Modulation of Expression of Acyltransferases to Modify Hydroxycinnamic

Acid Content

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims benefit of priority of U.S. proivisonal application no.

61/745,247, filed December 21 , 2012, which application is herein incorporated by reference for all purposes.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

[0002] This invention was made with government support under Contract No. DE-AC02- 05CH11231 awarded by the U.S. Department of Energy. The government has certain rights in this invention.

BACKGROUND OF THE INVENTION

[0003] Grasses constitute about 20% of natural land cover (Kellogg, 2001 ) and the majority of cultivated biomass (57%) that can be sustainably produced in the U.S. (US-DOE, 2011). Rice straw, for example, represents approximately 23% of all agricultural waste, globally (Lai, 2005). The inefficiency of deconstructing cell walls into their component sugars represents a key limitation for production of biofuels from biomass via biological conversion (Lynd et al, 2008). On the other hand, root and leaf litter composition significantly affects soil carbon storage (Zhou et al., 2012). The cell wall components of whole grains also have beneficial effects in human health and various impacts on food processing (Fincher, 2009). For these reasons, grass cell wall properties critically impact unmanaged and managed ecosystems and economic uses.

[0004] In contrast to the cell walls of dicotyledenous plants (type I), cell walls of grasses and other Commelinoid monocots (type II) consist of up to 40% dry weight of the polysaccharide xylan, even in primary wails (reviewed in: (Carpiia, 1996; Vogei, 2008; Scheller and Ufvskov, 2010)). Grass xylan is substituted with arabinofuranose side chains and infrequently with glucuronic acid (Obel et al, 2006). Of apparent significance to the structure of grass cell walls, ferulic acid (FA, Figure 1 A) esterifies to a fraction of the arabinose sidechains of xylan (re viewed in (Buanafina, 2009)). Dehydrodirners of ferulate (diferulates) form through oxidative coupling likely mediated by peroxidases (Takahama and Oniki, 1994; Bunzel et al., 2008) and cross- link adjacent xylan strands to one another (Ishii, 1991 ; Allerdings et al., 2005). Furthermore, the observation of ether linkages between ferulate and monolignols suggests that ferulie acid on arabinoxylan may nucleate lignin polymerization (Bunzef et al., 2004), Another hydroxycinnamate, para-coumaric acid (p-CA, Figure 1 A), is also ester-linked to grass cell walls. p-Coumaryl esters are more abundant on lignin, but have also been found to be esterified to grass arabinoxylan (Mueller-Harvey et al, 1986; Ishii et al, 1990; Faulds et al, 2004; Ralph, 2010). Though p-CA is readily oxidized to its radical, p-CA dimers have not been observed (Ralph et al., 1994). Rather p-coumaryl substiruents may act as "radical catalysts" rapidly passing the radical to synapyl alcohols and facilitating lignin polymerization (Takaha ia and Oniki, 1994; Ralph, 2010). [0005] FA on arabinoxylan, and especially diferulates, are thought to act to strengthen primary and secondary cell walls. For example, diferuiate accumulation anticorrelates with fescue leaf elongation (MacAdam and Grabber, 2002). Similarly, hydroxycinnamate amounts anticorrelate with rice interaode expansion (Sasayama et al., 201 1). Cell wall FA content inversely correlates with enzymatic sugar release parameters in vitro (Grabber et al., 1998; Grabber et al., 1998; Lam et al., 2003; Casler and Jung, 2006). in addition, both cell wall-associated diferulates and free and ceil wall-associated FA and p-CA deter fungal pathogens and insect pests of grasses (Santiago et al, 2007; Santiago et al., 2008; Lanoue et al, 2009).

[0006] Despite their importance, the proteins that incorporate hydroxycinnamates into grass ceil walls are not well- characterized. Recently, Mitchell et al. (2007) proposed that a subclade of proteins with the Pfam domain, PF02458, for which transcripts are more abundant in grasses relative to dicots, might incorporate FA into grass walls. PF02458 domain-containing proteins are acyl CoA-dependent acyltransferases present in plants, fungi, and a few bacteria, in plants, these enzymes have been named BAHD acyliransferase, based on the first biochemically characterized family members. They catalyze the addition of an acyl group from the thioester of coenzyme A primarily to oxygen nucleophiles of diverse acceptor molecules in plant secondary metabolism (reviewed in: (D'Auria, 2006)).

[0007] There are over 50 BAHD members in most sequenced vascular plants (Table I). The BAHD enzymes group robustly into five clades (D'Auria, 2006), though more recently subclades have been proposed (Tuominen et al., 201 1). Several characterized members use hydroxycinnamoyl-CoAs as substrates, including the hydroxycinnamoyl- CoA:shikimate/quinate hydroxycinnamoyltransferase (HCT) involved in synthesis of lignin precursors (Hoffmann et al., 2003). Other recent reports have described suberin and cutin feralovl transferases from Arabidopsis thaliana that act to transfer hydroxyciiinamoyi-CoA o)- hydroxy fatty acids acyf acceptors (Molina et al., 2009; Rautengarten et al., 2012). Of importance for the possibility that the BAHD acvltransferase subclade identified by Mitchell, hereafter (he "Mitchell clade", might be involved in arabinoxylan modification, other BAHD enzymes catalyze the addition of esters to sugar acceptors, such as in anthocyanin biosynthesis (IJnno et al., 2007). indeed, Piston et al. found that rice plants simultaneously engineered with reduced expression of four genes from this clade show a -20% reduction in FA in young leaves (Piston et al., 2010), Furthermore, Withers et al. have recently described the biochemical characterization of one of the members of the "Mitchell clade", PMT or here called OsAT4, which possesses p-coumaryl-CoA:monolignol aclytransferase activity (Withers et al, 2012).

[0008] There is a need to increase the digestibility of grass plants. This invention addresses that need. BRIEF SUMMARY OF THE INVENTION

1000.9] The invention is based, in part, on the discovery that the "Mitchell clade" of BAHD acyltrasferases is expanded and diverged in grasses relative to dicots and more primitive plants. The invention is further based, in part, on the discovery that mutants in four of these genes have altered cell wail hydroxycinnamate content. Further, manipulating expression of these genes, e.g., overexpressioxi AT10, AT 15, AT7, and/or ATS; or decreasing expression of AT 5, increases arabinoxyian-associated ester-linked p-CA while simultaneously decreasing arabinoxylan-associated FA. Thus, in some aspects, the invention provides methods for engineering grass plants to reduce FA. content and increase saceharification, recombinant pl nts produced by such engineering and methods of using the plants for improved biofuel and feed prodcution.

[0010] In one aspect, the invention provides a method of engineering a plant to decrease the ferulic acid content in a plant, the method comprising: introducing an expression cassette into the plant, wherein the expression cassette comprises a polynucleotide encoding an ATIO, AT7, ATI 5, or ATS acyltransferase wherein the acyltranferase has at least 70% identity to a sequence selected from SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, or SEQ ID NO:8, and culturing the plant under conditions in which the acyltransferase is expressed. In some embodiments, the polynucleotide is operably linked to a promoter endogenous to the plant. In some embodiments, the expression cassette comprises a promoter to which the polynucleotide is operably linked. In some embodiments, the promoter is a tissue-specific promoter, e.g., a promoter that drives expression in cell wall. In some embodiments, the polynucleotide has at least 70% identity to SEQ ID NO: l, SEQ ID NO:3, SEQ ID NO:5, or SEQ ID NO:7,

[0011] In a further aspect, the invention provides a method of engineering a plant to decrease the ferulic acid content in a plant, (he method comprising: modifying the plant to decrease expression of an ATS polypeptide having at least 70% identity to SEQ ID O:8.

[0012] In an additional aspect, the invention provides a grass plant, e.g., rice, corn, switchgrass, sorghum, millet, miscanthus, sugarcane, alfalfa, wheat, soy, rye, barley, turfgrass, hemp, bamboo, rape, sunflower, or brachypodium, genetically modified to over express AT10 ATI 5, AT7, and/or ATS. In some embodiments, a plant engineered in accordance with the invention, or progeny of said plant, comprises a polynucleotide encoding an ATI O, ATI 5, AT7, or ATS operably linked to a heterologous promoter. In some embodiments, the plant comprises a heterologous polynucleotide encoding an ATIO, AT15, AT7, or ATS protein.

[0013] In another aspect, the invention provides a plant, e.g., a grass plant, comprising a polynucleotide ATS inhibitor that inhibits expression of a gene encoding ATS.

[0014] In a further aspect, the invention provides biomass comprising a plant or a part of a plant genetically modified as described herein to overexpress ATIO, AT15, AT7, or ATS; or to disrupt ATS expression. The invention additionally pro vides a method of obtaining an increased amount of soluble sugars from a plant in a saccliarification reaction, the method comprising subjecting the plant biomass a saccharification reaction, thereby increasing the amount of soluble sugars that can be obtained from the plant as compared to a wild-type plant BRIEF DESCRIPTION OF THE DRAWINGS

[0015] Figure 1. (A) Structures of relevant hydroxycinnamic acids. (B) Inferred Bayesian phylogeny of the rice "Mitchell Clade" BAHD acyl CoA-utilizing enzymes that includes the following: the rice acyltransferases (QsAT); the Arabidopsis gene, AT3G62160, that allowed this clade to be identified by Mitchell (2007); biochemically characterized BAHD-IV and BAHD-III proteins as an outgroup (ACT and VAAT, refs); Arabidopsis proteins that use hydroxycinnamoyl-CoA adducts (HCT and SFT) as substrates; and the rice genes that cluster with the Arabidopsis HCT (HCT-like). Proteins are identified by the locus ID that encodes them or their Genbank ID, followed by their designated abbreviations. Clade credibility values are 100 unless shown. The two major acyitransferase groups are designated clade i and ii. Color intensity of the circles indicates the level of RNA expression in terms of counts of Sanger ESTs and representation in massively parallel signature sequences (MPSS) data.

[0016] Figure 2. Screening results of the cell wall soluble hydroxycinnamate composition of selected T-DNA mutant rice lines. (A) Average ferulic acid content from an alcohol insoluble residue (AIR) preparation. (13) para-Coumaric acid content from AIR. (C) The ratio of ferulic acid (FA) to p-coumaric acid (p-CA), which is not subject to weighing errors. Error bars indicate standard deviations, 2 to 3 plants for each genotype were measured

independently. Data are for homozygous negative segregant plants (solid bars) and homozygous mutant plants (hashed or striped bars). Light grey and cross-hatching indicate v alues for the leaf blade and dark red and horizontal stripes for the leaf sheath. Each plant line is designated by the repository ID and the putative target gene. The first three samples (2A-20021 , 2A-40095, and 4A-03423) are from a side tiller harvested 7-weeks after transplanting to the greenhouse, which can be compared to indicate variation at this stage in hydroxycinnamic acid content. The last two, 1B-00523 and 5A-00394, were harvested 10- weeks after transplanting. A line putatively targeting a rice extosin, 5A-00394, demonstrates that heightened HCA levels are typical in older adult plants relative to younger adult plants.

[0017] Figure 3. Genomic positions and gene expression data for GsATlO-D! activation tagged lines ( A) Representation of the portion of the rice chromosomes near the T-DNA insertion sites. Exons are represented by wide bars with the direction of transcription indicated by arrows. The insertion site is represented by the triangle, with the left border, nearest the CaMV 35S transcriptional enhancer elements, represented by 'L\ cDMA regions targeted for amplification in qPCR are depicted as black bands, 'R stands for

retrotransposon and 'hypoth.' indicates hypothetical. OsFBK16 is an F-box and kelch-domain containing protein. (B) Average relative gene expression determined via qPCR shows that among genes within 20 kb of the insertion site only acyitransferase expression is altered significantly in young leaves of homozygous plants with the T-DNA insertion (hashed) compared with negative segreganis (solid). The observed minor variations in other nearby genes were not consistent among the 3 biological replicates assayed (not shown). Error bars represent the standard deviation of 3-4 biological replicates. Genes with significantly higher expression (p<0.01, unpaired, 2-tailed, Student's t-test) are marked with an asterisk.

[0018] Figure 4. (A) OsATlO-Dl plants (4A-03423.5 progeny) are not significantly different in size compared with the negative segregant, wild type (4A-03423.1 progeny) at senescence, 7 months after planting, (B) dr '' biomass and (C) whole plant seed at senescence for OsATl O-Dl plants. Grey bars indicate wild type (WW, 4A-03423.1 progeny), and hatched bars indicate mutant (TT, 4A-Q3423.5 and 4A-03423.12 progeny). N=12. Error bars represent 2*SEM, ' *' indicates significant differences at p<0.05 (unpaired, 2-tailed, Student's t-test). [0019] Figure 5. OsATlO-Dl shows alterations in cell wall hydroxycinnamic acids. Data are for a negative segregant family lacking the insert (grey bars, progeny of 4A-03423.1) and two mutant families homozygous for the insert (cross hatched bars, progeny of 4A-03423.5,; and horizontal hatched bars, progeny of 4A-03423.12) for y oung leaves and a pool of mature aerial, vegetative material (i.e., mature straw). AIR is alcohol insoluble residue. dsAlR is destarched alcohol insoluble residue. Error bars are 2*SEM of 3 to 5 biological replicates. * indicates significance via two-tailed, unpaired Student's t-test at p < 0.05 and ** indicates significance at p < 0,01. (A) Ferulic acid content. (B) p-Coumaric acid content. (C) The ratio of ferulic acid (F A) to p-couraaric acid (p-C A), which is not subject to weighing or extraction efficiency errors. (13) FA dimer amounts and the ratio of FA:FA Dimer for young leaf samples from A-C.

[0020] Figure 6. Independent OsAtlO over expression lines (cross-hatch) also show altered ratios of hydroxy cinnamic acids (HCA) relative to wild-type lines (solid). (A) qRT-PCR shows that primary transgenic (Transg) Ubi::OsA.tl 0 lines 4 and 5 have increased expression of OsAtlO relative to the wild type (WT) Kitaake (Kit) and line 1, which lack the transgene. Relative expression is normalized to the average of the results with WT plants. (B)

Hydroxycinnamic acid (i.e., ferulic acid, p-coumaric acid, and the sum of ferulic acid dimer peaks) content of a young leaf from wild type and primary transgenic plants. (C) FA:p-CA ratio, but not the FA:FA dimer ratio is altered in the OsAtl O over expression lines.

[0021] Figure 7. The cell wall alteration in OsATlO-Dl hydroxcinnamates is

predominantly in the TFA-soluble fraction. Data are for mature straw from wild type (solid, 4A-03423.5 progeny) and mutant (hatched, 4A-03423.1 progeny). P indicates the pellet and S the supernatant after trifluoroacetate treatment (TFA) or mock (no TFA). The times indicates the minutes of TFA treatment. * indicates significance via unpaired, 2-tailed Student's t-test at p < 0.05 and ** indicates significance at p < 0.01. (A) Ferulic acid content in AIR. (B) p-Coumaric acid content in AIR. (C) The ratio of feruiie acid to p-couniaric acid.

[0022] Figure 8. The modified hydroxycinnamates in OsAT10-D l are attached to a five- carbon sugar, (A) Liquid chromatography-tnass spectrometry shows the total ion abundances in the ethyl acetate extracts for (a) wild type and (b) mutant after 50 niM TFA and 2 M NaOH and (e) wild type and (d) mutant after 50 niM TFA treatment only. Labeled peaks were consistent both with standards, when available, and with mass spectra. trans-Cinnamate was added as an extraction control, (B) The major ion in the mass spectrum for unknown peak 1 is consistent with a para-coumarylated five-carbon sugar. (C) The major ion in the mass spectrum for unknown peak 2 is consistent with a feruloylated five-carbon sugar.

[0023] Figure 9. OsATlO-D l mature straw has increased glucose content relative to wild type (4A-03423.5 progeny vs. 4A-03423.1 progeny, respectively). Wild-type samples are solid and mutant samples are hatched. Grey is from whole tissue, blue is AIR, and maroon is destrached AIR. Error bars show 2*SEM of three replicates. '**' indicates a difference at p < 0.01 and at p < 0.05 via unpaired, 2-tailed, Student's t-test (A) Mass analysis shows significant increases in glucose both after trifluoroacetate (TFA) and after additional treatment with sulfuric acid (TFA+H2S04), as well as with the sum of the two treatments. (B) Analysis of the molecular fraction (moJ %) of monomelic sugars released by TFA from various biomass fractions shows significant increases in mutant glucose and concomitant decreases in xylose, arabinose, and other sugars.

[0024] Figure 10, Principal component analysis of pyro lysis-mo iecuiar beam- mass spectrometry data for 4A-03423 corroborate the change in extractable phenolics, but show no difference in lignin composition. (A) First two components for total biomass (negative in PC I ) and AIR (positive in PCI) for 4A-03423. i pool (WT, diamonds and squares) and 4A- 03423.1 pool (Mutant triangles and X's), (B) Loadings plot for PC2 of A, The mass to charge ratios of the four most differentially identified ions are shown the ions that are overrepresented in mutant tissue are 120 (4 -vinyl phenol or 2,3-Dihydrobenzofuran), 91 (fragment of 2,3-Dihydrobenzofuran and most phenols) and 94 (phenol). The ion that is underrepresented in the mutants is 150 (coumaryl alcohoi/coniferyl alcohol). (C) For samples consisting of the residue remaining after 2 N NaOH extraction, PCA poorly distinguishes mutant and wild type, indicating that the principle components of variation are extractable and, therefore, cannot be polymeric lignin. Symbols are as in (A).

[0025] Figure 1 1. OsATl()-Dl exhibits increased enzymatic and fungal deconstructability. (A) An enzyme cocktail of cellulase and β-glucosidase releases more sugar from destarched AIR from rice straw of OsATl O-Dl (red diamonds, 4A-03423.5 progeny) than from wild- type AIR (light grey circles, 4A-03423.1 progeny). AIR was prefreated at 100 degrees for one hour at pH 5.5 prior to addition of enzyme. Error bars sho w the values of the two technical replicates. (B) PeniciUium sp. YT02 releases greater amounts of sugar from rice straw of OsATlO-Dl (diamonds, 4A-03423.5 progeny) than from wild type straw (circles, 4A- 03423.1 T2 progeny) pretreated via acid-explosion. Grey symbols indicate glucose, red symbols xylose, and while symbols arabinose. Error bars show 2*SEM of five replicate cultures. (C) Xylanase activity (dashed lines, red symbols) in the fungal-straw slurry is enhanced in the presence of the mutant straw (diamonds) relative to the wild type straw (circles); whereas, carboxymethyi cellulase actitvity (solid lines, grey symbols) is unchanged. IU is nmoles of sugar per minute per rnL. Error bars show 2*SEM of five replicate cultures.

[0026] Figure 12 (Supplemental Figure 1). Inferred Bayesian phy togeny for clade V BAUD CoA acyltransferases identified from diverse species based on grouping closely with the biochemically characterized proteins that are similar to the "Mitchell clade" of BAHD proteins, namely BanAAT, and the taxol biosynthesis genes. Branch likelihood scores are 95% if not specified. The phylogeny was built using Mr.Bayes3. L2 with 1 ,5 X106 generations, until the split frequencies decreased below 0.01. Subciades i and si, described in the text and Figure I B, are marked.

10027] Figure 13 (Supplemental Figure 2). Quantitative gene expression analysis suggests no change in the expression of other closely related acyltransferases the OsAT10-Dl (4A- 03423.5, + insert, cross-hatched bars) and negative segregant lines (4A-03423.1 , - insert, solid bars). Shown are the average relative expression data for each target gene and related BAHD acyltransferases in young leaves. Error bars are 2*SEM of three to four biological replicates,

[0028] Figure 14 (Supplemental Figure 3). OsATlO-Dl shows consistent alterations in cell wall hydroxycinnamic acids. Data are for young leaves from progeny of negative segregant (NS) wild-type line (4A-03423.1.9, grey bars) and a line that is homozygous for the insert (4A-03423.5.6, crossliatched bars). The average and error bars indicate 2*SEM for the shown biological young leaf replicates. * indicates significance via Student's t-test at p < 0.05 and ** indicates significance at p < 0.01. (A) Ferulic acid content in an alcohol insoluble residue (ATR) preparation. (B) p-Coumaric acid content from AIR. (C) The ratio of ferulic acid (FA) to p-CGumaric acid (p-CA), which is not subject to weighing or extraction efficiency errors. 02 ] F gure 15 (Supplemenatal Figure 4). Sugar analysis confirms that xylose, not glucose, is a major constituent released by the 50 mM TFA treatments.

[0030] Figure 16 (Supplemental Figure 5). Destarched AIR from OsATl 0-Dl mature straw has increased glucose content relative to that of the wild type, but no other significant changes by mass. Wild-type (4A-03423.1 progeny) samples are solid and mutant (4A- 03423.5 progeny) samples are hatched. Error bars show 2*SEM of three replicates.

indicates a difference at p < 0.05 via unpaired, two-tailed Student's t-test. (A) Mass analysis shows significant increases in glucose (Glc), but not xylose (Xyl) and arabinose (Ara). (B) Mass analysis shows no significant changes in galactose (Gal), fucose (Fuc), rhammnose (Rha), galacturonic acid (GalA), or glucuronic acid (GlcA). [0031] Figure 17 (Supplemental Figure 6). Thermogravimetric analysis defects no mass difference upon heatmg between wild-type and mutant mature straw. (A) Example gravimetric traces throughout heating. The first heating phase (red fine, right axis) represents heating in the absence of oxygen and the second represents heatmg in the presence of oxygen (combustion). Data are normalized to values at 30 minutes ( 177 °C), which represent the initial dry weights. (B) Selected times report on biomass composition. WT and OsATl O-Dl are indistinguishable in terms of the mass of char (blue bars) remaining after pyrolysis at 800 °C (blue bars, t = 1 12'), the ash content after combustion (red bars, 1=250'), and, by extension, the fraction of the char that is combustible (yellow bars, difference between char and ash). This provides further evidence that there is no difference in the lignin composition or content between the two genotypes. Switehgrass, oak, and duckweed samples are shown for comparison. Values are % of the dry weigh; and averages were taken, when replicates were available. When shown, error bars are 2*SEM of 2-4 technical replicates.

[0032] Figure 18 (Supplemental Figure 7). Enzymatic activity in media during Penicillium sp. ΥΊΌ2 incubation with wild-type (circles) and OsA.T10-Dl mutant (diamonds) straw. FPA (dashed lines, red symbols) is the activity on cellulose filter paper, β-glucosidase activity uses cellobiose as a substrate. IU is nmoles of sugar per minute per mL. Data are normalized for me of total protein. Error bars show 2*SEM of fi ve replicate cultures. [0033] Figure 19. Genomic positions and gene expression data of the OsAT5-Dl activation tagged line. Genomic positions and gene expression data for the OsAT5-Dl activation tagged line (A) Representation of the portion of the rice chromosome near the T-DNA insertion site. Exons are represented by wide bars with the direction of transcription indicated by arrows. The insertion site is represented by the triangle, with the left border, nearest the transcriptional enhancer elements, represented by 'L'. cDNA Regions targeted for amplification in qPCR are depicted as black bands, RT stands for retrotransposon and hypoth indicates hypothetical. (B) Average normalized gene expression determined via qPCR shows that among genes within 20 kbp of the insertion site only acy transferase expression is altered significantly in young leaves of homozygous plants with the T-DNA insertion (hashed) compared with negative segregants (solid). Error bars represent the standard deviation of 3-4 biological replicates. Genes with significantly higher expression (p<Q.01, Student's t- test) are marked with an asterisk,

[0034] Figure 20. OsAT5-Dl shows alterations in cell wail hydroxycinnamic acids. Data are for two separately grown batches (#1 and #2) of plants of a near isogenic family lacking the insert (grey bars, progeny of the near isogenic wild type line 2A-20021.10.2) and a family homozygous for the insert (cross-hatched bars, progeny of the OsAT5-Dl mutant line 2A- 20021.1 1,7). Samples for batch #1 were harvested from seedlings 35 days post germination. The expanding leaf samples for batch #2 were harvested at 8 weeks post germination and the mature tiller at 16 weeks post germination. Values are the average of 5 to 12 individual plants. Error bars mark the 95% confidence interval for the mean. * indicates significance via Student's t-test at p < 0.05 and ** indicates significance at p < 0.01. (A) Ferulic acid content in an alcohol insoluble residue (AIR.) preparation. (B) p-Coumaric acid content from AIR. (C) The ratio of ferulic acid (FA) to p-coumaric acid (CA), which is not subject to weighing or extraction efficiency errors. (D) Major FA dimer species and the ratio of FA to dimer for the Batch #1 expanded leaf samples.

[0035] Figure 21. Alignment of illustrative AT 10 polypeptide sequences. [0036] Figure 22. Alignment of illustrative ATI 5 polypeptide sequences. [0037] Figure 23. Alignment of illustrative AT7 polypeptide sequences. [0038] Figure 24. Alignment of illustrative ATS polypeptide sequences. DETAILED DESCRIPTION OF THE INVENTION

I. Definitions

[0039] As used herein, the term "AT 10 acyl transferase" refers to a CoA p-coumaryl transferase that functions in the modification of grass arabinoxylan. The term encompasses variants and interspecies homologs to the specific polypeptides described herein. A nucleic acid that encodes an AT 10 acyl transferase refers to a gene, pre-mRNA, mRNA, and ihe like, including nucleic acids encoding polymorphic variants, alleles, mutants, and interspecies homologs of the particular amino acid sequences described herein. Thus, in some embodiments, an Ail 0 acyl transferase gene encodes a polypeptide having an amino acid sequence that has at least 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater, amino acid sequence identity, preferably over a region of at least about 25, 50, 100, 200 or more amino acids, or over the length of the entire polypeptide, to an amino acid sequence of SEQ ID NO:2; or to amino acids 4 to 434 of SEQ ID NO:2; or to any one of the AT10 amino acid sequences shown in Figure 21. Examples of AT 10 genes and the proteins encoded by the genes are shown in Figure 21.

[0040] As used herein, the term "AT 15 acyl transferase" refers to a CoA feruJoyl transferase that functions in the modification of a molecule that effects the amount of ferulic acid incorporated into grass cell wall. The term encompasses variants and interspecies homologs to the specific polypeptides described herein. A nucleic acid that encodes an AT 15 acyl transferase refers to a gene, pre-mRNA, mRNA, and the like, including nucleic acids encoding polymorphic variants, alleles, mutants, and interspecies homologs of the particular amino acid sequences described herein. Thus, in some embodiments, an AT 15 acyl transferase encodes a polypeptide having an amino acid sequence that has at least 70%, typically at least 75%, 80%, 85%, 90%, preferably 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater, amino acid sequence identity, preferably over a region of at least aboui 25, 50, 100, 200 or more amino acids, or over ihe length of the entire polypeptide, to an amino acid sequence of SEQ ID NO:4, or to amino aicd 5 to 429 of SEQ ID NQ:4, or to any one of the ATI 5 amino acid sequences shown in Figure 22. Examples of AT15 genes and the proteins encoded by the genes are shown in Figure 22. [0041] As used herein, the term "AT? acyl transferase" refers to a CoA feruloyl transferase that functions in the modification of grass cell walls. The term encompasses variants and interspecies homologs to the specific polypeptides described herein. A nucleic acid that encodes an AT7 acyl transferase refers to a gene, pre-mRNA, mRNA, and the like, including nucleic acids encoding polymorphic variants, alleles, mutants, and interspecies homologs of the particular amino acid sequences described herein. Thus, in some embodiments, an AT7 acyl transferase encodes a polypeptide having an amino acid sequence that has at least 70%, typically at least 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater, amino acid sequence identity, preferably over a region of at least about 25, 50, 100, 200 or more amino acids, or over the length of the entire polypeptide, to an amino acid sequence of SEQ ID NO:6 or to amino acid residues 9 to 439 of SEQ ID O:6, or to any one of the AT7 amino acid sequences shown in Figure 23. Examples of AT7 genes and the proteins encoded by the genes are shown in Figure 2.3.

[0042] As used herein, the term "AT5 acyl transferase" refers to a CoA feruioyl transferase that functions in the modification of grass cell wall components. The term encompasses variants and interspecies homologs to the specific polypeptides described herein. A nucleic acid that encodes an ATS acyl transferase refers to a gene, pre -mRNA, mRN A, and the like, including nucleic acids encoding polymorphic variants, alleles, mutants, and interspecies homologs of the particular amino acid sequences described herein. Thus, in some embodiments, an AT7 acyl transferase encodes a polypeptide having an amino acid sequence that has at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater, amino acid sequence identity, preferably over a region of at least about 25, 50, 100, 200 or more amino acids, or over the length of the entire polypeptide, to an amino acid sequence of SEQ ID NO:8, or to amino acids 5 to 429 of SEQ ID NO:8, or to any one of the AT5 amino acid sequences shown in Figure 24. Examples of ATS genes and the proteins encoded by the genes are shown in Figure 24.

[0043] The terms "increased level of activity," or "increased activity" refer interchangeably to an increase in the amount of activity of an ATI 0, ATI 5, AT7, or AT5 acvltransferase protein in a grass plant engineered to increase expression of the acvltransferase compared to the amount of activity in a wild-type (i.e., naturally occurring) plant. In some embodiments, increased activity results from increased expression levels. An increased level of activity or increased level of expression can be an increase in the amount of activity or expression of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% or greater, compared to a wildtype plant. In some embodiments, the increased acvltransferase activity or expression is localized to one or more tissues of the engineered plant, such as cell walls and/ or leaves. Increased expression or activity of the acyltransferase gene or protein can be assessed by any number of assays, including, but not limited to, measuring the level of RNA encoded by the ΑΤΊ 0, ATI5, AT7, or ATS acyltransferase gene, the level of AT 10, AT 15, AT7, or ATS protein, the level of AT 10, AT 15, AT7, or ATS enzymatic activity, or by measuring the ceil wall ferulic acid and optionally, ^-coumaric acid content in comparison to the amount in a wild-type plant.

[0044] The terms "reduced level of activity," "reduced activity" and "decreased activity " refer interchangeably to a reduction in the amount of activity of ATS protein in a plant engineered to decrease AT5 compared to the amount of activity in a wild-type (i.e., naturally occurring) plant. In some embodiments, reduced activity results from reduced expression levels. A reduced level of activity ora. reduced level of expression can be a reduction in the amount of activity or expression of ATS of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% or greater. In some embodiments, the reduced level of activity or reduced level of expression occurs, throughout all the tissues of the engineered plant. In some

embodiments, the reduction in the amount of activity or expression is localized to one or more tissues of the engineered plant, such as the cell wall. In some embodiments, the ATS is not reduced in amount, but is modified in amino acid sequence so that the enzymatic activity is reduced directly or indirectly. Decreased expression or activity of an ATS gene or protein can be assessed by any number of assays, including, but not limited to, measuring the level of RNA encoded by the ATS gene, the level of ATS protein, the level of ATS enzymatic activity, or by measuring the ceil wall ferulic acid and/or p-coumaric acid content.

[0045] The terms "polynucleotide" and "nucleic acid" are used interchangeably and refer to a single or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5' to the 3' end. A nucleic acid of the present invention will generally contain phosphodiester bonds, although in some cases, nucleic acid analogs may be used that may have alternate backbones, comprising, e.g., phosphoramidate, phosphorothioate,

phosphorodithioate, or O-methylphophoroamidite linkages (see Eckstein, Oligonucleotides and Analogues: A Practical Approach, Oxford University Press); positive backbones: non- ionic backbones, and non-ribose backbones. Thus, nucleic acids or polynucleotides may also include modified nucleotides that permit correct read-through by a polymerase.

"Polynucleotide sequence" or "nucleic acid sequence" includes both the sense and antisense strands of a nucleic acid as either individual single strands or in a duplex. As will be appreciated by those in the art, the depiction of a single strand also defines the sequence of the complementary strand; thus the sequences described herein also provide the complement of the sequence. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. The nucleic acid may be DNA, both genomic and cDNA, RNA or a hybrid, where the nucleic acid may contain combinations of deoxyribo- and ribo-nucleotides, and combinations of bases, including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosine, isoguanine, etc. [0046] The term "substantially identical," used in the context of two nucleic acids or polypeptides, refers to a sequence that has at least 50% sequence identity with a reference sequence. Percent identity can be any integer from 50% to 100%. Some embodiments include at least: 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, compared to a reference sequence using the programs described herein; preferably BLAST ^' using standard parameters, as described below. For example, an ATI 0 polypeptide may have a sequence that is at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to a sequence of SEQ ID NO:2.

[0047] Two nucleic acid sequences or polypeptide sequences are said to be "identical" if the sequence of nucleotides or amino acid residues, respectively, in the two sequences is the same when aligned for maximum correspondence as described below. The terms "identical" or percent "identity," in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using one of the following sequence comparison algorithms or by marutal alignment and visual inspection. When percentage of sequence identity is used in reference to proteins or peptides, it is recognized that residue positions that are not identical often differ by conservative amino acid substitutions, where amino acids residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservati ve substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated according to, e.g., the algorithm of Meyers & Miller, Computer Applic. Biol. Sci. 4: 1 1-17 ( 1988) e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, California, USA).

[0048] For sequence comparison, typically one sequence acts as a reference sequence, to which tesi sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identiiies for the test sequences relative to the reference sequence, based on the program parameters.

[0049] A "comparison window," as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may ^¬ be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homolog algorithm of Smith & Waterman, Adv. Appl. Math. 2 :482 (1981 ), by the homology alignment algorithm of Needleman & Wunsch, J. Mot Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipmart, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wl), or by manual alignment and visual inspection.

[0050] Algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST ^' and BLAST 2.0 algorithms, which are described in Altschul et al. (1990) ,/. Mol. Biol. 215: 403-410 and Altschul et al. (1977) Nucleic Acids Res. 25: 3389- 3402, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (NCBI) web site. The algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Aitschul et al, supra). These initial neighborhood word hits acts as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment The BLASTN program (for nucleotide sequences) uses as defaults a word size (W) of 28, an expectation (E) of 10, M=l, N=-2, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a word size (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. ScL USA 89: 10915 (1989)). [0051] The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Aitschul, Proc. Nat'L Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.01, more preferably

-5 -20

less than about 10 , and most preferably less than about 10 .

[0052] Nucleic acid or protein sequences that are substantially identical to a reference sequence include "conservatively modified variants." With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are "silent variations," which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine) can be modified to yield a functionally identical molecule.

Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.

[0053] A s to amino acid sequences, one of skill will recognize that individual substitutions, in a nucleic acid, peptide, polypeptide, or protein sequence which alters a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art.

[0054] The following six groups each contain amino acids that are illustsrative conservative substitutions for one another: 1) Alanine (A), Serine (S), Threonine (T);

2) Aspartic acid (D), Glutamic acid (E);

3) Asparagine (N), Glutamine (Q);

4) Arginine (R), Lysine (K);

5) Isoleucine (ΐ), Leucine (L), Methionine (M), Valine (V); and

6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

(see, e.g., Creighton, Proteins (1984)),

[0055] Another indication that nucleotide sequences are substantially identical is if two molecules hybridize to each other, or a third nucleic acid, under stringent conditions.

Stringent conditions are sequence dependent and will be different in different circumstances. Generally, stringent conditions are selected to be about 5°C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Typically, stringent conditions will be those in which the salt concentration is about 0.02 molar at pH 7 and the temperature is at least about 60°C. For example, stringent conditions for hybridization, such as RNA-DNA hybridizations in a blotting technique are those which include at least one wash in 0.2X SSC at 55°C for 20 minutes, or equivalent conditions. [0056] The term "promoter," as used herein, refers to a polynucleotide sequence capable of driving transcription of a DNA sequence in a ceil. Thus, promoters used in the

polynucleotide constructs of the invention include cis- and trans- acting transcriptional control elements and regulatory sequences that are involved in regulating or modulating the timing and/or rate of transcription of a gene. For example, a promoter can be a cis- acting transcriptional control element, including an enhancer, a promoter, a transcription terminator, an origin of replication, a chromosomal integration sequence, 5' and 3' untranslated regions, or an intronic sequence, which are involved in transcriptional regulation. These cis-acting sequences typically interact with proteins or other biomolecules to carry out (turn on/off, regulate, modulate, etc.) gene transcription. Promoters are located 5' to the transcribed gene, and as used herein, include the sequence 5' from the translation start codon (i.e., including the 5' untranslated region of the mRNA, typically comprising 100-200 bp). Most often the core promoter sequences lie within 1-2 kb of the translation start site, more often within 1 kbp and often within 500 bp of the translation start site. By convention, the promoter sequence is usually provided as the sequence on the coding strand of the gene it controls. In the context of this application, a promoter is typically referred to by the name of the gene for which it naturally regulates expression. A promoter used in an expression construct of the invention is referred to by the name of the gene. Reference to a promoter by name includes a wildtype, native promoter as well as variants of the promoter that retain the ab lity to induce expression. Reference to a promoter by name is not restricted to a particular plants species, but also encompasses a promoter from a corresponding gene in other plant species.

[0057] A "constitutive promoter" in the context of this invention refers to a promoter that is capable of initiating transcription in nearly ail cell types, whereas a "cell type -specific promoter" or "tissue-specific promoter" initiates transcription only in one or a few particular cell types or groups of cells forming a tissue. In some embodiments, a promoter is tissue - specific if the transcription levels initiated by the promoter in the cell wall are at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 50-fold, 100-fold, 500-fold, 1000-fold higher or more as compared to the transcription levels initiated by the promoter in non-cell wall tissues

[0058] A polynucleotide is "heterologous" to an organism or a second polynucleotide sequence if it originates from a foreign species, or, if from the same species, is modified from its original form. For example, when a polynucleotide encoding a polypeptide sequence is said to be operably linked to a heterologous promoter, it means that the polynucleotide coding sequence encoding the polypeptide is derived from one species whereas the promoter sequence is derived from another, different species; or, if both are derived from the same species, the coding sequence is not naturally associated with the promoter (e.g., is a genetically engineered coding sequence, e.g., from a different gene in (he same species, or an allele from a different ecotype or variety).

[0059] The term "operably linked" refers to a functional relationship between two or more polynucleotide (e.g., DNA) segments. Typically, it refers to the functional relationship of a tra scriptio al regulatory sequence to a transcribed sequence. For example, a promoter or enhancer sequence is operably linked to a DNA or RNA sequence if it stimulates or modulates the transcription of the DNA or RNA sequence in an appropriate host cell or other expression system. Generally, promoter transcriptional regulatory sequences that are operably linked to a transcribed sequence are physically contiguous to the transcribed sequence, i.e., they are cis-acting. However, some transcriptional regulatory sequences, such as enhancers, need not be physically contiguous or located in close proximity to the coding sequences whose transcription they enhance.

[006(5] The term "expression cassette" or "DNA construct" or "expression construct" refers to a nucleic acid construct that, when introduced into a host cell, results in transcription and/or translation of an RNA or polypeptide, respectively. Antisense or sense constructs that are not or cannot be translated are expressly included by this definition. In the case of both expression of transgenes and suppression of endogenous genes (e.g. , by antisense, RNAi, or sense suppression) one of skill will recognize that the inserted polynucleotide sequence need not be identical, but may be only substantially identical to a sequence of the gene from which it was derived. As explained herein, these substantially identical variants are specifically covered by reference to a specific nucleic acid sequence. One example of an expression cassette is a polynucleotide construct that comprises a polynucleotide sequence encoding a AT 10 protein operably linked to a heterologous promoter. In some embodiments, an expression cassette comprises a polynucleotide sequence encoding a AT 10 protein that is targeted to a position in a plant genome such that expression of the polynucleotide sequence is driven by a promoter that is present in the plant

[0061] The term "plant" as used herein can refer to a whole plant or part of a plant, e.g., seeds, and includes plants of a variety of pfoidy levels, including aneuploid, polyploid, diploid and haploid. The term "plant part," as used herein, refers to shoot vegetative organs and'or structures (e.g., leaves, stems and tubers), branches, roots, flowers and floral organs (e.g. , bracts, sepals, petals, stamens, carpels, anthers), ovules (including egg and central cells), seed (including zygote, embryo, endosperm, and seed coat), fruit (e.g., the mature ovary), seedlings, and plant tissue (e.g., vascular tissue, ground tissue, and the like), as well as individual plant cells, groups of plant cells (e.g., cultured plant ceils), protoplasts, plant extracts, and seeds. The class of plants that can be used in the methods of the invention is generally as broad as the class of higher and lower plants amenable to transformation techniques, including angiosperms (monocotyiedonous and dicotyledonous plants), gymnosperms, ferns, bryophyt.es, and multicellular algae.

[0062] The term "biomass," as used herein, refers to plant material that is processed to provide a product, e.g., a biofuel such as ethanol, or livestock feed, or a cellulose for paper and pulp industry products. Such plant material can include whole plants, or parts of plants, e.g., stems, leaves, branches, shoots, roots, tubers, and the like. [0063] The term "decreased ferulic acid content" in the context of this invention refers to a decreased amount of ferulic acid present in cell wall or leaf in an engineered plant of the present invention as compared to a wild-type (i.e., naturally occurring) plant. In the current invention, ferulic acid is typically considered to be decreased when the amount of ferulic acid in the cell wall or leaf is decreased by at least 10%, at least 20, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more relative to the amount of the ferulic acid in the cell wall or leaf in a wild- type plant. Ferulic acid content can be assessed using any method known in the art. .

[0064] The term "decreased ferulic acid content" also encompasses embodiments where the ratio of ferulic acid to /.'-coumaric acid is decreased relative to a wild type plant. Thus, in some embodiments, the amount of ferulic acid may be the same as a wild-type plant, but relative to the to >-coumaric acid content, may be increased, thus decreasing the ration of ferulic acid to ferulic acid to p-coumaric acid when compared to a wildtype plant. In the current invention, the raio of ferulic acid to p-coumaric acid is typically considered to be decreased when the ratio in the ceil wall or leaf is decreased by at least 10%, at least 20, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more relative to the ratio of the amount of the ferulie acid in the cell wall or leaf in a wild-type plant,

[0065] The term "sacc arification reaction" refers to a process of converting biomass, usually cellulosic or lignocellulosic biomass, into monomeric sugars, such as glucose and xylose.

[0066] The term "soluble sugar" refers to monomeric, dimeric, or trimeric sugar that is produced from the saccharification of biomass.

[0067] The term "increased amount," when referring to an amount of sugar or soluble sugar obtained from an engineered plant of the present invention, refers to an increase in the amount or yield of sugar that is obtained from saccharification of biomass per amount of starting material, in comparison to corresponding biomass from a wild-type (i.e., naturally occurring) plant. In the context of the present invention, "corresponding biomass from a wild-type plant" refers to plant material that is from the same part of the plant as the biomass from a plant engineered to have modified hydroxycinnamic acid levels. As understood in the art, increased amount or increased yield is based upon comparisons of the same amount of corresponding plant material.

[0068] The term "conversion reaction," as used herein, refers to a reaction that converts biomass into a form of bioenergy. Examples of conversion reactions include, but are not limited to, combustion (burning), gasification, pyroiysis, and polysaccharide hydrolysis (enzymatic or chemical).

[0069] The term "mcreased production," when referring to an amount of bioenergy production obtained from an engineered plant of the present invention, refers to an increased amount of bioenergy that is produced from subjecting biomass from an engineered plant to a conversion reaction (e.g., combustion, gasification, pyroiysis, or polysaccharide hydrolysis) as compared to the amount of bioenergy that is produced from corresponding biomass from a wild-type (i.e., naturally occurring) plant.

II. Introduction

[0070] The invention relates to acyltransferases that modify the hydroxycinnamic acid content in grass plant cell walls. These acyltranferases include AT 10, AT 15, AT7, and ATS. Plants, e.g., grasses, that are modified to overexpress ATI 0, AT 15, and AT7; and/or are modified to decrease expression of AT ^' 5 have reduced ferulic acid content and accordingly, provide an increased yield, relative to a wild-type plant, in obtaining sugars from plant wall material. In some embodiments, plants, e.g., grass plants, may be modified to overexpress ATS, resulting in an increase of feruioyl esters. Not to be bound by theory, depending on the cell wall precursor that is modified, increasing the level of feruioyl esters present may introduce relatively easily broken bonds that reduce cell wall recalcitrance. For example, increasing ester linkages within the lignin polymer may improve the solubilization of lignin under mild alkaline conditions compared to native lignin. Accordingly, in this embodiment, increasing ferulic acid content of a plant, such as a grass plan, may provide an increased yield, relative to a wild-type plant in which ATS is not modified, in obtaining sugars from plant wail material.

[0071] Plants can be engineered to overexpress an acyltransferase by genetically modifying a plant to overexpress one or more of ATS, AT10, AT 15, or AT7 acyltransferase genes as described herein. In some embodiments, overexpresson is targeted to various tissues, e.g., cell wall and/or leaf, using a tissue-specific promoter. An example of a method for fine-tuning ATS, ATIO, AT 15, or AT7 expression to increase expression in the cell wall is taught in PCT/US2012/023182, which is incorporated by reference. Similarly, ferulic acid content in a plant, e.g., a grass plant, can be increased by genetically modifying a cell to decrease expression of ATS as described herein.

[0072] In some embodiments, a plant may be genetically modified, to disrupt expression of an endogenous AT10, A I 5, AT ^' 7, and/or ATS gene and then further modified to express the AT10, AT 15, AT7, and/or ATS gene in a tissue of interest, e.g., cell wail and/or leaf.

[0073] The invention additionally provides methods of generating genetically modified plants that overexpress or have reduced levels of ATIO, AT15, AT7, and/or ATS acyltransferase activity and methods of using such plants, e.g., as biomass for degradation reactions to produce soluble sugars or as forage plants.

[0074] As used herein in describing nucleic acids and polypeptides of the invention, an "AT" nucleic acid or polypeptides refers to an AT10, AT15, AT7, or ATS polynucleotide or polypeptide. Acy ransferase nucleic acid and polypeptide sequences

[0075] The invention employs various routine recombinant nucleic acid techniques.

Generally, the nomenclature and the laboratory procedures in recombinant DNA technology described below are those well known and commonly employed in the art. Many manuals that provide direction for performing recombinant DNA manipulations are available, e.g., Sambrook & Russell, Molecular Cloning, A Laboratory Manual (3rd Ed, 2001); and Current Protocols in Molecular Biology (Ausubei, el ah, John Wiley and Sons, New York, 2009).

A T10

[0076] ATI 0 nucleic acid and polypeptide sequences suitable for use in the invention mciude ATI 0 nucleic acid sequences that encode a plant AT10 polypeptide as illustrated by the sequences shown in Figure 21, or a substantially identical variant. Such a substantially identical variant typically has at least 70%, or at least 75%, 80%, 85%, 90%, or 95% identity to SEQ ID NG:2. In some embodiments, the variant has at least 70%, or at least 75%, 80%, 85%, 90%, or 95% identity to an AT 10 sequence shown in Figure 21. In some embodiments, a nucleic acid that encodes an AT 10 polypeptide of the invention has at least 60%, often at least 70%, or at least 75%, 80%, 85%, or 90% identity to the nucleic acid sequence of SEQ ID NO: 1. The Pfam domain of SEQ ID NO:2 corresponds to amino acids 4 to 434 of SEQ ID NO:2. ATI 0 proteins are additionally characterized by the presence of a motif HXXXD at positions 182-186 of SEQ ID NO:2. [0077] A comparison of AT 10 sequences is provided in Figure 21. As shown in Figure 21, there are highly conserved regions of the polypeptide sequences. These conserved sequences are not strictly conserved 100% across the various plant protein sequences. For example, one of skill can obtain a variant by using the sequence alignments to identify residues within the conserved sequences that would be expected to retain AT 10 function as well as residues outside of the conserved regions that would be expected to be tolerant to substitution,

[0078] AT 10 activity can be assessed using any number of assays, including assays that evaluate the liydroxycimiamie acid content of cell wall and/or leaf. AT 10 activity can be assessed by increasing the expression of ATI 0 in plant cells. Examples of assays include, but are not limited to the following illustrative assays. Activity may assayed by creation of a transgenic plant by incorporation into the plant genome of an AT 10 gene that is associated with a promoter that increases AT 10 expression compared to wild-type levels. Alternatively, transient expression assays, such as through infiltration or dipping of plant cells into an Agrobacterium solution, can be used. For both of these assays the read out is measurement of an increase in the cell wall content of p-coumaryl esters associated with cell wall matrix polysaccharide. For this assay, biomass, or a cell wall extraction thereof, is treated with 2M NaOH. The resulting supernatant, or an extract there of, can be analyzed for changes in hydroxycinnamate content via high performance liquid chromatography with UV absorbance detection or another similar method. Alternatively, an in vitro assay can be used to indicate activity of ATiO in attachment of a hydroxycinnamate (e.g., FA or pCA) onto a 5-carbon sugar. This activity can be measured again via liquid chromatography (LC)-UV detection or LC-mass spectrometry, among others

AT1S

[0079] ATI 5 nucleic acid and polypeptide sequences suitable for use in the invention include AT 15 nucleic acid sequences that encode a plant AT 15 poly peptide as illustrated by the sequences shown in Figure 22, or a substantially identical variant. Such a variant typically has at least 75%, 80%, 85%, 90%, or 95% identity to SEQ ID NO:4. In some embodiments, the variant has at least 75%, 80%, 85%, 90%, or 95% identity to an ATI 5 sequence shown in Figure 22. In some embodiments, a nucleic acid that encodes an AT 15 polypeptide of the invention has at least 60%, often at least 70%, or at least 75%, 80%, 85%, or 90% identity to SEQ ID NO:3. The Pfam domain of SEQ ID NO:4 corresponds to amino acids 5 to 41 1 of SEQ ID NQ:4, AT15 proteins are additionally characterized by the presence of a motif , HXXXD. This motif occurs neaer position 164 in SEQ ID NO:4.

[008(5] A comparison of ATI 5 sequences is provided in Figure 22. As shown in Figure 22, there are highly conserved regions of the polypeptide sequences. These conserved sequences are not strictly conserved 100% across the various plant protein sequences. For example, one of skill can obtain a variant by using the sequence alignments to identify residues within the conserved sequences that would be expected to retain AT 15 function as well as residues outside of the conserved regions that would be tol erant to substitution.

[0081] AT 15 activity can be assessed using any number of assays, including assays that evaluate the hydroxycinnamic acid content of cell wall and/or leaf. Examples of assays include, but are not limited to the following illustrative assays. AT15 activity can be assessed by increasing the expression of AT15 in plant cells. This can be accomplished through creation of a transgenic plant by incorporation into the plant genome of an AT 15 gene that is associated with a promoter that increases AT 15 expression compared to wild-type levels. Alternatively, transient expression assays, such as through infiltration or dipping of plant cells into an Agrobactenum solution, can be used. For both of these assays the read out is measurement of an decrease in the cell wall content of hydroxycinnamyl esters associated with cell wall matrix polysaccharide. For this assay, biomass, or a cell wall extraction thereof, is treated with 2.M NaOH. T he resulting supernatant, or an extract thereof, can be analyzed for changes in hydroxycinnamate content via high perfonnance liquid

chromatography with UV absorbance detection or another similar method.

All

[0082] AT7 nucleic acid and polypeptide sequences suitable for use in the invention include AT7 nucleic acid sequences that encode a plant AT7 polypeptide as illustrated by the sequences shown in Figure 23, or a substantially identical variant. Such a variant typically has at least least 70%, or at least 75%, 80%, 85%, 90%, or 95% identity to SEQ ID NO:6. In some embodiments, the variant has at least 75%, 80%, 85%, 90% or 95% identity to identity to an AT7 sequence shown in Figure 23. In some embodiments, a nucleic acid that encodes an AT7 polypeptide of the invention has at least 60%, often at least 70%, or at least 75%, 80%, 85%, or 90% identity to SEQ ID NO:5. The Pfam domain of SEQ ID NO:6 corresponds to amino acids 9 to 439 of SEQ ID sIO:6. AT7 polypeptides are additionally characterized by the presence of a motif HXXXD. This motif occurs near position 176 in SEQ ID NO:6.

[0083] A comparison of AT7 sequences is provided in Figure 23. As shown in Figure 23, there are highly conserved regions of the polypeptide sequences. These conserv ed sequences are not strictly conserved 100% across the various plant protein sequences. For example, one of skill can obtain a variant by using the sequence alignments to identify residues within the conserved sequences that would be expected to retain AT7 function as well as residues outside of the conserved regions that would be tolerant to substitution.

[0084] AT7 activity can be assessed using any number of assays, including assays that evaluate the hydroxycinnamic acid content of cell wall and'Or leaf. Examples of assays include, but are not limited to the following illustrative assays. AT7 activity can be assessed by increasing the expression of AT7 in plant cells. This can be accomplished through creation of a transgenic plant by incorporation into the plant genome of an AT7 gene that is associated with a promoter that increases AT7 expression compared to wild- type levels. Alternatively, transient expression assays, such as through infiltration or dipping of plant cells into an Agrobacterium solution, can be used. For both of these assays the read out is measurement of an decrease in the cell wail content of hydroxycinnatnyl esters associated with ceil wall matrix polysaccharide. For this assay, biomass, or a cell wall extraction thereof, is treated with 2M aOFi. The resulting supernatant, or an extraci thereof, can be analyzed for changes in hydroxycinnamate content via high performance liquid chromatography with LTV absorbance detection or another similar method.

ATS

[0085] ATS nucleic acid and polypeptide sequences that are targeted for disruption in accordance with the invention include ATS nucleic acid sequences that encode a plant ATS polypeptide as illustrated by the sequences shown in Figure 24, or a substantially identical variant. Such a variant typically has at least 60% identity, or at least 65%, 70%, 75%, 80%, 85%, 90%, or 95% identity to SEQ ID NQ:8, In some embodiments, the variant has at least 70%, 75%>, 80%, 85%>, 90% or 95% identity to identity to an ATS sequence shown in Figure 24. In some embodiments, a nucleic acid that encodes an ATS polypeptide of the invention has at least 60%, often at least 70%, or at least 75%, 80%, 85%, or 90% identity to SEQ ID NO 17. The Pfam domain of SEQ ID NO: 8 corresponds to amino acids 5 to 429 of SEQ ID NO:8. ATS polypeptides are additionally characterized by the presence of a motif , HXXXD. This motif occurs near position 170 in SEQ ID NO:8. [0086] A comparison of ATS amino acid sequences is provided in Figure 24. As shown in Figure 24, there are highly conserved regions of the polypeptide sequences. These conserved sequences are not strictly conserved 100% across the various plant protein sequences. For example, one of skill can obtain a nucleic acid encoding a variant polypeptide by using the sequence alignments to identify residues within the conserved sequences that would be expected to retain ATS function as well as residues outside of the conserved regions that would be tolerant to substitution.

[0087] ATS activity can be assessed using any number of assays, including assays that evaluate the hydroxycinnamic acid content of cell wall and/or leaf. Examples of assays include, but are not limited to the following illustrative assays. ATS activity can be assessed by increasing the expression of ATS in plant cells. This can be accomplished through creation of a transgenic plant by incorporation into the plant genome of an ATS gene that is associated with a promoter that increases ATS expression compared to wild- type levels. Alternatively, transient expression assays, such as through infiltration or dipping of plant cells into an Agrobacteriusn solution, can be used. For both of these assays the read out is measurement of an decrease in the cell wall content of hydroxycinnamyf esters associated with cell wall matrix polysaccharide. For this assay, biomass, or a ceil wall extraction thereof, is treated with 2M NaOH. The resulting supernatant, or an extract thereoi ^" , can be analyzed for changes in hydroxycinnamate content via high performance liquid

chromatography with UV absorha ce detection or another similar method.

[0088] Isolation or generation AT polynucleotide sequences can be accomplished by a number of techniques. Cloning and expression of AT genes in accordance with the invention are generally discussed in the context of ATI 0 genes. One of skill understands that these techniques can be employed to overexpress AT7, AT 15, or AT5 genes. Recombinant expression techniques can also be used to disrupt ATS expression. In some embodiments, oligonucleotide probes based on the sequences disclosed here can be used to identify the desired polynucleotide in a cDNA or genomic DNA library from a desired plant species. Probes may be used to hybridize with genomic DNA or cD A sequences to isolate homologous genes in the same or different plant species.

[0089] Alternatively, the nucleic acids of interest can be amplified from nucleic acid samples using routine amplification techniques. For instance, PGR may be used to amplify the sequences of the genes directly from mRNA, from cDNA, from genomic libraries or cDNA libraries, PGR and other in vitro amplification methods may also be useful, for example, to clone nucleic acid sequences that code for proteins to be expressed, to make nucleic acids to use as probes for detecting the presence of the desired mRNA in samples, for nucleic acid sequencing, or for other purposes.

[0090] Appropriate primers and probes for identifying a ATI 0 gene from plant cells such as moss or spikemoss, can be generated from comparisons of the sequences provided herein. For a general overview of PGR see PGR Protocols: A Guide to Methods and Applications. (Innis, M, Geifand, D., Sninsky, J. and White, T., eds.), Academic Press, San Diego (1990).

[0091] AT 10, AT 15, AT7, and ATS nucleic acid sequences for use in the invention includes genes and gene products identified and characterized by techniques such as hybridization and/or sequence analysis using exemplary nucleic acid sequences, e.g., SEQ ID NO: l , SEQ ID NO:3, SEQ ID NQ:5, and SEQ ID NO:7. Preparation of recombinant vectors

[0092] To use isolated sequences in the above techniques, recombinant DNA vectors suitable for transformation of plant cells, such as grass crop plant cells, are prepared.

Techniques for transformation are well known and described in the technical and scientific literature. For example, a DNA sequence encoding an AT 10, AT7, ATI 5, or ATS polypeptide (described in further detail below), can be combined with transcriptional and other regulatory sequences which will direct the transcription of the sequence from ihe gene in the intended cells, e.g., grass or other crop plant cells. In some embodiments, an expression vector that comprises an expression cassette that comprises the AT 10, AT7, AT15, or ATS gene further comprises a promoter operabiy linked to the ATI 0, AT7, AT15, or ATS gene. In other embodiments, a promoter and'or other regulatory elements that direct transcription of the AT 10, AT7, ATI 5, or ATS gene are endogenous to the plant and an expression cassette comprising the AT 10, AT7, ATI 5, or ATS gene is introduced, e.g., by homologous recombination, such that the heterologous AT 10, AT7, AT 15, or ATS gene is operabiy linked to an endogenous promoter and is expression driven by the endogenous promoter.

[0093] Regulatory sequences include promoters, which may be either constitutive or inducible, or tissue-specific.

[0094] In some embodiments, recombinant vectors may be prepared to disrupt gene expression, e.g., ATS gene expression. For example, such a recombinant vector may encode an RNA that disrupts expression of an endogenous gene. Such embodiments are described in greater detail in the section below relating to engineering of plants to decrease expression of an AT gene of interest.

Tissue-Specific Promoters [0095] In some embodiments, a plant promoter to direct expression of an AT gene, e.g.,

AT 10, AT7, AT 15, or ATS gene, in a specific tissue is employed (tissue-specific promoters). Tissue-specific promoters are transcriptional control elements that are only active in particular cells or tissues at specific times during plant development, such as in vegetative tissues or reproductive tissues, [0096] Examples of tissue-specific promoters under developmental control include promoters that initiate transcription only (or primarily only) in certain tissues, such as vegetative tissues, cell walls, including e.g., roots or leaves. A variety of promoters specifically active in vegetative tissues, such as leaves, stems, roots and tubers are known. For example, promoters controlling patatin, the major storage protein of the potato tuber, can be used (see, e.g., Kim, Plant Mol Biol. 26:603-615, 1994; Martin, Plant J. 1 1 :53-62, 1997). The ORF13 promoter from Agrobacierium rhizogenes thai exhibits high aetiviiv in roots can also be used (Hansen, Mol. Gen. Genet. 254:337-343, 1997). Other useful vegetative tissue- specific promoters include: the tarin promoter of the gene encoding a globulin from a major taro (Colocasia esculenta L. Schott) corm protein family, Sarin (Bezerra, Plant Mol. Biol. 28: 137- 144, 1995); the curculin promoter active during taro corm development (de Castro, Plant Cell 4: 1549- 1559, 1992.) and the promoter for the tobacco root-specific gene TobRB7, whose expression is localized to root meristem and immature central cylinder regions (Yamamoto, Plant Cell 3:371 -382, 1991).

[0097] Leaf-specific promoters, such as the ribulose biphosphate carboxylase (RBCS) promoters can be used. For example, the tomato RBCS 1, RBCS2 and RBCS3A genes are expressed in leaves and light-grown seedlings, only RBCS1 and RBCS2 are expressed in developing tomato fruits (Meier, FEBS Lett. 415:91 -95, 1997). A ribulose bisphosphate carboxylase promoters expressed almost exclusively in mesophyll cells in leaf blades and leaf sheaths at high le vels {e.g., Matsuoka, Plant J. 6:31 1-319, 1994), can be used. Another leaf- specific promoter is the light harvesting chlorophyll a/b binding protein gene promoter (see, e.g., Shiina, Plant Physiol 1 15:477-483, 1997; Casaf , Plant Physiol. 1 16: 1533- 1538, 1998). The Arabidopsis thaliana myb-related gene promoter (AtmybS) (Li, el at, FEBS Lett.

379: 1 17-121 1996), is leaf-specific. The AtmybS promoter is expressed in developing leaf tric omes, stipules, and epidermal cells on the margins of young rosette and cauline leaves, and in immature seeds. AtmybS mR A appears between fertilization and the 16 cell stage of embryo development and persists beyond the heart stage, A leaf promoter identified in maize {e.g., Busk et l, Plant J. 1 : 1285-1295, 1997) can also be used.

[0098] Another class of useful vegetative tissue-specific promoters are meristematic (root tip and shoot apex) promoters. For example, the "SHOOTMER1STEMLESS" and

"SCARECROW" promoters, which are active in the developing shoot or root apical meristems, {e.g., Di Laurenzio, et al, Cell 86:423-433, 1996; and, Long, et al., Nature

379:66-69, 1996); can be used. Another useful promoter is that which controls the expression of 3-hydroxy-3- methylglutaryl coenzyme A reductase HMG2 gene, whose expression is restricted to meristematic and floral (secretory zone of the stigma, mature pollen grains, gynoecium vascular tissue, and fertilized ovules) tissues (see, e.g. , Enjuto, Plant Cell. 7:517- 527, 1995). Also useful are kn I -related genes from maize and other species which show meristem-specitic expression, (see, e.g.. Granger, Plant Mol. Biol. 31 :373-378, 1996;

Kerstetter, Plant Cell 6: 1877- 1887, 1994; Hake, Philos. Trans. R. Soe. Lond. B. Biol. Sci. 350:45-51 , 1995). For example, the Arabidopsis thaliana KNAT1 promoter (see, e.g., Lincoln, Plant Cell 6: 1859-1 876, 1994) can be used.

[0099] In some embodiments, the promoter is substantially identical to the native promoter of a promoter that drives expression of a gene involved in secondary wall deposition.

Examples of such promoters are promoters from IRX1, IRX3, IRX5, IRX8, IRX9, IRX14, IRX7, IRX10, GAUT13, or GAUT14 genes. Specific expression in fiber cells can be accomplished by using a promoter such as the NSTl promoter and specific expression in vessels can be accomplished by using a promoter such as VND6 or VND7. (See, e.g., PCT/US2012/023182 for illustrative promoter sequences). [0100] One of skill will recognize that a tissue-specific promoter may drive expression of operabiy linked sequences in tissues other than the target tissue. Thus, as used herein a tissue-specific promoter is one that drives expression preferentially in the target tissue, but may also lead to some expression in other tissues as well.

Constitutive Promoters [0101] A promoter, or an active fragment thereof, can be employed which will direct expression of a nucleic acid encoding a fusion protein of the invention, in all or most transformed cells or tissues, e.g. as those of a regenerated plant. Such promoters are referred to herein as "constitutive" promoters and are active under most environmental conditions and states of development or cell differentiation. Examples of constitutive promoters include those from viruses which infect plants, such as the cauliflower mosaic virus (CaMV) 35S transcription initiation region (see, e.g., Dagless, Arch. Virol. 142: 183-191 , 1997); the Γ- or 2'- promoter derived from T-DNA of Agrobacterium tumefaciens (see, e.g., Mengiste supra ( 1997); O'Grady, Plant Mol. Biol. 29:99-108, 1995); the promoter of the tobacco mosaic virus; the promoter of Figwort mosaic virus (see, e.g. , Maiti, Transgenic Res. 6: 143-156, 1997); actin promoters, such as the Arabidopsis actin gene promoter (see, e.g., Huang, Plant Mol. Biol. 33: 125-139, 1997); alcohol dehydrogenase (Adh) gene promoters (see, e.g., Miliar, Plant Mol. Biol. 31 :897-904, 1996); ACT1 1 from Arabidopsis (Huang et ai, Plant Mol. Biol. 33: 125-139, 1996), Cat3 from Arabidopsis (GenBank No. U43147, Zhong el al, Mol Gen. Genet. 251 : 196-203, 1996), the gene encoding stearoyJ-acyi carrier protein desaturase from Brassica napus (Genbank No. X74782, Solocombe et al, Plant Physiol 104: 1167- 1 176, 1994), GPcl from maize (GenBank No. X15596, Martinez el al, J. Mol Biol 208:551-565, 1989), Gpc2 from maize (GenBank No. U45855, Manjunath et al, Plant Mol Biol, 33:97- 1 12, 1997), other transcription initiation regions from various plant genes known to those of skill. See also Holtorf, "Comparison of different constitutive and inducible promoters for the overexpression of transgenes in Arabidopsis thalkma," Plant Mol. Biol 29:637-646, 1995). inducible Promoters 10102] in some embodiments, a plant promoter may direct expression of the nucleic acids under the influence of changing environmental conditions or developmental conditions. Examples of environmental conditions that may effect transcription by inducible promoters include anaerobic conditions, elevated temperature, drought or other environmental stress, or the presence of light. Examples of developmental conditions that may effect transcription by inducible promoters include senescence and embryogenesis. Such promoters are referred to herein as "inducible" promoters. For example, the invention can incorporate drought-specific promoter such as the drought-inducible promoter of maize (Busk el al, Plant,!, 1 1 : 1285-95, 1997); or alternatively the cold, drought, and high salt inducible promoter from potato (Kirch Plant Mol. Biol 33:897-909, 1997). [0103] Suitable promoters responding to biotic or abiotic stress conditions include the pathogen inducible PRPl -gene promoter (Ward et al, Plant. Mol Biol 22:361 -366, 1993), the heat inducible hsp80-promoter from tomato (U.S. Pat. No. 5,187,267), cold inducible alpha-amyiase promoter from potato (PCT Publication No. WO 96/12814) or the wound - inducible pinll-promoter (European Patent No. 375091 ). For other examples of drought, cold, and salt-mducible promoters, such as the RD29A promoter, see, e.g., Yamaguchi- Shinozalei el al, Mol. Gen. Genet. 236:331-340, 1993 are also known.

[0104] Alternatively, plant promoters which are inducible upon exposure to plant hormones, such as auxins, may be used to express an AT 10, AT7, AT 15, or AT5 gene. For example, the invention can use the auxin-response elements E l promoter fragment (AuxREs) in the soybean (Glycine max L.) (Liu, Plant Physiol. 1 15:397-407, 1997); the auxin- responsive Arabidopsis GST6 promoter (also responsive to salicylic acid and hydrogen peroxide) (Chen, Plant J. 10: 955-966, 1996); the auxm-inducible parC promoter from tobacco (Sakai, 37:906-913, 1996); a plant biotin response element (Streit, Mol Plant Microbe interact, 10:933-937, 1997); and, the promoter responsive to the stress hormone abscisic acid (Sheen, Science 274: 1900- 1902, 1996).

10105] Plant promoters inducible upon exposure to chemicals reagents that may be applied to the plant, such as herbicides or antibiotics, are also useful for expressing an AT 10, AT7, AT 15, or AT5 gene in accordance with the iwention. For example, the maize In2-2 promoter, activated by benzenesulfonamide herbicide safeners, can be used (De Veyider, Plant Cell Physiol, 38:568-577, 19997); application of different herbicide safeners induces distinct gene expression patterns, including expression in the root, hydathodes, and the shoot apical meristem. An AT 10, AT7, AT 15, or ATS coding sequence can also be under the control of, e.g. , a tetracycline-inducible promoter, such as described with transgenic tobacco plants containing the Avena sativa L. (oat) arginine decarboxylase gene (Masgrau, Plant J. 1 1 :465-473, 1997); or, a salicylic acid-responsive element (Stange, Plant . J. 1 1 : 1315-1324, 1997; Uknes et al, Plant Cell 5: 159-169, 1993); Bi et al, Plant J. 8:235-245, 1995). [0106] Examples of useful inducible regulatory elements include copper-inducibie regulatory elements (Mett et al, Proc. Natl. Acad. Sci. USA 90:4567-4571, 1993); Furst et al, Cell 55:705-717, 1988); tetracycline and chlor-tetracycline-inducible regulatory elements (Gatz et al, Plant J. 2:397-404, 1992); Roder et al., Mol Gen. Genet. 243:32-38, 1994); Gate, Meth. Cell Biol. 50:41 1-424, 1995); ecdysone inducible regulatory elements

(Christopherson et al, Proc. Natl. Acad. Sci. USA 89:6314-6318, 1992; Kreutzweiser et al, Ecotoxicol Environ. Safety 28:14-24, 1994); heat shock inducible regulatory elements (Takahashi et al, Plant Physiol. 99:383-390, 1992; Yabe et al, Plant Cell Physiol. 35: 1207- 1219, 1994; Ueda et al, Mol Gen. Genet. 250:533-539, 1996); and lac operon elements, which are used in combination with a consiiiutively expressed lac repressor to confer, for example, IPTG-inducible expression (Wilde et al, EMBO J. 1 1 : 1251-1259, 1992). An inducible regulatory element useful in the transgenic plants of the invention also can be, for example, a nitrate-inducible promoter derived from the spinach nitrite reductase gene (Back et al, Plani Mol. Biol. 17:9 (1991)) or a light- inducible promoter, such as that associated with the small subunit of RuBP carboxylase or the Lt CP gene families (Feinbaum et al., Mol. Gen. Genet. 226:449 (1991 ); Lam and Chua, Science 248:471 (1990)). Expression using a positive feed hack loop

[0107] In further embodiments, a plant can be engineered to overexpress AT 10, AT7, AT 15, or ATS using a positive feedback loop to express AT 10, AT7, AT 15, or ATS in a desired tissue. In such an embodiment, a promoter for use in an AT 10, AT7, ATI 5, or ATS expression construct is responsive to a transcription factor that mediates expression in the desired tissue. The AT10, AT7, AT15, or ATS expression construct is used in a genentically modified plant comprising an expression construe! encoding a transcription factor hwere expression is also driven by a promoter that is responsive to the transcription factor.

Examples of such expression systems are provided in PCT/U S2012/023182.

[0108] In some embodiments in which a positive feed back loop is employed, the plant is genetically modified to express a transcription factor that regulates the production of secondary cell wail. Examples of such transcription factors include NST1 , ST2, NST3, SND2, 8ND3, MYB103, MBY85, MYB46, MYB83, MYB58, and MYB63 (See, e.g., Mitsuda et al. Plant Cell 17:2993-3006 (2005); Mitsuda et al. Plant Cell 19:270-80 (2007); Ohashi-Ito et al, Plant Cell 22:3461-73 (2010); Zhong et at, Plant Cell 20:2763-82 (2008); Zhong et al. Plant Cell 19:2776-92 (2007); KG et al, Plant J. 60:649-65 (2009); and McCarthy et al, Plant Cell Physiol. 50: 1950-64 (2009)).

[0109] Illustrative examples of gene and protein sequences and/or accession numbers for NST.1 , NST2, N8T3, S D2, SND3, MYB103, MBY85, MYB46, MYB83, MYB58, and MYB63 are provided in PCT/US2012/023182.

[0 10] In some embodiments, the polynucleotide encoding the transcription factor that regulates secondary cell wall production is operably linked to a promoter that is a downstream target of the transcription factor. Similarly, the AT 10, AT7, ATI 5, or AT5 nucleic acid sequence is also linked to a promoter that is a downstream target of the transcription factor. The promoter may be the same promoter or differnet promoters. In such an embodiment, a promoter is suitable for use with the transcription factor that regulates secondary cell wall production if expression of the promoter is induced, directly or indirectly, by the transcription factor to be expressed, and if the promoter is expressed in the desired location, e.g., the stem of the plant. [0111] In some embodiments, a native IRX1 , IRX3, IRX5, IRX8, IRX9, IRX14, IRX7, or IRX10, GAUT13, or GAUT14 promoter, or active variant thereof, is employed. Additional emhodimens for expressing AT 10, AT7, AT 15, or ATS

[0112] In another embodiment, the ATI 0, AT7, AT 15, or ATS polynucleotide is expressed through a transposable element. This allows for constitutive, yet periodic and infrequent expression of the constitutively active polypeptide. The invention also provides for use of tissue-specific promoters derived from viruses including, e.g., the tobamovirus suhgenomic promoter (Kumagai, Proc. Natl Acad. Sci. USA. 92: 1679-1683, 1995); the rice tungro baciiliform virus (RTBV), which replicates only in phloem cells in infected rice plants, with its promoter which drives strong phloem-specific reporter gene expression; the cassava vein mosaic virus (CVMV) promoter, with highest activity in vascular elements, in leaf mesophyll ceils, and in root tips (Verdaguer, Plant Mol. Biol. 31 : 1 129- 1 139, 1996).

[0113] A vector comprising an A ^' TIO, AT7, ATI 5, or ATS nucleic acid sequence will typically comprise a marker gene that confers a selectable phenotype on the cell to which it is introduced. Such markers are known. For example, the marker may encode antibiotic resistance, such as resistance to kanamycin, G418, bleomycin, hygromycin, and the like. [0114] AT 10, AT7, AT 15, or ATS nucleic acid sequences of the invention are expressed recombinantly in plant cells as described. As appreciated by one of skill in the art, expression constructs can be designed taking into account such properties as codon usage frequencies of the plant in which the AT nucleic acid is to be expressed. Codon usage frequencies can be tabulated using known methods (see, e.g., Nakaimtra et al. Nucl. Acids Res. 28:292, 2000). Codon usage frequency tables are available in the art (e.g., from the Codon Usage Database at the internet site www.kazusa.or.jp/codon/.)

[01 IS] Additional sequence modifications may be made that are also known to enhance gene expression in a plant. These include elimination of sequences encoding spurious polyadenylation signals, exon-intron splice site signals, transposon-like repeats, and other such well-characterized sequences ihai may be deleterious to gene expression. The G-C content of the sequence may be adjusted to levels average for a given cellular host as calculated by reference to known genes expressed in the host cell. When possible, the sequence may also be modified to avoid predicted hairpin secondary mR A structures.

Production of Transgenic Plants [0116] As detailed herein, the present invention provides for transgenic plants comprising recombinant expression cassettes either for expressing heterologous AT 10, AT ^' 7, AT15, or ATS for overexpressing endogenous AT 10, AT7, ATI 5, or ATS using recombinant technology. It should be recognized that the term "transgenic plants" as used here encompasses the plant or plant eel! in which the expression cassette is introduced as well as progeny of such plants or plant cells that contain the expression cassette, including the progeny that have the expression cassette stably integrated in a chromosome.

[0117] Once an expression cassette comprising a polynucleotide encoding an AT10, AT7, AT 15, or ATS polypeptide (or a polynucleotide sequence designed to suppress or inhibit expression of an AT gene, e.g., ATS, as described below) has been constructed, standard techniques may be used to introduce the polynucleotide into a plant in order to modify gene expression. See, e.g., protocols described in Ammirato et al. (1984) Handbook of Plant Cell Culture— Crop Species. Macmilian Publ. Co, Shimamoto et ai. (1989) Nature 338:274-276; Fromm et al. (1990) Bio/Technology 8:833-839; and Vasil et al. (1990) Bio/Technology 8:429-434.

[0118] ^' Transformation and regeneration of plants is known in the art, and the selection of the most appropriate transformation technique will be determined by the practitioner.

Suitable methods may include, but are not limited to: eiectroporation of plant protoplasts; iiposome-mediated transformation; polyethylene glycol (PEG) mediated transformation; transformation using viruses; micro-injection of plant cells; micro-projectile bombardment of plant cells; vacuum infiltration; and Agrobacterium iumeficiem mediated transformation. Transformation means introducing a nucleotide sequence in a plant in a manner to cause stable or transient expression of the sequence. Examples of these methods in various plants include: U.S. Pat. Nos. 5,571 ,706; 5,677,175; 5,510,471 ; 5,750,386; 5,597,945; 5,589,615;

5,750,871 ; 5,268,526; 5,780,708; 5,538,880; 5,773,269; 5,736,369 and 5,610,042.

[0119] Transformed plant cells derived by any of the above transformation techniques can be cultured to regenerate a whole plant that possesses the transformed genotype and thus the desired phenotype such as enhanced drought-resistance. Such regeneration techniques rely- on manipulation of certain phytobormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker which has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in E vans et al. Protoplasts Isolation and Culture, Handbook of Plant Cell Culture, pp. 124-176, MacMillilan Publishing Company, New York, 1983; and Binding, Regeneration of Plants, Plant Protoplasts, pp. 21-73, CRC Press, Boca Raton, 1985. Regeneration can also be obtained from plant callus, explants, organs, or parts thereof. Such regeneration techniques are described generally, e.g., in Klee et ah Ann. Rev. of Plant Phys. 38:467-486, 1987.

[0120] One of skill will recognize that after the expression cassette is stably incorporated in transgenic plants and confirmed to be operable, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed.

[0121] in some embodiments, the plant into which the expression construct comprising a nucleic acid sequence that encodes AT 10, AT7, ATI 5, or ATS (or that is designed to inhibit expresson of ATS) is introduced is the same species of plant from which the AT sequence, and/ or the promoter driving expression of the AT sequence, is obtained. In some embodiments, the plant into which the expression construct is introduced is a different species of plant compared to the species from which the AT and/or promoter sequence was obtained.

[0122] Plants that overexpress AT10, AT7, AT15, or ATS can be identified using any known assay, including analysis of R A, protein, or hydroxy cinnamic ester content. With respect to this aspect of the invention, the plants have altered hydroxycinnamic acid levels, e.g., decreased ferulic acid. Hydroxycinnamic ester levels can be determined directly or indirectly. An example of an assay measuring hydroxycinnamic ester levels in the cell wall is provided in the Examples section. For this assay, biomass, or a cell wall extraction thereof, is treated with 2M NaOH. The resulting supernatant, or an extract thereof, can be analyzed for changes in hydroxycinnamate content via high performance liquid chromatography with IJV absorbance detection or another similar method.

Modification of plants to decrease AT expression

[0123] in one aspect, the invention also provides a plant in which expression of an AT gene as described herein, e.g., an ATS gene is inhibited, thereby resulting in modified levels of hydroxycinnamic acid in the plant. As understood in the art, in some embodiments, it may be desirable to inhibit expression of AT10, AT7, or AT15 generally in a plant and restore expression in tissue of interests, e.g., grass cell wall. Technicques described in this section with reference to inhibition of ATS can also be used to inhibit AT 10, AT7, and/or ATI 5, if desired. [0124] In some embodiments, the plant is modified to have a level of ATS activity that is reduced throughout the entire plant. n some embodiments, the plant is modified to reduce ATS activity in a subset of cells or tissues of the plant. The genetic background of the plant can be modified according to any method known in the art, such as antisense, siRNA, microRNA, dsR A, sense suppression, mutagenesis, or use of a dominant negative inhibition strategy. In some embodiments, the level of expression of the protein is reduced.

Gene silencing techniques

[0125] In some embodiments, expression of a ATS is inhibited by an antisense

oligonucleotide. In antisense technology, a nucleic acid segment from the desired gene is cloned and operably linked to a promoter such that the antisense strand of RNA will be transcribed. The expression cassette is then transformed into plants and the antisense strand of RNA is produced. In plant cells, it has been suggested that antisense RNA inhibits gene expression by preventing the accumulation of mRNA which encodes the enzyme of interest, see, e.g., Sheehy et ai, Proc. Nat. Acad. Sci. USA, 85:8805-8809 (1988); Pnueli et ai, The Plant Cell 6: 175- 1 86 (1994); and Hiatt et al, U.S. Patent No. 4,801 ,340.

[0126] The antisense nucleic acid sequence transformed into plants will be substantially identical to at least a portion of the endogenous gene or genes to be repressed. The sequence, however, does not have to be perfectly identical to inhibit expression. Thus, an antisense or sense nucleic acid molecule encoding only a portion of an ATS-encoding sequence can be useful for producing a plant in which expression of AT5 is inhibited. For antisense suppression, the introduced sequence also need not be full length relative to either the primary transcription product or fully processed mRNA. Generally, higher homology can be used to compensate for the use of a shorter sequence. Furthermore, the introduced sequence need not have the same intron or exon pattern, and homology of on-coding segments may be equally effective. In some embodiments, a sequence of at least, e.g., 20, 25, 30, SO, 100, 200, or more continuous nucleotides (up to mRNA full length) substantially identical to a ATS mRNA, or a complement thereof, can be used.

[0127] Catalytic RNA molecules or ribozymes can also be used to inhibit expression of a gene encoding an AT5 polypeptide. It is possible to design ribozymes that specifically pair with virtually any target RNA and cleave the phosphodiester backbone at a specific location, thereby functionally inactivating the target RNA. In carrying out this cleavage, the ribozyme is not itself altered, and is thus capable of recycling and cleaving other molecules, making it a true enzyme. The inclusion of ribozyme sequences within antisense RNAs confers RNA- cleaving acti vity upon them, thereby increasing the activity of the constructs.

[0128] A number of classes of ribozymes have been identified. One class of ribozymes is derived from a number of small circular RNAs that are capable of self-cleavage and replication in plants. The RNAs replicate either alone (viroid RN As) or with a helper virus (satellite RNAs). Examples include RNAs from avocado sunblotch viroid and the satellite RNAs from tobacco ringspot virus, lucerne transient streak virus, velvet tobacco motile vims, solanum nodifloram mottle vims and subterranean clover mottle vims. The design and use of target RNA-specific ribozymes is described in Haseloff et al Nature, 334:585-591 (1988), [0129] Another method by which expression of a gene encoding an ATS polypeptide can be inhibited is by sense suppression (also known as co-suppression). Introduction of expression cassettes in which a nucleic acid is configured in the sense orientation with respect to the promoter has been shown to be an effective means by which to block the transcription of target genes. For an example of the use of this method to modulate expression of endogenous genes, see Napoli et al. The Plant Cell 2:279-289 (1990); Flavell, Proc. Natl Acad. Set, USA 91 :3490-3496 (1994); Kooter and MoL Current Opin. Biol 4: 166-171 (1993): and U.S. Patents Nos. 5,034,323, 5,231,020, and 5,283,184.

[0130] Generally, where inhibition of expression is desired, some transcription of the introduced sequence occurs. The effect may occur where the introduced sequence contains no coding sequence per se, but only intron or untranslated sequences homologous to sequences present in the primary transcript of the endogenous sequence. The introduced sequence generally will be substantially identical to the endogenous ATS sequence intended to be repressed. This minimal identity will typically be greater than about 65%, but a higher identity can exert a more effective repression of expression of the endogenous sequences. In some embodiments, sequences with substantially greater identity are used, e.g., at least about 80%, at least about 95%, or 100% identity are used. As with antisense regulation, further discussed below, the effect can be designed and tested to apply to any other proteins within a similar family of genes exhibiting homology or substantial homology.

[0131] For sense suppression, the introduced sequence in the expression cassette, needing less than absolute identity, also need not be full length, relative to either the primary transcription product or fully processed mRNA. Furthermore, the introduced sequence need not have the same intron or exon pattern, and identity of non-coding segments will be equally effective. In some embodiments, a sequence of the size ranges noted above for antisense regulation is used, i.e., 30-40, or at least about 20, 50, 100, 200, 500 or more nucleotides.

[0132] Endogenous gene expression may also be suppressed by means of RNA interference (RNAi) (and indeed co-suppression can be considered a type of RNAi), which uses a double- stranded RNA having a sequence identical or similar to the sequence of the target gene.

RNAi is the phenomenon in which when a double-stranded RNA having a sequence identical or similar to that of the target gene is introduced into a cell, ihe expressions of both the inserted exogenous gene and target endogenous gene are suppressed. The double-stranded RNA may be formed from two separate complementary RNAs or may be a single RNA with internally complementary sequences that form a double-stranded RNA. Although complete details of the mechanism of RNAi are still unknown, it is considered that the introduced double-stranded RNA is initially cleaved into small fragments, which then serve as indexes of the target gene in some manner, thereby degrading the target gene. RNAi is known to be also effective in plants (see, e.g., Chuang, C. F. & Meyerowitz, E. M., Proc. Natl. Acad. Sci. USA 97: 4985 (2000); Waterhouse et al, Proc. Natl. Acad. Sci. USA 95 : 13959- 13964 (1998);

Tabara et al. Science 282:430-431 (1998); Matthew, Comp Fund Genom 5: 240-244 (2004); Lu, et al. Nucleic Acids Res. 32(21):el71 (2004)).

[0133] Thus, in some embodiments, inhibition of a gene encoding an ATS polypeptide is accomplished using RNAi techniques. For example, to achieve suppression of the expression of a DN A encoding a protein using RNAi, a double-stranded RNA having the sequence of a DN A encoding the protein, or a substantially similar sequence thereof (including those engineered not to translate the protein) or fragment thereof, is introduced into a plant of interest. As used herein, RNAi and dsRNA both refer to gene-specific silencing that is induced by ihe introduction of a double-stranded RNA molecule, see e.g., U.S. Pat. Nos. 6,506,559 and 6,573,099, and includes reference to a molecule that has a region that is double-stranded, e.g., a short hairpin RNA molecule. The resulting plants may then be screened for a phenotype associated with the target protein, for example, screening for an increase in the extractabili y of sugar from the plants as compared to wild-type plants, and/or by monitoring steady-state RNA levels for transcripts encoding the protein. Although the genes used for RNAi need not be completely identical to the target gene, they may be at least 70%, 80%, 90%, 95% or more identical to the target gene sequence. See, e.g., U.S,. Patent Publication No. 2004/0029283. The constructs encoding an RNA molecule with a stem-loop structure that is unrelated to the target gene and that is positioned distally to a sequence specific for the gene of interest may also be used to inhibit target gene expression. See, e.g., U.S. Patent Publication No. 2003/0221211.

[0134] The RNAi polynucleotides may encompass the full-length target RNA or may correspond to a fragment of the target RNA. In some cases, the fragment will have fewer than 100, 200, 300, 400, 500 600, 700, 800, 900 or 1,000 nucleotides corresponding to the target sequence. In addition, in some embodiments, these fragments are at least, e.g., 50, 100, 150, 2.00, or more nucleotides in length. I some cases, fragments for use in RNAi will be at least substantially similar to regions of a target protein that do not occur in other proteins in the organism or may be selected to have as little similarity to other organism transcripts as possible, e.g., selected by comparison to sequences in analyzing publicly-available sequence databases.

[0135] Expression vectors that continually express siRNA in transiently- and stably- transfected have been engineered to express small hairpin RNAs, which get processed in vivo into siRNAs molecules capable of carrying out gene-specific silencing (Brummelkamp ei al,

Science 296:550-553 (2002), and Paddison, ei at. Genes & Dev. 16:948-958 (2002)). Post- transcriptional gene silencing by double-stranded RNA is discussed in further detail by Hammond et al. Nature Rev Gen 2: 1 10-119 (2001 ), Fire ei at Nature 391 : 806-81 1 (1998) and Timmons and Fire Nature 395: 854 (1998). [0136] Yet another way to suppress expression of an endogenous AT5 gene is by recombinant expression of a micro RNA that suppresses a target (e.g., a gene encoding a iignin or xylan biosynthesis enzyme). Artificial microRNAs are single-stranded RNAs (e.g., between 18-25-mers, generally 21-mers), that are not normally found in plants and that are processed from endogenous miRNA precursors. Their sequences are designed according to the determinants of plant miRNA target selection, such that the artificial microRNA specifically silences its intended target gene(s) and are generally described in Schwab et al, The Plant Cell 18: 1121 -1 133 (2006) as well as the internet-based methods of designing such microRNAs as described therein. See also, US Patent Publication No. 2008/0313773.

[0137] Another example of a method to reduce levels of ATS employs riboswitch techniques (see, e.g., U.S. Patent Application Publication Nos. US20100286082, and US201 10245326). [0138] In some embodiments, the level of expression of ATS is reduced by generating a plant that has a mutation in a gene encoding an AT5 enzyme. One method for abolishing or decreasing the expression of a gene encoding ATS is by insertion mutagenesis using the T- DNA of Agrobaclerium tumefaciens. After generating the insertion mutants, the mutants can be screened to identify those containing the insertion in the gene of interest. Mutants containing a single mutation event at the desired gene may be crossed to generate homozygous plants for the mutation (Koiicz et al. (1992) Methods in Arabidopsis Research. World Scientific).

[0139] Alternatively, random mutagenesis approaches may be used to generate new alleles that will generate truncated or defective (non- functional or poorly active) enzymes or unstable RNA, or to disrupt or "knock-out" the expression of a gene encoding an ATS enzyme using either chemical or msertional mutagenesis or irradiation.

Methods of Using Plants Having Modified ΑΤ1Θ, ΑΤΪ5, AT7 and/or ATS expression

[0140] The nucleic acid constructs of the invention can be used to modulate the hydroxycinnamic acid of cell walls of essentially any plant, but in particular grass plants. The plant may be a monocotyledonous plant or a dicotyledonous plant. In some

embodiments of the invention, the plant is a green field plant. Tn some embodiments, the plant is a gymnosperm or conifer. Thus, the invention has use over a broad range of plants, including species from the genera Asparagus, Atropa, Avena, Brassica, Cannabis, Citrus, Citrullus, Capsicum, Cucumis, Cucurbita, Daucus, Fragaria, Glycine, Gossypium,

Helianthus, Iieterocaliis, Hordeum, Hyoscvamus, Lactuca, Linum, Lolium, Lycopersicon, Malus, Manihot, Majorana, Medicago, Nicotiana, Oryza, Pameum, Panneserum, Persea, Pisum, Pyrus, Prunus, Raphanus, SecaJe, Senecio, Sinapis, Solatium, Sorghum, Trigonella, Triticum, Vitis, Vigna, and, Zea. Tn some embodiments, the plant is com, switchgrass, sorghum, miscanthus, sugarcane, poplar, pine, wheat, rice, soy, cotton, barley, turf grass, tobacco, potato, bamboo, rape, sugar beet, sunflower, willow, and eucalyptus. In further embodiments, the plant is reed canarygrass (Phalaris arundinacea), Miscanthus x giganteus, Miscanthus sp,, sericea lespedeza (Lespedeza cuneata), millet, ryegrass {Lolium multiflorum, Lolium sp.), timothy, Kochia (Kochia scoparia), forage soybeans, alfalfa, clover, sunn hemp, kenaf, bahiagrass, bermudagrass, daiiisgrass, pangolagrass, big bluest ein, indiangrass, fescue {Festuca sp.), Dactylis sp., Brachypodium distachyon, smooth bromegrass, orchardgrass, or Kentucky bluegrass among others. In some embodiments, the plant is an ornamental plant. In some embodiment, the plant is a vegetable- or fruit-producing plant. In some

embodiments, the plant is a plant that is suitable for generating bioraass, including plants as noted above, e.g., Arabidopsis, poplar, eucalyptus, rice, corn, switchgrass, sorghum, millet, miscanthus, sugarcane, pine, alfalfa, wheat, soy, barley, turfgrass, tobacco, hemp, bamboo, rape, sunflower, willow, Jatropha, and Brachypodium.

[0141] Plants, parts of plants, or plant biomass material from plants having modified AT 10, AT 15, AT7 and/or ATS expression can be used for a v ariety of purposes. In embodiments, the plants, parts of plants, or plant biomass material may be used in a conversion reaction to generate an increased amount of bioenergy as compared to wild-type plants. For example, the plants, parts of plants, or plant biomass material can be used in a saccharification reaction to generate an increased amount of soluble and fermentable sugar compared to wild-type plants. In some embodiments, the plants, parts of plants, or plant biomass material are used to increase biomass yield or simplify downstream processing for wood industries (such as paper, pulping, and construction) as compared to wild-type plants. In some embodiments, the plants, parts of plants, or plant biomass material are used to increase the quality of wood for construction purposes. In some embodiments the plants, or parts of plants are used to improve the quality of textile fiber or simplify the downstream processing for textile industry. In some embodiments the plants, or parts of plants, are used as a raw material for pectin production. [0142] Methods of conversion, for example biomass gasification, are known in the art. Briefly, in gasification plants or plant biomass material (e.g., leaves and stems) are ground into small particles and enter the gasifier along with a controlled amount of air or oxygen and steam. The heat and pressure of the reaction break apart the chemical bonds of the biomass, forming syngas, which is subsequently cleaned to remove impurities such as sulfur, mercury, particulates, and trace materials. Syngas can then be converted to products such as ethanol or other biofuels.

[0143] Methods of enzymatic saccharification are also known in the art. Briefly, plants or plant biomass material (e.g., leaves and stems) are optionally pre-treated with hot water, dilute acid, alkali, or ionic liquid followed by enzymatic saccharification using a mixture of ceiluiases and hemicellulases and peetinases in buffer and incubation of the plants or plant biomass material with the enzymatic mixture. Following incubation, the yield of the saccharification reaction can be readily determined by measuring the amount of reducing sugar released, using a standard method for sugar detection, e.g. the dimtrosalicyiic acid method well known to those skilled in the art. Plants engineered in accordance with the invention provide a higher sugar yield as compared to wild-type plants.

[0144] In some embodiments, grass plants having modified AT 10, AT 15, AT7, or ATS expression are used as forage plants for application in which an improvement in digestibility is desired.

EXAMPLES

[0145] The following examples are provided to illustrate, but not limit the claimed invention. Example 1. The "Mitchell Clade" of BAHD Acyltransferases is Expanded and Diverged in Grasses

[0146] Mitchell et al. (2007) identified what is referred to in this examples section as the "Mitchell clade" of BAHD acyl CoA acyltransferases on the basis of high gene expression in grasses relative to dicots. We systematically characterized the distribution of this clade in selected plant species and compared the clade with other characterized BAHD proteins. We identified BAHD proteins from a diverse set of sequenced plants and analyzed the phylogenetic relationships among them and a reference set of BAHDs (Table I). To gain higher sensitivity relative to local sequence alignment (i.e., BLAST) for recognizing sequences with low, but potentially still significant, homology, we used a hidden Markov model to identify putative BAHD proteins (Finn et al, 201 1). We then inferred an initial model of the phylogenetic relationships among the putative BAHD proteins from each genome and the set of biochemically characterized BAHD proteins cataloged by D'Auria (2006) with a. neighbor-joining algorithm (Tamura et al., 201 1). Active BAHD proteins can be identified by a HXXXD motif. A variation of this motif can also be present in an active protein in which the histidine is replaced by a serine (see, e.g., one of the known

biochemically active proteins for the family, BAFT (NCBI ID: AAL92459) involved in taxol biosynthesis (Walker et al., 2002).

[0147] As observed by Tuominen et al., the distribution of BAHD proteins varies among species (Table I, Supplemental Figure 1, and LEB and PC, in prep). The "Mitchell clade" is embedded within Clade V, or Clade Va of Tuominen et al. The analysis revealed that the

"Mitchell clade" includes a biochemically characterized banana alcohol CoA acyltransferase, BarsAAT (Beekwilder et al., 2004), and is also related to a group of BAUD proteins that participate in taxol biosynthesis (Figure 1 and Supplemental Figure 1).

[0148] Using Bayesian analysis, we found that multiple proteins with similarity to the "Mitchell clade" are present in the gra ss genomes that were available at the time of the analysis, Sorghum hicolor and Brachypodium dystachion (Tabie T, Supplemental Fig. 1), In contrast, the annotated genomes of Arabidopsis lhaliana, Glycine max, and Medicago Iruncatida encode only single members of this clade. The other recently characterized cutin- and suberin-feruloyl transferases (Molina et al,, 2009; Rautengarten et al., 2012), though part of clade V, are not part of the "Mitchell clade". The clade is entirely absent from the annotated proteins of Populus trichocarpa and the primitive plants, Selaginella and

Physcomietrella. Thus, the "Mitchell clade" appears to be conserved and expanded in grasses and banana relative to dicotyledonous species and more primitive plants. This is consistent with this clade functioning in aspects of Commelinoid metabolism that diverge from metabolism of dicot and more basal plants, such as synthesis of type II ceil walls. [0149] The analysis described above also revealed that the "Mitchell clade" of BAHD acvhransferases was missing several members. Instead of possessing 12 members in rice (Mitchell et al,, 2007; Piston et al,, 2010), the group consists of 20 closely related members that are further subdivided into two subclades (1 and ii. Figure 1). In rice, the 10 genes in subclade i are all supported by Sanger-based expressed sequence tag (EST)-evidence;

whereas, only 3 of the 10 members of subclade ii w ere identified via traditional EST sequencing (Figure 1). In addition, the multi-species tree reveals that most proteins of subclade i are represented in all three grass species examined and are more similar to the non- grass proteins (Supplemental Fig 1). In contrast, subclade ii contains more species-specific expansions and/or contractions, consistent with the possibility that some of the members are pseudogen.es. To facilitate communication about the putative "Mitchell clade"

acyltransferases, we have given the clade members of rice preliminary names with the format Oryza sativa acyltransferase, OsATl through OsAT20. As mentioned above, OsAT4 was recently named PMT and found to be capable of esterifying monolignols (Withers et al,, 2012). Screen of Mutants for Altered Cell Wall Hydroxycinnamic Acid Content

[0150] We screened indexed rice mutants related to Mitchell clade" of BAHD CoA acyltransferases for altered cell wall content, Tabie II describes the mutant lines that we characterized. We screened progeny of each of these lines for the presence of the insertion, did not detect an insert in four lines, and for two lines, did not identify any progeny that were homozygous for the insert (Table 11).

[0151] For the remaining 1 1 lines, we characterized the alkali-labile hydroxycinnamoyl ester content of cell wall alcohol insoluble residue (AIR) from leaves and leaf sheaths. We compared side tillers of homozygous, mutant and negative segregant, wild-type plants seven to ten weeks after planting. From this, we found four possible cell wall hydroxycrnnamic acid phenotypes (T able II, Figure 2). Three of the preliminary phenotypes were in putative mutants of subclade i proteins, and one was a mutant in a subclade ii protein. Homozygous mutant progeny of 2A-20021 , predicted to increase expression of OsAtS, exhibited reduced p-CA in leaf sheaths relative to negative segregant wild-type progeny (-50% less).

Homozygous mutant progeny of 2A -40095, possessing the transcriptional activator sequences but inserted toward the end of the coding sequence for OsAt7, exhibited reduced FA in leaf sheaths (-60% less). Homozygous mutant progeny of 4A-03423 (OsATlO-Dl), however, which were predicted to increase expression of OsAtlO, exhibited reduced FA (-60% less) and increased p-CA (-300% more) in sheaths and leaves. Homozygous mutant progeny of 1B-00523, which were predicted to increase expression of OsATI S, a subclade it member, exhibited reduced FA in leaves relative to negative segregant, wild-type progeny (-60% less). In contrast, the other lines showed no change in FA or p-C A in the developmental stages and tissues examined. For example, our experiment included line 5A-00394, which is predicted to have activated expression of a putative rice exostosi (GT47) gene, LOC Osl Og 10080. This line showed no alteration in cell wall hydroxycinnamic acids in leaf blades or sheaths (Figure 2).

Gene expression and developmental phenotypes of OsATlO-Dl [0152] The T-DNA insertion site for line 4A-03423, hereafter referred to as OsATlO-Dl , is approximately 8.5 kb downstream of the transcriptional start site for OsAtlO (Figure 3A). The insert is oriented so that the activating sequences are proximate to OsAtlO and thus is in range observed to activate expression (Jeong et al., 2006). RT-qPCR indicated that the expression of OsA lO was indeed increased by > 100-fold in the leaves of homozygous OsATlO-Dl plants (Figure 3B). In OsATlO-Dl, the expression genes other than OsAtlO that were proximate to the site of the T-DNA insertion did not vary significantly relative to the wild type (Figure 3B). The expression of related OsAt genes did not vary significantly in OsATl O-Dl (Supplemental Figure 2), reducing the possibility that the observed phenotype is due to compensation at the level of gene expression of a related acyltransferase. OsATlO-Dl lines exhibited no change in size and dry mass at maturity (Figure 4A & 4B). However, a -20 to 30% decrease in total seed mass per plant for the mutant compared to the wild type (Figure 4C) was observed.

Cell walls of OsAilO over expression lines are heritable altered in ester-linked

hydroxycinnamic acids

[0153] For OsATlO-Dl , we confirmed the inheritance of the altered cell wall

hydroxycmnamate phenotype in young leaves and mature tillers of plants from two subsequent generations (Figure 5 and Supplemental Figure 3). This line has a ~50% decrease in ester-linked FA in young leaf tissue (Figure 5A). The same tissue shows an -300% increase in ester-linked p-CA (Figure 5B). The change in both components is most clearly exhibited as a change in the ratio of FA to p-CA (Figure 5C). The ratio is the most reliable as it is independent of potential variation in the absolute amounts due to variation in sample mass and extraction efficiency. We were also able to quantify the four most abundant ferulate dimers. ough signals were low for some dimer species, most showed decreases compared to wild-type amounts (Figure 5D). We found that the dimers decreased proportionally to the decrease in FA in the young leaf tissues (Figure 5D). This can be most clearly seen as the similar ratio of FA compared to the sum of the dimer species (Figure 5D). In addition, we found similar trends but less extreme changes in pools of total aerial tissues harvested after senescence for the same plants from each genotype (Figure 5). These mature straw samples possessed a -40% less FA and -80% more p-CA, Measurements were independent of whether total, AIR or destarched AIR preps were used, but these different samples do show the technical replicate- ability of the analysis. [0154] To gather further evidence that the phenotype in the activation tagged line was due to over expression of Os AT 10, we generated two additional OsAtlO over expression lines utilizing the maize ubiquitinl promoter (Figure 6). Contrary to our typical experience for high efficiency transformation with the japo ica cultivar, Kitaake (Jung et al, 2008), we were only able to regenerate two independent transformants that possessed the transgene from tissue culture (Figure 6A). This result suggest that the OsAtlO construct interferes with transformation efficiency. Both of the confirmed transgenic lines did show increased expression of OsAtlO compared to the non-transgenic plants (Figure 6A). Furthermore, AIR from young leaf tissue of the primary transgenics also exhibited a qualitatively similar change in bydroxycinnamic acids compared with the QsATI O-Dl line (Figure 6B). In particular, the ratio of FA:p-CA was dramatically decreased in both lines, though the absolute amounts of FA and p-CA varied relative to the non-transgenics. Specifically , Ubi::OsAtlO-4 has a sharp decrease in FA, with a relatively smaller increase in p-CA and Ubi::OsAtlO-5 showed no change in FA, but a dramatic increase in p-CA. (Figure 6B). As with the other over expression lines, the FA:diferulate ratios do not vary from those observed for the non- transgenics (Figure 6C).

The Difference in OsATI0-Dl Hydroxycinnamates is Predominantly TFA-Soluhle and is Linked to a 5-Carbon Sugar

[0155] in grasses, hydroxycinnamoyl esters have been found to be attached to matrix polysaccharides, glucuranoarabirioxyian or xyloglucan, or to lignin. We examined which cell wall fraction harbored the alteration in FA and p-CA in the OsATlO-Dl mutant. To accomplish this, we subjected AIR from mutant and wild-type mature rice straw with a relatively mild, 50 mM trifluoroacetate (TFA) treatment to release the matrix

polysaccharides. At multiple time points, we removed a fraction of the supernatant. We then saponified both the supernatants and pellet with the typical 2 N NaOH treatment followed by HPLC analysis of the products. The results demonstrat.de that the alteration in FA and p-CA amounts in OsATlO-DI is primarily in the matrix polysaccharide fraction of the cell wall (Figure 7). For both the wild type and QsATIO-Dl, the FA is predominantly associated with the TFA fraction, with less than 20% of the FA remaining in the pellet after TFA treatment for both genotypes (Figure 7A). The reverse is observed for the p-CA for the wild type, in which -70% of the p-CA remains in the pellet (Figure 7B). However, for the mutant only 55% of the p-CA is in the pellet after TFA treatment, though the absolute amouni of p-CA in the TFA pellet are very similar for the wild type and mutant (Figure 7B). Thus, we conclude the additional p-CA in the cell w ^r alf of the OsATlO-DI is in the TFA-sofuhle matrix polysaccharide fraction. This can be clearly seen in the FA:p-CA ratio plot, in which the ratio of FA:p-CA is most drastically changed in the supernatants after TFA treatment;

whereas, the FA:p-CA ratio is the same within error for the mutant and wild type in the residue remaining after TFA treatment (i.e., pellet, Figure 7C). These data suggest that in mature rice straw, the change in p-CA in the matrix polysaccharide fraction approaches a -300% increase of OsATl 0-Dl over the wild type, rather than the smaller ~70% increase when total ester- linked p-CA is considered. Consistent with the typical location of p-CA on lignin, this magnitude of increase in the mutant compared to the wild type is more similar to that seen in young leaf tissue, which in the wild type possess a relatively lower percentage of p-CA compared to FA (Figure 5). 15 ] Further analysis of the TFA soluble fractions supports the assertion that the glucuranoarabinox lan is modified by OsAtlO activation. First, the sugars released by TFA treatment in this experiment predominantly consist of xylose, consistent with the model that OsATlO functions in arabmoxylan modification (Supplemental Figure 4). n contrast, the pellet contains less than 20% of the total amount of xylose. Furthermore, via LC-MS, we detected two major new ion peaks in the TFA-soiubilized ethylacetate extract compared to extract that had been treated with NaOH or with hydroxycinnamate standards (Figure 8A). The mass spectra of these peaks are consistent with the major unknown peak in the mutant (unknown peak 1) consisting of p-CA esterified to a five-carbon sugar (m/z = 295.0285, Figure 8B); whereas, the predominant peak in the wild type (unknown peak two) is consists of FA esterifsed to a five carbon sugar (m/z = 325.083, Figure 8C). Because arabinose and xylose have the same molecular weight they are indistinguishable in this experiment;

however, our strong expectation from nuclear magnetic resonance ( MR) data from the literature is that the esterified sugar is arabinose (Buanafina, 2009; Ralph, 2010), Relative quantification of the ion counts of each of these peaks in the mutant vs. the wild type is consistent with the results measured via HPLC. That is, compared with the wild type, OsATl ⁽ )-Dl has ~4.6-fold more pCA-sugar and 2.5-fold less FA-sugar (Figure 8A). The relative amounts of FA and p-CA after saponification are also consistent with our pre vious results (Figure 8A).

The OsATlO-Dl line has an increase in cell wall glucose content [0157] Compensatory changes are often seen among the components of the cell wall

(Humphrey et ai, 2007). Quantification of sugars released by acid treatment of total, AIR, and destarched (ds) AIR preparations suggests that the glucose content is increased by -20% (weight/weight) in AIR and dsAIR for the mutant relative to the wild type (Figure 9A). We observed the difference both with TFA treatment, which liberates matrix polysaccharides and amorphous celiulose, and when the TFA residue is further treated with sulfuric acid, which liberates cellulose (Figure 9A). That the difference persists after destarching is consistent with a change in the cell wall content, not starch. By mass, we did not observe any other significant changes in sugar amounts in the mutant compared to the wild type (Supplemental Figure 5), Expressing sugar data as percent of molecules (mol%) is more precise because it excludes weighing and other experimental errors. When the TFA-solubiiized sugars are expressed in terms of moi%, the data also indicate an increase in glucose content, on the order of 10 to 20% (Figure 9B), Xylose, arabinose, and the sum of minor cell wall sugars decrease proportionally to the glucose increase (10-20%), suggesting that the change in cell wall polysaccharide content in the mutant is isolated to the glucose-containing polymers.

The OsATlO-Dl shows no alierations in lignin content or composition

[0158] To further explore the extent of cell wall changes in the mutants relative to the wild type, we also measured lignin content and composition. We hypothesized that the possible alteration in pools of hydroxycinnamyl-CoA adducts in the OsATlO-Dl line might lead to alterations in lignin amount or content, in terms of syringyl (S), guiacyl (G), and coumaryl (H) subunits. Due to the presence of H residues in grass lignin, ail methods of lignin analy sis are not equally accurate for grasses relative to dicots. For our analysis, we used two methods suitable for grasses - acetyibromide solubilization (Grabber et al,, 1996; Fukushima and Hatfield, 2004) and pyrolysis-molecular beam mass spectrometry (py-MBMS) (Evans and Milne, 1987; Agblevor et al, 1994). "Lignin" analy ses of whole tissue or AIR typically include all classes of phenylpropanoids, both esterified and non-esterified, though some esterified hydroxycinnamates are associated soley with arabinoxylan. Since our previous analysis had determined that there is a difference in OsATlO-Dl in ester-linked phenolics, we quantified lignin content and composition with and without removing esterified

hydroxycinnimates via saponification.

[0159] OsATlO-Dl mature aerial tissue, and separate, young leaf and sheath samples show no significant difference in mass percent acetyibromide soluble lignin after saponification relative to the wild type. We obtained a similar result via py-MBMS, which also revealed no difference in the S:G lignin ratio in the mutant compared to the wild type after saponification. For OsATlO-Dl, we also collected py-MBMS data for unprocessed straw and AIR. When analyzed together via principle component analysis (PCA), the first component clearly separates the saponified and unsaponified samples and explains 85% of the variation between the samples (not shown). Separate analysis of the saponified and unsaponified samples reveals distinctions between the wild type and mutant in the unsaponified samples (Figure 10A). Principle component 1 (PCI) explains the alcohol extraction (30% of the variation) and principle component 2 (PC2) explains differences between the wild-type and mutant samples (19% of the variation). The loadings for PC2 show that the major ions that distinguish the wild-type and mutant samples are phenofics (Figure 10B). Thus, the MS fragmentation pattern is consistent with an interpretation in which there is an increase of p- CA, as reflected by peaks 120, 94, and 91, and a decrease in ferulic acid, as reflected in the drop in the coniferyl ion, peak 150 (Evans and Milne, 1987), Note that the "tails" of phenyfpropanoid molecules are typically absent in these spectra due to MS fragmentation. The observed differences in phenylpropanoids between OsATl()-Dl and the wild type are iikeiy associated with ester-linked hydroxycinna mates and not lignin, because PCA no longer distinguishes the samples after saponification (Figure 10C).

[016(5] A limitation of the pyrolysis method for determining lignin composition is that it inaccurately measures H-lignin, which volatilizes poorly and instead turns to char upon heating. Because of the increase in p-CA, a precursor of H-lignin, in OsATlG-Dl cell walls relative to the wild type, we sought to determine whether there is an increase in the char content of OsATl O-Dl using a thennogravimetric (TO) pyrolysis instrument, Duplicate runs per genotype of the TG did not detect a difference in the mass remaining from mature straw after pyrolysis (Supplemental Figure 7), again consistent with there being no difference in core lignin composition or content between OsATlO-Dl and the wild type.

The OsATIO-Dl line shows an increase in saccharijication [0161] Several researchers have observed a correlation between ferulate esters in grass biomass and digestibility among diverse canarygrass and lolium accessions (Lam et al., 2003; Casier and Jung, 2006). The phenotype of the OsAi lQ-Dl line provided the opportunity to determine whether there is also an increase in enzymatic digestibility with reduced FA content when comparing two near-isogenic plant fines, with little to no variation besides the difference in ceil wall hydroxycinnamic acid content. We found that destarched AIR after mild pre-treatment followed by incubation with a cellulase cocktail and β-glucosidase resulted in the release of approximately 20% more reducing sugar from the mutant compared with the wild type at all time points examined (Figure 1 1 A). We note that this might be explained solely by the increase in glucose content, which is quantitatively similarity . [01 2] We also determinee if the improvement in digestibility impacted a biological saccharification agent. For this, we exposed acid-explosion pretreated, coarsely chopped rice straw from the wild type and OsATlO-Dl to the mesophiiic fungus, Penicillium sp. YT02. This recently characterized fungus shows significantly higher xylanase and β-glucosidase with various insoluble lignocellulosic substrates in comparison with the commonly used fungal strain, Trichoderma reesei (ATCC 24449) (Kovacs et al, 2009), and may be a promising strain for industrial bioprocessing of cellulosic plant biomass (L. Gao and J. Zhou, in prep). Qualitatively consistent with the enzymatic deconstruetion results, YT02 incubation released more glucose, xylose, and arabmose into the medium from acid explosion pretreated OsATl O-D 1 straw than from wild-type straw (Figure 1 1 B). A veraged over the entire time course ( 12 to 120 hours), the improvement in y ield is more dramatic with the fungus than with enzymes alone, with the fungus releasing 46% more glucose, 82% more xylose, and 25% more arabinose for a total sugar yield increase of -40%. In the fungal treatments, the hiomass-derived sugars initially accumulate, due to the action of enzymes excreted by the fungus. At later time points (>72 hrs,), the fungus metabolizes the sugars, incorporating them into fungal biomass. Ceiluiase and β-giucosidase enzymatic activity in the slurry is unchanged on the mutant straw (Figure 1 1 C and Supplemental Figure 8), suggesting that the fungus grew similarly on both. In contrast and of relevance to the nature of the change caused by the increased expression of OsATK), xylanase activity is dramatically enhanced, especially at later time points (Figure 1 1 C).

OsATS

[01 3] Figure 19 provides shows the genomic positions and gene expression data of the OsAT5-Dl activation tagged line. Genomic positions and gene expression data for the

OsAT5-Dl activation tagged line (A) Representation of the portion of the rice chromosome near the T-DNA insertion site. Exons are represented by wide bars with the direction of transcription indicated by arrows. The insertion site is represented by the triangle, with the left border, nearest the iranscriptional enhancer elements, represented by 'L'. cDNA Regions targeted for amplification in qPCR are depicted as black bands. RT stands for retrotransposon and hypoth indicates hypothetical. (B) Average normalized gene expression determined via qPCR shows that among genes within 20 kbp of the insertion site only acyltransferase expression is altered significantly in young leaves of homozygous plants with the T-DNA insertion (hashed) compared with negative segregants (solid). Error bars represent the standard deviation of 3-4 biological replicates. Genes with significantly higher expression (p<G.01, Student's t-test) are marked with an asterisk. [0164] Figure 20 provides data demonstrating that OsATS-Dl shows alterations in cell wall hydroxycinnamic acids. Data are for two separately grown batches (#1 and #2) of plants of a near isogenic family lacking the insert (grey bars, progeny of the near isogenic wild type line 2A-20021.10.2) and a family homozygous for the insert (cross-hatched bars, progeny of the OsAT5-D l mutant line 2A-20021.1 1.7), Samples for batch #1 were harvested from seedlings 35 days post germination. The expanding leaf samples for batch #2 were harvested at 8 weeks post germination and the mature tiller at 16 weeks post germination. Values are the average of 5 to 12 individual plants. Error bars mark the 95% confidence interval for the mean. * indicates significance via Student's t-test at p < 0.05 and ** indicates significance at p < 0.01 , (A.) Ferulic acid content in an alcohol insoluble residue (AIR) preparation. (B) p-Coumaric acid content from AIR. (C) The ratio of ferulic acid (FA) to p-coumaric acid (CA), which is not subject to weighing or extraction efficiency errors. (D) Major FA dimer species and the ratio of FA to dimer for the Batch #1 expanded leaf samples.

[§165] Figure 19. Genomic positions and gene expression data of the OsATS-Dl activation tagged line. Genomic positions and gene expression data for the OsAT5-Dl activation tagged line (A) Representation of the portion of the rice chromosome near the T-DNA insertion site. Exons are represented by wide bars with the direction of transcription indicated by arrows. The insertion site is represented by the triangle, with the left border, nearest the transcriptional enhancer elements, represented by 'L'. cDNA Regions targeted for amplification in qPCR are depicted as black bands, RT stands for retrotransposon and hypoth indicates hypothetical. (B) Average normalized gene expression determined via qPCR shows that among genes within 20 kbp of the insertion site only acyliransferase expression is altered significantly in young leaves of homozygous plants with the T-DNA insertion (hashed) compared with negative segregants (solid). Error bars represent the standard deviation of 3-4 biological replicates. Genes with significantly higher expression (p<0.01. Student's t-test) are marked with an asterisk,

[0166] Figure 20. OsAT5-Dl shows alterations in cell wail hydroxycinnamic acids. Data are for two separately grown batches (#1 and #2.) of plants of a near isogenic family lacking the insert (grey bars, progeny of the near isogenic wild type line 2A-20021.10.2) and a family homozygous for the insert (cross-hatched bars, progeny of the OsAT5-Dl mutant line 2A- 20021.1 1,7). Samples for batch #1 were harvested from seedlings 35 days post germination. The expanding leaf samples for batch #2 were harvested at 8 weeks post germination and the mature tiller at 16 weeks post germination. Values are the average of 5 to 12 individual plants. Error bars mark the 95% confidence interval for the mean. * indicates significance via Student's t-test at p < 0.05 and ** indicates significance at p < 0.01. (A) Ferulic acid content in an alcohol insoluble residue (AIR) preparation. (B) p-Coumaric acid content from AIR. (C) The ratio of ferulic acid (FA) to p-couniaric acid (CA), which is not subject to weighing or extraction efficiency errors. (D) Major FA dimer species and the ratio of FA to dimer for the Batch #1 expanded leaf samples.

Discussion

[0167] Hydroxycinnamyl esters in cell walls influence basic and applied plant traits including growth properties, disease resistance, and food and feed quality (Santiago et al,, 2007; Buanafma, 2009). The molecular mechanism of incorporation of hydroxycinnamates into cell walls remains largely obscure. Here, we present results showing that over expression of GsAtlO in the OsATlO-Dl line decreases FA and increases p-CA in leaf blades, leaf sheaths, and mature straw (Figure 5). We have also confirmed that over expression of OsAtlO in two other independent lines, Ubi::OsAtlO-4 and Ubi::QsAtl O-5, alters the ratio of FA to p-CA in a manner similar to OsATlO-Dl, namely by causing a dramatic decrease in the FA:p-CA ratio relative to wild -type genotypes (Figure 6).

Distribution ofBAHD CoA Acyltransferases across Plants

[0168] Our phyiogenetie analysis shows that, with one exception, sequenced angiosperms that we examined have annotated proteins within the "Mitchell clade" of BAHD acyl CoA- utiiizing acyltransierase proteins, identified by being highly expressed in grasses (Mitchell et al., 2007). However, there has been a distinct expansion of this clade in grasses, with 12.-20 members in grasses compared to 0-2 in other species (Table I). The presence and expression of a protein in the Mitchell clade in banana (order Zingerberales, BanAAT (Beekwilder et al, 2004)), is consistent with the presence of hydroxycinnamates in banana ceil walls (Carpita, 1996).

[0169] A mutant in the most closely related Arabidopsis protein, AT3G62160, was recently examined for a change in hydroxycinnamates in the cell wall and other extracellular polymers, though no differences were identified (Rautengarten et al., 2012). Though the function of the Arabidopsis protein remains to be determined, that result is consistent with a model of neofunctionalization or subneofunctionalization of the "Mitchell clade" ofBAHD acyltransferases in Commelinoid monocots (He and Zhang, 2005). In this model, a duplicated "Mitchell clade" member in the progenitor of Commelinoids acquired the ability to modify a cell wall-related substrate. Subsequently, the conservation of additional clade members that we observe is consistent with selection for further additional gene duplication events.

The Cell Wall Target of Os AT 10 is Arabinoxylan

[0170] Previous results have found that p-coumaroyl esters are almost exclusively bonded to lignin; whereas, FA is predominantly esterfied to glucuranoarabinoxylan. However, enzymatic release experiments have provided some prior evidence that p-CA is also incorporated into the polysaccharides of grass cell walls (Mueller-Harvey et al., 1986; Ishii et al., 1990; Faulds et al, 2004). We find that mature rice straw has -20% of p-CA associated with matrix polysaccharide (Figure 7). This may also be the location of the p-CA in the young leaf tissue, which we expect to have very low lignin amounts (Figure 6). We found that the hydroxycinnamic acid changes in OsATl O-D l are predominantly on the TFA-soluble matrix polysaccharide fraction, not the acid-resistant lignin (Figure 7). Indeed, we were able to confirm that the hydroxycinnamoyl groups in the TFA-released fraction are ester-linlied to a 5-carbon sugar. Since this sugar-hydroxycinnamoyi species migrate in narrow bands in the LC-MS analysis, we strongly suspect that these represent only arabinose esters, which have been commonly described (Mueller-Harvey et al., 1986; Buanafma, 2009). Thus, it is unlikely ihai this peak also consists of feruloylaied-x lose, which has been described from bamboo xyloglucan (Ishii et al., 1990). Furthermore, we have no evidence to suggest that OsATIO functions as a p-coumaroyl Co A monolignol acyltransferase that has been described in recent publications (Hatfield et al., 2009; Withers et al., 2012). Rather, it seems likely that the native function of OsATIO is to incorporate p-CA into cell wail 5 -carbon sugars, likely the arabinose of arabinoxylan. This is consistent with the notion that different '"Mitchell clade" members may have different functions.

[0171] We observed that OsATlO-Dl had an ~30G-fold increase in gene expression, but only a 3-fold increase in p-CA. While this could be caused by the cell wall phenotype being an indirect result of increased OsAtlO expression, this trivial explanation is unlikely based on previous results. The observations that silencing "Mitchell clade" members decreases rice cell wall hydroxycmnamate content (Piston et al., 2010) and that biochemical analysis of one of them, PMT (OsAT4), demonstrates function on a cell wall substrate makes the trivial explanation unlikely. Instead, the difference suggests that other parts of the cell wall hemicellulose-incorporation pathway are limiting in the presence of the excess amount of acyltransferase. Indeed, dramatic changes in, for example, the monolignol biosynthesis enzymes, 4-CGumaryl CoA ligase of Arabidopsis, cause comparatively small changes in enzyme activity and iignin composition (Lee et al, 1997). Assuming that the altered polysaccharide is arabmoxyian, one possibility is that the frequency of hydroxycinnamoyl- arabinose incorporation is controlled by the glycosyltransferases that synthesize

arabinoxylan. Another observation that remains to be completely resolved is the decrease in sugar-feruloylation that accompanies the increase in p-coumarylation in cell wails of mutant plants. Some specificity in the level of modification of arabinose may explain this observation. Alternatively or in addition, since p-CA is a precursor of FA, the increased activity of the putative p-CA transferase, OsATIO, may reduce the amount of feruloyi-CoA available for modification of the bemicellulose. Further experiments will be needed to test these models. "Mitchell Clade " Acyltransferase Have Different Effects on Cell Wall Hydroxycinnamoyl Esters

[0172] Both our data and that of Piston et al. (2010) pro vide genetic evidence that changing the expression of "'Mite hell clade" CoA acyltransferases alters the amounts of cell wall hydroxycinnamyi esters. Superficially, our result that OsATIO over expression decreases cell wall feruiate appears to conflict with that of Piston et ai. (2010), who reported that simultaneous reduced expression of OsAT6 through OsATl 0 (i.e., construct pAFT-B) causes a -20% reduction in the amount of FA in mature leaves. One possibility is that in OsATIO- Dl a change in expression of other related acyltransferases causes the observed phenorype. However, our results showing that there is no measurable change in selected related acyltransferases in the over expression lines (Supp Fig 2), make this model less likely.

[0173] Instead, the various results with "Mitchell clade" members is consistent with the model that differing OsATs have different functions. First, this model explains the apparent conflict between Piston et al.'s results and ours. If all of the OsATs function to incorporate FA into arabinoxylan, it seems likely that the effect of reducing expression 2- to 5-fold for four to five OsAT members would give greater than the observed 20% reduction in FA. Further, Piston et al. detected no effect on wall hydroxycinnamates in lines with

simultaneously reduced expression of QsAtl, OsAt2, OsAtl I, and OsAtl2 (i.e., construct pAFT-A). Thus, we suspect that Piston et al. observed small or no effects because their constructs caused multiple small effects. Indeed, while several studies have found that BAHD acyltransferases often have promiscuous specificities (D'Auria, 2006), work with anthocyanidin-malonyl transferases (DmSMATi), have measured discrimination for a hydroxyiated substrate over a maloynaited one (Unno et al., 2007). Thus, it is not improbable to hypothesize that different acyltransferases may have differential affinities for the two hydroxyci namyl CoA addicts. This is also consistent with the report of Withers et al. that OsAT4 (PMT) acts on monolignols (Withers et al., 2012), rather than polysaccharides.

Glucose polysaccharide, hut not lignin, compensation in OsATlO-Dl [0174] Several cases of compensatory changes in plant cell wall composition have been observed. For example, the cell walls of an Arabidopsis mutant with dramatically reduced xylan, irxl Oirxl OL, possess by mass more glucose, arabinose, and galactose compared with those of wild-type plants (Wu et al., 2009). Also, other Arabidopsis and rice xylan mutants have reduced lignin content (Scheller irx 9 and irx 7 paper, (Chen et al., in prep)). Similarly, poplar saplings (Populus tremuloides) in which a phenyipropanoid biosynthesis gene for 4- coumaryl-CoA ligase is silenced produce less lignin but more cellulose (Hu et al, 1999). However, compensatory changes are not uniformly observed in response to reduced amounts of a particular cell wall component. For example, no consistent changes in polysaccharide content are observed in switchgrass plants with lignin reduced by silencing of the phenyipropanoid biosynthesis genes thai encode caffeic acid 3-O-niethyltransferase or cinnamyl alcohol dehydrogenase (Fu et al, 201 1 ; Fu et al., 201 1).

[0175] The mature cell walls of OsATlO-Dl exhibits a ~15 to 20% increase by mass and moi% in both TFA-soluble glucose, corresponding to mixed linkage glucose and amorphous cellulose, and TFA-insofuble glucose, representing crystalline cellulose (Figure 9). The increase in crystalline cellulose is of a similar magnitude to that observed in poplar silenced for 4-coumaryl-CoA ligase ( 15%, (Hu et al, 1999)). In contrast, chemical, mass

spectrometry, and therm ogravimetric assays did not detect alterations in lignin content or composition in the OsATlO-Dl mutant line (Table III, Figure 9, and Supplemental Figure 5). This suggests that lignin amounts are not sensitive to changes in phenyipropanoid pathway flux that may be caused by increased OsATlO activity. The observations that FA and glucose levels change but lignin does not might be due to spatial and temporal separation of the incorporation of hydroxycinnamates into a precursor of arabinoxylan and the synthesis of lignin. Generally, our results contribute to an emerging view that plants possess specific molecules that are able to sense and trigger responses to specific changes in cell wall composition and/or function; however, the nature of those sensors remains obscure

(Humphrey et al, 2007). Cell wall hydroxycinnamyl esters may contribute to plant reproduction

[0176] Correlative studies suggest that FA dimerizaiion has a role in halting plant growth via inhibition of cell wall elongation and expansion (MacAdam and Grabber, 2002; Qbei et al, 2002; Sasayama et al,, 201 1). Thus, we might have expected plants with reduced FA dimer content to either be smaller, due to decreased ability to support themselves, or be larger, due to greater expansion of cells during growth. ndeed, the progeny of a maize line with reduced ferulate esters at the seedling stage, has recently been found to increase biomass by -8% in field trials (Jung and Phillips, 2010). However, we observed no effect on vegetative growth for greenhouse-grown OsAtlO over expression lines (Figure 4). We were also unable to detect changes in the breaking force of OsATlO-Dl seedling leaves compared with those of the negative segregant (FL, R. Gan, and LEB unpublished), suggesting that this modification does not cause changes in leaf biophysics. OsATlO-Dl does exhibit reduced seed yields per plant by -20% (Figure 4). This observation correlates with the difficulty of isolating homozygous knockout lines for various OsATs (Table 11, F. Piston and J.

Dubcovsky personal communication). On the other hand the low ferulate maize lines did not exhibit a change in ear mass at the stage examined (Jung and Phillips, 2010). From a practical perspective, restoring grain yield in plants engineered to over express OsAtlO would be an important consideration for development of a dual-use crop for both food and biofuel/feed purposes, but would be less crucial for dedicated fuel and feed grasses. One way to accomplish this might be to use a promoter with low expression in reproductive tissues. Heightened Saccharification of OsATIO-Dl

[0177] A major impetus for this work was to understand if a specific genetic reduction of the amount of cell wall-associated FA would improve the yields of cell wall sugars from modified plants for biofuel and feed production. W ^T e found that the decreased amount of FA and proportional decrease in FA dimers releasable from OsATlO-Dl , did indeed lead to greater sugar yields in both enzymatic and fungal saccharification assays (Figure 1 1 ).

However, the quantitative similarity between the improvement in cellulose-mediated digestion and cell wall glucose content (-20%) suggest that with the mild pretreatment conditions used the improvement in enzymatic digestibility may not be due to altered cellulose access bility, but rather cellulose content. On the other hand, the larger improvement in glucose yield (~45%) from acid pretreatment and fungal digestion is consistent with improvements in the accessibility of glucose-containing polysaccharides. The improvement in fungal xylose release was particularly dramatic (85%) and correlates with an increase in fungal xylanase production (Figure 1 1), as if due to a positive feedback loop between xylose and xylanase expression. The enhanced xylanase activity of YT02 on the mutant straw is consistent with the model that the modifications in the mutants are on the xylan polymer, which is made more accessible by reduced ability to cross-link with each other and lignin. The acid-based pretreatment and the synthes s by the fungus of a suite of enzymes, presumably including diverse xylanases, in the fungal assay might have accentuated the effects of the reduced ferulate content of the mutant relative to the wild type. In contrast, we do not expect that there is a major improvement in the quality of the xylan of the OsATlO-Dl because the xylan in the mutant appears to have higher absolute

hydroxycinnamyl esters substitution rates compared with the wild type.

Summary

[0178] We find that over expression of members of a grass-diverged and expanded cla de of BAHD CoA acyltransferases alter the amounts of hydroxycinnamic acids in grass cell walls. In particular, increased expression of OsAtl 0 increased p-C.A content but decreased FA content of rice matrix poly saccharide, consistent with the tentative assignment of this enzyme as a p-coumaryl CoA transferase. Similarly, increased expression of AT15 and AT7 resulted in decreased FA. Together with the recent report that OsAT4 has p-coumaryl

CoA:monoIignol transferase activity , this sugges ts that o ther members of the "Mitchell clade" of CoA acyltransferases likely possess feruiovl transferase activity. Of practical importance toward improving the efficiency of biofuel production and animal feed from grass biomass, we have found that the increased OsAtl 0 expression increases the glucose content of and improves the digestibility of mature straw. The fact that this is an over expression effect will facilitate rapid transfer to and testing of this gene in other grass species.

Materials and Methods Acyllransferase Identification and Phylogenetic Analysis [0179] To identify putative BAUD acyltransferases, we downloaded the hidden Markov model profile for PF02458 from the Pfam database and then searched the annotated coding sequences of diverse plant genomes to identify potential domains using HMMER v3.0 (Finn et al., 2011 ). We used the following genome annotation sources and versions, which were current at the time of the analysis: Arabidopsis thaliana, TA1 vlO; Brachypodium dystachyon, Phytozome V7.0; Soybean, Phytozome v7,0; Medicago trancatula, M†3.5; Rice, MSU v6.1 ; Physcomitrella patens, Phytozome v7.0; Poplar, Phytozome v7.0; Sorghum, Phytozome v7.0; Selaginella moellendorffii, Phytozome v7.0. To serve as a reference for phylogenetic analysis, we downloaded the sequences of 46 previously characterized BAHD enzymes from NCB1, and identified their conserved PF02458 domains as described above, e refer to these proteins as the D'Auria set (D'Auria, 2006). in addition, we randomly selected an outgroup of three PF02458- containing proteins from fungi. Ail phylogenetic analyses were conducted only with the Pfam domain protein sequences. If HM.MER3 identified multiple segments with similarity to the PF02458 domain for a single protein, those segments were concatenated. Redundant sequences, such as from alternative splice versions of a single locus, were noted in the sequence name and only represented once in subsequent analyses.

[0180] W ⁷ e determined the BAHD ciade of each predicted protein via comparison to the D'Auria set. To do this, we used Clustal2 (Larkin et al., 2007) with default settings to build an alignment of the D'Auria set followed by limited manual adjustments with BioEdit. We used this alignment as a profile for alignment of each species' predicted BAHD enzymes. Based on these alignments, we omitted sequences that lack the region immediately surrounding the highly conserved active-site motif, HXXXD, and also those that lack either the H or the D, or include of an extra amino acid between them. We then used MEGA5.05 (Tamura et al., 201 1) to infer and visualize neighbor-joining phylogenetic trees for each species' BAHD proteins in conjunction with the D'Auria set and the outgroup sequences. Parameters were: amino acid substitutions according to the Jones-Taylor-Thorton model, gamma distribution of mutation rate among sites, distribution shape parameter of one, and gaps treated by pair-wise deletion. Five hundred bootstraps were used to identify a consensus tree for each species. Though the bootstrap values were often lower than 50%, the previously delineated BAHD clades unfailingly grouped together (D'Auria, 2006). The proteins encoded by the highly grass-expressed genes belong to Clade V. From the species BAHD trees, we identified clade V proteins, to which, from each species for further analysis. [0181] Clade V proteins from the diverse plant species examined were aligned, then the alignments manually edited. To achieve a high level of confidence we analyzed the relationships among the rice acyltransferase proteins of interest using Bayesian analysis, in addition to the methods described above. Using MrBayes3.1.2 (Huelsenbeck and Ronquist, 2001), the parameters for that analysis were as follows: the WAG model for amino acid substitutions (analysis with a subset of the data showed that this was the most probably fixed rate model for the data set), with a gamma rate distribution with some invariable residues. We ran the simulation for 125,000 generation until the average standard deviation of split frequencies stabilized below 0.01. Plant Lines and Growth Conditions

[0182] We selected mutant lines for the target genes from RiceGE, which summarizes rice T-DNA flanking sequence database (An et al, 2005; Jeong et al., 2006). The initial screen was conducted on the segregating progeny of the primary transgenics, the line numbers for which are listed in Table Π. Seeds from the stock center were sterilized with a 40% commercial bleach solution and germinated on a half-strength Murashige and Skoog (MS) medium containing 1.5% sucrose, 0.55 mM myo-inositol and 0.2% phytagel at 28 °C with continuous white light. After seven days, the seedlings were transplanted into iopsoii and grown in a greenhouse (20-30 °C, 60 to 80% relative humidity). Natural day lengths <14 hours were supplemented with artificial lighting. For genotyping, 10-20 mg leaf samples from 10- 24 segregating progeny of the first generation were harvested, frozen in liquid nitrogen, and ground with a Qiagen Tissuelyser (17 Hz, 1 minute). The samples were vortexed in 200 iiL DNA extraction buffer containing 100 mM Tris-HCf (pH 9.5), 1 M KG, and 10 mM EDTA (pH 8.0), incubated at 65 °C for 30 min, diluted with 1 mL of H20, and centrifuged for 10 min at the maximum speed. The supernatant was used as template the template for genotyping by PGR. PGR. conditions were as follows: 94 °C, 5 min; 35 cycles of 95 °C for 35 sec, 56 °C for 45 sec, and 72 °C for 45 sec; 72 °C for 5 minutes. Genotyping primers are described in Supplemental Table S I . We confirmed and fitrther characterized the next two generations in selfed progeny of homozygous mutant and negative segregant, wild- type plants of fine 4A-03423, which we have named OsATlO-Dl . Specifically we characterized mutant progeny of 4A-03423.5, 4A-03423.12, and 4A-03423.1.9 and negative segregant progeny of 4A-03423.5 and 4A-03423.5.6. In this nomenclature, the period indicates each new generation and the numbers following the period indicate the parent plant of the analyzed progeny.

Generation of Ubi:()sAllO lines

[0183] We amplified a 1541 base pair fragment encoding OsATIO (LOC_Os06g39390.1) including both the start and stop codons from Nipponbare seedling cDNA with the cloning primers listed in Supplemental Table SI, The PGR fragment was gel purified, cloned into pENTR-DTOPO (Invitrogen), and confirmed by sequencing. We then recombined the gene into the final pCAMBIAl 300-Ubi-GW-Nos construct (Park et al., 2010). This binary vector contains a Gateway cassette, flanked by the maize IJbil promoter and the 3 '-terminator of nopaline synthase from Agrobacterium tumefaciens, and the Hpt2 gene, which confers resistance to hygromycin. We used Argrobacte ium tumefaciens ERA 105 to transform fresh caili from the rice japonica cultivar, Kitaake, as previously described (Cheng et al., 1997). After regeneration of piantleis, plants were transferred to the greenhouse under conditions described above, and genotyped with primers for Hpt2 (Supplemental Table SI). Quantitative RT-PCR

[0184] We measured gene expression in young leaf samples. The samples were harvested 33 days after transplanting to the greenhouse and consisted of the top recen tly emerged or greater- than two-thirds emerged leaf of the 2nd or 3rd tiller. We attempted to choose morphologically and developmentally similar leaves for analysis, based on leaf length and degree of emergence/expansion. Leaves were split vertically down the mid-vein and one half dried for hydi xyeinnamic acid analysis, as described below . The other half was frozen in liquid nitrogen, ground to a powder and the A extracted with 1 mL of Trizol reagent (Invitrogen) with subsequent processing according the manufacturer's protocol. The resulting total RNA was then purified by digestion with DNasel and cleaned up on a Nucleospin RNA II column (Macherey-Nagel) according to the manufacturer's protocol. RNA quality was checked on a 1.4% agarose gel after denaturation with glyoxal reagent (Ambion). We synthesized cDNA from 1 jig of total RNA with VILO-Superscript (Invitrogen).

[01 5] We used quantitative real time PGR to measure the expression of each target gene and potential off targets. Using an established procedure for identifying control primers (Vandesompele et al, 2002), we screened primers for three highly expressed rice genes

(Ubq5, eEfla, and 18S rRNA (Jain et al, 2006)) and two moderately expressed genes (Abp and Cc55 (Jain, 2009)) for stability of expression across a set of cDNAs made from 28 rice, aerial vegetative samples collected throughout development (Supplemental Table 1, LEB and PGR in prep). Based on geNORM analysis, we used primers for Ubq5 and Cc55, the two most stably expressed genes for our samples, for internal controls in the qPCR reactions. Reactions were run in a Bio-Rad CFX thermocycler, using SsoFAST EvaGreen mastermix (Bio-Rad). Reaction efficiencies were calculated with LinRegPCR, which calculates the average efficiency for each primer pair based on all the reactions using those primers per plate (Ruijter et al., 2009). Efficiency-adjusted gene expression was normalized with the geometric mean of the control primers (Vandesompele et al., 2002), using the following equation: EAtl 0Cq(Atl 0)/SQRT(ECc55Cq(Cc55) X Eubq5Cq(Ubq5)), where E and Cq indicates the average reaction efficiency and cycle number at which the threshold fluorescence level was exceeded for the designated genes, respectively.

Cell Wail Analyses

Preparation of Alcohol Insoluble Residue (AIR) [0186] Due to the significant changes in ceil wall content across development, we took care to harvest developmentally similar plant organs and parts for comparisons between wild-type and mutant plants in all experiments. Samples harvested for the initial screen % ^r ere dried at 65 °C and samples from subsequent generations at 45 °C for 72 hours. Immature tissue was ground by two rounds of shaking at 1200 rpm with two stainless steal balls 90 sec each. Mature aerial tissue was milled with a Wiley Mill with a 5 mm screen followed by and Udy mill with a 1 mm screen. Ground tissue (5 to 500 mg) was treated with 95% ethanol (1 :4 w'/v) at 100 °C for 30 niin. After the treatment, the supernatant was removed by

centrifugation (10,000 g, 10 min) and the residue was subsequently washed three to five times with 70% ethanol and dried at ~35 °C under vacuum using a centrivap. The dried powder obtained after 70% ethanol wash is designated as alcohol insoluble residue (AIR). The AIR was destarched as described by Obro et al. (2004). AIR was treated with amylase (0.3 U/10 mg biomass Termamyl, Novozymes, Bagsvaerd, Denmark) in 3-(N-morpholino) propanesuffonic acid (MOPS) buffer (50 mM, pH 7.0) at 85 °C for 1 h followed by amyloglucosidase (0.33 U/10 mg biomass) and pullulanase (0.04 U/10 mg biomass) in acetate buffer, 200 mM, pH 4.5 for 2 h at 50 °C. Amyloglucosidase and pullulanase were purchased from Megazyme (Bray, Ireland). The reactions were stopped by adding 3 volumes of cold 95% ethanol, vortexed, and centrifuged at 10,000 g for 10 min. The residue obtained after centrifugation was washed three times with 70% ethanol and dried at 32 °C using a CeniriVap Vacuum Concentrator (Labconco Corp, MO).

Analysis of Hydroxycinnamic Acids

[0187] To release esterified hydroxycinnamic acids from the cell wall, ATR (1 to 10 mg, depending on the experiment, typically 3 mg) was saponified with 500 μΐ of 2 N NaOH for 24 h at 25 °C with mixing at 300 rpm. For analysis of later generations, we doped reactions with an extraction standard, trans-einnamic acid, but this improvement had not yet been developed for the initial screening. After saponification, the supernatant was acidified (pH < 2) with 100 ,ii,L concentrated HCL voriexed, and extracted three times with 300 iL ethyl acetate. The extracts were combined and evaporated to dryness using a CentriVap at 32 °C. The samples were dissolved in 50% (v/v) methanol prior to HPLC analysis. Care was taken to shield the samples from light during the entire process of extraction to prevent the isonierization of hydroxy einnamaies in light.

[0188] Quantification of hydroxycinnamic acids was carried out on a Dionex Ultimate 3000 high pressure liquid chromatography (HPLC) system (Thermoflsher-Dionex,

Sunnyvale, C , USA) with UV detection. Samples were separated on a reverse-phase C 18 column a Synergy 4u Fusioii-RP 80 A column (250 x 2 mm, Plienomenex, Torrance, CA) with a flow of 0.3 ml min- 1 and a gradient of solvent A (0.2%, v/v, TFA) and solvent B (acetonitrile) as follows: 0-5 rnin, 10% B isocratic; 5-25 min, 10-30% B linear; 25-40 min, 30% B isocratic; 40-45 min, 30-35% B linear; 45-46 min, 35-100% B linear; 46-51 min, 100% B isocratic; 51 -53 min 100- 10% B linear; 53-60 min 10% B isocratic. The column temperature was maintained at 30 °C and detection was carried out at 320 nm. Drs, J. Ralph and F. Lu kindly provided the ferulate dehydrodimers, which were treated with 2 NaOH prior to running as standards (Ralph et ak, 1994). To confirm that the species with corresponding retention times were diferulates, we also collected the two major dimer peaks from the HPLC and then their identity verified their mass by LC-MS.

Hydroxycinn m te fractionation

[01 9] To determine whether the changes in hydroxycinnamate content were associated with the matrix polysaccharide or the lignin fractions, 6 mg of destarched AIR were mixed with 600 uL of either 0.05 M trifluoroacetate (TFA) or water. Samples were incubated with shaking at 100 °C for up to 690 minutes. At each time point, a fraction of the sample was removed and frozen. Once all the samples were collected, they were thawed and treated with 2 N NaOH for 24 hrs at 2.5 °C followed by neutralization with concentrated HCl. (Control duplicates remained frozen during the NaOH incubation and then were treated with NaOH and HCl). trans-Cinnamic acid was doped into the samples before they were extracted three times with 300 uL of ethyl acetate. Combined exiracts were dried with no heat via speed vac and resuspended in 50:50 MeOH before HPLC analysis. For quantification of sugars released by TFA, D-xylose was measured using a D-xylose test kit (Megazyme) and D-glucose was measured using a D-fructose /D-glucose (LQR) kit (Megazyme). Both kits were used essentially according to manufacturer's directions, but with reduced volumes for use with a microplate reader. Xylose and glucose supplied with the kits were used to generate standard curves for quantification.

High Performance Liquid Chromatography-Electrospray lonization-Mass Spectrometry

[0190] HPLC separation of the 50 mM TFA-treated samples was performed using an Agilent (Santa Clara, CA) 1290 HPLC system equipped with a Phenomenex (Torrance, CA) Kinetex reversed phase column (ODS-18, 100 mm x 2.1 mm, 2,6 μηι particle size). Mobile phase A consisted of 5% acetonitrile and 0.1% formic acid in HPLC-grade submicron filtered water (Fisher Scientific, Pittsburg, PA). Mobile phase B consisted of 0.1% formic acid in 100% acetonitriie. These mobile phase solutions were filtered and vacuum-degassed prior to use. A binary gradient at 0.3 mL/min flow rate was applied as follows: 90% solvent A and 10% solvent B from 0 to 4 min, linear gradient to 30% solvent B from 4 to 8 min, linear gradient to 50% solvent B from 8 to 9 min, 50% solvent B from 9 to 12 min, linear gradient from 12 to 13 100% solvent B, 100% solvent B from 13 to 15 min, and linear gradient to return the mobile phase to 90% solvent A and 10% solvent B from 15 to 16 min, which was maintained for an additional 5 min before the next sample was injected. The HPLC column eluent was introduced into an Agilent 6538 LLHD Accurate Mass QTOF (Santa Clara, CA) equipped with an electrospray ionization source operated in negative ion mode. Nitrogen gas was used as a nebulizing and drying gas with a drying gas temperature of 325 °C and 0 L/min flow rate. Fragmentor voltage was 160V and capillary voltage was 3500V. Data was collected with Mass Hunter Acquisition (B.04.00, 201 1) and analyzed with Mass Hunter Qualitative (B.04.00, 201 1). Monosaccharide composition by HPAEC

[0191] Destarched AIR (2-5 mg) was treated with 2 M TFA at 120 °C for 1 h. Next the hydrolysate was completely dried using a CentriVap at 32 °C. Monosaccharides produced by TFA hydrolysis were then redissolved in nanopure water and analyzed by high-performance anion exchange chromatography (HPAEC) with pulsed amperometric detection on an Dionex UltimateICS-3000 system equipped with an electrochemical detector and a 4 ^χ 250 mm CarboPac PA20 column (0Bro et al, 2004), The monosaccharides used as the external standards were obtained from Sigma Aldrich, USA. and Alfa Aesar, MA, USA.

Lignin Quantification using Acetyl Bromide 192] Lignin was quantified via acetylbromide solubilization (Fukushima and Hatfield, 2004), followed by quantification in a 96-well plate as described. Breifly, AIR (5 mg) was incubated with 300 ,uL of freshly prepared acetyl bromide (25% v/v in acetic acid, Alfa Aesar, MA, USA)) in screw-capped eppendorf tubes (VW # 16466-044) at 50 °C for 3 h in a thermomixer at 1050 rpm, with vortexing every 15 min for the fast hour. After centrifuging, 100 μϋ of the solution wa s transferred to a fresh tube, followed by addition of 400 μΙ_ of 2 N N aOH and 70 μΕ of freshly prepared 0.5 M hydroxylamine hydrochloride. Next, 57 μΕ of the solution was transferred to a uv-compatible 96-well plate, followed by addition of 200 uL of glacial acetic acid. Absorption was measured at 280 nm with a BioTek SynergyHT. The lignin content in the samples was determined with an extinction coefficient of 17.75 Lg-lcm- 1 corresponding to average values for grass samples (Fukushima and Hatfield, 2004).

Pathlength was determined by measuring the height of the plate.

Pyrolysis Molecular Beam Mass Spectrometry

[0193] A commercially available molecular beam mass spectrometer (MBMS) designed specifically for biomass analysis was used for pyrolysis vapor analysis (Skyes et al, 2010). Approximately 4 mg of air-dried 20 mesh biomass was introduced into the quartz pyrolysis reactor via 80 μ,Ε deactivated stainless steel Eco-Cups provided with the autosampler. Mass spectral data from m/z 30-450 were acquired on a Merlin Automation data system version 3.0 using 17 eV electron impact ionization. Lignin estimates and S:G ratios were determined by summing the intensities of peaks assigned to lignin compounds as described (Skyes et al, 2010). Several lignin peaks were omitted in the syringyl or guaiacyl summations due to individual peaks having associations with both S and G precursors (Evans and Milne, 1987). Thermogravimeiric Analysis

[0194] Thennogravimetric experiments were ran using a Netzsch STA 449 F3 TG-DTA instrument. Approximately 50 mg of the ground samples were weighed and then loaded into the thermal analyzer. The samples were measured in 50 mL/min gas flow. The gas was initially He; and the temperature was held at 35 °C for 15 minutes and then increased to 800 °C at 10 K/min. The samples were then cooled to 140 °C and the gas flow was switched to 60% air in He, The samples were then again heated to 800 °C at 5 K/min and then cooled to 290 °C and the gas flow was switched back to He. The weight data reported in Supplemenatal Figure 5B was corrected for variations in water content by normalizing to the weight at 177 °C, 30 minutes into the experiment.

Enzymatic Saccharification Assay

[§195] AIR (2-5 mg) was pretreated by shaking at 30 °C in 500 μΙ_ of 100 mM Citrate buffer (pH 5.0) followed by incubation at 100 °C for 1 hour. After cooling on the bench, 1 :2000 (final dilution) NS50013, which contain a cellulose cocktail, and 1 : 10,000 (final dilution) NSSOOlO, which contains β-giucosidase, from the Novozymes Biomass Kit were added to the slurry. Reactions were incubated at 50 °C with shaking with periodic removal of time-points, which were stopped by freezing. Released reducing sugars were quantified by 3,5-dinitrosalicilate (DNS) assay · Chose. 1987).

Fungal. Deconstruction and Enzymatic Assays [0196] Pretreatment of rice straw. Prior to steam pre -treatment, wild- type and mutant rice straw were soaked in 1.2% H2S04 overnight. Steam-based pretreatment was performed by loading the samples into an autoclave gun and treating them at 191 °C with a residence time of 2 min. Pretreated materials were then released by rapid depressurization to allow the material to explode, breaking apart the lignin and hemi-cellulose from the cellulose. The pre- treated materials were collected, filtered, washed with distilled water, and stored at 4 °C for subsequent degradation experiments using a modified Hagglund's method (Hagglund, 1951).

[0197] Rice straw degradation. The pretreated wild-type and mutant rice straw was supplemented with 100 mL of Mandel's media in 500-mL flasks (Mandels et al., 1970). Spores from Penicillium sp. YT02 were collected from agar plates with a 0.9% NaCl solution, the adjusted to a concentration of 5.0x 1012 spores mL-1, and used as inoculum [10% (v/v)] for fungal degradation. [01 8] Protein content. Fungal growth was estimated by the protein content in the supernatant. Mid-log fungal cell culture suspension was collected by centrifugation (14,000 x g) for 20 min at room temperature. The supernatant was collected and protein content was determined via the Bradford method. [01 9] Enzymatic activities. Total cellulase activity was determined against Whatman no.1 filter paper (Sigma-Aidrich, St. Louis, MO) using the DNS method (Xiao et ai. 2004). Total endoglucanase activity was determined with earboxyinethylcellulose (CMC) (Claeyssens and Aerts, 1992) followed by reducing sugar measurements with DNS (Ghose, 1987). β- glucosidase activity was determined with p-nitrophenyl-P-d-glucoside and the liberation of p- nitrophenol was accompanied by absorption spectroscopy at 410 nm (Ghose, 1987). Xylanase activity was assayed as described elsewhere (Gessesse and Gashe, 1997). One international unit (IU) was defined as the enzymatic activity needed for the release of 1 mmoi of sugar equivalents per unit volume per minute. To improve accuracy, activity values are expressed relative to the protein concentration in the media (IU/mg). [0200] Saccharides. Fungal cultures were centrifuged and the supernatants analyzed for saccharide content by HPLC using an Aminex HPX-87H (Bio-Rad, Hercules, CA, USA) organic acid column ai 65 °C. The mobile phase was 5 mM sulphuric acid ai a flow rate of 0.5 mL min-1. A. refractive index detector was used.

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[0202] It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, accession numbers, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.

ILLUSTRATIVE SEQUENCES

SEQ ID NO:l AT 10 Acyltransferase cDNA Sequence

LOC_OS06G39390.1

ATGGGCGTCTTCGCCGTCACCAAGGTGTCCGAGGGCCCCGTCCGGCCGTCCGCAGCGACG CCGTCGGAGACGCTGCCGCTCGCCTGGGTCGACCGCTACCCGACGCACCGCGGCCTCGTC GAGTCCGTGCACATCTACCTCCGCCGCGACGACGCCGCCGTCGAGGCGCCGTGCGCCGAC GGCGGCGTCATCGTCGAGGGAAAGAAGAAGAATAATAAGCCGGCGGCGGCGGTGGTGCGC GGCGCGCTGGCGGACGCGCTGGTGCACTACTACCCGTTCGCGGGGCGGATCGTGGAGGAC GAGCGGTCGCCGGGGCGGCCTGCCGTGCTGTGCTCCGGCGAGGGCGTCTACTTCGTGGAG GCCGCCGCCAACTGCACCCTCGCCGACGTCAACCACCTGGAGCGGCCGCTGCTGCTGTCC AAGGAGGACCTCGTGCCGTGCCCGACGCCGGAGCAGTGGCCCGTCGAGCCGCACAACAGC CTCGCCATGATCCAGGTGACGACGTTCACCTGCGGCGGCTTCGTGATCGGGCTGCGCACC AACCACGCGGTGGCGGACGGCACCGGCGCCGCCCAGTTCATGAACGCCGTCGGCGACCTC GCCCGCGGCCTCCCGGAGCCGCGGGTGAAGCCGATCTGGGCGCGCGACCGCTTCCCGGAC CCGGACATCAAGCCCGGCCCGCTGCCGGAGCTCCCCGTGCTGCCGCTCCAGTACATCGCC TTCGACTTCCCCGCCGCCTACCTCGGCAAGCTCAAGGCGCAGTACGCCGCCACCGCCGGC GCCAGCAAGATCTGCTCCGCCTTCGACATCGTCATCGCCAAGCTCTGGCAGTGCCGGACG CGCGCCATCGCCGCCGACCCCGCCGCGGCCGTCAAGCTCTGCTTCTTCGCCAGCGCCCGC CAGGTGCTCGGCCTGGAGACCGGCTACTGGGGCAACGCCATCTTCCCGGTGAAGGTGTCC GCGGCGGCGGGGGAGGTGGCGGCGTCGTCGGTGATCGAGCTCGTCGGCGTGGTCCGGGAG GCGAAGCGGCGGATGGCCGGCGAGTGCCTGCGCTGGGCGGAGGGGCGCACCGGCGGCGCC GACCCGTTCCAGATGACGTTCGACTACGAGTCCGTGTACGTGTCGGACTGGAGCAAGCTC GGGTTCAACGACGTCGACTACGGGTACGGCGCGCCGTCGGCGGCGGGGCCGCTGGTGAAC TGCGACCTCATCTCGTCGGTGATCGTCATGCGGGCGCCGGCGCCGCTCGCCGGCACGCGG CTGCTGGCGAGCTGCGTCACCAAGGAGCACGCCGACGACTTCGCCGCCAGGATGAGGGAG GATCTCGTCTAA

SEQ ID O:2 ATI 0 Acyltransferase Protein Sequence

LOC _Os06g39390.1 (encoded by SEQ ID NO: l)

MGVFAVTKVSEGPVRPSAATPSETLPLA VIjRypTHRGLVESVHIYLRRDDAAVEAPCAD GGVIVEGKKK NKPAAAVVRGALADALVHYYPFAGRIVEDERSPGRPAVLCSGEGVYFVE AAA CTLADV HLERPLLLSKEDLVPCPTPEQWPVBPH SL^IQVTTFTCGGFVIGLRT NKAVADGTGAAQFMNAVGDLARGLPEPRVKPIWARDRFPDPDIKPGPLPELPVLPLQYIA FDFPAAYLGKLKAQYAATAGAS ICSAFDIVIAKLWQCRTRAIAADPAAAVKLCFFASAR QVLGLE GYWG AIFPVKVSAAAGEVAASSVIELVGVVREAKRRMAGECLRWAEGRTGGA DPFQMTFDYESVY VSDWSKLGFNDVDYGYGAPSAAGPLV CDLISSVI V RAPAPLAGTR LLASCVTKEHADDFAARMREDLiV*

SEQ ID NO:3 ATI 5 Acyltransferase cDNA Sequence

LOC_OS 10G01920.1

ATGAGTATTGTGGTGAGCAAGTCAGCGCCGGTGGTCGTCCGGCCATCGGAGCCGGCCACA TCGACGGCCGACAAGATCCTTCTGTCAACTTTGGACAAGCCTGTTGCCACGATACCAGTG ACCGTGCTACTTGCGTTCGACCACCCCATCCATGACGCCACCGCGGAGACCATCAAGACG GCTCTCGCTCAATCACTCGTCCACTACTATCCTATCGCCGGCCGCATTTCCTGCGACAAT GACGACGGCGGCCATTTCTACATCGACTGCACCGGCGAGGATCTCGGGGTCACGTTCGTG GCCGCGTCXXiCCAACTGCACCATGGAGGAGCTCATGTGTCTCGTCGACGACCAGGCTCC C GACGACGAGACAGCGGTGGTGCAGCAGCTCGCCTTCAACTGCACGCCCGACGACCTTCAT CACCGTCTGCTGTGGGTGCAGGTCACCACTCTCAACTGTGGAGGCTTCGTCGTCGGGGTG ACATGGAGCCATGGCGTGGCTGACGGTCCCGGCATAGCACAGTTCATACAAGCCGTCGGC GAGCTCGCCCGTGGCCTGCCATCGCCGTCCGTCGTCCCGGTCAGGTTGGACGACAAGATC GCAACCCAAGCCGTACCTCCCTTCACCATGGCCGTTCATCGCTTCATATCCGGCCTCAAG CCAGTATCAAACCTCGACGTACGCAACGTCACCGTCTCATCTAGCCTTATCAACCACATC ATCGTCGGAGCTCGTCGTCGTGCCACCGTGTTCGAGGCGGTCGCCGCCGTGCTCTGGCAG TGCCGTACACGGGTGGTGATGACGGATCCTGAGGCCCCCGCCGTGCTGCTCTTCGCGGTG AACGCACGCAAGTACCTCGGCGCCAAGGACGGCTACTACGGATGCTGCACCGCCATGCAC ATGGCCGTGTCCAAGTCCGGCACGGTGGCCAACGGCGACATCATGAAGTTGGTCGGCATC ATACGCCGCGCCAAGGAGCAGATACCGGAGCAGCTGAAGGCAGACGACGGCGAGATGATG CTACGGACGATGGTAGGGGAGAAGCAGGTGAATGGATACGAGAGCCTGCTCTACTTGACA TCCTGGCGAAACATCGGGTTCGAGGACGTCGATTTCGGCAGCGGGAAGACGGCGAGGGTG ATGACCTACCCGCCGAGGATGCTGTCCATGATGCCCAGGATTGCGCCCATCTGCTTCATG CTCAAGGCCACAGAGGAAGGGGTCAGGGTCATGTCAGACTGTGTTACGGCTGACCACGCC GAT G C C T T C TAT CAAGAJ-LAT AG C C AAG C T C AAAG C C AC C A C C T G A

SEQ ID NO:4 AS 15 Acyltransferase Protein Sequence

LOC_ OS 10G01920.1 (encoded by SEQ ID NO:3)

MS I WS KS AF VVVRP S E PAT S T A KI LLSTLD PVAT I PVTVLLAFDHP ΙΗΏΑΤΑΕΤ I KT ALAQSLVHYYPIAGRISCDNDDGGHFYIDCTGEDLGVTFVAASANCTMEELMCLVDDQAP DDETAVVQQLAFNCTPDDLKHRLLWVQVTTLNCGGFVVGVTwSKGVADGPGIAQFIQAVG ELARGLPSPSVVPVRLDDKIATQAVPPFTMAVKRFISGLKPVSNLDVRNVTVSSSLINHI IVGARREATVFEAVAAVL QCRTRVVMTDPEAPAVLLFAVNARKYLGAKDGYYGCCTAMH MAYS KS GTVA GD IMKLVG 1 1 RRAKE QIPEQL KADDGEMMLRTMVGEKQV GYESLLYLT SWIWIGFEDVDFGSGKTARVMTYPPR LSJWPRIAPICFMLKATBEGWVMSD ⁽ ^TADHA DAFYQE I AKLKATT *

SEQ ID NO:5 AT7 Acyl transferase cDNA Sequence

LOC_Os05g08640.1

ATGGCGGCGGCGGCGCCGGACAAGGCGGTGGAGCGGCTGTCCCAGAAGCTGGTGCACCCG TCGTCCCCCACGCCGTCGGCCCCGCTCCGCCTCTCCTGGCTCGACCGCTACCCCACCCAG ATGGCGCTCATCGAGTCGCTCCACGTCTTCAAGCCCGACCCGGCGAGGGACGCCGCGGGG CAGGGGCTCGCCCCCGCGCGCGCCATCGAGACGGCCCTCGCGAGAGCCCTCGTCGAGTAC TACCCGCTCGCCGGGAGGCTCGCCGTCTCCCGGGACTCCGGCGAGCTCCAGGTGGATTGC TGCGGCGGCGCCGGCGGCCATGGCGGGGTGTGGTTCATCGAGGCGGCTGTCCCGTGCCGG CTCGAGGACGTGGATTACCTCGAGTACCCTCTCGCCATCTCCAAGGACGAGCTGCTCCCC CACCCGCGCCCCCGCCCCACCCGCGACGAGGAAGACAAGCTCATCCTGCTCGTCCAGGTG ACGACGTTCGCGTGCGGCGGGTTCGTGGTGGGGTTCAGGTTCAGCCACGCGGTGGCGGAC GGCCCGGGGGCGGCGCAGTTCATGGGCGCGGTCGGCGAGCTCGCCCGCGGCGGCGAGCGC ATCACGGTGGCCCCGTCGTGGGGGCGCGACGCGGTGCCCGACCCGGCCGGCGCCATGGTC GGCGCCCTCCCGGAGCCGGCCGGCGCGTCCCGCCTCGAGTACCTCGCCATCGACATCTCC GCCGACTACATCAACCACTTCAAGTCCCAGTTCGCGGCGGCCACCGGCGGCGCCCGCTGC TCCGCCTTCGAGGTGCTCATCGCCAAGGCATGGCAGAGCCGCACCCGCGCCGCCGCGTTC GACCCCTCGACGCCGATCAACCTCTCCTTCGCCATGAACGCCCGGCCGCTCCTCCTCCCG CGCGGCGGCGCCGGGTTCTACGGCAACTGCTACTACATCATGCGGGTGGCCTCCACCGCC GGGAGGGTGGCGACGGCGAGCGTCACCGACGTGGTGAGGATGATCCGGGAGGGGAAGAAG CGGCTCCCGTCGGAGTTCGCGCGGTGGGCCGCCGGAGAGATGGCCGGAGTCGACCCGTAC CAGATCACCTCCGACTACCGGACGCTGCTGGTCTCCGACTGGACGCGGCTGGGCTTCGCC GAGGTGGACTACGGGTGGGGCCCACCGGGCCACGTCGTGCCGCTCACGAACCTGGACTAC ATCGCCACGTGTATCCTCGTCAAGCCCTGGGCCCACAAACCAGGGGCACGGCTCATCACC CAGTGCGTCACACCCGACCGCGTCACCGCCTTCCACGACGCCATGGTGGACATCAACTAA SEQ ID NO:6 AT7 Protein Sequence

LOC_Os05g08640.1 (encoded by SEQ ID NO:5)

AAAAPD AVERLSQKLVHPSSPTPSAPLRLSWLDRYP QMALIESLHVFKPDPARDAAG QGLAPARAIETALARALVEYYPLAGRLAVSRDSGELQVDCCGGAGGKGGVWFIEAAVPCR LEDVDYLEYPLAI SKDELLPHPRPRPTRDEEDKLILLVQVTTFACGGFVVGFRFSHAVAD GPGAAQFMGAVGELARGGER TTVAPSWGRDAVPDPAGAMVGALPEPAGASRLEYLAIDI S ADYI HFKSQFAAATGGARCSAFEVL IAKAWQSRTRAAAF PSTPINLSFAMNARPLLLP RGGAGFYGNCYYIMRVASTAGRVATASVTDVVRMIREGKKRLPSEFARWAAGEMAGVDPY QITSDYRTLLVSDWTRLGFAEVDYGWGPPGHVVPLTN ^' LD IATCILVKPWAHKPGARLIT QCVTPDRVTAFHDAMVE)IN*

SEQ ID NO: 7 ATS cDNA sequence

LOC_Os05gl 9910.1

ATGGTCGCTGTCACCGTGA GAGGAAGTCCCGGAACTTCGTCGGGCCGTCTCCTCCGACG CCGCCGGCCGAGATCACGACGACGCTCGAGCTGTCGTCCATCGACCGCGTGCCCGGGCTG CGCCACAACGTGCGGTCCCTGCACGTGTTCCGCCGCCACAAGAACAGCGGGCCCGTCGTC GACGGTGATAGCAGGAGGCCGGCCGCCGTGATCCGCGCGGCGCTCGCCCGGGCGCTGGCG GACTACCCGGCGTTCGCCGGCCGATTCGTCGGCTCCCTGCTGGCCGGCGACGCCTGCGTC GCGTGCACCGGCGAGGGCGCGTGGTTCGTGGAGGCAGCCGCGGACTGCAGCCTCGACGAC GTGAACGGCCTCGAGTACCCGCTCATGATCTCCGAGGAGGAGCTGCTGCCTGCCCCCGAG GACGGCGTCGACCCTACCAGTATTCCAGTCATGATGCAGGTGACTGAATTCACTTGTGGA GGATTTATCTTGGGCCTTGTGGCAGTCCACACCCTTGCTGATGGACTTGGAGCAGCACAA TTCATCACTGCAG AGCTGAATTGGCCCGTGGCATGGACAAGCTCAGGGTGGCTCCCGTG TGGGATCGCTCGCTGATACCGAACCCACCTAAGCTCCCTCCTGGGCCACCACCATCGTTC CAGTCCTTTGGTTTTCAGCATTTCTCCACAGATGTCACCTCTGACCGTATAGCTCACGTG AAGGCTGAGTACTTCCAGACCTTTGGCCAGTATTGTTCCACCTTTGATGTTGCTACTGCT AAGGTTTGGCAGGCCAGGACACGGGCCGTCGGGTACAAACCGGAGATCCAGGTCCATGTG TGTTTCTTTGCAAACACGCGTCACCTGCTCACGCAGGTTCTCCCAAAAGATGGGGGCTAC TATGGCAACTGCTTTTATCCAGTGACTGTGACAGCAATAGCTGAGGATGTTGCCACCAAA GAGTTGCTTGATGTGATCAAGATAATTCGGGATGGAAAGGCGAGGCTCCCCATGGAGTTT GCAAAGTGGGCTTCAGGGGATGTGAAAGTTGATCCCTACGCATTGACATTTGAACACAAT GTGCTTTTTGTGTCTGATTGGACGAGGTTAGGATTCTTCGAGGTAGACTATGGGTGGGGT ACACCTAATCACA CATACCATTCACT ATGCAGACTACATGGCAGTCGCAGTGC TGGT GCTCCACCAATGCCAAAGAAAGGGACCCGGATTATGACACAGTGTGTGGAGAACAAGTGT ATCAAGGAGTTCCAAGATGAGATGAAGGCCTTCATATAA

SEQ ID NO:8 ATS polypeptide sequence

LOC _Os05gl 9910.1 (encoded by SEQ ID NO:7)

MVAVTVMRKSRNFVGPSPPTPPAEITTTLFLSSIDRVPGLRHNVRSLHVFRRHKNSGPVV DGDSRRPAAVIRAALARALADYPAFAGRFVGSLLAGDACVACTGEGAWFVEAAADCSLDD VNGLEYPLMISEEELLPAPEDGVDPTSIPVMMQVTBFTCGGFILGLVAVHTLADGLGAAQ FITAVAELARGMDKLRVAPV DRSLIPNPPKLPPGPPPSFQSFGFQHFSTDVTSDRIAHV KAEYFQTFGQYCSTFDVATAKV QARTRAVGY PEIQVI-IVCFFA TRHLLTQVLP DGGY YGNCFYPVTVTAI EDVATKELLDVIKIIRDGKARLP EFAKWASGDVKVDPYALTFEHN VLFVSDWTRLGFFEVDYG GTPNHIIPFTYADYMAVAVLGAPPMPKKGTRIMTQCVENKC IKEFQDEMKAFI*

Table !. BAND CoA acyltrarssfe rases encoded in son TO sequenced p!ars t genomes.

Species # putative BAHD Ciade V: AT C!ade i ^c AT Ciade ii ^c proteins: Tota! (# Perfect

Total {# Perfect HXXXD) ^a

HXXXD) ³

Physcomitrella patens 17 (16) 8 (7) 0 0 Seiaginei!a moellendorffii 74 (65) 19 (19) 0 0 Oryza sativa 122 (1 17) 61 (60) 10 10 Sorghum biocolor 89 (85) 49 (48) 8 4 Brachypodium dystachion 83 (78) 38 (38) 12 4 Arabidopsis thaliana 64 (61 ) 25 (25) 1 0 Popu!us tricocarpa 125 (121 ) 25 (24) 0 0 Medicago iruncatula 89 (83) 30 (27) 1 0 Glycine max 142 ( 135) 70 (65) 2 0 ^a Consists of nonredundant predicted protein sequences identified via HMME 3.0 based on PFAM v. 25 and that contain the region surrounding the conserved active site motif, HXXXD, though proteins with single amino acid variations in either the H or D are included. The

number in parentheses is the number with the strict HXXXD motif. See Results for

justification.

b As in D'Auria 2006.

c Acy [transferase (AT) protein c!ades delineated in Figure 1 and Supplemental Figure 1 .

tble SL Summary of the rice acyltransferase mutant analysis.

Locus ID EST Mutant Line c ^d Line Class Insert immature leaf and sheath cell wall jme ^a (LOG J ^b Count ⁰ ID (PFGJ (putative) Detected hydroxycsrirsamlc acid p enotype ^e

3At1 Os01g42880 86 3 A- 13924 DJ AT ' No ND ⁹

sAt2 Os01g42870 25 NA ^h

sAt3 Os05g04584 49 3A-02783 DJ AT No ND

3At4 Os01g18744 50 3A-02300 DJ Insert/ AT ^! Yes, no ND

homozygotes

3A-09297 DJ Insert/AT No ND

sAt5 Os05g 19910 17 2A-20021 ¹ DJ AT Yes Leaf and sheath: increase in FA:p-CA ratio

1 C-03624 HY insert ^x No ND

3At6 Os01g08380 76 1 C-06931 HY Insert No ND

3A-G8459 DJ AT No ND

2D-4G810 HY AT Yes None

sAt7 Os05g08640 15 2A-40095 HY Insert/AT Yes Sheath: decrease FA

sAt8 Os06g39470 5 NA

sAt9 Os01g09010 200 NA

3 At 10 Os06g39390 41 4A-03423 ^! DJ AT Yes Leaf: decrease FA, increase p-CA

Sheath: decrease FA, increase p-CA

3At1 1 Os04g 1 1810 0 NA

3At12 Os04g09590 0 3A-16373 DJ AT Yes None

2D-41616 HY AT Yes None

sAt13 Os10g01930 0 2D-10182 DJ I sert/AT Yes, no ND

homozygotes

3At14 Os10g02000 9 NA

3 At 15 Os10g01920 0 1 B-00523 DJ AT Yes Leaf: decrease FA

3 At 16 Os10g01800 0 2D-40243 DJ AT Yes None

3 At 17 Os10g03360 0 NA

3Αί18 Os10g03390 1 4A-04176 DJ AT Yes None

sAt19 Os04g09260 7 NA

3At20 Os06g48560 0 NA

Totals 20 17 1 1 confirmed, 4 phenotypes

(for 1 1 2 no

genes) homozyg . for

insert

Dryza sativa (Os) acyltransferase (At) gene names were assigned arbitrarily based on an early phylogenic analysis, that has since been revised. \nnotation SUvG

sum of ESTs from ail organs/stages from rice Sanger EST data available through 2009.

)J and HW indicate O. sativa var. japonica cv. Dongjin and cv. Hwayoung, respectively

^■ or homozygous mutants relative to negative segregant wild-type siblings. CA signifies para-coumanc acid. FA signifies feruiic acid. A change in :CA ratio is only mentioned when a phenotype in neither FA nor CA alone appear to change.

,T signifies a putative activation tagged line in the T-DNA insert possesses transcription activation sequences.

iD signifies not determined.

vlA signifies that no rice activation lines were available at the inception of the study.

¾sert/AT signifies that the T-DNA possesses transcription activation sequences and is inserted within, or <300 base pairs away from, the gene. )sAT5-D1

isert signifies that the T-DNA is inserted within, or <300 base pairs away from, the gene.

)sAT10-D1

Tab!e 111. Lignin Amounts and S:G Ratios from AIR after 2 N NaOH extraction for

greenhouse grown mutant and wiidtype plants.

Standardize

Parental ABSL ³ d Ugnin ^c

Line Genotype Materia! (% mass) S/G ratio ^b (% mass}

WT- 4A-03423.1 mature straw 5.5 ± 0.5 0.87 ± 0.01 5.7 ± 0.2

AT10-D1 4A-03423.5 mature straw 5.5 ± 0.5 0.75 ± 0.1 1 5.5 ± 0.1

AT10-D1 4A-03423.12 mature straw 5.7 ± 0,6 ND

WT 4A-03423 leaf sheath ND 0.39 ± 0.05 5.9 ± 0.1

AT10-D1 4A-G3423 leaf sheath ND 0.36 ± 0.13 5.5 ± 0.7

WT 4A-03423 leaf blade ND 0.52 ± 0.13 3.4 ± 0.1

AT10-D1 4A-G3423 leaf blade ND 0.52 ± 0.09 3.4 ± 0.3 ^a Acetylbromide soluble !ignin expressed in terms of mg/mg for pools of straw, measured in triplicate, or 2 to 3 individual bioreplicates, measured in duplicate. Errors are standard deviations.

"Average ± standard deviation of singiicate measurements of 2 to 3 plants for the earlier generation, and two technical replicates of pools of 12 plants for the later generation

samples, as determined by py-MBMS.

⁰ As determined via py-MBMS and calibrated for each type of rice sample (i.e., straw, leaf, sheath) based on the ABSL data.

α negative segregant, wild type.

e ND = not determined

OC_Os05g08640 os05g08640_F4qPCR A AACCAGG GG C ACG G CTCAT os05g08640_R4q PCR TTG ATGTCCACCATG G CGTCGT exp eri m en ta I OC_Os05g l9910 os05g l 9910_543F catcactgcagtagctgaattgg os05g l9910_634R gcttaggtgggttcggtatcagc experimental OC_Os06g39370 Os06g39370_Fl TGCCTTCTAGAAATCTGAAGCGTAT Os06g39370_Rl TTGCTGTACAAACTCGAACTCTGC experimental OC_Os06g39380 Os06g39380_Fl ACAGAAAAACCACGGCCTAATAGA Os06g39380_Rl CTCTTTTCACTCCCACCCTTGTCT exp eri m e n ta I OC_Os06g39390 06g39390-RT2-5' GACCCGTTCCAGATGACGTT 05g39390-RT2-3' GATGAGGTCGCAGTTCACCA experimental OC_Os06g39400 Os06g39400_Fl GCGCATGGAAGGGCAAAAACAGC Os06g39400_Rl CTGCTCCAGAAAAAGCTCGATCGGT experimental OC_Os06g 39470 Os06g39470_359F agtacccgctcatggtggac Os06g39470_467R aactgcgtgacctggacaa experimental OC_Os04g35910 CC55 Rl -5' AAGGAGAAAGCCGAACAACG CC55 RT1 -3' TCCTCAAGTTTCTTCCTGTAGGC control OC_Os01g22490 UBQ5 RT 1 -5' ACCACTTCGACCGCCACTACT UB05 RT1-3' ACG CCTAAG CCTGCTG GTT control

:. Cloning

rimers

ene targeted 5' primer name 5' primer sequence 3' primer name 3' primer sequence

Os06g39390-rev-

OC _ Os06g39390 Os06g39390-for-2 CACCAGCAGCAGCAGCAGCAGCA stop2 TACCACGCATGTCACAAAG

Supplemental Table !L Average ± standard deviation of sugar composition of the media during the course of Penicilliurn sp. YT02 incubation with OSAT10-D1 and negative segregant, wild type. N - 5.

Glucose Xylose ¾rabinoss

Time WT Mut Δ WT ut Δ WT Mut Δ

(hrs) (mg/mL) (mg/mL) % (mg/mL) (mg/mL) % (mg/mL) (mg/mL) %

0.42 ± 0.42 ± 0 0.17 + 0.32 + 88 0.05 ± 0.05 + 0

12 0.01 0.02 0.03 0.04 0.02 0.01

1,4 + 0.1 1.5 + 0.4 3 0.7 ± 0.3 1.4 + 0.5 106 0.14 ± 0.24 + 71

24 0.05 0.01

2.1 +0,1 2.3 + 0,2 9 0.8 + 0.2 1.8 + 0.4 116 0.27 +. 0,40 ± 48

36 0.03 0.01

2.7 + 0,1 4.4 + 0,3 65 1.2 + 0.5 2.3 + 0.2 95 0.5 + 0,2 0,39 ±

48 0.02 19

3.5 + 0,1 4.7 + 0,3 35 1.7 + 0.3 2.7 + 0.2 64 0.6 + 0,2 0,63 ± 5

60 0.02

3.4 + 0.1 6.1 ± 0.2 82 1.8 + 0.1 3.7 ±0.4 102 0.5 ± 0.5 0.60 ± 25

72 0.03

3.3 + 0.1 4.8 ± 0.1 47 2.0 ±0.2 2.9 ±0.2 45 0.6 ± 0.3 0.80 ± 35

84 0.05

1.8 + 0.1 3.4 ± 0.2 97 1.4 + 0.1 2.5 ±0.2 84 0.5 ± 0.2 0.64 ± 28

96 0.03

120 1.1 +0.1 1.4 ± 0.1 28 1.6 + 0.1 2.4 + 0.2 48 0.5 ± 0.2 0.48 ± 7

0.03

Avg 46 82 25

Galactose Mannose Ce obiose

Tims WT Mut Δ WT Mut Δ WT Mut Δ

(hrs) (mg/mL) [mg/mL) % (mg/mL) (mg/mL) % (mg/rnL) (mg/ L) %

0.02 ± 0.02 ± 0 0.04 ± 0.04 + 0 0.20 ± 0.09 ± 0.01 -55

12 0.01 0.01 0.01 0.01 0.01

0.11 ± 0.04 ± -62 0.18 ± 0.16 + -9 0.38 ± 0.36 ± 0.02 -4

24 0.02 0.01 0.02 0.01 0.01

0.09 ± 0.10 ± 11 0.14 ± 0.20 + 48 0.54 ± 0.35 ± 0.02 -35

36 0.03 0.01 0.06 0.03 0.01

0.18 ± 0.16 ± -13 0.42 ± 0.23 + -44 0.70 + 0.55 + 0.04 -22

48 0.06 0.01 0.04 0.04 0.01

0.15 + 0.27 ± 80 0.38 + 0.45 + 20 0.85 + 0.81 + 0.05 -5

60 0.02 0.03 0.03 0.03 0.02

0.16 + 0.12 ± -25 0.24 ± 0.48 + 100 0.95 + 1.2 + 0.2 27

72 0.04 0.02 0.04 0.02 0.01

0.15 + 0.40 ± 170 0.15 + 0.30 + 103 0.73 + 0.80 + 0.05 10

84 0.02 0.03 0.03 0.02 0.03

0.65 ± 0.24 ± -63 0.10 + 0.40 + 300 0.60 + 0.80 + 0.04 34

96 0.01 0.01 0.02 0.02 0.02

120 0.36 ± 0.03 ± -17 0.36 + 0.30 + -17 0.37 + 0.78 + 0.02 110

0.01 0.02 0.05 0.01 0.03

63