Patent Publication Number: US-8110389-B2

Title: Family 6 cellulase with decreased inactivation by lignin

Description:
FIELD OF THE INVENTION 
     The present invention relates to modified Family 6 cellulases. More specifically, the invention relates to modified  Trichoderma reesei  Family 6 (TrCel6A) cellulases with decreased inactivation by lignin. The present invention also relates to genetic constructs comprising nucleotide sequences encoding for modified TrCel6A cellulases, methods for the production of the modified TrCel6A cellulase from host strains and the use of the modified TrCel6A cellulases in the hydrolysis of lignocellulosic substrates. 
     BACKGROUND OF THE INVENTION 
     More than half of organic carbon on earth is found in the cell walls of plants. Plant cell walls comprise three main compounds: cellulose, hemicellulose, and lignin. Collectively these compounds are called “lignocellulose,” and they represent a potential source of sugars and other organic molecules for fermentation to ethanol or other high-value products. 
     The conversion of lignocellulosic biomass to ethanol has become a key feature of emerging energy policies due to the environmentally favorable and sustainable nature of cellulosic ethanol. There are several technologies being developed for cellulose conversion. Of interest here is a method by which lignocellulosic biomass is subjected to a pretreatment that increases its susceptibility to hydrolytic enzymes, followed by enzymatic hydrolysis to sugars and the fermentation of those sugars to ethanol or other high-value organic molecules (e.g. butanol). Common pretreatment methods include dilute acid steam explosion (U.S. Pat. No. 4,461,648), ammonia freeze explosion (AFEX; Holtzapple et al., 1991), and organosolv extraction (U.S. Pat. No. 4,409,032). Hydrolysis and fermentation systems may be either separate (sequential hydrolysis and fermentation; SHF) or coincident (simultaneous saccharification and fermentation; SSF). In all instances, the hemicellulose and cellulose are broken down to sugars that may be fermented, while the lignin becomes separated and may be used either as a solid fuel or as a source for other organic molecules. 
     The choice of enzymes for conversion of pretreated lignocellulosic biomass to sugars is highly dependent upon the pretreatment method. Dilute acid steam explosion results in significant chemical hydrolysis of the hemicellulose, thereby making enzymes for the conversion of hemicellulose to sugars less relevant to the process. In contrast, AFEX and organosolv extraction both leave hemicellulose and cellulose largely intact. Organosolv extraction, unlike dilute acid steam explosion or AFEX removes a significant portion of the lignin from substrate. In all instances, the primary target for enzymatic hydrolysis is the cellulose, which is converted to sugars using a combination of cellulase enzymes. 
     There are two principle types of cellulase enzymes: endoglucanases, which cleave glycosidic bonds in the middle of cellulose chains, and in doing so, create new chain ends, and cellobiohydrolases, which cleave short oligosaccharides from the ends of cellulose chains. Glucosidases digest short oligosaccharides into monosaccharides. These three enzyme components thus act synergistically to create an efficient cellulolytic enzyme system. Most cellulases have a similar modular structure, which consists of a catalytic domain, linker peptide and a carbohydrate-binding module (CBM). 
     Modified cellulase enzymes and methods for modification have been extensively described. For example, variants of  Trichoderma reesei  Cel7A and Cel6A to improve thermostability have been reported (U.S. Pat. No. 7,375,197; WO 2005/028636; U.S. Publication No. 2007/0173431; U.S. Publication No. 2008/167214; WO 2006/074005; U.S. Publication No. 2006/0205042; U.S. Pat. No. 7,348,168; WO 2008/025164). In particular, substitution of the serine at position 413 in  T. reesei  Cel6A with a proline, or substitution of the amino acid at the equivalent to position 413 with a proline in other Family 6 cellulases confers increased thermostability (WO 2008/025164). Mutations at the equivalent of positions 103, 136, 186, 365 and 410 within the catalytic domain of  T. reesei  Cel6A and other Family 6 cellulases have been shown to lead to reduced inhibition by glucose (U.S. Patent Publication No: 2009/0186381). Variants with resistance to proteases and to surfactants for detergent formulations have been created for textile applications (WO 99/01544; WO 94/07998; and U.S. Pat. No. 6,114,296). 
     The negative effects of lignin on cellulase enzyme systems are well documented. Removal of lignin from hardwood (aspen) was shown to increase sugar yield by enzymatic hydrolysis (Kong et al., 1992). Similarly, removal of lignin from softwood (Douglas fir) was shown to improve enzymatic hydrolysis of the cellulose, an effect attributed to improved accessibility of the enzymes to the cellulose (Mooney et al., 1998). Other groups have demonstrated that cellulases purified from  Trichoderma reesei  bind to isolated lignin (Chemoglazov et al., 1988) and have speculated on the role of the different binding domains in the enzyme-lignin interaction (Palonen et al., 2004). Binding to lignin and inactivation of  Trichoderma reesei  cellulases has been observed when lignin is added back to a pure cellulose system (Escoffier et al., 1991). Only in one instance was lignin reported to not have any significant effect on cellulases (Meunier-Goddik and Penner, 1999). Other reports suggest that some hemicellulases may be resistant to, and even activated by, lignin and lignin breakdown products (Kaya et al., 2000). Thus, it is generally recognized that lignin is a serious limitation to enzymatic hydrolysis of cellulose. 
     CBMs are reportedly involved in lignin binding. For example, removal of the CBM from  Trichoderma  Cel7A essentially eliminates binding to alkali extracted lignin and to residual lignin prepared by enzyme hydrolysis (Palonen et al., 2004). 
     Catalytic domains are also reportedly involved in binding lignin. Cel7B from  Humicola  sp., which does not possess a CBM, is bound extensively by lignin (Berlin et al., 2005b). Similarly  Trichoderma  Cel5A core, devoid of a CBM, does not bind enzymic lignin and binds alkali extracted lignin to a lesser extent than does the full-length protein (Palonen et al., 2004). 
     The development of lignin resistant cellulases with preserved cellulose binding affinity and native cellulolytic activity represents a large hurdle in the commercialization of cellulose conversion to soluble sugars including glucose for the production of ethanol and other products. A variety of methods have been suggested to reduce the negative impact of lignin on the cellulase system. Non-specific binding proteins (e.g. bovine serum albumin; BSA) have been shown to block interactions between cellulases and lignin surfaces (Yang and Wyman, 2006; US24185542 A1; US26088922 A1; WO05024037 A2, A3; WO09429474 A1). Other chemical blocking agents and surfactants have been shown to have a similar effect (Tu et al., 2007; U.S. Pat. No. 7,354,743). While it has been proposed to seek out and identify lignin-resistant variants of cellulase enzymes (Berlin et al., 2005a), no successful work in this direction has been previously documented. 
     SUMMARY OF THE INVENTION 
     The present invention relates to modified cellulase enzymes. More specifically, the present invention relates to modified  Trichoderma reesei  Family 6 (TrCel6A) cellulases with decreased inactivation by lignin. The present invention also relates to genetic constructs comprising nucleotide sequences encoding for modified TrCel6A cellulases, methods for the production of the modified TrCel6A cellulase from host strains and the use of the modified TrCel6A cellulases in the hydrolysis of lignocellulosic substrates. 
     It is an object of the invention to provide a modified TrCel6A cellulase with decreased inactivation by lignin. 
     The present invention relates to a modified TrCel6A cellulase comprising one or more amino acid substitutions selected from the group consisting of: 
     substitution of a basic amino acid at one or more of positions 129 and 410 by a charge-neutral or an acidic amino acid; 
     substitution of a charge-neutral amino acid at one or more of positions 322 and 363 by an acidic amino acid; and 
     substitution of an amino acid at position 186 by a threonine; 
     the modified TrCel6A cellulase having an amino acid sequence that exhibits from about 47% to about 99.9% identity to amino acid 83-447 of SEQ ID NO: 1. Furthermore, the modified TrCel6A cellulase may comprise one or more amino acid substitutions selected from the group consisting of K129E, S186T, A322D, Q363E, R410G, and R410Q. The modified TrCel6A cellulase is capable of hydrolyzing polysaccharides using an inverting mechanism. 
     The position of the one or more amino acid substitution defined above may be determined from sequence alignment of the amino acids corresponding to amino acids 83-447 of SEQ ID NO: 1 of a parental TrCel6A cellulase enzyme with amino acids 83-447 comprising the catalytic domain of the  Trichoderma reesei  Cel6A amino acid sequence as defined in SEQ ID NO: 1. 
     The modified TrCel6A cellulase may be derived from a parental TrCel6A cellulase that is otherwise identical to the modified TrCel6A cellulase except for the substitution of the naturally occurring amino acid at one or more of positions 129, 186, 322, 363, or 410. For example, this invention includes a modified TrCel6A cellulase as defined above further comprising one or more amino acid substitutions selected from the group consisting of Y103H, Y103K, Y103R, Y103A, Y103V, Y103L, Y103P, L136V, L136I, and S413P or any other additional mutations at positions other than 129, 186, 322, 363, or 410, provided that the enzyme exhibits Cel6A cellulase activity. 
     The present invention also relates to a modified TrCel6A cellulase, as defined above, that exhibits at least a 15% reduction in the extent of deactivation by lignin relative to that of a parental TrCel6A cellulase from which the modified TrCel6A cellulase is derived 
     The present invention also relates to a modified Family 6 cellulase selected from the group consisting of: 
     TrCel6A-K129E-S413P (SEQ ID NO: 37); 
     TrCel6A-S186T-S413P (SEQ ID NO: 38); 
     TrCel6A-A322D-S413P (SEQ ID NO: 39); 
     TrCel6A-Q363E-S413P (SEQ ID NO: 40); 
     TrCel6A-R410G-S413P (SEQ ID NO: 41); 
     TrCel6A-R410Q-S413P (SEQ ID NO: 42); 
     TrCel6A-K129E-S186T-A322D-Q363E-S413P (SEQ ID NO: 43); and 
     TrCel6A-K129E-S186T-A322D-Q363E-R410Q-S413P (SEQ ID NO: 44). 
     The present invention relates to genetic constructs comprising a nucleic acid sequence encoding a modified TrCel6A cellulase comprising one or more amino acid substitutions selected from the group consisting of: 
     substitution of a basic amino acid at one or more of positions 129 and 410 by a charge-neutral or an acidic amino acid; 
     substitution of a charge-neutral amino acid at one or more of positions 322 and 363 by an acidic amino acid; and 
     substitution of an amino acid at position 186 by a threonine, 
     the modified TrCel6A cellulase having an amino acid sequence that exhibits from 47% to 99.9% identity to amino acids 83-447 of SEQ ID NO: 1. The nucleic acid sequence may be operably linked to other nucleic acid sequences regulating its expression and secretion from a host microbe. The other nucleic sequences regulating the expression and secretion of the modified TrCel6A cellulase may be derived from the host microbe used for expression of the modified TrCel6A cellulase. The host microbe may be a yeast, such as  Saccharomyces cerevisiae , or a filamentous fungus, such as  Trichoderma reesei.    
     The invention also relates to a genetic construct as defined above, wherein the modified TrCel6A cellulase encoded by the genetic construct further comprises one or more amino acid substitutions selected from the group consisting of Y103H, Y103K, Y103R, Y103A, Y103V, Y103L, Y103P, L136V, L136I, and S413P, or any other additional mutations at positions other than 129, 186, 322, 363 or 410, provided that the enzyme exhibits Cel6A cellulase activity. 
     The invention also relates to a genetically modified microbe comprising a genetic construct encoding a modified TrCel6A cellulase and capable of expression and secretion of a modified TrCel6A cellulase comprising one or more amino acid substitutions selected from the group consisting of: 
     substitution of a basic amino acid at one or more of positions 129 and 410 by a charge-neutral or an acidic amino acid; 
     substitution of a charge-neutral amino acid at one or more of positions 322 and 363 by an acidic amino acid; and 
     substitution of an amino acid at position 186 by a threonine, 
     the modified TrCel6A cellulase having an amino acid sequence that exhibits 47% to 99.9% identity to amino acids 83-447 of SEQ ID NO: 1. In one embodiment, the genetically modified microbe is capable of expression and secretion of a modified TrCel6A cellulase further comprising one or more amino acid substitutions selected from the group consisting of Y103H, Y103K, Y103R, Y103A, Y103V, Y103L, Y103P, L136V, L136I, and S413P, or any other additional mutations at positions other than 129, 186, 322, 363, or 410. The genetically modified microbe may be a yeast or filamentous fungus. For example, the genetically modified microbe may be a species of  Saccharomyces, Pichia, Hansenula, Trichoderma, Hypocrea, Aspergillus, Fusarium, Humicola  or  Neurospora.    
     The present invention also relates to a process for hydrolysing cellulose in the presence of lignin with a modified TrCel6A cellulase. 
     The invention also relates to a process of producing a modified TrCel6A cellulase as defined above, including transformation of a yeast or fungal host with a genetic construct comprising a DNA sequence encoding a modified TrCel6A cellulase, selection of recombinant yeast or fungal strains expressing a modified TrCel6A cellulase, culturing the selected recombinant strains in submerged liquid fermentations under conditions that induce the expression of a modified TrCel6A cellulase and recovering the modified TrCel6A cellulase thus produced by separation of the culture filtrate from the host microbe. 
     The inventors have made the discovery that substitution of a basic or charge-neutral amino acid at position 129, 322, 363 or 410 or of the amino acid at position 186 by a threonine, results in a decrease in the extent of deactivation of the modified TrCel6A cellulase by lignin relative to that of a parental TrCel6A cellulase from which it is derived. As shown in  FIG. 8 , all of these amino acids are located on the surface of the TrCel6A cellulase. 
     Modified TrCel6A cellulases of the present invention can exhibit at least a 15% reduction in the extent of deactivation by lignin relative to that of a parental TrCel6A cellulase from which the modified TrCel6A cellulase is derived. This decreased lignin inactivation contributes to increased activity for the hydrolysis of a cellulose substrate in a hydrolysis reaction containing the modified TrCel6A cellulase, cellulose and lignin relative to the parental TrCel6A cellulase from which the modified TrCel6A cellulase is derived. 
     Such TrCel6A cellulases find use in a variety of applications in industry that require high cellulose-hydrolyzing activity in the presence of lignin. For example, modified TrCel6A cellulase, as described herein, may be used in industrial processes in which lignocellulosic substrates are converted to fermentable sugars used for the production of fuel alcohols, sugar alcohols or other products. 
    
    
     
       DESCRIPTION OF THE DRAWINGS 
       These and other features of the invention will become more apparent from the following description in which reference is made to the appended drawings wherein: 
         FIG. 1  shows an amino acid sequence alignment among selected fungal cellulases from Glycosyl Hydrolase Family 6 and a consensus Family 6 cellulase sequence. A graphical representation of the frequency of occurrence of the amino acid at each position of the consensus Family 6 cellulase among the 36 fungal Family 6 cellulases is shown below the aligned sequences. The catalytic aspartic acid residues at the equivalent positions 175 and 221 in TrCel6A are indicated by arrows. The highly conserved amino acids at the equivalent of positions 129, 186, 363, 322, and 410 in TrCel6A are indicated with an asterisk. For cellulases with a cellulose-binding domain, only the catalytic core sequences are presented. 
         FIG. 2  depicts plasmid vector YEp352/PGK91-1ΔNheI-α ss -TrCel6A-S413P directing the expression and secretion of native and modified TrCel6A from recombinant  Saccharomyces cerevisiae.    
         FIG. 3  contains two scatter plots. Panel A is a scatter plot of enzyme activity in the presence of BSA-treated lignin (+BSA) versus enzyme activity in the presence of untreated lignin (−BSA) for high-throughput assay 1 (Example 6). The data relate to the screening of one 96-well culture plate containing parental (TrCel6A-S413P) and modified TrCel6A cellulases or filtrates from empty vector transformants (Negative Controls). Panel B is a scatter plot of enzyme activity in the presence of BSA-treated lignin (+BSA) versus enzyme activity in the presence of untreated lignin (−BSA) for high-throughput assay 2 (Example 7). The data relate to the screening of one 96-well culture plate containing parental (TrCel6A-S413P) and modified TrCel6A cellulases or filtrates from empty vector transformants (Negative Controls). 
         FIG. 4  is a bar graph showing ±BSA lignin ratios for modified TrCel6A cellulases normalized to ±BSA lignin ratios for the parental TrCel6A-S413P cellulase as measured in high throughput assay 1 (Example 6). 
         FIG. 5  contains two scatter plots. Panel A is a scatter plot of enzyme activity in the presence of BSA-treated lignin (+BSA) versus enzyme activity in the presence of untreated lignin (−BSA) for high-throughput assay 1 (Example 6). The data relate to the screening of the modified cellulase TrCel6A-K129E-S186T-A322D-Q363E-S413P and the parental cellulase TrCel6A-S413P. Panel B is a scatter plot of enzyme activity in the presence of BSA-treated lignin (+BSA) versus enzyme activity in the presence of untreated lignin (−BSA) for high-throughput assay 2 (Example 7). The data relate to the screening of the modified cellulases TrCel6A-K129E-S 186T-A322D-Q363E-S413P, TrCel6A-K129E-S186T-A322D-Q363E-R410Q-S413P and the parental cellulase TrCel6A-S413P. 
         FIG. 6  shows the lignin inactivation time course results for TrCel6A-S413P and TrCel6A-K129E-S186T-A322D-Q363E-R410Q-S413P. Residual TrCel6A activity as a function of time in the lignin slurry was measured and analyzed as described in Example 9. 
         FIG. 7  is a scatter plot of the relative K L  and the relative specific activities of modified TrCel6A cellulases and TrCel6A-S413P as determined in lignin inactivation time course assays. 
         FIG. 8  shows the space-filling (CPK) model for the crystal structures of  T. reesei  Cel6A using coordinates from PDB files 1CB2. The view to the right is a 180 degree rotation around the centered vertical axis of the view on the left. 
         FIG. 9  shows an identity matrix for the alignment of the amino acids corresponding to amino acids 83-447 of SEQ ID NO: 1 for each of 36 Family 6 cellulase amino acid sequences to each other. 
         FIG. 10  shows a 10% SDS-PAGE gel of the purified parental and modified TrCel6A enzymes. Purified TrCel6A cellulases (5 μg each) were separated by 10% SDS-PAGE and the gel stained with Coomassie Brilliant Blue R250. In this figure, TrCel6A Aggregate 1 (lane 10) and TrCel6A Aggregate 2 (lane 11) refer to TrCel6A-K129E-S 186T-A322D-Q363E-S413P and TrCel6A-K129E-S186T-A322D-Q363E-R410Q-S413P, respectively. TrCel6A purified from  Trichoderma  cellulase (lane 2) and molecular mass standards (lane 1) are shown for reference. 
     
    
    
     DESCRIPTION OF PREFERRED EMBODIMENT 
     The present invention relates to modified cellulases. More specifically, the invention relates to modified  Trichoderma reesei  Family 6 (TrCel6A) cellulases with decreased inactivation by lignin. The present invention also relates to genetic constructs comprising nucleic acid sequences encoding for modified TrCel6A cellulases, methods for the production of the modified TrCel6A cellulase from host strains and the use of the modified TrCel6A cellulase in the hydrolysis of cellulose in the presence of lignin. 
     The present invention provides a modified TrCel6A cellulase with decreased inactivation by lignin and thus, increased cellulose hydrolyzing activity in a hydrolysis reaction comprising the modified TrCel6A cellulase, cellulose and lignin, relative to the cellulose-hydrolyzing activity of a parental TrCel6A cellulase from which the modified TrCel6A cellulase is derived, in a hydrolysis reaction of equivalent composition. 
     The following description is of a preferred embodiment by way of example only and without limitation to the combination of features necessary for carrying the invention into effect. 
     Modified TrCel6A Cellulases 
     A cellulase enzyme is classified as a Family 6 cellulase if it exhibits similarity in its primary, secondary and tertiary protein structures relative to those of other Family 6 cellulases. For example, all Family 6 cellulases comprise two aspartic acid (D) residues which may serve as catalytic residues. These aspartic acid residues are found at positions 175 and 221 (see  FIG. 1 ; based on TrCel6A,  Trichoderma reesei  Cel6A, amino acid numbering). Most of the Family 6 cellulases identified thus far are mesophilic; however, this family also includes thermostable cellulases from  Thermobifida fusca  (TfCel6A and TfCel6B) and the alkalophilic cellulases from  Humicola insolens  (HiCel6A and HiCel6B). Family 6 cellulases also share a similar three dimensional structure: an alpha/beta-barrel with a central beta-barrel containing seven parallel beta-strands connected by five alpha-helices. The three dimensional structures of several Family 6 cellulases are known, such as TrCel6A (Rouvinen, J., et al. 1990),  Thermobifida fusca  endo-beta-1,4-glucanase Cel6A (TfCel6A, Spezio, M., et al. 1993),  Humicola insolens  cellobiohydrolase Cel6A (HiCel6A, Varrot, A., et al. 1999),  Humicola insolens  endo-beta-1,4-glucanase Cel6B (HiCel6B, Davies, G. J., et al. 2000) and  Mycobacterium tuberculosis  H37Rv Cel6A (MtCel6A, Varrot, A., et al. 2005). 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 % Amino Acid Sequence Identity of Fungal Family 6 Cellulases to TrCel6A 
               
            
           
           
               
               
               
               
            
               
                   
                   
                   
                 Identity with 
               
               
                   
                   
                   
                 TrCel6A catalytic 
               
               
                   
                   
                   
                 domain (83-447) 
               
               
                 SEQ ID 
                 Organism 
                 Protein 
                 (%) 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 2 
                 
                   Hypocrea koningii 
                 
                 cellobiohydrolase II (Cbh2) 
                 98.9 
               
               
                 3 
                   Trichoderma viride  CICC 13038 
                 cellobiohydrolase II (CbhII; Cbh2) 
                 98.9 
               
               
                 4 
                   Hypocrea koningii  3.2774 
                 cellobiohydrolase II (Cbh2; CbhII) 
                 98.1 
               
               
                 5 
                   Hypocrea koningii  AS3.2774 
                 cbh2 
                 97.8 
               
               
                 6 
                 
                   Trichoderma parceramosum 
                 
                 cellobiohydrolase II (CbhII) 
                 97.8 
               
               
                 7 
                   Aspergillus nidulans  FGSC A4 
                 cellobiohydrolase (AN5282.2) 
                 72.4 
               
               
                 8 
                   Aspergillus niger  CBS 513.88 
                 An12g02220 
                 72.4 
               
               
                 9 
                   Aspergillus oryzae  RIB 40 
                 AO090038000439 
                 67.8 
               
               
                 10 
                   Aspergillus niger  CBS 513.88 
                 An08g01760 
                 67.7 
               
               
                 11 
                   Acremonium cellulolyticus  Y-94 
                 cellobiohydrolase II (Acc2) 
                 67.3 
               
               
                 12 
                 
                   Talaromyces emersonii 
                 
                 cellobiohydrolase II (CbhII) 
                 66.8 
               
               
                 13 
                   Gibberella zeae  K59 
                 Cel6 - Cel6 
                 66.1 
               
               
                 14 
                 
                   Fusarium oxysporum 
                 
                 endoglucanase B 
                 66.1 
               
               
                 15 
                   Neurospora crassa  OR74A 
                 NCU09680.1 (64C2.180) 
                 65.9 
               
               
                 16 
                   Aspergillus nidulans  FGSC A4 
                 AN1273.2 
                 65.5 
               
               
                 17 
                 
                   Aspergillus tubingensis 
                 
                 unnamed protein product (fragment) 
                 65.5 
               
               
                 18 
                   Magnaporthe grisea  70-15 
                 MG05520.4 
                 65.4 
               
               
                 19 
                 
                   Chaetomium thermophilum 
                 
                 unnamed protein product 
                 65.1 
               
               
                 20 
                   Chaetomium thermophilum  CT2 
                 cellobiohydrolase (Cbh2) 
                 65.0 
               
               
                 21 
                 
                   Stilbella annulata 
                 
                 unnamed protein product 
                 64.9 
               
               
                 22 
                 
                   Humicola insolens 
                 
                 avicelase2 (Avi2) 
                 63.7 
               
               
                 23 
                 
                   Humicola insolens 
                 
                 cellobiohydrolase (CBHII) - Cel6A 
                 63.1 
               
               
                 24 
                   Cochliobolus heterostrophus  C4 
                 cellobiohydrolase II (CEL7) 
                 59.6 
               
               
                 25 
                   Agaricus bisporus  D649 
                 cellobiohydrolase II (Cel3; Cel3A) 
                 57.7 
               
               
                 26 
                   Polyporus arcularius  69B-8 
                 cellobiohydrolase II (Cel2) 
                 57.1 
               
               
                 27 
                   Lentinula edodes Stamets  CS-2 
                 cellulase - Cel6B 
                 56.3 
               
               
                 28 
                   Lentinula edodes  L54 
                 cellobiohydrolase (CbhII-1) 
                 56.0 
               
               
                 29 
                 
                   Malbranchea cinnamomea 
                 
                 unnamed protein product 
                 54.9 
               
               
                 30 
                 
                   Phanerochaete chrysosporium 
                 
                 cellobiohydrolase II 
                 54.9 
               
               
                 31 
                 
                   Volvariella volvacea 
                 
                 cellobiohydrolase II-I (CbhII-I) 
                 53.8 
               
               
                 32 
                 
                   Chrysosporium lucknowense 
                 
                 cellobiohydrolase (EG6; CBH II) - Cel6A 
                 49.5 
               
               
                 33 
                 
                   Pleurotus sajor-caju 
                 
                 cellobiohydrolase II 
                 47.2 
               
               
                 34 
                 
                   Trametes versicolor 
                 
                 ORF 
                 47.0 
               
               
                 35 
                   Neurospora crassa  OR74A 
                 NCU03996.1 
                 46.8 
               
               
                 36 
                   Magnaporthe grisea  70-15 
                 MG04499.4 
                 45.1 
               
               
                   
               
            
           
         
       
     
     As shown in  FIG. 1 , there is a high degree of conservation of primary amino acid sequence among Family 6 cellulases. Multiple alignment across 36 currently known Family 6 cellulase amino acid sequences of fungal origin shows that most naturally occurring Family 6 cellulases exhibit from about 47% to about 100% amino acid sequence identity to amino acids 83-447 comprising the catalytic domain of TrCel6A (Table 1) and from about 70% to 100% amino acid sequence identity to at least one other Family 6 cellulase. Family 6 cellulases of bacterial origin show a much lower degree of amino acid sequence identity to TrCel6A or to other Family 6 cellulases of fungal origin. TrCel6A is a member of glycoside hydrolase Family 6, which comprises enzymes that hydrolyses b-1,4 glycosidic bonds with inversion of anomeric configuration, referred to herein as an “inverting mechanism”. Family 6 glycoside hydrolases are defined by the CAZy system which is accepted as a standard nomenclature for such enzymes (see URL: cazy.org). 
     By “TrCel6A numbering”, it is meant the numbering corresponding to the position of amino acids based on the amino acid sequence of TrCel6A (SEQ ID NO: 1). As set forth below, and as is evident by  FIG. 1 , Family 6 cellulases exhibit a substantial degree of sequence similarity. Therefore, by aligning the amino acids to optimize the sequence similarity between the Family 6 catalytic domains of cellulase enzymes, and by using the amino acid numbering of TrCel6A as the basis for numbering, the positions of amino acids within other Family 6 cellulases can be determined relative to TrCel6A. 
     Methods to align amino acid sequences are well known and available to those of skill in the art and include BLAST (Basic Local Alignment Search Tool, URL: blast.ncbi.nlm.nih.gove/Blast.chi; Altschul et al., 1990; using the published default settings) which is useful for aligning two sequences and CLUSTALW (URL: ebi.cak.ak/Tools/clustalw2/index.html) for alignment of two or more sequences. 
     By “modified TrCel6A cellulase” or “modified cellulase”, it is meant a  Trichoderma reesei  Family 6 cellulase of SEQ ID NO: 1 which comprises one or more amino acid substitutions selected from the group consisting of: 
     substitution of a basic amino acid at one or more of positions 129 and 410 by a charge-neutral or an acidic amino acid; 
     substitution of a charge-neutral amino acid at one or more of positions 322 and 363 by an acidic amino acid; and 
     substitution of an amino acid at position 186 by a threonine. 
     For example, which is not to be considered limiting, the modified TrCel6A cellulase may comprise one or more amino acid substitutions selected from the group consisting of K129E, S186T, A322D, Q363E, R410G, and R410Q. 
     As defined herein, “basic amino acid” refers to any one of histidine, lysine or arginine, “acid amino acid” refers to any one of aspartic acid or glutamic acid and “charge-neutral amino acid” is any amino acid that is not a basic or acidic amino acid. 
     It will be understood that modified TrCel6A cellulase may be derived from a wild-type TrCel6A cellulase or from a TrCel6A cellulase that already contains other amino acid substitutions. 
     A “modified TrCel6A cellulase” may also be defined as an enzyme capable of hydrolyzing polysaccharides using an inverting mechanism and having one or more amino acid substitutions, introduced by genetic engineering techniques, selected from the group consisting of: 
     substitution of a basic amino acid at one or more of positions 129 and 410 by a charge-neutral or an acidic amino acid; 
     substitution of a charge-neutral amino acid at one or more of positions 322 and 363 by an acidic amino acid; and 
     substitution of an amino acid at position 186 by a threonine; 
     and which is characterized by having an amino acid sequence that is from about 47% to about 99.9% identical to the amino acids 83 to 447 of the TrCel6A amino acid sequence (SEQ ID NO: 1). For example, a modified TrCel6A cellulase may have an amino acid sequence that is about 47%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99.9% identical to the amino acids 83-447 of SEQ ID NO: 1. One of skill in the art will appreciate that the amino acid sequence of a given TrCel6A cellulase may be modified by the addition, deletion or substitution of one or more amino acids and still be considered a modified TrCel6A cellulase, given that the basic structure and function of the enzyme is retained. 
     The modified TrCel6A cellulase of the present invention is encoded by a nucleic acid sequence that can be generated using genetic material or nucleic acid or amino acid sequence information specific to the desired modified TrCel6A cellulase or to a corresponding parental TrCel6A cellulase. As is known by one of skill in the art, such material or sequence information can be used to generate a nucleic acid sequence encoding a desired modified TrCel6A cellulase using one or more molecular biology techniques for altering amino acid sequences including, but not limited to, site-directed mutagenesis, cassette mutagenesis, random mutagenesis, synthetic oligonucleotide construction, cloning, sub-cloning, amplification by PCT, in vitro synthesis and other genetic engineering techniques (Eijsink V G, et al. 2005). It will be understood that the modified TrCel6A cellulase may be derived from any TrCel6A cellulase—i.e., it may be derived from a naturally-occurring or “wild-type” TrCel6A cellulase or from a TrCel6A cellulase that already contains other amino acid substitutions. 
     In one embodiment of the invention, the modified TrCel6A cellulase comprises an amino acid sequence that is from about 70% to 99.9% identical to amino acids 83-447 of SEQ ID NO: 1, and exhibits at least a 15% reduction in the extent of deactivation of the modified TrCel6A cellulase by lignin relative to that of a parental TrCel6A cellulase from which the modified TrCel6A cellulase is derived. The modified TrCel6A cellulase is capable of hydrolyzing polysaccharides using an inverting mechanism. 
     In other embodiments of the invention, the modified TrCel6A cellulase comprises an amino acid sequence that is from about 90% to about 99.9% identical to amino acids 83-447 of SEQ ID NO: 1, and exhibits at least a 15% reduction in the extent of deactivation of the modified TrCel6A cellulase by lignin relative to that of a parental TrCel6A cellulase from which the modified TrCel6A cellulase is derived. The modified TrCel6A cellulase is capable of hydrolyzing polysaccharides using an inverting mechanism. 
     By “wild type” or “native” TrCel6A cellulase, it is meant the cellulases of SEQ ID NO: 1, without any amino acid substitutions. 
     For the purposes of the present invention, a “parental TrCel6A cellulase” or “parental cellulase” is a TrCel6A cellulase that does not contain the amino acid substitution(s) present in the modified TrCel6A cellulase, namely one or more amino acid substitutions selected from the group consisting of: 
     substitution of a basic amino acid at one or more of positions 129 and 410 by a charge-neutral or an acidic amino acid; 
     substitution of a charge-neutral amino acid at one or more of positions 322 and 363 by an acidic amino acid; and 
     substitution of an amino acid at position 186 by a threonine, 
     but that is otherwise identical to the modified TrCel6A cellulase. As such, the parental TrCel6A cellulase may be a TrCel6A cellulase that contains amino acid substitutions at other positions that have been introduced by genetic engineering or other techniques and that is capable of hydrolyzing polysaccharides using an inverting mechanism. By way of example, the parental cellulase corresponding to a modified TrCel6A cellulase having basic amino acids substitutions at positions 129 and 410 to charge-neutral or acidic amino acids would be a TrCel6A cellulase that does not have charge-neutral or acidic amino acids at both of these positions, but that would be otherwise identical to the modified TrCel6A. However, the parental cellulase and the modified TrCel6A may contain amino acid substitutions at other positions provided that these amino acid substitutions are present in both the modified and parental cellulases. The parental cellulase could also be a wild-type enzyme. By comparing the activity of the modified TrCel6A cellulase with a parental cellulase that is identical to the modified cellulase except for the amino acid substitutions introduced in accordance with the invention, the effect of these amino acid substitutions on the activity of the enzyme in the presence of lignin can be quantified using the assays described below. 
     Alternatively, after production of a modified TrCel6A cellulase comprising one or more amino acid substitutions selected from the group consisting of: 
     substitution of a basic amino acid at one or more of positions 129 and 410 by a charge-neutral or an acidic amino acid; 
     substitution of a charge-neutral amino acid at one or more of positions 322 and 363 by an acidic amino acid; and 
     substitution of an amino acid at position 186 by a threonine, 
     the modified TrCel6A cellulase may be subsequently further modified to contain additional amino acid substitutions. The modified TrCel6A cellulase being capable of hydrolyzing polysaccharides using an inverting mechanism. 
     In order to assist one of skill in the art regarding where other amino acid substitutions (other than positions 129, 186, 322, 363 and 410) of a given TrCel6A cellulase may be made to produce an active enzyme, an alignment of thirty-six Family 6 cellulases derived from fungal sources is provided in  FIG. 1  along with a graph showing the frequency of occurrence of each amino acid of the consensus sequence at each position. Using the information provided in  FIG. 1 , one of skill in the art would recognize regions of low sequence conservation among Family 6 cellulases and could introduce additional amino acid substitutions in these regions provided that the enzyme exhibits Cel16A cellulase activity. 
     Decreasing the Inactivation of TrCel6A Cellulases by Lignin 
     The decrease in the inactivation of the modified TrCel6A cellulase by lignin is determined by measuring the degradation of cellulose or other suitable cellulase substrate (such as beta-glucan) in the presence and absence of lignin and then taking the ratio of activity in the presence of lignin to the activity in the absence of lignin. The lignin present in such a cellulose hydrolysis reaction can be part of the insoluble substrate, such as in pre-treated lignocellulose, or be isolated in a soluble or insoluble form. If the lignin is isolated or purified, the inactivation of the modified or parental TrCel6A cellulase by lignin is determined by measuring the cellulase activity in equivalent hydrolysis reactions, wherein one of the reactions contains a sufficient amount of lignin to reduce the cellulase activity. Alternatively, isolated lignin that has been treated to be less deactivating by coating with a non-specific protein such as bovine serum albumin (BSA), a surfactant or other chemical can be added to the control reaction in the same amounts as the untreated lignin. If the lignin is part of the insoluble substrate, the inactivation of the modified or parental TrCel6A cellulase by lignin is determined by taking the ratio of cellulase activity on a bleached substrate (from which the lignin has been removed, for example, by an oxidant such as chlorine dioxide) and the cellulase activity on an unbleached, lignin-containing substrate. A modified TrCel6A cellulase with decreased inactivation by lignin will show a higher activity ratio (+untreated, isolated lignin: no lignin or treated lignin) than the parental TrCel6A cellulase. 
     There are several assays for measuring cellulase activity of the modified and parental TrCel6A cellulases known to one of skill in the art. It should be understood, however, that the practice of the present invention is not limited by the method used to assess the activity of the modified TrCel6A cellulase. 
     For example, hydrolysis of cellulose can be monitored by measuring the enzyme-dependent release of reducing sugars, which are quantified in subsequent chemical or chemienzymatic assays known to one of skill in the art, including reaction with dinitrosalisylic acid (DNS). Hydrolysis of polysaccharides can also be monitored by chromatographic methods that separate and quantify soluble mono-, di- and oligo-saccharides released by the enzyme activity. In addition, soluble colorimetric substrates may be incorporated into agar-medium on which a host microbe expressing and secreting a parental or modified Family 6 cellulase is grown. In such an agar-plate assay, activity of the cellulase is detected as a colored or colorless halo around the individual microbial colony expressing and secreting an active cellulase. 
     The effect of amino acid substitutions at positions 129, 186, 322, 363 and 410 on the lignin inactivation of a parental TrCel6A was determined via a comparative study of the relative cellulose-hydrolyzing activities of the parental TrCel6A-S413P and the modified TrCel6A cellulases in the presence of isolated, untreated lignin (−BSA) and treated lignin (+BSA), as described in Example 6. For each protein, the ratio of the two activities is normalized to 1.0 for the parental TrCel6A-S413P. The results are shown in  FIG. 4 . All of the modified Family 6 cellulases show at least a 15% higher ratio of activity after pre-incubation with untreated lignin: activity after pre-incubation with BSA-treated lignin. 
     In a preferred embodiment, the modified TrCel6A cellulase exhibits at least a 15% decrease in its inactivation by lignin relative to a parental cellulase as measured in the assays described in Examples 6 and 7. For example, the modified TrCel6A cellulase may exhibit from about 15% to about 400%, or any amount therebetween, decrease in its inactivation by lignin relative to a parental cellulase. The modified TrCel6A cellulase may exhibit 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 75%, 100%, 150%, 200%, 250%, 300%, 350% or 400% decrease in its inactivation by lignin relative to a parental cellulase. 
     Genetic Constructs Encoding Modified TrCel6A Cellulase 
     The present invention also relates to genetic constructs comprising a nucleic acid sequence encoding a modified TrCel6A cellulase. The modified cellulase-encoding nucleic acid sequence may be operably linked to regulatory nucleic acid sequences directing the expression and secretion of the modified TrCel6A cellulase from a host microbe. By “regulatory DNA sequences” it is meant a promoter and a DNA sequence encoding a secretion signal peptide. The regulatory DNA sequences are preferably functional in a fungal host. The regulatory DNA sequences may be derived from nucleic acid sequences that are highly expressed and secreted in the host microbe under industrial fermentation conditions. In a preferred embodiment, the regulatory sequences are derived from one or more of the nucleic acids sequences encoding  Trichoderma reesei  cellulase or hemicellulase. 
     The genetic construct may further comprise a nucleic acid sequence encoding a selectable marker to enable isolation of a genetically modified microbe transformed with the construct as is commonly known to those of skill in the art. The selectable marker may confer resistance to an antibiotic or the ability to grow on medium lacking a specific nutrient to the host organism that otherwise could not grow under these conditions. However, the present invention is not limited by the choice of selectable marker or nucleic acid sequence encoding the selectable marker, and one of skill in the art may readily determine an appropriate marker. In a preferred embodiment, the selectable marker confers resistance to hygromycin, phleomycin, kanamycin, geneticin, or G418, complements a deficiency of the host microbe in one of the trp, arg, leu, pyr4, pyr, ura3, ura5, his, or ade genes or confers the ability to grow on acetamide as a sole nitrogen source. 
     The genetic construct may further comprise other nucleic acid sequences, for example, transcriptional terminators, nucleic acid sequences encoding peptide tags, synthetic sequences to link the various nucleic acid sequences together, origins of replication, and the like. However, it should be understood that the practice of the present invention is not limited by the presence of any one or more of these other nucleic acid sequences. 
     Genetically Modified Microbes Producing Modified TrCel6A Cellulases 
     The modified TrCel6A cellulase may be expressed and secreted from a genetically modified microbe produced by transformation of a host microbe with a genetic construct encoding the modified TrCel6A cellulase. The host microbe may be a yeast or a filamentous fungus, particularly those microbes that are members of the phylum  Ascomycota . Genera of yeasts useful as host microbes for the expression of modified TrCel6A cellulases of the present invention include  Saccharomyces, Pichia, Hansenula, Kluyveromyces, Yarrowia , and  Arxula . Genera of fungi useful as microbes for the expression of modified TrCel3A beta-glucosidases of the present invention include  Trichoderma, Hypocrea, Aspergillus, Fusarium, Humicola, Neurospora , and  Penicillium . Typically, the host microbe is one from which the gene(s) encoding any or all Family 6 cellulase have been deleted. In a most preferred embodiment, the host microbe is an industrial strain of  Trichoderma reesei.    
     The genetic construct may be introduced into the host microbe by any number of methods known by one skilled in the art of microbial transformation, including but not limited to, treatment of cells with CaCl 2 , electroporation, biolistic bombardment, PEG-mediated fusion of protoplasts (e.g. White et al., WO 2005/093072). After selecting the recombinant fungal strains expressing the modified TrCel6A cellulase, they may be cultured in submerged liquid fermentations under conditions that induce the expression of the modified TrCel6A cellulase. Preferably, the modified TrCel6A cellulase is produced in submerged liquid culture fermentation and separated from the cells at the end of the fermentation. The cells may be separated by filtration, centrifugation, or other processes familiar to those skilled in the art. The cell-free cellulase-containing fraction may then be concentrated (for example, via ultrafiltration), preserved, and/or stabilized prior to use. 
     Therefore the present invention also provides a process for producing a modified TrCel6A cellulase. The method comprises growing a genetically modified microbe comprising a nucleotide sequence encoding a modified TrCel6A cellulase, in a culture medium under conditions that induce expression and secretion of the modified TrCel6A cellulase, and recovering the modified TrCel6A cellulase from the culture medium. The modified TrCel6A cellulase comprising one or more amino acid substitutions selected from the group consisting of: 
     substitution of a basic amino acid at one or more of positions 129 and 410 by a charge-neutral or an acidic amino acid; 
     substitution of a charge-neutral amino acid at one or more of positions 322 and 363 by an acidic amino acid; and 
     substitution of an amino acid at position 186 by a threonine, 
     wherein amino acids 83-447 of the modified TrCel6A cellulase are from about 47% to about 99.9% identical to amino acids 83-447 of SEQ ID NO: 1. 
     Production of Modified TrCel6A Cellulases 
     A modified TrCel6A cellulase of the present invention may be produced in a fermentation process using a genetically modified microbe comprising a genetic construct encoding the modified TrCel6A cellulase, e.g., in submerged liquid culture fermentation. 
     Submerged liquid fermentations of microorganisms, including  Trichoderma  and related filamentous fungi, are typically conducted as a batch, fed-batch or continuous process. In a batch process, all the necessary materials, with the exception of oxygen for aerobic processes, are placed in a reactor at the start of the operation and the fermentation is allowed to proceed until completion, at which point the product is harvested. A batch process for producing the modified TrCel6A cellulase of the present invention may be carried out in a shake-flask or a bioreactor. 
     In a fed-batch process, the culture is fed continuously or sequentially with one or more media components without the removal of the culture fluid. In a continuous process, fresh medium is supplied and culture fluid is removed continuously at volumetrically equal rates to maintain the culture at a steady growth rate. 
     One of skill in the art is aware that fermentation medium comprises a carbon source, a nitrogen source and other nutrients, vitamins and minerals which can be added to the fermentation media to improve growth and enzyme production of the host cell. These other media components may be added prior to, simultaneously with or after inoculation of the culture with the host cell. 
     For the process for producing the modified TrCel6A cellulase of the present invention, the carbon source may comprise a carbohydrate that will induce the expression of the modified TrCel6A cellulase from a genetic construct in the genetically modified microbe. For example, if the genetically modified microbe is a strain of  Trichoderma , the carbon source may comprise one or more of cellulose, cellobiose, sophorose, and related oligo- or poly-saccharides known to induce expression of cellulases and beta-glucosidase in  Trichoderma.    
     In the case of batch fermentation, the carbon source may be added to the fermentation medium prior to or simultaneously with inoculation. In the cases of fed-batch or continuous operations, the carbon source may also be supplied continuously or intermittently during the fermentation process. For example, when the genetically modified microbe is a strain of  Trichoderma , the carbon feed rate is between 0.2 and 2.5 g carbon/L of culture/h, or any amount therebetween. 
     The process for producing the modified TrCel6A cellulase of the present invention may be carried at a temperature from about 20° C. to about 40° C., or any temperature therebetween, for example from about 25° C. to about 37° C., or any temperature therebetween, or from 20, 22, 25, 26, 27, 28, 29, 30, 32, 35, 37, 40° C. or any temperature therebetween. 
     The process for producing the modified TrCel6A cellulase of the present invention may be carried out at a pH from about 3.0 to 6.5, or any pH therebetween, for example from about pH 3.5 to pH 5.5, or any pH therebetween, for example from about pH 3.0, 3.2, 3.4, 3.5, 3.7, 3.8, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.2, 5.4, 5.5, 5.7, 5.8, 6.0, 6.2, 6.5 or any pH therebetween. 
     Following fermentation, the fermentation broth containing the modified TrCel6A cellulase may be used directly, or the modified TrCel6A cellulase may be separated from the fungal cells, for example by filtration or centrifugation. Low molecular solutes such as unconsumed components of the fermentation medium may be removed by ultra-filtration. The modified Family 6 cellulase may be concentrated, for example, by evaporation, precipitation, sedimentation or filtration. Chemicals such as glycerol, sucrose, sorbitol and the like may be added to stabilize the cellulase enzyme. Other chemicals, such as sodium benzoate or potassium sorbate, may be added to the cellulase enzyme to prevent growth of microbial contamination. 
     Cellulose Hydrolysis Process Using the Modified TrCel6A Cellulase 
     The modified TrCel6A cellulase of the present invention is used for the enzymatic hydrolysis of cellulose in a hydrolysis reaction further comprising lignin. For example, the modified TrCel6A cellulase of the present invention is used for the enzymatic hydrolysis of a pretreated lignocellulosic substrate. The modified TrCel6A cellulase of the present invention may be used in industrial processes such as the production of fermentable sugars, sugar alcohols or fuel alcohols. 
     The modified TrCel6A cellulase enzyme of the invention can be used for the enzymatic hydrolysis of a “pretreated lignocellulosic substrate.” A pretreated lignocellulosic substrate is a material of plant origin that, prior to pretreatment, contains at least 20% cellulose (dry wt), more preferably greater than about 30% cellulose, even more preferably greater than 40% cellulose, for example 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 55, 60, 65, 70, 75, 80, 85, 90% or any % therebetween, and at least 10% lignin (dry wt), more typically at least 12% (dry wt) and that has been subjected to physical and/or chemical processes to make the fiber more accessible and/or receptive to the actions of cellulolytic enzymes. 
     After pretreatment, the lignocellulosic feedstock may contain higher levels of cellulose. For example, if acid pretreatment is employed, the hemicellulose component is hydrolyzed, which increases the relative level of cellulose. In this case, the pretreated feedstock may contain greater than about 20% cellulose and greater than about 12% lignin. In one embodiment, the pretreated lignocellulosic feedstock contains greater than about 20% cellulose and greater than about 10% lignin. 
     Lignocellulosic feedstocks that may be used in the invention include, but are not limited to, agricultural residues such as corn stover, wheat straw, barley straw, rice straw, oat straw, canola straw, and soybean stover; fiber process residues such as corn fiber, sugar beet pulp, pulp mill fines and rejects or sugar cane bagasse; forestry residues such as aspen wood, other hardwoods, softwood, and sawdust; grasses such as switch grass, miscanthus, cord grass, and reed canary grass; or post-consumer waste paper products. 
     The lignocellulosic feedstock may be first subjected to size reduction by methods including, but not limited to, milling, grinding, agitation, shredding, compression/expansion, or other types of mechanical action. Size reduction by mechanical action can be performed by any type of equipment adapted for the purpose, for example, but not limited to, a hammer mill. 
     Non-limiting examples of pretreatment processes include chemical treatment of a lignocellulosic feedstock with sulfuric or sulfurous acid, or other acids; ammonia, lime, ammonium hydroxide, or other alkali; ethanol, butanol, or other organic solvents; or pressurized water (See U.S. Pat. Nos. 4,461,648, 5,916,780, 6,090,595, 6,043,392, 4,600,590, Weil et al. (1997)). 
     The pretreatment may be carried out to hydrolyze the hemicellulose, or a portion thereof, that is present in the lignocellulosic feedstock to monomeric sugars, for example xylose, arabinose, mannose, galactose, or a combination thereof. Preferably, the pretreatment is carried out so that nearly complete hydrolysis of the hemicellulose and a small amount of conversion of cellulose to glucose occurs. During the pretreatment, typically an acid concentration in the aqueous slurry from about 0.02% (w/w) to about 2% (w/w), or any amount therebetween, is used for the treatment of the lignocellulosic feedstock. The acid may be, but is not limited to, hydrochloric acid, nitric acid, or sulfuric acid. For example, the acid used during pretreatment is sulfuric acid. 
     One method of performing acid pretreatment of the feedstock is steam explosion using the process conditions set out in U.S. Pat. No. 4,461,648. Another method of pretreating the feedstock slurry involves continuous pretreatment, meaning that the lignocellulosic feedstock is pumped through a reactor continuously. Continuous acid pretreatment is familiar to those skilled in the art; see, for example, U.S. Pat. No. 5,536,325; WO 2006/128304; and U.S. Pat. No. 4,237,226. Additional techniques known in the art may be used as required such as the process disclosed in U.S. Pat. No. 4,556,430. 
     As noted above, the pretreatment may be conducted with alkali. In contrast to acid pretreatment, pretreatment with alkali does not hydrolyze the hemicellulose component of the feedstock, but rather the alkali reacts with acidic groups present on the hemicellulose to open up the surface of the substrate. The addition of alkali may also alter the crystal structure of the cellulose so that it is more amenable to hydrolysis. Examples of alkali that may be used in the pretreatment include ammonia, ammonium hydroxide, potassium hydroxide, and sodium hydroxide. The pretreatment is preferably not conducted with alkali that is insoluble in water, such as lime and magnesium hydroxide. 
     An example of a suitable alkali pretreatment, variously known as Ammonia Freeze Explosion, Ammonia Fiber Explosion or Ammonia Fiber Expansion (“AFEX” process), involves contacting the lignocellulosic feedstock with ammonia or ammonium hydroxide in a pressure vessel for a sufficient time to enable the ammonia or ammonium hydroxide to alter the crystal structure of the cellulose fibers. The pressure is then rapidly reduced, which allows the ammonia to flash or boil and explode the cellulose fiber structure. (See U.S. Pat. Nos. 5,171,592, 5,037,663, 4,600,590, 6,106,888, 4,356,196, 5,939,544, 6,176,176, 5,037,663 and 5,171,592). The flashed ammonia may then be recovered according to known processes. 
     The pretreated lignocellulosic feedstock may be processed after pretreatment but prior to the enzymatic hydrolysis by any of several steps, such as dilution with water, washing with water, buffering, filtration, or centrifugation, or a combination of these processes, prior to enzymatic hydrolysis, as is familiar to those skilled in the art. 
     The pretreated lignocellulosic feedstock is next subjected to enzymatic hydrolysis. By the term “enzymatic hydrolysis”, it is meant a process by which cellulase enzymes act on cellulose to convert all or a portion thereof to soluble sugars. Soluble sugars are meant to include water-soluble hexose monomers and oligomers of up to six monomer units that are derived from the cellulose portion of the pretreated lignocellulosic feedstock. Examples of soluble sugars include, but are not limited to, glucose, cellobiose, cellodextrins, or mixtures thereof. The soluble sugars may be predominantly cellobiose and glucose. The soluble sugars may be predominantly glucose. 
     The enzymatic hydrolysis process preferably converts about 80% to about 100% of the cellulose to soluble sugars, or any range therebetween. More preferably, the enzymatic hydrolysis process converts about 90% to about 100% of the cellulose to soluble sugars, or any range therebetween. In the most preferred embodiment, the enzymatic hydrolysis process converts about 98% to about 100% of the cellulose to soluble sugars, or any range therebetween. The enzymatic hydrolysis process may be batch hydrolysis, continuous hydrolysis, or a combination thereof. The hydrolysis process may be agitated, unmixed, or a combination thereof. 
     The enzymatic hydrolysis process is preferably carried out at a temperature of about 45° C. to about 75° C., or any temperature therebetween, for example a temperature of 45, 50, 55, 60, 65, 70, 75° C., or any temperature therebetween, and a pH of about 3.5 to about 7.5, or any pH therebetween, for example a temperature of 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, or pH therebetween. The initial concentration of cellulose in the hydrolysis reactor, prior to the start of hydrolysis, is preferably about 4% (w/w) to about 15% (w/w), or any amount therebetween, for example 4, 6, 8, 10, 12, 14, 15% or any amount therebetween. The combined dosage of all primary cellulase enzymes may be about 1 to about 100 mg protein per gram cellulose, or any amount therebetween, for example 1, 5, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100 mg protein per gram cellulose or any amount therebetween. The hydrolysis may be carried out for a time period of about 12 hours to about 200 hours, or any time therebetween, for example, the hydrolysis may be carried out for a period of 15 hours to 100 hours, or any time therebetween, or it may be carried out for 12, 14, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 120, 140, 160, 180, 200 or any time therebetween. It should be appreciated that the reaction conditions are not meant to limit the invention in any manner and may be adjusted as desired by those of skill in the art. 
     The enzymatic hydrolysis process is typically carried out in a hydrolysis reactor. The cellulase enzyme is added to the pretreated lignocellulosic feedstock (also referred to as the “substrate”) prior to, during, or after the addition of the substrate to the hydrolysis reactor. 
     The cellulase enzyme may be a cellulase enzyme mixture comprising the modified TrCel6A cellulase and other cellulase enzymes produced in one or more submerged liquid culture fermentations. The modified TrCel6A cellulase and other cellulase enzymes thus produced may be separated from the cells at the end of the fermentation by filtration, centrifugation, or other processes familiar to those skilled in the art. The cell-free cellulase-containing fraction(s) may then be concentrated (for example, via ultrafiltration), preserved, and/or stabilized prior to use. Alternatively, the modified TrCel6A cellulase and other cellulase enzymes are not separated from the cells, but are added to the enzymatic hydrolysis with the cells. 
     EXAMPLES 
     The present invention will be further illustrated in the following examples. However, it is to be understood that these examples are for illustrative purposes only and should not be used to limit the scope of the present invention in any manner. 
     Example 1 describes the strains and vectors used in the following examples. Example 2 describes the cloning of the TrCel6A-S413P gene and transformation in yeast. Example 3 summarizes the preparation of the error prone-PCR library of TrCel6A-S413P. Example 4 describes the expression of modified TrCel6A cellulases from microculture. Example 5 describes the isolation and preparation of lignin. Examples 6 and 7 describe the high-throughput screening assays to identify modified TrCel6A cellulases with decreased inactivation by lignin. Example 8 describes the preparation of aggregate modified TrCel6A cellulases. Example 9 describes the expression and purification of parental and modified TrCel6A cellulases. Example 10 summarizes the testing of purified parental and modified TrCel6A cellulases in high-throughput assay 1 and assay 2. Finally, Example 11 describes the testing of purified parental and modified TrCel6A cellulases in lignin inactivation time course experiments. 
     Example 1 
     Strains and Vectors 
       Saccharomyces cerevisiae  strain YDR483W BY4742 [14317] (MATα his3Δ1 leu2Δ0 lys2 Δ0 ura3 Δ0 Δkre2) was obtained from ATCC (#4014317). The YEp352/PGK91-1 vector was obtained from the National Institute of Health. The YEpFLAG ΔKpn10-S413P vector is described in U.S. Patent Application 60/841,507. The YEpFLAG-1 vector was obtained from Sigma as a part of the Amino-Terminal Yeast FLAG Expression Kit. 
     Example 2 
     Cloning of the TrCel6A-S413P Gene into the YEp352/PGK91-1 and Transformation in Yeast 
     In order to facilitate cloning using NheI and KpnI restriction enzymes, the unique NheI site at position 1936 of the YEp352/PGK91-1 vector was blunted using the DNA Polymerase I large (Klenow) fragment to generate YEp352/PGK91-1 ΔNheI. The TrCel6A-S413P gene was amplified by PCR from YEpFLAG ΔKpn10-S413P vector (U.S. Patent Provisional No. 60/841,507) using primers 5′NheCel6A and 3′BglKpnCel6A. In parallel, the yeast alpha-factor leader sequence was amplified by PCR from the YEpFLAG-1 vector (Sigma) using primers (5′BglAlphaSS and 3′NheAlphaSS) to introduce BglII at the 5′ end and an NheI site at 3′ end of the amplicon. 
     The yeast alpha-factor leader sequence was isolated by BglII/NheI digestion and a three piece ligation performed with the TrCel6A-S413P gene (isolated by NheI/BglII digestion) and YEp352/PGK91-1 ΔNheI vector (isolated by BglII digestion). The resulting vector YEp352/PGK91-1 ΔNheI-alpha ss -TrCel6A-S413P ( FIG. 2 ) was transformed in yeast strain BY4742 using the procedure described by Gietz, R. D. and Woods, R. A. (2002). Primer sequences are listed below: 
     
       
         
           
               
            
               
                 5′BglAlphaSS: 
               
            
           
           
               
            
               
                 (SEQ ID NO: 46) 
               
            
           
           
               
            
               
                 5′ACC AAA AGA TCT ATG AGA TTT CCT TCA ATT 
               
               
                   
               
               
                 3′NheAlphaSS: 
               
            
           
           
               
            
               
                 (SEQ ID NO: 47) 
               
            
           
           
               
            
               
                 5′TGA GCA GCT AGC CCT TTT ATC CAA AGA TAC 
               
               
                   
               
               
                 5′NheCel6A: 
               
            
           
           
               
            
               
                 (SEQ ID NO: 48) 
               
            
           
           
               
            
               
                 5′AAA AGG GCT AGC TGC TCA AGC GTC TGG GGC 
               
               
                   
               
               
                 3′BglKpnCel6A: 
               
            
           
           
               
            
               
                 (SEQ ID NO: 49) 
               
            
           
           
               
            
               
                 5′GAG CTC AGA TCT GGT ACC TTA CAG GAA CGA TGG GTT 
               
            
           
         
       
     
     Example 3 
     Making Error Prone-PCR Libraries 
     Random mutagenesis libraries were generated using a Mutazyme® II DNA polymerase method. For the Mutazyme® II DNA polymerase method, a series of four independent PCR were performed using 10, 20, 30, 40 ng of YEp352/PGK91-1 ΔNheI-α ss -TrCel6A-S413P vector and the Mutazyme® II DNA polymerase with primers YalphaN21 and 3′PGK-term. The amplification was done for 25 cycles. The four PCR products were pooled and diluted to 10 ng/μL. A second PCR mutagenesis step was performed using 30 ng of pooled PCR product with Mutazyme® II DNA polymerase using the same primers for 30 amplification cycles. The YEp352/PGK91-1ΔNheI-α ss -TrCel6A-S413P vector was digested with NheI and KpnI and the empty vector fragment was isolated. This linear fragment and the final amplicon were transformed simultaneously and cloned by in vivo recombination into yeast strain BY4742 (Butler et al., 2003). 
     
       
         
           
               
               
            
               
                 YalphaN21: 
                   
               
               
                 5′AGC ACA AAT AAC GGG TTA TTG 
                 (SEQ ID NO: 45) 
               
               
                   
               
               
                 3′PGK-term: 
               
               
                 5′GCA ACA CCT GGC AAT TCC TTA CC 
                 (SEQ ID NO: 56) 
               
            
           
         
       
     
     Example 4 
     Expression and Isolation of Parental and Modified TrCel6A Cellulases from Microplate Cultures 
     This example describes the selection and expression of TrCel6A-S413P and modified TrCel6A cellulases from  Saccharomyces cerevisiae  for use in high-throughput screening assays (Examples 6 and 7). 
       Saccharomyces cerevisiae  transformants from Example 3 were grown on plates containing synthetic complete medium (SC: 2% agar w/v, 0.17% yeast nitrogen base w/v, 0.078%-Ura drop-out supplement w/v, 2% glucose w/v, 2% casamino acids w/v, 0.5% ammonium sulfate w/v, pH 5.5) and 0.12% Azo-barley-beta-glucan (Megazyme) for 4 days at 30° C. 
     Colonies showing visible clearing halos after an overnight incubation at 45° C. were selected for liquid media pre-cultures by toothpick inoculation of 0.15 mL synthetic complete media (SC: 0.17% yeast nitrogen base w/v, 0.078%-Ura drop-out supplement w/v, 2% glucose w/v, 2% casamino acids w/v, 0.5% ammonium sulfate w/v) in 96-well microplates. Pre-cultures were grown overnight (16-18 hr) at 30° C. with orbital shaking to stationary phase. For expression culture inoculation, 25 μL of pre-culture was used to inoculate 1 mL of SC media in deepwell microplates containing one glass bead. Expression cultures were grown for 3 days at 30° C. with orbital shaking and humidity control. Plates were centrifuged at 710×g for 5 minutes to pellet cells and supernatant was aspirated for screening assays (Examples 6 and 7). To the remaining pre-culture, stocks were prepared by the addition of glycerol to a final concentration of 15% and stored at −80° C. 
     Example 5 
     Preparation of Lignin 
     Wheat straw was pretreated using the methods described in U.S. Pat. No. 4,461,648. Following pretreatment, sodium benzoate was added at a concentration of 0.5% as a preservative. The pretreated material was then washed with six volumes of lukewarm (˜35° C.) tap water using a Buchner funnel and filter paper. 
     A sample of pretreated wheat straw (167 g wet; 30% solids; 60% cellulose) was added to 625 mL of 82% H 2 SO 4  with stirring in a 1 L flask, then stoppered and incubated at 50° C. with shaking for 4 hours. The remaining solids were filtered to dampness using a Buchner funnel and a glass fiber filter, resuspended in 1 L of water and adjusted to pH 4.5 with NaOH. The solids were filtered and washed with ˜8 L water. The solids are referred to herein as “lignin”. 
     Bovine serum albumin (BSA) treatment of lignin was performed by incubating equal amounts (w/w) of lignin and BSA, at a concentration of 30 g/L in 50 mM citrate buffer (pH 5) containing 0.1% sodium benzoate, for 5 days at 50° C. with shaking. 
     Example 6 
     High-Throughput Screening of  Trichoderma reesei  Cel6A Gene Libraries for Modified Family 6 Cellulase with Resistance to Lignin—Assay 1 
     This example describes the screening of modified TrCel6A cellulases in order to identify those with resistance to inactivation by lignin in comparison to the parent TrCel6A-S413P that had been cloned into  Saccharomyces cerevisiae.    
     Yeast expressed TrCel6A-S413P pre-binding to cellulose. An aliquot (0.175 mL) of supernatant from culture containing modified TrCel6A cellulase as described in Example 4 was added to two separate microplate wells containing 0.05 mL cellulose at a concentration of 0.167% w/v, and incubated for 90 minutes at 4° C. with orbital shaking. Microplates were then centrifuged at 2800×g for 3 min and 0.175 mL of supernatant was removed. An additional aliquot of supernatant (0.175 mL) from each modified TrCel6A was added to the same microplate wells and incubated for another 90 minutes under the same conditions. Microplates were again centrifuged at 2800×g for 3 min and 0.175 mL of supernatant was removed. A 0.175 mL volume of 50 mM citrate buffer (pH 5) was added to all wells and immediately the microplates were centrifuged at 2800×g for 3 min. Supernatant (0.175 mL) was removed. 
     Cellulose hydrolysis. Each modified TrCel6A cellulase was incubated with both 2.68% (w/v) lignin and BSA-treated lignin (0.10 mL) for 2 hours at 50° C. with orbital shaking. Following this period,  Trichoderma reesei  Cel7B and Cel5A (40 mg protein/g cellulose) and 125 IU/g cellulose  A. niger  beta-glucosidase were added and the incubation proceeded for an additional 3 hours. Microplates were centrifuged for 3 min at 2800×g and an aliquot of supernatant was sampled for glucose. Enzyme activity was measured via the detection of glucose using a standard glucose oxidase/peroxidase coupled reaction assay (Trinder, 1969). A sample of the data from one screening plate is shown in  FIG. 3 , panel A. 
     Contained in each 96-well microplate were six parental TrCel6A-S413P controls used for comparison. A ±BSA-treated lignin ratio was calculated for all modified TrCel6A cellulases and parental TrCel6A-S413P cellulase by dividing the cellulase activity in the presence of untreated lignin by the cellulase activity in the presence of BSA-treated lignin. The activity ratio for each modified TrCel6A cellulase was compared to the average of six parental TrCel6A-S413P controls on a particular microplate and positives (those having increased ratios) were selected at the 95% confidence level using a t-test. All positive cellulases were produced again in microculture and re-screened to reduce the number of false positives. Plasmid DNA comprising genes encoding modified TrCel6A cellulases with decreased lignin inactivation was isolated from yeast cultures grown from the glycerol stocks prepared in Example 4. The modified TrCel6A cellulase genes were subjected to DNA sequencing to identify mutations that confer altered substrate specificity. 
     Example 7 
     High-Throughput Screening of  Trichoderma reesei  Cel6A Gene Libraries for Modified Family 6 Cellulase with Resistance to Lignin—Assay 2 
     This example describes an additional screening of modified TrCel6A cellulases for those resistant to lignin using another high-throughput assay. 
     An aliquot (0.15 mL) of yeast supernatant as described in Example 4 was pre-incubated with lignin (1.6% w/v) in a 0.25 mL citrate buffered (50 mM; pH 5) reaction. An equivalent aliquot of supernatant from each modified cellulase was also pre-incubated with lignin (1.6% w/v) which was pre-treated with BSA. Pre-incubation was performed for 5.5 hours, in a 96-well microplate containing 1 glass bead, at 50° C. with orbital shaking (NB Innova 44). Contained in each 96-well microplate were six parent TrCel6A-S413P controls used for comparison. Following pre-incubation, microplates were centrifuged for 5 min at 2800×g and the supernatant was aspirated for residual activity assays. 
     Supernatant (0.05 mL) was incubated with 0.5% beta-glucan in a 100 μL citrate buffered (50 mM; pH 5) reaction. Residual activity assays were performed for 16 hours for samples pre-incubated with lignin and 3 hours for samples pre-incubated with BSA-treated lignin, in a PCR plate, at 50° C. A glucose standard curve was placed in the first column of the PCR ranging from 3 to 0.05 mg/mL. Following incubation, 0.08 mL of DNS reagent was added to all wells and the plates were boiled for 10 min. An aliquot (0.15 mL) was transferred to a microplate and the absorbance was measured at 560 nm. Residual enzyme activity was determined by converting A 560  values to reducing equivalents using the glucose standard curve. A sample of the data from one screening plate is shown in  FIG. 3 , panel B. An activity ratio was calculated for all modified TrCel6A cellulases and the parental TrCel6A-S413P controls by dividing the residual enzyme activity in the presence of untreated lignin by the residual enzyme activity in the presence of BSA-treated lignin. The activity ratio for each modified TrCel6A was compared to the average of six parental TrCel6A-S413P controls on a particular microplate and positives (those having increased ratios) were selected at the 95% confidence level using a t-test. All positive modified TrCel6A cellulases were produced again in microculture and re-screened to reduce the number of false positives. 
     DNS Reagent Contains: 
     
       
         
           
               
               
               
             
               
                   
                   
               
               
                   
                 Component 
                 g/L 
               
               
                   
                   
               
             
            
               
                   
               
            
           
           
               
               
               
            
               
                   
                 3,5-Dinitosalicylic acid (Acros) 
                 20 
               
               
                   
                 Sodium hydroxide (Fisher) 
                 20 
               
               
                   
                 Phenol (Sigma) 
                 4 
               
               
                   
                 Sodium metabisulfate (Fisher) 
                 1 
               
               
                   
                   
               
            
           
         
       
     
     Example 8 
     Making the Aggregate Modified TrCel6A Cellulases 
     Lignin-resistant mutations were combined into two aggregate modified TrCel6A cellulases. Table 2 shows the steps performed to generate the aggregate modified TrCel6A cellulases, TrCel6A-K129E-S 186T-A322D-Q363E-S413P and TrCel6A-K129E-S 186T-A322D-Q363E-R410Q-S413P. 
     
       
         
           
               
               
               
               
            
               
                 PSP4-C 
                 5′-GGCCACTGCTGCAGCAGCTGTCGCAGAAGTTCCCTCTTTTATGTGGC-3′ 
                 (SEQ ID NO: 50) 
                   
               
               
                   
               
               
                 PSP5-C 
                 5′-GCCACATAAAAGAGGGAACTTCTGCGACAGCTGCTGCAGCAGTGGCC-3′ 
                 (SEQ ID NO: 51) 
               
               
                   
               
               
                 PSP6-B 
                 5′-GCCCTTGCCTCGAATGGCGAATACACTATTGCCGATGGTGGCGTCGCC-3′ 
                 (SEQ ID NO: 52) 
               
               
                   
               
               
                 PSP7-B 
                 5′-GGCGACGCCACCATCGGCAATAGTGTATTCGCCATTCGAGGCAAGGGC-3′ 
                 (SEQ ID NO: 53) 
               
               
                   
               
               
                 PSP8 
                 5′-TACACGCAAGGCAACGATGTCTACAACGAGAAG-3′ 
                 (SEQ ID NO: 54) 
               
               
                   
               
               
                 PSP9 
                 5′-CTTCTCGTTGTAGACATCGTTGCCTTGCGTGTA-3′ 
                 (SEQ ID NO: 55) 
               
               
                   
               
               
                 DK091 
                 5′-GACAGCAGTGCGCCACAGTTTGAC C CCCACTGT-3′ 
                 (SEQ ID NO: 57) 
               
               
                   
               
               
                 DK092 
                 5′-ACAGTGGG G GTCAAACTGTGGCGCACTGCTGTC-3′ 
                 (SEQ ID NO: 58) 
               
            
           
         
       
     
     To perform gap repair, the vector YEp352/PGK91-1-α ss -NKE was digested with NheI and KpnI and purified on gel. The digested YEp352/PGK91-1-α ss -NKE vector and the amplicons were transformed in yeast ( Saccharomyces cerevisiae  strain BY4742) using the procedure described by Gietz, R. D. and Woods, R. A., (2002). 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Generation of modified TrCel6A cellulases by PCR 
               
            
           
           
               
               
               
               
               
               
            
               
                 PCR 
                 Step 
                 Template 
                 Primer 1 
                 Primer 2 
                 Amplicon 
               
               
                   
               
               
                 1 
                 1 
                 YEp352/PGK91-1-α ss -NKE 
                 YαN21 
                 PSP9 
                 PCR 1 Step 1 
               
               
                   
                   
                 TrCel6A- S413P-Q363E 
               
               
                   
                 1 
                 YEp352/PGK91-1-α ss -NKE 
                 PSP8 
                 3′PGK-Term 
                 PCR 1 Step 1 
               
               
                   
                   
                 TrCel6A- S413P-Q363E 
               
               
                   
                 2 
                 Both PCR 1 Step 1 megaprimers 
                 YαN21 
                 3′PGK-Term 
                 PCR 1 Step 2 
               
               
                 2 
                 1 
                 PCR 1 Step 2 
                 YαN21 
                 PSP7B 
                 PCR 2 Step 1 
               
               
                   
                 1 
                 PCR 1 Step 2 
                 PSP6B 
                 3′PGK-Term 
                 PCR 2 Step 1 
               
               
                   
                 2 
                 Both PCR 2 Step 1 megaprimers 
                 YαN21 
                 3′PGK-Term 
                 PCR 2 Step 2 
               
               
                 3 
                 1 
                 PCR 2 Step 2 
                 YαN21 
                 PSP5C 
                 PCR 3 Step 1 
               
               
                   
                 1 
                 PCR 2 Step 2 
                 PSP4C 
                 3′PGK-Term 
                 PCR 3 Step 1 
               
               
                   
                 2 
                 Both PCR 3 Step 1 megaprimers 
                 YαN21 
                 3′PGK-Term 
                 PCR 3 Step 2 
               
               
                 4 
                 1 
                 PCR 3 Step 2 
                 YαN21 
                 DK092 
                 PCR 4 Step 1 
               
               
                   
                 1 
                 PCR 3 Step 2 
                 DK091 
                 3′PGK-Term 
                 PCR 4 Step 1 
               
            
           
           
               
               
               
               
            
               
                   
                 2 
                 Both PCR 4 Step 1 megaprimers 
                 Both fragments were cloned in 
               
               
                   
                   
                   
                 YEp352/PGK91-1-α ss -NKE using the Gap 
               
               
                   
                   
                   
                 repair method in yeast. 
               
               
                   
                   
               
            
           
         
       
     
     Example 9 
     Expression and Purification of TrCel6A-S413P and Modified TrCel6A Cellulases from Large Scale Cultures 
     500 mL of sterile YPD medium (10 g/L yeast extract, 20 g/L peptone and 20 g/L glucose) was inoculated with 10 mL of an overnight culture of transformed  S. cerevisiae  grown from cells freshly picked from an agar plate. The 500 mL cultures were then incubated for 96 hours at 30° C. with orbital shaking. 
     After incubation, the broth from each culture was centrifuged for 10 minutes at 16,700×g and the pellet (containing yeast cells) discarded. The pH of the supernatant was adjusted to 5.0 and then allowed to cool to 4° C. for an hour. Subsequent to cooling, 625 g (NH 4 ) 2 SO 4  was added to bring the yeast supernatant to 93% saturation. Precipitation was allowed to occur over a period of 2 hours at 4° C. with constant stirring. After centrifugation for 15 minutes at 16,700×g, the supernatant was discarded. 
     The pellet was resuspended with pipetting in 20 mL of 50 mM citrate, pH 5.0. Once the pellet was resuspended, 80 mL of 0.1 M sodium acetate, 200 mM glucose and 1 mM gluconic acid lactone, pH 5.0 was added. Samples were then incubated at 4° C. for 30 min with gentle stirring. Each sample was then centrifuged at 710×g for 3 minutes to pellet any insoluble material. The supernatant was removed carefully with a pipette to prevent disruption of the pellet and retained. The TrCel6A cellulase in each sample was purified by APTC affinity chromatography as described by (Piyachomkwan et al., 1997). Purified TrCel6A cellulases were buffer exchanged into 50 mM citrate, pH 5.0 and concentrated using a Centricon (Millipore) centrifugal concentrator with a 5 kDa NMWL polyethersulfone membrane. Protein concentrations were measured by UV absorbance (280 nm) using an extinction coefficient of ε 280 nm =2.062 mL·mg −1 ·cm. 
     Example 10 
     Assaying Purified Aggregate Modified TrCel6A Cellulases in High-Throughput Assay 1 and Assay 2 
     TrCel6A-S413P, TrCel6A-K129E-S186T-A322D-Q363E-S413P and TrCel6A-K129E-S 186T-A322D-Q363E-R410Q-S413P were expressed and purified as described in Example 10. The TrCel6A cellulases were tested in high-throughput assay 1 and assay 2 as described in Examples 6 and 7. The concentration of TrCel6A was 0.02 mg/mL. The ±BSA-lignin ratio was normalized to TrCel6A-S413P and P-values were calculated for the aggregate modified TrCel6A cellulases ( FIG. 5  and Table 3). 
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Normalized ±BSA-lignin ratios and P-values for 
               
               
                 the aggregate modified TrCel6A cellulases. 
               
            
           
           
               
               
               
            
               
                   
                 Assay 1 
                 Assay 2 
               
            
           
           
               
               
               
               
               
            
               
                   
                 Normalized ±BSA 
                   
                 Normalized ±BSA 
                   
               
               
                   
                 Lignin Ratio 
                 P-value 
                 Lignin Ratio 
                 P-value 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
            
               
                 TrCel6A-S413P 
                 1.00 
                 — 
                 1.00 
                 — 
               
               
                 TrCel6A-K129E-S186T- 
                 1.36 
                 0.001 
                 1.63 
                 &lt;0.001 
               
               
                 A322D-Q363E-S413P 
               
               
                 TrCel6A-K129E-S186T- 
                 — 
                 — 
                 2.14 
                 &lt;0.001 
               
               
                 A322D-Q363E-R410Q- 
               
               
                 S413P 
               
               
                   
               
            
           
         
       
     
     Example 11 
     Testing Purified Modified TrCel6A Cellulases in Lignin Inactivation Time Course Assays 
     Purified TrCel6A (0.06 mg) cellulases were incubated with untreated lignin (1.04 mg) in stoppered, glass flasks in a total volume of 2 mL of 50 mM citrate buffer, pH 5.0. Incubations were done at 50° C. with orbital shaking. 0.2 mL samples were collected from each flask at 0, 0.5, 1, 2, 3, 4, 6, 14 and 24 hr. Each sample was centrifuged to separate the lignin and stored at 4° C. 
     Upon completion of the time course, each sample was mixed briefly to resuspend the pellet and 0.05 mL of slurry containing both soluble and insoluble material added to a microtitre plate containing 3 glass beads/well. To each well, 0.02 mL of a dilute preparation of  Trichoderma  cellulase devoid of cellobiohydrolase activity (1 μg total protein) and purified  Trichoderma  Cel3A (1.4 μg) were added to complement TrCel6A hydrolysis activity. Finally a 0.2 mL slurry of delignified cellulose (0.25% cellulose) was added to each well. The assay plate was incubated at 50° C. for 2 hr with orbital shaking. The plate was then centrifuged at 710×g for 2 min and the glucose concentrations measured as described in Example 6. 
     Glucose concentrations were converted to TrCel6A activity, expressed as mg glucose produced/hr/mg of TrCel6A protein. The activity measured at t=0 hr, in the absence of incubation with lignin, was the enzyme&#39;s specific activity. Activities measured throughout the time course were divided by the activity measured at t=0 in order to calculate a relative residual activity of TrCel6A. For the purposes of analyzing the results, measurements of relative residual activity were considered representative of the relative residual active TrCel6A concentration. Standard curves were used to demonstrate that changes in TrCel6A concentration and activity were linear over the concentrations of enzyme and substrate used in this assay. 
     The residual TrCel6A versus time data were modeled using Equation 1. In this equation, E represents the enzyme, L represents lignin, EL represents a reversible enzyme-lignin complex and EL* represents an irreversible enzyme-lignin complex. K L  represents [E][L]/[EL] at steady state while k L  is a rate constant describing the rate of conversion of the reversible to the irreversible enzyme-lignin complex. A minimum of two replicate data sets for each modified TrCel6A cellulase were generated. 
     Sample lignin inactivation time course results are shown in  FIG. 6  for TrCel6A-S413P and TrCel6A-K129E-S186T-A322D-Q363E-R410Q-S413P. At each time during the 24 hr incubation with lignin, residual activity of TrCel6A-K129E-S186T-A322D-Q363E-R410Q-S413P is greater than TrCel6A-S413P, indicating that a larger fraction of the modified TrCel6A was active at each time point. As controls, TrCel6A-S413P and TrCel6A-K129E-S186T-A322D-Q363E-R410Q-S413P were incubated in the absence of lignin under otherwise the same experimental conditions. These controls demonstrate that both TrCel6A cellulases were stable in solution in the absence of lignin over the duration of these assays. Therefore, an increase in the relative residual activity of a modified TrCel6A cellulase relative to TrCel6A-S413P in the presence of lignin is due to a reduced rate of inactivation due to the presence of lignin rather than any potential improvement in thermal stability of the modified TrCel6A. 
     Modeling was done using 4th order Runge-Kutta spreadsheet in Microsoft Excel. In order to model the residual TrCel6A versus time results in a given experiment, the results for TrCel6A-S413P were fit by varying K L  and k L . Error minimization was done by the method of least squares as known to those of skill in the art. For modeling modified TrCel6A cellulases, the k L  value was fixed to that determined for TrCel6A-S413P in the same experiment and varying K L . Standard errors in the model fit to at least duplicate data sets were determined using a model comparison approach (Motulsky, H., and A. Christopoulos (2004)). The K L  determined for each modified TrCel6A cellulase was divided by the K L  determined for TrCel6A-S413P in order to calculate a relative K L . Similarly, the specific activity of each modified TrCel6A was divided by the specific activity of TrCel6A-S413P in order to calculate a relative specific activity. Modified TrCel6A cellulases with a K L  significantly higher (P&lt;0.05, Student&#39;s t-test) than TrCel6A-S413P are shown in Table 4. A scatter plot of the relative K L  and relative specific activity of each lignin-resistant modified TrCel6A cellulase and TrCel6A-S413P is shown in  FIG. 7 . 
     
       
         
           
               
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                   
                 Equation 1 
               
               
                 
                   
                     
                       
                         E 
                         ⁢ 
                         
                             
                         
                         + 
                         
                             
                         
                         ⁢ 
                         
                           L 
                           ⁢ 
                           
                               
                           
                           ⁢ 
                           
                             ⟵ 
                             
                               ⟶ 
                               
                                 K 
                                 L 
                               
                             
                           
                           ⁢ 
                           
                               
                           
                           ⁢ 
                           EL 
                           ⁢ 
                           
                               
                           
                           ⁢ 
                           
                             ⟶ 
                             
                               k 
                               L 
                             
                           
                           ⁢ 
                           
                               
                           
                           ⁢ 
                           
                             EL 
                             * 
                           
                         
                       
                     
                   
                 
               
               
                   
               
            
           
           
               
            
               
                 Lignin inactivation constants (K L ) 
               
               
                 for modified TrCel6A cellulases 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                   
                   
                 Relative 
               
               
                   
                 Relative 
                 Standard 
                 P- 
                 Specific 
               
               
                 TrCel6A 
                 K L   
                 Error 
                 value 
                 Activity 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 TrCel6A-K129E-S413P 
                 2.1 
                 0.11 
                 &lt;0.001 
                 1.09 
               
               
                 TrCel6A-S186T-S413P 
                 2.3 
                 0.07 
                 &lt;0.001 
                 0.99 
               
               
                 TrCel6A-A322D-S413P 
                 3.1 
                 0.15 
                 &lt;0.001 
                 1.10 
               
               
                 TrCel6A-Q363E-S413P 
                 2.9 
                 0.16 
                 &lt;0.001 
                 1.03 
               
               
                 TrCel6A-R410G-S413P 
                 1.6 
                 0.20 
                 0.009 
                 0.75 
               
               
                 TrCel6A-R410Q-S413P 
                 1.3 
                 0.04 
                 0.02 
                 0.84 
               
               
                 TrCel6A-S413P 
                 1.0 
                 0.09 
                 — 
                 1.00 
               
               
                   
               
            
           
         
       
     
     This assay demonstrated that six modified TrCel6A cellulases had significantly higher K L  values and therefore were more resistant to lignin inactivation, compared to TrCel6A-S413P. 
     The purified TrCel6A enzymes, parental and modified, were separated by 10% SDS-PAGE and visualized by Coomassie blue staining ( FIG. 10 ). This gel demonstrates that the relative purity of the modified TrCel6A enzymes (lanes 4-11) were similar to TrCel6A-S413P (lane 3). The major band observed for modified and parental TrCel6A enzymes had an apparent molecular mass of about 60 kDa. In this figure, TrCel6A Aggregate 1 (lane 10) and TrCel6A Aggregate 2 (lane 11) refer to TrCel6A-K129E-S186T-A322D-Q363E-S413P and TrCel6A-K129E-S186T-A322D-Q363E-R410Q-S413P, respectively. TrCel6A purified from  Trichoderma  cellulase (lane 2) and molecular mass standards (lane 1) are shown for reference. 
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         Butler, T. and Alcalde, M. (2003) In Methods in Molecular Biology, vol. 231: (F. H. Arnold and G. Georgiou, editors), Humana Press Inc. Totowa (N.J.), pages 17-22. 
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