Patent Publication Number: US-2012040408-A1

Title: Processing cellulosic biomass

Description:
RELATED APPLICATION INFORMATION  
     The present application claims benefit of and priority to U.S. Provisional Application No. 61/074,497, filed on Jun. 20, 2008, the contents of which are herby incorpoarted by reference in their entirety. 
    
    
     GOVERNMENT SUPPORT 
     This invention was made with U.S. government support under the United States Department of Agriculture and Department of Energy Biomass Grant No. DE-PS36-06G096002F to Edenspace Systems Corporation and contract No. DE-AC36-08G028308 between the United States Department of Energy and the Alliance for Sustainable Energy, LLC, manager and operator of the National Renewable Energy Laboratory. The government of the United States of America has certain rights in the invention. 
    
    
     SEQUENCE LISTING 
     The present specification makes reference to a Sequence Listing (submitted electronically as a .txt file named “sequence listing.txt” concurrently with other documents associated with this application on Jun. 19, 2009). The .txt file was generated on Jun. 19, 2009 and is 39 kb in size. The entire contents of the Sequence Listing are herein incorporated by reference. 
     BACKGROUND OF THE INVENTION 
     Rising oil prices have increased the cost-competitiveness of ethanol as a fuel, which has captured a substantial share of the U.S. fuel market. Federal agencies such as the U.S. Department of Agriculture (USDA) have begun to implement programs of preferred procurement of biofuels such as ethanol as a fuel additive. The potential market for the biofuels in industries such as transportation fuel is one of the largest in the U.S. economy. 
     The ability to produce ethanol from low-cost biomass has been called the “key” to making ethanol competitive as a gasoline additive (J. DiPardo, “Outlook for biomass ethanol production and demand”, EIA Forecasts, 2002). Joint USDA/DOE studies forecast the ability to produce up to approximately 100 billion gallons per year from forestland and agricultural land combined (R.D. Perlack et al., “Biomass as feedstock for a bioenergy and bioproducts industry: The technical feasibility of a billion-ton annual supply”, 2005, ORNL/TM-2005/66). Lignocellulosic production would also help to increase the net energy balance of corn ethanol. The conversion of lignocellulosic feedstocks into ethanol has advantages, including ready availability of large amounts of feedstock, avoidance of burning or land filling the materials, and relatively easy conversion of glucose (produced by hydrolysis of cellulose) into ethanol. Most studies show substantial energy advantages of using cellulosic feedstocks (e.g., Farrell et al., Science, 2006, 311: 506-508). 
     Today, most fuel ethanol is produced from corn (maize) grain, which is milled, pretreated with heat and acid to break down lignin and cellulose, treated with amylase enzymes to hydrolyze starch to sugars, fermented, and distilled. While substantial progress has been made in reducing costs of ethanol production, substantial challenges remain. One such challenge is to reduce the costs of pretreating the biomass to remove lignin and hemicellulose. Another challenge is to reduce the cost of microbially-produced enzymes that are often used in processing lignocellulosic biomass. 
     Improved techniques are still needed to reduce the cost of biofuel feedstocks for ethanol production. 
     SUMMARY OF THE INVENTION 
     The present invention encompasses the surprising finding that expression of even low levels of microbial enzyme polypeptides in plants can significantly reduce processing required to promote hydrolysis of celluloses in lignocelluloytic biomass from such plants. Lignocellulolytic biomass from plants that transgenically express low levels of microbial lignocellulolytic enzyme polypeptides, for example, can be processed in less severe conditions than can lignocellulolytic biomass from nontransgenic plants. The present invention demonstrates, for example, that processing may be accomplished at lower temperatures, with lower amounts of added enzyme polypeptides, in shorter times, and/or reduced acid concentrations. 
     Without wishing to be bound by any particular theory, the present inventors propose that expression of microbial lignocellulolytic enzyme polypeptides during the life of the plant may weaken cell walls, possibly through nicking or other damage to cellulose, hemicellulose, and/or various cross-linking molecules such as lignin and ferulic acid that make up the cell wall. However, high expression of active lignocellulolytic enzyme polypeptides can be toxic to plants. Without wishing to be bound by any particular theory, the present inventors propose that use of microbial lignocellulolytic enzyme polypeptides having relatively low activity during the life of the plant may be beneficial. Without wishing to be bound by any particular theory, the present inventors further propose that use of thermostable enzyme polypeptides having relatively high activity under conditions of relatively high temperature may be beneficial in certain applications, as it may allow for higher activity under conditions commonly used in processing of cellulosic biomass. 
     In some embodiments, the present invention utilizes enzyme polypeptides with greater activity at higher temperatures (e.g., thermophilic enzyme polypeptides), so that the enzyme polypeptides are less active during the life of the plant and are more active during treatments performed after harvest. For example, in some embodiments, the present invention utilizes enzyme polypeptides found in thermophilic microbes (e.g., bacteria). 
     The present invention provides improved systems for the processing of cellulosic biomass. In some embodiments, such systems are useful in ethanol production. In some embodiments, provided are transgenic plants, the genomes of which comprise a recombinant polynucleotide encoding at least one lignocellulolytic enzyme polypeptide operably linked to a promoter sequence, wherein the polynucleotide is optimized for expression in the plant, wherein the at least one lignocellulolytic enzyme polypeptide is produced at a level less than about 0.5% of total soluble protein. 
     In some embodiments, the present invention provides a transgenic plant, the genome of which is augmented with a recombinant polynucleotide encoding at least one lignocellulolytic enzyme polypeptide operably linked to a promoter sequence, wherein the polynucleotide is optimized for expression in the plant, wherein the at least one lignocellulolytic enzyme polypeptide is produced under control of a constitutive promoter. In some embodiments, the lignocellulolytic enzyme polypeptide is produced during the life of the plant. In some embodiments, the lignocellulolytic enzyme polypeptide is active during the life of the plant. In some embodiments, the lignocellulolytic enzyme polypeptide is present in all plant tissues during the life of the plant. In some embodiments, the lignocellylolytic enzyme polypeptide is present in only some plant tissues during the life of the plant. In some embodiments, the lignocellulolytic enzyme polypeptide is present in the cell wall and/or the endoplasmic reticulum during the life of the plant. 
     In some embodiments, the present invention provides a transgenic plant, the genome of which is augmented with a recombinant polynucleotide encoding at least one lignocellulolytic enzyme polypeptide that is or is homologous to a lignocellulolytic enzyme polypeptide found in a thermophilic microorganism (e.g., bacterium, fungus, etc.). In some such embodiments, the thermophilic organism is a microorganism that is a member of a genus selected from the group consisting of  Aeropyrum, Acidilobus, Acidothermus, Aciduliprofundum, Anaerocellum, Archaeoglobus, Aspergillus, Bacillus, Caldibacillus, Caldicellulosiruptor, Caldithrix, Cellulomonas, Chaetomium, Chloroflexus, Clostridium, Cyanidium, Deferribacter, Desulfotomaculum, Desulfurella, Desulfurococcus, Fervidobacterium, Geobacillus, Geothermobacterium, Humicola, Ignicoccus, Marinitoga, Methanocaldococcus, Methanococcus, Methanopyrus, Methanosarcina, Methanothermobacter, Nautilia, Pyrobaculum, Pyrococcus, Pyrodictium, Rhizomucor, Rhodothermus, Staphylothermus, Scylatidium, Spirochaeta, Sulfolobus, Talaromyces, Thermoascus, Thermobifida, Thermococcus, Thermodesulfobacterium, Thermodesulfovibrio, Thermomicrobium, Thermoplasma, Thermoproteus, Thermothrix, Thermotoga, Thermus , and  Thiobacillus ; in some such embodiments, the thermophilic microorganism is a bacterium that is a member of a species selected from the group consisting of  Acidothermus cellulolyticus  and  Pyrococcusi . In some embodiments, the thermophilic microorganism is a fungal organism or cell; in some such embodiments, the thermophilic microorganism is  Talaromyces emersonii.    
     A plant utilized in accordance with the present invention may be a monocotyledonous plant or a dicotyledonous plant. In certain embodiments, the plant is a crop plant. In some embodiments, the plant is selected from the group consisting of corn, switchgrass, sorghum, miscanthus, sugarcane, poplar, pine, wheat, rice, soy, cotton, barley, turf grass, tobacco, bamboo, rape, sugar beet, sunflower, willow, and eucalyptus. 
     In another aspect, the present invention provides methods for cost-effective processing of lignocellulosic biomass. Inventive methods comprise steps of pretreating a plant part obtained from at least one transgenic plant of the invention under conditions to promote accessibility of celluloses within the lignocellulosic biomass and treating the plant part under conditions that promote hydrolysis of cellulose to fermentable sugars. In some such methods, the at least one lignocellulolytic enzyme polypeptide is expressed at a level less than or equal to about 0.5% of total soluble protein. 
     In certain embodiments, the step of pretreating comprises incubating the plant part in acid and heating the plant part. In some embodiments, the step of pretreating is performed at a temperature less than about 175° C., less than about 145° C., or less than about 115° C. 
     In some embodiments, the method further comprises applying external lignocellulolytic enzyme polypeptides to the plant part prior to the treating step. Such a method will result in increased ethanol production compared to a method in which the plant part is obtained from a non-transgenic plant. 
     In some embodiments, the amount of externally applied lignocellulolytic enzyme polypeptide required to achieve a given level of hydrolysis is less than the amount of externally applied lignocellulolytic enzyme polypeptide required to achieve the same level of hydrolysis of comparable lignocellulosic biomass from a plant part that is not obtained from a transgenic plant. In some embodiments, a greater level of hydrolysis is obtained from the plant part obtained from a transgenic plant than from a plant part obtained from a non-transgenic that is processed under the same conditions. 
     In some embodiments, at least two lignocellulolytic enzyme polypeptides are externally applied and the at least two lignocellulolytic enzyme polypeptides together have at least two different enzyme activities. In some embodiments, the externally applied lignocellulolytic enzyme polypeptide has at least two different enzyme activities. In some embodiments, the at least two different enzyme activities are selected from the group consisting of exoglucanase, endoglucanase, hemi-cellulase, beta-glucosidase, beta-glucanase, lignin peroxidase, laccase, Mn peroxidase, acetyl xylan esterase, ferulic acid esterase, alpha-glucuronidase, pectin methyl esterase, and pectate lyase. In some embodiments, the at least two different enzyme activities are selected from the group consisting of exoglucanase, endoglucanase, hemi-cellulase, beta-glucosidase, and combinations thereof. In some embodiments, the at least two different enzyme activities comprise exoglucanase, endoglucanase, hemi-cellulase, and beta-glucosidase. 
     In some embodiments, the at least one externally applied lignocellulolytic enzyme polypeptide is capable of hydrolyzing cellulose to glucose monomers. 
     In some embodiments, the promoter sequence is a sequence of a promoter selected from the group consisting of a constitutive promoter, a developmentally-specific promoter, a tissue-specific promoter, and an inducible promoter. In some embodiments the promoter is a constitutive promoter selected from the group consisting of the actl promoter and the 35S CMV promoter. In some embodiments the lignocellulolytic enzyme polypeptide is expressed in one or more targeted sub-cellular compartments or organelles. In some embodiments, the targeted sub-cellular compartments or organelles are selected from the group consisting of apoplast, chloroplast, vacuole, endoplasmic reticulum, cell wall, and combinations thereof. In some embodiments, the lignocellulolytic enzyme polypeptide is expressed in at least two sub-cellular compartments or organelles. 
     In certain embodiments, prior to the treating step, the plant part is not pretreated or is pretreated under conditions of heat and acid that are less harsh than conditions used in pretreatment of biomass from non-transgenic plants. 
     In some embodiments, the sequence for the lignocellulolytic polypeptide is fused to a signal peptide sequence. In some embodiments, the signal peptide sequence encodes a secretion signal that allows localization to a cell compartment or organelle selected from the group consisting of cytosol, vacuole, nucleus, endoplasmic reticulum, mitochondria, apoplast, peroxisomes, and plastid (including chloroplast). In some embodiments, the signal peptide sequence encodes a secretion signal from sea anemone equistatin. In some embodiments, the signal peptide sequence encodes a retention signal comprising a KDEL motif 
     In some embodiments, the lignocellulolytic enzyme polypeptide is expressed in a plant part selected from the group consisting of stems, leaves, grain, cobs, husks, roots, branches, bark, and combinations thereof 
     In some embodiments, the lignocellulolytic enzyme polypeptide expressed by the transgenic plant is selected from the group consisting of cellulases, hemicellulases, ligninases, and combinations thereof. In some embodiments, the lignocellulolytic enzyme polypeptide comprises and endoglucanase. In some embodiments, the endoglucanase comprises E1 endo-1,4-β-glucanase; in some such embodiments, the amino acid sequence of the E1 endo glucanase comprises the sequence of SEQ ID NO. 2. 
     These and other objects, advantages and features of the present invention will become apparent to those of ordinary skill in the art having read the following detailed description. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWING 
         FIG. 1  is a map of the pBI12l vector used in the transformation of tobacco as reported in Example 1. The following sequences are abbreviated; NOS promoter (N-p), neomycin phospho-transferase II (NPTII), NOS terminator (N-t), cauliflower mosaic virus 35S promoter (35S), β-glucuronidase (GUS), agrobacteria right border sequence (RB), left border (LB). 
         FIG. 2  is a map of the pBI121-E1 vector in between the right and left border sequences used in the transformation of tobacco as reported in Example 1. The E1 construct contains the VSPβ signal peptide fused to the N-terminus of the E1 catalytic domain. The following sequences are abbreviated; NOS promoter (N-p), neomycin phospho-transferase II (NPTII), NOS terminator (N-t), cauliflower mosaic virus 35S promoter (35S), β-glucuronidase (GUS), agrobacteria right border sequence (RB), left border (LB). 
         FIG. 3  is a graph showing glucose production from dried E1-FLC and W38 (wild-type) tobacco biomass equilibrated in citrate buffer (pH 4.5) for 24 hours at 50° C. with or without added Cellulase AN, glucoamylase, and hemicellulase. Error bars indicate ±1 standard deviation (n=3). 
         FIG. 4  shows the results of Southern blot analysis of genomic DNA from corn plants, probed with the E1-cat. Lane 1: 10 pg of Sac 1 E1 fragment from pMZ766; Lanes 2-3: untransformed corn control (lane 2: DNA undigested and lane 3: DNA digested); Lanes 4-13: five independent pMZ766 transformants; (lanes 4, 6, 8, 10, and 12: DNA not digested; lanes 5, 7, 9, 11, and 13: DNA digested with Sac I). Size of bands is lkb. 
         FIG. 5  shows Western blots of transgenic corn samples as compared to that of transgenic rice and transgenic tobacco. (A) Western blot of 1 μg total soluble protein from transgenic maize plants expressing E1. Lanes: +, positive tobacco control (Austin-Philipps); −C, negative control (untransformed); 1-10, transgenic maize lines representing at least 5 different transformation events; 11, transgenic rice. Lanes representing different transformation events: 1-5, transformed with pMZ766E1cat and pBY520; 6, transformed with pMZ766E1cat and pDN302; 7, transformed with E1 binary vector construct 2 and pBY520; 8-9, transformed with pMZ766E1cat and pBY520; 10, transformed with pMZ766E1cat and pDM302. Samples in lanes 1, 2, 5, and 6 were from transgenic corn expressing E1 (three lines expressed E1 from pMZ766E1cat and pBY520 and one line expressed E1 from pMZ766E1cat and pDM302). No E1 was detected in lanes 3, 4, 7, 8, 9, and 10. (B) Western blot of 2 μg total soluble protein from transgenic maize plants expressing E1. Lanes: +, positive tobacco control (Austin-Phillips); −C, negative maize control (untransformed); 1-6, transgenic maize lines representing at least four different transformation events; 7, transgenic rice. Lanes representing different transformation events: transformed with pMZ766E1 cat and pBY520; 4, transformed with pMZ766E1cat and pDM302; 5, transformed with E1 binary vector construct 2 and pBY520; 6, transformed with pMZ766E1cat and pDM302. A faint band was detected in lane 3; no bands were detected in any other lane for samples of transformed corn. 
         FIG. 6(A)  is a picture of E1 transgenic maize leaf tissue obtained by immunofluorescent confocal laser microscopy image microscopy using an E1-specific primary antibody and an FITC-conjugated anti-mouse secondary antibody. This picture shows that E1 transgenic leaf tissue exhibits apparent storage of E1 in the plant apoplast.  FIG. 6(B)  is a confocal microscopy image of leaf tissue from an untransformed control maize leaf showing no expression of E1 enzyme. 
         FIG. 7  shows the cellulase activity of crude extract from transgenic tobacco expressing E1. The red carboxy-methyl-cellulose in the Petri dish has been hydrolyzed by the application of E1 extract or commercially available cellulase enzymes (Cellulase AN, BIO-CAT) to form clear areas. No cellulase activity was observed from wild type tobacco extract. 
         FIG. 8  is a graph illustrating the increased production of glucose from hydrolysis of transgenic tobacco biomass expressing the E1 endoglucanase compared to wild-type biomass. Glucose levels were measured from E1 and wild-type samples before and after AFEX (ammonia fiber explosion) treatment. 
         FIG. 9  shows two pictures allowing visualization of E1 hydrolysis of CMC (carboxyl-methyl-cellulose) using Congo Red staining Leaf tips of untransformed (left) and transgenic E1 (right) tobacco (A) before and (B) after incubation at 65° C. for thirty minutes and the staining with Congo Red. 
         FIG. 10  presents data showing glucan conversion rates of E1 transgenic and wildtype corn stover. Transgenic E1 biomass is more readily hydrolyzable to glucose than wild type biomass is. E1 corn under low (15 mg enzyme/g biomass) and high (100 mg/g) external enzyme loading conditions consistently provided higher levels of glucan conversion than untransformed (WT) corn across a wide range of pretreatment temperatures after 24 hours of pretreatment. 
         FIG. 11  depicts a map of pEDEN122, which is designed for expression of CBH-E in plants. 
         FIG. 12  depicts agarose gels that show results from a PCR analysis to screen corn plants regenerated from immature embryos transformed with pEDEN122, an expression plasmid for CBH-E. Presence of CBH-E (“exocellulase”) and of the selectable marker was detected using primers for each gene. 
         FIG. 13  shows effects of in planta exoglucanase (in this case CBH-E) expression on enzyme dosage requirements and digestibility in corn biomass. The “pretreated” group of samples was pretreated with dilute sulfuric acid. Samples were incubated with low (0.4 mg/g) or high (8 mg/g) concentration of commercial cellulase cocktail (Novozymes Celluclast 1.5 L). 
     
    
    
     DEFINITIONS 
     Throughout the specification, several terms are employed that are defined in the following paragraphs. 
     As used herein, the terms “about” and “approximately,” in reference to a number, are used herein to include numbers that fall within a range of 20%, 10%, 5%, or 1% in either direction (greater than or less than) the number unless otherwise stated or otherwise evident from the context (except where such number would exceed 100% of a possible value). 
     As used herein, the phrase “externally applied,” when used to describe enzyme polypeptides used in the processing of biomass, refers to enzyme polypeptides that are not produced by the organism whose biomass is being processed. “Externally applied” enzyme polypeptides, as used herein, do not include enzyme polypeptides that are expressed (whether endogenously or transgenically) by the organism (e.g., plant) from which the biomass is obtained. 
     As used herein, the term “extract,” when used as noun, refers to a preparation from a biological material (such as lignocellulolytic biomass) in which a substantial portion of proteins are in solution. In some embodiments of the invention, the extract is a crude extract, e.g., an extract that is prepared by disrupting cells such that proteins are solubilized and optionally removing debris, but not performing further purification steps. In some embodiments of the invention, the extract is further purified in that certain substances, molecules, or combinations thereof are removed. 
     As used herein, the term “gene” refers to a discrete nucleic acid sequence responsible for a discrete cellular product and/or performing one or more intracellular or extracellular functions. More specifically, the term “gene” refers to a nucleic acid that includes a portion encoding a protein and optionally encompasses regulatory sequences, such as promoters, enhancers, terminators, and the like, which are involved in the regulation of expression of the protein encoded by the gene of interest. The gene and regulatory sequences may be derived from the same natural source, or may be heterologous to one another. The definition can also include nucleic acids that do not encode proteins but rather provide templates for transcription of functional RNA molecules such as tRNAs, rRNAs, etc. Alternatively, a gene may define a genomic location for a particular event/function, such as the binding of proteins and/or nucleic acids. 
     As used herein, the term “gene expression” refers to the conversion of the information, contained in a gene, into a gene product. A gene product can be the direct transcriptional product of a gene (e.g., mRNA, tRNA, rRNA, antisense RNA, ribozyme structural RNA or any other type of RNA) or a protein produced by translation of an mRNA. Gene products also include RNAs that are modified by processes such as capping, polyadenylation, methylation, and editing, proteins post-translationally modified, and proteins modified by, for example, methylation, acetylation, phosphorylation, ubiquitination, ADP-ribosylation, myristilation, and glycosylation. 
     The terms “genetically modified” and “transgenic” are used herein interchangeably. A transgenic or genetically modified organism is one that has a genetic background which is at least partially due to manipulation by the hand of man through the use of genetic engineering. For example, the term “transgenic cell”, as used herein, refers to a cell whose DNA contains an exogenous nucleic acid not originally present in the non-transgenic cell. A transgenic cell may be derived or regenerated from a transformed cell or derived from a transgenic cell. Exemplary transgenic cells in the context of the present invention include plant calli derived from a stably transformed plant cell and particular cells (such as leaf, root, stem, or reproductive cells) obtained from a transgenic plant. A “transgenic plant” is any plant in which one or more of the cells of the plant contain heterologous nucleic acid sequences introduced by way of human intervention. Transgenic plants typically express DNA sequences, which confer the plants with characters different from that of native, non-transgenic plants of the same strain. The progeny from such a plant or from crosses involving such a plant in the form of plants, seeds, tissue cultures and isolated tissue and cells, which carry at least part of the modification originally introduced by genetic engineering, are comprised by the definition. 
     As used herein, the term “lignocellulolytic enzyme polypeptide” refers to a polypeptide that disrupts or degrades lignocellulose, which comprises cellulose, hemicellulose, and lignin. The term “lignocelluloytic enzyme polypeptide” encompasses, but is not limited to, cellulases, hemicellulases, ligninases, and related polypeptides. In some embodiments, disruption or degradation of lignocellulose by a lignocellulolytic enzyme polypeptide leads to the formation of substances including monosaccharides, disaccharides, polysaccharides, and phenols. In some embodiments, a lignocellulolytic enzyme polypeptide shares at least 50%, 60%, 70%, 80% or more overall identity with a polypeptide whose amino acid sequence is set forth in Table 1. Alternatively or additionally, in some embodiments, a lignocellulolytic enzyme polypeptide shows at least 90%, 95%, 96%, 97%, 98%, 99%, or greater identity with at least one sequence element found in a polypeptide whose amino acid sequence is set forth in Table 1, which sequence element is at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. It will be appreciated that the present invention describes use of lignocellulolytic enzyme polypeptides generally, but also use of particular lignocellulolytic enzyme polypeptides (e.g.,  Acidothermus cellulolyticus  E1 endo-1,4-β-glucanase polypeptide,  Acidothermus cellulolyticus  xylE polypeptide,  Acidothermus cellulolyticus  gux1 polypeptide,  Acidothermus cellulolyticus  aviIII polypeptide,  Talaromyces emersonii  cbhE polypeptide, and  Pyrococcus furiosus  faeE (ferulic acid esterase) polypeptide). 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Non-limiting examples of lignocellulolytic enzyme 
               
               
                 polypeptides that may be used in accordance with the invention. 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                   
                 GenBank 
                   
               
               
                 Gene 
                 Microbial 
                   
                 Accession 
                   
               
               
                 name 
                 species 
                 Amino Acid Sequence 
                 Number 
                 SEQ ID NO.: 
               
               
                   
               
               
                 E1 
                 
                   Acidothermus 
                 
                 AGGGYWHTSGREILDANNVPVRIAGINWFGFETCNYVVHGLW 
                 U33212 
                 2 
               
               
                   
                 
                   cellulo- 
                 
                 SRDYRSMLDQIKSLGYNTIRLPYSDDILKPGTMPNSINFYQM 
                   
                   
               
               
                   
                 
                   lyticus 
                 
                 NQDLQGLTSLQVMDKIVAYAGQIGLRIILDRHRPDCSGQSAL 
                   
                   
               
               
                   
                   
                 WYTSSVSEATWISDLQALAQRYKGNPTVVGFDLHNEPHDPAC 
                   
                   
               
               
                   
                   
                 WGCGDPSIDWRLAAERAGNAVLSVNPNLLIFVEGVQSYNGDS 
                   
                   
               
               
                   
                   
                 YWWGGNLQGAGQYPVVLNVPNRLVYSAHDYATSVYPQTWFSD 
                   
                   
               
               
                   
                   
                 PTFPNNMPGIWNKNWGYLFNQNIAPVWLGEFGTTLQSTTDQT 
                   
                   
               
               
                   
                   
                 WLKTLVQYLRPTAQYGADSFQWTFWSWNPDSGDTGGILKDDW 
                   
                   
               
               
                   
                   
                 QTVDTVKDGYLAPIKSSIFDPVG 
                   
                   
               
               
                   
               
               
                 gux 1 
                 
                   Acidothermus 
                 
                 MGAPGLRRRLRAGIVSAAALGSLVSGLVAVAPVAHAAVTLKA 
                 YP872376 
                 5 
               
               
                   
                 
                   cellulo- 
                 
                 QYKNNDSAPSDNQIKPGLQLVNTGSSSVDLSTVTVRYWFTRD 
                   
                   
               
               
                   
                 
                   lyticus 
                 
                 GGSSTLVYNCDWAAMGCGNIRASFGSVNPATPTADTYLQLSF 
                   
                   
               
               
                   
                   
                 TGGTLAAGGSTGEIQNRVNKSDWSNFDETNDYSYGTNTTFQD 
                   
                   
               
               
                   
                   
                 WTKVTVYVNGVLVWGTEPSGATASPSASATPSPSSSPTTSPS 
                   
                   
               
               
                   
                   
                 SSPSPSSSPTPTPSSSSPPPSSNDPYIQRFLTMYNKIHDPAN 
                   
                   
               
               
                   
                   
                 GYFSPQGIPYHSVETLIVEAPDYGHETTSEAYSFWLWLEATY 
                   
                   
               
               
                   
                   
                 GAVTGNWTPFNNAWTTMETYMIPQHADQPNNASYNPNSPASY 
                   
                   
               
               
                   
                   
                 APEEPLPSMYPVAIDSSVPVGHDPLAAELQSTYGTPDIYGMH 
                   
                   
               
               
                   
                   
                 WLADVDNIYGYGDSPGGGCELGPSAKGVSYINTFQRGSQESV 
                   
                   
               
               
                   
                   
                 WETVTQPTCDNGKYGGAHGYVDLFIQGSTPPQWKYTDAPDAD 
                   
                   
               
               
                   
                   
                 ARAVQAAYWAYTWASAQGKASAIAPTIAKAAKLGDYLRYSLF 
                   
                   
               
               
                   
                   
                 DKYFKQVGNCYPASSCPGATGRQSETYLIGWYYAWGGSSQGW 
                   
                   
               
               
                   
                   
                 AWRIGDGAAHFGYQNPLAAWAMSNVTPLIPLSPTAKSDWAAS 
                   
                   
               
               
                   
                   
                 LQRQLEFYQWLQSAEGAIAGGATNSWNGNYGTPPAGDSTFYG 
                   
                   
               
               
                   
                   
                 MAYDWEPVYHDPPSNNWFGFQAWSMERVAEYYYVTGDPKAKA 
                   
                   
               
               
                   
                   
                 LLDKWVAWVKPNVTTGASWSIPSNLSWSGQPDTWNPSNPGTN 
                   
                   
               
               
                   
                   
                 ANLHVTITSSGQDVGVAAALAKTLEYYAAKSGDTASRDLAKG 
                   
                   
               
               
                   
                   
                 LLDSIWNNDQDSLGVSTPETRTDYSRFTQVYDPTTGDGLYIP 
                   
                   
               
               
                   
                   
                 SGWTGTMPNGDQIKPGATFLSIRSWYTKDPQWSKVQAYLNGG 
                   
                   
               
               
                   
                   
                 PAPTFNYHRFWAESDFAMANADFGMLFPSGSPSPTPSPTPTS 
                   
                   
               
               
                   
                   
                 SPSPTPSSSPTPSPSPSPTGDTTPPSVPTGLQVTGTTTSSVS 
                   
                   
               
               
                   
                   
                 LSWTASTDNVGVAHYNVYRNGTLVGQPTATSFTDTGLAAGTS 
                   
                   
               
               
                   
                   
                 YTYTVAAVDAAGNTSAQSSPVTATTASPSPSPSPSPTPTSSP 
                   
                   
               
               
                   
                   
                 SPTPSPTPSPTSTSGASCTATYVVNSDWGSGFTTTVTVTNTG 
                   
                   
               
               
                   
                   
                 TRATSGWTVTWSFAGNQTVTNYWNTALTQSGKSVTAKNLSYN 
                   
                   
               
               
                   
                   
                 NVIQPGQSTTFGFNGSYSGTNTAPTLSCTASZ 
                   
                   
               
               
                   
               
               
                 XylE 
                 
                   Acidothermus 
                 
                 MGHHAMRRMVTSASVVGVATLAAATVLITGGIAHAASTLKQG 
                 YP871941 
                 6 
               
               
                   
                 
                   cellulo- 
                 
                 AEANGRYFGVSASVNTLNNSAAANLVATQFDMLTPENEMKWD 
                   
                   
               
               
                   
                 
                   lyticus 
                 
                 TVESSRGSFNFGPGDQIVAFATAHNMRVRGHNLVWHSQLPGW 
                   
                   
               
               
                   
                   
                 VSSLPLSQVQSAMESHITAEVTHYKGKIYAWDVVNEPFDDSG 
                   
                   
               
               
                   
                   
                 NLRTDVFYQAMGAGYIADALRTAHAADPNAKLYLNDYNIEGI 
                   
                   
               
               
                   
                   
                 NAKSDAMYNLIKQLKSQGVPIDGVGFESHFIVGQVPSTLQQN 
                   
                   
               
               
                   
                   
                 MQRFADLGVDVAITELDDRMPTPPSQQNLNQQATDDANVVKA 
                   
                   
               
               
                   
                   
                 CLAVARCVGITQWDVSDADSWVPGTFSGQGAATMFDSNLQPK 
                   
                   
               
               
                   
                   
                 PAFTAVLNALSASASVSPSPSPSPSPSPSPSPSPSPSPSPSP 
                   
                   
               
               
                   
                   
                 SPSPSPSSSPVSGGVKVQYKNNDSAPGDNQIKPGLQVVNTGS 
                   
                   
               
               
                   
                   
                 SSVDLSTVTVRYWFTRDGGSSTLVYNCDWAVMGCGNIRASFG 
                   
                   
               
               
                   
                   
                 SVNPATPTADTYLQLSFTGGTLPAGGSTGEIQSRVNKSDWSN 
                   
                   
               
               
                   
                   
                 FTETNDYSYGTNTTFQDWSKVTVYVNGRLVWGTEPSGTSPSP 
                   
                   
               
               
                   
                   
                 TPSPSPTPSPSPSPSPSPSPSPSPSPSPSPSSSPSSGCVASM 
                   
                   
               
               
                   
                   
                 RVDSSWPGGFTATVTVSNTGGVSTSGWQVGWSWPSGDSLVNA 
                   
                   
               
               
                   
                   
                 WNAVVSVTGTSVRAVNASYNGVIPAGGSTTFGFQANGTPGTP 
                   
                   
               
               
                   
                   
                 TFTCTTSADLZ 
                   
                   
               
               
                   
               
               
                 aviIII 
                 
                   Acidothermus 
                 
                 MAATTQPYTWSNVAIGGGGFVDGIVFNEGAPGILYVRTDIGG 
                 YP872377 
                 7 
               
               
                   
                 
                   cellulo- 
                 
                 MYRWDAANGRWIPLLDWVGWNNWGYNGVVSIAADPINTNKVW 
                   
                   
               
               
                   
                 
                   lyticus 
                 
                 AAVGMYTNSWDPNDGAILRSSDQGATWQITPLPFKLGGNMPG 
                   
                   
               
               
                   
                   
                 RGMGERLAVDPNNDNILYFGAPSGKGLWRSTDSGATWSQMTN 
                   
                   
               
               
                   
                   
                 FPDVGTYIANPTDTTGYQSDIQGVVWVAFDKSSSSLGQASKT 
                   
                   
               
               
                   
                   
                 IFVGVADPNNPVFWSRDGGATWQAVPGAPTGFIPHKGVFDPV 
                   
                   
               
               
                   
                   
                 NHVLYIATSNTGGPYDGSSGDVWKFSVTSGTWTRISPVPSTD 
                   
                   
               
               
                   
                   
                 TANDYFGYSGLTIDRQHPNTIMVATQISWWPDTIIFRSTDGG 
                   
                   
               
               
                   
                   
                 ATWTRIWDWTSYPNRSLRYVLDISAEPWLTFGVQPNPPVPSP 
                   
                   
               
               
                   
                   
                 KLGWMDEAMAIDPFNSDRMLYGTGATLYATNDLTKWDSGGQI 
                   
                   
               
               
                   
                   
                 HIAPMVKGLEETAVNDLISPPSGAPLISALGDLGGFTHADVT 
                   
                   
               
               
                   
                   
                 AVPSTIFTSPVFTTGTSVDYAELNPSIIVRAGSFDPSSQPND 
                   
                   
               
               
                   
                   
                 RHVAFSTDGGKNWFQGSEPGGVTTGGTVAASADGSRFVWAPG 
                   
                   
               
               
                   
                   
                 DPGQPVVYAVGFGNSWAASQGVPANAQIRSDRVNPKTFYALS 
                   
                   
               
               
                   
                   
                 NGTFYRSTDGGVTFQPVAAGLPSSGAVGVMFHAVPGKEGDLW 
                   
                   
               
               
                   
                   
                 LAASSGLYHSTNGGSSWSAITGVSSAVNVGFGKSAPGSSYPA 
                   
                   
               
               
                   
                   
                 VFVVGTIGGVTGAYRSDDGGTTWVRINDDQHQYGNWGQAITG 
                   
                   
               
               
                   
                   
                 DPRIYGRVYIGTNGRGIVYGDIAGAPSGSPSPSVSPSASPSL 
                   
                   
               
               
                   
                   
                 SPSPSPSSSPSPSPSPSSSPSSSPSPSPSPSPSPSRSPSPSA 
                   
                   
               
               
                   
                   
                 SPSPSSSPSPSSSPSSSPSPTPSSSPVSGGVKVQYKNNDSAP 
                   
                   
               
               
                   
                   
                 GDNQIKPGLQVVNTGSSSVDLSTVTVRYWFTRDGGSSTLVYN 
                   
                   
               
               
                   
                   
                 CDWAAIGCGNIRASFGSVNPATPTADTYLQLSFTGGTLAAGG 
                   
                   
               
               
                   
                   
                 STGEIQNRVNKSDWSNFTETNDYSYGTNTVFQDWSKVTVYVN 
                   
                   
               
               
                   
                   
                 GRLVWGTEPSGTSPSPTPSPSPTPSPSPSPSPGGDVTPPSVP 
                   
                   
               
               
                   
                   
                 TGVVVTGVSGSSVSLAWNASTDNVGVAHYNVYRNGVLVGQPT 
                   
                   
               
               
                   
                   
                 VTSFTDTGLAAGTAYTYTVAAVDAAGNTSAPSTPVTATTTSP 
                   
                   
               
               
                   
                   
                 SPSPSPTPSPTPSPTPSPSPSPSLSPSPSPSPSPSPSPSLSP 
                   
                   
               
               
                   
                   
                 SPSTSPSPSPSPTPSPSSSGVGCRATYVVNSDWGSGFTATVT 
                   
                   
               
               
                   
                   
                 VTNTGSRATSGWTVAWSFGGNQTVTNYWNTLLTQSGASVTAT 
                   
                   
               
               
                   
                   
                 NLSYNNVIQPGQSTTFGFNATYAGTNTPPTPTCTTNSD 
               
               
                   
               
            
           
         
       
     
     As used herein, the term “nucleic acid construct” refers to a polynucleotide or oligonucleotide comprising nucleic acid sequences not normally associated in nature. A nucleic acid construct of the present invention is prepared, isolated, or manipulated by the hand of man. The terms “nucleic acid”, “polynucleotide” and “oligonucleotide” are used herein interchangeably and refer to a deoxyribonucleotide (DNA) or ribonucleotide (RNA) polymer either in single- or double-stranded form. For the purposes of the present invention, these terms are not to be construed as limited with respect to the length of the polymer and should also be understood to encompass analogs of DNA or RNA polymers made from analogs of natural nucleotides and/or from nucleotides that are modified in the base, sugar and/or phosphate moieties. 
     As used herein, the term “operably linked” refers to a relationship between two nucleic acid sequences wherein the expression of one of the nucleic acid sequences is controlled by, regulated by or modulated by the other nucleic acid sequence. Preferably, a nucleic acid sequence that is operably linked to a second nucleic acid sequence is covalently linked, either directly or indirectly, to such second sequence, although any effective three-dimensional association is acceptable. A single nucleic acid sequence can be operably linked to multiple other sequences. For example, a single promoter can direct transcription of multiple RNA species. 
     As will be clear from the context, the term “plant”, as used herein, can refer to a whole plant, plant parts (e.g., cuttings, tubers, pollen), plant organs (e.g., leaves, stems, flowers, roots, fruits, branches, etc.), individual plant cells, groups of plant cells (e.g., cultured plant cells), protoplasts, plant extracts, seeds, and progeny thereof. The class of plants which can be used in the methods of the present invention is as broad as the class of higher plants amenable to transformation techniques, including both monocotyledonous and dicotyledonous plants, as well as certain lower plants such as algae. The term includes plants of a variety of a ploidy levels, including polyploid, diploid and haploid. In certain embodiments of the invention, plants are green field plants. In other embodiments, plants are grown specifically for “biomass energy”. For example, suitable plants include, but are not limited to, corn, switchgrass, sorghum, miscanthus, sugarcane, poplar, pine, wheat, rice, soy, cotton, barley, turf grass, tobacco, bamboo, rape, sugar beet, sunflower, willow, and eucalyptus. Using transformation methods, genetically modified plants, plant cells, plant tissue, seeds, and the like can be obtained. 
     The term “polypeptide”, as used herein, generally has its art-recognized meaning of a polymer of at least three amino acids. However, the term is also used to refer to specific functional classes of polypeptides, such as, for example, lignocellulolytic enzyme polypeptides (including, for example,  Acidothermus cellulolyticus  E1 endo-1,4-β-glucanase polypeptide,  Acidothermus cellulolyticus  xylE polypeptide, Acidothermus cellulolyticus gux1 polypeptide,  Acidothermus cellulolyticus  aviIII polypeptide,  Talaromyces emersonii  cbhE polypeptide, and  Pyrococcus furiosus  faeE (ferulic acid esterase) polypeptide). For each such class, the present specification provides specific examples of known sequences of such polypeptides. Those of ordinary skill in the art will appreciate, however, that the term “polypeptide” is intended to be sufficiently general as to encompass not only polypeptides having the complete sequence recited herein (or in a reference or database specifically mentioned herein), but also to encompass polypeptides that represent functional fragments (i.e., fragments retaining at least one activity) of such complete polypeptides. Moreover, those of ordinary skill in the art understand that protein sequences generally tolerate some substitution without destroying activity. Thus, any polypeptide that retains activity and shares at least about 30-40% overall sequence identity, often greater than about 50%, 60%, 70%, or 80%, and further usually including at least one region of much higher identity, often greater than 90% or even 95%, 96%, 97%, 98%, or 99% in one or more highly conserved regions, usually encompassing at least 3-4 and often up to 20 or more amino acids, with another polypeptide of the same class, is encompassed within the relevant term “polypeptide” as used herein. Other regions of similarity and/or identity can be determined by those of ordinary skill in the art by analysis of the sequences of various polypeptides presented herein. 
     As used herein, the terms “promoter” and “promoter element” refer to a polynucleotide that regulates expression of a selected polynucleotide sequence operably linked to the promoter, and which effects expression of the selected polynucleotide sequence in cells. The term “plant promoter”, as used herein, refers to a promoter that functions in a plant. In some embodiments of the invention, the promoter is a constitutive promoter, i.e., an unregulated promoter that allows continual expression of a gene associated with it. A constitutive promoter may in some embodiments allow expression of an associated gene throughout the life of the plant. Examples of constitutive plant promoters include, but are not limited to, rice actl promoter, Cauliflower mosaic virus (CaMV) 35S promoter, and nopaline synthase promoter from  Agrobacterium tumefaciens . In some embodiments of the invention, the promoter is a tissue-specific promoter that selectively functions in a part of a plant body, such as a flower. In some embodiments of the invention, the promoter is a developmentally specific promoter. In some embodiments of the invention, the promoter is an inducible promoter. In some embodiments of the invention, the promoter is a senescence promoter, i.e., a promoter that allows transcription to be initiated upon a certain event relating to the age of the organism. 
     As used herein, the term “protoplast” refers to an isolated plant cell without cell walls which has the potency for regeneration into cell culture or a whole plant. 
     As used herein, the term “regeneration” refers to the process of growing a plant from a plant cell (e.g., plant protoplast, plant callus or plant explant). 
     As used herein, the term “stably transformed”, when applied to a plant cell, callus or protoplast refers to a cell, callus or protoplast in which an inserted exogenous nucleic acid molecule is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome. The stability is demonstrated by the ability of the transformed cells to establish cell lines or clones comprised of a population of daughter cells containing the exogenous nucleic acid molecule. 
     As used herein, the term “transformation” refers to a process by which an exogenous nucleic acid molecule (e.g., a vector or recombinant DNA molecule) is introduced into a recipient cell, callus or protoplast. The exogenous nucleic acid molecule may or may not be integrated into (i.e., covalently linked to) chromosomal DNA making up the genome of the host cell, callus or protoplast. For example, the exogenous polynucleotide may be maintained on an episomal element, such as a plasmid. Alternatively, the exogenous polynucleotide may become integrated into a chromosome so that it is inherited by daughter cells through chromosome replication. Methods for transformation include, but are not limited to, electroporation, magnetoporation, Ca 2−  treatment, injection, particle bombardment, retroviral infection, and lipofection. 
     The term “transgene”, as used herein, refers to an exogenous gene which, when introduced into a host cell through the hand of man, for example, using a process such as transformation, electroporation, particle bombardment, and the like, is expressed by the host cell and integrated into the cell&#39;s DNA such that the trait or traits produced by the expression of the transgene is inherited by the progeny of the transformed cell. A transgene may be partly or entirely heterologous (i.e., foreign to the cell into which it is introduced). Alternatively, a transgene may be homologous to an endogenous gene of the cell into which it is introduced, but is designed to be inserted (or is inserted) into the cell&#39;s genome in such a way as to alter the genome of the cell (e.g., it is inserted at a location which differs from that of the natural gene or its insertion results in a knockout). A transgene can also be present in a cell in the form of an episome. A transgene can include one or more transcriptional regulatory sequences and other nucleic acids, such as introns. Alternatively or additionally, a transgene is one that is not naturally associated with the vector sequences with which it is associated according to the present invention. 
     Detailed Description of Certain Embodiments 
     As mentioned above, the present invention relates to improved systems and strategies for reducing costs and increasing yields of ethanol production from lignocellulosic biomass. 
     I. Lignocellulolytic Enzyme Polypeptides 
     In one aspect, the present invention provides plants engineered (i.e., genetically transformed) to produce one or more lignocellulolytic enzyme polypeptides. Suitable lignocellulolytic enzyme polypeptides include enzymes that are involved in the disruption and/or degradation of lignocellulose. Lignocellulosic biomass is a complex substrate in which crystalline cellulose is embedded within a matrix of hemicellulose and lignin. Lignocellulose represents approximately 90% of the dry weight of most plant material with cellulose making up between 30% to 50% of the dry weight of lignocellulose and hemicellulose making up between 20% and 50% of the dry weight of lignocellulose. 
     Disruption and degradation (e.g., hydrolysis) of lignocellulose by lignocellulolytic enzyme polypeptides leads to the formation of substances including monosaccharides, disaccharides, polysaccharides and phenols. Lignocellulolytic enzyme polypeptides include, but are not limited to, cellulases, hemicellulases and ligninases. Representative examples of lignocellulolytic enzyme polypeptides are presented in Table 1. 
     A—Cellulases 
     Cellulases are enzyme polypeptides involved in cellulose degradation. Cellulase enzyme polypeptides are classified on the basis of their mode of action. There are two basic kinds of cellulases: the endocellulases, which cleave the polymer chains internally; and the exocellulases, which cleave from the reducing and non-reducing ends of molecules generated by the action of endocellulases. Cellulases include cellobiohydrolases, endoglucanases, and β-D-glucosidases. Endoglucanases randomly attack the amorphous regions of cellulose substrate, yielding mainly higher oligomers. Cellulobiohydrolases are exocellulases which hydrolyze crystalline cellulose and release cellobiose (glucose dimer). Both types of enzymes hydrolyze β-1,4-glycosidic bonds. β-D-glucosidases or cellulobiase converts oligosaccharides and cellubiose to glucose. 
     According to the present invention, plants may be engineered to comprise a gene encoding a cellulase enzyme polypeptide. Alternatively, plants may be engineered to comprise more than one gene encoding a cellulase enzyme polypeptide. For example, plants may be engineered to comprise one or more genes encoding a cellulase of the cellobiohydrolase class, one or more genes encoding a cellulase of the endoglucanase class, and/or one or more genes encoding a cellulase of the β-D-glucosidase class. 
     Examples of endoglucanase genes that can be used in the present invention can be obtained from  Aspergillus aculeatus  (U.S. Pat. No. 6,623,949; WO 94/14953),  Aspergillus kawachii  (U.S. Pat. No. 6,623,949),  Aspergillus oryzae  (Kitamoto et al., Appl. Microbiol. Biotechnol., 1996, 46: 538-544; U.S. Pat. No. 6,635,465),  Aspergillus nidulans  (Lockington et al., Fungal Genet. Biol., 2002, 37: 190-196),  Cellulomonas fimi  (Wong et al., Gene, 1986, 44: 315-324),  Bacillus subtilis  (MacKay et al., Nucleic Acids Res., 1986, 14: 9159-9170),  Cellulomonas pachnodae  (Cazemier et al., Appl. Microbiol. Biotechnol., 1999, 52: 232-239),  Fusarium equiseti  (Goedegebuur et al., Curr. Genet., 2002, 41: 89-98),  Fusarium oxysporum  (Hagen et al., Gene, 1994, 150: 163-167; Sheppard et al., Gene, 1994, 150: 163-167),  Humicola insolens  (U.S. Pat. No. 5,912,157; Davies et al., Biochem J., 2000, 348: 201-207),  Hypocrea jecorina  (Penttila et al., Gene,1986, 45: 253-263),  Humicola grisea  (Goedegebuur et al., Curr. Genet., 2002, 41: 89-98),  Micromonospora cellulolyticum  (Lin et al., J. Ind. Microbiol., 1994, 13: 344-350),  Myceliophthora thermophila  (U.S. Pat. No. 5,912,157), Rhizopus oryzae (Moriya et al., J. Bacteriol., 2003, 185: 1749-1756),  Trichoderma reesei  (Saloheimo et al., Mol. Microbiol., 1994, 13: 219-228), and  Trichoderma viride  (Kwon et al., Biosci. Biotechnol. Biochem., 1999, 63: 1714-1720; Goedegebuur et al., Curr. Genet., 2002, 41: 89-98). 
     In certain embodiments, plants are engineered to comprise the endo-1,4-β-glucanase E1 gene (GenBank Accession No. U33212, See Table 1). This gene was isolated from the thermophilic bacterium  Acidothermus cellulolyticus. Acidothermus cellulolyticus  has been characterized with the ability to hydrolyze and degrade plant cellulose. The cellulase complex produced by A. cellulolyticus is known to contain several different thermostable cellulase enzymes with maximal activities at temperatures of 75° C. to 83° C. These cellulases are resistant to inhibition from cellobiose, an end product of the reactions catalyzed by endo- and exo-cellulases. 
     The E1 endo-1,4-β-glucanase is described in detail in U.S. Pat. No. 5,275,944. This endoglucanase demonstrates a temperature optimum of 83° C. and a specific activity of 40 μmol glucose release from carboxymethylcellulose/min/mg protein. This E1 endoglucanase was further identified as having an isoelectric pH of 6.7 and a molecular weight of 81,000 daltons by SDS polyacrylamide gel electrophoresis. It is synthesized as a precursor with a signal peptide that directs it to the export pathway in bacteria. The mature enzyme polypeptide is 521 amino acids (aa) in length. The crystal structure of the catalytic domain of about 40 kD (358 aa) has been described (J. Sakon et al., Biochem., 1996, 35: 10648-10660). Its pro/thr/ser-rich linker is 60 aa, and the cellulose binding domain (CBD) is 104 aa. The properties of the cellulose binding domain that confer its function are not well-characterized. Plant expression of the E1 gene has been reported (see for example, M. T. Ziegler et al., Mol. Breeding, 2000, 6: 37-46; Z. Dai et al., Mol. Breeding, 2000, 6: 277-285; Z. Dai et al., Transg. Res., 2000, 9: 43-54; and T. Ziegelhoffer et al., Mol. Breeding, 2001, 8: 147-158). 
     Examples of cellobiohydrolase genes that can be used in the present invention can be obtained from  Acidothermus cellulolyticus, Acremonium cellulolyticus  (U.S. Pat. No. 6,127,160),  Agaricus bisporus  (Chow et al., Appl. Environ. Microbiol., 1994, 60: 2779-2785),  Aspergillus aculeatus  (Takada et al., J. Ferment. Bioeng., 1998, 85: 1-9),  Aspergillus niger  (Gielkens et al., Appl. Environ. Microbiol., 65: 1999, 4340-4345),  Aspergillus oryzae  (Kitamoto et al., Appl. Microbiol. Biotechnol., 1996, 46: 538-544),  Athelia rolfsii  (EMBL accession No. AB103461),  Chaetomium thermophilum  (EMBL accession Nos. AX657571 and CQ838150),  Cullulomonas fimi  (Meinke et al., Mol. Microbiol., 1994, 12: 413-422),  Emericella nidulans  (Lockington et al., Fungal Genet. Biol., 2002, 37: 190-196),  Fusarium oxysporum  (Hagen et al., Gene, 1994, 150: 163-167),  Geotrichum  sp. 128 (EMBL accession No. AB089343),  Humicola grisea  (de Oliviera and Radford, Nucleic Acids Res., 1990, 18: 668; Takashima et al., J. Biochem., 1998, 124: 717-725),  Humicola nigrescens  (EMBL accession No. AX657571), Hypocrea koningii (Teeri et al., Gene, 1987, 51: 43-52),  Mycelioptera thermophila  (EMBL accession No. AX657599),  Neocallimastix patriciarum  (Denman et al., Appl. Environ. Microbiol., 1996, 62: 1889-1896),  Phanerochaete chrysosporium  (Tempelaars et al., Appl. Environ. Microbiol., 1994, 60: 4387-4393),  Thermobifida fusca  (Zhang, Biochemistry, 1995, 34: 3386-3395),  Trichoderma reesei  (Terri et al., BioTechnology, 1983, 1: 696-699; Chen et al., BioTechnology, 1987, 5: 274-278), and  Trichoderma viride  (EMBL accession Nos. A4368686 and A4368688). 
     Examples of β-D-glucosidase genes that can be used in the present invention can be obtained from  Aspergillus aculeatus  (Kawaguchi et al., Gene, 1996, 173: 287-288),  Aspergillus kawachi  (Iwashita et al., Appl. Environ. Microbiol., 1999, 65: 5546-5553),  Aspergillus oryzae  (WO 2002/095014),  Cellulomonas biazotea  (Wong et al., Gene, 1998, 207: 79-86),  Penicillium funiculosum  (WO 200478919),  Saccharomycopsis fibuligera  (Machida et al., Appl. Environ. Microbiol., 1988, 54: 3147-3155),  Schizosaccharomyces pombe  (Wood et al., Nature, 2002, 415: 871-880), and  Trichoderma reesei  (Barnett et al., BioTechnology, 1991, 9: 562-567). 
     Other examples of cellulases that can be used in accordance with the present invention include family 48 glycoside hydrolases such as gux 1 from  Acidothermus cellulolyticus , avicelases such as aviIII from  Acidothermus cellulolyticus , and cbhE from  Talaromyces emersonii . (See Table 1.) 
     Transgene expression of cellulases in plants for the conversion of cellulose to glucose has been reported (see, for example, Y. Jin Cai et al., Appl. Environ. Microbiol., 1999, 65: 553-559; C. R. Sanchez et al., Revista de Microbiologica, 1999, 30: 310-314; R. Cohen et al., Appl. Environ., 2995, 71: 2412-2417; Z. Dai et al., Transg. Res., 2005, 14: 627-543). 
     B—Hemicellulases 
     Hemicellulases are enzyme polypeptides that are involved in hemicellulose degradation. Hemicellulases include xylanases (including endo-xylanases, exo-xylanases, and beta-xylosidases), arabinofuranosidases, acetyl xylan esterases, glucuronidases, mannanases, galactanases, arabinases, xyloglucanases, beta-glucanases, and ferulic acid esterases. Similar to cellulase enzyme polypeptides, hemicellulases are classified on the basis of their mode of action: the endo-acting hemicellulases attack internal bonds within the polysaccharide chain; the exo-acting hemicellulases act progressively from either the reducing or non-reducing end of polysaccharide chains. 
     According to the present invention, plants may be engineered to comprise a gene encoding a hemicellulase enzyme polypeptide. Alternatively, plants may be engineered to comprise more than one gene encoding a hemicellulase enzyme polypeptide. For example, plants may be engineered to comprise one or more genes encoding a hemicellulase of the xylanase class, one or more genes encoding a hemicellulase of the arabinofuranosidase class, one or more genes encoding a hemicellulase of the acetyl xylan esterase class, one or more genes encoding a hemicellulase of the glucuronidase class, one or more genes encoding a hemicellulase of the mannanase class, one or more genes encoding a hemicellulase of the galactanase class, and/or one or more genes encoding a hemicellulase of the arabinase class. 
     Examples of endo-acting hemicellulases include endoarabinanase, endoarabinogalactanase, endoglucanase, endomannanase, endoxylanase, and feraxan endoxylanase. Examples of exo-acting hemicellulases include α-L-arabinosidase, β-L-arabinosidase, α-1,2-L-fucosidase, α-D-galactosidase, β-D-galactosidase, β-D-glucosidase, β-D-glucuronidase, β-D-mannosidase, β-D-xylosidase, exo-glucosidase, exo-cellobiohydrolase, exo-mannobiohydrolase, exo-mannanase, exo-xylanase, xylan α-glucuronidase, and coniferin β-glucosidase. 
     Hemicellulase genes can be obtained from any suitable source, including fungal and bacterial organisms, such as  Aspergillus, Disporotrichum, Penicillium, Neurospora, Fusarium, Trichoderma, Humicola, Thermomyces , and  Bacillus . Examples of hemicellulases that can be used in the present invention can be obtained from  Acidothermus cellulolyticus, Acidobacterium capsulatum  (Inagaki et al., Biosci. Biotechnol. Biochem., 1998, 62: 1061-1067),  Agaricus bisporus  (De Groot et al., J. Mol. Biol., 1998, 277: 273-284),  Aspergillus aculeatus  (U.S. Pat. No. 6,197,564; U.S. Pat. No. 5,693,518),  Aspergillus kawachii  (Ito et al., Biosci. Biotechnol. Biochem., 1992, 56: 906-912),  Aspergillus niger  (EMBL accession No. AF108944),  Magnaporthe grisea  (Wu et al., Mol. Plant Microbe Interact., 1995, 8: 506-514),  Penicillium chrysogenum  (Haas et al., Gene, 1993, 126: 237-242),  Talaromyces emersonii  (WO 02/24926), and  Trichoderma reesei  (EMBL accession Nos. X69573, X69574, and AY281369). 
     In certain embodiments, plants are engineered to comprise the  A. cellulolyticus  endoxylanase xylE (see the Examples section). 
     C—Ligninases 
     Ligninases are enzyme polypeptides that are involved in the degradation of lignin. Lignin-degrading enzyme polypeptides include, but are not limited to, lignin peroxidases, manganese-dependent peroxidases, hybrid peroxidases (which exhibit combined properties of lignin peroxidases and manganese-dependent peroxidases), and laccases. Hydrogen peroxide, required as co-substrate by the peroxidases, can be generated by glucose oxidase, aryl alcohol oxidase, and/or lignin peroxidase-activated glyoxal oxidase. 
     According to the present invention, plants may be engineered to comprise a gene encoding a ligninase enzyme polypeptide. Alternatively, plants may be engineered to comprise more than one gene encoding a ligninase enzyme polypeptide. For example, plants may be engineered to comprise one or more genes encoding a ligninase of the lignin peroxidase class, one or more genes encoding a ligninase of the manganese-dependent peroxidase class, one or more genes encoding a ligninase of the hybrid peroxidase class, and/or one or more genes encoding a ligninase of the laccase class. 
     Lignin-degrading genes may be obtained from  Acidothermus cellulolyticus, Bjerkandera adusta, Ceriporiopsis subvermispora  (see WO 02/079400),  Coprinus cinereus, Coriolus hirsutus, Humicola insolens, Humicola lanuginosa, Mucor miehei, Myceliophthora thermophila, Neurospora crassa, Penicillium purpurogenum, Phanerochaete chrysosporium, Phlebia radiata, Pleurotus eryngii, Thielavia terrestris, Trametes villosa, Trametes versicolor, Trichoderma harzianum, Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma reesei , or  Trichoderma viride.    
     Examples of genes encoding ligninases that can be used in the invention can be obtained from Bjerkandera adusta (WO 2001/098469),  Ceriporiopsis subvermispora  (Conesa et al., J. Biotechnol., 2002, 93: 143-158),  Cantharellus cibariusi  (Ng et al., Biochem. and Biophys. Res. Comm., 2004, 313: 37-41),  Coprinus cinereus  (WO 97/008325; Conesa et al., J. Biotechnol., 2002, 93: 143-158),  Lentinula edodes  (Nagai et al., Applied Microbiol. and Biotechnol., 2002, 60: 327-335, 2002),  Melanocarpus albomyces  (Kiiskinen et al., FEBS Letters, 2004, 576: 251-255, 2004),  Myceliophthora thermophila  (WO 95/006815),  Phanerochaete chrysosporium  (Conesa et al., J. Biotechnol., 2002, 93: 143-158; Martinez, Enz, Microb, Technol, 2002, 30: 425-444),  Phlebia radiata  (Conesa et al., J. Biotechnol., 2002, 93: 143-158),  Pleurotus eryngii  (Conesa et al., J. Biotechnol., 2002, 93: 143-158),  Polyporus pinsitus  (WO 96/000290),  Rigidoporus lignosus  (Garavaglia et al., J. of Mol. Biol., 2004, 342: 1519-1531),  Rhizoctonia solani  (WO 96/007988),  Scytalidium thermophilum  (WO 95/033837),  Tricholoma giganteum  (Wang et al., Biochem. Biophys. Res. Comm., 2004, 315: 450-454), and  Trametes versicolor  (Conesa et al., J. Biotechnol., 2002, 93: 143-158). 
     For example, plants may be engineered to comprise one or more lignin peroxidases. Genes encoding lignin peroxidases may be obtained from  Phanerochaete chrysosporium  or  Phlebia radiata . Lignin-peroxidases are glycosylated heme proteins (MW 38 to 46 kDa) which are dependent on hydrogen peroxide for activity and catalyze the oxidative cleavage of lignin polymer. At least six (6) heme proteins (H1, H2, H6, H7, H8 and H10) with lignin peroxidase activity have been identified Phanerochaete chrysosporium in strain BKMF-1767. In certain embodiments, plants are engineered to comprise the white rot filamentous  Phanerochaete chrysosporium  ligninase (CGL5) (H. A. de Boer et al., Gene, 1988, 69(2): 369) (see the Examples section). 
     D—Other Lignocellulolytic Enzyme Polypeptides 
     In addition to cellulases, hemicellulases and ligninases, lignocellulolytic enzyme polypeptides that can be used in the practice of the present invention also include enzymes that degrade pectic substances or phenolic acids such as ferulic acid. Pectic substances are composed of homogalacturonan (or pectin), rhamno-galacturonan, and xylogalacturonan. Enzymes that degrade homogalacturonan include pectate lyase, pectin lyase, polygalacturonase, pectin acetyl esterase, and pectin methyl esterase. Enzymes that degrade rhamnogalacturonan include alpha-arabinofuranosidase, beta-galactosidase, galactanase, arabinanase, alpha-arabinofuranosidase, rhamnogalacturonase, rhamnogalacturonan lyase, and rhamnogalacturonan acetyl esterase. Enzymes that degrade xylogalacturonan include xylogalacturonosidase, xylogalacturonase, and rhamnogalacturonan lyase. 
     Phenolic acids include ferulic acid, which functions in the plant cell wall to cross-link cell wall components together. For example, ferulic acid may cross-link lignin to hemicellulose, cellulose to lignin, and/or hemicellulose polymers to each other. Ferulic acid esterases cleave ferulic acid from the arabinose side-chains of xylan, disrupting cross linkages to lignin. 
     Other enzymes that may enhance or promote lignocellulose disruption and/or degradation include, but are not limited to, amylases (e.g., alpha amylase and glucoamylase), esterases, lipases, phospholipases, phytases, proteases, and peroxidases. 
     E—Combinations of Lignocellulolytic Enzyme Polypeptides 
     According to the present invention, plants may be engineered to comprise a gene encoding a lignocellulolytic enzyme polypeptide, e.g., a cellulase enzyme polypeptide, a hemicellulase enzyme polypeptide, or a ligninase enzyme polypeptide. Alternatively, plants may be engineered to comprise two or more genes encoding lignocellulolytic enzyme polypeptides, e.g., enzymes from different classes of cellulases, enzymes from different classes of hemicellulases, enzymes from different classes of ligninases, or any combinations thereof. For example, combinations of genes may be selected to provide efficient degradation of one component of lignocellulose (e.g., cellulose, hemicellulose, or lignin). Alternatively, combinations of genes may be selected to provide efficient degradation of the lignocellulosic material. 
     In certain embodiments, genes are optimized for the substrate (e.g., cellulose, hemicellulase, lignin or whole lignocellulosic material) in a particular plant (e.g., corn, tobacco, switchgrass). Tissue from one plant species is likely to be physically and/or chemically different from tissue from another plant species. Selection of genes or combinations of genes to achieve efficient degradation of a given plant tissue is within the skill of artisans in the art. 
     In some embodiments, combinations of genes are selected to provide for synergistic enzymes activity (i.e., genes are selected such that the interaction between distinguishable enzymes or enzyme activities results in the total activity of the enzymes taken together being greater than the sum of the effects of the individual activities). 
     Efficient lignocellulolytic activity may be achieved by production of two or more enzymes in a single transgenic plant. As mentioned above, plants may be transformed to express more than one enzyme, for example, by employing the use of multiple gene constructs encoding each of the selected enzymes or a single construct comprising multiple nucleotide sequences encoding each of the selected enzymes. Alternatively, individual transgenic plants, each stably transformed to express a given enzyme, may be crossed by methods known in the art (e.g., pollination, hand detassling, cytoplasmic male sterility, and the like) to obtain a resulting plant that can produce all the enzymes of the individual starting plants. 
     Alternatively or additionally, efficient lignocellulolytic activity may be achieved by production of two or more lignocellulolytic enzyme polypeptides in separate plants. For example, three separate lines of plants (e.g., corn), one expressing one or more enzymes of the cellulase class, another expressing one or more enzymes of the hemicellulase class and the third one expressing one or more enzymes of the ligninase class, may be developed and grown simultaneously. The desired “blend” of enzymes produced may be achieved by simply changing the seed ratio, taking into account farm climate and soil type, which are expected to influence enzyme yields in plants. 
     Other advantages of this approach include, but are not limited to, increased plant health (which is known to be adversely affected as the number of introduced genes increases), simpler transformations procedures and great flexibility in incorporating the desired traits in commercial plant varieties for large-scale production. 
     G—Thermophilic and Thermostable Enzyme Polypeptides 
     It may be sometimes desirable to use transgenic plants expressing thermophilic and/or thermostable enzyme polypeptides. For example, enzyme polypeptides whose optimal range of temperature for activity (thermophilic enzyme polypeptides) may be expressed in transgenic plants in accordance with the invention. Without wishing to be bound by any particular theory, the limited activity or absence of activity during growth of the plant (at moderate or low temperatures, at which the enzyme polypeptide is less active) may be beneficial to the health of the plant. Alternatively or additionally, and without wishing to be bound by any particular theory, such enzyme polypeptides may facilitate increased hydrolysis because of their high activity at high temperature conditions commonly used in the processing of cellulosic biomass. 
     In some embodiments, the present invention provides a transgenic plant, the genome of which is augmented with a recombinant polynucleotide encoding at least one lignocellulolytic enzyme polypeptide that exhibits low activity at a temperature below about 60° C., below about 50° C., below about 40° C., or below about 30° C. In some embodiments, the present invention provides a transgenic plant, the genome of which is augmented with a recombinant polynucleotide encoding at least one lignocellulolytic enzyme polypeptide that exhibits high activity at a temperature above about 50° C., above about 60° C., above about 70° C., above about 80° C., or above about 90° C. 
     In some embodiments, the present invention provides a transgenic plant, the genome of which is augmented with a recombinant polynucleotide encoding at least one lignocellulolytic enzyme polypeptide that is or is homologous to a lignocellulolytic enzyme polypeptide found in a thermophilic microorganism (e.g., bacterium, fungus, etc.). In some such embodiments, the thermophilic organism is a bacterium that is a member of a genus selected from the group consisting of  Aeropyrum, Acidilobus, Acidothermus, Aciduliprofundum, Anaerocellum, Archaeoglobus, Bacillus, Caldibacillus, Caldicellulosiruptor, Caldithrix, Cellulomonas, Chloroflexus, Clostridium, Cyanidium, Deferribacter, Desulfotomaculum, Desulfurella, Desulfurococcus, Fervidobacterium, Geobacillus, Geothermobacterium, Ignicoccus, Marinitoga, Methanocaldococcus, Methanococcus, Methanopyrus, Methanosarcina, Methanothermobacter, Nautilia, Pyrobaculum, Pyrococcus, Pyrodictium, Rhodothermus, Staphylothermus, Scylatidium, Spirochaeta, Sulfolobus, Thermoascus, Thermobifida, Thermococcus, Thermodesulfobacterium, Thermodesulfovibrio, Thermomicrobium, Thermoplasma, Thermoproteus, Thermothrix, Thermotoga, Thermus , and  Thiobacillus ; in some such embodiments, the thermophilic microorganism is a bacterium that is a member of a species selected from the group consisting of  Acidothermus cellulolyticus  and  Pyrococcus furiosus . In some embodmients, the thermophilic organism is a fungal organism that is a member of a genus selected from the group consisting of  Aspergillus, Chaetomium, Humicola, Rhizomucor , and  Talaromyces . In some such embodiments, the thermophilic organism is  Talaromyces emersonii.    
     II. Nucleic Acid Constructs 
     In many embodiments of the present invention, genomes of transgenic plants comprise recombinant polynucleotides that are introduced into such genomes as part of one or more nucleic acid constructs. Nucleic acid constructs to be used in the practice of the present invention generally encompass expression cassettes for expression in the plant of interest. The cassette generally includes 5′ and 3′ regulatory sequences operably linked to a nucleotide sequence encoding a lignocellulolytic enzyme polypeptide (e.g., a cellulase, a hemicellulase or ligninase). 
     Expression Cassettes 
     Techniques used to isolate or clone a gene encoding an enzyme (e.g., a lignocellulolytic enzyme polypeptide) are known in the art and include isolation from genomic DNA, preparation from cDNA, or a combination thereof. The cloning of a gene from such genomic DNA, can be effected, e.g., by using polymerase chain reaction (PCR) or antibody screening or expression libraries to detect cloned DNA fragments with shared structural features (Innis et al., “PCR: A Guide to Method and Application”, 1990, Academic Press: New York). Other nucleic acid amplification procedures such as ligase chain reaction (LCR), ligated activated transcription (LAT) and nucleotide sequence-based amplification (NASBA) may be used. 
     The expression cassette will generally include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region, a coding sequence for a lignocellulolytic enzyme polypeptide, and a transcriptional and translational termination region functional in plants. The transcriptional initiation region, i.e., the promoter, can be native or analogous (i.e., found in the native plant) or foreign or heterologous (i.e., not found in the native plant) to the plant host. Additionally, the promoter can be the natural sequence or alternatively a synthetic sequence. 
     In certain embodiments, the promoter is a constitutive plant promoter, i.e., an unregulated promoter that allows continual expression of a gene associated with it. Examples of plant promoters include, but are not limited to, the 35S cauliflower mosaic virus (CaMV) promoter, a promoter of nopaline synthase, and a promoter of octopine synthase. Examples of other constitutive promoters used in plants are the 19S promoter and promoters from genes encoding actin and ubiquitin. Promoters may be obtained from genomic DNA by using polymerase chain reaction (PCR), and then cloned into the construct. 
     The constitutive promoter may allow expression of an associated gene throughout the life of a plant. In some embodiments, the lignocellulolytic enzyme polypeptide is produced throughout the life of the plant. In some embodiments, the lignocellulolytic enzyme polypeptide is active through the life of the plant. Alternatively or additionally, a constitutive promoter may allow expression of an associated gene in all or a majority of plant tissues. In some embodiments, the lignocellulolytic enzyme polypeptide is present in all plant tissues during the life of the plant. 
     Other sequences that can be present in nucleic acid constructs are sequences that enhance gene expression such as intron sequences and leader sequences. Examples of introns that have been reported to enhance expression include, but are not limited to, the introns of the Maize AdhI gene and introns of the Maize bronzel gene (J. Callis et. al., Genes Develop. 1987, 1: 1183-1200). Examples of non-translated leader sequences that are known to enhance expression include, but are not limited to, leader sequences from Tobacco Mosaic Virus (TMV, the “omegasequence”), Maize Chlorotic Mottle Virus (MCMV), and Alfalfa Mosaic Virus (AlMV) (see, for example, D. R. Gallie et al., Nucl. Acids Res. 1987, 15: 8693-8711; J. M. Skuzeski et. al., Plant Mol. Biol. 1990, 15: 65-79). 
     The transcriptional and translational termination region can be native with the transcription initiation region, can be native with the operably linked polynucleotide sequence of interest, or can be derived from another source. Convenient termination regions are available from the T 1 -plasmid of  A. tumefaciens , such as the octopine synthase and nopaline synthase termination regions (An et al., Plant Cell, 1989, 1: 115-122; Guerineau et al., Mol. Gen. Genet. 1991, 262: 141-144; Proudfoot, Cell, 1991, 64: 671-674; Sanfacon et al., Genes Dev. 1991, 5: 141-149; Mogen et al., Plant Cell, 1990, 2:1261-1272; Munroe et al., Gene, 1990, 91:151-158; Ballas et al., Nucleic Acids Res., 1989, 17: 7891-7903; and Joshi et al., Nucleic Acid Res., 1987, 15: 9627-9639). 
     Where appropriate, the gene(s) or polynucleotide sequence(s) encoding the enzyme(s) of interest may be modified to include codons that are optimized for expression in the transformed plant (Campbell and Gowri, Plant Physiol., 1990, 92: 1-11; Murray et al., Nucleic Acids Res., 1989, 17: 477-498; Wada et al., Nucl. Acids Res., 1990, 18: 2367, and U.S. Pat. Nos. 5,096,825; 5,380,831; 5,436,391; 5,625,136, 5,670,356 and 5,874,304). Codon optimized sequences are synthetic sequences, and preferably encode the identical polypeptide (or an enzymatically active fragment of a full length polypeptide which has substantially the same activity as the full length polypeptide) encoded by the non-codon optimized parent polynucleotide that encodes a lignocellulolytic enzyme polypeptide. 
     Other Polynucleotide Sequences 
     Optional components of nucleic acid constructs include one or more marker genes. Marker genes are genes that impart a distinct phenotype to cells expressing the marker gene and thus allow transformed cells to be distinguished from cells that do not have the marker. Such genes may encode either a selectable or screenable marker. The characteristic phenotype allows the identification of cells, groups of cells, tissues, organs, plant parts or whole plants containing the construct. Many examples of suitable marker genes are known in the art. The marker may also confer additional benefit(s) to the transgenic plant such as herbicide resistance, insect resistance, disease resistance, and increased tolerance to environmental stress (e.g., drought). 
     Alternatively, a marker gene can provide some other visibly reactive response (e.g., may cause a distinctive appearance such as color or growth pattern relative to plants or plant cells not expressing the selectable marker gene in the presence of some substance, either as applied directly to the plant or plant cells or as present in the plant or plant cell growth media). It is now well known in the art that transcriptional activators of anthocyanin biosynthesis, operably linked to a suitable promoter in a construct, have widespread utility as non-phytotoxic markers for plant cell transformation. 
     Examples of markers that provide resistance to herbicides include, but are not limited to, the bar gene from Streptomyces hygroscopicus encoding phosphinothricin acetylase (PAT), which confers resistance to the herbicide glufosinate; mutant genes which encode resistance to imidazalinone or sulfonylurea such as genes encoding mutant form of the ALS and AHAS enzyme (Lee at al., EMBO J., 1988, 7: 1241; Miki et al., Theor. Appl. Genet., 1990, 80: 449; and U.S. Pat. No. 5,773,702); genes which confer resistance to glycophosphate such as mutant forms of EPSP synthase and aroA; resistance to L-phosphinothricin such as the glutamine synthetase genes; resistance to glufosinate such as the phosphinothricin acetyl transferase (PAT and bar) gene; and resistance to phenoxy propionic acids and cyclohexones such as the ACCAse inhibitor-encoding genes (Marshall et al., Theor. Appl. Genet., 1992, 83: 435). 
     Examples of genes which confer resistance to pests or disease include, but are not limited to, genes encoding a  Bacillus thuringiensis  protein such as the delta-endotoxin (U.S. Pat. No. 6,100,456); genes encoding lectins (Van Damme et al., Plant Mol. Biol., 1994, 24: 825); genes encoding vitamin-binding proteins such as avidin and avidin homologs which can be used as larvicides against insect pests; genes encoding protease or amylase inhibitors, such as the rice cysteine proteinase inhibitor (Abe et al., J. Biol. Chem., 1987, 262: 16793) and the tobacco proteinase inhibitor I (Hubb et al., Plant Mol. Biol., 1993, 21: 985); genes encoding insect-specific hormones or pheromones such as ecdysteroid and juvenile hormone, and variants thereof, mimetics based thereon, or an antagonists or agonists thereof; genes encoding insect-specific peptides or neuropeptides which, upon expression, disrupts the physiology of the pest; genes encoding insect-specific venom such as that produced by a wasp, snake, etc.; genes encoding enzymes responsible for the accumulation of monoterpenes, sesquiterpenes, asteroid, hydroxamic acid, phenylpropanoid derivative or other non-protein molecule with insecticidal activity; genes encoding enzymes involved in the modification of a biologically active molecule (U.S. Pat. No. 5,539,095); genes encoding peptides which stimulate signal transduction; genes encoding hydrophobic moment peptides such as derivatives of Tachyplesin which inhibit fungal pathogens; genes encoding a membrane permease, a channel former or channel blocker (Jaynes et al., Plant Sci., 1993, 89: 43); genes encoding a viral invasive protein or complex toxin derived therefrom (Beachy et al., Ann. Rev. Phytopathol., 1990, 28: 451); genes encoding an insect-specific antibody or antitoxin or a virus-specific antibody (Tavladoraki et al., Nature, 1993, 366: 469); and genes encoding a developmental-arrestive protein produced by a plant, pathogen or parasite which prevents disease. 
     Examples of genes which confer resistance to environmental stress include, but are not limited to, mtld and HVA1, which are genes that confer resistance to environmental stress factors; rd29A and rd19B, which are genes of Arabidopsis thaliana that encode hydrophilic proteins which are induced in response to dehydration, low temperature, salt stress, or exposure to abscisic acid and enable the plant to tolerate the stress (Yamaguchi-Shinozaki et al., Plant Cell, 1994, 6: 251-264). Other genes contemplated can be found in U.S. Pat. Nos. 5,296,462 and 5,356,816. 
     Tissue-Specific Expression 
     In certain embodiments, lignocellulolytic enzyme polypeptide expression is targeted to specific tissues of the transgenic plant such that the lignocellulolytic enzyme is present in only some plant tissues during the life of the plant. For example, tissue specific expression may be performed to preferentially express enzymes in leaves and stems rather than grain or seed (which can reduce concerns about human consumption of genetically modified organism (GMOs)). Tissue-specific expression has other benefits including targeted expression of enzyme(s) to the appropriate substrate. 
     Tissue specific expression may be functionally accomplished by introducing a constitutively expressed gene in combination with an antisense gene that is expressed only in those tissues where the gene product (e.g., lignocellulolytic enzyme polypeptide) is not desired. For example, a gene coding for a lignocellulolytic enzyme polypeptide may be introduced such that it is expression in all tissues using the 35S promoter from Cauliflower Mosaic Virus. Expression of an antisense transcript of the gene in maize kernel, using for example a zein promoter, would prevent accumulation of the lignocellulolytic enzyme polypeptide in seed. Hence the enzyme encoded by the introduced gene would be present in all tissues except the kernel. 
     Moreover, several tissue-specific regulated genes and/or promoters have been reported in plants. Some reported tissue-specific genes include the genes encoding the seed storage proteins (such as napin, cruciferin, β-conglycinin, and phaseolin) zein or oil body proteins (such as oleosin), or genes involved in fatty acid biosynthesis (including acyl carrier protein, stearoyl-ACP desaturase, and fatty acid desaturases (fad 2-1)), and other genes expressed during embryo development, such as Bce4 (Kridl et al., Seed Science Research, 1991, 1: 209). Examples of tissue-specific promoters, which have been described include the lectin (Vodkin, Prog. Clin. Biol. Res., 1983, 138: 87; Lindstrom et al., Der. Genet., 1990, 11: 160), corn alcohol dehydrogenase 1 (Dennis et al., Nucleic Acids Res., 1984, 12: 983), corn light harvesting complex (Bansal et al., Proc. Natl. Acad. Sci. USA, 1992, 89: 3654), corn heat shock protein, pea small subunit RuBP carboxylase, Ti plasmid mannopine synthase, Ti plasmid nopaline synthase, petunia chalcone isomerase (van Tunen et al., EMBO J., 1988, 7:125), bean glycine rich protein 1 (Keller et al., Genes Dev., 1989, 3: 1639), truncated CaMV 35s (Odell et al., Nature, 1985, 313: 810), potato patatin (Wenzler et al., Plant Mol. Biol., 1989, 13: 347), root cell (Yamamoto et al., Nucleic Acids Res., 1990, 18: 7449), maize zein (Reina et al., Nucleic Acids Res., 1990, 18: 6425; Kriz et al., Mol. Gen. Genet., 1987, 207: 90; Wandelt et al., Nucleic Acids Res., 1989, 17 2354), PEPCase, R gene complex-associated promoters (Chandler et al., Plant Cell, 1989, 1: 1175), and chalcone synthase promoters (Franken et al., EMBO J., 1991, 10: 2605). Particularly useful for seed-specific expression is the pea vicilin promoter (Czako et al., Mol. Gen. Genet., 1992, 235: 33). 
     Subcellular Specific Expression 
     In some embodiments, lignocellulolytic enzyme polypeptide expression is targeted to specific cellular compartments or organelles, such as, for example, the cytosol, the vacuole, the nucleus, the endoplasmic reticulum, the cell wall, the mitochondria, the apoplast, the peroxisomes, plastids, or combinations thereof. In some embodiments of the invention, the lignocellulolytic enzyme polypeptide is expressed in one or more subcellular compartments or organelles, for example, the cell wall and/or endoplasmic reticulum, during the life of the plant. 
     Directing the lignocellulolytic enzyme polypeptide to a specific cell compartment or organelle may allow the enzyme to be localized such that it will not come into contact with the substrate during plant growth. The enzyme would not act until it is allowed to contact its substrate, e.g., following physical disruption of the cell integrity by milling. 
     Targeting expression of a lignocellulolytic enzyme polypeptide to the cell wall (as in the apoplast) can help overcome the difficulty of mixing hydrophobic cellulose and hydrophilic enzymes that makes it hard to achieve efficient hydrolysis with external enzymes. 
     In some embodiments, the invention provides plants engineered to express a lignocellulolytic enzyme polypeptide (or more than one lignocellulolytic enzyme polypeptide) in more than one subcellular compartments or organelles. By using promoters targeted at different locations in the plant cell, one can increase the total enzyme produced in the plant. Thus, for example, using an apoplast promoter with the E1 gene, and a chloroplast promoter with the E1 gene, in a plant would increase total production of E1 compared to a single promoter/E1 construct in the plant. Furthermore, by using promoters targeted at different locations in the plant in the case of expression of multiple lignocellulolytic enzyme polypeptides, one can minimize in vivo (pre-processing) deconstruction of the cell wall that occurs when multiple synergistic enzymes are present in a cell. For example, combining an endoglucanase with an apoplast promoter, a hemicellulase with a vacuole promoter, and an exoglucanase with a chloroplast promoter, sequesters each enzyme in a different part of the cell and achieves the advantages listed above. This method circumvents the limit on enzyme mass that can be expressed in a single organelle or location of the cell. 
     The localization of a nuclear-encoded protein (e.g., enzyme polypeptide) within the cell is known to be determined by the amino acid sequence of the protein. The protein localization can be altered by modifying the nucleotide sequence that encodes the protein in such a manner as to alter the protein&#39;s amino acid sequence. The polynucleotide sequences encoding ligno-cellulolytic enzymes can be altered to redirect the cellular localization of the encoded enzymes by any suitable method (see, e.g., Dai et al., Trans. Res., 2005, 14: 627, the entire contents of which are herein incorporated by reference). In some embodiments of the invention, protein localization is altered by fusing a sequence encoding a signal peptide to the sequence encoding the enzyme polypeptide. Signal peptides that may be used in accordance with the invention include a secretion signal from sea anemona equistatin (which allows localization to apoplasts) and secretion signals comprising the KDEL motif (which allows localization to endoplasmic reticulum). 
     Expression Vectors 
     Nucleic acid constructs according to the present invention may be cloned into a vector, such as, for example, a plasmid. Vectors suitable for transforming plant cells include, but are not limited to, Ti plasmids from  Agrobacterium tumefaciens  (J. Darnell, H.F. Lodish and D. Baltimore, “ Molecular Cell Biology”,  2 nd  Ed., 1990, Scientific American Books: New York), a plasmid containing a β-glucuronidase gene and a cauliflower mosaic virus (CaMV) promoter plus a leader sequence from alfalfa mosaic virus (J. C. Sanford et al., Plant Mol. Biol. 1993, 22: 751-765) or a plasmid containing a bar gene cloned downstream from a CaMV 35S promoter and a tobacco mosaic virus (TMV) leader. Other plasmids may additionally contain introns, such as that derived from alcohol dehydrogenase (Adhl), or other DNA sequences. The size of the vector is not a limiting factor. 
     For constructs intended to be used in  Agrobacterium -mediated transformation, the plasmid may contain an origin of replication that allows it to replicate in  Agrobacterium  and a high copy number origin of replication functional in  E. coli.  This permits facile production and testing of transgenes in  E. coli  prior to transfer to  Agrobacterium  for subsequent introduction in plants. Resistance genes can be carried on the vector, one for selection in bacteria, for example, streptomycin, and another that will function in plants, for example, a gene encoding kanamycin resistance or herbicide resistance. Also present on the vector are restriction endonuclease sites for the addition of one or more transgenes and directional T-DNA border sequences which, when recognized by the transfer functions of  Agrobacterium,  delimit the DNA region that will be transferred to the plant. 
     Methods of preparation of nucleic acid constructs and expression vectors are well known in the art and can be found described in several textbooks such as, for example, J. Sambrook, E. F. Fritsch and T. Maniatis, “Molecular Cloning: A Laboratory Manual”, 1989, Cold Spring Harbor Laboratory: Cold Spring Harbor, and T. J. Silhavy, M. L. Berman, and L. W. Enquist, “Experiments with Gene Fusions”, 1984, Cold Spring Harbor Laboratory: Cold Spring Harbor; F.M. Ausubel et al., “Current Protocols in Molecular Biology”, 1989, John Wiley &amp; Sons: New York. 
     Additional desirable properties of the transgenic plants may include, but are not limited to, ability to adapt for growth in various climates and soil conditions; well studied genetic model system; incorporation of bioconfinement features such as male (or total) sterile flowers; incorporation of phytoremediation features such as contaminant hyperaccumulation, greater biomass, or promotion of contaminant-degrading mycorrhizae. 
     III. Preparation of Transgenic Plants 
     Nucleic acid constructs, such as those described above, can be used to transform any plant including monocots and dicots. In some embodiments, plants are green field plants. In other embodiments, plants are grown specifically for “biomass energy” and/or phytoremediation. Examples of suitable plants for use in the methods of the present invention include, but are not limited to, corn, switchgrass, sorghum, miscanthus, sugarcane, poplar, pine, wheat, rice, soy, cotton, barley, turf grass, tobacco, bamboo, rape, sugar beet, sunflower, willow, and eucalyptus. Using transformation methods, genetically modified plants, plant cells, plant tissue, seeds, and the like can be obtained. 
     Transformation according to the present invention may be performed by any suitable method. In certain embodiments, transformation comprises steps of introducing a nucleic acid construct, as described above, into a plant cell or protoplast to obtain a stably transformed plant cell or protoplast; and regenerating a whole plant from the stably transformed plant cell or protoplast. 
     Cell Transformation 
     Delivery or introduction of a nucleic acid construct into eukaryotic cells may be accomplished using any of a variety of methods. The method used for the transformation is not critical to the instant invention. Suitable techniques include, but are not limited to, non-biological methods, such as microinjection, microprojectile bombardment, electroporation, induced uptake, and aerosol beam injection, as well as biological methods such as direct DNA uptake, liposomes and  Agrobacterium -mediated transformation. Any combinations of the above methods that provide for efficient transformation of plant cells or protoplasts may also be used in the practice of the invention. 
     Methods of introduction of nucleic acid constructs into plant cells or protoplasts have been described. See, for example, “ Methods for Plant Molecular Biology ”, Weissbach and Weissbach (Eds.), 1989, Academic Press, Inc; “ Plant Cell, Tissue and Organ Culture: Fundamental Methods”,  1995, Springer-Verlag: Berlin, Germany; and U.S. Pat. Nos. 4,945,050; 5,036,006; 5,100,792; 5,240,855; 5,302,523; 5,322,783; 5,324,646; 5,384,253; 5,464,765; 5,538,877; 5,538,880; 5,550,318; 5,563,055; and 5,591,616). 
     In particular, electroporation has frequently been used to transform plant cells (see, for example, U.S. Pat. No. 5,384,253). This method is generally performed using friable tissues (such as a suspension culture of cells or embryogenic callus) or target recipient cells from immature embryos or other organized tissue that have been rendered more susceptible to transformation by electroporation by exposing them to pectin-degrading enzymes or by mechanically wounding them in a controlled manner. Intact cells of maize (see, for example, K. D&#39;Halluin et al., Plant cell, 1992, 4: 1495-1505; C. A. Rhodes et al., Methods Mol. Biol. 1995, 55: 121-131; and U.S. Pat. No. 5,384,253), wheat, tomato, soybean, and tobacco have been transformed by electroporation. As reviewed, for example, by G. W. Bates (Methods Mol. Biol. 1999, 111: 359-366), electroporation can also be used to transform protoplasts. 
     Another method of transformation is microprojectile bombardment (see, for example, U.S. Pat. Nos. 5,538,880; 5,550,318; and 5,610,042; and WO 94/09699). In this method, nucleic acids are delivered to living cells by coating or precipitating the nucleic acids onto a particle or microprojectile (for example tungsten, platinum or gold), and propelling the coated microprojectile into the living cell. Microprojectile bombardment techniques are widely applicable, and may be used to transform virtually any monocotyledonous or dicotyledonous plant species (see, for example, U.S. Pat. Nos. 5,036,006; 5,302,523; 5,322,783 and 5,563,055; WO 95/06128; A. Ritala et al., Plant Mol. Biol. 1994, 24: 317-325; L. A. Hengens et al., Plant Mol. Biol. 1993, 23: 643-669; L. A. Hengens et al., Plant Mol. Biol. 1993, 22: 1101-1127; C. M. Buising and R. M. Benbow, Mol. Gen. Genet. 1994, 243: 71-81; C. Singsit et al., Transgenic Res. 1997, 6: 169-176). 
     The use of  Agrobacterium -mediated transformation of plant cells is well known in the art (see, for example, U.S. Pat. No. 5,563,055). This method has long been used in the transformation of dicotyledonous plants, including  Arabidopsis  and tobacco, and has recently also become applicable to monocotyledonous plants, such as rice, wheat, barley and maize (see, for example, U.S. Pat. No. 5,591,616). In plant strains where  Agrobacterium -mediated transformation is efficient, it is often the method of choice because of the facile and defined nature of the gene transfer.  Agrobacterium -mediated transformation of plant cells is carried out in two phases. First, the steps of cloning and DNA modifications are performed in  E. coli,  and then the plasmid containing the gene construct of interest is transferred by heat shock treatment into  Agrobacterium,  and the resulting  Agrobacterium  strain is used to transform plant cells. 
     Transformation of plant protoplasts can be achieved using methods based on calcium phosphate precipitation, polyethylene glycol treatment, electroporation, and combinations of these treatments (see, e.g., I. Potrykus et al., Mol. Gen. Genet. 1985, 199: 169-177; M. E. Fromm et al., Nature, 1986, 31: 791-793; J. Callis et al., Genes Dev. 1987, 1: 1183-1200; S. Omirulleh et al., Plant Mol. Biol. 1993, 21: 415-428). 
     Alternative methods of plant cell transformation, which have been reviewed, for example, by M. Rakoczy-Trojanowska (Cell Mol. Biol. Lett. 2002, 7: 849-858), can also be used in the practice of the present invention. 
     The successful delivery of the nucleic acid construct into the host plant cell or protoplast may be preliminarily evaluated visually. Selection of stably transformed plant cells can be performed, for example, by introducing into the cell, a nucleic acid construct comprising a marker gene which confers resistance to some normally inhibitory agent, such as an antibiotic or herbicide. Examples of antibiotics which may be used include the aminoglycoside antibiotics neomycin, kanamycin and paromomycin, or the antibiotic hygromycin. Examples of herbicides which may be used include phosphinothricin and glyphosate. Potentially transformed cells then are exposed to the selective agent. Cells where the resistance-conferring gene has been integrated and expressed at sufficient levels to permit cell survival will generally be present in the population of surviving cells. 
     Alternatively, host cells comprising a nucleic acid sequence of the invention and which express its gene product may be identified and selected by a variety of procedures, including, DNA-DNA or DNA-RNA hybridization and protein bioassay or immunoassay techniques such as membrane, solution or chip-based technologies for the detection and/or quantification of nucleic acid or protein. 
     Plant cells are available from a wide range of sources including the American Type Culture Collection (Rockland, Md.), or from any of a number of seed companies including, for example, A. Atlee Burpee Seed Co. (Warminster, Pa.), Park Seed Co. (Greenwood, S.C.), Johnny Seed Co. (Albion, Me.), or Northrup King Seeds (Hartsville, S.C.). Descriptions and sources of useful host cells are also found in I. K. Vasil, “Cell Culture and Somatic Cell Genetics of Plants”, Vol. I, II and II; 1984, Laboratory Procedures and Their Applications Academic Press: New York; R.A. Dixon et al., “ Plant Cell Culture—A Practical Approach”,  1985, IRL Press: Oxford University; and Green et al., “Plant Tissue and Cell Culture”, 1987, Academic Press: New York. 
     Plant cells or protoplasts stably transformed according to the present invention are provided herein. 
     Plant Regeneration 
     In plants, every cell is capable of regenerating into a mature plant, and in addition contributing to the germ line such that subsequent generations of the plant will contain the transgene of interest. Stably transformed cells may be grown into plants according to conventional ways (see, for example, McCormick et al., Plant Cell Reports, 1986, 5: 81-84). Plant regeneration from cultured protoplasts has been described, for example by Evans et al., “ Handbook of Plant Cell Cultures ”, Vol. 1, 1983, MacMilan Publishing Co: New York; and I. R. Vasil (Ed.), “ Cell Culture and Somatic Cell Genetics of Plants ”, Vol. I (1984) and Vol. II (1986), Acad. Press: Orlando. 
     Means for regeneration vary from species to species of plants, but generally a suspension of transformed protoplasts or a Petri plate containing transformed explants is first provided. Callus tissue is formed and shoots may be induced from callus and subsequently roots. Alternatively, somatic embryo formation can be induced in the callus tissue. These somatic embryos germinate as natural embryos to form plants. The culture media will generally contain various amino acids and plant hormones, such as auxin and cytokinins Glutamic acid and proline may also be added to the medium. Efficient regeneration generally depends on the medium, on the genotype, and on the history of the culture. 
     Regeneration from transformed individual cells to obtain transgenic whole plants has been shown to be possible for a large number of plants. For example, regeneration has been demonstrated for dicots (such as apple;  Malus pumila;  blackberry,  Rubus;  Blackberry/raspberry hybrid,  Rubus;  red raspberry,  Rubus;  carrot;  Daucus carota;  cauliflower;  Brassica oleracea;  celery;  Apium graveolens;  cucumber;  Cucumis sativus;  eggplant; solanum melongena; lettuce;  Lactuca sativa;  potato;  Solanum tuberosum;  rape;  Brassica napus;  soybean (wild);  Glycine Canescens;  strawberry;  Fragaria  x  ananassa;  tomato;  Lycopersicon esculentum;  walnut;  Juglans regia;  melon;  Cucumis melo;  grape;  Vitis vinifera;  mango; and  Mangifera indica ) as well as for monocots (such as rice;  Oryza sativa;  rye,  Secale cereale;  and Maize). 
     Primary transgenic plants may then be grown using conventional methods. Various techniques for plant cultivation are well known in the art. Plants can be grown in soil, or alternatively can be grown hydroponically (see, for example, U.S. Pat. Nos. 5,364,451; 5,393,426; and 5,785,735). Primary transgenic plants may be either pollinated with the same transformed strain or with a different strain and the resulting hybrid having the desired phenotypic characteristics identified and selected. Two or more generations may be grown to ensure that the subject phenotypic characteristics is stably maintained and inherited and then seeds are harvested to ensure that the desired phenotype or other property has been achieved. 
     As is well known in the art, plants may be grown in different media such as soil, growth solution or water. 
     Selection of plants that have been transformed with the construct may be performed by any suitable method, for example, with Northern blot, Southern blot, herbicide resistance screening, antibiotic resistance screening or any combinations of these or other methods. The Southern blot and Northern blot techniques, which test for the presence (in a plant tissue) of a nucleic acid sequence of interest and of its corresponding RNA, respectively, are standard methods (see, for example, Sambrook &amp; Russell, “ Molecular Cloning”,  2001, Cold Spring Harbor Laboratory Press: Cold Spring Harbor). 
     IV. Uses of Inventive Transgenic Plants 
     The transgenic plants and plant parts disclosed herein may be used advantageously in a variety of applications. More specifically, the present invention, which involves genetically engineering plants for both increased biomass and expression of lignocellulolytic enzyme polypeptides, results in downstream process innovations and/or improvements in a variety of applications including ethanol production, phytoremediation and hydrogen production. 
     A—Ethanol Production 
     Plants transformed according to the present invention provide a means of increasing ethanol yields, reducing pretreatment costs by reducing acid/heat pretreatment requirements for saccharification of biomass; and/or reducing other plant production and processing costs, such as by allowing multi-applications and isolation of commercially valuable by-products. 
     Plant Culture. As already mentioned above, farmers can grow different transgenic plants of the present invention (e.g., different variety of transgenic corn, each expressing a lignocellulolytic enzyme polypeptide or a combination of enzyme polyeptides) simultaneously, achieving the desired “blend” of enzyme polypeptides produced by changing the seed ratio. 
     Plant Harvest. Transgenic plants of the present invention can be harvested as known in the art. For example, current techniques may cut corn stover at the same time as the grain is harvested, but leave the stover lying in the field for later collection. However, dirt collected by the stover can interfere with ethanol production from lignocellulosic material. The present invention provides a method in which transgenic plants are cut, collected, stored, and transported so as to minimize soil contact. In addition to minimizing interference from dirt with ethanol production, this method can result in reduction in harvest and transportation costs. 
     Pretreatment. Conventional methods include physical, chemical, and/or biological pretreaments. For example, physical pretreatment techniques can include one or more of various types of milling, crushing, irradiation, steaming/steam explosion, and hydrothermolysis. Chemical pretreatment techniques can include acid, alkaline, organic solvent, ammonia, sulfur dioxide, carbon dioxide, and pH-controlled hydrothermolysis. Biological pretreatment techniques can involve applying lignin-solubilizing microorganisms (T.-A. Hsu, “ Handbook on Bioethanol: Production and Utilization ”, C. E. Wyman (Ed.), 1996, Taylor &amp; Francis: Washington, D.C., 179-212; P. Ghosh and A. Singh, A., Adv. Appl. Microbiol., 1993, 39: 295-333; J. D. McMillan, in “Enzymatic Conversion of Biomass for Fuels Production”, M. Himmel et al., (Eds.), 1994, Chapter 15, ACS Symposium Series 566, American Chemical Society: B. Hahn-Hagerdal, Enz. Microb. Tech., 1996, 18: 312-331; and L. Vallander and K. E. L. Eriksson, Adv. Biochem. Eng./Biotechnol., 1990, 42: 63-95). The purpose of the pretreatment step is to break down the lignin and carbohydrate structure to make the cellulose fraction accessible to cellulolytic enzymes. 
     Simultaneous use of transgenic plants that express one or more cellulases, one or more hemicellulases and/or one or more ligninases according to the present invention reduces or eliminates expensive grinding of the biomass, reduces or eliminates the need for heat and strong acid required to strip lignin and hemicellulose away from cellulose before hydrolyzing the cellulose. 
     In some embodiments, lignocellulosic biomass of plant parts obtained from inventive transgenic plants is more easily hydrolyzable than that of nontransgenic plants. Thus, the extent and/or severity of pretreatment required to achieve a particular level of hydrolysis is reduced. Therefore, the present invention in some embodiments provides improvements over existing pretreatment methods. Such improvements may include one or more of: reduction of biomass grinding, elimination of biomass grinding, reduction of the pretreatment temperature, elimination of heat in the pretreatment, reduction of the strength of acid in the pretreatment step, elimination of acid in the pretreatment step, and any combination thereof. 
     In some embodiments, lower temperatures of pretreatment may be used to achieved a desired level of hydrolysis. In some embodiments, pretreating is performed at temperatures below about 175° C., below about 145° C., or below about 115° C. For example, under some conditions, the yield of hydrolysis products from lignocellulosic biomass from transgenic plant parts pretreated at about 140° C. is comparable to the yield of hydrolysis products from nontransgenic plant parts pretreated at about 170° C. Under some conditions, the yield of hydrolysis products from lignocellulosic biomass from transgenic plant parts pretreated at about 170° C. is above about 60%, above about 70%, above about 80%, or above about 90% of theoretical yields. Under some conditions, the yield of hydrolysis products from lignocellulosic biomass from transgenic plant parts pretreated at about 140° C. is above about 60%, above about 70%, or above about 80% of theoretical yields. Under some conditions, the yield of hydrolysis products from lignocellulosic biomass from transgenic plant parts pretreated at about 110° C. is above about 40%, above about 50%, or above about 60% of theoretical yields. Such yields from transgenic plant parts can represent an increase of up to about 20% of yields from nontransgenic plant parts. 
     In some embodiments, one or more such improvement(s) is/are observed in inventive transgenic plants expressing a lignocellulolytic enzyme polypeptide at a level less than about 0.5%, less than about 0.4%, less than about 0.3%, less than about 0.2%, or less than about 0.1% of total soluble protein. Without wishing to be bound by any particular theory, the inventors propose that low levels of enzyme expression may facilitate modifying the cell wall, possibly by nicking cellulose or hemicellulose strands. Such modification of the cell wall may make the biomass more susceptible to pretreatment. Thus, biomass from inventive transgenic plants expressing low levels of lignocellulolytic enzymes may require less pretreatment, and/or pretreatment in less severe conditions. 
     In certain embodiments, the pretreated material is used for saccharification without further manipulation. In other embodiments, it may be desired to process the plant tissue so as to produce an extract comprising the lignocellulolytic enzyme polypeptide(s). In this case, the extraction is carried out in the presence of components known in the art to favor extraction of active enzymes from plant tissue and/or to enhance the degradation of cell-wall polysaccharides in the lignocellulosic biomass. Such components include, but are not limited to, salts, chelators, detergents, antioxidants, polyvinylpyrrolidone (PVP), and polyvinylpolypyrrolidone (PVPP). The remaining plant tissue may then be submitted to a pretreatment process. 
     Saccharification. 
     In saccharification (or enzymatic hydrolysis), lignocellulose is converted into fermentable sugars (i.e. glucose monomers) by lignocellulolytic enzyme polypeptides present in the pretreated material. If desired, external cellulolytic enzyme polypeptides (i.e., enzymes not produced by the transgenic plants being processed) may be added to this mixture. Extracts comprising lignocellulolytic enzyme polypeptides obtained as described above can be added back to the lignocellulosic biomass before saccharification. Here again, external cellulolytic enzyme polypeptides may be added to the saccharification reaction mixture. 
     In some embodiments, the amount of externally applied enzyme polypeptide that is required to achieve a particular level of hydrolysis of lignocellulosic biomass from inventive transgenic plants is reduced as compared to the amount required to achieve a similar level of hydrolysis of lignocellulosic biomass from nontransgenic plants. For example, in some embodiments, processing transgenic lignocellulosic biomass in the presence of as low as 15 mg externally applied cellulase per gram of biomass (15 mg/g) yields a similar level of hydrolysis as processing nontransgenic lignocellulosic biomass in the presence of 100 mg/g cellulase. This represents a reduction of almost 90% of cellulases needed for hydrolysis can be achieved when processing biomass from inventive transgenic plants. Such a reduction in externally applied cellulases used can represent significant cost savings. 
     In some embodiments, the amount of externally applied enzyme polypeptide that is required to achieve a particular level of hydrolysis of lignocellulosic biomass from inventive transgenic plants is reduced by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 67%, at least 70%, at least 75%, at least 80%, at least 83%, at least 85%, at least 86%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 95%, at least 97%, at least 98%, at least 99%, or more as compared to the amount required to achieve the same level of hydrolysis from a nontransgenic plant. 
     In some embodiments, the amount of externally applied enzyme polypeptide that is required to achieve a particular level of hydrolysis of lignocellulosic biomass from inventive transgenic plants is reduced by at least two fold, at least three fold, at least four fold, at least five fold, at least six fold, at least seven fold, at least eight fold, at least nine fold, at least ten fold, at least eleven fold, at least twelve fold, at least thirteen fold, at least fourteen fold, at least fifteen fold, at least twenty fold, at least twenty five fold, at least thirty fold, at least thirty-five fold, at least forty fold, at least forty-five fold, at least fifty fold, at least sixty fold, at least seventy fold, at least eighty fold, at least ninety fold, at least one hundred fold, or more as compared to the amount required to achieve the same level of hydrolysis from a nontransgenic plant. 
     In some embodiments, a mixture of enzyme polypeptides each having different enzyme activities (e.g., exoglucanase, endoglucanase, hemi-cellulase, beta-glucosidase, and combinations thereof), and/or an enzyme polypeptide having more than one enzyme activity (e.g., exoglucanase, endoglucanase, hemi-cellulase, beta-glucosidase, and combinations thereof) is added during a “treatment” step to promote saccharification. Without wishing to be bound by any particular theory, such combinations of enzyme activity, whether through the activity of an enzyme complex or other mixture of enzymes, may allow a greater degree of hydrolysis than can be achieved with a single enzyme activity alone. Commercially available enzyme complexes that can be employed in the practice of the invention include, but are not limited to, Accellerase™ 1000 (Genencor), which contains multiple enzyme activities, mainly exoglucanase, endoglucanse, hemi-cellulase, and beta-glucosidase. 
     Saccharification is generally performed in stirred-tank reactors or fermentors under controlled pH, temperature, and mixing conditions. A saccharification step may last up to 200 hours. Saccharification may be carried out at temperatures from about 30° C. to about 65° C., in particular around 50° C., and at a pH in the range of between about 4 and about 5, in particular, around pH 4.5. Saccharification can be performed on the whole pretreated material. 
     The present Applicants have shown that adding cellulases to E1-transformed plants increases total glucose production compared to adding cellulases to non-transgenic plants, which suggests that simply using transgenic E1 plants with current external cellulase techniques can substantially increase ethanol yields. The experiment also indicates that adding cellulases to E1 plants increases total glucose production compared to adding cellulases to non-transgenic plants. This is an important result since it suggests that simply using transgenic E1 plants with current external cellulase techniques can substantially increase ethanol yields in the presence or absence of pretreatment processes. 
     Fermentation. In the fermentation step, sugars, released from the lignocellulose as a result of the pretreatment and enzymatic hydrolysis steps, are fermented to one or more organic substances, e.g., ethanol, by a fermenting microorganism, such as yeasts and/or bacteria. The fermentation can also be carried out simultaneously with the enzymatic hydrolysis in the same vessels, again under controlled pH, temperature and mixing conditions. When saccharification and fermentation are performed simultaneously in the same vessel, the process is generally termed simultaneous saccharification and fermentation or SSF. 
     Fermenting microorganisms and methods for their use in ethanol production are known in the art (Sheehan, “The road to Bioethanol: A strategic Perspective of the US Department of Energy&#39;s National Ethanol Program” In: “ Glucosyl Hydrolases For Biomass Conversion ”, ACS Symposium Series 769, 2001, American Chemical Society: Washington, D.C.). Existing ethanol production methods that utilize corn grain as the biomass typically involve the use of yeast, particularly strains of  Saccharomyces cerevisiae.  Such strains can be utilized in the methods of the invention. While such strains may be preferred for the production of ethanol from glucose that is derived from the degradation of cellulose and/or starch, the methods of the present invention do not depend on the use of a particular microorganism, or of a strain thereof, or of any particular combination of said microorganisms and said strains. 
     Yeast or other microorganisms are typically added to the hydrolysate and the fermentation is allowed to proceed for 24-96 hours, such as 35-60 hours. The temperature of fermentation is typically between 26-40° C., such as 32° C., and at a pH between 3 and 6, such as about pH 4-5. 
     A fermentation stimulator may be used to further improve the fermentation process, in particular, the performance of the fermenting microorganism, such as, rate enhancement and ethanol yield. Fermentation stimulators for growth include vitamins and minerals. Examples of vitamins include multivitamin, biotin, pantothenate, nicotinic acid, meso-inositol, thiamine, pyridoxine, para-aminobenzoic acid, folic acid, riboflavin, and vitamins A, B, C, D, and E (Alfenore et al., “Improving ethanol production and viability of  Saccharomyces cerevisiae  by a vitamin feeding strategy during fed-batch process”, 2002, Springer-Verlag). Examples of minerals include minerals and mineral salts that can supply nutrients comprising phosphate, potassium, manganese, sulfur, calcium, iron, zinc, magnesium and copper. 
     Recovery. Following fermentation (or SSF), the mash is distilled to extract the ethanol. Ethanol with a purity greater than 96 vol. % can be obtained. 
     By-Products. The hydrolysis process of lignocellulosic raw material also releases by-products such as weak acids, furans, and phenolic compounds, which are inhibitory to the fermentation process. Removing such by-products may enhance fermentation. In particular, lignin and lignin breakdown products such as phenols, produced by enzymatic activity and by other processing activities, from the saccharified cellulosic biomass is likely to be important to speeding up fermentation and maintaining optimum viscosity. 
     Thus, in another aspect, the present invention provides methods of speeding up fermentation which comprise removing, from the hydrolysate, products of the enzymatic process that cannot be fermented. Such products comprise, but are not limited to, lignin, lignin breakdown products, phenols, and furans. In certain embodiments, products of the enzymatic process that cannot be fermented can be separated and used subsequently. For example, the products can be burned to provide heat required in some steps of the ethanol production such as saccharification, fermentation, and ethanol distillation, thereby reducing costs by reducing the need for current external energy sources such as natural gas. Alternatively, such by-products may have commercial value. For example, phenols can find applications as chemical intermediates for a wide variety of applications, ranging from plastics to pharmaceuticals and agricultural chemicals. Phenol condensed to with aldehydes (e.g., methanal) make resinous compounds, which are the basis of plastics which are used in electrical equipment and as bonding agents in manufacturing wood products such as plywood and medium density fiberboard (MDF). 
     Separation of by-products from the hydrolysate can be done using a variety of chemical and physical techniques that rely on the different chemical and physical properties of the by-products (e.g., lignin and phenols). Such techniques include, but are not limited to, chromatography (e.g., ion exchange, affinity, hydrophobic, chromatofocusing, and size exclusion), electrophoretic procedures (e.g., preparative isoelectric focusing), differential solubility (e.g., ammonium sulfate precipitation), SDS-PAGE, distillation, or extraction. 
     Some of the hydrolysis by-products, such as phenols, or fermentation/processing products, such as methanol, can be used as ethanol denaturants. Currently about 5% gasoline is added immediately to distilled ethanol as a denaturant under the Bureau of Alcohol, Tobacco and Firearms regulations, to prevent unauthorized non-fuel use. This requires shipping gasoline to the ethanol production plant, then shipping the gas back with the ethanol to the refinery. The gas also impedes the use of ethanol-optimized engines that make use of ethanol&#39;s higher compression ratio and higher octane to improve performance. Using transgenic plant derived phenols and/or methanol as denaturants in lieu of gasoline can reduce costs and increase automotive engine design alternatives. 
     Reducing Lignin Content. Another way of reducing lignin and lignin breakdown products that are not fermentable in hydrolysate is to reduce lignin content in transgenic plant of the present invention. Such methods have been developed and can be used to modify the inventive plants (see, for example, U.S. Pat. Nos. 6,441,272 and 6,969,784, U.S. Pat. Appln. No. 2003-0172395, US and PCT publication No. WO 00/71670). 
     Combined Starch Hydrolysis and Cellulolytic Material Hydrolysis. The transgenic plants and plant parts disclosed herein can be used in methods involving combined hydrolysis of starch and of cellulosic material for increased ethanol yields. In addition to providing enhanced yields of ethanol, these methods can be performed in existing starch-based ethanol processing facilities. 
     Starch is a glucose polymer that is easily hydrolyzed to individual glucose molecules for fermentation. Starch hydrolysis may be performed in the presence of an amylolytic microorganism or enzymes such as amylase enzymes. In certain embodiments of the invention, starch hydrolysis is performed in the presence of at least one amylase enzyme. Examples of suitable amylase enzymes include a-amylase (which randomly cleaves the α(1-4)glycosidic linkages of amylose to yield dextrin, maltose or glucose molecules) and glucoamylase (which cleaves the α(1-4) and α(1-6)glycosidic linkages of amylose and amylopectin to yield glucose). 
     In the inventive methods, hydrolysis of starch and hydrolysis of cellulosic material can be performed simultaneously (i.e., at the same time) under identical conditions (e.g., under conditions commonly used for starch hydrolysis). Alternatively, the hydrolytic reactions can be performed sequentially (e.g., hydrolysis of lignocellulose can be performed prior to hydrolysis of starch). When starch and cellulosic material are hydrolyzed simultaneously, the conditions are preferably selected to promote starch degradation and to activate lignocellulolytic enzyme polypeptide(s) for the degradation of lignocellulose. Factors that can be varied to optimize such conditions include physical processing of the plants or plant parts, and reaction conditions such as pH, temperature, viscosity, processing times, and addition of amylase enzymes for starch hydrolysis. 
     The inventive methods may use transgenic plants (or plant parts) alone or a mixture of non-transgenic plants (or plant parts) and plants (or plant parts) transformed according to the present invention. Suitable plants include any plants that can be employed in starch-based ethanol production (e.g., corn, wheat, potato, cassava, etc). For example, the present inventive methods may be used to increase ethanol yields from corn grains. 
     EXAMPLES  
     The following examples describe some of the preferred modes of making and practicing the present invention. However, it should be understood that these examples are for illustrative purposes only and are not meant to limit the scope of the invention. Furthermore, unless the description in an Example is presented in the past tense, the text, like the rest of the specification, is not intended to suggest that experiments were actually performed or data were actually obtained. 
     Example 1 
     Generation of Transgenic Tobacco 
     To generate the transgenic tobacco, wild-type tobacco was transformed with the E1 and then AtFLC genes using  Agrobacterium tumefaciens  as described below. 
     Description of the Donor. The endo-1,4-β-glucanase E1 gene (GenBank Accession No. U33212) was isolated from the thermophilic bacterium Acidothermus cellulolyticus. This bacterium was originally isolated from decaying wood in an acidic, thermal pool at Yellowstone National Park and deposited with the American Type Culture Collection (ATCC, Manassas, Va.) under collection number 43068 (A. Mohagheghi et al., Int. J. System. Baceril., 1986, 36: 435-443; Tucker et al., Biotechnology, 1989, 7: 817-820). As already mentioned herein, the bacterium has been characterized with the ability to hydrolyze and degrade plant cellulose. 
     For transformation into tobacco, the E1 catalytic domain was isolated from the genomic sequence and contained by 950-2020 listed in Accession No. U33212. To generate the E1-catalytic construct, a stop codon was introduced after the codon specifying Val-358 of E1 through Polymerase Chain Reaction (PCR), and the 5′ end of the gene was fused to the 21 amino acids in the amino-terminal soybean vegetative storage protein VSPβ (GenBank Accession No. M76980) (Ziegelhoffer et al., Mol. Breed, 2001, 8: 147-158) in order to target the protein to the apoplast. For cloning purposes, a SacI site was added to the 3′ end of the E1 gene following the stop codon and an XbaI site at the 5′end of the VSPI3 sequence. 
     The inhibitor Flowering Locus C gene, or FLC (accession # BK000546) is a dosage-dependent repressor of flowering in  Arabidopsis  (S. D. Michaels and R. M. Amasino, Plant Cell, 1999, 11: 949-956), which operates by negatively regulating the expression of genes that promote flowering, such as SOC1 and FT. The 591 by cDNA was isolated from  Arabidopsis  and used without modification for transformation into tobacco. 
     Description of the Recipient. The recipient organism was  Nicotiana tabacum  W38, a commonly used variety for laboratory studies. Tobacco is a very well characterized crop that has been cultivated for centuries. 
     Description of the Vector and the Transformation Process. The E1 transformation vector was constructed from an existing pBI121 binary Ti vector used for agrobacteria mediated transformation (Jefferson et al., EMBO J., 1987, 6: 3901). Through standard agrobacteria transformation, DNA sequences in between the right and left borders are stably transferred into the plant genome. The complete sequence of pBI121 is 14,758 by (GenBank Accession No. AF502128) and contains resistance to the antibiotic kanamycin and the GUS gene in between its right and left border sequence (as presented on  FIG. 1 ). For the development of pBI121-E1, the β-glucuronidase gene was excised through digestion with XbaI and SacI and replaced with the VSPβ/E1 construct (as shown on  FIG. 2 ). 
     Tobacco leaf explants were transformed with pBI121-E1 according to standard procedures (Horsch et al., Science, 1985, 227: 1229). Leaf explants were taken from the second and third fully expanded leaves of 3-week old in vitro shoot cultures of  Nicotiana tabacum  W38 maintained on MS medium. After pre-culture, explants were dropped into a suspension of  Agrobacterium  cells containing the modified pBI121 vector obtained from an overnight culture. Leaf pieces were selected on 100 mg/L kanamycin and plantlets (typically 2 or 3) developed 10-14 days later from callus formed along cut leaf edges. Plantlets were excised and rooted on MS media containing 100 mg/L kanamycin in Magenta GA7 boxes (Ziegelhoffer et al., Mol. Breed, 2001, 8: 147-158). 
     Transformed plants were confirmed through genomic PCR amplification of the E1 gene in parallel with measuring the hydrolysis of cellulose using leaf extracts (Ziegelhoffer et al., Mol. Breed, 2001, 8: 147-158). Plants positive for both the presence of the E1 gene and E1 activity were grown to maturity and seeds were collected for further work. Stable expression of the E1 gene and E1 activity were observed for multiple generations of tobacco after the transformation event. 
     Presence of E1 gene. To verify the presence of the E1 gene, the third or fourth leaf from the shoot apex can be used for protein extraction. Leaf samples can be harvested at 2-3 hours into the light period. Leaf tissues can be cut into approximately 1 cm 2  pieces and pooled for homogeneization. An enzyme assay, SDS-PAGE, and western blot can be carried out as described previously (Z. Dai et al., Transgenic Res., 2000, 9: 43-54). 
     E1 Activity. To assess E1 activity, the third or fourth leaf from the shoot apex of transgenic plants can be harvested. One half of the leaf tissues can be sliced into 1 cm×2 cm pieces and the other half used for direct extraction as described above. About 0.15 g of leaf pieces can be vacuum-infiltrated with 50 mM MES (pH 5.5) twice each for 10 minutes at 20 in. of mercury. The infiltrated leaf pieces can be transferred into 1.5 mL microcentrifuge tubes and centrifuged at 350 g for 10 minutes to obtain fluid from the intercellular space. About 15-25 μL of intercellular fluid can be used for E1 activity measurement and 30-50 μL of intercellular fluid can be used for protein quantification. 
     Example 2 
     Enzymatic Performance and Stability of E1 Tobacco 
     The stability properties of leaf protein concentrates and associated E1 cellulase activity in E1-FLC transgenic tobacco were characterized. 
     Leaf protein concentrates were prepared by macerating the tobacco leaves with ice in a blender at a ratio of 8:1 (w/1). Samples of these extracts were analyzed for cellulase activity using carboxy-methyl cellulose. As shown in  FIG. 16 , extract from E1 plants but not wild-type tobacco can hydrolyze cellulase. Samples of these concentrates were also subjected to various conditions to determine the effect of refrigeration at 2° C., pre-heating the sample at 90° C., acidification to pH 4.0 with lactic acid, and drying the plant material prior to addition to external cellulase (Spezyme CP from Genencor International, Inc., Palo Alto, Calif.). Nine combinations of these variables were studied in the presence and absence of added cellulase (25 μL cellulase per mL). 
     The stability/activity of the cellulase enzymes (both added/external and endogenous) within these concentrates were measured as a function of the hydrolysis of cellulose and glucose production. One (1) mL aliquots of each sample were added to 0.25 g of microcrystalline cellulose. The solution was brought to 10 mL in a pH 4.5 citrate buffer. The solutions were allowed to hydrolyze for 5 days, and the concentration of glucose was measured to assess cellulase activity of the sample. Long-term studies are underway to determine cellulase activity measurements for various times for up to 6 months. Hydrolysis of cellulose as a function of glucose concentration in the samples is presented in Table 2. 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Concentrations of glucose (g/L) from transgenic and non-transgenic 
               
               
                 tobacco after five (5) days of hydrolysis. 
               
            
           
           
               
               
            
               
                   
                 Tobacco Genotype and Treatment 
               
            
           
           
               
               
               
            
               
                 Pretreatment 
                 No Added Cellulase 
                 Added Cellulase 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                 pH 
                   
                 Control 
                 E1/FLC 
                 Control 
                 E1/FLC 
               
            
           
           
               
               
               
               
               
            
               
                 2° C. 
                 90° C. 
                 4.0 
                 Dry 
                 (glucose (g/L) 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 0 
                 0 
                 3.13 
                 3.72 
               
               
                 x 
                   
                   
                   
                 0 
                 1.43 
                 3.11 
                 4.19 
               
               
                   
                 x 
                   
                   
                 0 
                 0 
                 3.44 
                 4.50 
               
               
                 x 
                 x 
                   
                   
                 0 
                 0 
                 3.08 
                 5.74 
               
               
                   
                   
                 x 
                   
                 0 
                 0 
                 1.33 
                 0.57 
               
               
                 x 
                   
                 x 
                   
                 0 
                 0 
                 1.65 
                 0.79 
               
               
                 x 
                 x 
                 x 
                   
                 0 
                 0.40 
                 0.82 
                 1.57 
               
               
                   
                   
                   
                 x 
                 0 
                 0.34 
                 4.08 
                 5.58 
               
               
                   
                 x 
                   
                 x 
                 0 
                 0 
                 4.84 
                 4.92 
               
               
                   
               
            
           
         
       
     
     As is evident from Table 2, the addition of acid severely limits the activity of cellulase, which is greatest at about pH 4.9. Significantly, in all cases except those involving acid addition, the transgenic plant plus cellulase experiments produced more glucose that the control plus cellulase. This is strong evidence for the expression of cellulase activity in the transgenic tobacco. Some transgenic samples showed measurable glucose production even without added cellulase, whereas none of the controls showed such cellulase activity. Bacterial growth was seen in all room temperature acidified samples after only two weeks, and some growth was seen in one refrigerated sample after one month. As such, room temperature acidified storage appears unsuitable for long-term storage conditions. These results show that E1 tobacco can self-hydrolyze and that exogenous cellulose is more efficient with E1 tobacco. 
     This experiment indicates that E1 cellulase activity in a concentrate of E1 plants is quite stable, suggesting that the plant juice can be used as a source of cellulase to hydrolyze non-transgenic plant biomass, or added back to the transgenic plants themselves after pre-processing steps such as high heat or acid treatment are completed that might otherwise inactivate the enzyme. The experiment also indicates that adding cellulases to E1 plants increases total glucose production compared to adding cellulases to non-transgenic plants. This is an important result since it suggests that simply using transgenic E1 plants with current external cellulase techniques can substantially increase ethanol yields. 
     As mentioned above, the “cellulase” enzyme system is complex and comprises various activities, while the transgenic E1 tobacco plant only expresses one of these activities, namely the endoglucanase. Three samples in the experiment described above showed glucose event in the absence of a complex cellulose complex, which is an encouraging result. 
     Adding additional members of the cellulase complex would be expected to increase hydrolysis of the E1 tobacco biomass. To test this hypothesis, an endoglucanase, glucoamylase and hemicellulase (obtained from BIO-CAT, Troy, VA) were added to a non-transgenic tobacco and to an E1-FLC tobacco. As shown in  FIG. 3 , the results indicate that adding different enzyme types almost doubles glucose production in the transgenic tobacco, without chemical pretreatment. The E1-FLC tobacco was also found to produce a higher level of glucose than the E1-only tobacco used in the previous experiment. 
     This result suggests that creating additional plant genotypes expressing different members of the cellulase complex, such as ligninase and hemicellulase, could multiply the hydrolysis yield of E1 plants. The result also suggests that the E1 activity is not restricted to that of an endoglucanase. The increased production of glucose in the absence of external cellulases indicates that additional enzymatic hydrolysis of polysaccharides and disaccharides is occurring in a manner similar to that observed with exoglucanaes, indicating that E1 may be what has been termed a “processive” endoglucanase. 
     Example 3 
     Transformation of Corn with E1-FLC 
     To develop a system for transforming corn, rice was used as cereal model plant system for transfer of the E1 and the bar genes. To do so, the pZM766E1-cat was inserted into pCAMBIA (purchased from pCAMBIA Co (Camberra, Australia) containing the bar selectable marker gene and the gus color indicator gene. The plasmid was obtained under a Material Transfer Agreement (MTA) from Dr. K. Danna of Colorado State University. The E1 transgenic rice plants showed the integration of all three transgenes (E1, bar and gus) by PCR. Furthermore, they showed E1 production as high as 24% total soluble proteins and enzymatic activity of the E1 transgene. 
     Several independent corn transgenic lines were then developed using biolistic bombardment. Lines showing confirmed integration, expression, enzymatic activity and accumulation of the transgene product inside of the apoplast were retained for further testing and development as described below. 
     Explant Preparation and Biolistic Bombardment of Corn. The Applicants produced multi-meristem apical shoot primordia for biolistic bombardment of a mixture of E1 and bar constructs. Corn was grown in greenhouses. Immature embryos were produced, cultured and callus lines were produced, and the immature embryo-derived callus lines were bombarded with a 1:1 ratio of a plasmid containing the E1 gene and one of the three plasmids, each containing the bar selectable marker gene. 
     For the E1 plasmid, the pMZ766E1-cat was selected because in  Arabidopsis  this construct produced the E1 enzyme up to 26% of the total soluble proteins (M. T. Ziegler et al., Mol. Breeding, 2000, 6: 37-46). This construct contains the strong promoter and enhancer and an apoplast targeting element. Corn multi-meristems and the immature embryo-derived callus lines were co-transformed with the pZM766E1-cat and either the pGreen (Fig. XX0, pDM 302 ( FIG. 10 ), or the pBY520 ( FIG. 11 ), as each has its own potential advantages. 
     Confirmation Analysis of E1 Transgenic Corn. PCR was used on a few PPT-selected plantlets and confirmed the presence of the E1 and bar genes. Those plantlets which showed positive signals were selected for further studies. Although the copy numbers of E1 in corn plants using the gene unique site has not yet been determined, Southern blot analysis confirmed the stable integration of E1 transgene in several PCR positive corn lines (see  FIG. 7 ). The translation of E1 transgene in corn was confirmed using Western blots and compared to E1 translation in tobacco and rice (see  FIG. 8 ). 
     Preliminary Work on Apoplast Localization of E1 in Transgenic Corn. Based on previous experience with localization studies of other gene products (polyhydroxybutyrate) in corn via confocal microscopy, an E1 primary antibody and an appropriate secondary antibody were used to perform localization of E1 in transgenic corn tissue. Although most samples showed strong non-specific binding of the fluorescence conjugate to plant tissues, some samples showed possible localization of E1 in apoplast ( FIG. 9 ). None of the plant lines generated as described herein appeared to show adverse growth effects from the non-specific binding of E1 in their tissues. Increased localization of E1 in apoplast will be pursued using several different blocking agents to reduce any potential non-specific binding. 
     Summary of Results Obtained 
     The results obtained in the Examples reported herein provide strong support for the contention that tailoring crop plant traits can significantly improve biofuel yields and reduce biofuel production costs. Robust activity by a key cellulase enzyme, E1 endoglucanase, was demonstrated in transformed tobacco and corn. One E1 corn line has shown E1 production at more than 9% of total soluble proteins, a level approximately equal to the level of exogenous enzyme today added to cellulosic biomass for hydrolysis. Significantly, addition of exogenous enzymes led to higher glucose yields from E1 tobacco than non-transformed tobacco, suggesting that higher ethanol yields can be achieved simply by using today&#39;s hydrolysis techniques on E1 crop plants. The results obtained also showed that the FLC gene delays flowering in tobacco, as it had earlier been shown to do in  Arabidopsis,  a trait that is likely to be useful in bioconfinement of transgenes in bioenergy crops. FLC may also confer greater biomass. 
     Example 4 
     Increased Glucose Conversion from Transgenic Biomass 
     E1 and wild-type samples were air-dried to a moisture content of 16% and then subsets of the biomass were AFEX (i.e., Ammonia Fiber Explosion) pretreated according to standard techniques. The untreated and AFEX treated samples underwent concurrent hydrolysis reaction with the addition of the external cellulase enzymes, Spezyme and Novo 188. The reactions were incubated at 50° C. for 24 hours before determination of the glucose levels present. 
     Results are presented on  FIG. 13 . Increased levels of glucose were observed from hydrolysis of transgenic tobacco biomass expressing the E1 endoglucanase compared with wild-type biomass. Untreated E1 tobacco produced a greater level of glucose compared to wild-type biomass (6.0 g/L vs. 2.9 g/L). The level of glucose produced from untreated E1 tobacco was similar to that of AFEX pretreated biomass, suggesting that the incorporation of cellulase enzymes could lessen or eliminate the need for chemical pretreatment. (ammonia fiber explosion) 
     Example 5 
     Codon Optimized Gene Sequences for Expression of Microbial Cellulases in Plants 
     As already mentioned above, a method was developed to modify microbial genes for increased expression in plants. A composite plant codon usage table was constructed from the analysis of the sequenced genomes of  Zea mays, Arabidopsis thaliana,  and  Nicotiana tabacum.  The codon usage of each of those genomes were averaged together to obtain a composite codon usage from monocot and dicot plants, and this composite table was used as a template to modify microbial DNA sequences so that the microbial sequences have a codon usage better suited for expression in plants. 
     For increased transcriptional expression of the E1 endoglucanase from  Acidothermus cellulolyticus  (GenBank accession numbers U33212 (nucleotide sequence) and AAA75477 (amino acid sequence)) in plants, the microbial sequence of the gene was optimized using a composite plant codon usage table. The average codon usages in  Zea mays  and  Arabidopsis thaliana  were obtained from the Kazusa Codon Usage Database (http://www.kazusa.or.jp/codon/) and averaged together to produce the composite plant codon usage table. With optimization, the E1 sequence used for transformation into plants had SEQ ID NO. 1 as follows: 
     
       
         
           
               
            
               
                 ATGGGCTTCGTTCTCTTTTCTCAACTCCCCTCCTTCCTTCTCGTTTCTA 
               
               
                   
               
               
                 CTCTTCTTCTGTTCCTCGTAATCTCACATTCATGTCGCGCCGCAGGCGG 
               
               
                   
               
               
                 TGGTTATTGGCATACTTCCGGCAGAGAGATACTTGACGCTAACAACGTT 
               
               
                   
               
               
                 CCCGTACGCATCGCTGGTATTAATTGGTTTGGTTTCGAGACGTGCAATT 
               
               
                   
               
               
                 ATGTCGTTCACGGTCTTTGGTCTCGCGATTACCGTTCAATGCTGGATCA 
               
               
                   
               
               
                 AATAAAATCTCTCGGCTACAATACAATTCGCCTTCCCTACTCGGATGAT 
               
               
                   
               
               
                 ATCTTGAAACCAGGTACTATGCCCAACTCAATTAATTTTTATCAAATGA 
               
               
                   
               
               
                 ATCAAGACCTTCAAGGCCTGACATCCCTTCAAGTTATGGACAAGATAGT 
               
               
                   
               
               
                 TGCTTACGCAGGACAAATAGGACTTAGGATTATTCTCGACAGACACAGA 
               
               
                   
               
               
                 CCCGACTGCTCTGGCCAAAGCGCTCTCTGGTATACTTCATCCGTCAGTG 
               
               
                   
               
               
                 AAGCTACCTGGATCTCTGATCTTCAAGCACTTGCCCAACGTTACAAAGG 
               
               
                   
               
               
                 AAACCCTACTGTTGTTGGTTTCGATCTTCACAACGAACCTCACGATCCC 
               
               
                   
               
               
                 GCCTGTTGGGGCTGCGGAGACCCATCTATTGACTGGAGATTGGCCGCCG 
               
               
                   
               
               
                 AACGTGCTGGCAACGCAGTGCTGTCCGTAAATCCCAACCTGCTTATATT 
               
               
                   
               
               
                 TGTCGAAGGCGTACAATCCTATAATGGTGACTCCTATTGGTGGGGCGGA 
               
               
                   
               
               
                 AACTTGCAAGGCGCAGGACAGTATCCAGTTGTCCTCAATGTCCCGAATC 
               
               
                   
               
               
                 GTCTCGTTTACTCAGCACACGACTACGCTACTTCCGTATACCCGCAAAC 
               
               
                   
               
               
                 TTGGTTCAGCGACCCGACATTCCCAAATAACATGCCCGGTATCTGGAAT 
               
               
                   
               
               
                 AAAAATTGGGGTTATCTCTTCAACCAAAACATCGCGCCCGTTTGGCTTG 
               
               
                   
               
               
                 GAGAATTCGGCACTACTCTGCAATCGACTACAGACCAAACTTGGCTCAA 
               
               
                   
               
               
                 GACTCTTGTCCAGTACCTCAGACCTACAGCACAATACGGAGCAGACTCA 
               
               
                   
               
               
                 TTTCAATGGACATTTTGGTCCTGGAACCCGGATTCTGGCGATACTGGCG 
               
               
                   
               
               
                 GTATTCTTAAAGATGATTGGCAAACTGTTGACACTGTCAAGGACGGCTA 
               
               
                   
               
               
                 CCTCGCACCTATCAAATCCTCGATATTCGATCCAGTTGGC 
               
            
           
         
       
     
     Example 6 
     Processing of Biomass from Transgenic Corn Expressing Low Levels of E1  
     The present Example illustrates that the production of E1 in corn stover, even at very low levels, leads to increases in glucan conversion rates when compared to conversion rates of stover from untransformed (WT) corn. In the present Example, E1 was expressed in corn at levels less than about 0.1% TSP and led to increases in glucan conversion rates between about 3% and about 20% compared to untransformed corn. 
     Dried corn stover was ground, then acid pretreated for ten minutes in 0.5% sulfuric acid at three temperatures to cover a range of severity. The resulting slurry was brought to a neutral pH, and then hydrolyzed with either a low (15 mg Spezyme/g biomass) or high (100 mg/g) concentration of enzyme. All reactions were supplemented with β-glucosidase to prevent cellobiose inhibition. Glucose concentrations in the hydrozylate were analyzed by HPLC and compared against theoretical yields. Glucan conversion rates are presented in  FIG. 15  as percentages of theoretical yields. 
     In all conditions tested in this Example, E1 stover yielded higher levels of glucan conversion than WT stover. For stover pretreated at 140° C., the yield from E1 stover processed in the presence of low amounts of externally applied enzyme polypeptide was equivalent to the yield from WT stover processed in the presence of high amounts of externally applied enzyme polypeptide. Thus, E1 expression led to a reduction of almost 90% of the cellulases needed for hydrolysis. For stover processed in the presence of high amounts of externally applied enzyme polypeptide, the yield from E1 stover pretreated at 140° C. was comparable to the yield from WT stover pretreated at 170° C. Thus, E1 expression allowed lower pretreatment temperatures for a similar level of hydrolysis. Without additional cellulases, glucan conversion of E1 stover was equivalent to that of WT stover (about 1.5%), indicating that starting glucose concentrations in the biomass were similar but that the presence of E1 enabled more efficient enzymatic hydrolysis. 
     These results strongly suggest that current loading levels of externally applied enzymes can be substantially reduced by using glycozymes expressed in the plant. Furthermore, using glycozymes expressed in the plant may lower pretreatment temperatures required to achieve a particular level of hydrolysis. 
     Example 7 
     Characterization of Corn Plants Stably Transformed with a Construct for Expressing an Exoglucanase 
     The present Example presents experimental results characterizing corn plants that had been transformed with expression vectors for an exoglucanase. 
     Materials and Methods 
     Screening of Transgenic Plants 
     Corn plants were transformed with pEDEN122 ( FIG. 11 ), an expression vector encoding CBH-E (an exoglucanase expressed by Talaromyces emorsonii; see Table 3 for sequences) and selected for paromomycin resistance. Paromomycin-selected plants were screened by PCR for presence of CBH-E and npt II (the selectable marker) genes, using CBH-E and npt II primers as listed in Table 4. Plants for which positive signals for CBH-E and the selectable marker were detected by PCR (see  FIG. 12 ) were chosen for further study. 
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 CBH-E sequences 
               
            
           
           
               
               
               
            
               
                 SEQ 
                   
                   
               
               
                 ID 
                   
                   
               
               
                 NO 
                 Sequence 
                 Comment 
               
               
                   
               
               
                 3 
                 CCATGGATCCACAGCAAGCGGGTACGGCCACCGCGGAGAACCATCCCCCCCTTACGTGGC 
                 Codon- 
               
               
                   
                 AAGAATGCACCGCCCCCGGATCGTGCACTACTCAAAATGGCGCTGTGGTTCTCGATGCTA 
                 optimized 
               
               
                   
                 ACTGGCGGTGGGTTCACGATGTTAATGGTTACACTAACTGCTATACAGGCAATACATGGG 
                 nucleotide 
               
               
                   
                 ACCCGACCTACTGCCCTGACGACGAGACTTGCGCCCAGAACTGCGCACTTGATGGTGCGG 
                 sequence 
               
               
                   
                 ATTATGAAGGAACGTACGGAGTCACCTCCTCCGGCTCTTCCCTTAAGCTTAATTTCGTGA 
                   
               
               
                   
                 CAGGCAGCAATGTGGGATCAAGGCTCTATCTGCTCCAGGACGATTCTACCTACCAAATAT 
                   
               
               
                   
                 TCAAGCTCCTCAACAGAGAATTTTCCTTCGACGTCGACGTTTCTAATCTCCCTTGTGGCC 
                   
               
               
                   
                 TCAATGGTGCACTCTATTTCGTAGCCATGGACGCAGACGGCGGAGTCTCGAAATACCCAA 
                   
               
               
                   
                 ACAACAAGGCTGGTGCTAAGTATGGTACGGGATACTGCGATAGCCAGTGTCCACGCGATC 
                   
               
               
                   
                 TTAAATTTATTGACGGTGAAGCAAACGTAGAAGGTTGGCAGCCATCATCTAACAACGCAA 
                   
               
               
                   
                 ACACAGGTATCGGCGATCACGGCAGCTGTTGTGCTGAAATGGACGTCTGGGAAGCAAACT 
                   
               
               
                   
                 CAATATCCAATGCGGTTACCCCCCATCCTTGCGATACCCCAGGTCAGACGATGTGCTCTG 
                   
               
               
                   
                 GAGACGATTGTGGTGGAACCTACTCGAATGACCGCTATGCCGGCACCTGCGATCCAGATG 
                   
               
               
                   
                 GATGCGACTTCAATCCCTACCGCATGGGTAATACCTCATTCTACGGCCCCGGAAAAATAA 
                   
               
               
                   
                 TTGACACCACGAAGCCTTTCACTGTAGTAACTCAATTTTTGACTGACGACGGAACAGACA 
                   
               
               
                   
                 CCGGTACCCTGTCCGAGATCAAAAGATTCTACATCCAGAATTCAAACGTCATCCCTCAAC 
                   
               
               
                   
                 CTAATAGCGACATATCAGGCGTGACCGGTAACTCGATAACAACTGAGTTTTGCACAGCCC 
                   
               
               
                   
                 AGAAACAAGCGTTCGGCGACACAGACGATTTCTCCCAACACGGAGGCCTGGCAAAAATGG 
                   
               
               
                   
                 GAGCTGCGATGCAACAAGGCATGGTACTCGTGATGAGTCTTTGGGATGATTATGCTGCGC 
                   
               
               
                   
                 AAATGCTTTGGCTGGATTCCGATTATCCGACAGATGCAGACCCAACAACCCCAGGAATAG 
                   
               
               
                   
                 CTAGAGGCACCTGCCCAACTGATTCAGGCGTACCGAGCGATGTCGAAAGCCAGTCTCCTA 
                   
               
               
                   
                 ATTCTTACGTTACATACTCCAATATTAAGTTCGGACCAATTAACTCTACATTCACGGCCT 
                   
               
               
                   
                 CAGGAGATCT 
                   
               
               
                   
               
               
                 4 
                 MLRRALLLSSSAILAVKAQQAGTATAENHPPLTWQECTAPGSCTTQNGAVVLDANWRWVH 
                 Amino acid 
               
               
                   
                 DVNGYTNCYTGNTWDPTYCPDDETCAQNCALDGADYEGTYGVTSSGSSLKLNFVTGSNVG 
                 sequence 
               
               
                   
                 SRLYLLQDDSTYQIFKLLNREFSFDVDVSNLPCGLNGALYFVAMDADGGVSKYPNNKAGA 
                   
               
               
                   
                 KYGTGYCDSQCPRDLKFIDGEANVEGWQPSSNNANTGIGDHGSCCAEMDVWEANSISNAV 
                   
               
               
                   
                 TPHPCDTPGQTMCSGDDCGGTYSNDRYAGTCDPDGCDFNPYRMGNTSFYGPGKIIDTTKP 
                   
               
               
                   
                 FTVVTQFLTDDGTDTGTLSEIKRFYIQNSNVIPQPNSDISGVTGNSITTEFCTAQKQAFG 
                   
               
               
                   
                 DTDDFSQHGGLAKMGAAMQQGMVLVMSLWDDYAAQMLWLDSDYPTDADPTTPGIARGTCP 
                   
               
               
                   
                 TDSGVPSDVESQSPNSYVTYSNIKFGPINSTFTAS 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Primer sequences used for PCR analysis 
               
            
           
           
               
               
               
               
            
               
                   
                 Primer 
                 SEQ 
                   
               
               
                 Primer Name 
                 ID 
                 ID NO: 
                 Primer Sequence (5′ to 3′) 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 Exoglucanase (CBH-E)- 
                 ES455 
                 8 
                 ACA GGC AGC AAT GTG GGA TCA A 
               
               
                 forward 
                   
                   
                   
               
               
                   
               
               
                 Exoglucanase (CBH-E)- 
                 ES456 
                 9 
                 TGT TGC ATC GCA GCT CCC ATT T 
               
               
                 reverse 
                   
                   
                   
               
               
                   
               
               
                 Promoter-SM (D35S- 
                 ES531 
                 10 
                 TTC ATT TCA TTT GGA GAG GAC A 
               
               
                 nptII)-forward 
                   
                   
                   
               
               
                   
               
               
                 Promoter-SM (D35S- 
                 ES532 
                 11 
                 CAA GCT CTT CAG CAA TAT CAC G 
               
               
                 nptII)-reverse 
               
               
                   
               
            
           
         
       
     
     Enzyme Digestion, Sugar Yield Analysis, and Digestibility Assays 
     Extractive compounds were removed from exoglucanase-expressing and control corn stover composite samples using a standard ethanol-acetone extraction procedure and dried to completeness in a fume hood. The tare weight of empty sample tubes was recorded and then ground material from exoglucanase-expressing and control biomass (˜50 mg) was transferred to each tube. The dry weight of the sample plus the tube was recorded. Samples were then treated according to their experimental group. Half of the exoglucanase-expressing and control samples, the “Pretreated” group, were reconstituted in 100 mM sulfuric acid and heated at 120° C. for 10 minutes followed by neutralization with 0.5 N sodium hydroxide. The second half of the samples, the “Not Treated” group, was kept in their dry state. Following neutralization, samples in the Pretreated group were centrifuged and the supernatant was discarded. Samples in the Pretreated and Not Treated groups were reconstituted in buffer (sodium acetate pH 5.0, 5 mM CaCl2, and 0.02% sodium azide) containing either 0.4 mg or 8 mg Novozymes Celluclast 1.5 L/g of starting dry weight and 0.2 units of Novozymes 188 β-glucosidase. The samples were incubated at 50° C. for 24 h after which time the solids rinsed extensively with water to remove hydrolyzed materials liberated during the 24 h hydrolysis period. Samples were dried to completeness in a dehydrator and the final dry weight of the sample plus tube recorded. The amount of mass lost during the enzyme digestion was determined by subtracting the final sample weight from the starting weight. The digestibility of a sample was determined by calculating percentage of mass lost during the in vitro dry matter digestibility (IVDMD) procedure. Data were graphed and analyzed by one-way Analysis of Variance (ANOVA) with post-hoc testing using the Tukey method. 
     Results and Discussion 
     Corn plants identified as bearing CBH-E glucanase and selection marker genes were identified by PCR (see  FIG. 12 ) and analyzed for digestibility using an in vitro dry matter digestibility (IVDMD) assay. As seen in  FIG. 13 , the group of samples pretreated with dilute acid (“pretreated”) exhibited significantly increased digestibility relative to samples in the “not treated” group. Hydrolysis of pretreated exoglucanase-expressing corn material with either a low (0.4 mg/g) or high (8 mg/g) concentration of commercial cellulase cocktail (Novozymes Celluclast 1.5 L) exhibited substantially greater digestibility than pretreated control corn material ( FIG. 13 ). Furthermore, pretreated exoglucanase corn material hydrolyzed with a low dose (0.4 mg/g) of Celluclast 1.5 L had a significantly greater digestibility than pretreated control corn material hydrolyzed with a high dose (8 mg/g) of Celluclast 1.5 L. These results indicate that exoglucanase-expressing corn material can achieve efficient biomass conversion yields using much lower levels of exogenous enzymes than can non-transgenic corn. Therefore, transgenic expression of exoglucanase can translate into significant cost savings in biomass processing, e.g., for fuel production. 
     Other Embodiments 
     Other embodiments of the invention will be apparent to those skilled in the art from a consideration of the specification or practice of the invention disclosed herein. It is intended that the specification and examples be considered as exemplary only, with the true scope of the invention being indicated by the following claims.