon an event that displayed unusually small starch granules in the smaller half of the population of granules obtained from the bulk of two endosperm. Additional mature seed were retrieved for that transgenic event and endosperm isolated. A part of each endosperm was used for determination of starch granule size distribution, Western analysis of ZM-FtsZ2 protein expression, and PCR detection of the integrated DNA construct containing ZM-FtsZ2. Upon examining these parameters for 37 individual seed, 28 indicated the presence of the transgene nucleic acid and overexpression of the protein. There was a perfect correspondence between detection of the transgene and overexpression. Nine seed were wild-type, based upon PCR and Western analyses. The modal starch granule size of wild-type seed ranged from 18.4-22.6 microns and averaged 20.2 microns among wild-type endosperm. The 28 transgenic endosperm segregated within the same ear containing the wild-type seed. For the transgenic seed, the modal starch granule size ranged from 11.8-19.2 microns and averaged 16.4 microns across this class of endosperm. Overexpression of the ZM-FtsZ2 protein was easy to distinguish in transgenic, compared to wild-type, seed and resulted in a reduction of average size of endosperm starch granules.
EXAMPLE 6
Overexpression of Lec1 in Endosperm Does Not Result in Reduced Starch Granule Size
A construct was designed to express the Lec1 protein (non-plastid-associated) (SEQ ID NO:20) in the endosperm and embryo by utilizing the γ-zein and Ltp2 promoters, respectively. Endosperm were dissected from mature T1 seed and tested by Western blot analysis for overexpression of Lec1 protein. Nontransgenic endosperm of the same genotype used for plant transformation was used as a negative control to determine that Lec1 protein cannot be detected in mature endosperm of wild-type seed. Western blot analysis confirmed that Lec1 was overexpressed in the endosperm of transgenic plants, but not wild-type (data not shown). Pools were made of wild-type or transgenic endosperm, starch was isolated from the pools, and starch granule size was measured. There was no consistent effect on starch granule size (Table 4), and all of the measurements were in the range of natural variation. Therefore, expression of this non-plastid-associated protein in the endosperm of plants did not result in reduced starch granule size.







TABLE 4







Low Angle Laser Light Scattering (LALLS) determination of the size of


starch granules isolated from T1 wild-type endosperm and T1 transgenic


endosperm overexpressing the Zea mays Lec1 protein










Wild-type Starch Granule
Transgenic Starch Granule


Event
Modal Size (micron)
Modal Size (micorn)





4571021
17.0
16.7


4571022
16.3
15.4


4571023
16.2
16.4


4571024
15.1
14.0


4571025
15.7
15.5









EXAMPLE 7
Overexpression of Maize Xylose Isomerase in Endosperm Does Not Result in Reduced Starch Granule Size
A construct was designed to express the Zea mays xylose isomerase (XI) protein (non-plastid-associated) (SEQ ID NO:18) in the endosperm by utilizing the γ-zein promoter. Endosperm were dissected from mature seed across several generations and tested by Western blot analysis for overexpression of XI protein. Nontransgenic endosperm of the same genotype used for plant transformation, or segregating wild-type seed in later generations, were used as a negative control to determine the difference between native levels of XI protein expression in the endosperm and transgenic overexpression of the protein. Western blot analysis confirmed that XI was strongly overexpressed in the endosperm of transgenic plants and was easily distinguishable from wild-type plants (data not shown). Pools were made of T3 wild-type or transgenic endosperm, starch was isolated from the pools, and starch granule size was measured by low angle laser light scattering particle size determination. The XI protein was strongly overexpressed in transgenic endosperm, but starch granule size was nearly identical between wild-type and transgenic seed, as shown in Table 5. Therefore, overexpression of this non-plastid-associated protein in the endosperm of plants did not result in reduced starch granule size.







TABLE 5







Low Angle Laser Light Scattering (LALLS) determination of the size of


starch granules isolated from T3 wild-type endosperm and T3 transgenic


endosperm overexpressing the Zea mays xylose isomerase protein










Wild-type Starch Granule
Transgenic Starch granule


Event
Modal Size (micron)
Modal Size (micron)





1000685596
15.9
16.0


1000685662
15.2
15.6









The articles “a” and “an” are used herein to refer to one or more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one or more element.
Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.
All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

## Claims

1. A method for reducing starch granule size in a plant, comprising stably introducing into the genome of said plant a DNA construct comprising a polynucleotide operably linked to a promoter that drives expression in a plant and operably linked to a plastid transit peptide, wherein said polynucleotide comprises the nucleotide sequence set forth in SEQ ID NO:7 or a variant thereof, wherein said variant has at least 95% sequence identity to the nucleotide sequence of SEQ ID NO:7, and wherein expression of said DNA construct results in said starch granule having a reduced size.

2. The method of claim 1, wherein said DNA construct is introduced into the plant by transformation.

3. The method of claim 1, wherein said plant is a monocot.

4. The method of claim 3, wherein said monocot is maize.

5. The method of claim 1, wherein said plant is a dicot.

6. The method of claim 1, wherein said promoter is a tissue-preferred promoter.

7. The method of claim 6, wherein said promoter is an endosperm-specific promoter.

8. The method of claim 1, wherein said promoter is selected from the group consisting of γ-zein, 22-kD zein, opaque2, Brittle-1, waxy, and Legumin1A.

9. The method of claim 1, wherein said plant expresses at least one additional heterologous polypeptide.

10. The method of claim 9, wherein said additional heterologous polypeptide is selected from the group consisting of gamma zein and UDP glucose dehydrogenase.

11. The method of claim 1, wherein said transit peptide is an amyloplast transit peptide.

12. The method of claim 1, wherein said transit peptide is selected from the group consisting of Brittle-1, Curcuma soluble starch synthase, ribulose bisphosphate carboxylase (small subunit), 5-(enolpyruvyl) shikimate-3-phosphate synthase (EPSPS), tryptophan synthase, chorismate synthase, plastocyanin, the transit peptide for the plant plastid acyl carrier protein (ACP), the transit peptide for GBSSI (granule bound starch synthase I), and chlorophyll AB binding protein transit peptides.

13. A plant having a heterologous DNA construct stably introduced into its genome, said DNA construct comprising a polynucleotide operably linked to a promoter that drives expression in a plant and operably linked to a plastid transit peptide,
wherein said polynucleotide wherein said polynucleotide comprises the nucleotide sequence set forth in SEQ ID NO:7 or a variant thereof, wherein said variant has at least 95% sequence identity to the nucleotide sequence of SEQ ID NO:7, and wherein expression of said DNA construct results in said starch granule having a reduced size.

14. The plant of claim 13, wherein said transit peptide is selected from the group consisting of Brittle-1, Curcuma soluble starch synthase, ribulose bisphosphate carboxylase (small subunit), 5-(enolpyruvyl) shikimate-3-phosphate synthase (EPSPS), tryptophan synthase, chorismate synthase, plastocyanin, the transit peptide for the plant plastid acyl carrier protein (ACP), the transit peptide for GBSSI (granule bound starch synthase I), and chlorophyll AB binding protein transit peptides.

15. The plant of claim 13, wherein said plant is a monocot.

16. The plant of claim 15, wherein said monocot is maize.

17. The plant of claim 13, wherein said plant is a dicot.

18. The plant of claim 13, wherein said plant is a plant cell.

19. A transformed seed of the plant of claim 13.