FIELD OF THE INVENTION

[0001 ] The present invention relates to a modified cellulase enzyme and uses thereof, in particular to a modified Family 5 cellulase enzyme for use in treating cellulose-containing goods.

BACKGROUND OF THE INVENTION

[0002] Cellulase enzymes are widely used to improve the appearance and softness of cellulose-containing fabrics. One common application of cellulase enzymes is for treating denim fabrics so as to impart to them a "stone-washed" appearance. Such a process is known in the industry as "bio-stoning". Cellulase enzymes have largely replaced stones for generating the soft, faded denim that is desired by consumers. A second widespread application of cellulase enzymes is to remove cotton fuzz and loose surface fibers in or on the fabric. This process, known as "depilling" or "biopolishing", smooths the surface of the fabric, which in turn improves its softness and appearance. Cellulase treatment also aids in the prevention of subsequent formation of fiber pills that make the garments appear worn.

[0003] Fungi such as Trichoderma secrete a number of different cellulase enzymes (also referred to herein as an "enzyme mixture") that are individually known as components. The more prevalent of these enzyme components include cellobiohydrolase (CBH), endoglucanase (EG), and beta-glucosidase enzymes.

Cellulase enzyme components typically comprise a cellulose binding domain (CBD) and a catalytic domain. A region between these two domains known as a "linker" serves as a flexible spacer between the CBD and the catalytic domain.

[0004] The cellobiohydrolase (CBH) and endoglucanase (EG) components can be further divided into glycosyl hydrolase families (Davies and Henrissat, 1995), some of which have been identified as contributing to improvements in the look and feel of the fabric. Trichoderma reesei is a widely studied and industrially important fungus for the production of cellulases. It produces at least six genetically different cellulases: two cellobiohydrolases (Cel7A and Cel6A, formerly known as CBH I and II, respectively) and at least four endoglucanases (Cel7B, Cel5A, Cell2A and Cel45A, formerly known as EGI, EGII, EGIII and EGV, respectively).

[0005] Efforts have been made to improve the properties of cellulase mixtures for textile applications by varying the relative proportions of the cellobiohydrolase and endoglucanase components in a secreted enzyme mixture relative to the natural mixture. For instance, WO 92/17574 discloses an approach that involves adjusting the amounts of EG type components relative to CBH I type components (Cel7 A) so that the protein weight ratio is greater than 5: 1. Cotton-containing fabrics treated with such compositions exhibited decreased strength loss during textile treatment compared to fabrics containing greater amounts of CBHI type (Cel7A) components.

[0006] Improvements in depilling and bio-stoning have also been achieved by elevating the content of single components in the enzyme mixture. U.S. Patent No. 5,858,767 discloses Trichoderma cellulase preparations enriched in the CBHII cellobiohydrolase (Cel6A) in an otherwise normal background cellulase composition. Such compositions were found to improve the appearance of fabrics in depilling applications. U.S. Patent No. 5,874,293 discloses cellulase mixtures enriched in EGII endoglucanase (Cel5A) that show improvements in bio-stoning applications. EP 866 165 discloses enzyme compositions enriched in EGII (Cel5A) with improvements in depilling applications.

[0007] However, despite these efforts, there is a continuous need for improved cellulases and compositions thereof that are more efficient in fabric treatment and in other fields where cellulases have been traditionally used. In particular, there is a continuous need for more catalytically efficient cellulases to improve process economics. Such a need could be met by improving the specific activity of components in the enzyme mixture. By providing for a more active cellulase, less enzyme may be required, which in turn could significantly reduce processing costs.

[0008] Researchers have modified Family 5 cellulases (also referred to herein as "Cel5") by protein engineering with the aim of improving their activity for the efficient conversion of cellulose to glucose during the production of ethanol from biomass. In Acidothermus cellulolyticus Cel5A (SEQ ID NO: 13; AcCel5A), a Y245G mutation increased the activity of the enzyme on dilute-acid pretreated yellow poplar sawdust (Baker et al., 2005). Increased activity was mainly driven by a decrease in inhibition by cellobiose.

[0009] Variants of Bacillus subtilis (strain BME-15) Cel5A (SEQ ID NO:14; BsCel5A) carrying multiple catalytic domains and CBD mutations exhibited increased specific activity of up to 2.68 fold using carboxymethyl cellulose (CMC) as a substrate (Lin et al., 2008). However, the activity level reached by the best mutant was 4.88 U/mg, whereas Trichoderma EGII activity on the same substrate was reported to be 39.9 U/mg (Xiao et al., 2002).

[0010] In addition, the effect of genetic modification on the activity of

Trichoderma reesei Cel5A (TrCel5A; SEQ ID NO: l) at pH values higher than its optimal range has been examined. Commercially available endoglucanases from Trichoderma reesei have optimum activity in the pH range of 4-6. The goal of such studies is to increase the activity of the enzyme at higher pH values so that it can be utilized in industrial processes that operate at neutral or alkaline conditions.

[0011] Mutation N321T in the mature TrCel5A cellulase (without the secretion signal) was identified to increase the optimal pH of the enzyme by 0.6 to 0.8 pH units over the wild-type enzyme via directed evolution (Wang et al., 2005). Site-saturation of this position showed that an N to R substitution resulted in the highest shift in optimum pH with an increase of 1.4 pH units (Qin et al., 2008a). However, the specific activity of this variant was greatly decreased compared to wild-type. After subsequent error-prone PCR and DNA shuffling steps, a variant

Q139R/L218H/W276R/N342T (equivalent to Ql 18R/L197H/W255R/N321T in SEQ ID: 1) was isolated with an optimal pH increase of 1.4 units without significant loss in specific activity (Qin et al., 2008b).

[0012] Studies on a Family 5 alkalophilic cellulase NK1 from Bacillus cellulosilyticus (SEQ ID NO: 15; BcNKl) (formerly known as Bacillus sp. N-4) showed that the C-terminal portion of the catalytic domain is critical for the alkalophilicity of enzyme, especially residues S287 and A296 (Nakamura et al., 1991; Park et al., 1993). Mutating these residues for the equivalent residues in Bacillus subtilis neutral cellulase (BSC) made the Bacillus cellulosilyticus NK1 pH profile very similar to the Bacillus subtilis pH profile. Among these two mutations, S287N caused a greater effect on the pH profile than A296S.

SUMMARY OF THE INVENTION

[0013] It is an object of the present invention to provide a modified Family 5 cellulase.

[0014] The present invention relates to a modified Family 5 cellulase and an enzyme mixture comprising same. The present invention also relates to a genetic construct comprising nucleic acid sequences encoding the modified Family 5 cellulase, methods for the production of the modified Family 5 cellulase from host strains and the use of the modified Family 5 cellulase in textile treatment, including, but not limited to depilling and bio-stoning.

[0015] The present invention provides a modified Family 5 cellulase comprising a substitution of an amino acid at position 363 with an alanine, a serine or a threonine. Generally, the substituted amino acid at position 363 is non-native. For example, this means that the parental or wild-type cellulase from which the modified Family 5 cellulase is derived does not have an alanine, serine or threonine at position 363. The position of the amino acid substitution is determined from alignment of the modified Family 5 cellulase with a Trichoderma reesei Cel5A amino acid sequence as set forth in SEQ ID NO: 1, as described hereinafter. The present invention also relates to an enzyme mixture comprising the modified Family 5 cellulase as defined above.

[0016] The modified Family 5 cellulase and enzyme mixtures comprising same may be used to treat cellulose-containing goods. In one embodiment, the invention provides a process for bio-stoning that comprises a step of contacting the denim fabric or denim garments with the enzyme mixture or the modified Family 5 cellulase.

Furthermore, the present invention relates to a process for depilling that comprises a step of contacting the cellulose-containing goods with the modified Family 5 cellulase. In one example of the invention, in the step of contacting, the cellulose- containing goods are fabrics or garments.

[0017] The present invention also provides a detergent composition comprising the modified Family 5 cellulase. [0018] Moreover, the present invention provides a genetic construct comprising a nucleic acid sequence encoding the modified Family 5 cellulase. Also provided is a genetically modified microbe that comprises the genetic construct. The invention also relates to a process for producing the modified Family 5 cellulase, comprising the steps of growing the genetically modified microbe in a culture medium under conditions that induce the expression and secretion of the modified Family 5 cellulase and recovering an enzyme mixture comprising the modified Family 5 cellulase from the culture medium.

[0019] The present invention also provides an enzyme mixture comprising a modified Trichoderma reesei Cel5A enzyme that has at least a substitution of a glycine to an alanine at position 363. Further provided is an enzyme mixture comprising a Trichoderma reesei Cel5A enzyme having a G363 A, S or T amino acid substitution as set forth in SEQ ID NO: 17, SEQ ID NO: 18 or SEQ ID NO: 19, respectively.

[0020] The present invention also relates to a modified Family 5 cellulase comprising a substitution of an amino acid at position 363 with an alanine, a serine or a threonine and that exhibits an increase in specific activity of at least 1.2 fold relative to a parental Family 5 cellulase or a corresponding wild-type Family 5 cellulase.

[0021] In features of any of the foregoing embodiments of the invention, the modified Family 5 cellulase is derived from a fungal Family 5 cellulase enzyme. In a further feature of any of the foregoing embodiments of the invention, the substituted amino acid at position 363 is an alanine. In yet a further feature of any of the foregoing embodiments of the invention, the alanine at position 363 is non-native.

[0022] Modified Family 5 cellulases of the invention exhibit improvements in specific activity relative to the parental or wild-type enzyme. Family 5 cellulases exhibiting such improvements in specific activity have potential value in industries for the treatment of cellulose-containing goods such as depilling or bio-stoning, or for the production of fermentable sugar in the production of biofuel, biogas or other chemicals.

BRIEF DESCRIPTION OF THE DRAWINGS [0023] FIGURE 1 shows an amino acid sequence alignment among fifteen selected cellulases from Glycosyl Hydrolase (GH) Family 5, the percent sequence identity of each amino acid sequence to amino acids 71 to 397 of TrCel5A (SEQ ID NO: l) and a graphical representation of the frequency of occurrence of the consensus amino acid at each position of the alignment among the fifteen selected Family 5 cellulases. For cellulases with a cellulose-binding domain, only the catalytic core sequences are presented. The catalytic residues at the equivalent position 218 and 329 in TrCel5A are indicated with an arrow. The conserved residues at the equivalent position 130, 174, 217, 288, and 290 in TrCel5A are indicated with an asterisk.

[0024] FIGURE 2A is a vector map of YEp352/PGKxylss-Cel5 A used to express native TrCel5A from Saccharomyces cerevisiae and to perform site-saturation mutagenesis.

[0025] FIGURE 2B is a vector map of YEp352/PGKxylss-Cel5A-G363A used to express TrCel5A-G363A from Saccharomyces cerevisiae.

[0026] FIGURE 3A is a vector map of the transformation vector p ^A EG2-hph- TV3 used to delete the endogenous cel5a gene from Trichoderma reesei to create strain P285-6.

[0027] FIGURE 3B is a vector map of transformation vector Pc/x-Cel5A- G363A-pyr4-TV.

[0028] FIGURE 4 is an agarose gel showing PCR amplification of the integrated TrCel5A-G363A expression cassette from genomic DNA of genetically modified Trichoderma reesei strains. DNA from the parental strains, BTR213aux and P285- 6aux, and the TrCel5A-G363A expression vector were used as controls. The source of the template DNA is indicated at the top of each lane and the size of each DNA marker is indicated on the left of each panel.

[0029] FIGURE 5 shows the concentration of TrCel5 A, expressed as the mass percent of the component as a fraction of total secreted protein, from BTR213, P285-6 and their transformant Trichoderma reesei strains overexpressing TrCel5A-G363 A grown in 14 L fermentations. The strain names are shown under each bar. [0030] FIGURE 6 shows the composition of the major Trichoderma cellulase components, Cel5A, Cel7B, Cel6A and Cel7A, in cellulase mixtures produced by BTR213, P285-6 and their transformant strains overexpressing TrCel5A-G363A grown in 14 L fermentations. The strain names are shown under each bar.

[0031] FIGURE 7 shows the abundance of parental and modified TrCel5A (G363A) cellulases and the relative depilling activity of cellulase enzyme mixtures produced by strains expressing parental or modified TrCel5A cellulases. White bars indicate the abundance of modified TrCel5A plus parental (as % of total protein) produced by different T. reesei strains grown in 14 L fermentation (values are indicated on the middle of each bar). The amount of TrCel5A in each strain is indicated. Cross-hatched bars indicate the relative depilling activity of cellulase enzyme mixtures. Activity is expressed as the specific activity per unit of protein and normalized to depilling activity of a control cellulase enzyme mixture comprising only parental TrCel5 A and values are indicated on the top of each bar. The strain names are shown under each bar.

[0032] FIGURE 8 shows TrCel5A, TrCel5A-G363A and TrCel5A-G363S activity on acid swollen cellulose (ASC) determined by measuring reducing sugar (depicted as glucose equivalents in μΜ) released over 30 minutes as a function of pH.

[0033] FIGURE 9 shows TrCelSA, TrCel5A-G363A and TrCel5A-G363T activity on hydroxyethyl cellulose (HEC) determined by measuring the rate in change in viscosity with time (-Δη/Δΐ) as a function of pH.

[0034] FIGURE 10 shows the depilling efficacy of TrCel5A and TrCel5A- G363A as measured by percent weight loss of flannelette as a function of enzyme dose in mg of enzyme per g of substrate.

DETAILED DESCRIPTION OF THE INVENTION

[0035] 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. The headings provided are not meant to be limiting of the various embodiments of the invention. Terms such as "comprises",

"comprising", "comprise", "includes", "including" and "include" are not meant to be limiting. In addition, the use of the singular includes the plural, and "or" means "and/or" unless otherwise stated. Unless otherwise defined herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art.

Modified Family 5 Cellulases

[0036] The amino acid sequences for numerous naturally occurring Family 5 cellulases of fungal and bacterial origin have been elucidated (Wang et al., 1993). Regions of Family 5 cellulases are well conserved in most Family 5 cellulase enzymes and this has allowed the alignment of parts of the catalytic domains of family members (Wang et al., supra).

[0037] Table 1 below includes a representative list of fifteen known Family 5 cellulases and Figure 1 shows an amino acid sequence alignment among the cellulases provided in the table.

Table 1: Examples of known Family 5 cellulases

[0038] As used herein, the term "TrCel5A numbering" means that the amino acid position in an amino acid sequence is determined by alignment with a wild-type Trichoderma, also referred to herein as "TrCel5A", the amino acid sequence of which is provided in SEQ ID NO:l . The amino acid numbering is based on the sequence of the mature, secreted protein. By aligning the amino acids to optimize the sequence similarity between the Family 5 catalytic domains of cellulase enzymes, and by using the amino acid numbering of TrCel5A as the basis for numbering, the positions of amino acids within other Family 5 cellulases can be determined relative to TrCel5A.

[0039] With reference to Figure 1, there is a particularly high degree of conservation of certain amino acid residues among Family 5 cellulases. As shown in the figure, multiple alignment across these fifteen Family 5 cellulase amino acid sequences (Table 1) reveals that most naturally occurring Family 5 cellulases have conserved R130, H174, E217, E218, H288, Y290 and E329 residues, as determined by "TrCel5A numbering" (See also Wang et al., 1993).

[0040] As used herein, the term "Family 5 cellulase" or "Cel5" encompasses a carbohydrate active cellulase enzyme that contains a glycohydrolase (GH) Family 5 catalytic domain that is classified under EC 3.2.1.4. The term also includes any carbohydrate active enzyme that exhibits at least hydrolysis of (l→4)- -D-glucosidic linkages, including those enzymes with the conserved R130, H174, N217, E218, H288, Y290 and E329 residues (determined by TrCel5A numbering described above).

[0041] Enzymes of Family 5 share a common (beta/alpha) 8-barrel fold and a catalytic mechanism resulting in a net retention of the anomeric sugar conformation. Glycosyl hydrolase catalysis is driven by two carboxylic acids found on the side chain of aspartate and/or glutamate residues (Ly and Withers, 1999). In enzymes using a retaining mechanism, one residue, initially deprotonated, acts as a nucleophile attacking the glycosidic bond in the first step. This forms a glycosyl-enzyme specie which is broken down in a second step. The other catalytic residue serves as an acid/base catalyst that donates a proton to the departing free sugar. In the second step, this residue deprotonates a water molecule, which then breaks the covalent bond in the substrate-enzyme complex to complete the hydrolysis process. The product is then released and the catalytic residues are back to their original protonation state. In Family 5 enzymes, both catalytic residues are glutamates (URL cazy.org/) (Cantarel et al., 2008). In TrCel5A, residue E329 and E218 are the nucleophile and the acid/base respectively (Macarron et al., 1993). As mentioned previously, these two residues are highly conserved among family members (Wang et al., 1993). [0042] Many Family 5 cellulases, including the Trichoderma Cel5A enzyme (TrCel5A), comprise three domains (Stahlberg et al., 1988). In the case of

Trichoderma, the N-terminal region (SEQ ID NO: l residues 1 to 36) is a cellulose binding domain (CBD) belonging to CBM (carbohydrate-binding module) Family 1 (URL cazy.org/) (Cantarel et al, 2008). The C-terminal domain (SEQ ID NO:l residues 71 to 397) is the glycohydrolase (GH) Family 5 catalytic domain which is responsible for the catalytic activity. The region between these two domains (SEQ ID NO:l residues 37 to 70) is a linker rich in proline and hydroxy-amino acids (serine and threonine) that serves as a flexible spacer between the CBD and the catalytic domain.

[0043] By "modified Family 5 cellulase", it is meant a Family 5 cellulase that contains one or more genetic alteration introduced by molecular biology techniques. Such techniques include, but are not limited to, site-directed mutagenesis, cassette mutagenesis, random mutagenesis, including that conducted on isolated DNA or by exposing a microorganism to a mutagen, such as UV light, synthetic oligonucleotide construction, cloning, sub-cloning, amplification by PCR, in vitro synthesis and other genetic engineering techniques (Eijsink et al., 2005). It will be understood that the modified Family 5 cellulase may be derived from any suitable Family 5 cellulase. That is, it may be derived from a naturally-occurring or "wild-type" Family 5 cellulase or from a Family 5 cellulase that already contains other amino acid substitutions, deletions or insertions. For example, the Family 5 cellulase may be derived from a parental Family 5 cellulase, as defined hereinafter.

[0044] By the term "isolated", it is meant a Family 5 cellulase that exists in an environment that is different from the environment in which it exists in nature or that is different from a naturally-occurring composition. For example, the isolated Family 5 cellulase may be one of a consortium of cellulase enzymes secreted by a microbe, such as in a fermentation process described below. Following fermentation, the fermentation broth containing the modified Family 5 cellulase may be used directly, or the modified Family 5 cellulase may be separated from the fungal cells, for example by filtration or centrifugation. [0045] By the term "wild-type Family 5 cellulase" it is meant a Family 5 cellulase that does not contain any genetic alteration(s) introduced by molecular biology techniques, such as those described above.

[0046] By the term "parental Family 5 cellulase", it is meant a Family 5 enzyme that is identical to the modified Family 5 cellulase of the invention, except that it does not contain the amino acid substitution(s) introduced in accordance with the invention. For example, the parental Family 5 cellulase may not contain a G363X, wherein X is alanine, serine or threonine. The parental Family 5 cellulase and the modified Family 5 of the invention may contain other amino acid modifications in their sequences relative to a wild-type enzyme, provided that the sequences are identical except for the amino acid substitution of the invention.

[0047] By the term "corresponding wild-type Family 5 cellulase", it is meant a wild-type Family 5 cellulase from which the modified Family 5 cellulase of the invention is derived.

[0048] The modified Family 5 cellulase of the invention comprises at least a mutation at position 363 to an alanine, serine or threonine residue. Generally, the amino acid introduced at position 363 is "non-native", meaning that that it does not naturally occur at the corresponding position in the wild-type Family 5 cellulase sequence from which it is derived. The position of the 363 mutation is determined by alignment with a wild-type Trichoderma reesei Family 5 enzyme, referred to herein as TrCel5A numbering.

[0049] Sequence identity can be readily determined by alignment of the amino acids of the two sequences, either using manual alignment, or any sequence alignment algorithm as known to one of skill in the art, for example but not limited to, BLAST algorithm (BLAST and BLAST 2.0; Altschul et al., 1997; and Altschul et al., 1990), the algorithm disclosed by Smith and Waterman, 1981, by the homology alignment algorithm of Needleman and Wunsch, 1970, by the search for similarity method of Pearson and Lipman, 1988, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software

Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 1995 supplement)). In the case of conducting BLAST alignments and sequence identity determinations for cellulase enzymes, only the amino acid sequences comprising the catalytic domains are considered.

[0050] Additional mutations may be introduced into the modified Family 5 cellulase, provided that such mutations do not significantly compromise the structure and function of the enzyme. As would be appreciated by those of ordinary skill in the art, but without being limiting in any manner, additional mutations may be introduced in regions of low sequence conservation among Family 5 cellulases. The alignment of the Family 5 cellulases in Figure 1 includes a bar graph below the sequences showing the occurrence of each consensus amino acid at each position among the selected family members. The sequence information contained in Figure 1 may be used as guidance by those of ordinary skill in the art when introducing an additional mutation(s) besides that at position 363. For example, amino acid substitutions may be introduced at amino acid positions that have less than 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%) or 5% conservation relative to the consensus residue (SEQ ID NO: 16) as determined by alignment with the set of amino acid sequences provided in Figure 1.

[0051] The modified Family 5 cellulase of the invention may contain amino acid substitutions "consisting essentially of the amino acid substitution at position 363". By this it is meant that the modified Family 5 cellulase contains no more than 20 other amino acid substitutions in its sequence relative to a corresponding wild-type Family 5 cellulase. In another example of the invention, the modified Family 5 cellulase contains no more than 15 other amino acid substitutions, no more than 10 other amino acid substitutions or no more than 5 other amino acid substitutions in its sequence. As mentioned previously, such additional amino acid substitutions may be introduced at non-conserved positions in the amino acid sequence. In further embodiments, the modified Family 5 cellulase contains 1-20 or 1 -10 amino acid substitutions in its sequence relative to a corresponding wild-type Family 5 cellulase.

[0052] The additional amino acid substitutions may be introduced by standard molecular biology techniques such as random mutagenesis, site-directed mutagenesis or directed evolution. [0053] Although the CBD is not required for the Family 5 cellulase to be active, its presence can make the enzyme more catalytically efficient (Stahlberg et al., 1988; Ito et al, 2004). The replacement of T. reesei Cel7A and Cel6A CBDs for the native TrCel5 A CBD increases activity by about 1.7 times compared to the wild-type enzyme (Ito et al., 2004). Similarly, CBD mutants with increased binding to cellulose and activity on carboxymethyl cellulose were found through a combinatorial library targeting two CBD residues (Fukuda et al., 2006). In one example of the invention, the Family 5 cellulase is functionally linked to a cellulose binding domain with a high affinity for crystalline cellulose.

[0054] However, modified Family 5 cellulase enzymes of the invention need not contain a CBD. Indeed, it is well known that cellulases utilized in depilling applications can be "cored", meaning that the enzyme does not contain the CBD or both the linker and the CBD. U.S. Patent Nos. 5,700,686 and 5,916,799 (which are incorporated herein by reference) describe methods for removing cellulose binding domains by protease treatment, although cellulases that lack a CBD can also be produced by genetic modification.

[0055] Representative examples of Family 5 cellulases that do not contain an alanine at position 363 of the wild-type sequence (TrCel5A numbering) and that can be modified in accordance with the invention include enzyme species from the genera of Trichoderma, Hypocrea, Penicillium, Botryotinia, Macrophomina, Aspergillus, Orpinomyces, Acidothermus, Pestalotiopsis, Myceliophthora, Chrysosporium and Xylella. In one example of the invention, the modified Family 5 cellulase is derived from species selected from the group consisting of Trichoderma reesei (SEQ ID NO: l), Trichoderma viride, Hypocrea jecorina, Penicillium decumbens, Penicillium janthinellum (SEQ ID NO:2), Botryotinia fuckeliana, Xylella fastidiosa,

Macrophomina phaseolina (MpEgl2, SEQ ID NO:3), Aspergillus kawachii (SEQ ID NO:6), Aspergillus aculeatus (SEQ ID NO: 10), Orpinomyces joyonii (SEQ ID NO: 12) and Acidothermus cellulolyticus (SEQ ID NO: 13). The sequences of each of these Family 5 cellulases are publicly available. That is, they can be readily obtained by those of ordinary skill in the art from public databases.

[0056] Modified Family 5 cellulases of the invention may have conserved R130, HI 74, N217, E218, H288, Y290 and E329 residues (determined by TrCel5A numbering) and exhibit greater than about 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% sequence identity with the TrCel5A catalytic domain (amino acids 71-397 of SEQ ID NO. ).

[0057] In another embodiment of the invention, the modified Family 5 cellulase has greater than about 40%, 50%, 60%, 70%, 80% or 90% sequence identity with the TrCel5A catalytic domain (amino acids 71-397 of SEQ ID NO:l).

Measurement of the specific activity of modified Family 5 cellulases

[0058] The modified Family 5 cellulase enzyme of the invention exhibits improvements in specific activity. The improvement in specific activity may be measured relative to a parental Family 5 cellulase or relative to a corresponding wild- type Family 5 cellulase, as defined above.

[0059] The increase in specific activity of the modified Family 5 of the invention can be determined by measuring the degradation of cellulose or other suitable cellulase substrate. There are several known assays that can be used for measuring cellulase activity of the modified and parental Family 5 cellulases. 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 Family 5 cellulase.

[0060] For example, Family 5 activity can be monitored by measuring the enzyme-dependent creation of reducing sugars, which are quantified in subsequent chemical or chemi-enzymatic assays known to one of skill in the art. Hydrolysis of polysaccharides can also be monitored by chromatographic methods that separate and quantify soluble mono-, di- and oligo-saccharides released by the enzyme. A further method that can be utilized involves determining the change in viscosity with time as the enzyme acts on the substrate. In addition, soluble colorimetric substrates may be incorporated into agar-medium on which a host microbe expressing and secreting a parental or modified Family 5 cellulase enzyme is grown. In such an agar-plate assay, activity of the cellulase is detected as a coloured or colourless halo around the individual microbial colony expressing and secreting an active cellulase.

[0061] Examples 10 and 11 provide non-limiting examples of assays that can be employed to determine the activity of the modified Family 5 enzyme relative to a parental or wild-type Family 5 cellulase. For example, the activity of the modified Family 5 cellulase relative to a reference Family 5 cellulase enzyme can be quantified by measuring the reducing ends released from cellulose as measured by glucose equivalents (Example 10). Such an approach generally involves treating a

polysaccharide with an enzyme that cleaves glycosidic bonds between its subunits. The anomeric carbon liberated from this bond is termed a reducing end in that it can act as an agent to reduce an assay reagent to produce a measurable signal. Glucose can be used to generate a standard curve for such a reaction as each glucose molecule will have one anomeric carbon and thus one reducing end; the number of molecules and the number of reducing ends are therefore the same for glucose. Example 1 1 provides a viscometric assay to quantify Family 5 cellulase activity. As set forth therein, enzyme is added to a cellulose substrate, in this case a derivative of cellulose, and the viscosity in centipoise is recorded over the time course of the assay.

Endoglucanases such as Cel5 can hydrolyse glycosidic bonds throughout cellulose chains, not just the end, so their action can rapidly reduce the average length of a sample of cellulose chains. The reduction in molecular weight of the cellulose chains results in a decrease in the viscosity of the solution.

[0062] The specific activity of the modified Family 5 cellulase enzyme is determined by measuring the activity of the enzyme, typically in units of amount of glucose released per unit of time divided by the weight of the enzyme. For example, the specific activity may be determined in units of micromoles of glucose produced per minute per milligram of enzyme.

[0063] Improvements in the activity of the modified Family 5 cellulase relative to a parental or a wild-type Family 5 cellulase may be between about 1.2 fold and about 10 fold, between about 1.2 fold and about 5 fold, or between about 1.2 fold and about 4 fold, or between about 1.2 fold and about 3 fold or between about 1.2 fold and about 2 fold or between about 1.2 fold and about 1.9 fold or between about 1.2 fold and about 1.8 fold or between about 1.2 fold and about 1.7 fold or between about 1.2 fold and about 1.5 fold.

[0064] The improvement in activity of the modified Family 5 cellulase relative to the reference Family 5 cellulase (wild-type or parental) is determined by comparing the activities under identical reaction conditions as would be appreciated by those of ordinary skill in the art.

Measuring Increases in pH Optimum

[0065] The modified Family 5 cellulase of the invention may exhibit an increase in its pH optimum relative to a corresponding wild-type or parental enzyme. The pH optimum of the modified Family 5 cellulase may be increased by known techniques, including but not limited to random mutagenesis, site-directed mutagenesis or directed evolution. The pH optimum of modified Family 5 cellulases produced by such known methods may be determined using known methodologies including those set forth below.

[0066] As discussed previously, glycosyl hydrolase catalysis by Family 5 cellulases is driven by two carboxylic acids found on the side chain of the two glutamate residues (Ly and Withers, 1999). These amino acids possess two p a's: pK _a i and pKa2 for the carboxylic acid and the amine respectively. Shifts in the pH optimum of the modified Family 5 cellulase of the invention relative to a parental or wild-type Family 5 cellulase can be measured by determination of the pK _a i and/or pKa2 of the glutamate residues in the active site using techniques known to those of ordinary skill in the art.

[0067] Increases in the pH optimum of a Family 5 cellulase may also be determined by measuring the maximum effective pH of the enzyme relative to a reference Family 5 cellulase, such as a wild-type or parental Family 5 cellulase. The maximum effective pH is the highest pH at which a cellulase exhibits at least 80% of its optimal activity. The pH range for which at least 80% of the optimal (maximum) activity is determined and the highest pH is the maximum effective pH.

Genetic Constructs Encoding Modified Family 5 Cellulase

[0068] The present invention also relates to genetic constructs comprising a nucleic acid sequence encoding a modified Family 5 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 Family 5 cellulase from a host microbe. By "regulatory nucleic acid sequences" it is meant a promoter and a nucleic acid sequence encoding a secretion signal peptide. In an embodiment of the invention, the regulatory nucleic acid sequences are derived from genes that are highly expressed and secreted in the host microbe under industrial fermentation conditions. Without being limiting, the regulatory sequences may be derived from one or more of the Trichoderma reesei cellulase or hemicellulase genes.

[0069] The genetic construct may further comprise a selectable marker gene 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 gene typically confers resistance to (i) an antibiotic, or (ii) the ability to grow on medium lacking a specific nutrient to the host organism that otherwise could not grow under the selective conditions. However, the present invention is not limited by the choice of a particular selectable marker gene, and one of skill in the art may readily determine an appropriate marker gene. In one embodiment of the invention, the selectable marker gene confers resistance to hygromycin, phleomycin, kanamycin, geneticin, or G418, complements a deficiency of the host microbe in one of the trp, arg, leu, pyr, ura, his, or ade genes or confers the ability to grow on acetamide as a sole nitrogen source.

[0070] As would be appreciated by those of skill in the art, 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.

Genetically Modified Microbes Producing Modified Family 5 Cellulases

[0071] The modified Family 5 cellulase is expressed and secreted from a genetically modified microbe comprising a genetic construct encoding the modified Family 5 cellulase. The modified Family 5 cellulase may be part of an enzyme mixture containing other cellulase enzymes secreted by the host microbe.

[0072] By the term "enzyme mixture", it is meant any mixture comprising enzymes in addition to modified Family 5 cellulase. For example, the enzyme mixture may comprise cellulase enzymes secreted from a host microbe, including, but not limited to a fungal host strain. [0073] The host microbe may be any suitable yeast or a filamentous fungus, such as those microbes that are members of the phylum Ascomycota. Genera of yeasts useful as host microbes for the expression of modified Family 5 cellulases of the present invention include Saccharomyces spp, Pichia spp, Hansenula spp,

Kluyveromyces spp, Yarrowia spp, and Arxula spp. Genera of fungi useful as microbes for the expression of modified Family 5 cellulases of the present invention include Trichoderma spp, Hypocrea spp, Aspergillus spp, Fusarium spp, Humicola spp, Neurospora spp, and Penicillium spp. In a most preferred embodiment, the host microbe is an industrial strain of Trichoderma reesei.

[0074] The genetic construct may be introduced into the host microbe by a number of methods known by those of ordinary skill in the art, including but not limited to, treatment of cells with CaC12, electroporation, biolistic bombardment and PEG-mediated transformation of protoplasts (e.g. White et al., WO 2005/093072).

[0075] According to one embodiment of the invention, the modified Family 5 cellulase of the invention is overexpressed from the host microbe. Overexpression can be achieved by introducing into a host microbe a genetic construct containing the gene encoding the modified Family 5 cellulase. The mature Family 5 cellulase may be operably linked to regulatory sequences driving protein expression and secretion, including: i) a sequence encoding a secretion signal peptide from either a native, homologous or heterologous secreted protein; and ii) a constitutive or regulated promoter derived from a gene which is highly expressed in the host microbe under industrial fermentation conditions. In addition, a translational enhancer may be added to increase protein translation. Moreover, multiple copies of the genetic construct containing the gene encoding the modified Family 5 cellulase may be introduced into the microbe, thereby increasing expression levels.

[0076] The genetic construct may contain sequences that allow it to recombine with sequences in the genome of the host microbe so that it integrates into the host genome. The genetic construct may also integrate without any specific sequences with which it can recombine. For example, the construct can integrate by random insertion through non-homologous end-joining and recombination. Alternatively, the construct may remain in the host in non-integrated form, in which case it replicates independently from the host microbe's genome. [0077] The construct may integrate at any suitable locus within the host microbe's genome. In one embodiment of the invention, the host microbe possesses a disrupted cel5 gene and the genetic construct is inserted into a locus different from that of the wild-type cel5 gene. Since the microbe is deficient in the production of the corresponding wild-type Family 5 cellulase, only the modified Family 5 cellulase will be secreted by the microbe. Non-limiting examples of such microbe strains are the P976 transformants of Figures 4-6. These microbial strains are advantageous in that the activity of the modified Family 5 cellulase secreted from the microbe is not diluted by the less active wild-type Family 5 cellulase. However, it should be appreciated that the invention also includes expression of the modified Family 5 cellulase from a host microbe that also expresses one or more wild-type Family 5 cellulase gene(s). (See, for example, the P998 strains of Figures 4-6 which express TrCel5A from the endogenous wild-type gene as well as the modified TrCel5A). Alternatively, the genetic construct is inserted into the microbe's genome at the endogenous Family 5 cellulase locus so as to replace the wild-type gene.

[0078] It should be appreciated that the invention also encompasses changing the expression levels of the other cellulase components relative to corresponding unmodified host (parental host). That is, the enzyme mixture comprising the modified Family 5 cellulase of the invention may be obtained from a host strain that has been genetically modified so as to overexpress, underexpress or not express one or more of the other cellulase components. In addition to the overexpression techniques set forth above, the expression levels of the other cellulase components may be increased by the introduction of extra copies of corresponding cellulase component or by the introduction of a promoter upstream of the native gene that increases the level of expression of the native gene over endogenous levels. Changes in expression can also be achieved by mutagenesis and selection of strains with desired expression levels. Underexpression may be achieved by the production of strains deficient in the production of a specific cellulase component(s), using techniques know to those of ordinary skill in the art.

[0079] Moreover, expression levels can be modulated by adjusting the fermentation conditions, such as by changing the composition of the feed, or by altering the pH or temperature of the fermentation. Yet another means for adjusting expression levels of cellulase involves the modification of cellulase secretion pathways or modification of cellulase transcriptional and/or translational regulation systems and/or post-translational protein maturation machinery (e.g. transcription factors, protein chaperones).

[0080] After selecting the recombinant host strains expressing the modified Family 5 cellulase, they may be cultured in submerged liquid fermentations under conditions that induce the expression of the modified Family 5 cellulase. According to one example of the invention, the modified Family 5 cellulase is secreted by a genetically modified microbe grown 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 modified Family 5 cellulase-containing fraction may then be concentrated (for example, via ultrafiltration), preserved, and/or stabilized prior to use.

Production of Modified Family 5 Cellulases

[0081] The modified Family 5 cellulase of the present invention may be produced in a fermentation process using a genetically modified microbe comprising a genetic construct encoding the modified Family 5 cellulase, e.g., in submerged liquid culture fermentation.

[0082] Submerged liquid fermentations of microorganisms, such as 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 Family 5 cellulase of the present invention may be carried out in a shake-flask or a bioreactor.

[0083] 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. [0084] 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 genetically modified microbe.

These other media components may be added prior to, simultaneously with or after inoculation of the medium with the genetically modified microbe.

[0085] When producing the modified Family 5 cellulase of the present invention, the carbon source may comprise a carbohydrate that will induce the expression of the modified Family 5 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.

[0086] 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 4.0 g carbon/L of culture/h, or any amount therebetween.

[0087] The process for producing the modified Family 5 cellulase of the present invention may be carried at a temperature from about 20°C to about 50°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, 45 or 50°C or any temperature therebetween.

[0088] The process for producing the modified Family 5 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.

[0089] Following fermentation, the fermentation broth containing the modified Family 5 cellulase may be used directly, or the modified Family 5 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 5 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.

[0090] The modified Family 5 cellulase may be purified by affinity based purification technologies. Such technologies are well known in the art and include any suitable method to selectively bind a component of a biological mixture to a solid support based on a highly specific biological interaction such as that between antigen and antibody or enzyme and substrate. Moreover, the purification can comprise fractionation methods including selective precipitation such as ammonium sulfate precipitation, isoelectric precipitation, selective thermal denaturation or any other suitable method that selectively precipitates the cellulase components. In another example, the purification methodology can comprise chromatographic methods including gel filtration, size exclusion, anion exchange, cation exchange, gel electrophoresis, or other chromatic separation methods known in the art for physically separating proteins.

Treatment of Cellulose-Containing Goods Using the Modified Family 5 Cellulase

[0091] The modified Family 5 cellulase of the present invention may be used to treat "cellulose-containing goods". Such treatments include "depilling" or "bio- stoning".

[0092] The term "cellulose-containing goods" refers to fabrics, either as piece goods or goods sewn into garments or yarn, comprising cotton or non-cotton containing fibres. The cellulose-containing goods may be treated with the modified Family 5 cellulase of the invention either before or after dyeing and with or without a resinous finish. The term encompasses natural cellulosics and manmade cellulosics. Manmade cellulose containing fabrics include regenerated fabrics that are well known in the art such as rayon.

[0093] As used herein, the term "depilling" refers to the use of the modified Family 5 cellulase of the present invention in a controlled hydrolysis of cellulosic fibres in order to modify the surface of the cotton goods in a manner that clears the surface structure by reducing fuzzing. Such treatment can prevent pilling, improve fabric handling like softness and smoothness, which can result in clarification of colour and/or improve moisture adsorbability and dyeability.

[0094] Depilling treatment may be carried out during the fabric manufacturing process or in subsequent garment laundering. In either case, treatment is typically carried out by adding cotton goods to a rotating horizontal or vertical drum jet dyer, washing machine, or other device. Such treatments typically provide agitation and shear to the fabric, including loose fibrils. In addition to cellulase enzyme and fabric, other components may be added during depilling, including water, buffer, detergents or surfactants. After treatment, the fabric is removed from the machine or device and dried.

[0095] When depilling takes place in a typical manufacturing process, the treatment time may be between about 15 to about 120 minutes; treatment temperature may be about 35°C to about 60°C; the ratio of liquor to fabric may be between about 2.5: 1 and about 10: 1 by weight; and the pH may be about 4.0 to about 6.0. When depilling takes place in a typical garment laundering, the treatment time is about 10 to about 60 minutes, the treatment temperature is about 20°C to about 70°C, the ratio of liquor to fabric is between about 2.5:1 and about 10:1 by weight and the pH is about 4.0 to about 9.5 or about 4.0 to about 6.0.

[0096] The amount of cellulase mixture used to depill depends on the

concentration of active protein in the cellulase mixture, the amount of cotton goods being treated, the desired degree of depilling, the time of treatment and other parameters well-known to those of ordinary skill in the art. When used for depilling in a typical manufacturing process, an example of a dose of cellulase is between about 0.1 and about 7 g of enzyme protein per kilogram of fabric and more preferably between about 0.5 g and about 4 g of enzyme protein per kilogram of fabric. When used for depilling in a typical garment laundering, the preferred amount of cellulase is generally between about 0.01 g and about 3 g of enzyme protein per kilogram of fabric and more preferably between about 0.05 g and about 2.5 g of enzyme protein per kilogram of fabric. [0097] One non-limiting option for controlling the action of the enzyme is to destroy the enzyme after treatment by heating the solution, adding chemicals to destroy enzyme activity or by drying the cotton goods.

[0098] It is contemplated that the modified Family 5 cellulase can be

incorporated into detergent compositions. Such detergent compositions may be in any form known in the art. This includes as a liquid diluent, in granules, in emulsions, in gels, or in pastes. When a solid detergent composition is employed, the modified Family 5 cellulase is typically formulated as granules.

[0099] "Bio-stoning" of fabric, as used herein, means the use of enzymes in place of, or in addition to, the use of pumice stones for the treatment of fabric or garments, especially denim.

[00100] Bio-stoning typically has three steps: desizing, abrasion and after- treatment. Desizing involves removal of starch or other sizing agents usually applied to the warp yarns to prevent damage during the weaving process. Alpha-amylases can be used for such purpose. Abrasion may be performed with the modified Family 5 cellulase enzyme of the invention. Mechanical action is used to remove the dye and the treatment is usually carried out in washing machines, like drum washers. Such treatment produces a "stone-washed" or "worn" look. As a result of uneven dye removal there are contrasts between dyed areas and areas from which dye has been removed.

[00101] Abrasion treatments utilizing the modified Family 5 cellulase of the present invention may be carried out either alone or together with pumice stones (when it is desired to achieve a more heavily abraded finish).

[00102] Abrasion is generally followed by after-treatment that includes washing and rinsing steps during which detergents, optical brighteners, bleaching agents or softeners may be used. The enzymatic treatment may be stopped by high temperature and/or pH inactivation.

[00103] In bio-stoning, neutral to alkaline conditions are sometimes employed for the purpose of achieving a specific level of abrasion or colour to the jean, while minimizing the costs of processing aids such as acidic buffers. In embodiments of the invention, a modified Family 5 cellulase having a pH optimum that is increased relative to a parental Family 5 cellulase is utilized in the bio-stoning process.

Examples of pH ranges that can be employed in bio-stoning are 5-8.

[00104] Suitable enzyme dosages for imparting a stone-washed appearance to the fabric depend on the desired result, on the treatment method, and on the activity of the enzyme product. Examples of suitable enzyme dosages are about 0.05 to 5 percent, or about 0.5 to 2 percent of the weight of the treated fabric. It should be appreciated that the enzyme dosage greatly depends on the type of fabrics and machinery process conditions.

[00105] The temperature of the abrasion reaction can range from about 30°C to 80°C and is preferably between about 50°C and 60°C. The liquor ratio (the ratio of the volume of liquid per weight of fabric) may range from about 3:1 to 20: 1, preferably 5: 1 to 10: 1. The treatment time can range between 15 minutes to 90 minutes and preferably 30 minutes to 60 minutes.

Other Industrial Applications for the Modified Family 5 Cellulase

[00106] The modified Family 5 cellulase of the present invention can also be utilized in the production of biofuels or biogas. A cellulase enzyme mixture could be used to convert cellulose to glucose, which is subsequently converted to a biofuel or biogas. The glucose is subsequently fermented to a biofuel such as ethanol or butanol or a biogas such as methane.

[00107] Enzyme mixtures containing the modified Family 5 cellulase of the present invention could also be useful for improving the quality of animal feed, whereby plant material is treated with the enzymes prior to or during the feeding.

[00108] 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. EXAMPLES

[00109] Example 1 describes the strains and vectors used in subsequent examples. Examples 2 and 3 describe the cloning of the Trichoderma reesei Cel5A gene (referred to hereinafter as "trce/5a" or the "trce/5a gene"), transformation of the gene into yeast and the generation of site-saturation mutagenesis libraries of TrCel5 A. Examples 4 and 5 relate to the expression of modified TrCel5A from microculture and the high-throughput screening to identify modified Family 5 cellulases with increased specific activity. Examples 6 and 7 describe the cloning and expression in Trichoderma reesei of modified Family 5 cellulase with increased specific activity. Example 8 shows the expression and preparation of TrCel5 A and modified TrCel5 A from large scale culture. Examples 9 and 10 set forth assays for measuring the activity of TrCel5A enzymes. In Example 11, the weight loss of fabric was determined after treatment with TrCel5A and modified TrCel5A cellulases.

Example 1: Strains and vectors

[00110] Saccharomyces cerevisiae strain YNL219C BY4742 [11993] (MATa his3Al leu2A0 lys2A0 ura3A0 Aalg9) was obtained from ATCC (cat. No. 4011993). Escherichia coli strain DH5a (F- (|>801acZAM15 A(lacZYA-argF)U169 recAl endAl hsdR17(rk-, mk+) phoA supE44 thi-1 gyrA96 relAl λ-) was obtained from Invitrogen (cat. No. 18265-017). The YEp352/PGK91-lANheI-xylss-cbh2 vector is described in co-pending and co-owned, U.S. Publication No. 2008/0076152.

[00111] The host Trichoderma reesei strain used for the overexpression of TrCel5A-G363A was BTR213aux. This strain was isolated from strain RutC30 (ATCC cat. No. 56765). RutC30 strain was isolated as a high cellulase producing derivative of the progenitor strain QM6A (Montenecourt et al., 1979). Cellulase hyper-producing strains were generated from RutC30 by random mutation and/or selection. A strain referred to as M2C38 was isolated based on its ability to produce larger clearing zones than RutC30 on minimal media agar containing 1 % acid swollen cellulose and 4 g/L 2-deoxyglucose. Next, M2C38 was subjected to further random mutagenesis and the BTR213 strain was isolated by selection on lactose media containing 0.2 μg/mL carbendazim. A uridine auxotroph of BTR213, BTR213aux, was obtained through selection of mutants spontaneously resistant to 0.15% w/v 5- fluoroorotic-acid (FOA).

Example 2: Cloning of the trcelSa gene into YEp352/PGK91-lANheI-xylss and transformation in yeast

[001 12] To isolate T. reesei M2C38 genomic DNA, 50 mL of Potato Dextrose Broth (Difco) was inoculated with T. reesei M2C38 spores collected from a Potato Dextrose Agar plate with a sterile inoculation loop. The cultures were shaken at 200 rpm for 2-3 days at 28°C. The mycelia was filtered onto a GFA grade glass microfibre filter (Whatman) and washed with cold, deionized water. The fungal cakes were frozen in liquid nitrogen and crushed into a powder with a pre-chilled mortar and pestle. Subsequently, 0.5 g of the powdered biomass was resuspended in 5 mL of 100 mM Tris, 50 mM EDTA, pH 7.5 plus 1% sodium dodecyl sulphate (SDS). The lysate was centrifuged (5000 x g for 20 minutes, 4°C) to pellet cell debris. The supernatant was extracted with 1 volume buffer (10 mM Tris, 1 mM EDTA, pH 8.0) saturated phenol followed by extraction with 1 volume of buffer saturated

phenolxhlorofornr.isoamyl alcohol (25:24:1) in order to remove soluble proteins. DNA was precipitated from the solution by adding 0.1 volumes of 3 M sodium acetate, pH 5.2 and 2.5 volumes of cold 95% ethanol. After incubating for at least 1 hour at -20°C, the DNA was pelleted by centrifugation (5000 x g for 20 min., 4°C), rinsed with 10 mL 70% ethanol, air-dried and resuspended in 1 mL of 10 mM Tris, 1 mM EDTA, pH 8.0. RNA was digested by the addition of Ribonuclease A (Roche Diagnostics) added to a final concentration of 0.1 mg/mL and incubation at 37°C for one hour. Sequential extractions with one volume of buffer-saturated phenol and one volume of buffer-saturated phenol:chloroform:isoamyl alcohol (25:24:1) were used to remove the ribonuclease from the DNA solution. The DNA was again precipitated with 0.1 volumes of 3 M sodium acetate, pH 5.2 and 2.5 volumes of cold 95% ethanol, pelleted by centrifugation, rinsed with 70% ethanol, air-dried and

resuspended in 50 iL of 10 mM Tris, 1 mM EDTA, pH 8.0. The concentration of DNA was determined by measuring the absorbance of the solution at 260 nm (p. CI in Sambrook et al., 1989, which is incorporated herein by reference).

[001 13] The T. reesei cel5a gene, trcel5a, was amplified and modified to remove its intron by two-step PCR using trcel5a specific primers and the purified genomic DNA as a template. In the first PCR round, the first exon (coding DNA fragment) of trcel5a was amplified with primers 5'-EG2/VAe (SEQ ID NO:20) and 3'EG2-Delint (SEQ ID NO:21), whereas the second part was amplified with primers 5'EG2-Delint (SEQ ID NO:22) and Y-EG2Kpn (SEQ ID NO:23). These two amplicons were generated independently and shared a homologous sequence introduced with primers 3'EG2-Delint (SEQ ID NO:21) and 5'EG2-Delint (SEQ ID NO:22). In a second round of PCR, both products were ligated together and amplified with primers 5'- EG2Nhe and 3 ^, -EG2Kpn in order to generate the complete trcel5a gene without the intron. The final amplicon also contains the Nhel and Kpnl restriction sites upstream and downstream of the gene to allow cloning into the yeast vector. Introduction of the Nhel site had the effect of changing the first two amino acids of the mature protein resulting in mutations Ql A and Q2S.

[001 14] Primers used for removal of the intron from the trcel5a gene:

5 ' -EGlNhe 5 ' GAG CTA GC A CTG TCT GGG GCC AGT GTG G (SEQ ID NO:20)

3'EG2-Delint 5' GGT AAC GCA AGT GCC ATC TGT GGT ACA GCC AAA G (SEQ ID NO:21)

5'EG2-Delint 5' TGG CAC TTG CGT TAC C (SEQ ID NO:22)

3 '-EG2A/W 5 ' GAG GTA CCC TAC TTT CTT GCG AGA CAC GAG (SEQ ID NO:23)

[001 15] The Saccharomyces cerevisiael Escherichia coli vector, YEp352/PGK91 - 1 ANheI-xylss-cbh2, was digested with Nhel and Kpnl to release its trcel6a insert. The fragments were separated on an agarose gel and a ~7.1 kb linearized vector fragment was purified from the gel using QIAquick Gel Extraction Kit (Qiagen). The final trcel5a PCR amplicon was digested with Nhel and Kpnl, ligated into the empty vector fragment and then transformed into E. coli strain DH5a chemically competent cells. The resulting vector was called YEp352/PGKxylss-Cel5A (Figure 2A) and was transformed into the yeast strain YNL219C BY4742 [1 1993] using the procedure described by Gietz, R. D. and Woods, R. A. (2002). Example 3: Making TrCel5A-G363X site-saturation mutagenesis library

[001 16] A site-saturation library of the glycine at position 363 (G363X) of the mature native TrCel5A protein was made by two-step PCR using the

YEp352/PGKxylss-Cel5A vector (Figure 2A) as a template. In a first PCR round, the N-terminal region was amplified with primers XylSS (SEQ ID NO:24) and 3Έ2- G363X (SEQ ID NO:25), whereas the C-terminal region was amplified with primers 5'E2-G363X (SEQ ID NO:26) and 3'PGK-term (SEQ ID NO:27). These two amplicons were generated independently and shared a homologous sequence introduced with primers 3'E2-G363X (SEQ ID NO:25) and 5'E2-G363X (SEQ ID NO:26). In a second round of PCR, both products were ligated together and amplified with primers XylSS (SEQ ID NO:24) and 3'PGK-term (SEQ ID NO:27) in order to generate the complete trcel5a gene saturated at amino acid position 363.

[00117] Primers used for site-saturation mutagenesis:

XylSS 5' GAT CGT CGA CAT GGT CTC CTT CAC CTC CCT C (SEQ ID

NO:24)

3'E2-G363X 5' AAA TGA TCC GGC VNN CCA ACC AAC ATA (SEQ ID NO:25)

5'E2-G363X 5' TAT GTT GGT TGG NNB GCC GGA TCA TTT (SEQ ID NO:26) 3'PGK-term 5' GCA ACA CCT GGC AAT TCC TTA CC (SEQ ID NO:27) V stands for A, C or G whereas B stands for T, C or G.

[00118] To generate the TrCel5A-G363X library in the yeast expression vector, the YEp352/PGK91-lAN -xylss-cbh2 vector was digested with Nhel and Kpnl and the empty vector fragment was purified as described above. This linear fragment and the final trcel5a amplicon library were transformed simultaneously and cloned by in vivo recombination (Butler and Alcalde, 2003) into the yeast strain YNL219C BY4742 [11993].

Example 4: Isolation and expression of TrCelSA-G363X from microplate cultures [00119] This example describes the selection and expression of TrCel5A-G363X from Saccharomyces cerevisiae for use in a high-throughput screening assay

(Example 5).

[00120] 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) containing 0.16% Azo-CMC (Megazyme) for 3 days at 30°C.

[00121] Colonies showing visible clearing halos were selected for liquid media cultures by toothpick inoculation of 150 μΕ synthetic complete (SC) 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, pH 5.5) in 96-well microplates containing one glass bead (1.5 - 2.0 mm) per well. Pre-cultures were grown overnight (16 - 18 hours) at 30°C and 300 rpm to stationary phase. The glycerol stocks were prepared by the addition of glycerol to a final concentration of 15% and stored at -80°C.

[00122] The glycerol stocks were used to start liquid media pre-cultures by using 10 μΐ. of the glycerol stock to inoculate 150 μΐ, 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, pH 5.5) in 96-well microplates containing one glass bead (1.5 - 2.0 mm) per well. Pre-cultures were grown overnight (18 - 20 hours) at 30°C and 300 rpm to stationary phase. For expression of the culture inoculation, 20 μΐ. of pre-culture was used to inoculate 0.2 mL of SC media in microtitre plates containing one glass bead (1.5 - 2.0 mm). Expression cultures were grown for 3 days at 30°C and 250 rpm with humidity control. Plates were centrifuged at 1 ,600 x g for 5 minutes to pellet the cells and the supernatant was aspirated for screening assays.

Example 5: Screening of Trichoderma reesei Cel5A-G363X library for modified Family 5 cellulases with increased specific activity [00123] This example describes the screening of modified Trichoderma reesei TrCel5A cellulases for improved specific activity relative to the parental TrCel5A that had been cloned into Saccharomyces cerevisiae.

[00124] Modified TrCel5A cellulases from yeast microcultures, as described in Example 4, were tested in six 80 μΐ. Azo-CMC (Azo-carboxymethyl cellulose) activity assays, each at a different pH. An aliquot of supernatant from each microculture was added to 0.5% Azo-CMC (Megazyme) buffered with 50 mM citrate phosphate at pH 4.0, 5.0, 6.0, 6.5, 7.0 and 8.0 and incubated at 50°C for 10 minutes. To stop the reaction, 200 μΐ, of precipitant solution (0.3 M sodium acetate trihydrate, 0.02 M zinc acetate dehydrate, 80% v/v anyhydrous ethanol) was added and the plates were centrifuged at 2,844 x g for 10 minutes. A 0.1 mL aliquot of the supernatant was transferred to a microplate and the absorbance at 595 nm was measured.

Contained in each 96-well plate were six parental TrCel5A controls used for comparison.

[00125] The concentration of TrCel5A cellulase in the S. cerevisiae microcultures was determined by ELIS A. Microculture supernatants were diluted 160-fold while the purified component standard was diluted to 0.01-10 μg/mL (based on total protein) in phosphate-buffered saline, pH 7.2 (PBS) and incubated overnight at 4°C in microtitre plates (Costar EIA #9018). These plates were washed with PBS containing 0.1% Tween-20 (PBS/Tween) and then incubated in PBS containing 1% bovine serum albumin (PBS/BSA) for 1 hour at room temperature. Blocked microtitre wells were washed with PBS/Tween. Rabbit polyclonal antisera specific for TrCel5A was diluted (1 :4000) in PBS/BSA, added to the blocked microtitre plates and incubated for 2 hours at room temperature. Plates were washed and incubated with a goat anti- rabbit antibody coupled to horseradish peroxidase (Sigma #A6154), diluted 1 :2000 in PBS/BSA, for 1 hour at room temperature. After washing, tetramethylbenzidine was added to each plate and incubated for 30 minutes at room temperature. The absorbance at 360 nm was measured in each well and converted into protein concentration using the TrCel5A standard curve.

[00126] The specific activity of the modified and the parental TrCel5 A cellulases at each of the six pH values was calculated by dividing the absorbance value by the amount of the modified or parental TrCel5A cellulase, as determined by ELISA, present in the assay. The specific activities for the parental TrCel5A cellulase controls were fit with the following model to determine the pKa2 value:

[00127] A, which is a measured parameter, represents enzyme activity at the specific set experimental pH. A _max , pK _a i and pK^ are all parameters that are determined by fitting the model to the data. A _max represents the maximum activity of the enzyme, which will occur at its pH optimum. pK _a j and pKa2 represent the pH- dependence of the protonation of catalytically active residues.

[00128] A 95% confidence interval for the pK^ was determined and from that, the standard deviation on the pK^ was calculated. The same model was fit to the specific activities of each modified TrCel5A to calculate a pKa2- The pK^ of each modified TrCel5A was compared to the Ka2 of the parental TrCel5A controls and positives were selected at the 95% level of confidence using a i-test. To determine

improvements in specific activity, the model was used to calculate the specific activity of the parental and modified TrCel5A cellulase at a pH corresponding to each enzyme's pKa2- Positives were selected at the 95% confidence using a t-test. All positive modified TrCel5A endoglucanases were produced again in microculture and re-screened to reduce the number of false positives.

[00129] From that screening, plasmids from positive clones were isolated from the yeast cultures using the method modified from Hoffman and Winston (1987) transformed into E. coli strain DH5a, and subsequently sequenced. After sequencing, the TrCel5A-G363A, TrCel5A-G363S and TrCel5AG363T modified cellulases were identified and the vectors that carried these modified Family 5 cellulases were named YEp352/PGKxylss-Cel5A-G363A (Figure 2B), YEp352/PGKxylss-Cel5A-G363S and YEp352/PGKxylss-Cel5A-G363T, respectively.

Example 6: Expression of TrCel5A-G363A in Trichoderma reesei

Example 6.1: Host Trichoderma strain for the overexpression of TrCel5A-G363A

[00130] The host Trichoderma reesei strains used for the overexpression of modified TrCel5A-G363A were BTR213aux and P285-6aux. [00131] The BTR213aux was isolated as described in Example 1. The P285-6aux strain was generated by transformation of BTR213aux with the p ^A EG2-hph-TV3 vector (Figure 3 A) which resulted in the deletion of the endogenous cel5a gene as described in co-pending and co-owned WO 2010/060188.

Example 6.2: Construction of the Trichoderma reesei transformation vector

[00132] The integrative T. reesei transformation vector, Pc/x-Cel5A-G363A-pyr4- TV (Figure 3B), was constructed as follows. The yeast expression vector

YEp352/PGKxylss-cel5A-G363A possessing the modified trcel5a (described in Example 5) was digested with Nhel and Kpnl restriction enzymes. The DNA fragments were separated on agarose gels and the fragment corresponding to the mature TrCel5A-G363A coding region was gel extracted using Wizard® SV Gel and PCR clean-up System (Promega). The isolated fragment was li gated via Nhel and Kpnl restriction enzyme digestion and ligation to produce the Trichoderma transformation vector Pc/x-Cel5A-G363A-pyr4-TV, which operatively links the mature TrCel5A-G363A coding region with a fragment comprising the xyn2 secretion signal coding sequence linked to a chimeric cel7A/xyn2 promoter (described in U.S. Patent No. 6,015,703) and cel6a terminator. The generated Trichoderma

transformation vector, Pc/x-cel5A-G363A-pyr4-TV, contains the N. crassa pyr4 gene as a selectable marker. This construct was transformed into chemically-competent DH5a E. coli cells. The TrCel5A-G363A coding region in the generated

transformation vector was sequenced to verify the presence of the G363A mutation. To generate sufficient DNA for transformation into Trichoderma, E. coli cells containing transformed plasmid were grown overnight in 50 mL of liquid LB media supplemented with 100 μg/mL ampicilin with shaking at 37°C. Plasmid for the Trichoderma transformation was isolated using Wizard® Plus Midiprep kit (Promega) as described in the manufacture's protocol.

[00133] Since the trcelSa gene without the intron was used in the TrCel5A- G363 A expression cassette, the trcel5a-G363A gene in the final Pc/x-cel5A-G363A- pyr4-TV transformation vector is shorter than the native genomic T. reesei cel5a gene by 179 nucleotides, the size of the intron.

Example 6.3: Transformation in Trichoderma reesei [00134] TrCel5A-G363A overexpressing strains were generated by linearizing vector Pc/x-cel5A-G363 A-pyr4-TV with Sspl and transforming the vector into Trichoderma strains BTR213aux and P285-6aux by polyethylene glycol mediated transformation of protoplasts. Transformants were selected on minimal media plates lacking uridine to select for complementation of pyr4 auxotrophy in BTR213aux and P285-6aux.

[00135] The Trichoderma transformation was performed by the following procedure. 5 x 10 ⁶ spores of the BTR213 and P285-6 auxotrophs were plated onto sterile cellophane on Potato Dextrose agar supplemented with 5 mM uridine and were incubated for 20 hours at 30°C to facilitate spore germination and mycelial growth. Cellophane discs with mycelia were then transferred to 10 mL of a protoplasting solution containing 7.5 g/L driselase and 4 g/L beta-glucanase (InterSpex Products Inc., Cat. Nos. 0465-1 and 0439-2, respectively) in 50 mM potassium phosphate buffer, pH 6.5 containing 0.6 M ammonium sulfate (Buffer P). The fungal mycelia were digested for 5 hours with gentle agitation at 60 rpm. Protoplasts were separated from undigested mycelia by filtration through sterile No. 30 MIRACLOTH™ and collected into a sterile 50 mL round-bottom centrifuge tube and recovered by centrifugation at 1000-1500 x g for 10 minutes at room temperature. Protoplasts were washed with 5 mL of Buffer P and centrifuged again at 1000-1500 x g for 10 minutes at room temperature. Protoplasts were resuspended in 1 mL of STC buffer (1.2 M sorbitol, 10 mM CaCl ₂ , 10 mM Tris-HCL, pH 7.5). For transformation, 0.1 mL of resuspended protoplasts was combined with 10 μg of vector DNA and 0.025 mL of PEG solution (25% PEG 3350, 50 mM CaCl ₂ , 10 mM Tris-HCl, pH 7.5). After incubation in an ice water bath for 30 minutes, 1 mL of PEG solution was added and the mixture incubated for 5 minutes at room temperature. The transformation mix was diluted with 2 mL of STC buffer and the entire mix was added to 50 mL of molten MMSS agar media (Table 2 below) cooled to about 47°C, split in half, and poured over MMSS agar. Plates were incubated at 30°C until colony growth was visible. Transformants were transferred to individual plates containing MM agar (Table 2) and allowed to sporulate. Spores were collected and plated at high dilution on MM agar to isolate homokaryon transformants, which were then plated onto PDA to allow for growth and sporulation. Table 2: Minimal medium (MM)

Component* Amount per L

KH ₂ P0 ₄ 10 g

(NH ₄ ) ₂ S0 ₄ 6 g

Na ₃ Citrate-2H ₂ 0 3 g

FeS0 ₄ 7H ₂ 0 5 mg

MnS0 ₄ H ₂ 0 1.6 mg

ZnS0 ₄ -7H ₂ 0 1.4 mg

CaCl ₂ -2H ₂ 0 2 mg

Agar 20 g

20% Glucose f.s. 50 mL

1 M MgS0 ₄ -7H ₂ 0 f.s. 4 mL

pH to 5.5

*MMSS agar contains the same components as MM agar plus 1.2 M sorbitol, 6.6 g/L YNB (Yeast Nitrogen Base w/o Amino Acids from DIFCO Cat.

No.291940) and 1.92 g/L amino acids (-Ura DO Supplement from Sigma Cat. No. Y1501-20G).

Example 6.4: Characterization of Trichoderma reesei transformants

[00136] Chromosomal integration of the transformation vector in isolated T. reesei transformants was confirmed by PCR using the Extract-N-Amp™ Seed PCR Kit (Sigma) and primers XylSS (5' GAT CGT CGA CAT GGT CTC CTT CAC CTC CCT C-3'; SEQ ID NO:24) and KW127 (5'-GGA ACC ACA CCA TCG CAC ATC- 3'; SEQ ID NO:28). Template DNA preparation and PCR reactions were performed according to the manufacturer's recommendations. A fragment comprising the trcel3a-G363A coding region was amplified from the DNA isolated from all transformants but not DNA isolated from their parental strains (Figure 4).

[00137] To test the production of the modified TrCel5A-G363A cellulase, spores of Trichoderma transformants and the parental strain grown on PDA plates were suspended in sterile water and about 10 ⁴ -10 ⁶ spores per mL were used to inoculate each micro-culture in 24-deepwell plates. The components present in the micro- culture media are provided in Table 3 below.

Table 3: The composition of micro-culture media

Component* g/L

KH ₂ P0 ₄ 8

(NH ₄ ) ₂ S0 ₄ 12.7

MgS0 ₄ -7H ₂ 0 4

CaCl ₂ -2H ₂ 0 1.02 Corn steep liquor 5

CaC0 ₃ 20

Carbon source** 35

Trace elements* 2 mL/L

* Trace elements solution contains 5 g/L FeS0 ₄ -7H ₂ 0; 1.6 g/L MnS0 ₄ ¾0; 1.4 g/L ZnS0 ₄ -7H ₂ 0.

** Glucose, Solka floe, lactose, cellobiose, sophorose, corn syrup, or Avicel. The carbon source can be sterilized separately as an aqueous solution at pH 2 to 7 and added to the remaining media initially or through the course of the fermentation.

[00138] Cultures were grown for 6 days at 30°C with shaking at 250 rpm. The fungal cells were separated from the growth media containing the secreted protein by centrifugation at 12,000 rpm. The protein concentration was determined using the Bio-Rad Protein Assay (Cat. No. 500-0001 ). The relative abundance (in weight % of total secreted protein) of TrCel5A cellulases (modified and parental) was determined by ELISA. Culture supernatants and purified component standards were diluted to 0.01-10 μg mL in phosphate-buffered saline, pH 7.2 (PBS) and incubated overnight at 4°C in microtitre plates (Costar EIA #9018). These plates were washed with PBS containing 0.1% Tween-20 (PBS/Tween) and then incubated in PBS containing 1% bovine serum albumin (PBS/BSA) for one hour at room temperature. Blocked microtitre wells were washed with PBS/Tween. Rabbit polyclonal antiserum specific for TrCel5A was diluted in PBS/BSA, added to separate microtitre plates and incubated for 2 hours at room temperature. Plates were washed and incubated with a goat anti-rabbit antibody coupled to horseradish peroxidase (Sigma #A6154), diluted 1 :2000 in PBS/BSA, for one hour at room temperature. After washing,

tetramethylbenzidine was added to each plate and incubated for 30 minutes at room temperature. The absorbance at 360 nm was measured in each well and converted into a protein concentration using a TrCel5A standard curve. The concentration of total TrCel5A cellulase (modified and parental) was expressed as the mass percent of the component as a fraction of total secreted protein (Figure 5). Several strains producing the highest amounts of TrCel5A cellulase (modified and parental) were selected for further analysis in 14 L fermentations (Figure 6) and depilling assays (Figure 7).

Example 7: Enzyme production in 14 L fermentations [00139] Trichoderma spores of strains BTR213, P285-6 and selected

transformants grown on PDA media were suspended in sterile water and transferred to 2 L, baffled Erlenmeyer flasks containing 750 mL of liquid Berkley media (pH 5.5) supplemented with 5.1 g/L of corn steep liquor powder and 10 g/L glucose (Table 4). Flasks were incubated at 28°C for 3 days using an orbital agitator (Model G-52 New Brunswick Scientific Co.) running at 100 rpm.

Table 4: Berkley media for flasks

Component g/L

(NH ) ₂ S0 ₄ 10.4

KH ₂ P04 2.0

MgS0 ₄ -7H ₂ 0 0.31

CaCl ₂ -2H ₂ 0 0.53

Dry Corn Steep Liquor 5.1

Glucose 10

Trace elements* 1 mL/L

*Trace elements solution contains 5 g/L FeS0 ₄ -7H ₂ 0; 1.6 g/L MnS0 ₄ H ₂ 0; and 1.4 g/L ZnS0 ₄ -7H ₂ 0.

[00140] The contents of an inoculum flask were transferred to a 14 L pilot scale fermentation vessel (Model MF114 New Brunswick Scientific Co.) set up with 10 L of Initial Pilot Media (pH 5.5). The vessel was run in batch mode until glucose in the media was depleted. At this point, the carbon source containing cellulase inducing carbohydrates was added on a continuous basis from a stock that was 35.5% w/v of solids dissolved in water. Peristaltic pumps were used to deliver the carbon source at a feed rate of 0.4 grams of carbon per liter culture per hour. Operational parameters during both the batch and fed-batch portions of the run were: mixing by impeller agitation at 500 rpm, air sparging at 8 standard liters per minute, and a temperature of 28°C. Culture pH was maintained at 4.0-4.5 during batch growth and pH 3.5 during cellulase production using an automated controller connected to an online pH probe and a pump enabling the addition of a 10% ammonium hydroxide solution.

Periodically, 100 mL samples of broth were drawn for biomass and protein analysis.

Table 5: Initial media for fed-batch fermentations

Component g/L

(NH ₄ ) ₂ S0 ₄ 2.20

KH ₂ P0 ₄ 1.39

MgS0 ₄ -7H ₂ 0 0.70 CaCl ₂ -2H ₂ 0 0.185

Dry Corn Steep Liquor 6.00

Glucose 13.00

Trace elements* 0.38 mL/L

*Trace elements solution contains 5 g/L FeS0 ₄ -7H ₂ 0; 1.6 g/L MnS0 ₄ H ₂ 0; and 1.4 g/L ZnS0 ₄ -7H ₂ 0.

[00141] The concentration of fungal cells in the culture broth was determined using aliquots of 5-10 mL that had been weighed, vacuum filtered through glass microfiber filters, and oven dried at 100°C for 4 to 24 hours. The concentration of fungal cells was determined according to Equation 2 below.

/o _\ drv filter paver and cake (q~)— filter mass _{l ti} , , rr.L

Bicnnas ( \ = -^— - — x broth density (*/ , )Ϊ 1000— wet sample mass (a) ^J '

[00142] The protein concentration of the culture filtrate was determined using the BioRad protein assay. Colour intensity changes in the Coomassie Brilliant Blue G- 250 dye, that forms the basis of this assay, were quantified spectrophotometrically using absorbance measurements at 595 nm. The standard assay control used was a cellulase mixture of known composition and concentration. The final filtrates for enzyme analysis were collected after 162-170 hours.

[00143] The relative concentrations (in weight percent of total secreted protein) of four cellulase components (TrCel7A, TrCel6A, TrCel7B, total modified TrCel5A and parental TrCel5A) were determined by ELISA using a component specific antibody as described above (Example 6.4). The abundance of the three major cellulase components, Cel7A, Cel6A and Cel7B, is similar in the cellulase mixtures produced by transformants and parental strains. The abundance of TrCel5A cellulases

(modified and parental) in the P998A, P998D, P1013C and P1013D cellulase mixtures increased by about four-fold compared to that of the parental BTR213 cellulase mixture due to the overexpression of the modified TrCel5A-G363 A cellulase (Figure 6). The P285-6 transformants P976F, P976G, P976I, P976J, P976L and P976M produced cellulase mixtures comprising 14-25% modified TrCel5A-G363A cellulases (Figure 6).

Example 8: Depilling activity of enzyme produced by T. reesei transformants [00144] To test depilling activity, circles of flannelette with an approximate diameter of 1 1.5 cm were cut out of a larger piece of fabric and weighed. The fabric was then placed in plastic jars with screw-top lids, and held against the bottom of the jar with gaskets made of rubber tubing. Subsequently, 90 g of 0.5 cm diameter steel ball bearings were added to each jar. The enzymes were diluted to deliver 10-100 units of CMC activity (as determined by Ghose et al., 1987) and 1-10 mg of the total protein per jar. The diluted enzyme was added to the jars so that the total liquid in each jar was about 15 g.

[00145] The jars were then sealed with their lids and incubated at 50°C with 180 rpm orbital shaking for 2 hours in a shaker incubator. After incubation, 3 drops of 10 N NaOH were added to each jar to stop the enzymatic reaction. The liquid portion of each reaction was then passed through a preweighed glass fiber filter using a vacuum manifold and sidearm flasks. An additional 200 mL of water were added to each jar, still containing the immobilized flannelette disc, which was then closed and shaken by hand to release any fines trapped within the fabric. The filter papers were dried in a 100°C oven for a minimum of 4 hours. The weights of the filter papers and captured fines were measured and used to calculate the percent weight loss of the substrate relative to the starting mass of each fabric disc.

[00146] The loss of fabric weight was calculated using Equation 3 below:

(weight of the filter paver +· collected fines) ^' — (weight of filter paper

% weight loss = ) * 100 initial weight of the fabric

[00147] The depilling was expressed as specific depilling activity per unit of protein and normalized to depilling activity of enzyme produced by strain BTR213.

[00148] As shown in Figure 7, the overexpression of modified TrCel5A-G363A cellulase increased depilling activity of enzymes produced by either BTR213aux or P285-6aux transformants. These findings demonstrate that improved activity upon introduction of TrCel5A-G363A is observed whether the wild-type TrCel5A cellulase is present, as in the BTR213 transformants, or absent, as in the P285-6 transformants.

Example 9: Expression and preparation of parental and modified TrCel5A cellulases for subsequent activity assays [00149] TrCel5A, TrCel5A-G363A, TrCel5A-G363S and TrCel5A-G363T preparations were made from transformed S. cerevisiae strains as set forth below and their respective specific activities were subsequently determined in a reducing end assay and a viscosity assay (Examples 10 and 1 1).

[00150] 250 mL volumes of sterile SC*-Ura media (0.77 g/L -Ura drop out supplement, 1.7 g/L yeast nitrogen base, 5 g/L (NH ₄ ) ₂ S0 ₄ , 20 g/L casamino acids, 20 g/L glucose) were inoculated with 10 mL of overnight cultures of transformed Saccharomyces cerevisiae grown from cells freshly picked from an agar plate. The cultures were then incubated for 72 hours at 30°C with shaking at 250 rpm.

[00151] After incubation, the yeast cultures were centrifuged for 10 minutes at 3,300 x g. The supernatant was removed with a pipette and retained and the yeast cell pellet was discarded. The concentration of parental or modified TrCel5A in the supernatant was determined using an ELISA with a standard curve of purified TrCel5A. This TrCel5A (parental or modified) preparation was used in viscosity assays (Example 11) without further treatment.

[00152] For the reducing ends assay (Example 10), the supernatant was concentrated and desalted to reduce the background signal of the assay. The yeast culture supematants containing parental or modified TrCel5A cellulase were exchanged into a citrate-phosphate buffer (5 mM citrate, 5 mM phosphate, pH 6.0) using Centricon® plus-20 Biomax PES-5 (Amicon) filtration devices. The supematants were successively concentrated by passage through a Centricon® device in 3 centrifugation steps of 10-15 minutes at 3,450 x g to the minimum retention volume of the device. The flow-through was discarded after each step. The concentrated, retained enzyme solution was then re-suspended in buffer and centrifuged as described above. The flow-through was discarded and the protein accumulated on the membrane was re-suspended in 10 mL of buffer and transferred in a 50 mL Falcon™ tube. Buffer was added to 40 mL final volume. The concentration of buffer-exchanged parental or modified TrCel5A was determined using an ELISA with a standard curve of purified TrCel5A.

Example 10: Assay for creation of reducing ends by TrCel5A, TrCeI5A-G363A or TrCel5A-G363S [00153] Acid swollen cellulose (ASC) was produced from SigmaCell50 (Sigma- Aldrich) using procedures known to those skilled in the art. The ASC was slurried in water to a concentration of 3.5 g of cellulose/L and homogenized in five cycles of 1 minute "on" followed by 1 minute "off using a rotor-stator homogenizer with a probe diameter of 1 cm. The cellulose slurry or "ASC slurry" was then degassed under vacuum for 10 minutes with constant stirring.

[00154] Endoglucanases create new reducing ends in cellulose, some of which are associated with the insoluble substrate and some of which are associated with short, solubilized cellodextrins. The number of reducing ends in the substrate prior to enzymatic treatment and the reducing potential of the enzyme itself, collectively termed a no-activity control, can be directly measured by mixing enzyme and substrate under conditions of high pH (10 or higher) where enzymatic hydrolysis of cellulose will not occur.

[00155] Aliquots containing 125 μΙ_, of the ASC slurry were dispensed by pipetting into microplates with 96 wells of 2 mL volume each. The slurry was mixed on a stir plate during dispensing to ensure homogeneous substrate distribution. An equal volume of 100 mM Na Citrate/Phosphate buffer, of varying pH, was added to each well. The plate was sealed with aluminum sealing tape and preheated in a 50°C water bath for 15 minutes. The plate was unsealed and 125 μΐ, of buffer-exchanged TrCel5A, TrCel5A-G363A or TrCel5A-G363S was added to triplicate wells (0.4 g of enzyme were added to each reaction). The plate was resealed and returned to the 50°C waterbath to incubate for 30 minutes. To stop the reaction, the plate was unsealed and a volume of BCA working solution (0.971 g/L disodium 2,2'- bicinchoninate, 27.14 g/L Na ₂ C0 ₃ , 12.1 g/L NaHC0 ₃ , 0.624 g/L CuSOy5H ₂ 0, 0.631 g/L L-Serine) equivalent to the sample volume was added to all samples.

[00156] Standard curves were generated simultaneously for each pH tested on each reaction microplate and used for the conversion of absorbance signal to reducing ends concentration, as glucose equivalents. Six glucose concentrations were used as standard solutions: 0.1 g/L, 0.05 g/L, 0.025 g/L, 0.0125 g/L, 0.006 g/L and 0 g/L. Aliquots of 125 μΐ, of standard solutions were dispensed by pipetting in the microplate, along with equivalent volumes of pH buffer and TrCel5A. [00157] The BCA reaction to measure reducing ends (based on Zhang and Lynd, 2005) was carried out at 75°C for 30 minutes. The reaction was stopped by cooling the sealed plates under running room temperature water. The plate was centrifuged at 2,750 x g for 4 minutes to sediment the remaining insoluble ASC. Next, 200 μΐ. of supernatant from each well was transferred into a 96-well polystyrene microplate and the absorbance was read at 560 nm. Absorbance readings were converted into glucose equivalents using the standard curve and matching no-activity controls were subtracted from readings of wells with active enzyme and substrate. Corrected readings were converted into specific activities in units of micromoles of glucose produced per minute per milligram of enzyme.

[00158] The results of the empty vector controls were subtracted from those of the enzyme-containing samples for each pH point. For the control samples, an equivalent volume of empty vector supernatant (from the growth of S. cerevisiae containing an expression vector lacking a TrCel5 A gene) was used instead of TrCel5 A preparation. Equation 1 (see Example 5) was fit to the corrected data by minimization of the sum of the squared residuals and the best- fit values of pK _al , pK^ and A _max were determined.

[00159] Activity of parental and modified TrCel5A cellulases as a function of pH, as well as model fits is depicted in Figure 8. The upper and lower limits of the 95% confidence intervals for pK _a j, pKa2 and A _ma x were determined using the methods of Motulsky (2004). A t-test was performed to compare the A _max of TrCel5A-G363A and TrCel5A-G363S to wild-type, parental TrCel5A and to calculate a -value to determine whether the parameters of the modified Family 5 cellulase were

significantly different from those for the wild-type cellulase (Table 6).

Table 6: Determination of -values for A _max of TrCeI5A, TrCeI5A-G363A and TrCel5A-G363S on acid swollen cellulose

Amax Standard -value

Deviation

TrCel5A 36.4 1.3 TrCel5A-G363A 62.8 2.3 1.4E-13

TrCel5A-G363S 66.8 2.6 6.0E-14

[00160] These results show that the modified TrCel5A-G363A and TrCel5A- G363S cellulases are more active than the parental TrCel5A cellulase on acid swollen cellulose.

Example 11: Viscometric assay of activity of TrCel5A and TrCel5A-G363A.

[00161] A hydroxyethyl cellulose (HEC) stock solution was prepared by first warming 1 L of water in a glass beaker to 40°C on a heating plate. After warming, 50 g of HEC was slowly added and mixed with vigorous stirring using a stir bar. The beaker was covered with a plastic film to prevent evaporation and the cellulose was allowed to solubilize overnight at room temperature with mixing using a magnetic stir bar.

[00162] To assay TrCel5A activity (modified and parental), 15 g of HEC substrate was weighed into a disposable metal sample cup for the RVA-Super-4 viscometer (Newport Scientific). 5 mL of 400 mM Na Citrate/Phosphate buffer was added to the substrate and the vessel was pre-warmed in the instrument for two minutes at 50°C. Next, 2 mL of TrCel5A, TrCel5A-G363A or TrCel5A-G363T (not buffer-exchanged) was added to the pre-heated sample and allowed to react for 2.5 minutes, during which time the viscosity in centipoise was automatically recorded every second. For the control samples, an equivalent volume of empty vector supernatant (from the growth of S. cerevisiae containing an expression vector lacking a TrCel5A gene) was used instead of a preparation containing parental and/or modified TrCelA.

[00163] The slope of the plot of viscosity as a function of time was calculated after the mixing of the enzyme solution into the buffered substrate was complete (after approximately 20 seconds) and only for the apparently linear portion of the data.

[00164] For each pH point, the slopes of the empty vector curves were subtracted from those of enzyme samples. Equation 1 set forth in Example 5 was fit to the corrected data by minimization of the sum of the squared residuals and the best-fit values of pK _al , pKa. and A _max were determined. Values of pK _al from the BCA assay (Example 10) were used for these fits. TrCel5A activity as a function of pH, and model fits, are depicted in Figure 9. The upper and lower limits of the 95% confidence intervals for all three parameters were determined using the methods of Motulsky (2004). A Mest was performed to compare the A _max of TrCel5A-G363A and TrCel5A-G363T to TrCel5A and to calculate a -value to determine whether the parameters of the modified Family 5 cellulase were significantly different from those of the parental TrCel5A cellulase (Table 7).

Table 7: Determination of -values for A _max of TrCel5A, TrCel5A-G363A and TrCel5A-G363T on hydroxyethyl cellulose.

[00165] These results show that the modified TrCel5 A-G363 A and TrCel5 A- G363S cellulases are more active than the parental TrCel5A cellulase on

hydroxyethyl cellulose.

Example 12: Purification of TrCel5A and TrCel5A-G363A expressed from Trichoderma reesei.

[00166] A strain of Trichoderma reesei was grown in submerged liquid fermentation under conditions that induce cellulase production as described in Example 7. The crude mixture of Trichoderma proteins were secreted by the cells into the fermentation broth. The fungal cells were removed from the fermentation broth by filtration across a glass microfiber filter containing a Harborlite filter bed. TrCel5A or TrCel5A-G363A was separated from the crude filtrate by anion exchange chromatography using a DEAE-Sepharose column as described by Bhikhabhai et al. (1984). Purified TrCel5A or TrCel5A-G363A was concentrated and buffer exchanged into 50 mM sodium citrate, pH 5.0 using a stirred ultrafiltration cell (Amicon) and a 10 kDa nominal molecular weight cutoff polyethersulfone membrane.

Example 13: Assay of the depilling activity of TrCel5A and TrCel5A-G363A.

[00167] The effectiveness of an enzyme in removing small balls of fuzz, referred to as pills, from fabric is measured by direct weighing of released insoluble cellulose from fabric.

[00168] Depilling assays were conducted as described in Example 8. Stocks of purified TrCel5A or TrCel5A-G363A in 50 mM citrate, pH 5.0, were added to 6 jars in 1 mL increments from 2 to 7 mL. Additional citrate buffer was added to a final volume of 50 mL.

[00169] The slope of the plot for TrCel5A is 0.233 percent wt loss/(mg enzyme/g cellulose) and 0.311 percent wt loss/(mg enzyme/g cellulose) for TrCel5A-G363A, indicating a 34% increase in activity of the modified Family 5 cellulase by this measure. An -test was used to compare the global fit performed with two slopes and a single intercept with a model of one slope and one intercept, a null model in which TrCel5A and TrCel5A-G363A have equivalent activities (Motulsky, 2004). This null model is rejected (P = 0.0002) by the -test.

REFERENCES

Altschul, S. F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215:403-410.

Altschul, S.F., Madden T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nuc. Acids Res. 25:3389-3402.

Ausubel, F.M, Brent, R. Kingston, R.E., Moore, D.D., Seidman, J.G., Struhl, K. 1995 supplement Current Protocols in Molecular Biology, John Wiley & Sons, Ausubel et al., eds.

Baker, J. O., McCarley, J. R., Lovett, R., Yu, C. H., Adney, W. S., Rignall, T. R., Vinzant, T. B., Decker, S. R., Sakon, J., and Himmel, M. E. (2005) Catalytically enhanced endocellulase Cel5A from Acidothermus cellulolyticus. Appl. Biochem. Biotechnol. 121-124:129-148. Bhikhabhai, R., Johansson, G. and Petterson, G. (1984) Isolation of Cellulolytic Enzymes from Trichoderma reesei QM 9414. Journal of Applied Biochemistry, 6:336-345.

Butler, T. and Alcalde, M. (2003) In Methods in Molecular Biology, vol. 231 : (F. H. Arnold and G. Georgiou, editors), Humana Press Inc. Totowa (New Jersey), ppg. 17- 22).

Cantarel, B. L., Coutinho, P. M., Rancurel, C, Bernard, T., Lombard, V., and Henrissat, B. (2008) The Carbohydrate- Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic. Acids. Res. 37:D233-D238.

Davies, G and Henrissat, B. (1995) Structures and mechanisms of glycosyl hydrolases. Structure. 3(9): 853-9.

Eijsink, V.G. H, Gaseidnes, S., Borchert, T. V., van den Burg, B. (2005)

Directed evolution of enzyme stability. Biomolecular engineering. 22(l-3):21-30.

Fukuda, T., Ishikawa, T., Ogawa, M., Shiraga, S., Kato, M., Suye, S., and Ueda, M. (2006) Enhancement of cellulase activity by clones selected from the combinatorial library of the cellulose-binding domain by cell surface engineering. Biotechnol. Prog. 22:933-938.

Ghose, T. K. (1987) Measurement of cellulase activities. Pure & Appl. Chem.

59(2):257-268.

Gietz, R.D. and Woods, R. A. (2002) Transformation of yeast by the Liac/SS Carrier DNA/PEG Method. Methods in Enzymology 350:87-96.

Hoffman, C.S. and Winston, F. (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57:267- 272.

Ito, J., Fujita, Y., Ueda, M., Fukuda, H., and Kondo, A. (2004) Improvement of cellulose-degrading ability of a yeast strain displaying Trichoderma reesei endoglucanase II by recombination of cellulose-binding domains. Biotechnol. Prog. 20:688-691.

Lin, L., Meng, X., Liu, P., Hong, Y., Wu, G., Huang, X., Li, C, Dong, J., Xiao, L., Liu, Z. (2008) Improved catalytic efficiency of Endo-beta-l ,4-glucanase from

Bacillus subtilis BME-15 by directed evolution. Appl. Microbiol. Biotechnol. 82:671- 679.

Ly, H. D. and Withers, S. G. (1999) Mutagenesis of glycosidases. Annu. Rev.

Biochem. 68:487-522.

Macarron, R., van Beeumen, J., Henrissat, B., de la Mata, I., and Claeyssens, M. (1993) Identification of an essential glutamate residue in the active site of

endoglucanase III from Trichoderma reesei. FEBS Lett. 316:137-140. Montencourt, B.S., Schamhart, D. H. J., Cuskey, S. M, Eveleigh, D. E. (1979) Improvements in cellulase production by Trichoderma through mutation and selected breeding. Proc. 3 ^rd Annual Symp. On Fuels from Biomass, Golden Colorado, pp. 85- 89.

Motulsky, H. and Christopolous, A., 2004, "Fitting Models to Biological Data Using Linear and Nonlinear Regression: A Practical Guide to Curve Fitting", Oxford University Press (2004).

Nakamura, A., Fukumori, F., Horinouchi, S., Masaki, FL, Kudo, T., Uozumi, T., Horikoshi, K., and Beppu, T. (1991) Construction and characterization of the chimeric enzymes between the Bacillus subtilis cellulase and an alkalophilic Bacillus cellulase. J. Biol. Chem. 266: 1579-1583.

Needleman, S.B. and Wunsch, CD. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453.

Park, J. S., Hitomi, J., Horinouchi, S., and Beppu, T. (1993) Identification of two amino acids contributing the high enzyme activity in the alkaline pH range of an alkaline endoglucanase from a Bacillus sp. Protein Eng. 6:921 -926.

Pearson W.R. and Lipman D. (1988) J. Proc Natl Acad Sci. Improved tools for biological sequence comparison. 85(8):2444-8.

Qin, Y., Wei, X., Song, X., and Qu, Y. (2008a) The role of the site 342 in catalytic efficiency and pH optima of endoglucanase II from Trichoderma reesei as probed by saturation mutagenesis. Biocatal. Biotransformation. 26:378-382.

Qin, Y., Wei, X., Song, X., and Qu, Y. (2008b) Engineering endoglucanase II from Trichoderma reesei to improve the catalytic efficiency at a higher pH optimum. J. Biotechnol. 135: 190-195.

Sambrook, T., Fritsch, E. F. and Maniatis T. (1989) Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press.

Smith, T.F. and Waterman, M.S. (1981) Comparison of biosequences, Adv. Appl. Math., 2:482-489.

Stahlberg, J., Johansson, G., and Pettersson, G. (1988) A binding-site-deficient, catalytically active, core protein of endoglucanase III from the culture filtrate of Trichoderma reesei. Eur. J. Biochem. 173: 179-183.

Wang, T., Liu, X., Yu, Q., Zhang, X., Qu, Y., Gao, P., and Wang, T. (2005) Directed evolution for engineering pH profile of endoglucanase III from Trichoderma reesei. Biomol. Eng. 22:89-94.

Wang, Q., Tull, D., Meinke, A., Gilkes, N.R., Warren, A.J., Aebersold, R. and Withers, S.G. (1993) Glu280 is the nucleophile in the active site of Clostridium thermocellum CelC, a Family A endo-P-l ,4-glucanase. The Journal of Biological Chemistry. 268(19): 14096-14102. Xiao, Z., Wang, P., Qu, Y., Gao, P., and Wang, T. (2002) Cold adaptation of a mesophilic cellulase, EG III from Trichoderma reesei, by directed evolution.

Sci. China, C, Life Sci. 45:337-343.

Zhang, Y.-H.P. and Lynd, L.R. (2005) Determination of the number-average degree of polymerization of cellodextrins and cellulose with application to enzymatic hydrolysis. Biomacromolecules, 6: 1510-1515.