# Patent

## Title
Compositions isolated from forage grasses and methods for their use

## Abstract

Isolated polynucleotides encoding polypeptides active in lignin, fructan and tannin biosynthetic pathways are provided, together with expression vectors and host cells comprising such isolated polynucleotides. Methods for the use of such polynucleotides and polypeptides are also provided.

## Background
REFERENCE TO RELATED APPLICATIONS
This application claims priority to U.S. Provisional Patent Application No. 60/337,703 filed Nov. 7, 2001.


TECHNICAL FIELD OF THE INVENTION
This invention relates to polynucleotides isolated from forage grass tissues, specifically from Lolium perenne (perennial ryegrass) and Festuca arundinacea (tall fescue), as well as oligonucleotide probes and primers, genetic constructs comprising the polynucleotides, biological materials (including host cells and plants) incorporating the polynucleotides, polypeptides encoded by the polynucleotides, and methods for using the polynucleotides and polypeptides. More particularly, the invention relates to polypeptides involved in the lignin, tannin and fructan biosynthetic pathways, and to polynucleotides encoding such polypeptides.
BACKGROUND OF THE INVENTION
Over the past 50 years, there have been substantial improvements in the genetic production potential of ruminant animals (sheep, cattle and deer). Levels of meat, milk or fiber production that equal an animal's genetic potential may be attained within controlled feeding systems, where animals are fully fed with energy dense, conserved forages and grains. However, the majority of temperate farming systems worldwide rely on the in situ grazing of pastures. Nutritional constraints associated with temperate pastures can prevent the full expression of an animal's genetic potential. This is illustrated by a comparison between milk production by North American grain-fed dairy cows and New Zealand pasture-fed cattle. North American dairy cattle produce, on average, twice the milk volume of New Zealand cattle, yet the genetic base is similar within both systems (New Zealand Dairy Board and United States Department of Agriculture figures). Significant potential therefore exists to improve the efficiency of conversion of pasture nutrients to animal products through the correction of nutritional constraints associated with pastures.
Lignin Biosynthetic Pathway
Lignin is an insoluble polymer that serves as a matrix around the polysaccharide components of some plant cell walls, and that is primarily responsible for the rigidity of plant stems. Generally, the higher the lignin content, the more rigid the plant. For example, tree species synthesize large quantities of lignin, with lignin constituting 20%–30% of the dry weight of wood. The lignin content of grasses ranges from 2–8% of dry weight and changes during the growing season. In addition to providing rigidity, lignin aids in water transport within plants by rendering cell walls hydrophobic and water impermeable. Lignin also plays a role in disease resistance of plants by impeding the penetration and propagation of pathogenic agents.
Forage digestibility is affected by both lignin composition and concentration. Lignin is largely responsible for the digestibility, or lack thereof, of forage crops, with small increases in plant lignin content resulting in relatively high decreases (>10%) in digestibility (Buxton and Russell, Crop. Sci. 28:5358–558, 1988). For example, crops with reduced lignin content provide more efficient forage for cattle, with the yield of milk and meat being higher relative to the amount of forage crop consumed. During normal plant growth, an increase in the maturity of the plant stem is accompanied by a corresponding increase in lignin content and composition that causes a decrease in digestibility. This change in lignin composition is to one of increasing syringyl:guaiacyl (S:G) ratio. When deciding on the optimum time to harvest forage crops, farmers must therefore choose between a high yield of less digestible material and a lower yield of more digestible material.
Lignin is formed by polymerization of three different monolignols, para-coumaryl alcohol, coniferyl alcohol and sinapyl alcohol that are synthesized in a multistep pathway, with each step in the pathway being catalyzed by a different enzyme. The three monolignols are derived from phenylalanine or tyrosine in a multistep process and are then polymerized into lignin by a free radical mechanism. Following polymerization, para-coumaryl alcohol, coniferyl alcohol and sinapyl alcohol are converted into the p-hydroxyphenyl (H), guaiacyl (G) and syringyl (S) units of lignin, respectively. While these three types of lignin subunits are well known, it is likely that slightly different variants of these subunits may be involved in the lignin biosynthetic pathway in various plants. For example, studies suggest that both free monolignols and monolignol-4-coumarate esters may be substrates for lignin formation in grasses. The relative concentration of the monolignol residues in lignin varies among different plant species and within species. For example, the monolignol content for H/G/S of grasses, alfalfa and softwood gymnosperms is 22%/44%/34%, 7%/39%/54% and 14%/80%/6%, respectively (van Soest in “Nutritional Ecology of the Ruminant,” Cornell University Press, Ithaca, N.Y.). The composition of lignin may also vary among different tissues within a specific plant.
Coniferyl alcohol, para-coumaryl alcohol and sinapyl alcohol are synthesized by similar pathways (Whetten et al., Annu. Rev. Plant Physiol. Plant Mol. Biol. 49:585–609, 1998; Guo et al., Plant Cell 13:73–88, 2001). The first step in the lignin biosynthetic pathway is the deamination of phenylalanine or tyrosine by phenylalanine ammonia-lyase (PAL) or tyrosine ammonia-lyase (TAL), respectively. In maize, the PAL enzyme also has TAL activity (Rosler et al., Plant Physiol. 113:175–179, 1997). The product of TAL activity on tyrosine is 4-coumarate, whereas the product of PAL activity on phenylalanine is cinnamate which is then hydroxylated by cinnamate 4-hydroxylase (C4H) to form 4-coumarate. 4-Coumarate is hydroxylated by coumarate 3-hydroxylase (C3H) to give caffeate. The newly added hydroxyl group is then methylated by caffeic acid O-methyl transferase (COMT) to give ferulate. Several other methylation reactions can be catalyzed by COMT, including caffeoylaldehyde to coniferaldehyde, and 5-hydroxyconiferaldehyde to sinapaldehyde. 4-Coumarate, caffeate and ferulate can all be conjugated to coenzyme A by 4-coumarate: CoA ligase (4CL) to form 4-coumaryl CoA, caffeoyl CoA and feruloyl CoA, respectively. Caffeoyl CoA can then be methylated by the enzyme caffeoyl-CoA O-methyl transferase (CAMT).
Coniferaldehyde is hydroxylated to 5-hydroxyconiferaldehyde by ferulate 5-hydroxylase (F5H). Reduction of 4-coumaryl CoA, caffeoyl CoA and feruloyl-CoA to 4-coumaraldehyde, caffeoyl aldehyde and coniferaldehyde, respectively, is catalyzed by cinnamoyl-CoA reductase (CCR). Coumaraldehyde, caffeoyl aldehyde, coniferaldehyde and 5-hydroxyconfieraldehyde are further reduced by the action of cinnamyl alcohol dehydrogenase (CAD) to give coniferyl alcohol which is then converted into its glucosylated form for export from the cytoplasm to the cell wall by coniferol glucosyl transferase (CGT). Recently a sinapyl alcohol dehydrogenase (SAD) was described that converts sinapaldehyde to sinapyl alcohol (Li et al., Plant Cell 13:1567–1586, 2001). Following export, the de-glucosylated form of coniferyl alcohol is obtained by the action of coniferin beta-gulcosidase (CBG). Finally, polymerization of the three monolignols to provide lignin is catalyzed by phenolase (PNL), laccase (LAC) and peroxidase (PER). For a more detailed review of the lignin biosynthetic pathway, see Whetton R and Sederoff R, The Plant Cell, 7:1001–1013, 1995 and Whetten et al., Annu. Rev. Plant Physiol. Plant Mol. Biol. 49:585–609, 1998.
Both lignin levels and composition have been changed in a range of plant species by altering the expression of specific lignin biosynthetic enzymes. For example, anti-sense 4CL constructs in transgenic aspen trees reduced lignin content from 20 to 11% (a 45% reduction) but at the same time increased both cellulose levels (by 15%) and growth rate (Hu et al. Nature Biotechnol. 17:808–812, 1999). These trees had the same level of total carbon, suggesting that carbon partitioning had been altered. Reducing 4CL by either anti-sense or sense-suppression in tobacco plants led to an accumulation of hydroxycinnamic acids in cell walls as well as a reduction in both guaiacyl and syringyl lignin units (Kajita et al., Plant Cell. Physiol. 37:957–965, 1996). In transgenic tobacco plants in which levels of C4H were reduced by anti-sense or sense suppression, total lignin content was reduced, in addition to a reduction in syringyl lignin units (Sewalt et al., Plant Physiol. 115:41–50, 1997). Reducing the levels of PAL in tobacco plants by anti-sense or sense-suppression reduced total lignin content but did not change the syringyl-guaiacyl (S:G) lignin ration. In alfalfa, reducing expression of COMT through either anti-sense or gene silencing decreased total lignin by decreasing the amount of guaiacyl units and resulted in a near total loss of syringyl lignin units (Guo et al., Plant Cell 13:73–88, 2001). In contrast, reducing CCOMT expression through anti-sense or gene silencing in alfalfa plants also decreased total lignin by reducing the total amount of guaiacyl lignin units but had no effect on the amount of syringyl lignin. Reducing CCR expression by anti-sense in tobacco plants resulted in reduced lignin content and increased S:G ratios due to lower guaiacyl lignin units (Piquemal et al., Plant J. 13:71–83, 1998). A. thaliana plants where the F5H gene had been mutated contained only traces of syringyl lignin (Marita et al., Proc. Natl. Acad. Sci. USA 96:12323–12332, 1999).
Alteration of grass lignin composition may usefully be employed to maintain high forage digestibility throughout the year. This is most important when the plant is approaching flowering and/or during flowering. At this time, the entire lignin biosynthetic pathway will preferably be reduced, in particular lowering the amount of syringyl lignin units, thereby lowering the S:G ratio and maintaining the digestibility of the forage crop.
Several of the enzymes involved in the lignin biosynthetic pathway also have other functions within the plant. For example, PAL is a key enzyme of plant and fungi phenylpropanoid metabolism and catalyzes the first step in phenylpropanoid metabolism. It is involved in the biosynthesis of a wide variety of secondary metabolites such as flavonoids, furanocoumar in phytoalexins and cell wall components. These compounds have many important roles in plants during normal growth and in responses to environmental stress. PAL catalyzes the removal of an ammonia group from phenylalanine to form trans-cinnamate. PAL and the related histidine ammonia lyase are unique enzymes which are known to have the modified amino acid dehydroalanine (DHA) in their active site (Taylor et al., .J. Biol. Chem. 265:18192–18199, 1990). Phenylalanine and histidine ammonia-lyases (PAL) active site has a consensus of GTITASGDLVPLSYIA (SEQ ID NO: 219). The serine residue is central to the active site, and the region around this active site residue is well conserved (Langer et al., Biochem. 33:6462–6467, 1994).
C4H, which is a member of the cytochrome P450 monooxygenase superfamily, plays a central role in both phenylpropanoid metabolism and lignin biosynthesis where it anchors a phenylpropanoid enzyme complex to the endoplasmic reticulum (ER). The phenylpropanoid pathway controls the synthesis of lignin, flower pigments, signaling molecules, and a large spectrum of compounds involved in plant defense against pathogens and UV light. This is also a branch point between general phenylpropanoid metabolism and pathways leading to various specific end products. 4 CLs are a group of enzymes necessary for maintaining a continuous metabolic flux for the biosynthesis of plant phenylpropanoids, such as lignin and flavonoids that are essential to the survival of plants, because they serve important functions in plant growth and adaptation to environmental perturbations. Three isoforms of 4CL have been identified with distinct substrate preference and specificities. Expression studies in angiosperms revealed a differential behavior of the three genes in various plant organs and upon external stimuli such as wounding and UV irradiation or upon challenge with fungi. One isoform is likely to participate in the biosynthetic pathway leading to flavonoids whereas the other two are probably involved in lignin formation and in the production of additional phenolic compounds other than flavonoids (Ehlting et al., Plant J. 19:9–20, 1999).
F5H is involved in the phenylpropanoid biosynthesis pathway. It belongs to the CYP84 subfamily of the cytochrome P450 family and is known as cytochrome P450 84A1. F5H is one of the enzymes in the pathways leading to the synthesis of sinapic acid esters, but also has coniferaldehyde hydroxylase activity (Nair et al., Plant Physiol. 123:1623–1634, 2000). In the generalized pathway for phenylpropanoid metabolism, F5H catalyzes the formation of 5-hydoxyferulate (a precursor of sinapate) and sinapate in turn as the precursor for sinapine and for sinapoyl CoA in two bifurcated pathways (Chapple et al., Plant Cell 4:1413–1424, 1992). Sinapoyl CoA has been considered as the precursor for sinapyl alcohol, which is then polymerized into syringyl (S) lignin. In addition, CYP84 F5H product carries out the hydroxylation of coniferaldehyde (ConAld) to 5-OH ConAld (Nair et al., Plant Physiol. 123:1623–1634, 2000).
Peroxidases are heme-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyze a number of oxidative reactions. They belong to a superfamily consisting of 3 major classes. Class III consists of the secretory plant peroxidases, which have multiple tissue-specific functions in removal of hydrogen peroxide from chloroplasts and cytosol, oxidation of toxic compounds, biosynthesis of the cell wall, defense responses towards wounding, indole-3-acetic acid (IAA) catabolism and ethylene biosynthesis.
Fructan Biosynthetic Pathway
Plant carbohydrates can be divided into two groups depending on their function within the plant. Structural carbohydrates, such as cellulose, are usually part of the extracellular matrix. Non-structural, storage carbohydrates act as either long- or short-term carbohydrate stores. Examples of non-structural carbohydrates include starch, sucrose and fructans.
Fructans are polymers that are stored in the vacuole and that consist of linear and branched chains of fructose units (for review, see Vijn and Smeekens Plant Physiol. 120:351–359, 1999). They play an important role in assimilate partitioning and possibly in stress tolerance in many plant families. Grasses use fructans instead of starch as a water-soluble carbohydrate store (Pollock et al., in “Regulation of primary metabolic pathways in plants”, N. J. Kruger et al., (eds), Kluwer Academic Publishers, The Netherlands, pp195–226, 1999). Increasing the amount of fructans and sucrose in forage crops leads to an increase in the level of water-soluble carbohydrates and thereby enhances the nutritional value of the plants. In addition, increasing the amount of fructans in forage plants decreases m ethane production in animals fed the plants, thereby leading to lower greenhouse gas emissions, and decreases urea production in animals as less protein is degraded in the rumen (Biggs and Hancock, Trends in Plant Sci. 6:8–9, 2001). Fructans have also been implicated in protecting plants against water deficits caused by drought or low temperatures. Introduction of enzymes involved in the fructan biosynthetic pathway into plants that do not naturally synthesize fructans may be employed to confer cold tolerance and drought tolerance (Pilon-Smits, Plant Physiol. 107:125–130, 1995).
The number of fructose units within a fructan chain is referred to as the degree of polymerization (DP). In grasses, fructans of DP 6–10 are common. Such fructans of low DP are naturally sweet and are therefore of interest for use as sweeteners in foodstuffs. Long fructan chains form emulsions with a fat-like texture and a neutral taste. The human digestive system is unable to degrade fructans, and fructans of high D P may therefore be used as low-calorie food ingredients. Over-expression of enzymes involved in the fructan biosynthetic pathway may be usefully employed to produce quantities of fructans that can be purified for human consumption.
Five major classes of structurally different fructans have been identified in plants, with each class showing a different linkage of the fructosyl residues. Fructans found in grasses are of the mixed levan class, consisting of both (2-1)- and (2-6)-linked beta-D-fructosyl units (Pollock et al., in “Regulation of primary metabolic pathways in plants”, N. J. Kruger et al., (eds), Kluwer Academic Publishers, The Netherlands, pp195–226, 1999). Fructans are synthesized by the action of fructosyltransferase enzymes on sucrose in the vacuole. These enzymes are closely related to invertases, enzymes that normally hydrolyze sucrose.
Grasses use two fructosyltransferase enzymes to synthesize fructans, namely sucrose:sucrose 1-fructosyltransferase (1-SST) and sucrose:fructan 6-fructosyltransferase (6-SFT) (Pollock et al., in “Regulation of primary metabolic pathways in plants”, N. J. Kruger et al., (eds), Kluwer Academic Publishers, The Netherlands, pp195–226, 1999). 1-SST is a key enzyme in plant fructan biosynthesis, while 6-SFT catalyzes the formation and extension of beta-2,6-linked fructans that is typically found in grasses. Specifically, 1-SST catalyzes the formation of 1-kestose plus glucose from sucrose, while 6-SFT catalyzes the formation of bifurcose plus glucose from sucrose plus 1-kestose and also the formation of 6-kestose plus glucose from sucrose. Both enzymes can modify 1-kestose, 6-kestose and bifurcose further by adding additional fructose molecules. Over-expression of both 1-SST and 6-SFT in the same plant may be employed to produce fructans for use in human foodstuffs (Sevenier et al., Nature Biotechnol 16:843–846; Hellwege et al., Proc. Nat. Acad. Sci. USA 97:8699–8704,2000).
The synthesis of sucrose from photosynthetic assimilates in plants, and therefore the availability of sucrose for use in fructan formation, is controlled, in part, by the enzymes sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP). Sucrose plays an important role in plant growth and development, and is a major end product of photosynthesis. It also functions as a primary transport sugar and in some cases as a direct or indirect regulator of gene expression (for a review see Smeekens, Curr. Opin. Plant Biol. 1:230–234, 1998). SPS regulates the synthesis of sucrose by regulating carbon partitioning in the leaves of plants and therefore plays a major role as a limiting factor in the export of photoassimilates out of the leaf The activity of SPS is regulated by phosphorylation and moderated by concentration of metabolites and light (Huber et al., Plant Physiol. 95:291–297, 1991). Specifically, SPS catalyzes the transfer of glucose from UDP-glucose to fructose-6-phosphate, thereby forming sucrose-6-phosphate (Suc-6-P). Suc-6-P is then dephosphorylated by SPP to form sucrose (Lunn et al., Proc. Natl. Acad. Sci. USA 97:12914–12919, 2000). The enzymes SPS and SPP exist as a heterotetramer in the cytoplasm of mesophyll cells in leaves, with SPP functioning to regulate SPS activity. SPS is also important in ripening fruits, sprouting tubers and germinating seeds (Laporte et al., Planta 212:817–822, 2001).
Once in the vacuole, sucrose can be converted into fructan by fructosyltransferases as discussed above, or hydrolyzed into glucose and fructose by the hydrolase enzymes known as invertases (Sturm, Plant Physiol. 121:1–7, 1999). There are several different types of invertases, namely extracellular (cell wall), vacuolar (soluble acid) and cytoplasmic, with at least two isoforms of each type of invertase normally being found within a plant species. In addition to having different subcellular locations, the different types of invertases have different biochemical properties. For example, soluble and cell wall invertases operate at acidic pH, whereas cytoplasmic invertases work at a more neutral or alkaline pH. Invertases are believed to regulate the entry of sucrose into different utilization pathways (Grof and Campbell, Aust. J. Plant Physiol. 28:1–12, 2001). Reduced vacuolar or cytoplasmic invertase activity in sink tissues may increase the level of water-soluble carbohydrates in plants. Plants contain several isoforms of cell wall invertases (CWINV), which accumulate as insoluble proteins. CWINV plays an important role in phloem unloading and in stress response. It hydrolyzes terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructo-furanosides.
Another enzyme that acts upon sucrose in plants is soluble sucrose synthase (SUS). Recent results indicate that SUS is localized in the cytosol, associated with the plasma membrane and the actin cytoskeleton. Phosphorylation of SUS is one of the factors controlling localization of the enzyme (Winter and Huber, Crit. Rev. Biochem. Mol. Biol. 35:253–89, 2000). It catalyzes the transfer of glucose from sucrose to UDP, yielding UDP-glucose and fructose. Increasing the amount of SUS in a plant increases the amount of cellulose synthesis, whereas decreasing SUS activity should increase fructan levels. Increased SUS concentration may also increase the yield of fruiting bodies. SUS activity is highest in carbon sink tissues in plants and low in photosynthetic source tissues, and studies have indicated that SUS is the main sucrose-cleaving activity in sink tissues. Grasses have two isoforms of SUS that are encoded by separate genes. These genes are differentially expressed in different tissues.
Tannin Biosynthetic Pathway
Condensed tannins are polymerized flavonoids. More specifically, tannins are composed of catechin 4-ol and catechin monomer units, and are stored in the vacuole. In many temperate forage crops, such as ryegrass and fescue, foliar tissues are tannin-negative. This leads to a high initial rate of fermentation when these crops are consumed by ruminant livestock, resulting in both protein degradation and production of ammonia by the livestock. These effects can be reduced by the presence of low to moderate levels of tannin. In certain other plant species, the presence of high levels of tannins reduces palatability and nutritive value. Introduction of genes encoding enzymes involved in the biosynthesis of condensed tannins into a plant may be employed to synthesize flavonoid compounds that are not normally made in the plant. These compounds may then be isolated and used for treating human or animal disorders or as food additives.
Much of the biosynthetic pathway for condensed tannins is shared with that for anthocyanins, which are pigments responsible for flower color. Therefore, modulation of the levels of enzymes involved in the tannin biosynthetic pathway may be employed to alter the color of foliage and the pigments produced in flowers.
Most tannins described to date contain pro-cyanidin units derived from dihydroquercetin and pro-delphinidin units derived from dihydromyricetin. However, some tannins contain pro-pelargonidin units derived from dihydrokaempferol. The initial step in the tannin biosynthetic pathway is the condensation of coumaryl CoA with malonyl CoA to give naringenin-chalcone, which is catalyzed by the enzyme chalcone synthase (CHS). The enzyme chalcone isomerase (CHI) catalyzes the isomerization of naringenin chalcone to naringenin (also known as flavanone), which is then hydroxylated by the action of the enzyme flavonone 3-beta-hydroxylase (F3βH) to give dihydrokaempferol. The enzyme flavonoid 3′-hydroxylase (F3′OH) catalyzes the conversion of dihydrokaempferol to dihydroquercetin, which in turn can be converted into dihydromyricetin by the action of flavonoid 3′5′-hydroxylase (F3′5′OH). The enzyme dihydroflavonol-4-reductase (DFR) catalyzes the last step before dihydrokaempferol, dihydroquercetin and dihydromyricetin are committed for either anthocyanin (flower pigment) or proanthocyanidin (condensed tannin) formation. DFR also converts dihydrokaempferol to afzelchin-4-ol, dihydroquercetin to catechin-4-ol, and dihydromyricetin to gallocatechin-4-ol, probably by the action of more than one isoform. For a review of the tannin biosynthetic pathway, see, Robbins M. P. and Morris P. in Metabolic Engineering of Plant Secondary Metabolism, Verpoorte and Alfermann (eds), Kluwer Academic Publishers, the Netherlands, 2000.
While polynucleotides encoding some of the enzymes involved in the lignin, fructan and tannin biosynthetic pathways have been isolated for certain species of plants, genes encoding many of the enzymes in a wide range of plant species have not yet been identified. Thus there remains a need in the art for materials useful in the modification of lignin, fructan and tannin content and composition in plants, and for methods for their use.
SUMMARY OF THE INVENTION
The present invention provides enzymes involved in the lignin, fructan or tannin biosynthetic pathways that are encoded by polynucleotides isolated from forage grass tissues. The polynucleotides were isolated from Lolium perenne (perennial ryegrass) and Festuca arundinacea (tall fescue) tissues taken at different times of the year, specifically in winter and spring, and from different parts of the plants, including: leaf blades, leaf base, pseudostems, floral stems, roots, inflorescences and stems. The present invention also provides genetic constructs, expression vectors and host cells comprising the inventive polynucleotides, and methods for using the inventive polynucleotides and genetic constructs to modulate the biosynthesis of lignins, fructans and tannins.
In specific embodiments, the isolated polynucleotides of the present invention comprise a sequence selected from the group consisting of: (a) SEQ ID NO: 1–62 and 125–162; (b) complements of SEQ ID NO: 1–62 and 125–162; (c) reverse complements of SEQ ID NO: 1–62 and 125–162; (d) reverse sequences of SEQ ID NO: 1–62 and 125–162; (e) sequences having a 99% probability of being functionally or evolutionarily related to a sequence of (a)-(d), determined as described below; and (f) sequences having at least 75%, 80%, 90% or 98% identity to a sequence of (a)–(d), the percentage identity being determined as described below. Polynucleotides comprising at least a specified number of contiguous residues (“x-mers”) of any of SEQ ID NO: 1–62 and 125–162; and oligonucleotide probes and primers corresponding to SEQ ID NO: 1–62 and 125–162 are also provided. All of the above polynucleotides are referred to herein as “polynucleotides of the present invention.”
In further aspects, the present invention provides isolated polypeptides comprising an amino acid sequence of SEQ ID NO: 63–124 and 163–190, together with polypeptides comprising a sequence having at least 75%, 80%, 90% or 98% identity to a sequence of SEQ ID NO: 63–124 and 163–190, wherein the polypeptide possesses the same functional activity as the polypeptide comprising a sequence of SEQ ID NO: 63–124 and 163–190. The present invention also contemplates isolated polypeptides comprising at least a functional portion of a polypeptide comprising an amino acid sequence selected from the group consisting of: (a) SEQ ID NO: 63–124 and 163–190; and (b) sequences having at least 75%, 80%, 90% or 98% identity to a sequence of SEQ ID NO: 63–124 and 163–190.
In another aspect, the present invention provides genetic constructs comprising a polynucleotide of the present invention, either alone, in combination with one or more of the inventive sequences, or in combination with one or more known polynucleotides.
In certain embodiments, the present invention provides genetic constructs comprising, in the 5′–3′ direction: a gene promoter sequence; an open reading frame coding for at least a functional portion of a polypeptide of the present invention; and a gene termination sequence. An open reading frame may be orientated in either a sense or anti-sense direction. Genetic constructs comprising a non-coding region of a polynucleotide of the present invention or a polynucleotide sequence complementary to a non-coding region, together with a gene promoter sequence and a gene termination sequence, are also provided. Preferably, the gene promoter and termination sequences are functional in a host cell, such as a plant cell. Most preferably, the gene promoter and termination sequences are those of the original enzyme genes but others generally used in the art, such as the Cauliflower Mosaic Virus (CMV) promoter, with or without enhancers, such as the Kozak sequence or Omega enhancer, and Agrobacterium tumefaciens nopalin synthase terminator may be usefully employed in the present invention. Tissue-specific promoters may be employed in order to target expression to one or more desired tissues. The construct may further include a marker for the identification of transformed cells.
In a further aspect, transgenic cells, such as transgenic plant cells, comprising the constructs of the present invention are provided, together with tissues and plants comprising such transgenic cells, and fruits, seeds and other products, derivatives, or progeny of such plants.
In yet another aspect, methods for modulating the lignin, fructan or tannin content and composition of a target organism, such as a plant, are provided, such methods including stably incorporating into the genome of the target plant a genetic construct comprising a polynucleotide of the present invention. In a preferred embodiment, the target plant is a forage grass, preferably selected from the group consisting of Lolium and Festuca species, and most preferably from the group consisting of Lolium perenne and Festuca arundinacea. In a related aspect, a method for producing a plant having altered lignin, fructan or tannin composition is provided, the method comprising transforming a plant cell with a genetic construct comprising of the present invention to provide a transgenic cell, and cultivating the transgenic cell under conditions conducive to regeneration and mature plant growth.
In yet a further aspect, the present invention provides methods for modifying the activity of an enzyme in a target organism, such as a plant, comprising stably incorporating into the genome of the target organism a genetic construct of the present invention. In a preferred embodiment, the target plant is a forage grass, preferably selected from the group consisting of Lolium and Festuca species, and most preferably from the group consisting of Lolium perenne and Festuca arundinacea. 



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the activity of recombinant LpSPP (SEQ ID NO: 8) and FaSPP (SEQ ID NO 7) on dephosphorylating Suc-6-P and Fru-6-P. The pET41a extract was the vector control.
FIG. 2 shows the peroxidase activity of FaPER3 (SEQ ID NO: 50) and LpPER5 (SEQ ID NO: 52) as determined by oxidation of ABTS. Horseradish peroxidase of known activity (Sigma, St Louis, Mich.) was used as a positive control and boiled samples as a negative control.
FIG. 3 shows PCR verification of transgenic N. benthamiana plants transformed with Lp6-SFT1 (SEQ ID NO: 3). Genomic DNA was isolated from kanamycin resistant T2 N. benthamiana plants and the Lp6-SFT1 fragment was amplified using specific PCR primers.
FIG. 4 shows PCR verification of transgenic N. benthamiana plants transformed with Lp1-SST (SEQ ID NO: 1). Genomic DNA was isolated from kanamycin resistant T2 N. benthamiana plants and the Lp1-SST fragment was amplified using specific PCR primers. Plant number 5 is a non-transgenic control.
FIG. 5 shows the fructan level in transgenic N. benthamiana lines transformed with Lp6-SFT1 (SEQ ID NO: 3) and Lp1-SST (SEQ ID NO: 1).
FIG. 6 shows the sucrose synthesizing activity of FaSPS-N (SEQ ID NO: 9) with and without SPP (SEQ ID NO: 8) in mammalian cell extracts. The non-transfected cells are controls.
FIG. 7 shows the sucrose cleaving activity of FaSUS1 (SEQ ID NO: 13) in mammalian cell extracts.
FIG. 8 shows the invertase activity for vacuolar invertase (LpSINV1, SEQ ID NO: 25) and two cell wall invertases (LpCWINV1 and FaCWINV4, SEQ ID NO: 17 and 19); absence of invertase activity from an empty vector (pPICZαA) control is also shown.



DETAILED DESCRIPTION OF THE INVENTION
The polypeptides of the present invention, and the polynucleotides encoding the polypeptides, have activity in lignin, fructan and tannin biosynthetic pathways in plants. Using the methods and materials of the present invention, the lignin, fructan and/or tannin content of a plant may be modulated by modulating expression of polynucleotides of the present invention, or by modifying the polynucleotides or polypeptides encoded by polynucleotides. The isolated polynucleotides and polypeptides of the present invention may thus be usefully employed in the correction of nutritional imbalances associated with temperate pastures and to increase the yield of animal products from pastures.
The lignin, fructan and/or tannin content of a target organism, such as a plant, may be modified, for example, by incorporating additional copies of genes encoding enzymes involved in the lignin, fructan or tannin biosynthetic pathways into the genome of the target plant. Similarly, a modified lignin, fructan and/or tannin content can be obtained by transforming the target plant with anti-sense copies of such genes. In addition, the number of copies of genes encoding for different enzymes in the lignin, fructan and tannin biosynthetic pathways can be manipulated to modify the relative amount of each monomer unit synthesized, thereby leading to the formation of lignins, fructans or tannins having altered composition.
The present invention thus provides methods for modulating the polynucleotide and/or polypeptide content and composition of an organism, such methods involving stably incorporating into the genome of the organism a genetic construct comprising one or more polynucleotides of the present invention. In one embodiment, the target organism is a plant species, preferably a forage plant, more preferably a grass of the Lolium or Festuca species, and most preferably Lolium perenne or Festuca arundinacea. In related aspects, methods for producing a plant having an altered genotype or phenotype is provided, such methods comprising transforming a plant cell with a genetic construct of the present invention to provide a transgenic cell, and cultivating the transgenic cell under conditions conducive to regeneration and mature plant growth. Plants having an altered genotype or phenotype as a consequence of modulation of the level or content of a polynucleotide or polypeptide of the present invention compared to a wild-type organism, as well as components (seeds, etc.) of such plants, and the progeny of such plants, are contemplated by and encompassed within the present invention.
The isolated polynucleotides of the present invention have utility in genome mapping, in physical mapping, and in positional cloning of genes. Additionally, the polynucleotide sequences identified as SEQ ID NOS: 1–62 and 125–162 and their variants, may be used to design oligonucleotide probes and primers. Oligonucleotide probes and primers have sequences that are substantially complementary to the polynucleotide of interest over a certain portion of the polynucleotide. Oligonucleotide probes designed using the polynucleotides of the present invention may be employed to detect the presence and examine the expression patterns of genes in any organism having sufficiently similar DNA and RNA sequences in their cells using techniques that are well known in the art, such as slot blot DNA hybridization techniques. Oligonucleotide primers designed using the polynucleotides of the present invention may be used for PCR amplifications. Oligonucleotide probes and primers designed using the polynucleotides of the present invention may also be used in connection with various microarray technologies, including the microarray technology of Affymetrix (Santa Clara, Calif.).
In a first aspect, the present invention provides isolated polynucleotide sequences identified in the attached Sequence Listing as SEQ ID NO: 1–62 and 125–162, and polypeptide sequences identified in the attached Sequence Listing as SEQ ID NO: 63–124 and 163–190. The polynucleotides and polypeptides of the present invention have demonstrated similarity to the following polypeptides that are known to be involved in lignin, fructan and tannin biosynthetic processes:










TABLE 1





SEQ ID NO
SEQ ID NO




Polynucleotide
Polypeptide
Category
Description







 1 and 125
63 and 163
Fructan
Homolog of Sucrose: Sucrose




biosynthesis
1-fructosyl-transferase (1-SST)





isolated from Festuca arundinacea.





They contain a typical signature





of the glycosyl hydrolases family 32





(amino acid residues 120 to 133). The





glycosyl hydrolases family 32 domain





signature has a consensus of





HYQPxxH/NxxNDPNG, where D is the





active site residue (Henrissat, Biochem.





J. 280:309–316, 1991).


 2
64
Fructan
Homolog of Sucrose: Sucrose 1-fructosyl-




biosynthesis
transferase (1-SST) isolated from





Festuca arundinacea. It contains a





typical signature of the glycosyl





hydrolases family 32 (amino acid





residues 120 to 133). The glycosyl





hydrolases family 32 domain signature





has a consensus of HYQPxxH/NxxNDPNG,





where D is the active site residue





(Henrissat, Biochem. J. 280:309–316,





1991).


 3 and 126
65 and 164
Fructan
Homolog of Sucrose: fructan 6-fructosyl-




biosynthesis
transferase (6-SFT) isolated from





Festuca arundinacea. They contain





a typical signature of the glycosyl





hydrolases family 32 (amino acid reidues





90 to 564). The glycosyl hydrolases





family 32 domain signature has a





consensus of HYQPxxH/NxxNDPNG, where





D is the active site residue (Henrissat,





Biochem. J 280:309–316, 1991).


 4 and 127
66 and 165
Fructan
Homolog of Sucrose: fructan 6-fructosyl-




biosynthesis
transferase (6-SFT) isolated from





Lolium perenne. They contain a





typical signature of the glycosyl





hydrolases family 32 (amino acid





residues 96 to 107). The glycosyl





hydrolases family 32 domain signature





has a consensus of HYQPxxH/NxxNDPNG,





where D is the active site residue





(Henrissat, Biochem. J. 280:309–316,





1991).


 5
67
Fructan
Homolog of sucrose: fructan 6-fructosyl-




biosynthesis
transferase (6-SFT) isolated from





Festuca arundinacea.


 6 and 128
68 and 166
Fructan
Homolog of Sucrose: fructan 6-fructosyl-




biosynthesis
transferase (6-SFT) isolated from





Lolium perenne. They contain a





typical signature of the glycosyl





hydrolases family 32 (amino acid





residues 90 to 103). The glycosyl





hydrolases family 32 domain signature





has a consensus of HYQPxxH/NxxNDPNG,





where D is the active site residue





(Henrissat, Biochem. J. 280:309–316,





1991).


 7 and 129
69
Fructan
Homolog of Sucrose-6-phosphate phospho-




biosynthesis
hydrolase (SPP; EC 3.1.3.24) isolated





from Festuca arundinacea. This





enzyme belongs to the superfamily of





hydrolases, and has the three





conserved motifs found in these proteins





(Galperin and Koonin, Trends Biochem





Sci. 23:127–129, 1998). Motif I





(amino acid residues 10 to 19) contains





conserved Asp and a Thr residues, motif





II (amino acid residues 48 to 53)





contains a conserved Thr residue, and





Motif III (residues 167 to 220) contains





conserved Lys (position 167) and Asp





residues (position 202 and 206). These





conserved amino acid residues are





required for activity of the enzyme.


 8
70
Fructan
Homolog of Sucrose-6-phosphate phospho-




biosynthesis
hydrolase (SPP; EC 3.1.3.24) isolated





from Lolium perenne. This enzyme





belongs to the superfamily of





hydrolases, and has the three conserved





motifs found in these proteins (Galperin





and Koonin, Trends Biochem Sci.





23:127–129, 1998). Motif I (residues





10 to 19) contains conserved Asp and Thr





residues, motif II (amino acid residues





48 to 53) contains a conserved Thr





residue, and Motif III (amino acid





residues 167 to 220) contains conserved





Lys (position 167) and Asp residues





(position 202 and 206). These conserved





amino acid residues are required for





activity of the enzyme.


 9 and 130
71
Fructan
Homolog of sucrose phosphate synthase




biosynthesis
(SPS-1) isolated from Festuca





arundinacea.


10 and 131
72 and 167
Fructan
Homolog of sucrose phosphate synthase




biosynthesis
(SPS-1) isolated from Lolium perenne





and that is involved in the sucrose





synthesis pathway.


11 and 132
73 and 168
Fructan
Homolog of sucrose phosphate synthase




biosynthesis
(SPS-N) isolated from Lolium perenne





and that is involved in the sucrose





synthesis pathway.


12 and 133
74 and 169
Fructan
Homolog of sucrose synthase (SuS)




biosynthesis
isolated from Lolium perenne. These





molecules contain a leucine zipper





motif in amino acid position 191 to





213. Leucine zipper motifs are present





in many gene regulatory proteins





(Landschulz et al., Science





240:1759–1764, 1988).


13
75
Fructan
Homolog of sucrose synthase (SuS)




biosynthesis
isolated from Festuca arundinacea.





This molecule contains a leucine zipper





motif in amino acid position 191 to





213. Leucine zipper motifs are present





in many gene regulatory proteins





(Landschulz et al., Science





240:1759–1764, 1988).


14 and 134
76 and 170
Fructan
Homolog of sucrose synthase (SuS)




biosynthesis
isolated from Lolium perenne.


15
77
Fructan
Homolog of sucrose synthase (SuS)




biosynthesis
isolated from Festuca arundinacea.


16 and 135
78 and 171
Fructan
Homologue of cell wall invertase




biosynthesis
(CWINV) isolated from Festuca





arundinacea that belongs to the





family 32 of glycosyl hydrolases.





These molecules contain a conserved





peptide domain in amino acid residues





139 to 144 and 242–247, respectively.





The consensus peptide domain of





invertases is (WVYL)EC(PIL)D(LFI) with





the conserved Cys residue part of the





catalytic domain (Sturm, Plant Physiol.





121:1–7, 1999).


17
79
Fructan
Homolog of cell wall invertase (CWINV)




biosynthesis
isolated from Lolium perenne that





belongs to the family 32 of glycosyl





hydrolases. This molecule contains a





conserved pentapeptide bF-motif at amino





acid residues 70 to 74 and a peptide





domain in amino acid residues 250 to 255.





The consensus peptide domain of





invertases is (WVYL)EC(PIL)D(LFI) with





the conserved Cys residue part of the





catalytic domain (Sturm, Plant Physiol.





121:1–7, 1999). It also contains a





glycosyl hydrolases family 32 signature





region at amino acids 61 to 74 that





contains a conserved His residue





important in the catalytic reaction





(Reddy and Maley, J. Biol. Chem.





265:10817–10120, 1990).


18 and 136
80 and 172
Fructan
Homolog of cell wall invertase (CWINV)




biosynthesis
isolated from Lolium perenne that





belongs to the family 32 of glycosyl





hydrolases.


19
81
Fructan
Homolog of cell wall invertase (CWINV)




biosynthesis
isolated from Festuca arundinacea





that belongs to the family 32 of





glycosyl hydrolases. This molecule





contains a conserved pentapeptide





bF-motif at amino acid residues 60 to





64. The consensus peptide domain of





invertases is (WVYL)EC(PIL)D(LFI) with





the conserved Cys residue part of the





catalytic domain (Sturm, Plant Physiol.





121:1–7, 1999). It also contains a





glycosyl hydrolases family 32 signature





region at amino acids 51 to 64 that





contains a conserved His residue





important in the catalytic reaction





(Reddy and Maley, J. Biol. Chem.





265:10817–10120, 1990). A signal





peptide is present in amino acid





residues 1 to 24.


20 and 137
82 and 173
Fructan
Homolog of cell wall invertase (CWINV)




biosynthesis
isolated from Festuca arundinacea





that belongs to the family 32 of





glycosyl hydrolases. These molecules





contain a peptide domain in amino acid





residues 61 to 66 and 242–247,





respectively. The consensus peptide





domain of invertases is





(WVYL)EC(PIL)D(LFI) with the





conserved Cys residue part of the





catalytic domain (Sturm, Plant Physiol.





121:1–7, 1999).


21
83
Fructan
Homolog of cell wall invertase (CWINV)




biosynthesis
isolated from Festuca arundinacea





that belongs to the family 32 of





glycosyl hydrolases. This molecule





contains a conserved pentapeptide





bF-motif at amino acid residues 73 to





77 and a peptide domain in amino acid





residues 253 to 258. The consensus





peptide domain of invertases is





(WVYL)EC(PIL)D-(LFI) with the





conserved Cys residue part of the





catalytic domain (Sturm, Plant Physiol.





121:1–7, 1999). It also contains a





glycosyl hydrolases family 32





signature region at amino acid 64 to





77 that contains a conserved His





residue important in the catalytic





reaction (Reddy and Maley, J. Biol.





Chem. 265:10817-10120, 1990).


22 and 138
84 and 174
Fructan
Homolog of cell wall invertase (CWINV)




biosynthesis
isolated from Lolium perenne that





belongs to the family 32 of glycosyl





hydrolases. These molecules contain a





peptide domain in amino acid residues





174 to 179 and 234 to 239,





respectively. The consensus peptide





domain of invertases is





(WVYL)EC-(PIL)D(LFI) with





the conserved Cys residue part of the





catalytic domain (Sturm, Plant Physiol.





121:1–7, 1999).


23
85
Fructan
Homolog of cell wall invertase (CWINV)




biosynthesis
isolated from Festuca arundinacea





that belongs to the family 32 of





glycosyl hydrolases. This molecule





contains a conserved pentapeptide





bF-motif at amino acid residues 56 to





60. The consensus peptide domain of





invertases is (WVYL)EC(PIL)D(LFI)





with the conserved Cys residue part of





the catalytic domain (Sturm, Plant





Physiol. 121:1–7, 1999). It also





contains a glycosyl hydrolases family





32 signature region at amino acid 47





to 60 that contains a conserved His





residue that is important in the





catalytic reaction (Reddy and Maley,





J. Biol. Chem. 265:10817-10120,





1990). A signal peptide is present





in amino acid residues 1 to 22.


24 and 139
86 and 175
Fructan
Homolog of cell wall invertase (CWINV)




biosynthesis
isolated from Lolium perenne





that belongs to the family 32 of





glycosyl hydrolases. These molecules





contain a conserved pentapeptide





bF-motif at amino acid residues 244





to 249. The consensus peptide domain





of invertases is (WVYL)EC(PIL)D(LFI)





with the conserved Cys residue part of





the catalytic domain (Sturm, Plant





Physiol. 121:1–7, 1999). They





also contain a glycosyl hydrolases





family 32 signature region at amino





acid 56 to 69 that contains a 





conserved His residue that is





important in the catalytic reaction





(Reddy and Maley, J. Biol. Chem.





265:10817-10120, 1990). A signal





peptide is present in amino acid





residues 1 to 25.


25 and 140
87 and 176
Fructan
Homolog of vacuolar invertase (SINV)




biosynthesis
isolated from Lolium perenne 





that belongs to the family 32 of





glycosyl hydrolases. These molecules





contain a conserved pentapeptide





bF-motif at amino acid residues 136





to 140 and 138 to 142, respectively





and a peptide domain in amino





acid residues 317 to 322 and 319 to





324, respectively. The consensus





peptide domain of invertases is





(WVYL)EC(PIL)D(LFI) with the





conserved Cys residue part of the





catalytic domain (Sturm, Plant





Physiol. 121:1–7, 1999). It also





contains a glycosyl hydrolases





family 32 signature region at amino





acid 127 to 140 and 129 to 142 that





contains a conserved His residue





that is important in the catalytic





reaction (Reddy and Maley, J. Biol.





Chem. 265:10817-10120, 1990).


26 and 141
88 and 177
Fructan
Homolog of invertase (SINV)




biosynthesis
isolated from Lolium perenne





that belongs to the family 32 of





glycosyl hydrolases. These molecules





contain a peptide domain in amino





acid residues 143 to 148 and 184





to 189, respectively. The consensus





peptide domain of invertases is





(WVYL)EC(PIL)D(LFI) with the





conserved Cys residue part of the





catalytic domain (Sturm, Plant





Physiol. 121:1–7, 1999).


27
89
Lignin/Tannin
Homolog of 4-Coumarate: CoA ligase




biosynthesis
(4CL, EC 6.2.1.12) isolated from





Lolium perenne The molecule





has two conserved AMP binding





regions at amino acid residues 182





to 193 and 383 to 389 (Hu et al.,





Proc. Natl. Acad. Sci. USA





95:5407–5412, 1998). The





AMP-binding domain signature





consists of two binding site





motifs. The consensus of the first





motif is LPYSSGTTGLPK (Etchegaray





et al., Biochem. Mol. Biol. Int.





44:235–243, 1998). The region





very rich in glycine, serine, and





threonine followed by a conserved





lysine. In most of these proteins,





the residue that follows the Lys





at the end of the pattern is a Gly.





The second motif consensus sequence





is GEIC(V/I)RG(Hu et al., Proc.





Natl. Acad. Sci. USA 95:5407–5412,





1998).


28 and 142
90
Lignin/Tannin
Homolog of 4-Coumarate: CoA ligase




biosynthesis
(4CL, EC 6.2.1.12) isolated from





Lolium perenne. The molecule





has two conserved AMP binding





regions at amino acid residues 195





to 206 and 395 to 401 (Hu et al.,





Proc. Natl. Acad. Sci. USA





95:5407–5412, 1998). The





AMP-binding domain signature





consists of two binding site motifs.





The consensus of the first motif





is LPYSSGTTGLPK (Etchegaray et al.,





Biochem. Mol. Biol. Int.





44:235–243, 1998). The region very





rich in glycine, serine, and theonine





followed by a conserved lysine. In





most of these proteins, the residue





that follows the Lys at the end of





the pattern is a Gly. The second





motif consensus sequence is GEIC(V/I)





RG (Hu et al., Proc. Natl. Acad. Sci.





USA 95:5407–5412, 1998).


29
91
Lignin/Tannin
Homolog of 4-Coumarate:CoA ligase




biosynthesis
(4CL, EC 6.2.1.12) isolated from





Festuca arundinacea. The molecule





has two conserved AMP binding regions





at amino acid residues 195 to 206 and





395 to 401 (Hu et al., Proc. Natl.





Acad. Sci. USA 95:5407–5412, 1998).





The AMP-binding domain signature





consists of two binding site motifs.





The consensus of the first motif is





LPYSSGTTGLPK (Etchegaray et al., 





Biochem. Mol. Biol. Int. 44:235–243,





1998). The region very rich in glycine,





serine, and threonine followed by a





conserved lysine. In most of these





proteins, the residue that follows





the Lys at the end of the pattern is a





Gly. The second motif consensus





sequence is GEIC(V/I)RG (Hu et al.,





Proc. Natl. Acad. Sci. USA 95:5407–54 12,





1998).


30 and 143
92 and 178
Lignin/Tannin
Homolog of 4-Coumarate:CoA ligase




biosynthesis
(4CL, EC 6.2.1.12) isolated from





Lolium. The molecules have two





conserved AMP binding regions at amino





acid residues 194 to 205 and 394 to





400 (Hu et al., Proc. Natl. Acad. Sci.





USA 95:5407–5412, 1998). The AMP-





binding domain signature consists of two





binding site motifs. The consensus of the





first motif is LPYSSGTTGLPK (Etchegaray





et al., Biochem. Mol. Biol. Int.





44:235–243, 1998). The region very





rich in glycine, serine, and threonine





followed by a conserved lysine. In most





of these proteins, the residue that





follows the Lys at the end of the pattern





is a Gly. The second motif consensus





sequence is GEIC(V/I)RG (Hu et al., Proc.





Natl. Acad. Sci. USA 95:5407–5412,





1998).


31
93
Lignin/Tannin
Homolog of 4-Coumarate:CoA ligase (4CL,




biosynthesis
EC 6.2.1.12) isolated from Festuca 





arundinacea. The molecule has two





conserved AMP binding regions at amino





acid residues 194 to 206 and 482 to 490





(Hu et al., Proc. Natl. Acad. Sci. USA





95:5407–5412, 1998). The AMP-binding





domain signature consists of two binding





site motifs. The consensus of the first





motif is LPYSSGTTGLPK (Etchegaray et





al., Biochem. Mol. Biol. Int. 44:235–243,





1998). The region very rich in glycine,





serine, and threonine followed by a





conserved lysine. In most of these proteins,





the residue that follows the Lys at the end





of the pattern is a Gly. The second motif





consensus sequence is GEIC(V/I)RG (Hu et





al., Proc. Natl. Acad. Sci. USA





95:5407–5412, 1998).


32 and 144
94 and 179
Lignin/Tannin
Homolog of cinnamic acid 4-hydroxylase




biosynthesis
(C4H) isolated from Lolium perenne. The





molecules have a conserved cytochrome P450





region in amino acids 436 to 445 that





contains a conserved Cys residue involved





in heme binding (Miles et al., Biochim





Biophys Acta 1543:383–407, 2000).


33
95
Lignin/Tannin
Homolog of cinnamic acid 4-hydroxylase




biosynthesis
(C4H) isolated from Festuca arundinacea.





The molecule has a conserved Cytochrome





P450 region in amino acids 440 to 449 that





contains a conserved Cys residue involved





in heme binding. The cytochrome P450





cysteine heme-iron ligand signature 





consensus is FG × GRRSCPG where the con-





served C is the heme iron ligand (Miles et





al., Biochim. Biophys. Acta 1543:383-407,





2000). It also contains an aldehyde de-





hydrogenases active site (Hempel et al.,





Adv. Exp. Med. Biol. 436:53–59, 1999) at





amino acid residues 428 to 435. A hy-





drophobic signal peptide region is





present in amino acid residues 1 to 24.


34 and 145
96 and 180
Lignin
Homolog of cinnamyl-alcohol dehydrogenase




biosynthesis
(CAD; EC 1.1.1.195) isolated from Lolium





perenne. These molecules contain a conserved





zinc-containing alcohol dehydrogenase





domain (Joernvall et al., Eur. J. Biochem.





167:195–201, 1987) in amino acid





residues 69 to 83, with a conserved His





residue at position 70. They also contain





a cytochrome C family heme-binding site





signature (Mathews, Prog. Biophys. Mol.





Biol. 45:1–56, 1985) in residues 45 to





50.


35
97
Lignin
Homolog of cinnamyl-alcohol dehydrogenase




biosynthesis
(CAD; EC 1.1.1.195) isolated from Festuca





arundinacea. CAD belongs to the family





of zinc-binding dehydrogenases. This





molecule contains a conserved zinc-





containing alcohol dehydrogenases domain





(Joernvall et al., Eur. J. Biochem.





167:195–201, 1987) in amino acid





residues 69 to 83, with a conserved His





residue at position 70. It also contains





a Cytochrome C family heme-binding site





signature. The cytochrome C family heme-





binding site signature is CGICHT. In the





cytochrome C protein family, the heme





group is covalently attached by thioether





bonds to two conserved cysteine residues.





The consensus sequence for this site is





Cys-X-X-Cys-His and the histidine residue





is one of the two axial ligands of the





heme iron. This arrangement is shared by





all proteins known to belong to cytochrome





C family (Mathews, Prog. Biophys. Mol.





Biol. 45:1–56, 1985).


36 and 146
98
Lignin
Homolog of caffeoyl coenzyme A O-




biosynthesis
methyltransferase (CCoAOMT) (EC 2.1.1.104)





isolated from Lolium perenne.


37
99
Lignin
Homolog of caffeoyl coenzyme A O-




biosynthesis
methyltransferase (CCoAOMT) (EC 2.1.1.104)





isolated from Festuca arundinacea.


38 and 147
100 and 181
Lignin
Homolog of cinnamoyl CoA:NADP




biosynthesis
oxidoreductase (CCR, EC 1.2.1.44) isolated





from Lolium perenne that catalyzes the





conversion of cinnamoyl CoA esters to their





corresponding cinnamaldehydes in the first





specific step in the synthesis of the





lignin monomers. A hydrophobic region





typical of a signal peptide is present in





amino acid residues 1 to 24.


39 and 148
101
Lignin
Homolog of cinnamoyl CoA:NADP oxidoreductase




biosynthesis
(CCR, EC 1.2.1.44) isolated from Festuca





arundinacea that catalyzes the





conversion of cinnamoyl CoA esters to their





corresponding cinnamaldehydes in the first





specific step in the synthesis of the





lignin monomers.


40 and 149
102 and 182
Lignin
Homolog of caffeic acid 3-O-methyltrans-




biosynthesis
ferase (COMT1) isolated from Festuca





arundinacea A conserved consensus





phosphopantetheine attachment site was





identified in amino acid residues 47 to 62.





This domain is involved in the attachment





of activated fatty acid and amino-acid





groups, with the Ser residue at position 52





crucial for the phosphopantetheine attach-





ment (Pugh and Wakil, J. Biol. Chem.





240:4727–4733, 1965).


41 and 150
103
Lignin
Homolog of caffeic acid 3-O-methyltrans-




biosynthesis
ferase (COMT1) isolated from Lolium perenne





A conserved consensus phosphopantetheine





attachment site was identified in amino





acid residues 47 to 62. This domain is





involved in the attachment of activated fatty





acid and amino-acid groups, with the Ser





residue at position 52 crucial for the phos-





phopantetheine attachment (Pugh and Wakil,





J. Biol. Chem. 240:4727–4733, 1965).


42
104
Lignin
Homolog of caffeic acid 3-O-methyltransferase




biosynthesis
(COMT1) isolated from Festuca arundinacea





A conserved consensus phosphopantetheine





attachment site was identified in amino acid





residues 47 to 62. This domain is involved





in the attachment of activated fatty acid





and amino-acid groups, with the Ser residue





at position 52 crucial for the





phosphopantetheine attachment (Pugh and





Wakil, J. Biol. Chem. 240:4727–4733, 1965).


43
105
Lignin
Homolog of caffeic acid 3-O-methyltransferase




biosynthesis
(COMT1) isolated from Lolium perenne A





conserved consensus phosphopantetheine





attachment site was identified in amino acid





residues 47 to 62. This domain is involved in





the attachment of activated fatty acid and





amino-acid groups, with the Ser residue at





position 52 crucial for the phosphopantetheine





attachment (Pugh and Wakil, J. Biol. Chem.





240:4727–4733, 1965).


44 and 151
106 and 183
Lignin
Homolog of ferulate 5-hydroxylase (F5H)




biosynthesis
isolated from Lolium perenne. The





molecules have a conserved cytochrome P450





region in amino acids 463 to 472 that contains





a conserved Cys residue involved in heme





binding (Miles et al., Biochim Biophys Acta





1543:383–407, 2000). A signal peptide is





present in amino acid residues 1 to 30.


45
107
Lignin
Homolog of ferulate 5-hydroxylase (F5H)




biosynthesis
isolated from Festuca arundinaceae. The





molecule has a conserved cytochrome P450





region in amino acids 462 to 471 that contains





a conserved Cys residue involved in heme





binding (Miles et al., Biochim Biophys Acta





1543:383–407, 2000). A signal peptide is





present in amino acid residues 1 to 30.


46 and 152
108
Lignin/Tannin
Homolog of phenylalanine ammonia-lyase (EC




biosynthesis
4.3.1.5) (PAL) isolated from Lolium





perenne. The polypeptide has a con-





served PAL-histidase region in amino acid





residues 193 to 209.


47 and 153
109 and 184
Lignin/Tannin
Homolog of phenylalanine ammonia-lyase (EC




biosynthesis
4.3.1.5) (PAL) isolated from Festuca





arundinacea. A conserved phenylalanine





and histidine ammonia-lyases active site





signature has been identified in amino acid





residues 195 to 210


48
110
Lignin
Homolog of peroxidase (PER) isolated from




biosynthesis
Festuca arundinacea. The conserved





peroxidase I region is present in amino





acid residues 188 to 199 and contains a





conserved His residue at position 196 in the





active site, and the conserved peroxidase





2 region is present in amino acid residues





60 to 71, with a conserved His residue at





position 69 that is involved in heme





binding (Kimura and Ikeda-Saito, Proteins





3:113–120, 1988). A signal peptide is





present in amino acid residues 1 to 27.


49
111
Lignin
Homolog of peroxidase (PER) isolated from




biosynthesis
Lolium perenne. The conserved peroxidase





I region is present in amino acid residues





199 to 209 and contains a conserved His





residue at position 208 in the active site.





A signal peptide is present in amino acid





residues 1 to 33.


50
112
Lignin
Homolog of peroxidase (PER) isolated from




biosynthesis
Festuca arundinacea. The conserved





peroxidase I region is present in amino acid





residues 180 to 190 and contains a





conserved His residue at position 188 in





the active site, and the conserved





peroxidase 2 region is present in amino acid





residues 55 to 66, with a conserved His





residue at position 64 that is involved in





heme binding (Kimura and Ikeda-Saito,





Proteins 3:113–120, 1988). A signal peptide





is present in amino acid residues 1 to 22.


51 and 154
113
Lignin
Homolog of peroxidase (PER) isolated from




biosynthesis
Lolium perenne. The conserved peroxidase





I region is present in amino acid residues





199 to 209 and contains a conserved His





residue at position 207 in the active site,





and the conserved peroxidase 2 region is





present in amino acid residues 70 to 80, with





a conserved His residue at position 78 that





is involved in heme binding (Kimura and





Ikeda-Saito, Proteins 3:113–120, 1988). A





signal peptide is present in amino acid





residues 1 to 20.


52 and 155
114
Lignin
Homolog of peroxidase (PER) isolated from




biosynthesis
Lolium perenne. The conserved peroxidase





I region is present in amino acid residues





198 to 208 and contains a conserved His





residue at position 206 in the active site





(Kimura and Ikeda-Saito, Proteins 3:113–120,





1988). A signal peptide is present in amino





acid residues 1 to 34.


53, 156, and
115, 185, and
Lignin
Homolog of peroxidase (PER) isolated from


162
190
biosynthesis
Lolium perenne. The conserved peroxidase I





region is present in amino acid residues





157 to 168, 188 to 199, and 190 to 201,





respectively and contain a conserved His





residue at position 165, 196 and 198,





respectively in the active site, and the





conserved peroxidase 2 region is present in





amino acid residues 29 to 41, 60 to 72 and 62





to 74, respectively, with a conserved His





residue at position 38, 69 and 71,





respectively that is involved in heme binding





(Kimura and Ikeda-Saito, Proteins 3:113–120,





1988).


54
116
Lignin
Homolog of peroxidase (PER) isolated from




biosynthesis
Festuca arundinacea. The conserved





peroxidase I region is present in amino acid





residues 176 to 186 and contains a conserved





His residue at position 184 in the active





site, and the conserved peroxidase 2 region





is present in amino acid residues 55 to 67,





with a conserved His residue at position 64





that is involved in heme binding (Kimura and





Ikeda-Saito, Proteins 3:113–120, 1988). A





signal peptide is present in amino acid





residues 1 to 22.


55
117
Tannin
Homolog of chalcone isomerase (CHI) isolated




Biosynthesis
from Lolium perenne. The molecule contains





a chalcone isomerase region at amino acid





residues 1 to 213.


56
118
Tannin
Homolog of chalcone isomerase (CHI). The




Biosynthesis
molecule contains a chalcone isomerase region





at amino acid residues 23 to 235.


57 and 157
119 and 186
Tannin
Homolog of Chalcone Synthase (CHS) isolated




Biosynthesis
from Lolium perenne and that is an





important enzyme in flavonoid synthesis. The





molecules contain a conserved chalcone syn-





thase active site (Lanz et al., J. Biol.





Chem. 266:9971–9976, 1991) at amino acid





residues 166 to 175, with the conserved Cys





residue at position 167.


58 and 158
120 and 187
Tannin
Homolog of dihydroflavonal-4-reductase




Biosynthesis
(DFR) isolated from Festuca arundinacea.


59 and 159
121 and 188
Tannin
Homolog of dihydroflavonal-4-reductase




Biosynthesis
(DFR) isolated from Lolium perenne.


60 and 160
122 and 189
Tannin
Homolog of dihydroflavonal-4-reductase




Biosynthesis
(DFR) isolated from Lolium perenne.





These molecules contain a conserved





ATP/GTP binding site at amino acid residues





84 to 91 and 86 to 93, respectively, known





as the “A” sequence (Walker et al.,





EMBO J. 1:945–951, 1982) or “P-loop”





(Saraste et al., Trends Biochem. Sd.





15:430–434, 1990).


61 and 161
123
Tannin
Homolog of flavanone 3-βhydroxylase




biosynthesis
(F3βH) isolated from Lolium perenne.


62
124
Tannin
Homolog of flavanone 3-βhydroxylase




Biosynthesis
(F3βH) isolated from Festuca arundinacea.









All the polynucleotides and polypeptides provided by the present invention are isolated and purified, as those terms are commonly used in the art. Preferably, the polypeptides and polynucleotides are at least about 80% pure, more preferably at least about 90% pure, and most preferably at least about 99% pure.
The word “polynucleotide(s),” as used herein, means a polymeric collection of nucleotides, and includes DNA and corresponding RNA molecules and both single and double stranded molecules, including RNAi, HnRNA and mRNA molecules, sense and anti-sense strands of DNA and RNA molecules, and comprehends cDNA, genomic DNA, and wholly or partially synthesized polynucleotides. A polynucleotide of the present invention may be an entire gene, or any portion thereof. As used herein, a “gene” is a DNA sequence which codes for a functional protein or RNA molecule. Operable anti-sense polynucleotides may comprise a fragment of the corresponding polynucleotide, and the definition of “polynucleotide” therefore includes all operable anti-sense fragments. Anti-sense polynucleotides and techniques involving anti-sense polynucleotides are well known in the art and are described, for example, in Robinson-Benion et al., Methods in Enzymol.254(23): 363–375, 1995 and Kawasaki et al., Artific. Organs 20(8): 836–848, 1996.
In specific embodiments, the present invention provides isolated polynucleotides comprising a sequence of SEQ ID NO: 1–62 and 125–162; polynucleotides comprising variants of SEQ ID NO: 1–62 and 125–162; polynucleotides comprising extended sequences of SEQ ID NO: 1–62 and 125–162 and their variants, oligonucleotide primers and probes corresponding to the sequences set out in SEQ ID NO: 1–62 and 125–162 and their variants, polynucleotides comprising at least a specified number of contiguous residues of any of SEQ ID NO: 1–62 and 125–162 (x-mers), and polynucleotides comprising extended sequences which include portions of the sequences set out in SEQ ID NO: 1–62 and 125–162, all of which are referred to herein, collectively, as “polynucleotides of the present invention.” Polynucleotides that comprise complements of such polynucleotide sequences, reverse complements of such polynucleotide sequences, or reverse sequences of such polynucleotide sequences, together with variants of such sequences, are also provided.
The definition of the terms “complement(s),” “reverse complement(s),” and “reverse sequence(s),” as used herein, is best illustrated by the following example. For the sequence 5′ AGGACC 3′, the complement, reverse complement, and reverse sequence are as follows:











complement
3′ TCCTGG 5′




 



reverse complement
3′ GGTCCT 5′



 



reverse sequence
5′ CCAGGA 3′.






Preferably, sequences that are complements of a specifically recited polynucleotide sequence are complementary over the entire length of the specific polynucleotide sequence.
As used herein, the term “x-mer,” with reference to a specific value of “x,” refers to a polynucleotide comprising at least a specified number (“x”) of contiguous residues of: any of the polynucleotides provided in SEQ ID NO: 1–62 and 125–162. The value of x may be from about 20 to about 600, depending upon the specific sequence.
Polynucleotides of the present invention comprehend polynucleotides comprising at least a specified number of contiguous residues (x-mers) of any of the polynucleotides identified as SEQ ID NO: 1–62 and 125–162, or their variants. Similarly, polypeptides of the present invention comprehend polypeptides comprising at least a specified number of contiguous residues (x-mers) of any of the polypeptides identified as SEQ ID NO: 63–124 and 163–190. According to preferred embodiments, the value of x is at least 20, more preferably at least 40, more preferably yet at least 60, and most preferably at least 80. Thus, polynucleotides of the present invention include polynucleotides comprising a 20-mer, a 40-mer, a 60-mer, an 80-mer, a 100-mer, a 120-mer, a 150-mer, a 180-mer, a 220-mer, a 250-mer; or a 300-mer, 400-mer, 500-mer or 600-mer of a polynucleotide provided in SEQ ID NO: 1–62 and 125–162, or a variant of one of the polynucleotides corresponding to the polynucleotides provided in SEQ ID NO: 1–62 and 125–162. Polypeptides of the present invention include polypeptides comprising a 20-mer, a 40-mer, a 60-mer, an 80-mer, a 100-mer, a 120-mer, a 150-mer, a 180-mer, a 220-mer, a 250-mer; or a 300-mer, 400-mer, 500mer or 600-mer of a polypeptide provided in SEQ ID NO: 63–124 and 163–190, or a variant thereof.
Polynucleotides of the present invention were isolated by high throughput sequencing of cDNA libraries comprising forage grass tissue collected from Lolium perenne and Festuca arundinacea. Some of the polynucleotides of the present invention may be “partial” sequences, in that they do not represent a full-length gene encoding a full-length polypeptide. Such partial sequences may be extended by analyzing and sequencing various DNA libraries using primers and/or probes and well known hybridization and/or PCR techniques. Partial sequences may be extended until an open reading frame encoding a polypeptide, a full-length polynucleotide and/or gene capable of expressing a polypeptide, or another useful portion of the genome is identified. Such extended sequences, including full-length polynucleotides and genes, are described as “corresponding to” a sequence identified as one of the sequences of SEQ ID NO: 1–62 and 125–162 or a variant thereof, or a portion of one of the sequences of SEQ ID NO: 1–62 and 125–162 or a variant thereof, when the extended polynucleotide comprises an identified sequence or its variant, or an identified contiguous portion (x-mer) of one of the sequences of SEQ ID NOS: 1–62 and 125–162 or a variant thereof. Similarly, RNA sequences, reverse sequences, complementary sequences, anti-sense sequences and the like, corresponding to the polynucleotides of the present invention, may be routinely ascertained and obtained using the cDNA sequences identified as SEQ ID NOS: 1–62 and 125–162.
The polynucleotides identified as SEQ ID NOS: 1–62 and 125–162 contain open reading frames (“ORFs”) or partial open reading frames encoding polypeptides and functional portions of polypeptides. Additionally, open reading frames encoding polypeptides may be identified in extended or full length sequences corresponding to the sequences set out as SEQ ID NOS: 1–62 and 125–162. Open reading frames may be identified using techniques that are well known in the art. These techniques include, for example, analysis for the location of known start and stop codons, most likely reading frame identification based on codon frequencies, etc. These techniques include, for example, analysis for the location of known start and stop codons, most likely reading frame identification based on codon frequencies, etc. Suitable tools and software for ORF analysis are well known in the art and include, for example, GeneWise, available from The Sanger Center, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom; Diogenes, available from Computational Biology Centers, University of Minnesota, Academic Health Center, UMHG Box 43 Minneapolis Minn. 55455; and GRAIL, available from the Informatics Group, Oak Ridge National Laboratories, Oak Ridge, Tenn. Once a partial open reading frame is identified, the polynucleotide may be extended in the area of the partial open reading frame using techniques that are well known in the art until the polynucleotide for the full open reading frame is identified.
Once open reading frames are identified in the polynucleotides of the present invention, the open reading frames may be isolated and/or synthesized. Expressible genetic constructs comprising the open reading frames and suitable promoters, initiators, terminators, etc., which are well known in the art, may then be constructed. Such genetic constructs may be introduced into a host cell to express the polypeptide encoded by the open reading frame. Suitable host cells may include various prokaryotic and eukaryotic cells, including plant cells, mammalian cells, bacterial cells, algae and the like.
The polynucleotides of the present invention may be isolated by high throughput sequencing of cDNA libraries prepared from forage grass tissue, as described below in Example 1. Alternatively, oligonucleotide probes and primers based on the sequences provided in SEQ ID NOS: 1–62 and 125–162 can be synthesized as detailed below, and used to identify positive clones in either cDNA or genomic DNA libraries from forage grass tissue cells by means of hybridization or polymerase chain reaction (PCR) techniques. Hybridization and PCR techniques suitable for use with such oligonucleotide probes are well known in the art (see, for example, Mullis et al., Cold Spring Harbor Symp. Quant. Biol., 51:263, 1987; Erlich, ed., PCR technology, Stockton Press: NY, 1989; and Sambrook et al., eds., Molecular cloning: a laboratory manual, 2nd ed., CSHL Press: Cold Spring Harbor, N.Y., 1989). In addition to DNA-DNA hybridization, DNA-RNA or RNA-RNA hybridization assays are also possible. In the first case, the mRNA from expressed genes would then be detected instead of genomic DNA or cDNA derived from mRNA of the sample. In the second case, RNA probes could be used. Artificial analogs of DNA hybridizing specifically to target sequences could also be employed. Positive clones may be analyzed by restriction enzyme digestion, DNA sequencing or the like.
The polynucleotides of the present invention may also, or alternatively, be synthesized using techniques that are well known in the art. The polynucleotides may be synthesized, for example, using automated oligonucleotide synthesizers (e.g., Beckman Oligo 1000M DNA Synthesizer; Beckman Coulter Ltd., Fullerton, Calif.) to obtain polynucleotide segments of up to 50 or more nucleic acids. A plurality of such polynucleotide segments may then be ligated using standard DNA manipulation techniques that are well known in the art of molecular biology. One conventional and exemplary polynucleotide synthesis technique involves synthesis of a single stranded polynucleotide segment having, for example, 80 nucleic acids, and hybridizing that segment to a synthesized complementary 85 nucleic acid segment to produce a 5 nucleotide overhang. The next segment may then be synthesized in a similar fashion, with a 5 nucleotide overhang on the opposite strand. The “sticky” ends ensure proper ligation when the two portions are hybridized. In this way, a complete polynucleotide of the present invention may be synthesized entirely in vitro.
Oligonucleotide probes and primers complementary to and/or corresponding to SEQ ID NOS: 1–62 and 125–162, and variants of those sequences, are also comprehended by the present invention. Such oligonucleotide probes and primers are substantially complementary to the polynucleotide of interest over a certain portion of the polynucleotide. An oligonucleotide probe or primer is described as “corresponding to” a polynucleotide of the present invention, including one of the sequences set out as SEQ ID NOS: 1–62 and 125–162 or a variant thereof, if the oligonucleotide probe or primer, or its complement, is contained within one of the sequences set out as SEQ ID NOS: 1–62 and 125–162 or a variant of one of the specified sequences.
Two single stranded sequences are said to be substantially complementary when the nucleotides of one strand, optimally aligned and compared, with the appropriate nucleotide insertions and/or deletions, pair with at least 80%, preferably at least 90% to 95%, and more preferably at least 98% to 100%, of the nucleotides of the other strand. Alternatively, substantial complementarity exists when a first DNA strand will selectively hybridize to a second DNA strand under stringent hybridization conditions.
In specific embodiments, the oligonucleotide probes and/or primers comprise at least about 6 contiguous residues, more preferably at least about 10 contiguous residues, and most preferably at least about 20 contiguous residues complementary to a polynucleotide sequence of the present invention. Probes and primers of the present invention may be from about 8 to 100 base pairs in length, preferably from about 10 to 50 base pairs in length, and more preferably from about 15 to 40 base pairs in length. The probes can be easily selected using procedures well known in the art, taking into account DNA-DNA hybridization stringencies, annealing and melting temperatures, potential for formation of loops, and other factors which are well known in the art. Preferred techniques for designing PCR primers are disclosed in Dieffenbach and Dyksler, PCR Primer: a laboratory manual, CSHL Press: Cold Spring Harbor, N.Y., 1995. A software program suitable for designing probes, and especially for designing PCR primers, is available from Premier Biosoft International, 3786 Corina Way, Palo Alto, Calif. 94303–4504.
The isolated polynucleotides of the present invention also have utility in genome mapping, in physical mapping, and in positional cloning of genes.
The polynucleotides identified as SEQ ID NOS: 1–62 and 125–162 were isolated from cDNA clones and represent sequences that are expressed in the tissue from which the cDNA was prepared. RNA sequences, reverse sequences, complementary sequences, anti-sense sequences, and the like, corresponding to the polynucleotides of the present invention, may be routinely ascertained and obtained using the cDNA sequences identified as SEQ ID NOS: 1–62 and 125–162.
Identification of genomic DNA and heterologous species DNA can be accomplished by standard DNA/DNA hybridization techniques, under appropriately stringent conditions, using all or part of a polynucleotide sequence as a probe to screen an appropriate library. Alternatively, PCR techniques using oligonucleotide primers that are designed based on known genomic DNA, cDNA and protein sequences can be used to amplify and identify genomic and cDNA sequences.
In another aspect, the present invention provides isolated polypeptides encoded by the above polynucleotides. As used herein, the term “polypeptide” encompasses amino acid chains of any length, including full-length proteins, wherein the amino acid residues are linked by covalent peptide bonds. The term “polypeptide encoded by a polynucleotide” as used herein, includes polypeptides encoded by a polynucleotide that comprises a partial isolated polynucleotide sequence provided herein. In specific embodiments, the inventive polypeptides comprise an amino acid sequence selected from the group consisting of SEQ ID NO: 63–124 and 163–190, as well as variants of such sequences.
As noted above, polypeptides of the present invention may be produced recombinantly by inserting a polynucleotide sequence of the present invention encoding the polypeptide into an expression vector and expressing the polypeptide in an appropriate host. Any of a variety of expression vectors known to those of ordinary skill in the art may be employed. Expression may be achieved in any appropriate host cell that has been transformed or transfected with an expression vector containing a polynucleotide molecule that encodes a recombinant polypeptide. Suitable host cells include prokaryotes, yeast, and higher eukaryotic cells. Preferably, the host cells employed are plant, E. coli, insect, yeast, or a mammalian cell line such as COS or 293T. The polynucleotide sequences expressed in this manner may encode naturally occurring polypeptides, portions of naturally occurring polypeptides, or other variants thereof. The expressed polypeptides may be used in various assays known in the art to determine their biological activity. Such polypeptides may also be used to raise antibodies, to isolate corresponding interacting proteins or other compounds, and to quantitatively determine levels of interacting proteins or other compounds.
In a related aspect, polypeptides are provided that comprise at least a functional portion of a polypeptide having an amino acid sequence selected from the group consisting of sequences provided in SEQ ID NO: 63–124 and 163–190, and variants thereof. As used herein, the “functional portion” of a polypeptide is that portion which contains an active site essential for affecting the function of the polypeptide, for example, a portion of the molecule that is capable of binding one or more reactants. The active site may be made up of separate portions present on one or more polypeptide chains and will generally exhibit high binding affinity. Functional portions of a polypeptide may be identified by first preparing fragments of the polypeptide by either chemical or enzymatic digestion of the polypeptide, or by mutation analysis of the polynucleotide that encodes the polypeptide and subsequent expression of the resulting mutant polypeptides. The polypeptide fragments or mutant polypeptides are then tested to determine which portions retain biological activity, using methods well known to those of skill in the art, including the representative assays described below.
Portions and other variants of the inventive polypeptides may be generated by synthetic or recombinant means. Synthetic polypeptides having fewer than about 100 amino acids, and generally fewer than about 50 amino acids, may be generated using techniques well known to those of ordinary skill in the art. For example, such polypeptides may be synthesized using any of the commercially available solid-phase techniques, such as the Merrifield solid-phase synthesis method, where amino acids are sequentially added to a growing amino acid chain. See Merrifield, J. Am. Chem. Soc. 85:2149–2146, 1963. Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Perkin Elmer/Applied Biosystems, Inc. (Foster City, Calif.), and may be operated according to the manufacturer's instructions. Variants of a native polypeptide may be prepared using standard mutagenesis techniques, such as oligonucleotide-directed site-specific mutagenesis (Kunkel, Proc. Natl. Acad. Sci. USA 82:488–492, 1985). Sections of DNA sequences may also be removed using standard techniques to permit preparation of truncated polypeptides.
As used herein, the term “variant” comprehends nucleotide or amino acid sequences different from the specifically identified sequences, wherein one or more nucleotides or amino acid residues is deleted, substituted, or added. Variants may be naturally occurring allelic variants, or non-naturally occurring variants. Variant sequences (polynucleotide or polypeptide) preferably exhibit at least 75%, more preferably at least 80%, more preferably at least 90%, more preferably yet at least 95% and most preferably, at least 98% identity to a sequence of the present invention. The percentage identity is determined by aligning the two sequences to be compared as described below, determining the number of identical residues in the aligned portion, dividing that number by the total number of residues in the inventive (queried) sequence, and multiplying the result by 100.
Polynucleotides and polypeptides having a specified percentage identity to a polynucleotide or polypeptide identified in one of SEQ ID NO: 1–190 thus share a high degree of similarity in their primary structure. In addition to a specified percentage identity to a polynucleotide or polypeptide of the present invention, variant polynucleotides and polypeptides preferably have additional structural and/or functional features in common with a polynucleotide of the present invention. Polynucleotides having a specified degree of identity to, or capable of hybridizing to, a polynucleotide of the present invention preferably additionally have at least one of the following features: (1) they contain an open reading frame, or partial open reading frame, encoding a polypeptide, or a functional portion of a polypeptide, having substantially the same functional properties as the polypeptide, or functional portion thereof, encoded by a polynucleotide in the recited SEQ ID NO:; or (2) they contain identifiable domains in common. Similarly, polypeptides having a specified degree of identity to a polypeptide of the present invention preferably additionally have at least one of the following features: (1) they have substantially the same functional properties as the polypeptide in the recited SEQ ID NO:; or (2) they contain identifiable domains in common.
Polynucleotide or polypeptide sequences may be aligned, and percentages of identical nucleotides or amino acids in a specified region may be determined against another polynucleotide or polypeptide, using computer algorithms that are publicly available. The BLASTN and FASTA algorithms, set to the default parameters described in the documentation and distributed with the algorithm, may be used for aligning and identifying the similarity of polynucleotide sequences. The alignment and similarity of polypeptide sequences may be examined using the BLASTP algorithm. BLASTX and FASTX algorithms compare nucleotide query sequences translated in all reading frames against polypeptide sequences. The FASTA and FASTX algorithms are described in Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85:2444–2448, 1988; and in Pearson, Methods in Enzymol. 183:63–98, 1990. The FASTA software package is available from the University of Virginia by contacting the Assistant Provost for Research, University of Virginia, PO Box 9025, Charlottesville, Va. 22906-9025. The BLASTN software is available from the National Center for Biotechnology Information (NCBI), National Library of Medicine, Building 38A, Room 8N805, Bethesda, Md. 20894. The BLASTN algorithm Version 2.0.11 [Jan. 20, 2000] and Version 2.2.1 [Apr. 13, 2001] set to the default parameters described in the documentation and distributed with the algorithm, are preferred for use in the determination of polynucleotide variants according to the present invention. The use of the BLAST family of algorithms, including BLASTN, BLASTP and BLASTX, is described in the publication of Altschul et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Res. 25:3389–3402, 1997.
The following running parameters are preferred for determination of alignments and similarities using BLASTN that contribute to the E values and percentage identity for polynucleotides: Unix running command with the following default parameters: blastall -p blastn -d embldb -e 10 -G 0 -E 0 -r 1 -v 30 -b 30 -i queryseq -o results; and parameters are: -p Program Name [String]; -d Database [String]; -e Expectation value (E) [Real]; -G Cost to open a gap (zero invokes default behavior) [Integer]; -E Cost to extend a gap (zero invokes default behavior) [Integer]; -r Reward for a nucleotide match (BLASTN only) [Integer]; -v Number of one-line descriptions (V) [Integer]; -b Number of alignments to show (B) [Integer]; -i Query File [File In]; -o BLAST report Output File [File Out] Optional.
The following running parameters are preferred for determination of alignments and similarities using BLASTP that contribute to the E values and percentage identity of polypeptide sequences: blastall -p blastp -d swissprotdb -e 10 -G 0 -E 0 -v 30 -b 30 -i queryseq -o results; the parameters are: -p Program Name [String]; -d Database [String]; -e Expectation value (E) [Real]; -G Cost to open a gap (zero invokes default behavior) [Integer]; -E Cost to extend a gap (zero invokes default behavior) [Integer]; -v Number of one-line descriptions (v) [Integer]; -b Number of alignments to show (b) [Integer]; -I Query File [File In]; -o BLAST report Output File [File Out] Optional.
The “hits” to one or more database sequences by a queried sequence produced by BLASTN, BLASTP, FASTA, or a similar algorithm, align and identify similar portions of sequences. The hits are arranged in order of the degree of similarity and the length of sequence overlap. Hits to a database sequence generally represent an overlap over only a fraction of the sequence length of the queried sequence.
As noted above, the percentage identity of a polynucleotide or polypeptide sequence is determined by aligning polynucleotide and polypeptide sequences using appropriate algorithms, such as BLASTN or BLASTP, respectively, set to default parameters; identifying the number of identical nucleic or amino acids over the aligned portions; dividing the number of identical nucleic or amino acids by the total number of nucleic or amino acids of the polynucleotide or polypeptide of the present invention; and then multiplying by 100 to determine the percentage identity. By way of example, a queried polynucleotide having 220 nucleic acids has a hit to a polynucleotide sequence in the EMBL database having 520 nucleic acids over a stretch of 23 nucleotides in the alignment produced by the BLASTN algorithm using the default parameters. The 23-nucleotide hit includes 21 identical nucleotides, one gap and one different nucleotide. The percentage identity of the queried polynucleotide to the hit in the EMBL database is thus 21/220 times 100, or 9.5%. The percentage identity of polypeptide sequences may be determined in a similar fashion.
The BLASTN and BLASTX algorithms also produce “Expect” values for polynucleotide and polypeptide alignments. The Expect value (E) indicates the number of hits one can “expect” to see over a certain number of contiguous sequences by chance when searching a database of a certain size. The Expect value is used as a significance threshold for determining whether the hit to a database indicates true similarity. For example, an E value of 0.1 assigned to a polynucleotide hit is interpreted as meaning that in a database of the size of the EMBL database, one might expect to see 0.1 matches over the aligned portion of the sequence with a similar score simply by chance. By this criterion, the aligned and matched portions of the sequences then have a probability of 90% of being related. For sequences having an E value of 0.01 or less over aligned and matched portions, the probability of finding a match by chance in the EMBL database is 1% or less using the BLASTN algorithm. E values for polypeptide sequences may be determined in a similar fashion using various polypeptide databases, such as the SwissProt database.
According to one embodiment, “variant” polynucleotides and polypeptides, with reference to each of the polynucleotides and polypeptides of the present invention, preferably comprise sequences having the same number or fewer nucleotides or amino acids than each of the polynucleotides or polypeptides of the present invention and producing an E value of 0.01 or less when compared to the polynucleotide or polypeptide of the present invention. That is, a variant polynucleotide or polypeptide is any sequence that has at least a 99% probability of being related to the polynucleotide or polypeptide of the present invention, measured as having an E value of 0.01 or less using the BLASTN or BLASTX algorithms set at the default parameters. According to a preferred embodiment, a variant polynucleotide is a sequence having the same number or fewer nucleic acids than a polynucleotide of the present invention that has at least a 99% probability of being related to the polynucleotide of the present invention, measured as having an E value of 0.01 or less using the BLASTN algorithm set at the default parameters. Similarly, according to a preferred embodiment, a variant polypeptide is a sequence having the same number or fewer amino acids than a polypeptide of the present invention that has at least a 99% probability of being related as the polypeptide of the present invention, measured as having an E value of 0.01 or less using the BLASTP algorithm set at the default parameters.
In an alternative embodiment, variant polynucleotides are sequences that hybridize to a polynucleotide of the present invention under stringent conditions. Stringent hybridization conditions for determining complementarity include salt conditions of less than about 1 M, more usually less than about 500 mM, and preferably less than about 200 mM. Hybridization temperatures can be as low as 5° C., but are generally greater than about 22° C., more preferably greater than about 30° C., and most preferably greater than about 37° C. Longer DNA fragments may require higher hybridization temperatures for specific hybridization. Since the stringency of hybridization may be affected by other factors such as probe composition, presence of organic solvents, and extent of base mismatching, the combination of parameters is more important than the absolute measure of any one alone. An example of “stringent conditions” is prewashing in a solution of 6×SSC, 0.2% SDS; hybridizing at 65° C., 6×SSC, 0.2% SDS overnight; followed by two washes of 30 minutes each in 1×SSC, 0.1% SDS at 65° C. and two washes of 30 minutes each in 0.2×SSC, 0.1% SDS at 65° C.
The present invention also encompasses polynucleotides that differ from the disclosed sequences but that, as a consequence of the discrepancy of the genetic code, encode a polypeptide having similar enzymatic activity to a polypeptide encoded by a polynucleotide of the present invention. Thus, polynucleotides comprising sequences that differ from the polynucleotide sequences recited in SEQ ID NO: 1–62 and 125–162, or complements, reverse sequences, or reverse complements of those sequences, as a result of conservative substitutions are contemplated by and encompassed within the present invention. Additionally, polynucleotides comprising sequences that differ from the polynucleotide sequences recited in SEQ ID NO: 1–62 and 125–162, or complements, reverse complements or reverse sequences thereof, as a result of deletions and/or insertions totaling less than 10% of the total sequence length are also contemplated by and encompassed within the present invention. Similarly, polypeptides comprising sequences that differ from the polypeptide sequences recited in SEQ ID NO: 63–124 and 163–190 as a result of amino acid substitutions, insertions, and/or deletions totaling less than 10% of the total sequence length are contemplated by and encompassed within the present invention, provided the variant polypeptide has activity in a lignin, fructan or tannin biosynthetic pathway.
In another aspect, the present invention provides genetic constructs comprising, in the 5′–3′ direction, a gene promoter sequence; an open reading frame coding for at least a functional portion of a polypeptide of the present invention; and a gene termination sequence. The open reading frame may be orientated in either a sense or anti-sense direction. For applications where amplification of lignin, fructan or tannin synthesis is desired, the open reading frame may be inserted in the construct in a sense orientation, such that transformation of a target organism with the construct will lead to an increase in the number of copies of the gene and therefore an increase in the amount of enzyme. When down-regulation of lignin, fructan or tannin synthesis is desired, the open reading frame may be inserted in the construct in an anti-sense orientation, such that the RNA produced by transcription of the polynucleotide is complementary to the endogenous mRNA sequence. This, in turn, will result in a decrease in the number of copies of the gene and therefore a decrease in the amount of enzyme. Alternatively, regulation may be achieved by inserting appropriate sequences or subsequences (e.g., DNA or RNA) in ribozyme constructs.
Genetic constructs comprising a non-coding region of a gene coding for a polypeptide of the present invention, or a nucleotide sequence complementary to a non-coding region, together with a gene promoter sequence and a gene termination sequence, are also provided. As used herein the term “non-coding region” includes both transcribed sequences which are not translated, and non-transcribed sequences within about 2000 base pairs 5′ or 3′ of the translated sequences or open reading frames. Examples of non-coding regions which may be usefully employed in the inventive constructs include introns and 5′-non-coding leader sequences. Transformation of a target plant with such a genetic construct may lead to a reduction in the amount of lignin, fructan or tannin synthesized by the plant by the process of cosuppression, in a manner similar to that discussed, for example, by Napoli et al., Plant Cell 2:279–290, 1990; and de Carvalho Niebel et al., Plant Cell 7:347–358, 1995.
The genetic constructs of the present invention further comprise a gene promoter sequence and a gene termination sequence, operably linked to the polynucleotide to be transcribed, which control expression of the gene. The gene promoter sequence is generally positioned at the 5′ end of the polynucleotide to be transcribed, and is employed to initiate transcription of the polynucleotide. Gene promoter sequences are generally found in the 5′ non-coding region of a gene but they may exist in introns (Luehrsen, Mol. Gen. Genet. 225:81–93, 1991). When the construct includes an open reading frame in a sense orientation, the gene promoter sequence also initiates translation of the open reading frame. For genetic constructs comprising either an open reading frame in an anti-sense orientation or a non-coding region, the gene promoter sequence consists only of a transcription initiation site having a RNA polymerase binding site.
A variety of gene promoter sequences which may be usefully employed in the genetic constructs of the present invention are well known in the art. The promoter gene sequence, and also the gene termination sequence, may be endogenous to the target plant host or may be exogenous, provided the promoter is functional in the target host. For example, the promoter and termination sequences may be from other plant species, plant viruses, bacterial plasmids and the like. Preferably, gene promoter and termination sequences are from the inventive sequences themselves.
Factors influencing the choice of promoter include the desired tissue specificity of the construct, and the timing of transcription and translation. For example, constitutive promoters, such as the 35S Cauliflower Mosaic Virus (CaMV 35S) promoter, will affect the activity of the enzyme in all parts of the plant. Use of a tissue specific promoter will result in production of the desired sense or anti-sense RNA only in the tissue of interest. With DNA constructs employing inducible gene promoter sequences, the rate of RNA polymerase binding and initiation can be modulated by external stimuli, such as light, heat, anaerobic stress, alteration in nutrient conditions and the like. Temporally regulated promoters can be employed to effect modulation of the rate of RNA polymerase binding and initiation a t a specific time during development of a transformed cell. Preferably, the original promoters from the enzyme gene in question, or promoters from a specific tissue-targeted gene in the organism to be transformed, such as Lolium or Festuca, are used. Grass promoters different from the original gene may also be usefully employed in the inventive genetic constructs in order to prevent feedback inhibition. For example, the fructosyltransferase gene will be regulated by sucrose sensing systems; therefore removing the gene from under control of its normal promoter allows the gene to be active all the time. Other examples of gene promoters which may be usefully employed in the present invention include, mannopine synthase (mas), octopine synthase (ocs) and those reviewed by Chua et al., Science 244:174–181, 1989.
The gene termination sequence, which is located 3′ to the polynucleotide to be transcribed, may come from the same gene as the gene promoter sequence or may be from a different gene. Many gene termination sequences known in the art may be usefully employed in the present invention, such as the 3′ end of the Agrobacterium tumefaciens nopaline synthase gene. However, preferred gene terminator sequences are those from the original enzyme gene or from the target species to be transformed.
The genetic constructs of the present invention may also contain a selection marker that is effective in plant cells, to allow for the detection of transformed cells containing the inventive construct. Such markers, which are well known in the art, typically confer resistance to one or more toxins. One example of such a marker is the NPTII gene whose expression results in resistance to kanamycin or hygromycin, antibiotics which are usually toxic to plant cells at a moderate concentration (Rogers et al., in Weissbach A and H, eds., Methods for Plant Molecular Biology, Academic Press Inc.: San Diego, Calif., 1988). Alternatively, the presence of the desired construct in transformed cells can be determined by means of other techniques well known in the art, such as Southern and Western blots.
Techniques for operatively linking the components of the inventive genetic constructs are well known in the art and include the use of synthetic linkers containing one or more restriction endonuclease sites as described, for example, by Sambrook et al., (Molecular cloning: a laboratory manual, CSHL Press: Cold Spring Harbor, N.Y., 1989). The genetic construct of the present invention may be linked to a vector having at least one replication system, for example, E. coli, whereby after each manipulation, the resulting construct can be cloned and sequenced and the correctness of the manipulation determined.
The genetic constructs of the present invention may be used to transform a variety of plants, both monocotyledonous (e.g., grasses, maize/corn, grains, oats, rice, sorghum, millet, rye, sugar cane, wheat and barley), dicotyledonous (e.g., Arabidopsis, tobacco, legumes, alfalfa, oaks, eucalyptus, maple), and gymnosperms. In a preferred embodiment, the inventive genetic constructs are employed to transform grasses. Preferably the target plant is selected from the group consisting of Lolium and Festuca species, most preferably from the group consisting of Lolium perenne and Festuca arundinacea. Other plants that may be usefully transformed with the inventive genetic constructs include other species of ryegrass and fescue, including, but not limited to Lolium multiflorum (Italian ryegrass), Lolium hybridum (hybrid ryegrass), Lolium rigidum (Wimerra grass), Lolium temulentum (darnel), Festuca rubra (red fescue) and Festuca pratensis (meadow fescue). As discussed above, transformation of a plant with a genetic construct of the present invention will produce a modified lignin, fructan or tannin content in the plant.
The production of RNA in target cells may be controlled by choice of the promoter sequence, or by selecting the number of functional copies or the site of integration of the polynucleotides incorporated into the genome of the target organism. A target plant may be transformed with more than one construct of the present invention, thereby modulating the lignin, fructan and/or tannin biosynthetic pathways by affecting the activity of more than one enzyme, affecting enzyme activity in more than one tissue or affecting enzyme activity at more than one expression time. Similarly, a construct may be assembled containing more than one open reading frame coding for an enzyme encoded by a polynucleotide of the present invention or more than one non-coding region of a gene coding for such an enzyme. The polynucleotides of the present invention may also be employed in combination with other known sequences encoding enzymes involved in the lignin, fructan and/or tannin biosynthetic pathways. In this manner, more than one biosynthetic pathway may be modulated, or a lignin, fructan or tannin biosynthetic pathway may be added to a plant to produce a plant having an altered phenotype.
Techniques for stably incorporating genetic constructs into the genome of target plants are well known in the art and include Agrobacterium tumefaciens mediated introduction, electroporation, protoplast fusion, injection into reproductive organs, injection into immature embryos, high velocity projectile introduction and the like. The choice of technique will depend upon the target plant to be transformed. For example, dicotyledonous plants and certain monocots and gymnosperms may be transformed by Agrobacterium Ti plasmid technology, as described, for example by Bevan, Nucleic Acid Res. 12:8711–8721, 1984. Targets for the introduction of the genetic constructs of the present invention include tissues, such as leaf tissue, disseminated cells, protoplasts, seeds, embryos, meristematic regions; cotyledons, hypocotyls, and the like. Transformation techniques which may be usefully employed in the inventive methods include those taught by Ellis et al., Plant Cell Reports, 8:16–20, 1989; Wilson et al., Plant Cell Reports 7:704–707, 1989; Tautorus et al., Theor. Appl. Genet. 78:531–536, 198; Hiei et al., Plant J. 6:271–282, 1994; and Ishida et al., Nature Biotechnol. 14:745–750, 1996; U.S. Pat. No. 5,591,616; and European Patent Publication EP 672 752 A1. Once the cells are transformed, cells having the inventive DNA construct incorporated in their genome may be selected by means of a marker, such as the kanamycin resistance marker discussed above. Transgenic cells may then be cultured in an appropriate medium to regenerate whole plants, using techniques well known in the art. In the case of protoplasts, the cell wall is allowed to reform under appropriate osmotic conditions. In the case of seeds or embryos, an appropriate germination or callus initiation medium is employed. For explants, an appropriate regeneration medium is used. Regeneration of plants is well established for many species. The resulting transformed plants may be reproduced sexually or asexually, using methods well known in the art, to give successive generations of transgenic plants.
Polynucleotides of the present invention may also be used to specifically suppress gene expression by methods that operate post-transcriptionally to block the synthesis of products of targeted genes, such as RNA interference (RNAi), and quelling. For a review of techniques of gene suppression see Science, 288:1370–1372, 2000. Exemplary gene silencing methods are also provided in WO 99/49029 and WO 99/53050. Posttranscriptional gene silencing is brought about by a sequence-specific RNA degradation process which results in the rapid degradation of transcripts of sequence-related genes. Studies have provided evidence that double-stranded RNA may act as a mediator of sequence-specific gene silencing (see, e.g., review by Montgomery and Fire, Trends in Genetics, 14: 255–258, 1998). Gene constructs that produce transcripts with self-complementary regions are particularly efficient at gene silencing. A unique feature of this posttranscriptional gene silencing pathway is that silencing is not limited to the cells where it is initiated. The gene-silencing effects may be disseminated to other parts of an organism and even transmitted through the germ line to several generations.
The polynucleotides of the present invention may be employed to generate gene silencing constructs and or gene-specific self-complementary RNA sequences that can be delivered by conventional art-known methods to plant tissues, such as forage grass tissues. Within genetic constructs, sense and antisense sequences can be placed in regions flanking an intron sequence in proper splicing orientation with donor and acceptor splicing sites, such that intron sequences are removed during processing of the transcript and sense and antisense sequences, as well as splice junction sequences, bind together to form double-stranded RNA. Alternatively, spacer sequences of various lengths may be employed to separate self-complementary regions of sequence in the construct. During processing of the gene construct transcript, intron sequences are spliced-out, allowing sense and anti-sense sequences, as well as splice junction sequences, to bind forming double-stranded RNA. Select ribonucleases bind to and cleave the double-stranded RNA, thereby initiating the cascade of events leading to degradation of specific mRNA gene sequences, and silencing specific genes. Alternatively, rather than using a gene construct to express the self-complementary RNA sequences, the gene-specific double-stranded RNA segments are delivered to one or more targeted areas to be internalized into the cell cytoplasm to exert a gene silencing effect. Gene silencing RNA sequences comprising the polynucleotides of the present invention are useful for creating genetically modified plants with desired phenotypes as well as for characterizing genes (e.g., in high-throughput screening of sequences), and studying their functions in intact organisms.
EXAMPLE 1
Isolation of cDNA Sequences from L. Perenne and F. Arundinacea cDNA Libraries
L. perenne and F. arundinacea cDNA expression libraries were constructed and screened as follows. Tissue was collected from L. perenne and F. arundinacea during winter and spring, and snap-frozen in liquid nitrogen. The tissues collected include those obtained from leaf blades, leaf base, pseudostem, floral stems, inflorescences, roots and stem. Total RNA was isolated from each tissue type using TRIzol Reagent (BRL Life Technologies, Gaithersburg, Md.). mRNA from each tissue type was obtained using a Poly(A) Quik mRNA isolation kit (Stratagene, La Jolla, Calif.), according to the manufacturer's specifications. cDNA expression libraries were constructed from the purified mRNA by reverse transcriptase synthesis followed by insertion of the resulting cDNA in Lambda ZAP using a ZAP Express cDNA Synthesis Kit (Stratagene, La Jolla, Calif.), according to the manufacturer's protocol. T he resulting cDNA clones were packaged using a Gigapack II Packaging Extract (Stratagene, La Jolla, Calif.) employing 1 μl of sample DNA from the 5 μl ligation mix. Mass excision of the libraries was done using XL1-Blue MRF′ cells and XLOLR cells (Stratagene, La Jolla, Calif.) with ExAssist helper phage (Stratagene, La Jolla, Calif.). The excized phagemids were diluted with NZY broth (Gibco BRL, Gaithersburg, Md.) and plated out onto LB-kanamycin agar plates containing 5-bromo-4-chloro-3-indolyl-beta-D-galactosidase (X-gal) and isopropylthio-beta-galactoside (IPTG). Of the colonies plated and picked for DNA preparations, the large majority contained an insert suitable for sequencing. Positive colonies were cultured in NZY broth with kanamycin and DNA was purified following standard protocols. Agarose gel at 1% was used to screen sequencing templates for chromosomal contamination. Dye terminator sequences were prepared using a Biomek 2000 robot (Beckman Coulter Inc., Fullerton, Calif.) for liquid handling and DNA amplification using a 9700 PCR machine (Perkin Elmer/Applied Biosystems, Foster City, Calif.) according to the manufacturer's protocol.
The DNA sequences for positive clones were obtained using a Perkin Elmer/Applied Biosystems Division Prism 377 sequencer. cDNA clones were sequenced from the 5′ end. The polynucleotide sequences identified as SEQ ID NO: 4, 6, 11, 127, 128 and 132 were identified from L. perenne leaf cDNA expression libraries; the polynucleotide sequences identified as SEQ ID NO: 1, 14, 15, 26, 32, 36, 38, 41, 49, 125, 134, 141, 144, 147, and 150 were identified from L. perenne vegetative stem cDNA expression libraries; the polynucleotide sequences identified as SEQ ID NO: 17, 22, 25, 138, and 140 were identified from L. perenne leaf and pseudostem cDNA expression libraries; the polynucleotide sequences identified as SEQ ID NO: 43, 57, 61, 157, and 161 were identified from L. perenne pseudostem cDNA expression libraries; the polynucleotide sequences identified as SEQ ID NO: 10, 12, 28, 30, 34, 44, 60, 131, 133, 142, 143, 145, 151, and 160 were identified from L. perenne floral stem cDNA expression libraries; the polynucleotide sequences identified as SEQ ID NO: 8, 18, 46, 52, 53, 55, 59, 136, 152, 155, 156, 159, and 162 were identified from L. perenne stem cDNA expression libraries; the polynucleotide sequences identified as SEQ ID NO: 51 and 154 were identified from a L. perenne root cDNA expression library; the polynucleotide sequences identified as SEQ ID NO: 24, 27 and 139 were identified from L. perenne leaf blade cDNA expression libraries; the polynucleotide sequences identified as SEQ ID NO: 9, 37, 39, 40, 45, 130, 148, and 149 were identified from F. arundinacea basal leaf cDNA expression libraries; the polynucleotide sequences identified as SEQ ID NO: 19, 21, 29, 33, 35, 47, 48, and 153 were identified from F. arundinacea combined day 3 and day 6 basal leaves cDNA expression libraries; the polynucleotide sequence identified as SEQ ID NO: 54 was identified from a F. arundinacea combined day 3 and day 6 leaves cDNA expression library; the polynucleotide sequence identified as SEQ ID NO: 56 was identified from a F. arundinacea inflorescence cDNA expression library; the polynucleotide sequences identified as SEQ ID NO: 20 and 137 were identified from a subtracted F. arundinacea leaf blade cDNA expression library; the polynucleotide sequences identified as SEQ ID NO: 7, 23, 42, 50, 62, and 129 were identified from F. arundinacea pseudostem cDNA expression libraries; the polynucleotide sequences identified as SEQ ID NO: 2, 13, 16 and 135 were identified from F. arundinacea leaf cDNA expression libraries; and the polynucleotide sequences identified as SEQ ID NO: 3, 5, 31, and 126 were identified from a F. arundinacea inflorescence day 0 cDNA expression library.
BLASTN Polynucleotide Analysis
The isolated cDNA sequences were compared to sequences in the EMBL DNA database using the computer algorithm BLASTN. Comparisons of DNA sequences provided in SEQ ID NOS: 1–62 to sequences in the EMBL DNA database were made as of Oct. 19, 2001 using BLASTN algorithm Version 2.0.11 [Jan. 20, 2000], and the following Unix running command: blastall -p blastn d embldb -e 10-G0 -E0 -r 1 -v 30 b 30 -i queryseq -o. Comparisons of DNA sequences provided in SEQ ID NOS: 125–162 to sequences in the EMBL DNA database were made using BLASTN algorithm Version 2.2.1 [Apr. 13, 2001], and the following Unix running command: blastall -p blastn -d embldb -F F -e 10 -G0 -E0 -r 1 -v 2-b 2 -i queryseq -o.
The sequences of SEQ ID NO: 4–6, 9–11, 17–19, 21–26, 33, 44, 45, 48, 49, 51–55, 59, 60, 130–132, 136, 139, 146, 151, 154–156, 159, and 162 were determined to have less than 50% identity to sequences in the EMBL database using the computer algorithm BLASTN, as described above. The sequences of SEQ ID NO: 2, 3, 7, 8, 14, 16, 36–38, 46, 47, 50, 56–58, 61, 129, 135, 137, 138, 152, 153, 157, 158, 160 and 161 were determined to have less than 75% identity to sequences in the EMBL database using the computer algorithm BLASTN, as described above. The sequences of SEQ ID NOS: 1, 12, 13, 15, 20, 28, 31, 32, 35, 40, 62, 125–128, 133, 134, 142, 144 and 147 were determined to have less than 90% identity to sequences in the EMBL database using the computer algorithm BLASTN, as described above. Finally, the sequences of SEQ ID NOS: 29, 30, 39, 41–43, 141, 143, 148, and 149 were determined to have less than 98% identity to sequences in the EMBL database using the computer algorithm BLASTN, as described above.
BLASTP Polypeptide Analysis
The protein sequences corresponding to the isolated cDNA sequences were compared to sequences in the SwissProt/Trembl protein database using the computer algorithm BLASTP. Comparisons of protein sequences provided in SEQ ID NOS: 63–124 to sequences in the SwissProt/Trembl protein database were made as of Oct. 19, 2001 using BLASTP algorithm Version 2.0.11 [Jan. 20, 2000], and the following Unix running command: blastall -p blastp -dstdb-e 10 -G0 -E0 -v 30 -b 30 -i queryseq -o. Comparisons of protein sequences provided in SEQ ID NOS: 163–190 to sequences in the SwissProt/Trembl protein database were made using BLASTP algorithm Version 2.2.1 [Apr. 13, 2001], and the following Unix running command: blastall -p blastp dstdb -F F -e 10 -G0 -E0 v 2 -b 2 -i queryseq -o.
The sequences of SEQ ID NOS: 65–68, 72, 73, 78, 80, 81, 84, 85, 87, 88, 106, 107, 110, 111, 113–115, 117, 118 and 121 were determined to have less than 50% identity to sequences in the SwissProt/Trembl database using the computer algorithm BLASTP, as described above. The sequences of SEQ ID NOS: 71, 79, 82, 83, 86, 95, 98–100, 112, 116, 120, 122–124, 167, 168, 171–174, 185, 188, and 190 were determined to have less than 75% identity to sequences in the SwissProt/Trembl database using the computer algorithm BLASTP, as described above. The sequences of SEQ ID NOS: 63, 64, 69, 70, 74–77, 90, 91, 93, 94, 97, 101, 102, 104, 108, 109, 119, 175, 183, 187, and 189 were determined to have less than 90% identity to sequences in the SwissProt/Trembl database using the computer algorithm BLASTP, as described above. Finally, the sequences of SEQ ID NOS: 89, 92, 96, 103, 105, 163–165, 169, 170, 177, 179, 181, 184, and 186 were determined to have less than 98% identity to sequences in the SwissProt/Trembl database using the computer algorithm BLASTP, as described above.
BLASTX Polynucleotide Analysis
The isolated cDNA sequences were compared to sequences in the SwissProt/Trembl protein database using the computer algorithm BLASTX. Comparisons of DNA sequences provided in SEQ ID NOS: 1–62 to sequences in the SwissProt/Trembl protein database were made as of Oct. 19, 2001 using BLASTX algorithm Version 2.0.11 [Jan. 20, 2000], and the following Unix running command: blastall -p blastx -dstdb -e 10 -G0 -E0 -v 30 -b 30 -i queryseq -o. Comparisons of DNA sequences provided in SEQ ID NOS: 1–62 to sequences in the SwissProt/Trembl protein database were made using BLASTX algorithm Version 2.2.1 [Apr. 13, 2001], and the following Unix running command: blastall -p blastx -d stdb -F F -e 10 -G0 -E0 -v2 -b 2 -i queryseq -o.
The sequences of SEQ ID NOS: 11, 44, 45, 48, 49, 51, 52, 55, 130, 132, 155, 156, and 162 were determined to have less than 50% identity to sequences in the abase using the computer algorithm BLASTX, as described above. The NOS: 3–10, 16–26, 33, 36–38, 40–43, 50, 53, 54, 56, 58–62, 129, 131, 135–139, 146, 150, 151, 154, and 158–161 were determined to have less than 75% identity to sequences in the SwissProt/Trembl database using the computer algorithm BLASTX, as described above. The sequences of SEQ ID NOS: 1, 2, 12–15, 27, 28–32, 34, 35, 39, 46, 47, 57, 125–128, 133, 134, 141–145, 147–149, 152, 153, and 157 were determined to have less than 90% identity to sequences in the SwissProt/Trembl database using the computer algorithm BLASTX, as described above. Finally, the sequence of SEQ ID NO: 140 was determined to have less than 98% identity to sequences in the SwissProt/Trembl database using the computer algorithm BLASTX, as described above.
The location of open reading frames (ORFs), by nucleotide position, contained within the sequences of SEQ ID NO: 1–62 and 125–162, and the corresponding amino acid sequences are provided in Table 2 below. SEQ ID NO: 1–8, 10–15, 17, 19, 21, 23–25, 28–52, 54–59, 61–62 and 125–162 are believed to contain full-length ORFs.









TABLE 2





POLYNUCLEOTIDE

POLYPEPTIDE


SEQ ID NO:
ORF
SEQ ID NO:

















1
 56–2,020
63


2
 64–2,010
64


3
 64–1,926
65


4
 74–1,945
66


5
 40–1,911
67


6
 79–1,938
68


7
246–1,514
69


8
264–1,532
70


9
 84–3,272
71


10
 73–3,297
72


11
129–2,942
73


12
 46–2,472
74


13
113–2,539
75


14
 61–2,505
76


15
103–2,253
77


16
 3–1,439
78


17
 26–1,777
79


18
 2–1,174
80


19
 59-1,852
81


20
 2–1,201
82


21
 1–1,779
83


22
198–1,097
84


23
 27–1,772
85


24
 36–1,802
86


25
 78–2,084
87


26
 2–1,423
88


27
 3–1,622
89


28
 85–1,764
90


29
 72–1,751
91


30
127–1,800
92


31
137–1,810
93


32
 62–1,567
94


33
 80–1,597
95


34
 32–1,117
96


35
 86–1,171
97


36
 55–852
98


37
 75–872
99


38
149–1,240
100


39
 90–1,118
101


40
 28–1,110
102


41
 66–1,148
103


42
 64–1,146
104


43
 85–1,170
105


44
 88–1,683
106


45
 93–1,721
107


46
111–2,246
108


47
144–2,285
109


48
 22–993
110


49
 4–1,038
111


50
 87–1,067
112


51
 59–1,135
113


52
 18–1,052
114


53
 1–882
115


54
 80–1,015
116


55
322–1,014
117


56
172–762
118


57
118–1,299
119


58
 5–595
120


59
 14–1,003
121


60
 1–987
122


61
 65–1,174
123


62
103–1,245
124


125
 55–2,019
163


126
 63–1,925
164


127
 73–1,944
165


128
 71–1,930
166


131
 72–3,299
167


132
134–2,950
168


133
 45–2,471
169


134
 65–2,512
170


135
 74–1,819
171


136
170–1,855
172


137
 28–1,770
173


138
 26–1,733
174


139
 35–1,801
175


140
 71–2,083
176


141
 63–1,607
177


143
126–1,799
178


144
 61–1,566
179


145
 67–1,152
180


147
148–1,239
181


149
 27–1,109
182


151
 87–1,718
183


153
143–2,284
184


156
 46–1,017
185


157
117–1,313
186


158
 81–1,193
187


159
 12–1,001
188


160
 26–1,018
189


162
 50–1,027
190









SEQ ID NO: 125 and 163 are related to SEQ ID NO: 1 and 63, respectively; SEQ ID NO: 126 and 164 are related to SEQ ID NO: 3 and 65, respectively; SEQ ID NO: 127 and 165 are related to SEQ ID NO: 4 and 66, respectively; SEQ ID NO: 128 and 166 are related to SEQ ID NO: 6 and 68, respectively; SEQ ID NO: 129 is an extended sequence of SEQ ID NO: 7; SEQ ID NO: 130 is an extended sequence of SEQ ID NO: 9; SEQ ID NO: 131 and 167 are related to SEQ ID NO: 10 and 72, respectively; SEQ ID NO: 132 and 168 are related to SEQ ID NO: 11 and 73, respectively; SEQ ID NO: 133 and 169 are related to SEQ ID NO: 12 and 74, respectively; SEQ ID NO: 134 and 170 are related to SEQ ID NO: 14 and 76, respectively; SEQ ID NO: 135 and 171 are full-length sequences of SEQ ID NO: 16 and 78, respectively; SEQ ID NO: 136 and 172 are full-length sequences of SEQ ID NO: 18 and 80, respectively; SEQ ID NO: 137 and 173 are related to SEQ ID NO: 20 and 82, respectively; SEQ ID NO: 138 and 174 are full-length sequences of SEQ ID NO: 22 and 84, respectively; SEQ ID NO: 139 and 175 are related to SEQ ID NO: 24 and 86, respectively; SEQ ID NO: 140 and 176 are related to SEQ ID NO: 25 and 87, respectively; SEQ ID NO: 141 and 177 are full-length sequences of SEQ ID NO: 26 and 88, respectively; SEQ ID NO: 142 is related to SEQ ID NO: 28 and encodes the same amino acid sequence; SEQ ID NO: 143 and 178 are related to SEQ ID NO: 30 and 92, respectively; SEQ ID NO: 144 and 179 are related to SEQ ID NO: 32 and 94, respectively; SEQ ID NO: 145 and 180 are full-length sequences of SEQ ID NO: 34 and 96, respectively; SEQ ID NO: 146 is related to SEQ ID NO: 36 and encodes the same amino acid sequence; SEQ ID NO: 147 and 181 are related to SEQ ID NO: 38 and 100, respectively; SEQ ID NO: 148is related t o SEQ ID NO: 39, and encodes the same amino acid sequence; SEQ ID NO: 149 and 182 are related to SEQ ID NO: 40 and 102, respectively; SEQ ID NO: 150 is related to SEQ ID NO: 41 and encodes the same amino acid sequence; SEQ ID NO: 151 and 183 is related to SEQ ID NO: 44 and 106, respectively; SEQ ID NO: 152 is related to SEQ ID NO: 46, and encodes the same amino acid sequence; SEQ ID NO: 153 and 184 are related to SEQ ID NO: 47 and 109, respectively; SEQ ID NO: 154 is related to SEQ ID NO: 51, and encodes the same amino acid sequence; SEQ ID NO: 155 is related to SEQ ID NO: 52, and encodes the same amino acid sequence; SEQ ID NO: 156 and 185 are full-length sequences of SEQ ID NO: 53 and 115, respectively; SEQ ID NO: 162 and 190 are variants of SEQ ID NO: 156 and 185, respectively, with a difference in the 5′ region of SEQ ID NO: 156 and 162; SEQ NO: 157 and 186 are related to SEQ ID NO: 57 and 119, respectively; SEQ ID NO: 158 and 187 are related to SEQ ID NO: 58 and 120, respectively; SEQ ID NO: 159 and 188 are full-length sequences of SEQ ID NO: 59 and 121, respectively; SEQ ID NO: 160 and 189 are full-length sequences of SEQ ID NO: 60 and 122, respectively; and SEQ ID NO: 161 is related to SEQ ID NO: 61 and encodes the same amino acid sequence.
EXAMPLE 2 
Use of Sucrose Phosphate Phosphatase to Dephosphorylate Sucrose-6-Phosphate
The F. arundinacea and L. perenne FaSPP and LpSPP genes (SEQ ID NO: 7 and 8, respectively) share amino acid sequence identity with sucrose-6-phosphate phosphatase genes from other plant species (Lunn et al., Proc. Natl. Acad. Sci. USA 97:12914–12919, 2000). These genes were amplified by PCR using the primers given in SEQ ID NO: 191 and 192 to add an initiating methionine, and then cloned into the pET41a expression plasmid (Novagen, Madison, Wis.). These primers amplified nucleotides 263–1531 and 280–1548 for FaSPP and LpSPP, respectively. The resulting plasmids were transformed into E. coli BL21 cells using standard protocols, and protein expression was induced using IPTG.
The soluble recombinant protein was assayed for its ability to specifically dephosphorylate sucrose-6-phosphate (Suc-6-P) but not fructose-6-phosphate (Fru-6-P) using the procedure described by Lunn et al. (ibid.). The release of phosphate from Suc-6P and Fru-6-P was measured using the Fiske-Subbarow method of determining inorganic phosphate (SIGMA assay kit; Sigma, St Louis, Mich.), with the change in absorbance at 660 nm being proportional to the amount of phosphate released per unit time. As shown in FIG. 1, both the Festuca and Lolium SPP enzymes dephosphorylated Suc-6-P but not Fru-6-P, whereas control pET41 extract had no activity on either substrate.
EXAMPLE 3 
Peroxidase Activity of Grass Enzymes Demonstrated by Their Ability to Oxidize 2,2′Azino-Bis.3-Ethylbenzylthiazoline-6-Sulfonic Acid (Abts)
A number of L. perenne or F. arundinacea genes (SEQ ID NO: 48–54) share amino acid identity with peroxidase genes from other plant species (Hiraga et al., Plant Cell Physiol. 42:462–468, 2001). The putative amino acid secretion signal sequence was identified by signalP analysis of the Lolium and Festuca sequences and homology to known peroxidase proteins. Primers were designed to amplify DNA representing the mature protein (minus signal sequence; Table 3.). These genes were amplified by PCR to add an initiating methionine and then cloned into the pET25b expression plasmid (Novagen, Madison, Wis.). The resulting plasmid was transformed into E. coli AD494 (DE3) pLysS cells using standard protocols, and protein expression was induced using IPTG.












TABLE 3








Primers




SEQ ID NO
SEQ ID NO

SEQ
DNA bp
Protein


DNA
PROT
Gene
ID NO:
amplified
codons







50
112
FaPER3
193
156–1077
24–326





194


52
114
LpPER5
195
120–1052
35–344





196









The insoluble recombinant protein was solubilized and re-folded following protocols described for several recombinant Arabidopsis peroxidases (Teilum et al., Protein Exp. and Purif. 15:77–82, 1999). The insoluble inclusion bodies within E. coli were isolated from lysed cells by standard protocols and the recombinant protein solubilized in 8M urea. The solubilized peroxidase protein was refolded to gain active enzyme by diluting urea to 2M with 5 μM Heme, 0.25mM Glutathione reduced, and 0.45mM Glutathione oxidized, pH 8 (20 mM Tris-HCl). The refolded protein was used directly to assay peroxidase activity.
Peroxidase activity was measured by incubating recombinant peroxidase with pre-mixed ABTS/H2O2 liquid substrate (Sigma, St Louis, Mich.) and measuring ABTS oxidation by the increase in absorbance at 405 nm. Horseradish peroxidase of known activity (Sigma, St Louis, Mich.) was used as a positive control and boiled samples as a negative control. The results provided in FIG. 2 show that FaPER3 and LpPER5 (SEQ ID NO: 50 and 52, respectively) had similar activity to that of horseradish peroxidase in these assays.
EXAMPLE 4
Use of Grass Fructosyltransferase Genes to Synthesize Fructans
Transformation of N. benthamiana Plants with Fructosyltransferase Genes
Sense constructs containing a polynucleotide including the coding region of fructosyltransferase genes isolated from L. perenne Lp1-SST and Lp6SFT1 (SEQ ID NO: 125 and 126, respectively) were inserted into a pART27 derived binary vector and used to transform A. tumefaciens LBA4404 using published methods (see, An et al., “Binary Vectors,” in Gelvin and Schilperoort, eds., Plant Molecular Biology Manual, Kluwer Academic Publishers: Dordrecht, 1988). The presence and integrity of the binary vector in A. tumefaciens was verified by polymerase chain reaction (PCR). The primers px17 (SEQ ID NO: 207) and px18 (SEQ ID NO: 208) were used to confirm the presence of the Lp1-SST construct, whereas the primers px19 (SEQ ID NO: 209) and px 20 (SEQ ID NO: 210) were used to confirm the presence of the Lp6-SFT-1 construct.
The A. tumefaciens containing the sense gene constructs were used to transform N. benthamiana leaf discs (Burow et al., Plant Mol. Biol. Report 8:124–139, 1990). Several independent transformed plant lines were established for the sense construct for each fructosyltransferase gene. DNA was isolated from transformed plants containing the appropriate fructosyltransferase gene construct using the QIAGEN DNAeasy Plant Mini Kit (Qiagen, Valencia, Calif.). Presence of the fructosyltransferase gene was verified using PCR experiments as shown in FIGS. 3 and 4. For the Lp6-SFT1 gene, the forward and reverse primers given in SEQ ID NO: 197 and 198 were used, respectively. These primers amplify nucleotides 1572–1980 of the Lp6-SFT1 gene which corresponds to a 406 base pair fragment. For Lp1-SST, the forward and reverse primers given in SEQ ID NO: 199 and 200 were used, respectively. These primers amplify nucleotides 1332–1740 of Lp1-SST, corresponding to a 414 base pair fragment.
Effects of Fructosyltransferase Genes on Fructosyltransferase Concentration in Transformed Plants
Fructans are not normally found in N. benthamiana plants; hence, if introduction of the sense fructosyltransferase constructs was successful, it should be possible to extract fructans from the transformed plants. The concentration of fructosyltransferase in the transformed plants was determined using the Fructan Assay Kit (Megazyme International Ireland Ltd, Wicklow, Ireland). Briefly, 300 mg of leaf material from the independent transformed plant lines containing the fructosyltransferase sense constructs were extracted individually at 80° C. with 1 ml 80% ethanol, followed by two 1 ml extractions with water. The ethanol and water extracts were combined and frozen overnight at −20° C. Extracts were centrifuged at 20,000 g to pellet chlorophyll. Clarified extracts were treated with 1% PVP-40 to precipitate phenolic compounds. These extracts were then reduced in volume by rotary evaporation.
Fructan levels were determined in these extracts using the Megazyme Fructan Assay kit. Briefly, sucrose, starch and reducing sugars are removed from the plant carbohydrate extracts by using sucrase, β-amylase, pullulanase and maltase, and then converting the resulting reducing sugars to sugar alcohols. The remaining fructans are hydrolyzed with fructanase and the reducing sugars produced (glucose and fructose) are measured by the 4-hydroxybenzoic acid hydrazide (PAHBAH) reducing sugar method. The final extracts are assayed for absorbance at 410 nm. As shown in FIG. 5, fructans could be detected in both the Lp1-SST and Lp6-SFT-1 transgenic lines. Fructan levels were highest in lines 07, 09 and 12 for Lp1-SST, and lines 05 and 12 for Lp6SFT-1.
EXAMPLE 5 
Use of Sucrose Phosphate Synthase Enzymes to Synthesize Sucrose
A F. arundinacea gene (FaSPS-N; SEQ ID NO: 9) has been identified that shares amino acid sequence identity with sucrose phosphate synthase (SPS) from other plant species. SEQ ID NO: 7 and 8 are also SPS sequences, with SEQ ID NO: 7 being a Lolium perenne homologue of SEQ ID NO: 9. The FaSPS-N was cloned into the pcDNA3 mammalian expression plasmid and the resulting plasmid transfected into 293T mammalian cells (human embryonic kidney derived cells) using Lipofectamine 2000 reagent (Invitrogen, Carlsbad, Calif.).
Cell lysates from transfected cells were deionized on G25 spin columns and used in a sucrose synthesis assay. In this assay, mammalian cell extracts were tested for their ability to synthesize sucrose from fructose-6-phosphate and uridine 5′-diphosphoglucose. Following the synthesis reaction, hexoses were converted to sugar alcohols by boiling in the presence of 30% KOH. The sucrose synthesized was detected by the addition of 1.4% anthrone reagent in H2SO4 and incubating at 40° C. for 20 min. The change in absorbance at 620 nm is relative to sucrose in the reaction (Botha and Black, Aust. J. Plant Physiol. 27:81–85, 2000). In these experiments, introducing FaSPS-N alone into mammalian cells produced a sucrose synthesis activity that was not detected in non-transfected cells (FIG. 6).
A known cofactor for SPS is SPP. To test whether SPP is required for SPS activity, the L. perenne LpSPP gene (SEQ ID NO: 8) was cloned into the pcDNA3 mammalian expression plasmid. Both the FaSPS-N and LpSPP plasmids were co-transfected into 293T mammalian cells using Lipofectamine 2000 reagent (Invitrogen, Carlsbad, Calif.). Cell lysates from transfected cells were deionized on G25 spin columns and used in a sucrose synthesis assay as described above. As shown in FIG. 6, adding SPP did not significantly enhance or alter the sucrose synthesis activity of the cell extracts.
EXAMPLE 6
Use of Soluble Sucrose Synthase Enzymes to Cleave Sucrose
A F. arundinacea gene (FaSUS-1; SEQ ID NO: 13) was identified that shared amino acid sequence identity with soluble sucrose synthase enzymes (SUS) from other plant species. Three other soluble sucrose synthases were also identified (SEQ ID NO: 12, 14 and 15) with SEQ ID NO. 12 being a direct homologue from L. perenne. The FaSUS-1 gene was cloned into the pcDNA3 mammalian expression plasmid, which was transiently transfected into 293T mammalian cells (human embryonic kidney derived cells) using Lipofectamine 2000 reagent (Invitrogen Carlsbad, Calif.). Transfected cells were grown for several days before harvesting (by scraping cells in a sucrose synthase buffer). Harvested cells were frozen on dry ice and freeze-thawed twice before pelleting cell debris by centrifugation. The resulting supernatant (cell lysate) was deionized on G25 spin columns and then used in a sucrose cleavage assay as described by Sebkova et al. (Plant Physiol. 108:75–83, 1995). In these assays, the cell lysates were tested for their ability to cleave sucrose in the presence of UDP to produce fructose and uridine 5′-diphosphoglucose. Following a 30 min incubation at 30° C., the enzyme activity was stopped by boiling the tubes for 1 min. Both NAD and UDP-glucose dehydrogenase were added and the change in OD at 340 nM (production of NADPH) was measured. As shown in FIG. 7, significantly higher levels of sucrose cleavage were observed in cells transfected with FaSUS1 construct than in non-transfected control cells.
EXAMPLE 7
Use of Acid Invertases to Cleave Sucrose
A number of acid (vacuolar and cell wall) invertase genes from L. perenne and F. arundinacea (SEQ ID NOS: 17, 19, 21, 23 and 135–141) were identified that share amino acid sequence identity with acid invertases from other plant species (Unger et al., Plant Physiol. 104:1351–1357, 1994; Goetz and Roitsch, J. Plant Physiol. 157:581–585, 2000). These sequences were analysed by SignalP and homology to identify signal regions and propeptide sequences, and primers were designed to amplify the DNA sequence encoding the mature protein (Table 4).












TABLE 4





SEQ
SEQ






ID NO
ID NO

Primers SEQ
DNA bp
Protein


DNA
PROT
Gene
ID NO
amplified
codons







17
79
LpCWINV1
201
137–1803
38–583





202


19
81
FaCWINV4
203
134–1912
26–597





204


25
87
LpSINV1
205
387–2124
104–668 





206









The PCR fragments were cloned into pPICZαA vectors for expression in methylotrophic yeast Pichia pastoris (EasySelect TM Pichia Expression Kit, Invitrogen, Carlsbad, Calif.). The sequences were cloned in frame with the α-mating factor for secretion of the recombinant invertase protein into liquid media, following similar methods described for the expression of barley 6-SFT and fescue 1-SST in P. pastoris (Hochstrasser et al., FEBS Letters 440:356–360, 1998; Lüscher et al., Plant Physiol., 124:1217–1227, 2000). The media was concentrated 10 fold by Vivaspin 30 kDa spin column (VivaScience, Hannover, Germany) to concentrate recombinant protein and used directly to assay invertase activity. Recombinant protein was assayed with 100 mM sucrose in 500μl phosphate buffer pH 5.0, at 30° C. for 1 hour. Release of glucose by invertase activity was measured using a glucose HK assay kit (Sigma, St Louis, Mich.). FIG. 8 shows the glucose released by invertase activity in terms of glucose concentration in the assay mix. As shown in FIG. 8, invertase activity was observed for the vacuolar invertase (LpSINV1; SEQ NO: 25) and the two cell wall invertases (LpCWINV1 and FaCWINV4; SEQ NO: 17 and 19, respectively) but not for an empty vector (pPICZalphaA) control.
EXAMPLE 8 
Use of Tannin Genes to Modify Tannin Biosynthesis
Certain Arabidopsis mutants of the transparent testa (tt) phenotype do not make the anthocyanin pigment cyanidin and therefore have no seed coat color. The genes responsible for many of these mutants have now been identified as shown in Table 5.










TABLE 5





Enzyme
Abbreviation
Locus
Chromosome







Dihydroflavanol-4-reductase
DFR
tt3
5


Chalcone synthase
CHS
tt4
5


Chalcone isomerase
CHI
tt5
3


Flavanone 3-β-hydroxylase
F3βH
tt6
3









Over-expression of the maize genes for CHS, CHI and DFR has been shown to complement the Arabidopsis tt4, tt5 and tt3 mutants, respectively, thereby restoring cyanidin synthesis and seed coat color (Dong et al., Plant Physiol. 127:46–57, 2001). Complementation of these Arabidopsis mutants may therefore be employed to demonstrate the function of the inventive polynucleotides encoding enzymes involved in the tannin biosynthetic pathway.
Sense constructs containing a polynucleotide including the coding region of tannin genes isolated from L. perenne or F. arundinacea LpCHS, LpCHI, LpFβH, LpDFR1, FaCHI and FaF3βH (SEQ ID NO: 157, 55, 161, 159, 56 and 62, respectively) under the control of the CaMV 35S promoter were inserted into a binary vector and used to transform Agrobacterium tumefaciens LBA4404 using published methods (see, An G, Ebert P R, Mitra A, Ha SB, “Binary Vectors,” in Gelvin S B, Schilperoort R A, eds., Plant Molecular Biology Manual, Kluwer Academic Publishers: Dordrecht, 1988). The presence and integrity of the binary vector in A. tumefaciens was verified by polymerase chain reaction (PCR) using the primer pairs described in Table 6.











TABLE 6






SEQ ID
Transparent
Forward Primer
Reverse Primer


Gene
NO:
testa line
SEQ ID NO:
SEQ ID NO:



















LpCHS
157
tt4
211
212


LpCHI
55
tt5
213
214


LpF3βH
161
tt6
217
218


LpDFR1
159
tt3
215
216


FaCHI
56
tt5
213
214


FaF3βH
62
tt6
217
218









The A. tumefaciens containing the sense gene constructs are used to transform Arabidopsis by floral dipping (Clough and Bent, Plant J. 16:735–743, 1998). Several independent transformed plant lines were established for the sense construct for each of the tannin genes. Specifically, LpDFR1 constructs were transformed into Arabidopsis tt3 mutants, LpCHS constructs were transformed into Arabidopsis tt4 mutants, LpCHI and FaCHI constructs were transformed into Arabidopsis tt5 mutants, and LpF3βH and FaF3βH constructs were transformed into Arabidopsis tt6 mutants. Several independent transformed plant lines were established for the construct for each of the tannin genes. Transformed plants containing the appropriate tannin gene construct were verified using PCR.
The presence of cyanidin in the FaCHI transformed plants is demonstrated by a phenotypic change in plant seedling color and by analyzing cyanidin extracts made from transgenic plants grown under stressed conditions (Dong et al., Plant Physiol. 127:46–57, 2001). Briefly, cyanidins are extracted from plant tissue with an acid/alcohol solution (HCl/methanol) and water. Chlorophyll is removed by freezing the extracts followed by centrifugation at 4° C. at 20,000 g for 20 min. Any remaining chlorophyll is removed through a chloroform extraction. The absorbance at 530 nm is measured for each of the cyanidin extracts. Non-transgenic wild type and control Arabidopsis plants are used as controls.
SEQ ID NOS: 1–218 are set out in the attached Sequence Listing. The codes for nucleotide sequences used in the attached Sequence Listing, including the symbol “n,” conform to WIPO Standard ST.25 (1998), Appendix 2, Table 1.
All references cited herein, including patent references and non-patent publications, are hereby incorporated by reference in their entireties.
While in the foregoing specification this invention has been described in relation to certain preferred embodiments, and many details have been set forth for purposes of illustration, it will be apparent to those skilled in the art that the invention is susceptible to additional embodiments and that certain of the details described herein may be varied considerably without departing from the basic principles of the invention.

## Claims

1. An isolated polynucleotide comprising SEQ ID NO: 151.

2. A genetic construct comprising the isolated polynucleotide of claim 1.

3. An isolated transgenic cell comprising the construct according to claim 2.

4. A recombinant construct comprising, in the 5′–3′ direction:
(a) a gene promoter sequence;
(b) a polynucleotide sequence comprising nucleotides 87–1,718 of SEQ ID NO: 151; and
(c) a gene termination sequence.

5. The construct of claim 4, wherein the polynucleotide is in the sense orientation.

6. A transgenic plant cell comprising the construct of claim 4.

7. A transgenic plant comprising the transgenic plant cell according to claim 6, or fruit or seeds or progeny thereof, wherein the fruit, seeds or progeny thereof comprise a recombinant construct comprising, in the 5′–3′ direction:
(a) a gene promoter sequence;
(b) a polynucleotide sequence comprising nucleotides 87–1,718 of SEQ ID NO: 151; and
(c) a gene termination sequence.

8. A method for modulating the lignin composition of a plant, comprising stably incorporating into the genome of the plant the polynucleotide of claim 1, expressing said polynucleotide, thereby modulating the lignin composition of the plant.

9. The method of claim 8, wherein the plant is a grass.

10. The method of claim 9, wherein the plant is selected from the group consisting of Lolium perenne and Festuea arundinacea.

11. The method of claim 8 comprising stably incorporating into the genome of the plant a recombinant construct comprising, in the 5′–3′ direction:
(a) a gene promoter sequence;
(b) a polynucleotide sequence comprising nucleotides 87–1,718 of SEQ ID NO:151; and
(c) a gene termination sequence.

12. A method for producing a plant having altered lignin composition, comprising:
(a) transforming a plant cell with the construct of any one of claims 2 and 4 to provide a transgenic cell;
(b) expressing said polynucleotide, thereby altering the lignin composition; and
(c) cultivating the transgenic cell under conditions conducive to regeneration and mature plant growth.

13. A method for increasing the amount of an enzyme involved in a lignin biosynthetic pathway in a plant comprising stably incorporating into the genome of the plant the construct of any one of claims 2 and 4, expressing said polynucleotide, thereby increasing the amount of the encoded enzyme which is involved in a lignin biosynthetic pathway.

14. An isolated polynucleotide that encodes SEQ ID NO:183.

15. An isolated polynucleotide comprising a sequence selected from the group consisting of:
(a) full-length complement of SEQ ID NO: 151;
(b) frill-length reverse complement of SEQ ID NO: 151; and
(c) frill-length reverse sequence of SEQ ID NO: 151.

16. A recombinant genetic construct comprising the polynucleotide of claim 15.

17. A transgenic cell comprising the recombinant genetic construct of claim 16.

18. A transgenic plant comprising a transgenic plant cell according to claim 3, or fruit or seeds or progeny thereof, wherein the fruit, seeds or progeny thereof comprise a recombinant construct comprising SEQ ID NO: 151.