# Patent

## Title
GH61 glycoside hydrolase protein variants and cofactors that enhance GH61 activity

## Abstract

The present invention provides various GH61 protein variants comprising various amino acid substitutions. The GH61 protein variants have an improved ability to synergize with cellulase enzymes, thereby increasing the yield of fermentable sugars obtained by saccharification of biomass. In some embodiments, sugars obtained from saccharification are fermented to produce numerous end-products, including but not limited to alcohol.

## Background
The present application is a continuation-in-part of U.S. patent application. Ser. No. 13/215,193, filed Aug. 22, 2011, now U.S. Pat. No. 8,298,795, which claims priority to U.S. Prov. Appln. Ser. No. 61/375,788, filed Aug. 20, 2010. This application also claims the priority of U.S. Prov. Appln. Ser. No. 61/526,224, filed Aug. 22, 2011, and U.S. Prov. Appln. Ser. No. 61/601,997, filed Feb. 22, 2012, all of which are hereby incorporated in their entireties for all purposes.


REFERENCE TO A “SEQUENCE LISTING”, A TABLE, OR A COMPUTER PROGRAM LISTING APPENDIX SUBMITTED AS AN ASCII TEXT FILE
The Sequence Listing written in file CX35-101US2A_ST25.TXT, created on Aug. 20, 2012, 416,766 bytes, machine format IBM-PC, MS-Windows operating system, is hereby incorporated by reference.
FIELD OF THE INVENTION
The invention relates generally to the field of glycolytic enzymes and their use, and to the field of directed enzyme evolution or modification. More specifically, the present invention provides GH61 protein variants, and methods for the use of such protein variants in production of fermentable sugars and ethanol from cellulosic biomass.
BACKGROUND
Cellulosic biomass is a significant renewable resource for the generation of fermentable sugars. These sugars can be used as substrates for fermentation and other metabolic processes to produce biofuels, chemical compounds and other commercially valuable end-products.
The conversion of cellulosic biomass to fermentable sugars may begin with chemical, mechanical, enzymatic or other pretreatments to increase the susceptibility of cellulose to hydrolysis. Such pretreatment may be followed by the enzymatic conversion of cellulose to cellobiose, cello-oligosaccharides, glucose, and other sugars and sugar polymers, using enzymes that break down cellulose. These enzymes are collectively referred to as “cellulases” and include endoglucanases, beta-glucosidases and cellobiohydrolases.
SUMMARY OF THE INVENTION
The invention provides numerous variants of GH61 proteins. In some embodiments, these variants comprise amino acid substitutions as set forth herein. In some embodiments, these variants exhibit an improved ability to synergize with cellulase enzymes, thereby increasing the yield of fermentable sugars obtained by saccharification of cellulose-containing biomass. Sugars obtained from saccharification can be fermented to produce alcohol and other end-products. Thus, the GH61 variant proteins of this invention have important commercial applicability in the production of biofuels and other end-products. In some embodiments, the present invention provides GH61 variant proteins comprising an amino acid sequence that is substantially identical (for example, at least about 70%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% identical) to SEQ ID NO:2 or a fragment of SEQ ID NO:2 having GH61 activity as defined below. In some embodiments, the variant protein has one or more amino acid substitutions with respect to SEQ ID NO:2 or a fragment of SEQ ID NO:2. In some embodiments, the GH61 is at least 95% identical to SEQ ID NO:2 or a fragment of SEQ ID NO:2 having GH61 activity. In some embodiments, the GH61 variant proteins have increased thermoactivity compared with the GH61 wild-type protein of SEQ ID NO:2. In some further embodiments, the GH61 variant proteins have increased thermostability compared with the GH61 wild-type protein of SEQ ID NO:2.
In some embodiments, the present invention provides GH61 variants comprising substitution(s) in at least one of the positions as indicated herein. In some embodiments, the substitution(s) provide GH61 variants that have increased activity as compared to wild-type GH61. In some embodiments, the GH61 variants comprise at least one substitution selected from those listed in Table 1 and/or Table 2 in any combination, wherein the positions are numbered with reference to SEQ ID NO:2.
In some further embodiments, the GH61 variants provided herein comprise the any one or more of the mutations listed in Table 1 and/or Table 2 in any combination. It is not intended that the present invention be limited to the specific substitutions. Any two, three, four, or more than four substitutions find use in any combination that improves GH61 activity. Non-limiting illustrations of effective combinations are provided herein.
In some embodiments, a substitution or combination of substitutions in the amino acid sequence as provided herein results in the variant protein having increased GH61 activity in a saccharification reaction. In some embodiments, crystalline cellulose undergoes saccharification by cellulase enzymes that are contained in culture broth from M. thermophila cells. When measured in this manner, a GH61 variant protein of this invention causes increase in yield of fermentable sugars (e.g., glucose) to a degree that is about 1.5-fold, about 2-fold, about 3-fold, about 5-fold, about 8-fold, about 10-fold or more compared with the parental GH61 sequence (SEQ ID NO:2) or biologically active fragment, compared with a reference protein comprising SEQ ID NO:2 or the fragment, without any substitutions. It is not intended that the present invention be limited to the production of any particular fermentable sugar(s). It is also not intended that the present invention be limited to any specific level of improvement in the yield of fermentable sugar using at least one of the variants provided herein.
This invention also provides GH61 protein variants that are more resistant to the presence of enzyme inhibitors that may be present in commercial sources of biomass, or be generated as a result of pretreatment of the biomass substrate.
In some embodiments, the present invention provides GH61 variant proteins comprising amino acid sequences that are at least about at least about 60%, at least about 65%, at least about 70%, 75%, at least 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% identical to SEQ ID NO:2 or a fragment of SEQ ID NO:2 having GH61 activity, wherein the amino acid sequence of the variant protein has one or more amino acid substitutions with respect to SEQ ID NO:2 or the fragment.
In some embodiments, the present invention provides GH61 variant proteins comprising amino acid sequences that are at least about at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:2 or a fragment of SEQ ID NO:2 having GH61 activity, wherein the amino acid sequence of the variant protein has one or more amino acid substitutions with respect to SEQ ID NO:2 or the fragment, and wherein the substitution(s) in the amino acid sequence result in the variant protein having increased GH61 activity in a reaction where crystalline cellulose undergoes saccharification by cellulase enzymes that are contained in culture broth from M. thermophila cells, compared with a reference protein comprising SEQ ID NO:2 or the fragment, without any substitutions.
In some embodiments, the present invention provides GH61 variant proteins comprising amino acid sequences that are at least about 60%, at least about 65%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% identical to SEQ ID NO:2 or a fragment of SEQ ID NO:2 having GH61 activity, wherein the amino acid sequence of the variant protein has one or more amino acid substitutions with respect to SEQ ID NO:2 or the fragment, and wherein the polynucleotide encoding the GH61 variant protein comprises at least one mutation and/or mutation set selected from those listed in Table 1 and/or Table 2 in any combination, wherein the nucleotide positions of the substitutions are determined by alignment with SEQ ID NO:1.
In some embodiments, the present invention provides enzyme compositions comprising at least one GH61 variant of the present invention and/or at least one wild-type GH61 protein. In some embodiments, the present invention provides enzyme compositions comprising at least one GH61 variant protein of this invention is combined with one or more cellulase enzyme(s), including but not limited to endoglucanases (EG), beta-glucosidases (BGL), cellobiohydrolases (e.g., CBH1 and/or CBH2), and/or at least one wild-type GH61 protein. In some embodiments, the enzyme compositions further comprise one or more enzymes selected from cellulases, hemicellulases, xylanases, amylases, glucoamylases, proteases, esterases xylosidases, and lipases.
The invention also includes polynucleotides encoding GH61 variant proteins, recombinant cells expressing such polynucleotides and optionally one or more cellulase enzymes, and methods for increasing yield of fermentable sugars in a saccharification reaction by conducting the reaction in the presence of at least one GH61 protein of this invention.
In some embodiments, the present invention provides at least one polynucleotide comprising at least one nucleic acid sequence encoding at least one GH61 variant protein; at least one polynucleotide that hybridizes under stringent hybridization conditions to at least one polynucleotide encoding at least one GH61 variant protein; and/or at least one polynucleotide that hybridizes under stringent hybridization conditions to the complement of at least one polynucleotide encoding at least one polypeptide comprising at least one GH61 variant protein.
The present invention also provides recombinant nucleic acid constructs comprising at least one polynucleotide sequence encoding at least one GH61 protein, wherein the polynucleotide is selected from: (a) a polynucleotide that encodes a polypeptide comprising an amino acid sequence having at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 100% identity to SEQ ID NO:2, wherein the amino acid sequence comprises at least one substitution and/or substitution set provided herein; (b) a polynucleotide that hybridizes under stringent hybridization conditions to at least a fragment of a polynucleotide that encodes a polypeptide having the amino acid sequence of SEQ ID NO:2, and wherein the amino acid sequence comprises at least one substitution and/or at least one substitution set provided herein; and/or (c) a polynucleotide that hybridizes under stringent hybridization conditions to the complement of at least a fragment of a polynucleotide that encodes a polypeptide having the amino acid sequence of SEQ ID NO:2, and wherein the amino acid sequence comprises at least one substitution and/or at least one substitution set provided herein.
The present invention further provides recombinant nucleic acid constructs comprising at least one polynucleotide sequence encoding at least one GH61 protein, wherein the polynucleotide is selected from: (a) a polynucleotide that encodes a polypeptide comprising an amino acid sequence having at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or at least about 100% identity to SEQ ID NO:2, wherein the amino acid sequence comprises at least one substitution and/or substitution set provided herein; (b) a polynucleotide that hybridizes under stringent hybridization conditions to a polynucleotide that encodes a polypeptide having the amino acid sequence of SEQ ID NO:2, and wherein the amino acid sequence comprises at least one substitution and/or at least one substitution set provided herein; and/or (c) a polynucleotide that hybridizes under stringent hybridization conditions to the complement of a polynucleotide that encodes a polypeptide having the amino acid sequence of SEQ ID NO:2, and wherein the amino acid sequence comprises at least one substitution and/or at least one substitution set provided herein. In some embodiments of the nucleic acid constructs, the polynucleotide sequence is at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:1, and wherein the polynucleotide sequence comprises at least one mutation and/or at least one mutation set provided herein. Exemplary are those shown in Table 1 and Table 2, which may be incorporated into the polynucleotide in any combination.
In some embodiments, the present invention provides polynucleotides and nucleic acid constructs comprising polynucleotides encoding at least one GH61 variant and/or wild-type protein (e.g., any of SEQ ID NOS:2, 3, 5, 6, 8, 9, 11, 12, 14, 15, 17, 18, 20, 21, 23, 24, 26, 27, 29, 30, 32, 33, 35, 36, 38, 39, 41, 42, 44, 45, 47, 48, 50, 51, 53, 54, 56, 57, 59, 60, 62, 64, 65, 67, 68, 70, 71, 73, 74, 76, 77, 79, 80, 82, 83, 85, 86, 88, 89, 91, 93, 95, 96, 98, 99, 101, 102, 104, 105, 107, 108), operably linked to promoters. In some embodiments, the promoters are heterologous promoters. In some embodiments, the present invention provides expression constructs comprising polynucleotides and/or nucleic acid constructs that comprise polynucleotides encoding at least one GH61 variant and/or wild-type protein. In some embodiments, the expression constructs comprise at least one nucleic acid sequence operably linked to at least one additional regulatory sequence.
The present invention also provides recombinant host cells that express at least one polynucleotide sequence encoding at least one GH61 variant protein. In some embodiments, the host cell also expresses at least one polynucleotide sequence encoding at least one GH61 wild-type protein. In some embodiments, the expressed GH61 variant and/or wild-type protein is secreted from the host cell. In some embodiments, the host cell also produces at least one cellulase enzyme selected from endoglucanases (EG), beta-glucosidases (BGL), cellobiohydrolases (e.g., CBH1 and/or CBH2), xylanases, xylosidases, etc. In some embodiments, the host cell is a yeast, while in some other embodiments, the host cell is a filamentous fungal cell. In some further embodiments, the filamentous fungal cell is a Myceliophthora, a Thielavia, a Trichoderma, or an Aspergillus cell. In some embodiments, the filamentous fungal cell is Myceliophthora thermophila. In some additional embodiments, the host cell also produces at least one additional enzyme (e.g., esterase, protease, amylase, laccase, etc.).
In some additional embodiments, the present invention provides methods for producing at least one end-product from at least one cellulosic substrate. The substrate is contacted with at least one GH61 variant protein of the invention, and one or more cellulase enzymes. The fermentable sugars that are produced as a result are contacted with a microorganism in a fermentation to produce an end-product (e.g., an alcohol such as ethanol). The fermentation may be simultaneous with the saccharification, or may occur subsequently. It is not intended that the fermentation end-product be limited to any specific composition, as various end-products may be obtained from the fermentation reaction, including but not limited to alcohols.
The present invention also provides methods for producing fermentable sugars from cellulosic substrates, comprising contacting at the cellulosic substrate with at least one enzyme composition provided herein, under culture conditions whereby fermentable sugars are produced. In some embodiments the enzyme composition comprises a plurality of enzymes selected from at least one GH61 variant, at least one wild-type GH61, at least one endoglucanase (EG), at least one beta-glucosidase (BGL), at least one cellobiohydrolase (e.g., CBH1 and/or CBH2), at least one xylanase, at least one xylosidase, and/or at least one esterase. In some embodiments, the CBH1 is CBH1a. In further embodiments, the CBH2 is CHB2b. In some embodiments, the methods further comprise the step of pretreating the cellulosic substrate prior to the contacting step. In some embodiments, the enzyme composition is added concurrently with the pretreating step.
In some embodiments, the cellulosic substrate comprises wheat grass, wheat straw, barley straw, sorghum, rice grass, sugarcane, sugarcane straw, bagasse, switchgrass, corn stover, corn fiber, grains, or a combination thereof. In further embodiments, the fermentable sugars comprise glucose and/or xylose. In some embodiments, the methods further comprise the step of recovering the fermentable sugars. In some embodiments, the methods further comprise the step of contacting the fermentable sugars with a microorganism under conditions such that the microorganism produces at least one fermentation end product. In further embodiments, the fermentation end product is selected from alcohols, fatty alcohols, fatty acids, lactic acid, acetic acid, 3-hydroxypropionic acid, acrylic acid, succinic acid, citric acid, malic acid, fumaric acid, amino acids, 1,3-propanediol, ethylene, glycerol, butadiene, and/or beta-lactams. In some still further embodiments, the fermentation end product is an alcohol selected from ethanol and butanol. In some embodiments, the alcohol is ethanol. It is not intended that the fermentation end-product be limited to any specific composition(s), as various end-products can be produced using the present invention.
The present invention also provides methods for producing an end product from a cellulosic substrate, comprising: contacting the cellulosic substrate with at any enzyme composition provided herein, under conditions whereby fermentable sugars are produced from the substrate; and contacting the fermentable sugars with a microorganism in a fermentation to produce an end-product. In some embodiments, the methods comprise simultaneous saccharification and fermentation reactions (SSF). In some alternative embodiments, the methods comprise saccharification of the cellulosic substrate and fermentation in separate reactions (SHF). In some additional embodiments, the methods comprise production of at least one enzyme simultaneously with hydrolysis and/or fermentation (e.g., “consolidated bioprocessing”).
The present invention also provides methods for producing a fermentation end product from a cellulosic substrate, comprising obtaining fermentable sugars produced according to any method provided herein, and contacting the fermentable sugars with a microorganism in a fermentation to produce a fermentation end product. In some embodiments, the fermentation end product is selected from alcohols, fatty alcohols, fatty acids, lactic acid, acetic acid, 3-hydroxypropionic acid, acrylic acid, citric acid, malic acid, fumaric acid, succinic acid, amino acids, 1,3-propanediol, ethylene, glycerol, butadiene, and/or beta-lactams. In some embodiments, the fermentation end product is at least one alcohol selected from ethanol and butanol. In further embodiments, the alcohol is ethanol. In some still further embodiments, the microorganism is a yeast. In some embodiments, the methods further comprise the step of recovering the fermentation end product. It is not intended that the fermentation end-product be limited to any specific composition(s), as various end-products can be produced using the present invention. It is also not intended that the present invention be limited to any particular microorganism. It is further not intended that the present invention be limited to any particular yeast, as any suitable yeast finds use in the present invention.
The present invention also provides for use of at least one GH61 variant protein as provided herein to produce at least one fermentation end product. The present invention also provides for use of at least one GH61 variant protein provided herein to produce at least one fermentation end product selected from alcohols, fatty alcohols, fatty acids, lactic acid, acetic acid, 3-hydroxypropionic acid, acrylic acid, citric acid, malic acid, fumaric acid, succinic acid, amino acids, 1,3-propanediol, ethylene, glycerol, butadiene, and/or beta-lactams. In some embodiments, the fermentation end product is an alcohol selected from ethanol and butanol. In some embodiments, the alcohol is ethanol. It is not intended that the fermentation end-product be limited to any specific composition(s), as various end-products can be produced using the present invention.
A further embodiment of the invention is a composition comprising a GH61 protein, one or more cellulase enzymes, a cellulosic substrate, and an effective concentration of Cu++ and/or gallic acid, as further described and illustrated below. The GH61 protein may be any GH61 protein disclosed herein, such as a protein comprising an amino acid sequence at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% identical to SEQ ID NO:2, or a fragment thereof with GH61 activity. In some embodiments, the GH61 protein is a variant protein comprising all or part of SEQ ID NO:2 having GH61 activity, wherein the variant comprises one or more of the amino acid substitutions provided herein. In some embodiments, the cellulase enzyme(s) are selected from endoglucanases (EG), beta-glucosidases (BGL), cellobiohydrolases (e.g., CBH1 and/or CBH2), xylanases, xylosidases, etc. In some embodiments, the presence of Cu++, gallic acid, or both enhances activity of the GH61 protein, thereby increasing the rate of glucose production or reducing the amount of GH61 protein needed to supply GH61 activity in a saccharification reaction.
In another embodiment, the present invention provides methods for producing fermentable sugars from cellulosic substrate(s), in which a composition comprising at least one GH61, at least one cofactor, at least one additional cellulase enzyme, and at least one cellulosic substrate is cultured or maintained under conditions whereby fermentable sugars are produced from the substrate(s). The fermentable sugars can then be contacted with a microorganism under conditions such that the microorganism produces at least one fermentation end product, such as ethanol. A further embodiment of the invention is use of Cu++ to increase production of fermentable sugars from a saccharification reaction where cellulase activity is enhanced in the presence of a protein or protein variant with GH61 activity.
The present invention provides GH61 variant proteins comprising amino acid sequences that are at least about 75%, at least about 80%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to SEQ ID NO:2 or a fragment of SEQ ID NO:2 having GH61 activity, wherein the amino acid sequence of the variant protein has one or more amino acid substitutions with respect to SEQ ID NO:2 or the fragment. In some embodiments, the GH61 variant proteins comprise an amino acid sequence that is at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO:2 or a fragment of SEQ ID NO:2 having GH61 activity, wherein the amino acid sequence of the variant protein has one or more amino acid substitutions with respect to SEQ ID NO:2 or the fragment. In some embodiments, the GH61 variant proteins are at least 95% identical to SEQ ID NO:2 or a fragment of SEQ ID NO:2 having GH61 activity. In some embodiments, the GH61 variant proteins have increased thermoactivity, thermostability, and/or activity, as compared to the GH61 wild-type protein of SEQ ID NO:2. In some further embodiments, the GH61 variant proteins comprise at least one substitution(s) at one or more of the following amino acid positions: 20, 35, 42, 44, 45, 68, 87, 97, 103, 104, 127, 131, 132, 133, 134, 137, 139, 142, 143, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 190, 191, 192, 192, 205, 212, 215, 218, 232, 236, 239, 244, 246, 258, 270, 273, 317, 322, 323, 328, 330, and/or 341, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some embodiments, the GH61 variant proteins comprise at least one substitution(s) at one or more of the following amino acid positions: H20, N35, W42, Q44, P45, F68, T87, V97, P103, E104, S127, W131, F132, K133, I134. A137, Y139, A142, A143, I162, P163, S164, D165, L166, K167, A168, G169, N170, Y171, V172, L173, R174, H175, E176, I177, I178, A179, L180, H181, Q190, A191, Y192, Y192, S205, A212, S215, K218, S232, T236, G239, A244, A246, T258, G270, P273, N317, P322, T323, G328, S330, and/or C341, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some further embodiments, the GH61 variant proteins comprise at least one substitution(s) at one or more of the following amino acid positions: H20, N35, W42, E104, I134, S164, K167, A168, V172, I177, A179, and/or A191, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some additional embodiments, the GH61 variant proteins comprise at least two amino acid substitutions. In still some further embodiments, the GH61 variant proteins comprise at least one substitution set selected from: N35/E104/A168; W42/E104/K167; N35/W42/V97/A191; W42/E104; E104/K167; W42/A191; N35/W42/A191; V97/A191; and N35/E104/A191, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some embodiments, the GH61 variant proteins comprise at least one amino acid substitution comprising one or more of the following substitutions numbered with reference to SEQ ID NO:2: H20C/D, N35G, W42P, Q44V, P45T, F68Y, T87P, V97Q, P103E/H, E104C/D/H/Q, S127T, W131X, F132X, K133X, 134X, A137P, Y139L, A142W, A143P, I162X, P163X, S164X, D165X, L166X, K167A/X, A168P/X, G169X, N170X, Y171A/R, V172X, L173X, R174X, H175X, E176X, I177X, I178X, A179X, L180M/W, H181X, Q190E/H, A191N/T, Y192H, Y192Q, S205N, A212P, S215W, K218T, S232A, T236P, G239D, A244D, A246T, T258I, G270S, P273S, N317K, P322L, T323P, G328A, S330R, and/or C341R, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some additional embodiments, the GH61 variant proteins comprise one or more of the following substitutions: N35G, W42P, V97Q, E104H, K167A, A168P, and/or A191N, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some embodiments, the GH61 variant proteins comprise one or more of the following substitution sets: N35G/E104H/A168P; W42P/E104H/K167A; N35G/W42P/V97Q/A191N; W42P/E104H; E104H/K167A; W42P/A191N; N35G/W42P/A191N; V97Q/A191N; and/or N35G/E104H/A191N, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some additional embodiments, the GH61 variant proteins comprise the substitutions N35G/E104H/A168P, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some further embodiments, the GH61 variant proteins comprise the sequence set forth in any of SEQ ID NOS:4, 6, and/or 8. In some additional further embodiments, the GH61 variant proteins are encoded by at least one polynucleotide sequence set forth in SEQ ID NOS:3, 5, and/or 7. In some embodiments, the GH61 variant proteins comprise at least one substitution(s) at one or more of the following amino acid positions: 24, 28, 32, 34, 35, 40, 44, 45, 46, 49, 51, 54, 55, 56, 58, 64, 66, 67, 69, 70, 71, 78, 80, 82, 83, 88, 93, 95, 101, 104, 116, 118, 128, 130, 136, 137, 141, 142, 144, 145, 150, 155, 161, 164, 168, 184, 187, 199, 203, 205, 212, 218, 219, 230, 231, 232, 233, 234, 236, 237, 245, 253, 263, 266, 267, 268, 269, 270, 271, 280, 281, 282, 290, 295, 297, 303, 305, 310, 317, 320, 324, 326, 327, 329, 330, 332, 333, 336, 337, and/or 339, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some further embodiments, the GH61 variant proteins, comprise at least one substitution(s) at one or more of the following amino acid positions: S24, V28, Y32, R34, N35, T40, Q44, P45, N46, T49, I51, T54, A55, A56, Q58, E64, N66, S67, G69, T70, P71, S78, T80, G82, G83, V88, K93, N95, E101, E104, A116, N118, S128, R130, G136, A137, K141, A142, G144, R145, A150, G155, Q161, S164, A168, Q184, N187, R199, G203, S205, A212, K218, A219, V230, S231, S232, P233, D234, T236, V237, G245, S253, A263, P266, G267, G268, G269, G270, A271, A280, T281, S282, R290, S295, A297, P303, G305, K310, N317, T320, V324, A326, P327, S329, S330, S332, V333, E336, W337, and/or S339, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some further embodiments, the GH61 variant proteins comprise a plurality of amino acid substitutions as set forth herein. In some embodiments, the GH61 variant proteins comprise at least one substitution set selected from: N35/T40/E104/A168/P327; N35/P45/E104/A168/N317; N35/E104/A168/N317; N35/E104/A168/N317/S329; N35/E104/A137/A168/S232; N35/E104/A168/N317/T320; N35/E104/A168/D234; N35/T40/E104/A142/A168; N35/E104/R145/A168; N35/T40/S78/V88/E104/S128K/A168/D234; N35/E104/A168/S330; N35/E104/A168/G203/P266; N35/E104/A168/D234; N35/E104/A168/S330; N35/E104/A168/W337; R34/N35/E104/R145/A168; Y32/N35/E64/E104/A168; V28/N35/P45/E104/A168; N35/E104/G144/A168/V333; N35/N66/E104/A168; N35/E104/A168/P327; N35/E104/A168/G203; N35/E104/A168/S339; N35/P45/N46/E104/A150/A168; N35/E104/A168/S231; N35/T40/E104/A168/D234/P327; N35/E104/A168/S231; N35/E104/A168/N317; N35/E104/A168/S330; N35/E104/A168/S329; N35/E104/A168/P327; N35/P45/E104/A168; N35/E104/A116/A168; N35/T40/E104/A168/V230/P327; N35/E104/A168/S332; N35/E104/A168/G203; N35/E104/R145/A168/S329; N35/T40/T49/E104/A168/D234; /P327; N35/A56/E104/A168; N35/E104/Q161/A168; N35/E104/A168/S332; N35/P45/T49/E104/A168/N317/T320; N35/E104/A168/V237; N35/E104/A168/E336; N35/E104/A168/P233; N35/E104/R130/A168; N35/E104/A168/P327; N35/E104/A168/N317; N35/Q44/E104/A168; N35/E104/A168/A326; N35/E104/A168/N317; N35/T40/E104/S128/A168; N35/T80/E104/A168/P303; N35/E104/A116/A168; N35/E104/A168/S231/S295; N35/T40/E101/E104/A168/P327; N35/P45/E104/A168/A219/S232; N35/N46/E104/A168; N35/E104/A168/A326; N35/E104/A168/G203/T281; N35/E104/A168/E336; N35/T40/E104/S128/A142/A168; N35/E104/N118/A168; N35/E104/G155/A168; S24/N35/E104/A168/V237/P303; N35/E104/Q161/A168; N35/Q44/S67/E104/A168; V28/N35/E104/A168; N35/E104/A168/Q184; N35/T54/E104/A168; N35/N66/E104/A168; N35/E64/E104/A168; N35/E104/S164/A168/A271; N35/N66/E104/A168; N35/G83/E104/A168; N35/E104/K141/A168; N35/E104/A168/N317/T320; N35/E104/R130/A168; N35/E104/R145/A168; N35/T70/E104/A168; N35/E104/R130/A168; N35/E104/A168/Q184; N35/E104/A168/S329; N35/T49/E104/A168; Y32/N35/E104/A168; N35/E104/A168/S330; N35/Q58/E104/A168; Y32/N35/P71/E104/A168; N35/E104/A168/S330; N35/T80/E104/A168; N35/G82/E104/A168; N35/E104/A168/S295; N35/N66/E104/A168; N35/T54/E104/A168; N35/P45/E104/A168; N35/E104/S128/A168; N35/N66/N95/E104/S164/A168; /G267; N35/T54/E104/A168; N35/P45/E104/K141/A168; N35/E104/A168/S332; N35/E104/A168/A297; N35/E104/K141/R145/A168; N35/Q44/E104/A168/S231; N35/T40/T49/S78/E104/A142; /A168; N35/E104/S164/A168/S295; N35/E104/A168/N317; N35/P45/E104/A168; N35/G82/E104/A168; N35/N46/E104/A168/G203/A263; N35/Q58/E104/A168; N35/G69/E104/A168; N35/S67/E104/A168; N35/E104/A168/R199; N35/E104/A168/G203/G268/G269/G270; N35/E104/A168/V324; N35/E104/A168/P266; N35/E104/A168/G245; N35/N66/E104/A168; S24/N35/Q44/T80/E104/A168; N35/E104/A168/T236; N35/E104/A168/K310; N35/E104/R130/A168; N35/N66/S78/E104/A168/S253; N35/N66/E104/S164/A168/S282; N35/E104/A142/A168; N35/E104/A145/A168; N35/E104/A168/S231; N35/E104/A168/Q184; N35/E104/A168/K218; N35/E104/A168/P233; N35/T49/E104/A168/Q184; N35/T40/E104/A168/P327; N35/T54/E104/A168; N35/N66/E104/S164/A168/S231/S253; N35/E104/A168/G203; N35/T49/E104/A168; N35/E104/A168/P266/G267; N35/Q44/N66/E104/A168; N35/S67/E104/A168; N35/E104/A137/A168; N35/T49/E104/S128/A168; N35/T49/E104/A168/K218/N317; N35/I51/E104/A168; N35/E104/A168/A326; N35/P45/E104/A168/T320; N35/N66/E104/A168; N35/E104/A168/V237/P303; N35/P45/E104/A168/K218/N317; N35/T80/E104/A168; N35/A55/E104/A168; N35/E104/K141/A168/P266; N35/E104/A168/S330; N35/N66/E104/A168/R290; N35/E104/N118/A168; N35/E104/A168/A212; N35/K93/E104/R130/A168; N35/E104/A168/G267; N35/P45/T49/E104/A168/N317; N35/E104/A168/V230; N35/E104/A168/S329; N35/P45/E104/A168/A219; N35/S78/E104/S164/A168; N35/E104/A168/S205; N35/E104/A168/Q184; V28/N35/N46/Q58/E104/A168; N35/E104/A142/A168; N35/E104/A168/E336; N35/E104/A168/A280; N35/E104/A168/A219; N35/E104/A168/P303/G305; R34/N35/E104/A168/A280; N35/E104/A168/N187; N35/E104/G136/A168; N35/E104/A168/Q184; N35/T49/E104/A168/N317; N35/T40/T49/S78/E104/A168; R34/N35/K93/E104/R130/R145/A168/R199/K218/A280; N35/T40/E104/A142/A168; and N35/N66/E104/A168, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some further embodiments, the GH61 variant proteins comprise at least one amino acid substitution comprising one or more of the following substitutions numbered with reference to SEQ ID NO:2: S24Q; V28H; Y32S; R34E; N35G; T40A/G/L/S; Q44K; P45D/E/K/R/S; N46E/R; T49A/Q/R/Y; I51A; T54G/M/S/W; A55G; A56S; Q58H/P; E64L/S; N66A/D/G/L/M/Q/R/V; S67G/H/T; G69T; T70A; P71A; S78C/D; T80H/L/V; G82A/S; G83R; V88I; K93N/T; N95E; E101T; E104H; A116Q/S; N118E/S; S128K/L/N; R130E/G/H/K/Y; G136H; A137M/S; K141A/N/P/R; A142D/G/L; G144S; R145H/L/N/Q/T; A150Y; G155N; Q161E/R; S164E; A168P; Q184E/H/L/N/R; N187D; R199E; G203E/V/Y; S205T; A212M; K218L/T; A219R/T; V230I/Q; S231A/H/K/I; S232E; P233F/T; D234E/M/N; T236E; V237I; G245A; S253D/T; A263V; P266S; G267D/V; G268A; G269A; G270A; A271T; A280D/T; T281A; S282D; R290K; S295D/L/T; A297T; P303T; G305D; K310I; N317D/H/I/M/Q/R; T320A; V324M; A326C/Q/V; P327F/K/L/M; S329H/I/Q/T/Y; S330A/H/I/T/V; S332C/F/R; V333Q; E336L/R/S; W337R; and/or S339W, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some embodiments, the GH61 variant proteins comprise a plurality of substitutions and/or substitution sets as provided therein. In some additional embodiments, the GH61 variant proteins comprise one or more of the following substitution sets: N35G/T40A/E104H/A168P/P327M; N35G/P45D/E104H/A168P/N317R; N35G/E104H/A168P/N317R; N35G/E104H/A168P/N317D/S329Y; N35G/E104H/A137S/A168P/S232E; N35G/E104H/A168P/N317R/T320A; N35G/E104H/A168P/D234E; N35G/T40S/E104H/A142G/A168P; N35G/E104H/R145L/A168P; N35G/T40S/S78C/V88I/E104H/S128K/A168P/D234M; N35G/E104H/A168P/S330V; N35G/E104H/A168P/G203E/P266S; N35G/E104H/A168P/D234N; N35G/E104H/A168P/S330H; N35G/E104H/A168P/W337R; R34E/N35G/E104H/R145T/A168P; Y32S/N35G/E64S/E104H/A168P; V28H/N35G/P45K/E104H/A168P; N35G/E104H/G144S/A168/V333Q; N35G/N66Q/E104H/A168P; N35G/E104H/A168P/P327K; N35G/E104H/A168P/G203E; N35G/E104H/A168P/S339W; N35G/P45K/N46E/E104H/A150Y/A168P; N35G/E104H/A168P/S231K; N35G/T40A/E104H/A168P/D234E/P327M; N35G/E104H/A168P/S231H; N35G/E104H/A168P/N317M; N35G/E104H/A168P/S330Y; N35G/E104H/A168P/S329I; N35G/E104H/A168P/P327F; N35G/P45D/E104H/A168P; N35G/E104H/A116S/A168P; N35G/T40A/E104H/A168P/V230I/P327M; N35G/E104H/A168P/S332R; N35G/E104H/A168P/G203V; N35G/E104H/R145N/A168P/S329H; N35G/T40S/T49R/E104H/A168P/D234E; /P327M; N35G/A56S/E104H/A168P; N35G/E104H/Q161R/A168P; N35G/E104H/A168P/S332F; N35G/P45R/T49A/E104H/A168P/N317R/T320A; N35G/E104H/A168P/V237I; N35G/E104H/A168P/E336S; N35G/E104H/A168P/P233T; N35G/E104H/R130H/A168P; N35G/E104H/A168P/P327L; N35G/E104H/A168P/N317I; N35G/Q44K/E104H/A168P; N35G/E104H/A168P/A326V; N35G/E104H/A168P/N317H; N35G/T40L/E104H/S128K/A168P; N35G/T80V/E104H/A168P/P303T; N35G/E104H/A116Q/A168P; N35G/E104H/A168P/S231A/S295L; N35G/T40S/E101T/E104H/A168P/P327M; N35G/P45K/E104H/A168P/A219R/S232E; N35G/N46R/E104H/A168P; N35G/E104H/A168P/A326Q; N35G/E104H/A168P/G203E/T281A; N35G/E104H/A168P/E336R; N35G/T40S/E104H/S128K/A142G/A168P; N35G/E104H/N118S/A168P; N35G/E104H/G155N/A168P; S24Q/N35G/E104H/A168P/V237I/P303T; N35G/E104H/Q161E/A168P; N35G/Q44K/S67T/E104H/A168P; V28H/N35G/E104H/A168P; N35G/E104H/A168P/Q184L; N35G/T54G/E104H/A168P; N35G/N66M/E104H/A168P; N35G/E64L/E104H/A168P; N35G/E104H/S164E/A168P/A271T; N35G/N66A/E104H/A168P; N35G/G83R/E104H/A168P; N35G/E104H/K141A/A168P; N35G/E104H/A168P/N317Q/T320A; N35G/E104H/R130G/A168P; N35G/E104H/R145Q/A168P; N35G/T70A/E104H/A168P; N35G/E104H/R130K/A168P; N35G/E104H/A168P/Q184E; N35G/E104H/A168P/S329T; N35G/T49A/E104H/A168P; Y32S/N35G/E104H/A168P; N35G/E104H/A168P/S3301; N35G/Q58H/E104H/A168P; Y32S/N35G/P71A/E104H/A168P; N35G/E104H/A168P/S330T; N35G/T80V/E104H/A168P; N35G/G82A/E104H/A168P; N35G/E104H/A168P/S295T; N35G/N66G/E104H/A168P; N35G/T54S/E104H/A168P; N35G/P45S/E104H/A168P; N35G/E104H/S128L/A168P; N35G/N66D/N95E/E104H/S164E/A168P; /G267D; N35G/T54W/E104H/A168P; N35G/P45E/E104H/K141R/A168P; N35G/E104H/A168P/S332C; N35G/E104H/A168P/A297T; N35G/E104H/K141P/R145Q/A168P; N35G/Q44K/E104H/A168P/S231T; N35G/T40G/T49R/S78C/E104H/A142G; /A168P; N35G/E104H/S164E/A168P/S295D; N35G/E104H/A168P/N317Q; N35G/P45R/E104H/A168P; N35G/G82S/E104H/A168P; N35G/N46R/E104H/A168P/G203E/A263V; N35G/Q58P/E104H/A168P; N35G/G69T/E104H/A168P; N35G/S67G/E104H/A168P; N35G/E104H/A168P/R199E; N35G/E104H/A168P/G203E/G268A/G269A/G270A; N35G/E104H/A168P/V324M; N35G/E104H/A168P/P266S; N35G/E104H/A168P/G245A; N35G/N66R/E104H/A168P; S24Q/N35G/Q44K/T80H/E104H/A168P; N35G/E104H/A168P/T236E; N35G/E104H/A168P/K310I; N35G/E104H/R130Y/A168P; N35G/N66D/S78D/E104H/A168P/S253D; N35G/N66D/E104H/S164E/A168P/S282D; N35G/E104H/A142L/A168P; N35G/E104H/R145H/A168P; N35G/E104H/A168P/S231T; N35G/E104H/A168P/Q184R; N35G/E104H/A168P/K218L; N35G/E104H/A168P/P233F; N35G/T49A/E104H/A168P/Q184H; N35G/T40S/E104H/A168P/P327M; N35G/T54M/E104H/A168P; N35G/N66D/E104H/S164E/A168P/S231T/S253T; N35G/E104H/A168P/G203Y; N35G/T49Q/E104H/A168P; N35G/E104H/A168P/P266S/G267V; N35G/Q44K/N66V/E104H/A168P; N35G/S67H/E104H/A168P; N35G/E104H/A137M/A168P; N35G/T49A/E104H/S128N/A168P; N35G/T49R/E104H/A168P/K218L/N317Q; N35G/I51A/E104H/A168P; N35G/E104H/A168P/A326C; N35G/P45R/E104H/A168P/T320A; N35G/N66L/E104H/A168P; N35G/E104H/A168P/V237I/P303T; N35G/P45R/E104H/A168P/K218L/N317Q; N35G/T80L/E104H/A168P; N35G/A55G/E104H/A168P; N35G/E104H/K141N/A168P/P266S; N35G/E104H/A168P/S330A; N35G/N66D/E104H/A168P/R290K; N35G/E104H/N118E/A168P; N35G/E104H/A168P/A212M; N35G/K93N/E104H/R130Y/A168P; N35G/E104H/A168P/G267D; N35G/P45R/T49Y/E104H/A168P/N317D; N35G/E104H/A168P/V230Q; N35G/E104H/A168P/S329Q; N35G/P45K/E104H/A168P/A219R; N35G/S78D/E104H/S164E/A168P; N35G/E104H/A168P/S205T; N35G/E104H/A168P/Q184H; V28H/N35G/N46E/Q58H/E104H/A168P; N35G/E104H/A142D/A168P; N35G/E104H/A168P/E336L; N35G/E104H/A168P/A280T; N35G/E104H/A168P/A219T; N35G/E104H/A168P/P303T/G305D; R34E/N35G/E104H/A168P/A280T; N35G/E104H/A168P/N187D; N35G/E104H/G136H/A168P; N35G/E104H/A168P/Q184N; N35G/T49Y/E104H/A168P/N317R; N35G/T40A/T49Q/S78C/E104H/A168P; R34E/N35G/K93T/E104H/R130E/R145T/A168P/R199E/K218T/A280D; N35G/T40L/E104H/A142G/A168P; and/or N35G/N66G/E104H/A168P, wherein the amino acid positions are numbered with reference to SEQ ID NO:2. In some further embodiments, the GH61 variant proteins comprise a plurality of substitutions as provided herein. In some additional embodiments, the GH61 variant proteins comprise polypeptide sequences that are at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to any of SEQ ID NOS:2, 3, 5, 6, 8, and/or 9, and/or a biologically active fragment of any of SEQ ID NOS: 2, 3, 5, 6, 8, and/or 9, wherein the fragment has GH61 activity. In still some additional embodiments, the GH61 variant proteins comprise polypeptide sequences that are at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to any of SEQ ID NOS:2, 3, 5, 6, 8, and/or 9, and/or a biologically active fragment of any of SEQ ID NOS: 2, 3, 5, 6, 8, and/or 9, wherein the fragment has GH61 activity.
The present invention also provides GH61 variant proteins comprising amino acid sequences that are at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to any of SEQ ID NOS:2, 3, 5, 6, 8, and/or 9, or a fragment of SEQ ID NOS:2, 3, 5, 6, 8, and/or 9 having GH61 activity, wherein the amino acid sequence of the variant protein has one or more amino acid substitutions with respect to SEQ ID NOS:2, 3, 5, 6, 8, and/or 9 or the fragment, and wherein the substitution(s) in the amino acid sequences result in the variant proteins having increased GH61 activity in a reaction where crystalline cellulose undergoes saccharification by cellulase enzymes that are contained in culture broth from M. thermophila cells, compared with a reference protein comprising SEQ ID NO:2, 3, 5, 6, 8, and/or 9 or the fragment, without any substitutions. In some embodiments, the GH61 variant proteins comprise amino acid sequences that are at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any of SEQ ID NOS:2, 3, 5, 6, 8, and/or 9, or a fragment of SEQ ID NOS:2, 3, 5, 6, 8, and/or 9 having GH61 activity, wherein the amino acid sequence of the variant protein has one or more amino acid substitutions with respect to SEQ ID NOS:2, 3, 5, 6, 8, and/or 9 or the fragment, and wherein the substitution(s) in the amino acid sequences result in the variant proteins having increased GH61 activity in a reaction where crystalline cellulose undergoes saccharification by cellulase enzymes that are contained in culture broth from M. thermophila cells, compared with a reference protein comprising SEQ ID NO:2, 3, 5, 6, 8, and/or 9 or the fragment, without any substitutions. In some further embodiments, the present invention provides GH61 variant proteins encoded by polynucleotides, wherein the proteins comprise amino acid sequences that are at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to any of SEQ ID NOS:2, 3, 5, 6, 8, and/or 9 or a fragment of SEQ ID NO:2, 3, 5, 6, 8, and/or 9 having GH61 activity, wherein the amino acid sequence of the variant protein has one or more amino acid substitutions with respect to SEQ ID NO:2, 3, 5, 6, 8, and/or 9 or the fragment, and wherein the polynucleotide encoding the GH61 variant protein comprises at least one mutation and/or mutation set selected from t60c/c573g, t60c/c573g/g1026a, c573g, t60c/c291a/c573g, t60c/c291a, t60c/c876t, a312g, t60c, t379a/c380g/g381c, c300t, t204c/t379a/c380g/g381c/c385t, g1026a, c246t, c597g, c72t, c732g/c843t/c882t, c909t, c912g, g921a, c792t, g972t, g921a, t379a/c380g/g381c/c454a/c456a/c732t/c843t/c849t, c520a/c522g, t60c/c573g; t60c/c288t/c573g; t60c/c198t/c573g; and/or t60c/g399a/c573g; wherein the nucleotide positions are numbered with reference to SEQ ID NO:1. In still some further embodiments, the present invention provides GH61 variant proteins encoded by polynucleotides, wherein the proteins comprise amino acid sequences that are at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any of SEQ ID NOS:2, 3, 5, 6, 8, and/or 9 or a fragment of SEQ ID NO:2, 3, 5, 6, 8, and/or 9 having GH61 activity, wherein the amino acid sequence of the variant protein has one or more amino acid substitutions with respect to SEQ ID NO:2, 3, 5, 6, 8, and/or 9 or the fragment, and wherein the polynucleotide encoding the GH61 variant protein comprises at least one mutation and/or mutation set selected from t60c/c573g, t60c/c573g/g1026a, c573g, t60c/c291a/c573g, t60c/c291a, t60c/c876t, a312g, t60c, t379a/c380g/g381c, c300t, t204c/t379a/c380g/g381c/c385t, g1026a, c246t, c597g, c72t, c732g/c843t/c882t, c909t, c912g, g921a, c792t, g972t, g921a, t379a/c380g/g381c/c454a/c456a/c732t/c843t/c849t, c520a/c522g, t60c/c573g; t60c/c288t/c573g; t60c/c198t/c573g; and/or t60c/g399a/c573g; wherein the nucleotide positions are numbered with reference to SEQ ID NO:1.
The present invention also provides polynucleotides comprising a nucleic acid sequences encoding the GH61 variant proteins provided herein, as well as polynucleotides that hybridize under stringent hybridization conditions to at least one polynucleotide and/or a complement of at least one polynucleotide encoding GH61 variant proteins provided herein. In some embodiments, the present invention provides polynucleotide sequences encoding GH61 variant proteins, wherein the polynucleotide sequences are at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to any of SEQ ID NOS:1, 4, 7, and/or 10, or at least one polynucleotide that hybridizes under stringent hybridization conditions to at least one polynucleotide and/or complement of any of SEQ ID NOS:1, 4, 7, and/or 10. In some additional embodiments, the present invention provides polynucleotide sequences encoding GH61 variant proteins, wherein the polynucleotide sequences are at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to any of SEQ ID NOS:1, 4, 7, and/or 10, or at least one polynucleotides that hybridizes under stringent hybridization conditions to at least one polynucleotide and/or complement of any of SEQ ID NOS:1, 4, 7, and/or 10.
The present invention also provides recombinant nucleic acid constructs comprising at least one polynucleotide sequence encoding at least one GH61 protein, wherein the polynucleotide is selected from: (a) a polynucleotide that encodes a polypeptide comprising an amino acid sequence having at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity to SEQ ID NO:2, 3, 5, 6, 8, and/or 9, wherein the amino acid sequence comprises at least one substitution and/or substitution set provided herein; (b) a polynucleotide that hybridizes under stringent hybridization conditions to at least a fragment of a polynucleotide that encodes a polypeptide having the amino acid sequence of SEQ ID NO:2, 3, 5, 6, 8, and/or 9, and wherein the amino acid sequence comprises at least one substitution and/or at least one substitution set provided herein; and/or (c) a polynucleotide that hybridizes under stringent hybridization conditions to the complement of at least a fragment of a polynucleotide that encodes a polypeptide having the amino acid sequence of SEQ ID NO:2, 3, 5, 6, 8, and/or 9, and wherein the amino acid sequence comprises at least one substitution and/or at least one substitution set provided herein. In some embodiments, the recombinant nucleic acid constructs comprise at least one polynucleotide sequence encoding at least one GH61 protein, wherein the polynucleotide is selected from: (a) a polynucleotide that encodes a polypeptide comprising an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to SEQ ID NO:2, wherein the amino acid sequence comprises at least one substitution and/or substitution set provided herein; (b) a polynucleotide that hybridizes under stringent hybridization conditions to a polynucleotide that encodes a polypeptide having the amino acid sequence of SEQ ID NO:2, and wherein the amino acid sequence comprises at least one substitution and/or at least one substitution set provided herein; and/or (c) a polynucleotide that hybridizes under stringent hybridization conditions to the complement of a polynucleotide that encodes a polypeptide having the amino acid sequence of SEQ ID NO:2, and wherein the amino acid sequence comprises at least one substitution and/or at least one substitution set provided herein. In some additional embodiments, the recombinant nucleic acid constructs comprise at least one polynucleotide sequence at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identical to any of SEQ ID NOS:1, 4, 7, and/or 10, and wherein the polynucleotide sequence comprises at least one mutation and/or at least one mutation set provided herein. In some further additional embodiments, the recombinant nucleic acid constructs comprise polynucleotide sequences that are at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to any of SEQ ID NOS:1, 4, 7, and/or 10, and wherein the polynucleotide sequence comprises at least one mutation and/or at least one mutation set provided herein. In some embodiments, the polynucleotides and/or nucleic acid constructs provided herein comprise at least one polynucleotide sequence comprising at least one mutation or mutation set selected from t60c/c573g, t60c/c573g/g1026a, c573g, t60c/c291a/c573g, t60c/c291a, t60c/c876t, a312g, t60c, t379a/c380g/g381c, c300t, t204c/t379a/c380g/g381c/c385t, g1026a, c246t, c597g, c72t, c732g/c843t/c882t, c909t, c912g, g921a, c792t, g972t, g921a, t379a/c380g/g381c/c454a/c456a/c732t/c843t/c849t, c520a/c522g; t60c/c573g; t60c/c288t/c573g; t60c/c198t/c573g; and/or t60c/g399a/c573g. In some additional embodiments, the polynucleotide and/or nucleic acid construct comprise at least one nucleic acid sequence operably linked to a promoter. In some additional embodiments, the promoter is a heterologous promoter. In some further embodiments, the nucleic acid constructs further encode at least one enzyme in addition to the GH61 variant protein. In some embodiments, the nucleic acid constructs comprise at least one additional enzyme is selected from wild-type GH61 enzymes, endoglucanases (EG), beta-glucosidases (BGL), Type 1 cellobiohydrolases (CBH1), Type 2 cellobiohydrolases (CBH2), cellulases, hemicellulases, xylanases, xylosidases, amylases, glucoamylases, proteases, esterases, and lipases. In some further embodiments, at least one additional enzyme is selected from wild-type GH61 enzymes, endoglucanases (EG), beta-glucosidases (BGL), Type 1 cellobiohydrolases (CBH1), Type 2 cellobiohydrolases (CBH2), xylanases, and xylosidases.
The present invention also provides expression constructs comprising at least one polynucleotide or nucleic acid construct as provided herein. In some expression construct embodiments, the nucleic acid construct and/or the polynucleotide is operably linked to a promoter. In some embodiments, the promoter is heterologous. In some further embodiments of the expression constructs provided herein, the nucleic acid sequence is operably linked to at least one additional regulatory sequence.
The present invention also provides host cells that express at least one polynucleotide sequence encoding at least one GH61 variant protein provided herein. In some embodiments, the host cells produce at least one GH61 variant protein provided herein. In some additional embodiments, at least one GH61 variant protein is secreted from the host cells. In some further embodiments, the host cells further produce at least one enzyme selected from wild-type GH61 enzymes, endoglucanases (EG), beta-glucosidases (BGL), Type 1 cellobiohydrolases (CBH1), Type 2 cellobiohydrolases (CBH2), cellulases, hemicellulases, xylanases, xylosidases, amylases, glucoamylases, proteases, esterases, and lipases. In some additional embodiments, the host cell further produces at least one enzyme selected from wild-type GH61 enzymes, endoglucanases (EG), beta-glucosidases (BGL), Type 1 cellobiohydrolases (CBH1), and Type 2 cellobiohydrolases (CBH2). In some embodiments, the host cell is a yeast or filamentous fungal cell. In some embodiments, the filamentous fungal cell is a Myceliophthora, a Chrysosporium a Thielavia, a Trichoderma, or an Aspergillus cell. In some further embodiments, the filamentous fungal cell is Myceliophthora thermophila. In some additional embodiments, the host cell is a yeast cell. In some further additional embodiments, the host cell is Saccharomyces. In some further embodiments, the host cells further comprise at least one polynucleotide, polynucleotide construct, and/or expression construct as provided herein.
The present invention also provides methods of producing at least one GH61 variant protein comprising culturing the host cell set forth herein under conditions such that the host cell produces at least one GH61 variant proteins as provided herein. In some embodiments of the methods, the host cell further produces at least one additional enzyme selected from wild-type GH61 enzymes, endoglucanases (EG), beta-glucosidases (BGL), Type 1 cellobiohydrolases (CBH1), Type 2 cellobiohydrolases (CBH2), cellulases, hemicellulases, xylanases, xylosidases, amylases, glucoamylases, proteases, esterases, and lipases. In some embodiments of the methods, the host cell further produces at least one EG, at least one BGL, at least one CBH1, at least one CBH2, and/or at least one wild-type GH61 enzyme. In some further embodiments of the methods, the conditions comprise culturing at about pH 5, while in some alternative embodiments of the methods, the conditions comprise culturing at about pH 6.7. In some embodiments of the methods, the filamentous fungal cell is a Myceliophthora, a Chrysosporium, a Thielavia, a Trichoderma, or an Aspergillus cell. In some further embodiments of the methods, the filamentous fungal cell is a Myceliophthora thermophila. In some additional embodiments of the methods, the host cell is a yeast cell. In some further additional embodiments of the methods, the host cell is Saccharomyces. 
The present invention also provides enzyme compositions comprising at least one GH61 variant protein as provided herein. In some embodiments, the enzyme compositions further comprise one or more enzymes selected from wild-type GH61 enzymes, endoglucanases (EG), beta-glucosidases (BGL), Type 1 cellobiohydrolases (CBH1), and/or Type 2 cellobiohydrolases (CBH2), cellulases, hemicellulases, xylanases, xylosidases, amylases, glucoamylases, proteases, esterases, and lipases. In some additional embodiments, the enzyme compositions further comprise at least two additional enzymes selected from wild-type GH61 enzymes, endoglucanases (EG), beta-glucosidases (BGL), Type 1 cellobiohydrolases (CBH1), and/or Type 2 cellobiohydrolases (CBH2), cellulases, hemicellulases, xylanases, xylosidases, amylases, glucoamylases, proteases, esterases, and lipases. In some embodiments, the enzyme compositions are produced by the host cells provided herein. In some additional embodiments, the enzyme compositions further comprise a microorganism. In some further embodiments, the microorganism comprises M. thermophila. In some embodiments, the enzyme compositions further comprise at least one adjunct composition. In some additional embodiments, the enzyme compositions comprise at least one adjunct composition selected from divalent metal cations, reductants, surfactants, buffers, culture media, and enzyme stabilizing systems. In some further embodiments, the enzyme compositions comprise adjunct composition comprising copper and/or gallic acid. In some additional embodiments, the enzyme compositions find use in saccharification reactions.
The present invention also provides compositions comprising at least one GH61 protein, one or more cellulase enzymes, a cellulosic substrate, and Cu++, wherein the GH61 protein is at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% identical to any of SEQ ID NOS:2, 5, 6, 8, 9, 11, and/or 12, and/or a biologically fragment thereof with GH61 activity. In some embodiments, the present invention provides compositions comprising at least one GH61 protein, one or more cellulase enzymes, a cellulosic substrate, and Cu++, wherein the GH61 protein is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ ID NO:2, 5, 6, 8, 9, 11, and/or 12, and/or a biologically fragment thereof with GH61 activity. In some embodiments, the concentration of Cu++ is at least about 4 μM. In some embodiments, the concentration of Cu++ is between about 1 μM and about 100 μM, between about 4 μM and about 100 μM, or between about 5 μM and about 100 μM.
The present invention also provides compositions comprising at least one GH61 protein, one or more cellulase enzymes, a cellulosic substrate, and gallic acid, wherein the GH61 protein is at least about 70%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% identical to any of SEQ ID NO:2, 5, 6, 8, 9, 11, and/or 12, and/or a biologically fragment thereof with GH61 activity. The present invention also provides compositions comprising at least one GH61 protein, one or more cellulase enzymes, a cellulosic substrate, and gallic acid, wherein the GH61 protein is at least 70%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to any of SEQ ID NO:2, 5, 6, 8, 9, 11, and/or 12, and/or a biologically fragment thereof with GH61 activity. In some embodiments, the concentration of gallic acid in the compositions is at least about 0.1 mM. In some embodiments, the compositions comprise gallic acid at a concentration between about 1 mM and about 5 mM. In some embodiments, the concentration of gallic acid in the composition is at least 0.1 mM. In some embodiments, the compositions comprise gallic acid at a concentration between 1 mM and 5 mM. In some embodiments, the compositions comprise at least one GH61 protein comprising SEQ ID NO:2, 5, 6, 8, 9, 11, and/or 12, and/or a biologically active fragment thereof with GH61 activity. In some embodiments, the compositions comprise at least one GH61 variant protein as provided herein. In some embodiments, the compositions comprise at least one cellulase enzyme selected from endoglucanases (EG), beta-glucosidases (BGL), Type 1 cellobiohydrolases (CBH1), and/or Type 2 cellobiohydrolases (CBH2). In some embodiments, the compositions comprise at least one BGL, CBH1, and CBH2. In some additional embodiments, the compositions further comprise at least one additional enzyme. In some further embodiments, at least one additional enzyme is selected from hemicellulases, xylanases, xylosidases, amylases, glucoamylases, proteases, esterases, and lipases. In still some further embodiments of the compositions, the cellulosic substrate is selected from wheat grass, wheat straw, barley straw, sorghum, rice grass, sugarcane straw, bagasse, switchgrass, corn stover, corn fiber, grains, or any combination thereof.
The present invention also provides methods for producing fermentable sugars from a cellulosic substrate, comprising contacting the cellulosic substrate with at least one enzyme composition as provided herein under conditions whereby fermentable sugars are produced. In some embodiments, the methods further comprise pretreating the cellulosic substrate prior to the contacting. In some additional embodiments of the methods, the enzyme composition is added concurrently with pretreating. In some further embodiments of the methods, the cellulosic substrate comprises wheat grass, wheat straw, barley straw, sorghum, rice grass, sugarcane, sugarcane straw, bagasse, switchgrass, corn stover, corn fiber, grains, or any combination thereof. In some additional embodiments of the methods, the fermentable sugars comprise glucose and/or xylose. In some embodiments, the methods further comprise recovering the fermentable sugars. In some embodiments of the methods, the conditions comprise using continuous, batch, and/or fed-batch culturing conditions. In some further embodiments, the method is a batch process, while in some alternative embodiments, the method is a continuous process, and in some still further embodiments, the method is a fed-batch process. In some embodiments, the methods comprise any combination of batch, continuous, and/or fed-batch processes conducted in any order. In still some further embodiments, the methods are conducted in a reaction volume of at least 10,000 liters, while in some other embodiments, the methods are conducted in a reaction volume of at least 100,000 liters. In some embodiments, the methods further comprise use of at least one adjunct composition. In some embodiments, the adjunct composition is selected from at least one divalent metal cation, gallic acid, and/or at least one surfactant. In some embodiments, the divalent metal cation comprises copper and/or gallic acid. In some additional embodiments, the surfactant is selected from TWEEN®-20 non-ionic detergent and polyethylene glycol. In some further embodiments, the methods are conducted at about pH 5.0, while in some alternative embodiments, the methods are conducted at about pH 6.0. In some additional embodiments, the pH is in the range of about 4.5 to about 7. In some embodiments, the methods further comprise contacting the fermentable sugars with a microorganism under conditions such that the microorganism produces at least one fermentation end product. In some embodiments, the fermentation end product is selected from alcohols, fatty acids, lactic acid, acetic acid, 3-hydroxypropionic acid, acrylic acid, succinic acid, citric acid, malic acid, fumaric acid, amino acids, 1,3-propanediol, ethylene, glycerol, fatty alcohols, butadiene, and beta-lactams. In some further embodiments, the fermentation product is an alcohol selected from ethanol and butanol. In some still further embodiments, the alcohol is ethanol.
The present invention also provides methods for increasing production of fermentable sugars from a saccharification reaction comprising combining at least one cellulase substrate, one or more cellulase enzymes, and at least one GH61 protein wherein the protein is at least about 70%, about 75%, about 80%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% identical to SEQ ID NO:2, and an adjunct composition in a saccharification reaction, wherein the adjunct composition comprises Cu++ at a concentration of at least about 4 μM and/or gallic acid at a concentration of at least about 0.5 mM. The present invention also provides methods for increasing production of fermentable sugars from a saccharification reaction comprising combining at least one cellulase substrate, one or more cellulase enzymes, and at least one GH61 protein wherein the protein is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to SEQ ID NO:2, and an adjunct composition in a saccharification reaction, wherein the adjunct composition comprises Cu++ at a concentration of at least about 4 μM and/or gallic acid at a concentration of at least about 0.5 mM. In some embodiments, at least one GH61 protein comprises SEQ ID NO:2, 5, 6, 8, 9, 11, and/or a biologically active fragment thereof. In some embodiments of the methods, the GH61 protein is at least one GH61 protein variant as provided herein. In some embodiments, the methods further comprise use of at least one surfactant selected from TWEEN®-20 non-ionic detergent and polyethylene glycol. In some additional embodiments, the methods are conducted at about pH 5.0, while in some other embodiments, the methods are conducted at about pH 6.0.
The present invention also provides methods of producing at least one end product from at least one cellulosic substrate, comprising: a) providing at least one cellulosic substrate and at least one enzyme composition as provided herein; b) contacting the cellulosic substrate with the enzyme composition under conditions whereby fermentable sugars are produced from the cellulosic substrate in a saccharification reaction; and c) contacting the fermentable sugars with a microorganism under fermentation conditions such that at least one end product is produced. In some embodiments, the method comprises simultaneous saccharification and fermentation reactions (SSF), while in some alternative embodiments of the methods, saccharification of the cellulosic substrate and fermentation are conducted in separate reactions (SHF). In some additional embodiments, the methods comprise production of at least one enzyme simultaneously with hydrolysis and/or fermentation (e.g., “consolidated bioprocessing”; CBP). In some embodiments, the enzyme composition is produced simultaneously with the saccharification and fermentation reactions. In some additional embodiments at least one enzyme of said composition is produced simultaneously with the saccharification and fermentation reactions. In some embodiments, in which at least one enzyme and/or the enzyme composition is produced simultaneously with the saccharification and fermentation reactions, the methods are conducted in a single reaction vessel. In some embodiments, the methods further comprise use of at least one adjunct composition in the saccharification reaction. In some embodiments of the methods, at least one adjunct composition is selected from at least one divalent metal cation, gallic acid, and/or at least one surfactant. In some further embodiments of the methods, the divalent metal cation comprises copper. In some further embodiments of the methods, the adjunct composition comprises gallic acid. In some additional embodiments of the methods, the surfactant is selected from TWEEN®-20 non-ionic detergent and polyethylene glycol. In some embodiments, the method is conducted at about pH 5.0. In some embodiments, the method is conducted at about pH 6.0. In some further embodiments, the method is conducted at a pH in the range of about 4.5 to about 7.0. In some embodiments, the methods further comprise recovering at least one end product. In some embodiments of the methods the end product comprises at least one fermentation end product. In some further embodiments of the methods, the fermentation end product is selected from alcohols, fatty acids, lactic acid, acetic acid, 3-hydroxypropionic acid, acrylic acid, succinic acid, citric acid, malic acid, fumaric acid, an amino acid, 1,3-propanediol, ethylene, glycerol, fatty alcohols, butadiene, and beta-lactams. In some embodiments of the methods, the fermentation end product is at least one alcohol selected from ethanol and butanol. In some embodiments of the methods, the alcohol is ethanol. In some additional embodiments of the methods, the microorganism is a yeast. In some further embodiments, the yeast is Saccharomyces. In some further additional embodiments, the methods further comprise recovering at least one fermentation end product.
The present invention also provides for use of at least one GH61 variant protein provided herein to produce at least one fermentation end product. In some embodiments, at least one GH61 variant protein provided herein is used to produce at least one fermentation end product selected from alcohols, fatty acids, lactic acid, acetic acid, 3-hydroxypropionic acid, acrylic acid, citric acid, malic acid, fumaric acid, succinic acid, amino acids, 1,3-propanediol, ethylene, glycerol, butadiene, fatty alcohols, and beta-lactams. In some embodiments, the fermentation end product is at least one alcohol selected from ethanol and butanol. In some further embodiments, the alcohol is ethanol.
Additional embodiments of the invention are apparent from the present description.



DESCRIPTION OF THE DRAWINGS
FIG. 1 provides results of an experiment using recombinantly produced GH61a protein having the sequence shown in SEQ ID NO:2. The protein was tested for its ability to promote the activity of cellulases present in culture broth of M. thermophila. The graph shows the improvement in the yield of the fermentable sugar glucose that is attained by adding GH61 to the reaction.
FIG. 2 shows specific GH61 activity observed in a reaction where a wheat straw substrate was hydrolyzed by cellulase enzymes CBH1, CBH2, and beta-glucosidase. The results show that GH61a Variants 5 and 9 have a 2.0 to 2.9 fold improvement over the parental GH61 sequence (SEQ ID NO:2); and Variant 1 has a 3.0 to 3.9 fold improvement.
FIG. 3 shows the increase in glucose production in the presence of GH61 protein when Cu++ is included the reaction. In this Figure, n=4; and mean±SD. Panel A shows the increase with a GH61 variant protein “Variant 5,” while Panel B shows the increase with the wild-type GH61a protein (SEQ ID NO:2).
FIG. 4 shows activity of GH61a pre-incubated with 0 or 50 μM CuSO4, copper(II) ion at either saccharification pH 5.0 or pH 6.0. Panel A shows glucose production, while Panel B shows the total production of C5 sugars.
FIG. 5 shows activity of M. thermophila-produced GH61a Variant 1 on cellulosic substrates. Panel A shows the results on AVICEL® PH microcrystalline cellulose, and Panel B shows the results on phosphoric acid swollen cellulose (PASC), in the presence of ascorbic acid, gallic acid and pretreatment filtrate.
FIG. 6 provides results showing the effects of surfactants on saccharification. Panel A shows enzymatic hydrolysis activity of a cellulase mixture in the presence of TWEEN®-20, while Panel B shows the enzymatic hydrolysis activity of a cellulase mixture in the presence of PEG-4000.



DETAILED DESCRIPTION OF THE INVENTION
As described herein, the present invention provides GH61 proteins of the filamentous fungus Myceliophthora thermophila that have been genetically modified. These GH61 protein variants exhibit improved activity and other benefits, as compared to wild-type GH61 proteins.
Before modification, the GH61 protein having the sequence shown in SEQ ID NO:2 improves the yield of fermentable sugars produced from a cellulosic substrate through the activity of cellulase enzymes (e.g., endoglucanase, beta-glucosidase (BGL), cellobiohydrolase, and combinations of such enzymes; See, FIG. 1). The GH61 variant proteins of this invention have certain amino acid substitutions in relation to SEQ ID NO:2, either alone or in various combinations. GH61 variant proteins that have gone through one round of optimization, when included in a saccharification assay, improve the yield of fermentable sugars in such reactions by at least about 2-fold, about 3-fold, or more, in relation to the improvement in yield when wild-type GH61a (SEQ ID NO:2) is used instead. (See, FIG. 2). After multiple rounds of optimization, the GH61 activity can be improved by a further 1.5-fold, 2-fold, 3-fold or more.
The GH61 variant proteins of the present invention have important industrial applicability in the processing of cellulosic biomass to produce fermentable sugars, which in turn can be fermented or processed to produce commercially important fermentation products (e.g., “fermentation end-products” or “end-products”), including but not limited to, at least one alcohol, fatty acid, lactic acid, acetic acid, 3-hydroxypropionic acid, acrylic acid, succinic acid, citric acid, malic acid, fumaric acid, amino acid, 1,3-propanediol, ethylene, glycerol, fatty alcohol, butadiene, and/or beta-lactam. In further embodiments, the alcohol is ethanol, butanol, and/or a fatty alcohol. In some embodiments, the fermentation product is ethanol. In some still further embodiments, the fermentation product is a fatty alcohol that is a C8-C20 fatty alcohol. In some embodiments, the fermentation medium comprises at least one product from a saccharification process.
GH61 proteins, their production and use are generally described in PCT/US11/488,700. This application claims priority to U.S. Ser. No. 61/375,788, both of which are incorporated herein by reference in their entirety. Proteins, procedures, and uses described in these applications find use with the GH61 variant proteins of the present invention.
Definitions
All patents and publications, including all sequences disclosed within such patents and publications, referred to herein are expressly incorporated by reference. Unless otherwise indicated, the practice of the present invention involves conventional techniques commonly used in molecular biology, fermentation, microbiology, and related fields, which are known to those of skill in the art. Unless defined otherwise herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are described. Indeed, it is intended that the present invention not be limited to the particular methodology, protocols, and reagents described herein, as these may vary, depending upon the context in which they are used. The headings provided herein are not limitations of the various aspects or embodiments of the present invention.
Nonetheless, in order to facilitate understanding of the present invention, a number of terms are defined below. Numeric ranges are inclusive of the numbers defining the range. Thus, every numerical range disclosed herein is intended to encompass every narrower numerical range that falls within such broader numerical range, as if such narrower numerical ranges were all expressly written herein. It is also intended that every maximum (or minimum) numerical limitation disclosed herein includes every lower (or higher) numerical limitation, as if such lower (or higher) numerical limitations were expressly written herein.
As used herein, the term “comprising” and its cognates are used in their inclusive sense (i.e., equivalent to the term “including” and its corresponding cognates).
As used herein and in the appended claims, the singular “a”, “an” and “the” include the plural reference unless the context clearly dictates otherwise. Thus, for example, reference to a “host cell” includes a plurality of such host cells.
Unless otherwise indicated, nucleic acids are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively. The headings provided herein are not limitations of the various aspects or embodiments of the invention that can be had by reference to the specification as a whole. Accordingly, the terms defined below are more fully defined by reference to the specification as a whole.
As used herein, the term “produces” refers to the production of proteins (polypeptides) and/or other compounds by cells. It is intended that the term encompass any step involved in the production of polypeptides including, but not limited to, transcription, post-transcriptional modification, translation, and post-translational modification. In some embodiments, the term also encompasses secretion of the polypeptide from a cell.
As used in this disclosure, the term “GH61 protein” means a protein that has GH61 activity, including GH61 variants and wild-type GH61 enzymes. In some embodiments, the GH61 proteins have been purified from M. thermophila cells, while in other embodiments, they are structurally related to the amino acid sequences shown in Tables 1 and 2. The terms also encompasses species and strain homologs and orthologs comprising protein sequences listed in Tables 1 and 2, as well as variants, and fragments of such sequences (produced using any suitable means known in the art), having GH61 activity.
As used herein, the terms “variant,” “GH61 variant,” refer to a GH61 polypeptide or polynucleotide encoding a GH61 polypeptide comprising one or more modifications relative to wild-type GH61 or the wild-type polynucleotide encoding GH61 (such as substitutions, insertions, deletions, and/or truncations of one or more amino acid residues or of one or more specific nucleotides or codons in the polypeptide or polynucleotide, respectively), and biologically active fragments thereof. In some embodiments, the variant is derived from a M. thermophila polypeptide and comprises one or more modifications relative to wild-type M. thermophila GH61 or the wild-type polynucleotide encoding wild-type M. thermophila GH61, or a biologically active fragment thereof. In some embodiments, a “GH61 variant protein” (“GH61 variant polypeptide”) of the present invention is a protein that is structurally related to a reference protein comprising SEQ ID NO:2 or a fragment of SEQ ID NO:2 that has GH61 activity, but has one or more amino acid substitutions in relation to the reference protein. In some embodiments, the GH61 variant is a GH61a variant (i.e., a variant of GH61a enzyme). In some embodiments, the GH61 variant polypeptide is a “polypeptide of interest.” In some additional embodiments, the GH61 variant polypeptide is encoded by a “polynucleotide of interest.”
The terms “improved” or “improved properties,” as used in the context of describing the properties of a GH61 variant, refers to a GH61 variant polypeptide that exhibits an improvement in a property or properties as compared to the wild-type GH61 (e.g., SEQ ID NO:2) or a specified reference polypeptide. Improved properties may include, but are not limited to increased protein expression, increased thermoactivity, increased thermostability, increased pH activity, increased stability (e.g., increased pH stability or pH tolerance at various pH levels), increased product specificity, increased specific activity, increased substrate specificity, increased resistance to substrate or end-product inhibition, increased chemical stability, reduced inhibition by glucose, increased resistance to inhibitors (e.g., acetic acid, lectins, tannic acids, and phenolic compounds), and altered pH/temperature profile.
The term “biologically active fragment,” as used herein, refers to a polypeptide that has an amino-terminal and/or carboxy-terminal deletion and/or internal deletion, but where the remaining amino acid sequence is identical to the corresponding positions in the sequence to which it is being compared (e.g., a full-length GH61 variant of the invention) and that retains substantially all of the activity of the full-length polypeptide. A biologically active fragment can comprise about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, at about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% of a full-length GH61 polypeptide.
A GH61 variant protein of this invention having “increased GH61 activity” has more GH61 activity when that protein is present in a saccharification reaction with a specified substrate and specified cellulase enzyme(s), compared with a saccharification reaction conducted with the same substrate and enzyme(s) under the same conditions in the presence of a reference protein (e.g., including but not limited to wild-type GH61). The increase is determined by measuring the amount of fermentable sugar produced in the reaction in the presence of the GH61 variant protein, in the presence of the reference protein (Positive Control), and in the absence of either protein (Negative Control). The Improvement Over Positive Control (FIOPC) is calculated as ([Glucose production of the GH61 Variant Protein]−[Glucose production of the Negative Control])/([Glucose production of the Positive Control]−[Glucose production of the Negative Control]).
As used herein, “GH61 activity” is the functional activity of a GH61 protein that results in production of more fermentable sugar from a polysaccharide substrate when the GH61 protein is present in a saccharification reaction, compared with a saccharification reaction conducted under the same conditions in the absence of the GH61 protein.
A GH61 variant protein of this invention having “increased GH61 thermoactivity” has more GH61 activity in a saccharification reaction conducted at an elevated temperature (about 50° C., about 55° C., about 60° C., or higher) with a specified substrate and specified cellulase enzyme(s), compared with a saccharification reaction conducted under the same conditions in the presence of the reference protein (e.g., including but not limited to wild-type GH61).
GH61 proteins of this invention may be said to “enhance”, “promote”, or “facilitate” activity of one or more cellulase enzymes during hydrolysis of sugar polymers (e.g., cellulosic and/or lignocellulosic biomass) such that the enzyme(s) produce(s) more product over a particular time period, hydrolysis proceeds more rapidly, or goes further to completion when the GH61 protein is present, compared with a similar reaction mixture in which the GH61 protein is absent. This invention may be practiced by following GH61 activity in an empirical fashion using assay methods provided in this disclosure, without knowing the mechanism of operation of the GH61 variant protein being used. However, it is not intended that the present invention be limited to any particular assay system and/or method, as any suitable method known in the art finds use.
The terms “transform” or “transformation,” as used in reference to a cell, mean a cell has a non-native nucleic acid sequence integrated into its genome and/or as an episome (e.g., plasmid) that is maintained through multiple generations.
The term “introduced,” as used in the context of inserting a nucleic acid sequence into a cell, means that the nucleic acid has been conjugated, transfected, transduced or transformed (collectively “transformed”) or otherwise incorporated into the genome of and/or maintained as an episome in the cell. Thus, the term encompasses transformation, transduction, conjugation, transfection, and/or any other suitable method(s) known in the art for inserting nucleic acid sequences into host cells. Any suitable means for the introduction of nucleic acid into host cells find use in the present invention.
The terms “percent identity,” “% identity”, “percent identical”, and “% identical” are used interchangeably to refer to a comparison of two optimally aligned sequences over a comparison window. The comparison window may include additions or deletions in either sequence to optimize alignment. The percentage of identity is the number of positions that are identical between the sequences, divided by the total number of positions in the comparison window (including positions where one of the sequences has a gap). For example, a protein with an amino acid sequence that matches at 310 positions a sequence of GH61a (which has 323 amino acids in the secreted form), would have 310/323=95.9% identity to the reference. Similarly, a protein variant that has 300 residues (i.e., less than full-length) and matches the reference sequence at 280 positions would have 280/300=93.3% identity. Computer-implemented alignment algorithms useful in determining the degree of identity are known in the art, including the BLAST and BLAST 2.0 algorithms (See e.g., Altschul at al., J. Mol. Biol., 215: 403-410 [1990]; and Altschul et al., Nucl. Acids Res., 3389-3402 [1977]).
As used herein, “polynucleotide” refers to a polymer of deoxyribonucleotides or ribonucleotides in either single- or double-stranded form, and complements thereof.
As used herein, the term “allelic variant” refers to any of two or more (e.g., several) alternative forms of a gene occupying the same chromosomal locus. In some embodiments, allelic variation arises naturally through mutation and results in genetic polymorphism within populations. In some embodiments, gene mutations are silent (i.e., there is no change in the encoded polypeptide), while in some other embodiments the genes encode polypeptides that have altered amino acid sequences. An “allelic variant of a polypeptide” is a polypeptide encoded by an allelic variant of a gene.
As used herein, “cDNA” refers to a DNA molecule that can be prepared by reverse transcription from a mature, spliced, mRNA molecule obtained from a eukaryotic or prokaryotic cell. cDNA sequences lack intron sequences that may be present in the corresponding genomic DNA. The initial, primary RNA transcript is a precursor to mRNA that is processed through a series of steps, including splicing, before appearing as mature spliced mRNA.
As used herein, the term “coding sequence” refers to a polynucleotide that directly specifies the amino acid sequence of a polypeptide. The boundaries of the coding sequence are generally determined by an open reading frame, which begins with a start codon (e.g., ATG, GTG, or TTG) and ends with a stop codon (e.g., TAA, TAG, or TGA). In some embodiments, a coding sequence comprises genomic DNA, while in some alternative embodiments, the coding sequence comprises cDNA, synthetic DNA, and/or a combination thereof.
As used herein, the terms “control sequences” and “regulatory sequences” refer to nucleic acid sequences necessary and/or useful for expression of a polynucleotide encoding a polypeptide. In some embodiments, control sequences are native (i.e., from the same gene) or foreign (i.e., from a different gene) to the polynucleotide encoding the polypeptide. Control sequences include, but are not limited to leaders, polyadenylation sequences, propeptide sequences, promoters, signal peptide sequences, and transcription terminators. In some embodiments, at a minimum, control sequences include a promoter, and transcriptional and translational stop signals. In some embodiments, control sequences are provided with linkers for the purpose of introducing specific restriction sites facilitating ligation of the control sequences with the coding region of the polynucleotide encoding the polypeptide.
A nucleic acid construct, nucleic acid (e.g., a polynucleotide), polypeptide, or host cell is referred to herein as “recombinant” when it is non-naturally occurring, artificial or engineered. The present invention also provides recombinant nucleic acid constructs comprising at least one GH61 variant polynucleotide sequence that hybridizes under stringent hybridization conditions to the complement of a polynucleotide which encodes a polypeptide comprising the amino acid sequence of any of SEQ ID NOS:2, 3, 5, 6, 8, 9, 11, and/or 12.
The term “recombinant nucleic acid” has its conventional meaning. A recombinant nucleic acid, or equivalently, “polynucleotide,” is one that is inserted into a heterologous location such that it is not associated with nucleotide sequences that normally flank the nucleic acid as it is found in nature (for example, a nucleic acid inserted into a vector or a genome of a heterologous organism). Likewise, a nucleic acid sequence that does not appear in nature, for example a variant of a naturally occurring gene, is recombinant. A cell containing a recombinant nucleic acid, or protein expressed in vitro or in vivo from a recombinant nucleic acid are also “recombinant.” Examples of recombinant nucleic acids include a protein-encoding DNA sequence that is (i) operably linked to a heterologous promoter and/or (ii) encodes a fusion polypeptide with a protein sequence and a heterologous signal peptide sequence.
For purposes of this disclosure, a promoter is “heterologous” to a gene sequence if the promoter is not associated in nature with the gene. A signal peptide is “heterologous” to a protein sequence when the signal peptide sequence is not associated with the protein in nature. In some embodiments, “hybrid promoters” find use. Hybrid promoters are promoters comprising portions of two or more (e.g., several) promoters that are linked together to generate a sequence that is a fusion of the portions of the two or more promoters, which when operably linked to a coding sequence, mediates the transcription of the coding sequence into mRNA.
In relation to regulatory sequences (e.g., promoters), the term “operably linked” refers to a configuration in which a regulatory sequence is located at a position relative to a polypeptide encoding sequence such that the regulatory sequence influences the expression of the polypeptide. In relation to a signal sequence, the term “operably linked” refers to a configuration in which the signal sequence encodes an amino-terminal signal peptide fused to the polypeptide, such that expression of the gene produces a pre-protein.
Nucleic acids “hybridize” when they associate, typically in solution. Nucleic acids hybridize due to a variety of well-characterized physico-chemical forces, such as hydrogen bonding, solvent exclusion, base stacking and the like. As used herein, the term “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments, such as Southern and Northern hybridizations, are sequence dependent, and are different under different environmental parameters. An extensive guide to the hybridization of nucleic acids is found in Tijssen, 1993, “Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes,” Part I, Chapter 2 (Elsevier, New York), which is incorporated herein by reference. For polynucleotides of at least 100 nucleotides in length, low to very high stringency conditions are defined as follows: prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 μg/ml sheared and denatured salmon sperm DNA, and either 25% formamide for low stringencies, 35% formamide for medium and medium-high stringencies, or 50% formamide for high and very high stringencies, following standard Southern blotting procedures. For polynucleotides of at least 100 nucleotides in length, the carrier material is finally washed three times each for 15 minutes using 2×SSC, 0.2% SDS 50° C. (low stringency), at 55° C. (medium stringency), at 60° C. (medium-high stringency), at 65° C. (high stringency), or at 70° C. (very high stringency).
As used herein, a “vector” and “nucleic acid construct” comprise nucleic acid (e.g., DNA) constructs for introducing a DNA sequence into a cell. In some embodiments, the vector is an expression vector that is operably linked to a suitable control sequence capable of effecting the expression in a suitable host of the polypeptide encoded in the DNA sequence. The term “expression vector” refers to a DNA molecule, linear or circular, that comprises a segment encoding a polypeptide of the invention, and which is operably linked to additional segments that provide for its transcription (e.g., a promoter, a transcription terminator sequence, enhancers, etc.) and optionally a selectable marker.
As used herein, the term “isolated” refers to a nucleic acid, polypeptide, or other component that is partially or completely separated from components with which it is normally associated in nature. Thus, the term encompasses a substance in a form or environment that does not occur in nature. Non-limiting examples of isolated substances include, but are not limited to: any non-naturally occurring substance; any substance including, but not limited to, any enzyme, variant, polynucleotide, protein, peptide or cofactor, that is at least partially removed from one or more or all of the naturally occurring constituents with which it is associated in nature; any substance modified by the hand of man relative to that substance found in nature; and/or any substance modified by increasing the amount of the substance relative to other components with which it is naturally associated (e.g., multiple copies of a gene encoding the substance; and/or use of a stronger promoter than the promoter naturally associated with the gene encoding the substance). In some embodiments, a polypeptide of interest is used in industrial applications in the form of a fermentation broth product (i.e., the polypeptide is a component of a fermentation broth) used as a product in industrial applications such as ethanol production. In some embodiments, in addition to the polypeptide of interest (e.g., a GH61 variant polypeptide), the fermentation broth product further comprises ingredients used in the fermentation process (e.g., cells, including the host cells containing the gene encoding the polypeptide of interest and/or the polypeptide of interest), cell debris, biomass, fermentation media, and/or fermentation products. In some embodiments, the fermentation broth is optionally subjected to one or more purification steps (e.g., filtration) to remove or reduce at least one components of a fermentation process. Accordingly, in some embodiments, an isolated substance is present in such a fermentation broth product.
As used herein, the terms “peptide,” “polypeptide,” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues.
As used herein, the term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified (e.g., hydroxyproline, γ-carboxyglutamate, and O-phosphoserine). Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, (i.e., an α-carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, such as homoserine, norleucine, methionine sulfoxide, and methionine methyl sulfonium). Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid.
An “amino acid substitution” in a protein sequence is replacement of a single amino acid within that sequence with another amino acid. Unless indicated otherwise, variant GH61 proteins of this invention have substitutions as specifically indicated. In some embodiments, the variant GH61 proteins of the present invention also have other substitutions and/or alterations at any position in any combination with the substitutions specifically indicated.
Amino acids are referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
An amino acid or nucleotide base “position” is denoted by a number that sequentially identifies each amino acid (or nucleotide base) in the reference sequence based on its position relative to the N-terminus (or 5′-end). Due to deletions, insertions, truncations, fusions, and the like that must be taken into account when determining an optimal alignment, the amino acid residue number in a test sequence determined by simply counting from the N-terminus will not necessarily be the same as the number of its corresponding position in the reference sequence. For example, in a case where a test sequence has a deletion relative to an aligned reference sequence, there will be no amino acid in the variant that corresponds to a position in the reference sequence at the site of deletion. Where there is an insertion in an aligned reference sequence, that insertion will not correspond to a numbered amino acid position in the reference sequence. In the case of truncations or fusions there can be stretches of amino acids in either the reference or aligned sequence that do not correspond to any amino acid in the corresponding sequence.
As used herein, the terms “numbered with reference to” or “corresponding to,” when used in the context of the numbering of a given amino acid or polynucleotide sequence, refers to the numbering of the residues of a specified reference sequence when the given amino acid or polynucleotide sequence is compared to the reference sequence.
As used herein, the term “reference enzyme” refers to an enzyme to which another enzyme of the present invention (e.g., a “test” enzyme) is compared in order to determine the presence of an improved property in the other enzyme being evaluated. In some embodiments, a reference enzyme is a wild-type enzyme (e.g., wild-type GH61). In some embodiments, the reference enzyme is an enzyme with which a test enzyme of the present invention is compared in order to determine the presence of an improved property in the test enzyme being evaluated, including but not limited to improved thermoactivity, improved thermostability, improved activity, and/or improved stability. In some embodiments, a reference enzyme is a wild-type enzyme (e.g., wild-type GH61).
Amino acid substitutions in a GH61 protein are referred to in this disclosure using the following notation: The single-letter abbreviation for the amino acid being substituted; its position in the reference sequence (e.g., the wild-type “parental sequence” set forth in SEQ ID NO:2); and the single-letter abbreviation for the amino acid that replaces it. Thus, the following nomenclature is used herein to describe substitutions in a reference sequence relative to a reference sequence or a variant polypeptide or nucleic acid sequence: “R-#-V,” where # refers to the position in the reference sequence, R refers to the amino acid (or base) at that position in the reference sequence, and V refers to the amino acid (or base) at that position in the variant sequence. In some embodiments, an amino acid (or base) may be called “X,” by which is meant any amino acid (or base). As a non-limiting example, for a variant polypeptide described with reference to a wild-type GH61 polypeptide (e.g., SEQ ID NO:2), “N35G” indicates that in the variant polypeptide, the asparagine at position 35 of the reference sequence is replaced by glycine, with amino acid position being determined by optimal alignment of the variant sequence with SEQ ID NO:2. Similarly, “H20C/D” describes two variants: a variant in which the histidine at position 20 of the reference sequence is replaced by cysteine and a variant in which the serine at position 20 of the reference sequence is replaced by aspartic acid. In the example “W141X” indicates that the tryptophan at position 131 has been replaced with any amino acid.
As used herein in reference to nucleotide and amino acid sequences, the term “mutation” refers to any change in the sequence, as compared to a reference nucleotide or amino acid sequence, including but not limited to substitutions, deletions, additions, truncations, modifications, etc. Indeed, it is intended that any change in a reference (or “parent” or “starting”) nucleotide or amino acid sequence comprises a mutation in the sequence.
As used herein, the terms “amino acid mutation set”, “mutation set” when used in the context of amino acid sequences (e.g., polypeptides) refer to a group of amino acid substitutions, insertions, deletions and/or other modifications to the sequence. In some embodiments, “mutation set” refers to the nucleic acid mutation sets present in some of the GH61 variants provided in Table 1 and Table 2.
The term “amino acid substitution set,” “substitution set,” and “combination of amino acid substitutions” refer to a group (i.e., set of combinations) of amino acid substitutions. A substitution set can have about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more amino acid substitutions. In some embodiments, a substitution set refers to the set of amino acid substitutions that is present in any of the variant GH61 enzymes provided herein.
As used herein, the terms “nucleic acid substitution set” and “substitution set” when used in the context of nucleotide sequences (e.g., polynucleotides) refer to a group of nucleic acid substitutions. In some embodiments, mutation set refers to the nucleic acid substitution sets present in some of the variant GH61 proteins provided in Table 1 and Table 2.
As used herein, the terms “nucleic acid mutation set” and “mutation set” when used in the context of nucleotide sequences (e.g., polynucleotides) refer to a group of nucleic acid substitutions, insertions, deletions, and/or other modifications to the sequence. In some embodiments, “mutation set” refers to the amino acid mutation sets present in some of the GH61 variants provided in Table 1 and Table 2.
A “cellulase-engineered” cell is a cell comprising at least one, at least two, at least three, or at least four recombinant sequences encoding a cellulase or cellulase variant, and in which expression of the cellulase(s) or cellulase variant(s) has been modified relative to the wild-type form. Expression of a cellulase is “modified” when a non-naturally occurring cellulase variant is expressed or when a naturally occurring cellulase is over-expressed. One exemplary means to over-express a cellulase is to operably link a strong (optionally constitutive) promoter to the cellulase encoding sequence. Another exemplary way to over-express a cellulase is to increase the copy number of a heterologous, variant, or endogenous cellulase gene. The cellulase-engineered cell may be any suitable fungal cell, including, but not limited to Myceliophthora, Trichoderma, Aspergillus, cells, etc.
As used herein, the terms “host cell” and “host strain” refer to suitable hosts for expression vectors comprising DNA provided herein. In some embodiments, the host cells are prokaryotic or eukaryotic cells that have been transformed or transfected with vectors constructed using recombinant DNA techniques as known in the art. Transformed hosts are capable of either replicating vectors encoding at least one protein of interest and/or expressing the desired protein of interest. In addition, reference to a cell of a particular strain refers to a parental cell of the strain as well as progeny and genetically modified derivatives. Genetically modified derivatives of a parental cell include progeny cells that contain a modified genome or episomal plasmids that confer for example, antibiotic resistance, improved fermentation, etc. In some embodiments, host cells are genetically modified to have characteristics that improve protein secretion, protein stability or other properties desirable for expression and/or secretion of a protein. For example, knockout of Alp1 function results in a cell that is protease deficient. Knockout of pyr5 function results in a cell with a pyrimidine deficient phenotype. In some embodiments, host cells are modified to delete endogenous cellulase protein-encoding sequences or otherwise eliminate expression of one or more endogenous cellulases. In some embodiments, expression of one or more endogenous cellulases is inhibited to increase production of cellulases of interest. Genetic modification can be achieved by any suitable genetic engineering techniques and/or classical microbiological techniques (e.g., chemical or UV mutagenesis and subsequent selection). Using recombinant technology, nucleic acid molecules can be introduced, deleted, inhibited or modified, in a manner that results in increased yields of GH61 variant(s) within the organism or in the culture. For example, knockout of Alp1 function results in a cell that is protease deficient. Knockout of pyr5 function results in a cell with a pyrimidine deficient phenotype. In some genetic engineering approaches, homologous recombination is used to induce targeted gene modifications by specifically targeting a gene in vivo to suppress expression of the encoded protein. In an alternative approach, siRNA, antisense, and/or ribozyme technology finds use in inhibiting gene expression.
As used herein, the term “C1” refers to strains of Myceliophthora thermophila, including the fungal strain described by Garg (See, Garg, Mycopathol., 30: 3-4 [1966]). As used herein, “Chrysosporium lucknowense” includes the strains described in U.S. Pat. Nos. 6,015,707, 5,811,381 and 6,573,086; US Pat. Pub. Nos. 2007/0238155, US 2008/0194005, US 2009/0099079; International Pat. Pub. Nos., WO 2008/073914 and WO 98/15633, all of which are incorporated herein by reference, and include, without limitation, Chrysosporium lucknowense Garg 27K, VKM-F 3500 D (Accession No. VKM F-3500-D), C1 strain UV 13-6 (Accession No. VKM F-3632 D), C1 strain NG7C-19 (Accession No. VKM F-3633 D), and C1 strain UV18-25 (VKM F-3631 D), all of which have been deposited at the All-Russian Collection of Microorganisms of Russian Academy of Sciences (VKM), Bakhurhina St. 8, Moscow, Russia, 113184, and any derivatives thereof. Although initially described as Chrysosporium lucknowense, C1 may currently be considered a strain of Myceliophthora thermophila. Other C1 strains include cells deposited under accession numbers ATCC 44006, CBS (Centraalbureau voor Schimmelcultures) 122188, CBS 251.72, CBS 143.77, CBS 272.77, CBS122190, CBS122189, and VKM F-3500D. Exemplary C1 derivatives include but are not limited to modified organisms in which one or more endogenous genes or sequences have been deleted or modified and/or one or more heterologous genes or sequences have been introduced. Derivatives include, but are not limited to UV18#100f Δalp1, UV18#100f Δpyr5 Δalp1, UV18#100.f Δalp1 Δpep4 Δalp2, UV18#100.f Δpyr5 Δalp1 Δpep4 Δalp2 and UV18#1001Δpyr4 Δpyr5 ΔaIp1 Δpep4 Δalp2, as described in WO2008073914 and WO2010107303, each of which is incorporated herein by reference.
As used herein, the term “culturing” refers to growing a population of microbial cells under suitable conditions in a liquid, semi-solid, or solid medium.
In general, “saccharification” refers to the process in which substrates (e.g., cellulosic biomass and/or lignocellulosic biomass) are broken down via the action of cellulases to produce fermentable sugars (e.g. monosaccharides, including but not limited to glucose and/or xylose). In particular, “saccharification” is an enzyme-catalyzed reaction that results in hydrolysis of a complex carbohydrate to produce shorter-chain carbohydrate polymers and/or fermentable sugar(s) that are more suitable for fermentation or further hydrolysis. In some embodiments, the enzymes comprise cellulase enzyme(s) such as endoglucanases, beta-glucosidases, cellobiohydrolases (e.g., CBH1 and/or CBH1), a synthetic mixture of any of such enzymes, and/or cellulase enzymes contained in culture broth from an organism that produces cellulase enzymes, such as M. thermophila or recombinant yeast cells. Products of saccharification may include disaccharides, and/or monosaccharides such as glucose or xylose.
In some embodiments, the fermentable sugars produced by the methods of the present invention are used to produce an alcohol (e.g., including but not limited to ethanol, butanol, etc.). The variant GH61 proteins of the present invention find use in any suitable method to generate alcohols and/or other biofuels from cellulose and/or lignocellulose, and are not limited necessarily to those described herein. Two methods commonly employed are the separate saccharification and fermentation (SHF) method (See, Wilke et al., Biotechnol. Bioengin. 6:155-75 [1976]) or the simultaneous saccharification and fermentation (SSF) method (See e.g., U.S. Pat. Nos. 3,990,944 and 3,990,945). An additional method that finds use with the present invention is consolidated bioprocessing (CBP), which encompasses the combination of the biological steps used in the conversion of lignocellulosic biomass to bioethanol (e.g., production of cellulase(s), hydrolysis of the polysaccharides in the biomass, and fermentation of hexose and pentose sugars) in one reactor (See e.g., Vertes et al., Biomass to Biofuels: Strategies for Global Industries, John Wiley & Sons, Ltd., [2010], Hoboken, N.J., pp. 324-325).
The SHF method of saccharification comprises the steps of contacting cellulase with a cellulose-containing substrate to enzymatically break down cellulose into fermentable sugars (e.g., monosaccharides such as glucose), contacting the fermentable sugars with an alcohol-producing microorganism to produce alcohol (e.g., ethanol or butanol) and recovering the alcohol. In some embodiments, the method of consolidated bioprocessing (CBP) can be used, in which the cellulase production from the host is simultaneous with saccharification and fermentation either from one host or from a mixed cultivation.
In addition to SHF methods, a SSF method may be used. In some cases, SSF methods result in a higher efficiency of alcohol production than is afforded by the SHF method (See e.g., Drissen et al., Biocat. Biotransform., 27:27-35 [2009]). One disadvantage of SSF over SHF is that higher temperatures are required for SSF than for SHF. In some embodiments, the present invention provides GH61 polypeptides that have higher thermostability than a wild-type GH61s. Thus, it is contemplated that the present invention will find use in increasing ethanol production in SSF, as well as SHF methods.
As used herein “fermentable sugars” refers to fermentable sugars (e.g., monosaccharides, disaccharides and short oligosaccharides), including but not limited to glucose, xylose, galactose, arabinose, mannose and sucrose. In general, the term “fermentable sugar” refers to any sugar that a microorganism can utilize or ferment.
As used herein, the terms “adjunct material,” “adjunct composition,” and “adjunct compound” refer to any composition suitable for use in the compositions and/or saccharification reactions provided herein, including but not limited to cofactors, surfactants, builders, buffers, enzyme stabilizing systems, chelants, dispersants, colorants, preservatives, antioxidants, solubilizing agents, carriers, processing aids, pH control agents, etc. In some embodiments, divalent metal cations are used to supplement saccharification reactions and/or the growth of host cells producing GH61 variant proteins. Any suitable divalent metal cation finds use in the present invention, including but not limited to Cu++, Mn++, Co++, Mg++, Ni++, Zn++, and Ca++. In addition, any suitable combination of divalent metal cations finds use in the present invention. Furthermore, divalent metal cations find use from any suitable source.
In some embodiments, the host cells producing GH61 variant proteins of the present invention are grown under culture conditions comprising about pH 5, while in some other embodiments, the host cells are grown at about pH 6.7. In some embodiments, the host cells cultured at pH 5 provide improved saccharification in the presence of supplemented copper, when saccharification is conducted at about pH 5 or about pH 6.7. In some alternative embodiments, the host cells cultured at about pH 6.7 provide improved saccharification in the absence of supplemented copper when saccharification is conducted at about pH 5 or about pH 6.
As used herein, the terms “biomass,” “biomass substrate,” “cellulosic biomass,” “cellulosic feedstock,” and “cellulosic substrate” refer to any materials that contain cellulose. Biomass can be derived from plants, animals, or microorganisms, and may include, but is not limited to agricultural, industrial, and forestry residues, industrial and municipal wastes, and terrestrial and aquatic crops grown for energy purposes. Examples of cellulosic substrates include, but are not limited to, wood, wood pulp, paper pulp, corn fiber, corn grain, corn cobs, crop residues such as corn husks, corn stover, grasses, wheat, wheat straw, barley, barley straw, hay, rice, rice straw, switchgrass, waste paper, paper and pulp processing waste, woody or herbaceous plants, fruit or vegetable pulp, corn cobs, distillers grain, grasses, rice hulls, cotton, hemp, flax, sisal, sugar cane bagasse, sorghum, soy, switchgrass, components obtained from milling of grains, trees, branches, roots, leaves, wood chips, sawdust, shrubs and bushes, vegetables, fruits, and flowers and any suitable mixtures thereof. In some embodiments, the cellulosic biomass comprises, but is not limited to cultivated crops (e.g., grasses, including C4 grasses, such as switch grass, cord grass, rye grass, miscanthus, reed canary grass, or any combination thereof), sugar processing residues, for example, but not limited to, bagasse (e.g., sugar cane bagasse, beet pulp [e.g., sugar beet], or a combination thereof), agricultural residues (e.g. soybean stover, corn stover, corn fiber, rice straw, sugar cane straw, rice, rice hulls, barley straw, corn cobs, wheat straw, canola straw, oat straw, oat hulls, corn fiber, hemp, flax, sisal, cotton, or any combination thereof), fruit pulp, vegetable pulp, distillers' grains, forestry biomass (e.g., wood, wood pulp, paper pulp, recycled wood pulp fiber, sawdust, hardwood, such as aspen wood, softwood, or a combination thereof). Furthermore, in some embodiments, the cellulosic biomass comprises cellulosic waste material and/or forestry waste materials, including but not limited to, paper and pulp processing waste, newsprint, cardboard and the like. In some embodiments, the cellulosic biomass comprises one species of fiber, while in some alternative embodiments, the cellulosic biomass comprises a mixture of fibers that originate from different cellulosic biomasses. In some embodiments, the biomass may also comprise transgenic plants that express ligninase and/or cellulase enzymes (US 2008/0104724 A1).
The terms “lignocellulosic biomass” and “lignocellulosic feedstock” refer to plant biomass that is composed of cellulose and hemicellulose, bound to lignin. The biomass may optionally be pretreated to increase the susceptibility of cellulose to hydrolysis by chemical, physical and biological pretreatments (such as steam explosion, pulping, grinding, acid hydrolysis, solvent exposure, and the like, as well as combinations thereof). Various lignocellulosic feedstocks find use, including those that comprise fresh lignocellulosic feedstock, partially dried lignocellulosic feedstock, fully dried lignocellulosic feedstock, and/or any combination thereof. In some embodiments, lignocellulosic feedstocks comprise cellulose in an amount greater than about 20%, more preferably greater than about 30%, more preferably greater than about 40% (w/w). For example, in some embodiments, the lignocellulosic material comprises from about 20% to about 90% (w/w) cellulose, or any amount therebetween, although in some embodiments, the lignocellulosic material comprises less than about 19%, less than about 18%, less than about 17%, less than about 16%, less than about 15%, less than about 14%, less than about 13%, less than about 12%, less than about 11%, less than about 10%, less than about 9%, less than about 8%, less than about 7%, less than about 6%, or less than about 5% cellulose (w/w).
Furthermore, in some embodiments, the lignocellulosic feedstock comprises lignin in an amount greater than about 10%, more typically in an amount greater than about 15% (w/w). In some embodiments, the lignocellulosic feedstock comprises small amounts of sucrose, fructose and/or starch. The lignocellulosic feedstock is generally first subjected to size reduction by methods including, but not limited to, milling, grinding, agitation, shredding, compression/expansion, or other types of mechanical action. Size reduction by mechanical action can be performed by any type of equipment adapted for the purpose, for example, but not limited to, hammer mills, tub-grinders, roll presses, refiners and hydrapulpers. In some embodiments, at least 90% by weight of the particles produced from the size reduction have lengths less than between about 1/16 and about 4 in (the measurement may be a volume or a weight average length). In some embodiments, the equipment used to reduce the particle size reduction is a hammer mill or shredder. Subsequent to size reduction, the feedstock is typically slurried in water, as this facilitates pumping of the feedstock. In some embodiments, lignocellulosic feedstocks of particle size less than about 6 inches do not require size reduction.
As used herein, the term “pretreated lignocellulosic feedstock,” refers to lignocellulosic feedstocks that have been subjected to physical and/or chemical processes to make the fiber more accessible and/or receptive to the actions of cellulolytic enzymes, as described above.
A cellulosic substrate or lignocellulosic substrate is said to be “pretreated” when it has been processed by some physical and/or chemical means to facilitate saccharification. As described further herein, in some embodiments, the biomass substrate is “pretreated,” or treated using methods known in the art, such as chemical pretreatment (e.g., ammonia pretreatment, dilute acid pretreatment, dilute alkali pretreatment, or solvent exposure), physical pretreatment (e.g., steam explosion or irradiation), mechanical pretreatment (e.g., grinding or milling) and biological pretreatment (e.g., application of lignin-solubilizing microorganisms) and combinations thereof, to increase the susceptibility of cellulose to hydrolysis. Thus, the term “cellulosic biomass” encompasses any living or dead biological material that contains a polysaccharide substrate, including but not limited to cellulose, starch, other forms of long-chain carbohydrate polymers, and mixtures of such sources. It may or may not be assembled entirely or primarily from glucose or xylose, and may optionally also contain various other pentose or hexose monomers. Xylose is an aldopentose containing five carbon atoms and an aldehyde group. It is the precursor to hemicellulose, and is often a main constituent of biomass. In some embodiments, the substrate is slurried prior to pretreatment. In some embodiments, the consistency of the slurry is between about 2% and about 30% and more typically between about 4% and about 15%. In some embodiments, the slurry is subjected to a water and/or acid soaking operation prior to pretreatment. In some embodiments, the slurry is dewatered using any suitable method to reduce steam and chemical usage prior to pretreatment. Examples of dewatering devices include, but are not limited to pressurized screw presses (See e.g., WO 2010/022511, incorporated herein by reference) pressurized filters and extruders.
In some embodiments, the pretreatment is carried out to hydrolyze hemicellulose, and/or a portion thereof present in the cellulosic substrate to monomeric pentose and hexose sugars (e.g., xylose, arabinose, mannose, galactose, and/or any combination thereof). In some embodiments, the pretreatment is carried out so that nearly complete hydrolysis of the hemicellulose and a small amount of conversion of cellulose to glucose occurs. In some embodiments, an acid concentration in the aqueous slurry from about 0.02% (w/w) to about 2% (w/w), or any amount therebetween, is typically used for the treatment of the cellulosic substrate. Any suitable acid finds use in these methods, including but not limited to, hydrochloric acid, nitric acid, and/or sulfuric acid. In some embodiments, the acid used during pretreatment is sulfuric acid. Steam explosion is one method of performing acid pretreatment of biomass substrates (See e.g., U.S. Pat. No. 4,461,648). Another method of pretreating the slurry involves continuous pretreatment (i.e., the cellulosic biomass is pumped though a reactor continuously). This methods are well-known to those skilled in the art (See e.g., U.S. Pat. No. 7,754,457).
In some embodiments, alkali is used in the pretreatment. In contrast to acid pretreatment, pretreatment with alkali may not hydrolyze the hemicellulose component of the biomass. Rather, the alkali reacts with acidic groups present on the hemicellulose to open up the surface of the substrate. In some embodiments, the addition of alkali alters the crystal structure of the cellulose so that it is more amenable to hydrolysis. Examples of alkali that find use in the pretreatment include, but are not limited to ammonia, ammonium hydroxide, potassium hydroxide, and sodium hydroxide. One method of alkali pretreatment is Ammonia Freeze Explosion, Ammonia Fiber Explosion or Ammonia Fiber Expansion (“AFEX” process; See e.g., U.S. Pat. Nos. 5,171,592; 5,037,663; 4,600,590; 6,106,888; 4,356,196; 5,939,544; 6,176,176; 5,037,663 and 5,171,592). During this process, the cellulosic substrate is contacted with ammonia or ammonium hydroxide in a pressure vessel for a sufficient time to enable the ammonia or ammonium hydroxide to alter the crystal structure of the cellulose fibers. The pressure is then rapidly reduced, which allows the ammonia to flash or boil and explode the cellulose fiber structure. In some embodiments, the flashed ammonia is then recovered using methods known in the art. In some alternative methods, dilute ammonia pretreatment is utilized. The dilute ammonia pretreatment method utilizes more dilute solutions of ammonia or ammonium hydroxide than AFEX (See e.g., WO2009/045651 and US 2007/0031953). This pretreatment process may or may not produce any monosaccharides.
Additional pretreatment processes for use in the present invention include chemical treatment of the cellulosic substrate with organic solvents, in methods such as those utilizing organic liquids in pretreatment systems (See e.g., U.S. Pat. No. 4,556,430; incorporated herein by reference). These methods have the advantage that the low boiling point liquids easily can be recovered and reused. Other pretreatments, such as the OrganosolvTM process, also use organic liquids (See e.g., U.S. Pat. No. 7,465,791, which is also incorporated herein by reference). Subjecting the substrate to pressurized water may also be a suitable pretreatment method (See e.g., Weil et al., Appl. Biochem. Biotechnol., 68(1-2): 21-40 [1997], which is incorporated herein by reference). In some embodiments, the pretreated cellulosic biomass is processed after pretreatment by any of several steps, such as dilution with water, washing with water, buffering, filtration, or centrifugation, or any combination of these processes, prior to enzymatic hydrolysis, as is familiar to those skilled in the art. The pretreatment produces a pretreated feedstock composition (e.g., a “pretreated feedstock slurry”) that contains a soluble component including the sugars resulting from hydrolysis of the hemicellulose, optionally acetic acid and other inhibitors, and solids including unhydrolyzed feedstock and lignin. In some embodiments, the soluble components of the pretreated feedstock composition are separated from the solids to produce a soluble fraction.
In some embodiments, the soluble fraction, including the sugars released during pretreatment and other soluble components (e.g., inhibitors), is then sent to fermentation. However, in some embodiments in which the hemicellulose is not effectively hydrolyzed during the pretreatment one or more additional steps are included (e.g., a further hydrolysis step(s) and/or enzymatic treatment step(s) and/or further alkali and/or acid treatment) to produce fermentable sugars. In some embodiments, the separation is carried out by washing the pretreated feedstock composition with an aqueous solution to produce a wash stream and a solids stream comprising the unhydrolyzed, pretreated feedstock. Alternatively, the soluble component is separated from the solids by subjecting the pretreated feedstock composition to a solids-liquid separation, using any suitable method (e.g., centrifugation, microfiltration, plate and frame filtration, cross-flow filtration, pressure filtration, vacuum filtration, etc.). Optionally, in some embodiments, a washing step is incorporated into the solids-liquids separation. In some embodiments, the separated solids containing cellulose, then undergo enzymatic hydrolysis with cellulase enzymes in order to convert the cellulose to glucose. In some embodiments, the pretreated feedstock composition is fed into the fermentation process without separation of the solids contained therein. In some embodiments, the unhydrolyzed solids are subjected to enzymatic hydrolysis with cellulase enzymes to convert the cellulose to glucose after the fermentation process. In some embodiments, the pretreated cellulosic feedstock is subjected to enzymatic hydrolysis with cellulase enzymes.
As used herein, the term “recovered” refers to the harvesting, isolating, collecting, or recovering of protein from a cell and/or culture medium. In the context of saccharification, it is used in reference to the harvesting the fermentable sugars produced during the saccharification reaction from the culture medium and/or cells. In the context of fermentation, it is used in reference to harvesting the fermentation product from the culture medium and/or cells. Thus, a process can be said to comprise “recovering” a product of a reaction (such as a soluble sugar recovered from saccharification) if the process includes separating the product from other components of a reaction mixture subsequent to at least some of the product being generated in the reaction.
As used herein, the term “slurry” refers to an aqueous solution in which are dispersed one or more solid components, such as a cellulosic substrate.
“Increasing” yield of a product (such as a fermentable sugar) from a reaction occurs when a particular component present during the reaction (such as a GH61 protein) causes more product to be produced, compared with a reaction conducted under the same conditions with the same substrate and other substituents, but in the absence of the component of interest.
“Hydrolyzing” cellulose or other polysaccharide occurs when at least some of the glycosidic bonds between two monosaccharides present in the substrate are hydrolyzed, thereby detaching from each other the two monomers that were previously bonded.
A reaction is said to be “substantially free” of a particular enzyme if the amount of that enzyme compared with other enzymes that participate in catalyzing the reaction is less than about 2%, about 1%, or about 0.1% (wt/wt).
“Fractionating” a liquid (e.g., a culture broth) means applying a separation process (e.g., salt precipitation, column chromatography, size exclusion, and filtration) or a combination of such processes to provide a solution in which a desired protein (e.g., GH61 protein, cellulase enzyme, or combination thereof) comprises a greater percentage of total protein in the solution than in the initial liquid product.
GH61 Variant Proteins with Improved Activity
GH61 variant proteins of the present invention have certain amino acid substitutions in relation to wild-type GH61a protein. In saccharification reactions, wild-type GH61a protein increases the yield of fermentable sugars. An equivalent amount of GH61 variant proteins instead of the wild type increases the yield of fermentable sugars still further. The present invention provides numerous GH61 variants, as indicated herein. Substitutions that have been shown to improve GH61 activity are included in Table 1, below.







TABLE 1







GH61 Variants with Improved Activity











Silent


Var.
Amino Acid
Nucleotide


No.
Changes
Changes












1
N35G/E104H/A168P
t60c/c573g



(SEQ ID NO: 5)


2
W42P/E104H/K167A
t60c/c573g/




g1026a


3
N35G/W42P/V97Q/



A191N


4
W42P/E104H
c573g


5
E104H/K167A
t60c/c291a/




c573g


6
W42P/A191N
t60c/c291a


7
N35G/W42P/A191N
t60c/c291a


8
H20D


9
V97Q/A191N


10
N35G/E104H/A191N
t60c/c876t


11
E104H


12
E104Q


13
H20D/E104D/Q190H/



Y192H


14
H20D/Q190E/Y192Q
a312g


15
H20D/E104C


16
H20D/P103H/E104C


17
H20D/P103H
a312g


18
N35G/E104H
t60c/c573g


19
H20D/P103H/E104Q/



Q190E


20
H20D/P103H/E104C/



Y192Q


21
E104D
t60c


22
N35G/W42P
t60c/c573g


23
A137P


24
H20D/P103H/E104Q


25
P103E/E104D
t60c


26
N35G/F68Y/A191N
t379a/c380g/




g381c


27
W42P/A168P


28
H20D/E104C/Q190E/



Y192Q


29
A142W


30
N35G


31
H20C/Q190E


32
W42P/A212P/T236P


33
N35G/W42P/V97Q/
t60c/c573g



K167A/



A168P


34
V97Q/A168P
c573g


35
S232A


36
W42P/E104H/K167A/
c573g



A168P/Q190E


37
W42P/A168P/A212P/



T236P


38
N35G/V97Q/K167A


39
N35G/V97Q


40
N35G/A191N


41
S127T/K167A/



A191N


42
W42P


43
W42P/E104C/K167A/
t60c/c291a/



A168P
c573g


44
K167Q


45
W131V


46
E176C


47
K167I/P273S
c300t


48
W42P/T87P


49
W42P/A212P


50
K133H


51
D165N


52
D165A


53
A168D


54
K218T


55
P45T


56
Q44V


57
S164W


58
I177F


59
A191N


60
I134P


61
K133F


62
I134D


63
N35G/K167A
t60c/c291a/




c573g


64
I162R


65
N35G/K167A
t204c/t379a




c380g/




g381c/c385t


66
D165W/A246T


67
I162L


68
S164M


69
F132D/A244D


70
H181Q


71
I177G
g1026a


72
L166W


73
I162F


74
I134V


75
E176Q


76
H181S


77
I178A


78
K167A


79
V172K


80
I177H


81
I134N


82
K133Y


83
N35G/Y139L


84
A168G


85
T12A/I162G
c246t


86
D165E


87
D165M


88
I134M


89
A168P


90
I177D


91
S164P


92
H175T


93
N187K/S330R
c597g


94
H175R


95
L166H


96
I178L


97
L173H


98
I177T


99
N170Y


100
H175S


101
K167T


102
L166R


103
V172Y


′104
P163S/E176D


105
S164I


106
H175M


107
A168N


108
A179W


109
W131K/H175Q
g1026a


110
Y171A


111
N170H


112
P163R


113
A168C


114
G169T


115
R174F


116
W131Y


117
I134L


118
I177V


119
K167E


120
H175C


121
W131I


122
W42P/A143P


123
I178G
c72t


124
N170P


125
A179D/N317K
c732g/c843t/




c882t/c909t/




c912g


126
I162V


127
I178M


128
V172A


129
K167A/A191N
t60c/c291a


130
F132A


131
P163E


132
F132M


133
A179G


134
I177S


135
K167A
g921a


136
K167F


137
A168I


138
A179N


139
I134A
c792t


140
K167E
g972t


141
R174K


142
S164F


143
V172L


144
A168H


145
I134T


146
K167H


147
L166A


148
S164R


149
R174C


150
A179P


151
G169R
g1026a


152
L173M


153
D165K


154
E176S


155
F132L


156
F132I/A179I


157
F132P


158
S164Q


159
V172Q


160
W131D


161
W131Q


162
A179H


163
I134H/G270S


164
N170G


165
A168T


166
A179C


167
K133N


168
K167L


169
L180M


170
W131F


171
I134W
g1026a


172
I178H


173
N170A


174
V172H


175
A168H/S205N


176
I134H
g921a


177
S164C


178
S164K


179
I177C


180
I178Q


181
L180W


182
I177M


183
R174D


184
V172M


185
A179M


186
H175Y


187
I178P


188
L173A


189
N170E


190
N170F


191
N35G/A191N/T258I/
t379a/c380g/



T323P/
g381c/



G328A/C341R
c454a/c456a/




c732t/c843t/




c849t


192
A168R


193
D165I


194
I162M


195
K167V


196
A179S


197
E176N


198
I134L/P322L


199
P163L


200
H181D


201
N170S


202
R174G


203
I177R


204
K167C


205
L166Q


206
P163I


207
S164L/L166I


208
Y171R


209
F132P/Q190E/A191T


210
F132Q


211
I134C


212
I177A


213
E176R


214
G169A


215
G169K


216
H181A


217
I177L


218
A168G


219
A179R


220
D165T


221
K167R


222
L166V


223
N170C


224
I178R


225
R174H


226
S164H


227
W131R/L166I


228
I162A/A191T


229
L173F


230
N170Q


231
I177P


232
R174N


233
V172K/S215W


234
D165R


235
G239D
c520a/c522g


236
H175V


237
H181R


238
I134Y


239
V172F


240
V172G









Positions that were changed in variants with improved GH61 activity listed in Table 1 include 20, 34, 35, 42, 44, 45, 68, 87, 97, 103, 104, 127, 131, 132, 133, 137, 139, 142, 143, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 190, 191, 192, 192, 205, 212, 215, 218, 232, 236, 239, 244, 246, 258, 270, 273, 317, 322, 323, 328, 330, and 341, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.
Residues that were changed in variants with improved GH61 activity listed in Table 1 include H20, I134, N35, W42, Q44, P45, F68, T87, V97, P103, E104, S127, W131, F132, K133, A137, Y139, A142, A143, I162, P163, S164, D165, L166, K167, A168, G169, N170, Y171, V172, L173, R174, H175, E176, I177, I178, A179, L180, H181, Q190, A191, Y192, Y192, S205, A212, S215, K218, S232, T236, G239, A244, A246, T258, G270, P273, N317, P322, T323, G328, S330, and C341, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.
Substitutions occurring in variants with improved GH61 activity listed in Table 1 include H20C/D, I134X, N35G, W42P, Q44V, P45T, F68Y, T87P, V97Q, P103E/H, E104C/D/H/Q, S127T, W131X, F132X, K133X, A137P, Y139L, A142W, A143P, I162X, P163X, S164X, D165X, L166X, K167A/X, A168P/X, G169X, N170X, Y171A/R, V172X, L173X, R174X, H175X, E176X, I177X, I178X, A179X, L180M/W, H181X, Q190E/H, A191N/T, Y192H, Y192Q, S205N, A212P, S215W, K218T, S232A, T236P, G239D, A244D, A246T, T258I, G270S, P273S, N317K, P322L, T323P, G328A, S330R, and C341R, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.
As shown herein, the changed residues and substitutions of the GH61 variants of this invention may be combined in a manner that produces an effect that is cumulative or synergistic. Cumulative effects occur when adding an additional mutation increases the effect beyond those of the mutations already present. Synergistic effects occur when having two more mutations in a variant produces an effect than is more than the product of the mutations when incorporated by themselves. This invention includes without limitation any and all combinations of any two, three, four, five, six, seven, eight, nine, ten, or more than ten of the mutations listed in this disclosure.
Useful combinations include but are not limited to the mutations and mutation sets: N35G/E104H/A168P (SEQ ID NO:5); W42P/E104H/K167A; N35G/W42P/V97Q/A191N; W42P/E104H; E104H/K167A; W42P/A191N; N35G/W42P/A191N; V97Q/A191N; N35G/E104H/A191N; H20D/E104D/Q190H/Y192H; H20D/Q190E/Y192Q; H20D/E104C; H20D/P103H/E104C; H20D/P103H; N35G/E104H; H20D/P103H/E104Q/Q190E; H20D/P103H/E104C/Y192Q; N35G/W42P; H20D/P103H/E104Q; P103E/E104D; N35G/F68Y/A191N; W42P/A168P; H20D/E104C/Q190E/Y192Q; H20C/Q190E; W42P/A212P/T236P; N35G/W42P/V97Q/K167A/V97Q/A168P; W42P/E104H/K167A/A168P/Q190E; W42P/A168P/A212P/T236P; N35G/V97Q/K167A; N35G/V97Q; N35G/A191N; S127T/K167A/A191N; W42P/E104C/K167A/A168P; K167I/P273S; W42P/T87P; W42P/A212P; N35G/K167A; N35G/K167A; D165W/A246T; F132D/A244D; N35G/Y139L; T12A/I162G; N187K/S330R; P163S/E176D; W131K/H175Q; W42P/A143P; A179D/N317K; K167A/A191N; F132I/A179I; I134H/G270S; A168H/S205N; N35G/A191N/T258I/T323P/G328A/C341R; I134L/P322E; S164E/L1661; F132P/Q190E/A191T; W131R/L166I; I162A/A191T; and V172K/S215W, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.
GH61 Variant Proteins Made with Multiple Rounds of Activity Enhancement
GH61 variant proteins can be generated that have been further optimized by subjecting to multiple rounds of variation and selection. In some embodiments, additional rounds of optimization increase saccharification reaction yields beyond what is achieved with one round of variation and selection. Substitutions improving GH61 activity are compiled in Table 2 below.
Table 2 shows GH61a variants derived from the GH61a protein designated “Variant 1” (SEQ ID NO:5) in Table 1 with improved thermoactivity. The second-round variants usually retained the alterations of Variant 1 compared with wild-type GH61a (N35G/E104H/A168P), along with additional modifications.







TABLE 2







GH61 Variants with Improved Activity Compared to Variant 1











Silent


Var.
Amino Acid
Nucleotide


No.
Changes
Changes





241
N35G/T40A/E104H/
t60c/c573g



A168P/P327M


242
N35G/P45D/E104H/
t60c/c573g



A168P/N317R


243
N35G/E104H/A168P/
t60c/c573g



N317R


244
N35G/E104H/A168P/
t60c/c573g



N317L


245
N35G/T54H/E104H/
t60c/c573g



A168P


246
N35G/E104H/A168P/
t60c/c573g



N317D/S329Y


247
N35G/E104H/A137S/
t60c/c573g



A168P/S232E


248
N35G/E104H/A168P/
t60c/c573g



N317R/T320A


249
N35G/E104H/A168P/
t60c/c573g



D234E


250
N35G/T40S/E104H/
t60c/c573g



A142G/A168P


251
N35G/T40S/S78C/
t60c/c573g



V88I/E104H/S128K/



A168P/D234M


252
N35G/E104H/A168P/
t60c/c573g



S330V


253
N35G/E104H/A168P/
t60c/c573g



G203E/P266S


254
N35G/E104H/A168P/
t60c/c573g



D234N


255
N35G/E104H/A168P/
t60c/c573g



S286N/S329H


256
N35G/E104H/A168P/
t60c/c573g



S330H


257
N35G/E104H/A168P/
t60c/c573g



W337R


258
N35G/N66D/E104H/
t60c/c573g



S164E/A168P/G267T


259
N35G/E104H/A168P/
t60c/c573g



P233V


260
R34E/N35G/E104H/
t60c/c573g



R145T/A168P


261
S24Q/N35G/E104H/
t60c/c573g



A168P/V237I


262
Y32S/N35G/E64S/
t60c/c573g



E104H/A168P


263
N35G/E104H/A168P/
t60c/c573g



V333R


264
N35G/E104H/G144S/
t60c/c573g



A168P/V333Q


265
V28H/N35G/P45K/
t60c/c573g



E104H/A168P


266
N35G/E104H/A168P/
t60c/c573g



P327K


267
N35G/N66Q/E104H/
t60c/c573g



A168P


268
N35G/E104H/A168P/
t60c/c573g



G203E


269
N35G/E104H/A168P/
t60c/c573g



S339W


270
N35G/P45K/N46E/
t60c/c573g



E104H/A150Y/



A168P


271
N35G/E104H/R130S/
t60c/c573g



A168P


272
N35G/E104H/R145T/
t60c/c573g/



A168P
g891a


273
N35G/E104H/A168P/
t60c/c573g



S231K


274
N35G/T40A/E104H/
t60c/c573g



A168P/D234E/



P327M


275
N35G/E104H/A168P/
t60c/c573g



S231H


276
N35G/E104H/A168P/
t60c/c573g



N317M


277
N35G/E104H/A168P/
t60c/c573g



S330Y


278
N35G/E104H/A168P/
t60c/c573g



S329I


279
N35G/E104H/A168P/
t60c/c573g



S329R


280
N35G/N66D/E104H/
t60c/c573g



A168P/P322R/S329L


281
N35G/E104H/A168P/
t60c/c288t/



P327F
c573g


282
N35G/P45D/E104H/
t60c/c573g



A168P


283
N35G/E104H/A168P/
t60c/c573g



S332R


284
N35G/E104H/A116S/
t60c/c573g



A168P


285
N35G/T40A/E104H/
t60c/c573g



A168P/V230I/P327M


286
N35G/T49A/E104H/
t60c/c573g



A168P


287
N35G/E104H/A168P/
t60c/c573g



N317T


288
N35G/N46Y/E104H/
t60c/c573g



A168P


289
N35G/E104H/A168P/
t60c/c573g



G203V


290
N35G/E104H/A168P/
t60c/c573g



S329L


291
N35G/E104H/R145N/
t60c/c573g



A168P/S329H


292
N35G/A56S/E104H/
t60c/c573g



A168P


293
N35G/T40S/T49R/
t60c/c573g



E104H/A168P/



D234E/P327M


294
N35G/E104H/Q161R/
t60c/c573g



A168P


295
N35G/E104H/A168P/
t60c/c573g



S332F


296
N35G/P45R/T49A/
t60c/c573g



E104H/A168P/



N317R/T320A


297
N35G/E104H/A168P/
t60c/c573g



V237I


298
N35G/Q44K/T80V/
t60c/c573g



E104H/A168P


299
N35G/E104H/A168P/
t60c/c573g



E336S


300
N35G/E104H/A168P/
t60c/c573g



P233T


301
N35G/E104H/A168P/
t60c/c573g



S329Y


302
N35G/E104H/A168P/
t60c/c573g



P327L


303
N35G/E104H/A168P/
t60c/c573g



N317I


304
N35G/E104H/R130H/
t60c/c573g



A168P


305
N35G/Q44K/E104H/
t60c/c573g



A168P


306
N35G/N66D/E104H/
t60c/c573g



A168P


307
N35G/E104H/A168P/
t60c/c573g



S329V


308
N35G/E104H/A168P/
t60c/c573g



W337F


309
N35G/E104H/A168P/
t60c/c573g



N317H


310
N35G/T40L/E104H/
t60c/c573g



S128K/A168P


311
N35G/E104H/A168P/
t60c/c573g



A326V


312
N35G/T80V/E104H/
t60c/c573g



A168P/P303T


313
N35G/E104H/A168P/
t60c/c573g



S231A/S295L


314
N35G/E104H/A116Q/
t60c/c573g



A168P


315
N35G/E104H/A168P/
t60c/c573g



S330C


316
N35G/T40S/E101T/
t60c/c573g



E104H/A168P/



P327M


317
N35G/E104H/A168P
t60c/c573g



//A326Q


318
N35GN46R/E104H/
t60c/c573g



A168P


319
N35G/P45K/E104H/
t60c/c573g



A168P/A219R/



S232E


320
S24Q/N35G/E104H/
t60c/c573g



A168P/V237I/P303T


321
N35G/E104H/A168P/
t60c/c573g



G203E/T281A


322
N35G/A56N/E104H/
t60c/c573g



A168P


323
N35G/E104H/A168P/
t60c/c573g



E336G


324
N35G/E104H/A168P/
t60c/c573g



E336R


325
N35G/T40S/E104H/
t60c/c573g



S128K/A142G/



A168P


326
N35G/Q44K/S67T/
t60c/c198t/



E104H/A168P
c573g


327
N35G/E104H/A168P/
t60c/c573g



N317A


328
N35G/E104H/G155N/
t60c/c573g



A168P


329
N35G/E104H/Q161E/
t60c/c573g



A168P


330
N35G/E104H/N118S/
t60c/c573g



A168P


331
N35G/P45T/V97Q/
t60c/c573g



E104H/A168P/



G267S


332
V28H/N35G/E104H/
t60c/c573g



A168P


333
N35G/E104H/A168P/
t60c/c573g



Q184L


334
N35G/E104H/A168P/
t60c/c573g



N317V


335
N35G/Q44L/E104H/
t60c/c573g



A168P


336
N35G/E104H/A168P/
t60c/c573g



S330G


337
N35G/E104H/A168P/
t60c/c573g



T320A/V333W


338
N35G/E104H/A168P/
t60c/c573g



E336A


339
N35G/E104H/A168P/
t60c/c573g



N335S


340
N35G/N66M/E104H/
t60c/c573g



A168P


341
N35G/T54G/E104H/
t60c/c573g



A168P


342
N35G/E104H/A168P/
t60c/c573g



N317S


343
N35G/E64L/E104H/
t60c/c573g



A168P


344
N35G/E104H/S164E/
t60c/c573g



A168P/A271T


345
N35G/N66A/E104H/
t60c/c573g



A168P


346
N35G/G83R/E104H/
t60c/c573g



A168P


347
N35G/E104H/A168P/
t60c/c573g



N317Q/T320A


348
N35G/E104H/K141A/
t60c/c573g



A168P


349
N35G/P71T/E104H/
t60c/c573g



A168P


350
N35G/P71S/E104H/
t60c/c573g



A168P


351
N35G/E104H/R130G/
t60c/c573g



A168P


352
N35G/E104H/R145Q/
t60c/c573g



A168P


353
N35G/T70A/E104H/
t60c/c573g



A168P


354
N35G/E104H/A168P/
t60c/c573g



K218R


355
N35G/E104H/A168P/
t60c/c573g



Q184E


356
N35G/E104H/R130K/
t60c/c573g



A168P


357
N35G/Q58H/E104H/
t60c/c573g



A168P


358
Y32S/N35G/E104H/
t60c/c573g



A168P


359
N35G/E104H/A168P/
t60c/c573g



S329T


360
N35G/E104H/A168P/
t60c/c573g



S330I


361
Y32S/N35G/P71A/
t60c/c573g



E104H/A168P


362
N35G/E104H/A168P/
t60c/c573g



S330T


363
N35G/G82A/E104H/
t60c/c573g



A168P


364
N35G/T80V/E104H/
t60c/c573g



A168P


365
N35G/E104H/A168P/
t60c/c573g



S295T


366
N35G/N66G/E104H/
t60c/c573g



A168P


367
N35G/E104H/R145L/
t60c/c573g



A168P


368
N35G/S67H/E104H/
t60c/c573g



A168P/V230M


369
N35G/E104H/G136E/
t60c/c573g



A168P


370
N35G/T54S/E104H/
t60c/c573g



A168P


371
N35G/P45S/E104H/
t60c/c573g



A168P


372
N35G/E104H/A168P/
t60c/c573g/



A326M
c882t


373
N35G/N66D/N95E/
t60c/c573g



E104H/S164E/A168P/



G267D


374
N35G/E104H/A168P/
t60c/c573g



S332C


375
N35G/E104H/S128L/
t60c/c573g



A168P


376
N35G/T54W/E104H/
t60c/c573g



A168P


377
N35G/E104H/A168P/
t60c/c573g



G268A/G269A/



G270A


378
N35G/Q44K/E104H/
t60c/c573g



A168P/S231T


379
R34E/N35G/E104H/
t60c/c573g



A168P/A280D


380
N35G/E104H/A168P/
t60c/g399a/



A297T
c573g


381
N35G/E104H/K141P/
t60c/c573g



R145Q/A168P


382
N35G/P45E/E104H\/
t60c/c573g



K141R/A168P


383
N35G/N66T/E104H/
t60c/c573g



A168P


384
N35G/E104H/S164E/
t60c/c573g



A168P/S295D


385
N35G/E104H/A168P/
t60c/c573g



N317F


386
N35G/E104H/A168P/
t60c/c573g



N317Q


387
N35G/T40G/T49R/
t60c/c573g



S78C/E104H/A142G/



A168P


388
N35G/G82S/E104H/
t60c/c573g



A168P


389
N35G/Q58P/E104H/
t60c/c573g



A168P


390
N35G/N46R/E104H/
t60c/c573g



A168P/G203E/



A263V


391
N35G/P45R/E104H/
t60c/c573g



A168P


392
N35G/S67G/E104H/
t60c/c573g



A168P


393
N35G/E104H/A168P/
t60c/c573g



R199E


394
N35G/G69T/E104H/
t60c/c573g



A168P


395
N35G/E104H/A168P/
t60c/c573g



G203E/G268A/



G269A/G270A


396
N35G/E104H/A168P/
t60c/c573g



P266S


397
N35G/E104H/A168P/
t60c/c573g



V324M


398
N35G/E104H/A168P/
t60c/c573g



G245A


399
N35G/N66R/E104H/
t60c/c573g



A168P


400
N35G/E104H/A168P/
t60c/c573g



T236E


401
S24Q/N35G/Q44K/
t60c/c573g



T80H/E104H/A168P


402
N35G/E104H/S128D/
t60c/c573g



A168P


403
N35G/N66D/S78D/
t60c/c573g



E104H/A168P/



S253D


404
N35G/E104H/R130Y/
t60c/c573g



A168P


405
N35G/E104H/A168P/
t60c/c573g



K310I


406
N35G/E104H/R145E/
t60c/c573g



A168P


407
N35G/N66D/E104H/
t60c/c573g



S164E/A168P/S282D


408
N35G/E104H/K141P/
t60c/c573g



A168P


409
N35G/E104H/A168P/
t60c/c573g



Q184R


410
N35G/E104H/A168P/
t60c/c573g



S231T


411
N35G/N66V/E104H/
t60c/c573g



A168P


412
N35G/E104H/A142L/
t60c/c573g



A168P


413
N35G/E104H/R145H/
t60c/c573g



A168P


414
N35G/E104H/A168P/
t60c/c573g



K218L


415
N35G/E104H/K141T/
t60c/c573g



A168P


416
N35G/E104H/A168P/
t60c/c573g



P233F


417
N35G/T40S/E104H/
t60c/c573g



A168P/P327M


418
N35G/T54M/E104H/
t60c/c573g



A168P


419
S24T/N35G/E104H/S164E/
t60c/c573g



A168P


420
N35G/P45T/E104H/
t60c/c573g



A168P


421
N35G/N66D/E104H/
t60c/c573g



S164E/A168P/S231T/



S253T


422
N35G/G69H/E104H/
t60c/c573g



A168P


423
N35G/E104H/S128Y/
t60c/c573g



A168P


424
N35G/T49Q/E104H/
t60c/c573g



A168P


425
N35G/T49A/E104H/
t60c/c573g



A168P/Q184H


426
N35G/E104H/A168P/
t60c/c573g



G203Y


427
N35G/Q44K/N66V/E104H/
t60c/c573g



A168P


428
N35G/E104H/
t60c/c573g



A137M/A168P


429
N35G/E104H/A168P/
t60c/c573g



P327C


430
N35G/E104H/A168P/
t60c/c573g



T236R


431
N35G/I51A/E104H/
t60c/c573g



A168P


432
N35G/S67H/E104H/
t60c/c573g



A168P


433
N35G/E104H/A168P/
t60c/c573g



A326C


434
N35G/T49A/E104H/
t60c/c573g



S128N/A168P


435
N35G/T49R/E104H/
t60c/c573g



A168P/K218L/



N317Q


436
N35G/E104H/A168P/
t60c/c573g



P266S/G267V


437
N35G/E104H/A168P/
t60c/c573g



V237I/P303T


438
N35G/T49E/E104H/
t60c/c573g



A168P


439
N35G/P45R/E104H/
t60c/c573g



A168P/T320A


440
N35G/N66L/E104H/
t60c/c573g



A168P


441
N35G/P45R/E104H/
t60c/c573g



A168P/K218L/



N317Q


442
N35G/E104H/R145V/
t60c/c573g



A168P


443
N35G/N66D/E104H/
t60c/c573g



A168P/R290K


444
N35G/T80L/E104H/
t60c/c573g



A168P


445
N35G/A55G/E104H/
t60c/c573g



A168P


446
N35G/E104H/A168P/
t60c/c573g



S330A


447
N35G/E104H/K141N/
t60c/c573g



A168P/P266S


448
N35G/E104H/A142S/
t60c/c573g



A168P


449
N35G/E104H/A168P/
t60c/c573g



Q184G


450
N35G/E104H/N118E/
t60c/c573g



A168P


451
N35G/E104H/A168P/
t60c/c573g



A212M


452
N35G/E104H/A168P/
t60c/c573g



G267D


453
N35G/K93N/E104H/
t60c/c573g



R130Y/A168P


454
N35G/P45R/T49Y/
t60c/c573g



E104H/A168P/



N317D


455
N35G/E104H/A168P/
t60c/c573g



S329Q


456
N35G/E104H/A168P/
t60c/c573g



V230Q


457
N35G/P45K/E104H/
t60c/c573g



A168P/A219R


458
N35G/E104H/A142G/
t60c/c573g



A168P


459
N35G/E104H/A168P/
t60c/c573g



S205T


460
N35G/S78D/E104H/
t60c/c573g



S164E/A168P


461
N35G/E104H/R130E/
t60c/c573g



A168P


462
N35G/E104H/A168P/
t60c/c573g



Q184H


463
N35G/E104H/A116P/
t60c/c573g



A168P


464
N35G/E104H/A142D/
t60c/c573g



A168P


465
V28H/N35G/N46E/
t60c/c573g



Q58H/E104H/A168P


466
N35G/E104H/A168P/
t60c/c573g



A280T


467
R34E/N35G/E104H/
t60c/c573g



A168P/A280T


468
N35G/E104H/A168P/
t60c/c573g



E336L


469
N35G/T49D/E104H/
t60c/c573g



A168P


470
N35G/E104H/A168P/
t60c/c573g



A219T


471
N35G/E104H/A142W/
t60c/c573g



A168P


472
N35G/E104H/A168P/
t60c/c573g



P303T/G305D


473
N35G/Q44V/E104H/
t60c/c573g



A168P


474
N35G/E104H/A168P/
t60c/c573g



N187D


475
N35G/E104H/G136H/
t60c/c573g



A168P


476
S24Q/N35G/Q44K/E104H/
t60c/c573g



A168P/P303T/



S332D


477
N35G/E104H/
t60c/c573g



A168P/Q184N


478
N35G/E104H/A168P/
t60c/c573g



S332L


479
S24T/N35G/N66D/
t60c/c573g



S78D/E104H/A168P/



S205T/S253T


480
N35G/E104H/A168P/
t60c/c573g



P327A


481
N35G/T40A/T49Q/
t60c/c573g



S78C/E104H/A168P


482
N35G/T40L/E104H/
t60c/c573g



A142G/A168P


483
N35G/T49Y/E104H/
t60c/c573g



A168P/N317R


484
R34E/N35G/K93T/E104H/
t60c/c573g



R130E/R145T/



A168P/R199E/



K218T/A280D









Positions that were changed in variants with improved GH61 activity listed in Table 2 include 24, 28, 32, 34, 35, 40, 44, 45, 46, 49, 51, 54, 55, 56, 58, 64, 66, 67, 69, 70, 71, 78, 80, 82, 83, 88, 93, 95, 101, 104, 116, 118, 128, 130, 136, 137, 141, 142, 144, 145, 150, 155, 161, 164, 168, 184, 187, 199, 203, 205, 212, 218, 219, 230, 231, 232, 233, 234, 236, 237, 245, 253, 263, 266, 267, 268, 269, 270, 271, 280, 281, 282, 290, 295, 297, 303, 305, 310, 317, 320, 324, 326, 327, 329, 330, 332, 333, 336, 337, and 339, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.
Residues that were changed in variants with improved GH61 activity listed in Table 2 include S24, V28, Y32, R34, N35, T40, Q44, P45, N46, T49, I51, T54, A55, A56, Q58, E64, N66, S67, G69, T70, P71, S78, T80, G82, G83, V88, K93, N95, E101, E104, A116, N118, S128, R130, G136, A137, K141, A142, G144, R145, A150, G155, Q161, S164, A168, Q184, N187, R199, G203, S205, A212, K218, A219, V230, S231, S232, P233, D234, T236, V237, G245, S253, A263, P266, G267, G268, G269, G270, A271, A280, T281, S282, R290, S295, A297, P303, G305, K310, N317, T320, V324, A326, P327, S329, S330, S332, V333, E336, W337, and S339, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.
Substitutions occurring in variants with improved GH61 activity listed in Table 2 include S24Q, V28H, Y32S, R34E, N35G, T40A/G/L/S, Q44K, P45D/E/K/R/S, N46E/R, T49A/Q/R/Y, I51A, T54G/M/S/W, A55G, A56S, Q58H/P, E64L/S, N66A/D/G/L/M/Q/R/V, S67G/H/T, G69T, T70A, P71A, S78C/D, T80H/L/V, G82A/S, G83R, V88I, K93N/T, N95E, E101T, E104H, A116Q/S, N118E/S, S128K/L/N, R130E/G/H/K/Y, G136H, A137M/S, K141A/N/P/R, A142D/G/L, G144S, R145H/L/N/Q/T, A150Y, G155N, Q161E/R, S164E, A168P, Q184E/H/L/N/R, N187D, R199E, G203E/V/Y, S205T, A212M, K218L/T, A219R/T, V230I/Q, S231A/H/K/I, S232E, P233F/T, D234E/M/N, T236E, V237I, G245A, S253D/T, A263V, P266S, G267D/V, G268A, G269A, G270A, A271T, A280D/T, T281A, S282D, R290K, S295D/L/T, A297T, P303T, G305D, K310I, N317D/H/I/M/Q/R, T320A, V324M, A326C/Q/V, P327F/K/L/M, S329H/I/Q/T/Y, S330A/H/I/T/V, S332C/F/R, V333Q, E336L/R/S, W337R, and S339W.
In some embodiments, the changed residues and substitutions of the GH61 variants of this invention may be combined in a manner that produces an effect that is cumulative or synergistic. Cumulative effects occur when adding an additional mutation increases the effect beyond those of the mutations already present. Synergistic effects occur when having two more mutations in a variant produces an effect than is greater than the product of the mutations when incorporated by themselves. This invention includes without limitation any and all combinations of any two, three, four, five, six, seven, eight, nine, ten, or more than ten of the mutations listed in Table 1, Table 2, or both Tables.
Useful combinations of mutated positions include but are not limited to N35/T40/E104/A168/P327; N35/P45/E104/A168/N317; N35/E104/A168/N317; N35/E104/A168/N317/S329; N35/E104/A137/A168/S232; N35/E104/A168/N317/T320; N35/E104/A168/D234; N35/T40/E104/A142/A168; N35/E104/R145/A168; N35/T40/S78/V88/E104/S128K/A168/D234; N35/E104/A168/S330; N35/E104/A168/G203/P266; N35/E104/A168/D234; N35/E104/A168/S330; N35/E104/A168/W337; R34/N35/E104/R145/A168; Y32/N35/E64/E104/A168; V28/N35/P45/E104/A168; N35/E104/G144/A168/V333; N35/N66/E104/A168; N35/E104/A168/P327; N35/E104/A168/G203; N35/E104/A168/S339; N35/P45/N46/E104/A150/A168; N35/E104/A168/S231; N35/T40/E104/A168/D234/P327; N35/E104/A168/S231; N35/E104/A168/N317; N35/E104/A168/S330; N35/E104/A168/S329; N35/E104/A168/P327; N35/P45/E104/A168; N35/E104/A116/A168; N35/T40/E104/A168/V230/P327; and N35/E104/A168/S332.
Useful combinations of mutated residues further include but are not limited to N35/E104/A168/G203; N35/E104/R145/A168/S329; N35/T40/T49/E104/A168/D234/P327; N35/A56/E104/A168; N35/E104/Q161/A168; N35/E104/A168/S332; N35/P45/T49/E104/A168/N317/T320; N35/E104/A168/V237; N35/E104/A168/E336; N35/E104/A168/P233; N35/E104/R130/A168; N35/E104/A168/P327; N35/E104/A168/N317; N35/Q44/E104/A168; N35/E104/A168/A326; N35/E104/A168/N317; N35/T40/E104/S128/A168; N35/T80/E104/A168/P303; N35/E104/A116/A168; N35/E104/A168/S231/S295; N35/T40/E101/E104/A168/P327; N35/P45/E104/A168/A219/S232; N35/N46/E104/A168; N35/E104/A168/A326; N35/E104/A168/G203/T281; N35/E104/A168/E336; N35/T40/E104/S128/A142/A168; N35/E104/N118/A168; N35/E104/G155/A168; S24/N35/E104/A168/V237/P303; N35/E104/Q161/A168; N35/Q44/S67/E104/A168; V28/N35/E104/A168; N35/E104/A168/Q184; N35/T54/E104/A168; N35/N66/E104/A168; N35/E64/E104/A168; N35/E104/S164/A168/A271; N35/N66/E104/A168; N35/G83/E104/A168; N35/E104/K141/A168; and N35/E104/A168/N317/T320.
Useful combinations of mutated residues include but are not limited to N35/E104/R130/A168; N35/E104/R145/A168; N35/T70/E104/A168; N35/E104/R130/A168; N35/E104/A168/Q184; N35/E104/A168/S329; N35/T49/E104/A168; Y32/N35/E104/A168; N35/E104/A168/S330; N35/Q58/E104/A168; Y32/N35/P71/E104/A168; N35/E104/A168/S330; N35/T80/E104/A168; N35/G82/E104/A168; N35/E104/A168/S295; N35/N66/E104/A168; N35/T54/E104/A168; N35/P45/E104/A168; N35/E104/S128/A168; N35/N66/N95/E104/S164/A168; /G267; N35/T54/E104/A168; N35/P45/E104/K141/A168; N35/E104/A168/S332; N35/E104/A168/A297; N35/E104/K141/R145/A168; N35/Q44/E104/A168/S231; N35/T40/T49/S78/E104/A142; /A168; N35/E104/S164/A168/S295; N35/E104/A168/N317; N35/P45/E104/A168; N35/G82/E104/A168; N35/N46/E104/A168/G203/A263; N35/Q58/E104/A168; N35/G69/E104/A168; N35/S67/E104/A168; N35/E104/A168/R199; N35/E104/A168/G203/G268/G269/G270; N35/E104/A168/V324; N35/E104/A168/P266; N35/E104/A168/G245; N35/N66/E104/A168; and S24/N35/Q44/T80/E104/A168.
Useful combinations of mutated residues further include but are not limited to N35/E104/A168/T236; N35/E104/A168/K310; N35/E104/R130/A168; N35/N66/S78/E104/A168/S253; N35/N66/E104/S164/A168/S282; N35/E104/A142/A168; N35/E104/R145/A168; N35/E104/A168/S231; N35/E104/A168/Q184; N35/E104/A168/K218; N35/E104/A168/P233; N35/T49/E104/A168/Q184; N35/T40/E104/A168/P327; N35/T54/E104/A168; N35/N66/E104/S164/A168/S231/S253; N35/E104/A168/G203; N35/T49/E104/A168; N35/E104/A168/P266/G267; N35/Q44/N66/E104/A168; N35/S67/E104/A168; N35/E104/A137/A168; N35/T49/E104/S128/A168; N35/T49/E104/A168/K218/N317; N35/I51/E104/A168; N35/E104/A168/A326; N35/P45/E104/A168/T320; N35/N66/E104/A168; N35/E104/A168/V237/P303; N35/P45/E104/A168/K218/N317; N35/T80/E104/A168; N35/A55/E104/A168; N35/E104/K141/A168/P266; N35/E104/A168/S330; N35/N66/E104/A168/R290; N35/E104/N118/A168; N35/E104/A168/A212; N35/K93/E104/R130/A168; N35/E104/A168/G267; N35/P45/T49/E104/A168/N317; N35/E104/A168/V230; N35/E104/A168/S329; N35/P45/E104/A168/A219; N35/S78/E104/S164/A168; N35/E104/A168/S205; N35/E104/A168/Q184; V28/N35/N46/Q58/E104/A168; N35/E104/A142/A168; N35/E104/A168/E336; N35/E104/A168/A280; N35/E104/A168/A219; N35/E104/A168/P303/G305; R34/N35/E104/A168/A280; N35/E104/A168/N187; N35/E104/G136/A168; N35/E104/A168/Q184; N35/T49/E104/A168/N317; N35/T40/T49/S78/E104/A168; R34/N35/K93/E104/R130/R145/A168/R199/K218/A280; N35/T40/E104/A142/A168; and N35/N66/E104/A168.
Useful combinations of mutations further include but are not limited to N35G/T40A/E104H/A168P/P327M; N35G/P45D/E104H/A168P/N317R; N35G/E104H/A168P/N317R; N35G/E104H/A168P/N317D/S329Y; N35G/E104H/A137S/A168P/S232E; N35G/E104H/A168P/N317R/T320A; N35G/E104H/A168P/D234E; N35G/T40S/E104H/A142G/A168P; N35G/E104H/R145L/A168P; N35G/T40S/S78C/V88I/E104H/S128K/A168P/D234M; N35G/E104H/A168P/S330V; N35G/E104H/A168P/G203E/P266S; N35G/E104H/A168P/D234N; N35G/E104H/A168P/S330H; N35G/E104H/A168P/W337R; R34E/N35G/E104H/R145T/A168P; Y32S/N35G/E64S/E104H/A168P; V28H/N35G/P45K/E104H/A168P; N35G/E104H/G144S/A168P/V333Q; N35G/N66Q/E104H/A168P; N35G/E104H/A168P/P327K; N35G/E104H/A168P/G203E; N35G/E104H/A168P/S339W; N35G/P45K/N46E/E104H/A150Y/A168P; N35G/E104H/A168P/S231K; N35G/T40A/E104H/A168P/D234E/P327M; N35G/E104H/A168P/S231H; N35G/E104H/A168P/N317M; N35G/E104H/A168P/S330Y; N35G/E104H/A168P/S329I; N35G/E104H/A168P/P327F; N35G/P45D/E104H/A168P; N35G/E104H/A116S/A168P; N35G/T40A/E104H/A168P/V230I/P327M; and N35G/E104H/A168P/S332R.
Useful combinations of mutations further include but are not limited to N35G/E104H/A168P/G203V; N35G/E104H/R145N/A168P/S329H; N35G/T40S/T49R/E104H/A168P/D234E; /P327M; N35G/A56S/E104H/A168P; N35G/E104H/Q161R/A168P; N35G/E104H/A168P/S332F; N35G/P45R/T49A/E104H/A168P/N317R/T320A; N35G/E104H/A168P/V237I; N35G/E104H/A168P/E336S; N35G/E104H/A168P/P233T; N35G/E104H/R130H/A168P; N35G/E104H/A168P/P327L; N35G/E104H/A168P/N317I; N35G/Q44K/E104H/A168P; N35G/E104H/A168P/A326V; N35G/E104H/A168P/N317H; N35G/T40L/E104H/S128K/A168P; N35G/T80V/E104H/A168P/P303T; N35G/E104H/A116Q/A168P; N35G/E104H/A168P/S231A/S295L; N35G/T40S/E101T/E104H/A168P/P327M; N35G/P45K/E104H/A168P/A219R/S232E; N35G/N46R/E104H/A168P; N35G/E104H/A168P/A326Q; N35G/E104H/A168P/G203E/T281A; N35G/E104H/A168P/E336R; N35G/T40S/E104H/S128K/A142G/A168P; N35G/E104H/N118S/A168P; N35G/E104H/G155N/A168P; S24Q/N35G/E104H/A168P/V237I/P303T; N35G/E104H/Q161E/A168P; N35G/Q44K/S67T/E104H/A168P; V28H/N35G/E104H/A168P; N35G/E104H/A168P/Q184L; N35G/T54G/E104H/A168P; N35G/N66M/E104H/A168P; N35G/E64L/E104H/A168P; N35G/E104H/S164E/A168P/A271T; N35G/N66A/E104H/A168P; N35G/G83R/E104H/A168P; N35G/E104H/K141A/A168P; and N35G/E104H/A168P/N317Q/T320A.
Useful combinations of mutations further include but are not limited to N35G/E104H/R130G/A168P; N35G/E104H/R145Q/A168P; N35G/T70A/E104H/A168P; N35G/E104H/R130G/A168P; N35G/E104H/A168P/Q184E; N35G/E104H/A168P/S329T; N35G/T49A/E104H/A168P; Y32S/N35G/E104H/A168P; N35G/E104H/A168P/S330I; N35G/Q58H/E104H/A168P; Y32S/N35G/P71A/E104H/A168P; N35G/E104H/A168P/S330T; N35G/T80V/E104H/A168P; N35G/G82A/E104H/A168P; N35G/E104H/A168P/S295T; N35G/N66G/E104H/A168P; N35G/T54S/E104H/A168P; N35G/P45S/E104H/A168P; N35G/E104H/S128L/A168P; N35G/N66D/N95E/E104H/S164E/A168P/G267D; N35G/T54W/E104H/A168P; N35G/P45E/E104H/K141R/A168P; N35G/E104H/A168P/S332C; N35G/E104H/A168P/A297T; N35G/E104H/K141P/R145Q/A168P; N35G/Q44K/E104H/A168P/S231T; N35G/T40G/T49R/S78C/E104H/A142G; /A168P; N35G/E104H/S164E/A168P/S295D; N35G/E104H/A168P/N317Q; N35G/P45R/E104H/A168P; N35G/G82S/E104H/A168P; N35G/N46R/E104H/A168P/G203E/A263V; N35G/Q58P/E104H/A168P; N35G/G69T/E104H/A168P; N35G/S67G/E104H/A168P; N35G/E104H/A168P/R199E; N35G/E104H/A168P/G203E/G268A/G269A/G270A; N35G/E104H/A168P/V324M; N35G/E104H/A168P/P266S; N35G/E104H/A168P/G245A; N35G/N66R/E104H/A168P; and S24Q/N35G/Q44K/T80H/E104H/A168P.
Useful combinations of mutations further include but are not limited to N35G/E104H/A168P/T236E; N35G/E104H/A168P/K310I; N35G/E104H/R130Y/A168P; N35G/N66D/S78D/E104H/A168P/S253D; N35G/N66D/E104H/S164E/A168P/S282D; N35G/E104H/A142L/A168P; N35G/E104H/R145H/A168P; N35G/E104H/A168P/S231T; N35G/E104H/A168P/Q184R; N35G/E104H/A168P/K218L; N35G/E104H/A168P/P233F; N35G/T49A/E104H/A168P/Q184H; N35G/T40S/E104H/A168P/P327M; N35G/T54M/E104H/A168P; N35G/N66D/E104H/S164E/A168P/S231T/S253T; N35G/E104H/A168P/G203Y; N35G/T49Q/E104H/A168P; N35G/E104H/A168P/P266S/G267V; N35G/Q44K/N66V/E104H/A168P; N35G/S67H/E104H/A168P; N35G/E104H/A137M/A168P; N35G/T49A/E104H/S128N/A168P; N35G/T49R/E104H/A168P/K218L/N317Q; N35G/I51A/E104H/A168P; N35G/E104H/A168P/A326C; N35G/P45R/E104H/A168P/T320A; N35G/N66L/E104H/A168P; N35G/E104H/A168P/V237I/P303T; N35G/P45R/E104H/A168P/K218L/N317Q; N35G/T80L/E104H/A168P; N35G/A55G/E104H/A168P; N35G/E104H/K141N/A168P/P266S; N35G/E104H/A168P/S330A; N35G/N66D/E104H/A168P/R290K; N35G/E104H/N118E/A168P; N35G/E104H/A168P/A212M; N35G/K93N/E104H/R130Y/A168P; N35G/E104H/A168P/G267D; N35G/P45R/T49Y/E104H/A168P/N317D; N35G/E104H/A168P/V230Q; N35G/E104H/A168P/S329Q; N35G/P45K/E104H/A168P/A219R; N35G/S78D/E104H/S164E/A168P; N35G/E104H/A168P/S205T; N35G/E104H/A168P/Q184H; V28H/N35G/N46E/Q58H/E104H/A168P; N35G/E104H/A142D/A168P; N35G/E104H/A168P/E336L; N35G/E104H/A168P/A280T; N35G/E104H/A168P/A219T; N35G/E104H/A168P/P303T/G305D; R34E/N35G/E104H/A168P/A280T; N35G/E104H/A168P/N187D; N35G/E104H/G136H/A168P; N35G/E104H/A168P/Q184N; N35G/T49Y/E104H/A168P/N317R; N35G/T40A/T49Q/S78C/E104H/A168P; R34E/N35G/K93T/E104H/R130E/R145T/A168P/R199E/K218T/A280D; N35G/T40L/E104H/A142G/A168P; and N35G/N66G/E104H/A168P.
Production of GH61 Variant Proteins
In some embodiments, the GH61 variant proteins of this invention are produced by recombinant expression in a host cell. Any suitable method for recombinant expression in any suitable host cell finds use in the present invention. In some embodiments, a nucleotide sequence encoding the protein is obtained, and introduced into a suitable host cell by way of a suitable transfer vector or expression vector. In some embodiments, the nucleotide sequence is operably linked to a promoter that promotes expression in the host cell. The promoter sequence is often selected to optimize in a cell that is not M. thermophila, in which case the promoter is typically heterologous to the GH61 variant protein encoding sequence. In some embodiments, the host cell is a eukaryotic cell and the GH61 variant protein comprises a heterologous signal peptide at the N-terminus.
Optionally, in some embodiments, the encoding sequence is codon-optimized for the host cell (e.g., a particular species of yeast cell). Any suitable method for obtaining codon-optimized sequences find use in the present invention (e.g., GCG CodonPreference, Genetics Computer Group Wisconsin Package; Codon W, John Peden, University of Nottingham; and McInerney, Bioinform., 14:372-73 [1998]).
General reference texts relating to gene expression include but are not limited to the most recent editions of Protocols in Molecular Biology (Ausubel et al. eds.); Molecular Cloning: A Laboratory Manual (Sambrook et al. eds.); Advances In Fungal Biotechnology For Industry, Agriculture, And Medicine (Tkacz and Lange, 2004); and Fungi: Biology and Applications (K. Kavanagh ed., 2005).
In some embodiments, culture broth from GH61 protein-producing cells is collected and combined directly with cellulase enzymes in a saccharification reaction. In some alternative embodiments, the broth is fractionated to any extent desired to provide partially or substantially purified GH61 protein, following the activity during the separation process using a GH61 activity assay, using standard protein separation techniques, and following GH61 activity during fractionation with a suitable GH61 activity assay. Such protocols may combine one or more of the following methods (but are not limited to these particular methods): salt precipitation, solid phase binding, affinity chromatography, ion exchange chromatography, molecular size separation, and/or filtration. Protein separation techniques are generally described in Protein Purification: Principles, High Resolution Methods, and Applications, (J. C. Janson, ed., 2011); High Throughput Protein Expression and Purification: Methods and Protocols (S. A. Doyle ed., 2009).
The present invention provides GH61 variant protein having an amino acid sequence that is at least about 60%, at least about 65%, at least about 70%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to SEQ ID NO:2 or a fragment of SEQ ID NO:2 having GH61 activity. In some embodiments, the amino acid sequence of the variant proteins have one or more amino acid substitutions with respect to SEQ ID NO:2 or said fragment. In some embodiments, the substitution(s) that are present in the amino acid sequence result in the variant protein having increased GH61 activity in a saccharification reaction by certain cellulase enzymes under specified conditions, compared with a reference protein comprising SEQ ID NO:2 or said fragment, without any of the substitutions.
In some embodiments, GH61 variant proteins of this invention comprise one or more of SEQ ID NOS:5, 6, 8, 9, 11, and/or 12, or biologically-active fragments of these sequences having GH61 activity. These correspond to Variants 1 (SEQ ID NOS:5 and 6), Variant 5 (SEQ ID NOS: 8 and 9), and Variant 9 (SEQ ID NOS: 11 and 12). In some embodiments, the variants have more than about 2-fold, 3-fold, or more than 3-fold GH61 activity compared with wild-type GH61a (i.e., SEQ ID NO:2). The combined effect of multiple rounds of optimization yield GH61 variant proteins that have about 3-fold, about 5-fold, about 8-fold, or about 10-fold activity compared with the original parental sequence (SEQ ID NO:2).
Also provided are polynucleotides encoding such GH61 variant proteins, expression vectors comprising such polynucleotides, and host cells that have been transfected with such vectors so as to express the GH61 variant proteins that are encoded.
Fragments and Variants
GH61 variant proteins of this invention may comprise one or more substitutions, deletions, or additions in the sequence in addition to the substitutions highlighted above. By way of illustration, the GH61 protein may be longer or shorter by at least about 5, 10, 20, 40, 75, 100, 125, 150, or 200 amino acids; or by about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 15%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, or 80% of the total number of amino acids in the polypeptide, compared with SEQ ID NO:2. The variant or any of these fragments may also be part of a fusion protein in which a portion having GH61 activity is joined to one or more other sequences. Providing the protein retains a degree of GH61 activity or other commercial applicability, the variations may comprise any combination of amino acid substitutions at any position that is not specifically indicated otherwise. Depending on the circumstances, a conservative amino acid substitution may be preferred over other types of substitutions.
Where an amino acid substitution is a “conservative” substitution, the substituted amino acid that shares one or more chemical property with the amino acid it is replacing. Shared properties include the following: Basic amino acids: arginine (R), lysine (K), histidine (H); acidic amino acids: glutamic acid (E) and aspartic acid (D); uncharged polar amino acids: glutamine (Q) and asparagine (N); hydrophobic amino acids: leucine (L), isoleucine (I), valine (V); aromatic amino acids: phenylalanine (F), tryptophan (W), and tyrosine (Y); sulphur-containing amino acids: cysteine (C), methionine (M); small amino acids: glycine (G), alanine (A), serine (S), threonine (T), proline (P), cysteine (C), and methionine (M).
Obtaining Functional Fragments and Variants
Functional fragments of GH61 protein variants of this invention can be identified by standard methodology for mapping function within a polypeptide. In some embodiments, recombinant protein is expressed that has effectively been trimmed at the N- or C-terminus, and then tested in a GH61 activity assay. Trimming can continue until activity is lost, at which point the minimum functional unit of the protein would be identified. Fragments containing any portion of the protein down to the identified size would typically be functional, as would be fusion constructs containing at least the functional core of the protein.
To generate further variants that incorporate one or more amino acid changes in a GH61 encoding sequence, the skilled artisan can change particular nucleotides, and then retest the expressed protein for GH61 activity.
An effective way to generate a large collection of functional variants is to use a random mutation strategy. The standard texts Protocols in Molecular Biology (Ausubel et al. eds.) and Molecular Cloning: A Laboratory Manual (Sambrook et al. eds.) describe techniques employing chemical mutagenesis, cassette mutagenesis, degenerate oligonucleotides, mutually priming oligonucleotides, linker-scanning mutagenesis, alanine-scanning mutagenesis, and error-prone PCR. Other efficient methods include the E. coli mutator strains of Stratagene (See e.g., Greener et al., Methods Mol. Biol. 57:375 [1996]) and the DNA shuffling technique of Maxygen (See e.g., Patten et al., Curr. Opin. Biotechnol., 8:724 [1997]; Harayama, Tr. Biotechnol., 16:76 [1998]; U.S. Pat. Nos. 5,605,793 and 6,132,970). To increase variation, a technology can be used that generates more abrupt changes, such as DNA shuffling techniques.
Mutagenesis may be performed in accordance with any of the techniques known in the art, including random and site-specific mutagenesis. Directed evolution can be performed with any of the techniques known in the art to screen for production of variants including shuffling. Mutagenesis and directed evolution methods are well known in the art (See e.g., U.S. Pat. Nos. 5,605,793, 5,830,721, 6,132,970, 6,420,175, 6,277,638, 6,365,408, 6,602,986, 7,288,375, 6,287,861, 6,297,053, 6,576,467, 6,444,468, 5,811,238, 6,117,679, 6,165,793, 6,180,406, 6,291,242, 6,995,017, 6,395,547, 6,506,602, 6,519,065, 6,506,603, 6,413,774, 6,573,098, 6,323,030, 6,344,356, 6,372,497, 7,868,138, 5,834,252, 5,928,905, 6,489,146, 6,096,548, 6,387,702, 6,391,552, 6,358,742, 6,482,647, 6,335,160, 6,653,072, 6,355,484, 603,344, 6,319,713, 6,613,514, 6,455,253, 6,579,678, 6,586,182, 6,406,855, 6,946,296, 7,534,564, 7,776,598, 5,837,458, 6,391,640, 6,309,883, 7,105,297, 7,795,030, 6,326,204, 6,251,674, 6,716,631, 6,528,311, 6,287,862, 6,335,198, 6,352,859, 6,379,964, 7,148,054, 7,629,170, 7,620,500, 6,365,377, 6,358,740, 6,406,910, 6,413,745, 6,436,675, 6,961,664, 7,430,477, 7,873,499, 7,702,464, 7,783,428, 7,747,391, 7,747,393, 7,751,986, 6,376,246, 6,426,224, 6,423,542, 6,479,652, 6,319,714, 6,521,453, 6,368,861, 7,421,347, 7,058,515, 7,024,312, 7,620,502, 7,853,410, 7,957,912, 7,904,249, and all related US and non-US counterparts; Ling et al., Anal. Biochem., 254(2):157-78 [1997]; Dale et al., Meth. Mol. Biol., 57:369-74 [1996]; Smith, Ann. Rev. Genet., 19:423-462 [1985]; Botstein et al., Science, 229:1193-1201 [1985]; Carter, Biochem. J., 237:1-7 [1986]; Kramer et al., Cell, 38:879-887 [1984]; Wells et al., Gene, 34:315-323 [1985]; Minshull et al., Curr. Op. Chem. Biol., 3:284-290 [1999]; Christians et al., Nat. Biotechnol., 17:259-264 [1999]; Crameri et al., Nature, 391:288-291 [1998]; Crameri, et al., Nat. Biotechnol., 15:436-438 [1997]; Zhang et al., Proc. Nat. Acad. Sci. U.S.A., 94:4504-4509 [1997]; Crameri et al., Nat. Biotechnol., 14:315-319 [1996]; Stemmer, Nature, 370:389-391 [1994]; Stemmer, Proc. Nat. Acad. Sci. USA, 91:10747-10751 [1994]; WO 95/22625; WO 97/0078; WO 97/35966; WO 98/27230; WO 00/42651; WO 01/75767; and WO 2009/152336, all of which are incorporated herein by reference).
There are commercially available services and kits available to the skilled reader to use in obtaining variants of the claimed proteins. By way of illustration, systems specifically designed for mutagenesis projects include the following: the GeneTailorTM Site-Directed Mutagenesis System sold by InVitrogenTM Life Technologies; the BD DiversifyTM PCR Random Mutagenesis KitTM, sold by BD Biosciences/Clontech; the Template Generation SystemTM, sold by MJ Research Inc., the XL1-RedTM mutator strain of E. coli, sold by Stratagene; and the GeneMorph® Random Mutagenesis KitTM, also sold by Stratagene. By employing any of these systems in conjunction with a suitable GH61 activity assay, variants can be generated and tested in a high throughput manner.
Alternatively or in addition, the user may conduct further evolution of the encoded protein (See e.g., U.S. Pat. No. 7,981,614; US Pat. Appln. Publ. No. 2011/0034342; U.S. Pat. Nos. 7,795,030; 7,647,184; 6,939,689; and 6,773,900).
After each iteration of mutagenesis, the user can test and select the desired clones retaining GH61 activity. Optionally, the selected clones can be subject to further rounds of mutagenesis, until the desired degree of variation from the original sequence has been achieved.
Cellulase Enzymes and Compositions
The GH61 proteins of this invention are useful for increasing the yield of fermentable sugars in a saccharification reaction with one or more cellulase enzymes. The cellulase enzymes can be produced in the same cell as the GH61 protein or in a different cell. In either case, the cellulase enzymes can be expressed from a recombinant encoding region or from a constitutive gene. The cellulase enzymes can be provided in the form of a culture broth (with or without the microorganism producing the enzyme(s)) or supernatant, or purified to any extent desired.
The terms “cellulase” and “cellulase enzyme” broadly refer to enzymes that catalyze the hydrolysis of the beta-1,4-glycosidic bonds joining individual glucose units in a cellulose containing substrate. Examples of cellulase enzymes suitable for use with the GH61 proteins of this invention are described in more detail later in this section.
Endoglucanases (EGs), comprise a group of cellulase enzymes classified as E.C. 3.2.1.4. These enzymes catalyze the hydrolysis of internal beta-1,4 glycosidic bonds of cellulose. In some embodiments, the present invention comprises an endogenous M. thermophila endoglucanase such as M. thermophila EG2 (See, WO 2007/109441) or a variant thereof. In some additional embodiments, the EG is from S. avermitilis, having a sequence set forth in GenBank accession NP—821730, or a variant thereof (See e.g., US Pat. Appln. Publ. No. 2010/0267089 A1). In some additional embodiments, the EG is a Thermoascus aurantiacus EG or variant thereof. In some further embodiments, the EG is an endogenous EG from a bacteria, a yeast, or a filamentous fungus other than M. thermophila. Indeed, it is contemplated that any suitable EG will find use in combination with the GH61 proteins provided herein. It is not intended that the present invention be limited to any specific EG.
Beta-glucosidases (BGL), comprise a group of cellulase enzymes classified as E.C. 3.2.1.21. These enzymes hydrolyze cellobiose to glucose. In some embodiments, the BGL is an endogenous M. thermophila enzyme, or a variant thereof (See e.g., US Pat. Appln. Publ. No. 2011/0129881 A1; and US Pat. Appln. Publ. No. 2011/0124058 A1). In some alternative embodiments, the BGL is from Azospirillum irakense (CelA), or a variant thereof (See e.g., US Pat. Appln. Publ. No. 2011/0114744 A1; and PCT/US2010/038902). Indeed, it is contemplated that any suitable BGL will find use in combination with the GH61 proteins provided herein. It is not intended that the present invention be limited to any specific BGL.
Cellobiohydrolases comprise a group of cellulase enzymes classified as E.C. 3.2.1.91. Type 1 cellobiohydrolase (CBH1) hydrolyzes cellobiose processively from the reducing end of cellulose chains. Type 2 cellobiohydrolase (CBH2) hydrolyzes cellobiose processively from the nonreducing end of cellulose chains. In some embodiments, the CBH1 and/or CBH2 enzymes used in the present invention are endogenous to M. thermophila, while in some other embodiments, the CBH1 and/or CBH2 enzymes used in the present invention are obtained from bacteria, yeast, and/or a filamentous fungus other than M. thermophila. Indeed, it is contemplated that any suitable CBHs will find use in combination with the GH61 proteins provided herein. It is not intended that the present invention be limited to any specific CBHs. The invention provides compositions comprising a GH61 variant protein in combination with at least one, at least two, at least three, or more than three cellulases selected from EG, BGL, CBH1, CBH2, xylosidase, and/or xylanase. In some embodiments, enzymes are purified or partly purified before combining them, so that the combined mass of the GH61, EG, BGL, CBH1 and CBH2 is at least about 50% or at least about 70% of the total cell-free protein in compositions.
In addition to one or more cellulase enzymes such as those listed above, in some embodiments, GH61 variant enzymes are combined with other enzymes to produce mixtures with industrial applicability. Such combinations are useful, for example, in rendering a cellulose-containing source into an intermediate that is more amenable to hydrolysis by the cellulase enzymes in the mixture. For example, in some embodiments, enzymes are selected to digest or hydrolyze other components of a particular cellulosic biomass, such as hemicellulose, arabinogalactan, pectin, rhamnogalacturonan and/or lignin.
In some embodiments, the compositions comprise enzymes selected from endoxylanases (EC 3.2.1.8); β-xylosidases (EC 3.2.1.37); alpha-L-arabinofuranosidases (EC 3.2.1.55); alpha-glucuronidases (EC 3.2.1.139); acetylxylanesterases (EC 3.1.1.72); feruloyl esterases (EC 3.1.1.73); coumaroyl esterases (EC 3.1.1.73); alpha-galactosidases (EC 3.2.1.22); beta-galactosidases (EC 3.2.1.23); beta-mannanases (EC 3.2.1.78); beta-mannosidases (EC 3.2.1.25); endo-polygalacturonases (EC 3.2.1.15); pectin methyl esterases (EC 3.1.1.11); endo-galactanases (EC 3.2.1.89); pectin acetyl esterases (EC 3.1.1.6); endo-pectin lyases (EC 4.2.2.10); pectate lyases (EC 4.2.2.2); alpha rhamnosidases (EC 3.2.1.40); exo-poly-alpha-galacturonosidase (EC 3.2.1.82); 1,4-alpha-galacturonidase (EC 3.2.1.67); exopolygalacturonate lyases (EC 4.2.2.9); rhamnogalacturonan endolyases EC (4.2.2.B3); rhamnogalacturonan acetylesterases (EC 3.2.1.B11); rhamnogalacturonan galacturonohydrolases (EC 3.2.1.B11); endo-arabinanases (EC 3.2.1.99); laccases (EC 1.10.3.2); manganese-dependent peroxidases (EC 1.10.3.2); amylases (EC 3.2.1.1), glucoamylases (EC 3.2.1.3), proteases, lipases, and lignin peroxidases (EC 1.11.1.14). Any combination of one, two, three, four, five, or more than five enzymes find use in the compositions of the present invention.
Cellulase mixtures for efficient enzymatic hydrolysis of cellulose are known (See e.g., Viikari et al., Adv. Biochem. Eng. Biotechnol., 108:121-45 [2007]; and US Pat. Publns. 2009/0061484; US 2008/0057541; and US 2009/0209009, each of which is incorporated herein by reference). In some embodiments, mixtures of purified naturally occurring or recombinant enzymes are combined with cellulosic feedstock or a product of cellulose hydrolysis. In some embodiments, one or more cell populations, each producing one or more naturally occurring or recombinant cellulases, are combined with cellulosic feedstock or a product of cellulose hydrolysis.
In some embodiments, the GH61 variant polypeptides of the present invention are present in mixtures comprising enzymes other than cellulases that degrade cellulose, hemicellulose, pectin, and/or lignocellulose.
In some embodiments, the present invention provides at least one GH61 variant and at least one endoxylanase. Endoxylanases (EC 3.2.1.8) catalyze the endo hydrolysis of 1,4-beta-D-xylosidic linkages in xylans. This enzyme may also be referred to as endo-1,4-beta-xylanase or 1,4-beta-D-xylan xylanohydrolase. In some embodiments, an alternative is EC 3.2.1.136, a glucuronoarabinoxylan endoxylanase, an enzyme that is able to hydrolyze 1,4 xylosidic linkages in glucuronoarabinoxylans.
In some embodiments, the present invention provides at least one GH61 variant and at least one beta-xylosidase. Beta-xylosidases (EC 3.2.1.37) catalyze the hydrolysis of 1,4-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini. This enzyme may also be referred to as xylan 1,4-beta-xylosidase, 1,4-beta-D-xylan xylohydrolase, exo-1,4-beta-xylosidase or xylobiase.
In some embodiments, the present invention provides at least one GH61 variant and at least one α-L-arabinofuranosidase. Alpha-L-arabinofuranosidases (EC 3.2.1.55) catalyze the hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides. The enzyme acts on alpha-L-arabinofuranosides, alpha-L-arabinans containing (1,3)- and/or (1,5)-linkages, arabinoxylans, and arabinogalactans. Alpha-L-arabinofuranosidase is also known as arabinosidase, alpha-arabinosidase, alpha-L-arabinosidase, alpha-arabinofuranosidase, arabinofuranosidase, polysaccharide alpha-L-arabinofuranosidase, alpha-L-arabinofuranoside hydrolase, L-arabinosidase and alpha-L-arabinanase.
In some embodiments, the present invention provides at least one GH61 variant and at least one alpha-glucuronidase. Alpha-glucuronidases (EC 3.2.1.139) catalyze the hydrolysis of an alpha-D-glucuronoside to D-glucuronate and an alcohol.
In some embodiments, the present invention provides at least one GH61 variant and at least one acetylxylanesterase. Acetylxylanesterases (EC 3.1.1.72) catalyze the hydrolysis of acetyl groups from polymeric xylan, acetylated xylose, acetylated glucose, alpha-napthyl acetate, and p-nitrophenyl acetate.
In some embodiments, the present invention provides at least one GH61 variant and at least one feruloyl esterase. Feruloyl esterases (EC 3.1.1.73) have 4-hydroxy-3-methoxycinnamoyl-sugar hydrolase activity (EC 3.1.1.73) that catalyzes the hydrolysis of the 4-hydroxy-3-methoxycinnamoyl (feruloyl) group from an esterified sugar, which is usually arabinose in “natural” substrates, to produce ferulate (4-hydroxy-3-methoxycinnamate). Feruloyl esterase is also known as ferulic acid esterase, hydroxycinnamoyl esterase, FAE-III, cinnamoyl ester hydrolase, FAEA, cinnAE, FAE-I, or FAE-II.
In some embodiments, the present invention provides at least one GH61 variant and at least one coumaroyl esterase. Coumaroyl esterases (EC 3.1.1.73) catalyze a reaction of the form: coumaroyl-saccharide+H2O=coumarate+saccharide. In some embodiments, the saccharide is an oligosaccharide or a polysaccharide. This enzyme may also be referred to as trans-4-coumaroyl esterase, trans-p-coumaroyl esterase, p-coumaroyl esterase or p-coumaric acid esterase. The enzyme also falls within EC 3.1.1.73; it may also be referred to as a “feruloyl esterase.”
In some embodiments, the present invention provides at least one GH61 variant and at least one alpha-galactosidase. Alpha-galactosidases (EC 3.2.1.22) catalyze the hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans, galactans and arabinogalactans. This enzyme may also be referred to as “melibiase.”
In some embodiments, the present invention provides at least one GH61 variant and at least one beta-galactosidase. Beta-galactosidases (EC 3.2.1.23) catalyze the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In some embodiments, the polypeptide is also capable of hydrolyzing alpha-L-arabinosides. This enzyme may also be referred to as exo-(1->4)-beta-D-galactanase or lactase.
In some embodiments, the present invention provides at least one GH61 variant and at least one beta-mannanase. Beta-mannanases (EC 3.2.1.78) catalyze the random hydrolysis of 1,4-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans. This enzyme may also be referred to as “mannan endo-1,4-beta-mannosidase” or “endo-1,4-mannanase.”
In some embodiments, the present invention provides at least one GH61 variant and at least one beta-mannosidase. Beta-mannosidases (EC 3.2.1.25) catalyze the hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides. This enzyme may also be referred to as mannanase or mannase.
In some embodiments, the present invention provides at least one GH61 variant and at least one glucoamylase. Glucoamylases (EC 3.2.1.3) catalyzes the release of D-glucose from non-reducing ends of oligo- and poly-saccharide molecules. Glucoamylase is also generally considered a type of amylase known as amylo-glucosidase.
In some embodiments, the present invention provides at least one GH61 variant and at least one amylase. Amylases (EC 3.2.1.1) are starch cleaving enzymes that degrade starch and related compounds by hydrolyzing the alpha-1,4 and/or alpha-1,6 glucosidic linkages in an endo- or an exo-acting fashion. Amylases include alpha-amylases (EC 3.2.1.1); beta-amylases (3.2.1.2), amylo-amylases (EC 3.2.1.3), alpha-glucosidases (EC 3.2.1.20), pullulanases (EC 3.2.1.41), and isoamylases (EC 3.2.1.68). In some embodiments, the amylase is an alpha-amylase.
In some embodiments one or more enzymes that degrade pectin are included in enzyme mixtures that comprise at least one GH61 variant of the present invention. Pectinases catalyze the hydrolysis of pectin into smaller units such as oligosaccharide or monomeric saccharides. In some embodiments, the enzyme mixtures comprise any pectinase, for example an endo-polygalacturonase, a pectin methyl esterase, an endo-galactanase, a pectin acetyl esterase, an endo-pectin lyase, pectate lyase, alpha rhamnosidase, an exo-galacturonase, an exo-polygalacturonate lyase, a rhamnogalacturonan hydrolase, a rhamnogalacturonan lyase, a rhamnogalacturonan acetyl esterase, a rhamnogalacturonan galacturonohydrolase and/or a xylogalacturonase.
In some embodiments, the present invention provides at least one GH61 variant and at least one endo-polygalacturonase, Endo-polygalacturonases (EC 3.2.1.15) catalyze the random hydrolysis of 1,4-alpha-D-galactosiduronic linkages in pectate and other galacturonans. This enzyme may also be referred to as “polygalacturonase pectin depolymerase,” “pectinase,” “endopolygalacturonase,” “pectolase,” “pectin hydrolase,” “pectin polygalacturonase,” “poly-alpha-1,4-galacturonide glycanohydrolase,” “endogalacturonase,” “endo-D-galacturonase” or “poly(1,4-alpha-D-galacturonide) glycanohydrolase.”
In some embodiments, the present invention provides at least one GH61 variant and at least one pectin methyl esterase. Pectin methyl esterases (EC 3.1.1.11) catalyze the reaction: pectin+n H2O=n methanol+pectate. The enzyme may also been known as “pectin esterase,” “pectin demethoxylase,” “pectin methoxylase,” “pectin methylesterase,” “pectase,” “pectinoesterase,” or “pectin pectylhydrolase.”
In some embodiments, the present invention provides at least one GH61 variant and at least one endo-galactanase. Endo-galactanases (EC 3.2.1.89) catalyze the endohydrolysis of 1,4-beta-D-galactosidic linkages in arabinogalactans. The enzyme may also be known as “arabinogalactan endo-1,4-beta-galactosidase,” “endo-1,4-beta-galactanase,” “galactanase,” “arabinogalactanase,” or “arabinogalactan 4-beta-D-galactanohydrolase.”
In some embodiments, the present invention provides at least one GH61 variant and at least one pectin acetyl esterase. Pectin acetyl esterases catalyze the deacetylation of the acetyl groups at the hydroxyl groups of GaIUA residues of pectin.
In some embodiments, the present invention provides at least one GH61 variant and at least one endo-pectin lyase. Endo-pectin lyases (EC 4.2.2.10) catalyze the eliminative cleavage of (1→4)-alpha-D-galacturonan methyl ester to give oligosaccharides with 4-deoxy-6-O-methyl-α-D-galact-4-enuronosyl groups at their non-reducing ends. The enzyme may also be known as “pectin lyase,” “pectin trans-eliminase,” “endo-pectin lyase,” “polymethylgalacturonic transeliminase,” “pectin methyltranseliminase,” “pectolyase,” “PL,” “PNL,” “PMGL,” or “(1→4)-6-O-methyl-alpha-D-galacturonan lyase.”
In some embodiments, the present invention provides at least one GH61 variant and at least one pectate lyase. Pectate lyases (EC 4.2.2.2) catalyze the eliminative cleavage of (1→4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends. The enzyme may also be known “polygalacturonic transeliminase,” “pectic acid transeliminase,” “polygalacturonate lyase,” “endopectin methyltranseliminase,” “pectate transeliminase,” “endogalacturonate transeliminase,” “pectic acid lyase,” “pectic lyase,” alpha-1,4-D-endopolygalacturonic acid lyase,” “PGA lyase,” “PPase-N,” “endo-alpha-1,4-polygalacturonic acid lyase,” “polygalacturonic acid lyase,” “pectin trans-eliminase,” “polygalacturonic acid trans-eliminase,” or “(1→4)-alpha-D-galacturonan lyase,”
In some embodiments, the present invention provides at least one GH61 variant and at least one alpha-rhamnosidase. Alpha-rhamnosidases (EC 3.2.1.40) catalyze the hydrolysis of terminal non-reducing alpha-L-rhamnose residues in alpha-L-rhamnosides or alternatively in rhamnogalacturonan. This enzyme may also be known as “alpha-L-rhamnosidase T,” “alpha-L-rhamnosidase N,” or “alpha-L-rhamnoside rhamnohydrolase.”
In some embodiments, the present invention provides at least one GH61 variant and at least one exo-galacturonase. Exo-galacturonases (EC 3.2.1.82) hydrolyze pectic acid from the non-reducing end, releasing digalacturonate. The enzyme may also be known as “exo-poly-alpha-galacturonosidase,” “exopolygalacturonosidase,” or “exopolygalacturanosidase.”
In some embodiments, the present invention provides at least one GH61 variant and at least one-galacturan 1,4-alpha galacturonidase. Exo-galacturonases (EC 3.2.1.67) catalyze a reaction of the following type: (1,4-α-D-galacturonide)n+H2O=(1,4-α-D-galacturonide)n-i+D-galacturonate. The enzyme may also be known as “poly [1->4) alpha-D-galacturonide] galacturonohydrolase,” “exopolygalacturonase,” “poly(galacturonate) hydrolase,” “exo-D-galacturonase,” “exo-D-galacturonanase,” “exopoly-D-galacturonase,” or “poly(1,4-alpha-D-galacturonide) galacturonohydrolase.”
In some embodiments, the present invention provides at least one GH61 variant and at least one exopolygalacturonate lyase. Exopolygalacturonate lyases (EC 4.2.2.9) catalyze eliminative cleavage of 4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate from the reducing end of pectate (i.e., de-esterified pectin). This enzyme may be known as “pectate disaccharide-lyase,” “pectate exo-lyase,” “exopectic acid transeliminase,” “exopectate lyase,” “exopolygalacturonic acid-trans-eliminase,” “PATE,” “exo-PATE,” “exo-PGL,” or “(1→4)-alpha-D-galacturonan reducing-end-disaccharide-lyase.”
In some embodiments, the present invention provides at least one GH61 variant and at least one rhamnogalacturonanase. Rhamnogalacturonanases hydrolyze the linkage between galactosyluronic acid and rhamnopyranosyl in an endo-fashion in strictly alternating rhamnogalacturonan structures, consisting of the disaccharide [(1,2-alpha-L-rhamnoyl-(1,4)-alpha-galactosyluronic acid].
In some embodiments, the present invention provides at least one GH61 variant and at least one rhamnogalacturonan lyase. Rhamnogalacturonan lyases cleave alpha-L-Rhap-(1→4)-alpha-D-GalpA linkages in an endo-fashion in rhamnogalacturonan by beta-elimination.
In some embodiments, the present invention provides at least one GH61 variant and at least one rhamnogalacturonan acetyl esterase. Rhamnogalacturonan acetyl esterases catalyze the deacetylation of the backbone of alternating rhamnose and galacturonic acid residues in rhamnogalacturonan.
In some embodiments, the present invention provides at least one GH61 variant and at least one rhamnogalacturonan galacturonohydrolase. Rhamnogalacturonan galacturonohydrolases hydrolyze galacturonic acid from the non-reducing end of strictly alternating rhamnogalacturonan structures in an exo-fashion. This enzyme may also be known as “xylogalacturonan hydrolase.”
In some embodiments, the present invention provides at least one GH61 variant and at least one endo-arabinanase. Endo-arabinanases (EC 12.1.99) catalyze endohydrolysis of 1,5-alpha-arabinofuranosidic linkages in 1,5-arabinans. The enzyme may also be known as “endo-arabinase,” “arabinan endo-1,5-alpha-L-arabinosidase,” “endo-1,5-alpha-L-arabinanase,” “endo-alpha-1,5-arabanase,” “endo-arabanase,” or “1,5-alpha-L-arabinan 1,5-alpha-L-arabinanohydrolase.”.
In some embodiments, the present invention provides at least one GH61 variant and at least one enzyme that participates in lignin degradation in an enzyme mixture. Enzymatic lignin depolymerization can be accomplished by lignin peroxidases, manganese peroxidases, laccases, and/or cellobiose dehydrogenases (CDH), often working in synergy. These extracellular enzymes are often referred to as “lignin-modifying enzymes” or “LMEs.” Three of these enzymes comprise two glycosylated heme-containing peroxidases, namely lignin peroxidase (LIP), Mn-dependent peroxidase (MNP), and copper-containing phenoloxidase laccase (LCC).
In some embodiments, the present invention provides at least one GH61 variant and at least one laccase. Laccases are copper containing oxidase enzymes that are found in many plants, fungi and microorganisms. Laccases are enzymatically active on phenols and similar molecules and perform a one electron oxidation. Laccases can be polymeric and the enzymatically active form can be a dimer or trimer.
In some embodiments, the present invention provides at least one GH61 variant and at least one Mn-dependent peroxidase. The enzymatic activity of Mn-dependent peroxidase (MnP) in is dependent on Mn2+. Without being bound by theory, it has been suggested that the main role of this enzyme is to oxidize Mn2+ to Mn3+ (See e.g, Glenn et al., Arch. Biochem. Biophys., 251:688-696 [1986]). Subsequently, phenolic substrates are oxidized by the Mn3+ generated.
In some embodiments, the present invention provides at least one GH61 variant and at least one lignin peroxidase. Lignin peroxidase is an extracellular heme peroxidase that catalyses the oxidative depolymerization of dilute solutions of polymeric lignin in vitro. Some of the substrates of LiP, most notably 3,4-dimethoxybenzyl alcohol (veratryl alcohol, VA), are active redox compounds that have been shown to act as redox mediators. VA is a secondary metabolite produced at the same time as LiP by ligninolytic cultures of P. chrysosporium and without being bound by theory, has been proposed to function as a physiological redox mediator in the LiP-catalyzed oxidation of lignin in vivo (See e.g., Harvey, et al., FEBS Lett., 195:242-246 [1986]).
In some embodiments, the present invention provides at least one GH61 variant and at least one protease, amylase, glucoamylase, and/or a lipase that participates in cellulose degradation.
As used herein, the term “protease” includes enzymes that hydrolyze peptide bonds (peptidases), as well as enzymes that hydrolyze bonds between peptides and other moieties, such as sugars (glycopeptidases). Many proteases are characterized under EC 3.4, and are suitable for use in the invention. Some specific types of proteases include, cysteine proteases including pepsin, papain and serine proteases including chymotrypsins, carboxypeptidases and metalloendopeptidases.
As used herein, the term “lipase” includes enzymes that hydrolyze lipids, fatty acids, and acylglycerides, including phosphoglycerides, lipoproteins, diacylglycerols, and the like. In plants, lipids are used as structural components to limit water loss and pathogen infection. These lipids include waxes derived from fatty acids, as well as cutin and suberin.
In some additional embodiments, the present invention provides at least one GH61 variant and at least one expansin or expansin-like protein, such as a swollenin (See e.g., Salheimo et al., Eur. J. Biochem., 269:4202-4211 [2002]) or a swollenin-like protein. Expansins are implicated in loosening of the cell wall structure during plant cell growth. Expansins have been proposed to disrupt hydrogen bonding between cellulose and other cell wall polysaccharides without having hydrolytic activity. In this way, they are thought to allow the sliding of cellulose fibers and enlargement of the cell wall. Swollenin, an expansin-like protein contains an N-terminal Carbohydrate Binding Module Family 1 domain (CBD) and a C-terminal expansin-like domain. In some embodiments, an expansin-like protein or swollenin-like protein comprises one or both of such domains and/or disrupts the structure of cell walls (such as disrupting cellulose structure), optionally without producing detectable amounts of reducing sugars.
In some embodiments, the present invention provides at least one GH61 variant and at least one polypeptide product of a cellulose integrating protein, scaffoldin or a scaffoldin-like protein, for example CipA or CipC from Clostridium thermocellum or Clostridium cellulolyticum, respectively. Scaffoldins and cellulose integrating proteins are multi-functional integrating subunits which may organize cellulolytic subunits into a multi-enzyme complex. This is accomplished by the interaction of two complementary classes of domains (i.e. a cohesion domain on scaffoldin and a dockerin domain on each enzymatic unit). The scaffoldin subunit also bears a cellulose-binding module that mediates attachment of the cellulosome to its substrate. A scaffoldin or cellulose integrating protein for the purposes of this invention may comprise one or both such domains.
In some embodiments, the present invention provides at least one GH61 variant and at least one cellulose induced protein or modulating protein, for example as encoded by a cip1 or cip2 gene or similar genes from Trichoderma reesei (See e.g., Foreman et al., J. Biol. Chem., 278:31988-31997 [2003]).
In some embodiments, the present invention provides at least one GH61 variant and at least one member of each of the classes of the polypeptides described above, several members of one polypeptide class, or any combination of these polypeptide classes to provide enzyme mixtures suitable for various uses.
In some embodiments, the enzyme mixture comprises other types of cellulases, selected from but not limited to cellobiohydrolase, endoglucanase, beta-glucosidase, and glycoside hydrolase 61 protein (GH61) cellulases. These enzymes may be wild-type or recombinant enzymes. In some embodiments, the cellobiohydrolase is a type 1 cellobiohydrolase (e.g., a T. reesei cellobiohydrolase I). In some embodiments, the endoglucanase comprises a catalytic domain derived from the catalytic domain of a Streptomyces avermitilis endoglucanase (See e.g., US Pat. Appln. Pub. No. 2010/0267089; U.S. Pat. No. 8,206,960; and U.S. Pat. No. 8,088,608, each of which is incorporated herein by reference). In some embodiments, at least one cellulase in the mixtures of the present invention is derived from Acidothermus cellulolyticus, Thermobifida fusca, Humicola grisea, Myceliophthora thermophila, Chaetomium thermophilum, Acremonium sp., Thielavia sp, Trichoderma reesei, Aspergillus sp., or a Chrysosporium sp. In some embodiments, cellulase enzymes of the cellulase mixture work together resulting in decrystallization and hydrolysis of the cellulose from a biomass substrate to yield fermentable sugars, such as but not limited to glucose.
Some cellulase mixtures for efficient enzymatic hydrolysis of cellulose are known (See e.g., Viikari et al., Adv. Biochem. Eng. Biotechnol., 108:121-45 [2007]; and US Pat. Appln. Pubin. Nos. US 2009/0061484, US 2008/0057541, and US 2009/0209009, each of which is incorporated herein by reference in their entireties). In some embodiments, mixtures of purified naturally occurring or recombinant enzymes are combined with cellulosic feedstock or a product of cellulose hydrolysis. Alternatively or in addition, one or more cell populations, each producing one or more naturally occurring or recombinant cellulase, are combined with cellulosic feedstock or a product of cellulose hydrolysis.
In some embodiments, the enzyme mixture comprises commercially available purified cellulases. Commercial cellulases are known and available (e.g., C2730 cellulase from Trichoderma reesei ATCC No. 25921 available from Sigma-Aldrich, Inc.) Any suitable commercially available enzyme finds use in the present invention.
In some embodiments, the enzyme mixture comprises at least one isolated GH61 variant as provided herein and at least one or more isolated enzymes, including but not limited to at least one isolated CBH1a, isolated CBH2b, isolated endoglucanase (EG) (e.g., EG2 and/or EG1), and/or isolated beta-glucosidase (BGL). In some embodiments, at least 5%, at least 10%, at last 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% of the enzyme mixture is GH61. In some embodiments, the enzyme mixture further comprises a cellobiohydrolase type 1a (e.g., CBH1a), and GH61, wherein the enzymes together comprise at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, or at least 80% of the enzyme mixture. In some embodiments, the enzyme mixture further comprises a beta-glucosidase (BGL), GH61, and CBH, wherein the three enzymes together comprise at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, or at least 85% of the enzyme mixture. In some embodiments, the enzyme mixture further comprises an endoglucanase (EG), GH61, CBH2b, CBH1a, BGL, wherein the five enzymes together comprise at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, or at least 90% of the enzyme mixture. In some embodiments, the enzyme mixture comprises GH61, CBH2b, CBH1, BGL, and at least one EG, in any suitable proportion for the desired reaction.
In some embodiments, the enzyme mixture composition comprises isolated cellulases in the following proportions by weight (wherein the total weight of the cellulases is 100%): about 20%-10% of GH61, about 20%-10% of BGL, about 30%-25% of CBH1a, about 10%-30% of GH61, about 20%-10% of EG, and about 20%-25% of CBH2b. In some embodiments, the enzyme mixture composition comprises isolated cellulases in the following proportions by weight: about 20%-10% of GH61, about 25%-15% of BGL, about 20%-30% of CBH1a, about 10%-15% of EG, and about 25%-30% of CBH2b. In some embodiments, the enzyme mixture composition comprises isolated cellulases in the following proportions by weight: about 30%-20% of GH61, about 15%-10% of BGL, about 25%-10% of CBH1a, about 25%-10% of CBH2b, about 15%-10% of EG. In some embodiments, the enzyme mixture composition comprises isolated cellulases in the following proportions by weight: about 40-30% of GH61, about 15%-10% of BGL, about 20%-10% of CBH1a, about 20%-10% of CBH2b, and about 15%-10% of EG.
In some embodiments, the enzyme mixture composition comprises isolated cellulases in the following proportions by weight: about 50-40% of GH61, about 15%-10% of BGL, about 20%-5% of CBH1a, about 15%-10% of CBH2b, and about 10%-5% of EG. However, in some embodiments, the enzyme mixture composition comprises no EG (e.g., EG2). In some embodiments, the enzyme mixture composition comprises isolated cellulases in the following proportions by weight: about 10%-15% of GH61, about 20%-25% of BGL, about 30%-20% of CBH1a, about 15%-5% of EG, and about 25%-35% of CBH2b. In some embodiments, the enzyme mixture composition comprises isolated cellulases in the following proportions by weight: about 15%-5% of GH61, about 15%-10% of BGL, about 45%-30% of CBH1a, about 25%-5% of EG, and about 40%-10% of CBH2b. In some embodiments, the enzyme mixture composition comprises isolated cellulases in the following proportions by weight: about 10% of GH61, about 15% of BGL, about 40% of CBH1a, about 25% of EG, and about 10% of CBH2b.
In some embodiments, the enzyme mixtures provided herein further comprise at least one xylan-active enzyme and/or at least one ester-active enzyme. In some embodiments, the enzyme mixture compositions comprise about 0-25% xylanase (e.g., about 2%-5%, about 1%-10%, about 10%-15%, about 15%-25%, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, or about 15% xylanase) by weight. In some embodiments, the enzyme mixture compositions comprise about 0-15% xylosidase (e.g., about 2%-5%, about 1%-10%, about 10%-15%, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, or about 15% xylosidase) by weight. In some embodiments, the enzyme mixture compositions comprise about 0-15% esterase (e.g., about 2%-5%, about 1%-10%, about 10%-15%, about 1%, about 2%, about 3%, about 4%, about 5%, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, or about 15% esterase) by weight. It is contemplated that any suitable combination of enzymes and suitable enzyme concentrations will find use in the present invention, as applied using various saccharification reactions and conditions.
In some embodiments, the enzyme component comprises more than one CBH1a, CBH2b, EG, BGL, and/or GH61 variant enzyme (e.g., 2, 3 or 4 different enzymes), in any suitable combination. In some embodiments, an enzyme mixture composition of the invention further comprises at least one additional protein and/or enzyme. In some embodiments, enzyme mixture compositions of the present invention further comprise at least one additional enzyme other than at least one GH61 variant, BGL, CBH1a, wild-type GH61, and/or CBH2b. In some embodiments, the enzyme mixture compositions of the invention further comprise at least one additional cellulase, other than at least one GH61 variant, BGL, CBH1a, GH61, and/or CBH2b as described herein. In some embodiments, the GH61 polypeptide variant of the invention is also present in mixtures with non-cellulase enzymes that degrade cellulose, hemicellulose, pectin, and/or lignocellulose.
In some embodiments, GH61 polypeptide variant of the present invention is used in combination with other optional ingredients such as at least one buffer, surfactant, and/or scouring agent. In some embodiments, at least one buffer is used with the GH61 polypeptide variant of the present invention (optionally combined with other enzymes) to maintain a desired pH within the solution in which the GH61 variant is employed. The exact concentration of buffer employed depends on several factors which the skilled artisan can determine. Suitable buffers are well known in the art. In some embodiments, at least one surfactant is used in with the GH61 variant of the present invention. Suitable surfactants include any surfactant compatible with the GH61 variant and, optionally, with any other enzymes being used in the mixture. Exemplary surfactants include, but are not limited to anionic, non-ionic, and ampholytic surfactants. Suitable anionic surfactants include, but are not limited to, linear or branched alkylbenzenesulfonates; alkyl or alkenyl ether sulfates having linear or branched alkyl groups or alkenyl groups; alkyl or alkenyl sulfates; olefinsulfonates; alkanesulfonates, and the like. Suitable counter ions for anionic surfactants include, for example, alkali metal ions, such as sodium and potassium; alkaline earth metal ions, such as calcium and magnesium; ammonium ion; and alkanolamines having from 1 to 3 alkanol groups of carbon number 2 or 3. Ampholytic surfactants suitable for use in the practice of the present invention include, for example, quaternary ammonium salt sulfonates, betaine-type ampholytic surfactants, and the like. Suitable nonionic surfactants generally include polyoxalkylene ethers, as well as higher fatty acid alkanolamides or alkylene oxide adduct thereof, fatty acid glycerine monoesters, and the like. Mixtures of surfactants also find use in the present invention, as is known in the art.
Exemplary Mixtures of Cellulolytic Enzymes and Cofactors
As a further guide to the reader, yet without implying any limitation in the practice of the present invention, exemplary mixtures of components that may be used as catalysts in a saccharification reaction to generate fermentable sugars from a cellulosic substrate are provided herein. Concentrations are given in wt/vol of each component in the final reaction volume with the cellulose substrate. Also provided are percentages of each component (wt/wt) in relation to the total mass of the components that are listed for addition into each mixture (the “total protein”). This may be a mixture of purified enzymes and/or enzymes in a culture supernatant.
By way of example, the invention embodies mixtures that comprise at least four, at least five, or all six of the following components. In some embodiments, cellobiohydrolase 1 (CBH1) finds use; in some embodiments CBH1 is present at a concentration of about 0.14 to about 0.23 g/L (about 15% to about 25% of total protein). Exemplary CBH1 enzymes include, but are not limited to T. emersonii CBH1 (wild-type) (e.g., SEQ ID NO:125), M. thermophila CBH1a (wild-type) (e.g., SEQ ID NO:128), and the variants CBH1a-983 (SEQ ID NO:134) and CBH1a-145 (SEQ ID NO:131). In some embodiments, cellobiohydrolase 2 (CBH2) finds use; in some embodiments, CBH2 is present at a concentration of about 0.14 to about 0.23 g/L (about 15% to about 25% of total protein). Exemplary CBH2 enzymes include but are not limited to CBH2b from M. thermophila (wild-type) (e.g., SEQ ID NO:137). In some embodiments, endoglucanase 2 (EG2) finds use; in some embodiments, EG2 is present at a concentration of 0 to about 0.05 g/L (0 to about 5% of total protein). Exemplary EGs include, but are not limited to M. thermophila EG2 (wild-type) (e.g., SEQ ID NO:113). In some further embodiments, endoglucanase 1 (EG1) finds use; in some embodiments, EG1 is present at a concentration of about 0.05 to about 0.14 g/L (about 5% to about 15% of total protein). Exemplary EG1s include, but are not limited to M. thermophila EG1b (wild-type) (e.g., SEQ ID NO:110). In some embodiments, beta-glucosidase (BGL) finds use in the present invention; in some embodiments, BGL is present at a concentration of about 0.05 to about 0.09 g/L (about 5% to about 10% of total protein). Exemplary beta-glucosidases include, but are not limited to M. thermophila BGL1 (wild-type) (e.g., SEQ ID NO:116), variant BGL-900 (SEQ ID NO:122), and variant BGL-883 (SEQ ID NO:119). In some further embodiments, GH61 protein and/or protein variants find use; in some embodiments, GH61 enzymes are present at a concentration of about 0.23 to about 0.33 g/L (about 25% to about 35% of total protein). Exemplary GH61s include, but are not limited to M. thermophila GH61a wild-type (SEQ ID NO:2), Variant 1 (SEQ ID NO:5), Variant 5 (SEQ ID NO:8) and/or Variant 9 (SEQ ID NO:11), and/or any other GH61a variant proteins, as well as any of the other GH61 enzymes (e.g., GH61b, GH61c, GH61d, GH61e, GH61f, GH61g, GH61h, GH161i, GH61j, GH61k, GH61l, GH61m, GH61n, GH61o, GH61p, GH61q, GH61r, GH61s, GH61t, GH61u, GH61v, GH61w, GH61x, and/or GH61y) as provided herein.
In some embodiments, one, two or more than two enzymes are present in the mixtures of the present invention. In some embodiments, GH61p is present at a concentration of about 0.05 to about 0.14 g/L (e.g, about 1% to about 15% of total protein). Exemplary M. thermophila GH61p enzymes include those set forth in SEQ ID NOS:70 and 73. In some embodiments, GH61f is present at a concentration of about 0.05 to about 0.14 g/L (about 1% to about 15% of total protein). An exemplary M. thermophila GH61f is set forth in SEQ ID NO:29. In some additional embodiments, at least one additional GH61 enzyme provided herein (e.g., GH61b, GH61c, GH61d, GH61e, GH61g, GH61h, GH61i, GH61j, GH61k, GH61l, GH61m, GH61n, GH61n, GH61o, GH61q, GH61r, GH61s, GH61t, GH61u, GH61v, GH61w, GH61x, and/or GH61y, finds use at an appropriate concentration (e.g., about 0.05 to about 0.14 g/L [about 1% to about 15% of total protein]).
In some embodiments, at least one xylanase at a concentration of about 0.05 to about 0.14 g/L (about 1% to about 15% of total protein) finds use in the present invention. Exemplary xylanases include but are not limited to the M. thermophila xylanase-3 (SEQ ID NO:149), xylanase-2 (SEQ ID NO:152), xylanase-1 (SEQ ID NO:155), xylanase-6 (SEQ ID NO:158), and xylanase-5 (SEQ ID NO:161).
In some additional embodiments, at least one beta-xylosidase at a concentration of about 0.05 to about 0.14 g/L (e.g., about 1% to about 15% of total protein) finds use in the present invention. Exemplary beta-xylosidases include but are not limited to the M. thermophila beta-xylosidase (SEQ ID NO:164).
In still some additional embodiments, at least one acetyl xylan esterase at a concentration of about 0.05 to about 0.14 g/L (e.g., about 1% to about 15% of total protein) finds use in the present invention. Exemplary acetylxylan esterases include but are not limited to the M. thermophila acetylxylan esterase (SEQ ID NO:167).
In some further additional embodiments, at least one ferulic acid esterase at a concentration of about 0.05 to about 0.14 g/L (e.g., about 1% to about 15% of total protein) finds use in the present invention. Exemplary ferulic esterases include but are not limited to the M. thermophila ferulic acid esterase (SEQ ID NO:170).
In some embodiments, the enzyme mixtures comprise at least one GH61 variant protein as provided herein and at least one cellulase, including but not limited to any of the enzymes described herein. In some embodiments, the enzyme mixtures comprise at least one GH61 variant protein and at least one wild-type GH61 protein. In some embodiments, the enzyme mixtures comprise at least one GH61 variant protein and at least one non-cellulase enzyme. Indeed, it is intended that any combination of enzymes will find use in the enzyme compositions comprising at least one GH61 variant of the present invention.
The concentrations listed above are appropriate for a final reaction volume with the biomass substrate in which all of the components listed (the “total protein”) is about 0.75 g/L, and the amount of glucan is about 93 g/L, subject to routine optimization. The user may empirically adjust the amount of each component and total protein for cellulosic substrates that have different characteristics and/or are processed at a different concentration. Any one or more of the components may be supplemented or substituted with variants with common structural and functional characteristics, as described below.
Without implying any limitation, the following mixtures further describe some embodiments of the present invention.
Some mixtures comprise CBH1a within a range of about 15% to about 30% total protein, typically about 20% to about 25%; CBH2 within a range of about 15% to about 30%, typically about 17% to about 22%; EG2 within a range of about 1% to about 10%, typically about 2% to about 5%; BGL1 within a range of about 5% to about 15%, typically about 8% to about 12%; GH61a within a range of about 10% to about 40%, typically about 20% to about 30%; EG1b within a range of about 5% to about 25%, typically about 10% to about 18%; and GH61f within a range of 0% to about 30%; typically about 5% to about 20%.
In some mixtures, exemplary BGL1s include the BGL1 variant 900 (SEQ ID NO:122) and/or variant 883 (SEQ ID NO:119). In some embodiments, other enzymes are M. thermophila wild-type: CBH1a (SEQ ID NO:128), CBH2b (SEQ ID NO:137), EG2 (SEQ ID NO:113), GH61a (SEQ ID NO:2), EG1b (SEQ ID NO:110) and GH61f (SEQ ID NO:29). Any one or more of the components may be supplemented or substituted with variants having common structural and functional characteristics with the component being substituted or supplemented, as described below. In a saccharification reaction, the amount of glucan is generally about 50 to about 300 g/L, typically about 75 to about 150 g/L. The total protein is about 0.1 to about 10 g/L, typically about 0.5 to about 2 g/L, or about 0.75 g/L.
Some mixtures comprise CBH1 within a range of about 10% to about 30%, typically about 15% to about 25%; CBH2b within a range of about 10% to about 25%, typically about 15% to about 20%; EG2 within a range of about 1% to about 10%, typically about 2% to about 5%; EG1b within a range of about 2% to about 25%, typically about 6% to about 14%; GH61a within a range of about 5% to about 50%, typically about 10% to about 35%; and BGL1 within a range of about 2% to about 15%, typically about 5% to about 12%. Also included is copper sulfate to generate a final concentration of Cu++ of about 4 μM to about 200 μM, typically about 25 μM to about 60 μM. However, it is not intended that the added copper be limited to any particular concentration, as any suitable concentration finds use in the present invention and will be determined based on the reaction conditions.
In an additional mixture, an exemplary CBH1 is wild-type CBH1 from T. emersonii (SEQ ID NO:125), as well as wild-type M. thermophila CBH1a (SEQ ID NO:128), Variant 983 (SEQ ID NO:134), and Variant 145 (SEQ ID NO:131); exemplary CBH2 enzymes include the wild-type (SEQ ID NO:137), Variant 962 (SEQ ID NO:146), Variant 196 (SEQ ID NO:140), and Variant 287 (SEQ ID NO:143); an exemplary EG2 is the wild-type M. thermophila (SEQ ID NO:113); an exemplary EG1b is the wild-type (SEQ ID NO: 110); exemplary GH61a enzymes include wild-type M. thermophila (SEQ ID NO:2), Variant 1 (SEQ ID NO:5), Variant 5 (SEQ ID NO:11), and Variant 9 (SEQ ID NO:11); and exemplary BGLs include wild-type M. thermophila BGL (SEQ ID NO:116), Variant 883 (SEQ ID NO:119), and Variant 900 (SEQ ID NO:122). Any one or more of the components may be supplemented or substituted with other variants having common structural and functional characteristics with the component being substituted or supplemented, as described below. In a saccharification reaction, the amount of glucan is generally about 50 to about 300 g/L, typically about 75 to about 150 g/L. The total protein is about 0.1 to about 10 g/L, typically about 0.5 to about 2 g/L, or about 0.75 g/L.
Any or all of the components listed in the mixtures referred to above may be supplemented or substituted with variant proteins that are structurally and functionally related, as described herein.
In some embodiments, the CBH1 cellobiohydrolase used in mixtures of the present invention comprises at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to either SEQ ID NO:128 (M. thermophila), SEQ ID NO:125 (T. emersonii), or a fragment of either SEQ ID NO:128 or SEQ ID NO:125 having cellobiohydrolase activity, as well as variants of M. thermophila CBH1a (e.g., SEQ ID NO:131 and/or SEQ ID NO:133), and variant fragment(s) having cellobiohydrolase activity. Exemplary CBH1 enzymes include, but are not limited to those described in US Pat. Appln. Publn. No. 2012/0003703 A1, which is hereby incorporated herein by reference in its entirety for all purposes.
In some embodiments, the CBH2b cellobiohydrolase used in the mixtures of the present invention comprises at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to SEQ ID NO:127 or a fragment of SEQ ID NO:127, as well as at least one variant M. thermophila CBH2b enzyme (e.g., SEQ ID NO:140, 143, and/or 146) and/or variant fragment(s) having cellobiohydrolase activity. Exemplary CBH2b enzymes are described in U.S. Patent Appln. Ser. Nos. 61/479,800, 13/459,038, both of which are hereby incorporated herein by reference in their entirety for all purposes.
In some embodiments, the EG2 endoglucanase used in the mixtures of the present invention comprises at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to SEQ ID NO:113 or a fragment of SEQ ID NO:113 having endoglucanase activity. Exemplary EG2 enzymes are described in U.S. patent application Ser. No. 13/332,114, and WO 2012/088159, both of which are hereby incorporated herein by reference in their entirety for all purposes.
In some embodiments, the EG1b endoglucanase used in the mixtures of the present invention comprises at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to SEQ ID NO:110 or a fragment of SEQ ID NO:110 having endoglucanase activity.
In some embodiments, the BGL1 beta-glucosidase used the mixtures of the present invention comprises at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to SEQ ID NOS:116, 119, and/or 122, or a fragment of SEQ ID NOS:116, 119, and/or 122 having beta-glucosidase activity. Exemplary BGL1 enzymes include, but are not limited to those described in US Pat. Appln. Publ. No. 2011/0129881, WO 2011/041594, and US Pat. Appln. Publ. No. 2011/0124058 A1, all of which are hereby incorporated herein by reference in their entireties for all purposes.
In some embodiments, the GH61f protein used in the mixtures of the present invention comprises at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to SEQ ID NO:29, or a fragment of SEQ ID NO:29 having GH61 activity, assayed as described elsewhere in this disclosure.
In some embodiments, the GH61p protein used in the mixtures of the present invention comprises at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to SEQ ID NO:70, SEQ ID NO:73, or a fragment of such sequence having GH61p activity.
In some embodiments, the xylanase used in the mixtures of the present invention comprises at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to SEQ ID NO:149, SEQ ID NO:151, or a fragment of such sequence having xylanase activity.
GH61 Activity Assays
The cellulase enhancing activity of GH61 proteins of the invention can be determined using any suitable GH61 activity assay. For example, in some embodiments, a purified and/or recombinant GH61 protein of this invention is obtained, and then assayed for GH61 activity by combining it with cellulase enzymes in a saccharification reaction, and determining if there is an increase in glucose yield, as compared to the same saccharification reaction conducted without the GH61.
In one approach, GH61 activity can be assayed by combining a cellulosic substrate with cellulase enzymes (e.g., 5-10 mg total weight of cellulase enzymes per gram of substrate) in the presence and absence of GH61 protein. In some embodiments, the cellulase enzymes comprise a defined set of recombinant cellulase enzymes from M. thermophila. 
In another approach, broth from a culture of wild-type M. thermophila is used (with and without supplementation with GH61 protein and/or GH61 variants). GH61 activity is evidenced by enhanced glucose yield in the presence of exogenous GH61 (i.e., beyond any enhancement resulting from endogenous GH61 in the broth). It is also possible to use a broth supplemented with one or more purified enzymes.
Suitable enzymes include isolated recombinant enzymes cloned from M. thermophila, including but not limited to EG, BGL, CBH1, and/or CBH2, in any combination suitable for the chosen substrate to yield a measurable product.
In one exemplary assay for measuring GH61 activity from M. thermophila derived GH61 proteins and variant proteins, the cellulase enzymes used are M. thermophila BGL1 (e.g., SEQ ID NOS:116, 119, and/or 122); See e.g., Badhan et al., Biores. Technol., 98:504-10 [2007]); M. thermophila CBH1 (SEQ ID NOS:128, 131, and/or 134); and M. thermophila CBH2 (SEQ ID NOS:137, 140, 143 and/or 146). In some embodiments, endoglucanase is also used, such as M. thermophila EG2 (SEQ ID NO:113; See e.g., Rosgaard et al., Prog., 22:493-8 [2006]; and Badhan et al., supra).
Alternatively, commercially available preparations comprising a mixture of cellulase enzymes may be used, such as LaminexTM and SpezymeTM (Genencor), RohamentTM (Rohm GmbH), and CelluzymeTM, CerefloTM and UltrafloTM (Novozymes).
Assays with cellulose enzymes are typically done at 50° C., but in some embodiments, other temperatures find use (e.g., 35, 45, 55, 60, or 65° C.). In some embodiments, the GH61 enzymes and any other desired enzymes are combined with the substrate and incubated so as to produce fermentable sugars. The sugars are then recovered and quantitated for yield of glucose. One suitable substrate is wheat straw (e.g., pre-treated wheat straw). Other cellulosic substrates listed in this disclosure may be used as an alternative, including corn stover pretreated with sulfuric acid (See e.g., U.S. Pat. No. 7,868,227). Assay methods are known in the art. For example, the method of Harris et al., (Harris et al., Biochem., 49:3305-3316 [2010], incorporated herein by reference) finds use. In this method, corn stover is pretreated with sulfuric acid, washed, incubated with cellulase enzymes and GH61 for several days, and then the yield of sugars quantitated by refraction. Another method is described in U.S. Pat. No. 7,868,227 (incorporated herein by reference). In this method, the cellulosic substrate is PCS (corn stover pretreated with heat and dilute sulfuric acid, as described in WO 2005/074647; and a cellulose enzyme mixture is Cellucast®, a blend of cellulase enzymes from the fungus Trichoderma reesei (Sigma-Aldrich). Hydrolysis of PCS is conducted in a total reaction volume of 1.0 mL and a PCS concentration of 50 mg/mL in 1 mM manganese sulfate, 50 mM sodium acetate buffer pH 5.0. The test protein is combined with the base cellulase mixture at relative concentrations between 0 and 100% total protein. The protein composition is incubated with the PCS at 65° C. for 7 days. The combined yield of glucose and cellobiose is measured by refractive index detection.
GH61 activity is calculated as an increase in glucose production from the substrate by the cellulase(s) in the presence of GH61 protein, in comparison with the same reaction mixture in the absence of GH61 protein. Typically, the increase is dose-dependent within at least a 3-fold range of concentrations. GH61 activity can be expressed as a degree of “synergy”.
Use of GH61 Variant Protein to Promote Saccharification
The GH61 variant proteins of the present invention can be used industrially to promote or otherwise modulate the activity of cellulase enzymes.
In some embodiments, suitably prepared lignocellulose is subjected to enzymatic hydrolysis using one or more cellulase enzymes in the presence of one or more GH61 variant proteins or preparations according to this invention. Thus, in some embodiments, saccharification reactions are carried out by exposing biomass to GH61 variant protein and cellulases, which work in concert to break down the biomass. Typically, the cellulases include at least one endoglucanase (EG), at least one beta-glucosidase (BGL), at least one Type 1 cellobiohydrolase (CBH1), and/or at least one Type 2 cellobiohydrolase (CBH2). In some alternative embodiments, a minimum enzyme mixture is used, for example, comprising GH61 protein in combination with BGL and either CBH1 or CBH2, or both, but with substantially no EG.
Hydrolysis of the hemicellulose and cellulose components of a lignocellulosic feedstock yields a lignocellulosic hydrolysate comprising xylose and glucose. Other sugars typically present include galactose, mannose, arabinose, fucose, rhamnose, or a combination thereof. Regardless of the means of hydrolyzing the lignocellulosic feedstock (e.g., full acid hydrolysis or chemical pretreatment with or without subsequent enzymatic hydrolysis), the xylose and glucose generally make up a large proportion of the sugars present. In some embodiments, if the lignocellulosic hydrolysate is a hemicellulose hydrolysate resulting from acid pretreatment, xylose will likely be the predominant sugar and lesser amounts of glucose will be present. The relative amount of xylose present in the lignocellulosic hydrolysate will depend on the feedstock and the pretreatment that is employed.
The cells and compositions of the present invention (including culture broth and/or cell lysates) find use in the production of fermentable sugars from cellulosic biomass. The biomass substrate may be converted to a fermentable sugar by (a) optionally pretreating a cellulosic substrate to increase its susceptibility to hydrolysis; (b) contacting the optionally pretreated cellulosic substrate of step (a) with a composition, culture medium or cell lysate containing at least one GH61 variant and any additional cellulases under conditions suitable for the production of cellobiose and fermentable sugars such as glucose.
In some embodiments, each of the at least one GH61 variant and additional cellulase enzymes described herein are partially or substantially purified, and the purified proteins are added to the biomass. Alternatively or in addition, the various individual enzymes are recombinantly expressed in different cells, and the media containing the secreted proteins are added to the biomass. The GH61 variant protein(s) and cellulase enzymes are then reacted with the biomass at a suitable temperature for a suitable period.
In some embodiments, sugars produced by methods of this invention are used to produce an end product such as an alcohol, such as ethanol. Other end-products may be produced, such as acetone, amino acid(s) (e.g., glycine, or lysine), organic acids (e.g., lactic acid, acetic acid, formic acid, citric acid, oxalic acid, or uric acid), glycerol, diols (e.g., 1,3 propanediol or butanediol), or at least one hydrocarbon with 1 to 20 carbon atoms. In some embodiments, cellulosic biomass is treated with at least one composition of the present invention to prepare an animal feed.
In some embodiments, when GH61 protein (e.g., at least one GH61 variant) is used to increase the yield of fermentable sugars in a saccharification reaction, at least one divalent metal cation or additional cofactor or adjunct compound is added to the reaction at a concentration of about 1 to 100 uM. In some embodiments, the divalent metal cation (e.g., copper) is included at a concentration of about 1 to 90 uM, about 10 to 80 uM, about 15 to 75 uM, about 20 to 70 uM, about 30 to 60 uM, about 40 to 50 uM, about 5 to 10 uM, about 10 to 20 μM, about 15 to 25 uM, about 20 to 30 uM, about 25 to 35 uM, about 30 to 40 uM, about 35 to 45 uM, about 40 to 50 uM, about 45 to 55 uM, about 50 to 60 uM, about 55 to 65 uM, about 60 to 70 uM, about 65 to 75 uM, about 70 to 80 uM, about 75 to 85 uM, about 80 to 90 uM, about 85 to 95 uM, about 90 to 100 uM, about 95 to 100 uM, or about 1 uM, about 2 uM, about 3 uM, about 4 uM, about 5 uM, about 6 uM, about 7 uM, about 8 uM, about 9 uM, about 10 uM, about 11 uM, about 12 uM, about 13 uM, about 14 uM, about 15 uM, about 16 uM, about 17 uM, about 18 uM, about 19 uM, about 20 uM, about 25 uM, about 30 uM, about 35 uM, about 40 uM, about 45 uM, about 50 uM, about 55 uM, about 60 uM, about 65 uM, about 70 uM, about 75 uM, about 80 uM, about 85 uM, about 90 uM, about 95 uM, or about 100 uM. Divalent cations present in the reaction include, but are not limited to Cu++, Mn++, Co++, Mg++, Ni++, Zn++, and Ca++ at concentrations of 0.001 to 50 mM, 1 μM to 1 mM, or 10-50 μM. Indeed, it is not intended that the concentration of divalent metal cation(s) be limited to any particular value, as any suitable concentration finds use in the present invention and will depend upon the reaction conditions, as known in the art.
Fermentation of Sugars
In some embodiments, once a suitable cellulosic biomass substrate has been treated with cellulase(s) and at least one GH61 variant protein(s) according to this invention, sugars and other components in the product are fermented to produce various fermentation end products, including but not limited to biofuels, such as ethanol or alcohol mixtures. Depending on the substrate used, other components (e.g., long-chain esters) may also be present.
Fermentation is the process of extracting energy from the oxidation of organic compounds, such as carbohydrates, using an endogenous electron acceptor. Alcoholic fermentation is a process in which sugars such as xylulose, glucose, fructose, and sucrose are converted into a fermentation end product, including but not limited to biofuel. For example, the fermentation product may comprise alcohol (such as ethanol or butanol) and/or a sugar alcohol, such as xylitol.
In some embodiments, enzyme compositions comprising at least one GH61 variant of the present invention is reacted with a biomass substrate in the range of about 25° C. to 100° C., about 30° C. to 90° C., about 30° C. to 80° C., and about 30° C. to 70° C. In some embodiments, the biomass is reacted with the enzyme compositions at about 25° C., at about 30° C., at about 35° C., at about 40° C., at about 45° C., at about 50° C., at about 55° C., at about 60° C., at about 65° C., at about 70° C., at about 75° C., at about 80° C., at about 85° C., at about 90° C., at about 95° C. and at about 100° C. In general, the pH range is from about pH 3.0 to 8.5, pH 3.5 to 8.5, pH 4.0 to 7.5, pH 4.0 to 7.0 and pH 4.0 to 6.5. The incubation time may vary for example from 1.0 to 240 hours, from 5.0 to 180 hrs and from 10.0 to 150 hrs. For example, the incubation time is generally at least 1 h, at least 5 hrs, at least 10 hrs, at least 15 hrs, at least 25 hrs, at least 50 h, at least 100 hrs, at least 180, or longer. Incubation of the cellulase under these conditions and subsequent contact with the substrate may result in the release of substantial amounts of fermentable sugars from the substrate (e.g., glucose when the cellulase is combined with beta-glucosidase). For example at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or more fermentable sugar may be available as compared to the release of sugar by a wild-type polypeptide.
Any suitable micro-organism finds use in converting sugar in the sugar hydrolysate to ethanol or other fermentation products. These include yeast from the genera Saccharomyces, Hansenula, Pichia, Khtyveromyces, and Candida. Commercially available yeasts also find use, including but not limited to ETHANOLRED® SAFDISTIL®, THERMOSACC®, FERMIOL®, FERMIVIN®, or SuperstartTM.
In some embodiments, the yeast is genetically engineered to ferment both hexose and pentose sugars to at least one end-product, including but not limited to ethanol. Alternatively, in some embodiments, the yeast is a strain that has been made capable of xylose and glucose fermentation by one or more non-recombinant methods, such as adaptive evolution or random mutagenesis and selection. For example, in some embodiments, the fermentation is performed with recombinant Saccharomyces. In some embodiments, the recombinant yeast is a strain that has been made capable of xylose fermentation by recombinant incorporation of genes encoding xylose reductase (XEL) and xylitol dehydrogenase (XDH) (See e.g., U.S. Pat. Nos. 5,789,210, 5,866,382, 6,582,944 and 7,527,927; and EP 450 530) and/or gene(s) encoding one or more xylose isomerase (XI) (See e.g., U.S. Pat. Nos. 6,475,768 and 7,622,284). In some additional embodiments, the modified yeast strain overexpresses an endogenous and/or heterologous gene encoding xylulokinase (XK). Other yeast can ferment hexose and pentose sugars to at least one end-product, including but not limited to ethanol, such as yeast of the genera Hansenula, Pichia, Kluyveromyces and Candida (See e.g., WO 2008/130603).
A typical temperature range for the fermentation of xylose to ethanol using Saccharomyces spp. is between about 25° C. to about 37° C., although the temperature may be higher (up to 55° C.) if the yeast is naturally or genetically modified to be thermostable. The pH of a typical fermentation employing Saccharomyces spp. is between about 3 and about 6, depending on the pH optimum of the fermentation microorganism. The sugar hydrolysate may also be supplemented with additional nutrients required for growth and fermentation performance of the fermentation microorganism. For example, yeast extract, specific amino acids, phosphate, nitrogen sources, salts, trace elements and vitamins (See e.g., Verduyn et al., Yeast 8:501-170 [1992]; Jorgensen, Appl. Biochem. Biotechnol., 153:44-57 [2009]; and Zhao et al., J. Biotechnol., 139:55-60 [2009]). In some embodiments, the fermentation is conducted under anaerobic conditions, although aerobic or microaerobic conditions also find use.
Use of Copper, Gallic Acid, and Biomass Pretreatment Filtrate to Enhance GH61 Activity
In some embodiments, GH61 proteins and variants exhibit increased activity in a saccharification reaction when Cu++, gallic acid, and/or pretreatment filtrate are added. In some embodiments, wild-type GH61a (SEQ ID NO:2) and/or Variant 1 (SEQ ID NO:5) are used. Similarly, in some embodiments, the present invention encompasses the supplemental addition of Cu++, gallic acid, and/or pretreatment filtrate as an enhancing agent in saccharification reactions conducted using any of the GH61a variants shown in Tables 1 and 2, any of the other GH61 proteins described herein, and any active variant or fragment thereof such as may be obtained using any suitable method, including but not limited to the methods provided herein. In some embodiments, enhancing GH61 activity allows saccharification reactions to proceed more quickly and/or with less GH61 or cellulase enzyme.
In some embodiments, Cu++, gallic acid, and other potential cofactors are tested by titrating into a saccharification reaction comprising a GH61 protein, one or more cellulase enzymes (e.g., CBH1, CBH2, and/or BGL), and a cellulosic substrate, and measuring the relative rate of glucose production. Controls may include the combination of GH61 protein, cellulase enzymes, and substrate in the absence of the putative cofactor (to test the relative enhancement), and combinations of cellulase enzymes and substrate with or without cofactor in the absence of GH61 protein (to determine the effect of the putative cofactor on other enzymes in the reaction).
As shown herein, in some embodiments, Cu++ can enhance the activity of GH61a Variant 1 (SEQ ID NO:5). The source of Cu++ used in the example was CuSO4, although any effective copper source can be used as an alternative. Effective supplemental copper sources include copper salts and metallic copper, or mixtures thereof. Copper salts include copper(II) (Cu++) salts and copper(I) (Cu+) salts. Copper in metallic copper(0) and copper(I) salts can be oxidized to Cu++ in water by oxygen (e.g., by oxygen present in air). Suitable copper(II) and copper(I) salts include sulfates, chlorides, oxides, hydroxides, nitrates, carbonates, hydroxycarbonates (basic carbonates), oxychlorides, and acetates. Suitable sources of metallic copper include metallic copper refined from copper ores, including copper vessels and piping in contact with water and oxygen (e.g., in air).
In some embodiments, as shown herein, gallic acid and/or pretreated biomass filtrate can also be used to enhance the activity of GH61 protein. In some embodiments, the gallic acid and/or pretreated biomass filtrate are titrated to the optimal dose for the reaction conditions used. Thus, an effective concentration of gallic acid can be determined empirically by titrating it into the reaction mixture, depending on the enzymes being used and the total biomass. In some embodiments, in which gallic acid is utilized, an effective concentration of gallic acid is within the range of about 0.1 to 20 mM, about 0.5 to 5 mM, or about 1 to 2 mM. However, it is not intended that the present invention be limited to any particular concentration of gallic acid, as any suitable concentration finds use in the present invention, depending upon the reaction conditions.
A cofactor of GH61 in a reaction volume such as Cu++ is said to be “supplemented” if it has been added into the reaction volume as a separate reagent, which is in addition to any metal ions that may be bound to GH61 or other reactants beforehand. Depending on the amount or molar ratio of cofactors such as Cu++ already present in a GH61 preparation, addition of such cofactors into the reaction may increase the amount of glucose produced per weight of GH61 by 25%, 50%, 2-fold, or more.
Effective concentrations of supplemented Cu++ in the reaction volume may be readily determined empirically as described herein. Depending on reaction conditions, effective supplemented concentrations include but are not limited to 1 μM to 200 μM, 4 μM to 100 μM, 10 μM to 100 μM, or at least 1 μM, 4 μM, 10 μM, 20 μM, 30 μM, 40 μM, or 50 μM in the reaction volume (i.e., the concentration of supplemented copper in the reaction volume). However, it is not intended that the present invention be limited to any particular copper concentration or range of concentrations, as any suitable concentration finds use and will depend upon the reaction conditions used. In some embodiments, prior to or without copper supplementation, copper is present in the GH61 protein preparation, the other enzymes, the cellulase fermentation production media, the pretreated biomass, and/or any other component of the reaction volume (i.e., in some embodiments, there are other sources of copper present in the reaction than any copper added to the reaction as a supplement). Thus, in some embodiments, the reaction is conducted without the supplemental addition of copper as described herein.
In some embodiments, inclusion of copper and/or gallic acid in the reaction mixture at an effective concentration or ratio, less GH61 protein is needed to produce the same amount of fermentable sugars from the same cellulase enzymes. In some embodiments, this provides a cost reduction associated with saccharification reactions.
Vectors, Promoters, Other Expression Elements, Host Cells, and Signal Peptides.
There are numerous general texts that describe molecular biological techniques including the use of vectors, promoters, in vitro amplification methods including the polymerase chain reaction (PCR) and the ligase chain reaction (LCR) (See e.g., Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology, Volume 152 Academic Press, Inc., San Diego, Calif. (Berger); Sambrook et al., Molecular Cloning—A Laboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989; and Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols [as supplemented through 2009]). Introduction of a vector or a DNA construct into a host cell can be effected by any suitable method, including but not limited to calcium phosphate transfection, DEAE-Dextran mediated transfection, electroporation, or other common techniques (See Davis et al., 1986, Basic Methods in Molecular Biology). General references on cell culture techniques and nutrient media for fungal host cells include Gene Manipulations in Fungi, Bennett, J. W. et al., Ed., Academic Press, 1985; More Gene Manipulations in Fungi, Bennett, J. W. et al., Ed., Academic Press, 1991; and The Handbook of Microbiological Media, CRC Press, Boca Raton, Fla., 1993.
Vectors
The present invention makes use of recombinant constructs comprising at least one sequence encoding at least one GH61 variant as described above. In some embodiments, the present invention provides expression vectors comprising at least one GH61 variant polynucleotide operably linked to a heterologous promoter. Expression vectors of the present invention may be used to transform an appropriate host cell to permit the host to express the GH61 variant protein. Methods for recombinant expression of proteins in fungi and other organisms are well known in the art, and a number expression vectors are available or can be constructed using routine methods (See, e.g., Tkacz and Lange, 2004, Advances in fungal biotechnology for industry, agriculture, and medicine, Kluwer Academic/Plenum Publishers, New York; Zhu et al., Plasmid 6:128-33 [2009]; and Kavanagh, K. 2005, Fungi: biology and applications, Wiley, all of which are incorporated herein by reference).
Nucleic acid constructs of the present invention comprise a vector, such as, a plasmid, a cosmid, a phage, a virus, a bacterial artificial chromosome (BAC), a yeast artificial chromosome (YAC), and the like, into which a nucleic acid sequence of the invention has been inserted. Polynucleotides of the present invention can be incorporated into any one of a variety of expression vectors suitable for expressing a polypeptide. Suitable vectors include, but are not limited to chromosomal, nonchromosomal and synthetic DNA sequences (e.g., derivatives of SV40); bacterial plasmids; phage DNA; baculovirus; yeast plasmids; vectors derived from combinations of plasmids and phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox virus, pseudorabies, adenovirus, adeno-associated virus, retroviruses and many others. Any vector that transduces genetic material into a cell, and, if replication is desired, which is replicable and viable in the relevant host can be used.
In some embodiments, the construct further comprises regulatory sequences, including, for example, a promoter, operably linked to the protein encoding sequence. Large numbers of suitable vectors and promoters are known to those of skill in the art.
Promoters
In order to obtain high levels of expression in a particular host it is often useful to express the GH61 variant of the present invention under the control of a heterologous promoter. A promoter sequence may be operably linked to the 5′ region of the GH61 variant coding sequence using routine methods.
Examples of useful promoters for expression of GH61 enzymes include promoters from fungi. In some embodiments, a promoter sequence that drives expression of a gene other than a GH61 gene in a fungal strain may be used. As a non-limiting example, a fungal promoter from a gene encoding an endoglucanase may be used. In some embodiments, a promoter sequence that drives the expression of a GH61 gene in a fungal strain other than the fungal strain from which the GH61 variant was derived may be used. As a non-limiting example, if the GH61 variant is derived from C1, a promoter from a T. reesei GH61 gene may be used or a promoter as described in WO 2010/107303, such as but not limited to the sequences identified as SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, or SEQ ID NO:29 in WO 2010/107303.
Examples of other suitable promoters useful for directing the transcription of the nucleotide constructs of the present invention in a filamentous fungal host cell are promoters obtained from the genes for Aspergillus oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, Aspergillus niger neutral alpha-amylase, Aspergillus niger acid stable alpha-amylase, Aspergillus niger or Aspergillus awamori glucoamylase (glaA), Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease, Aspergillus oryzae triose phosphate isomerase, Aspergillus nidulans acetamidase, and Fusarium oxysporum trypsin-like protease (WO 96/00787, which is incorporated herein by reference), as well as the NA2-tpi promoter (a hybrid of the promoters from the genes for Aspergillus niger neutral alpha-amylase and Aspergillus oryzae triose phosphate isomerase), promoters such as cbh1, cbh2, egl1, egl2, pepA, hfb1, hfb2, xyn1, amy, and glaA (Nunberg et al., Mol. Cell Biol., 4:2306-2315 [1984]; Boel et al., EMBO J, 3:1581-85 [1984]; and European Pat. Publ. 137280, all of which are incorporated herein by reference), and mutant, truncated, and hybrid promoters thereof. In a yeast host, useful promoters can be from the genes for Saccharomyces cerevisiae enolase (eno-1), Saccharomyces cerevisiae galactokinase (gall), Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP), and S. cerevisiae 3-phosphoglycerate kinase. Other useful promoters for yeast host cells are known (See e.g., Romanos et al., Yeast 8:423-488 [1992], incorporated herein by reference. Promoters associated with chitinase production in fungi may be used (See, e.g., Blaiseau and Lafay, Gene 120243-248 [1992] (filamentous fungus Aphanocladium album); Limon et al., Curr. Genet, 28:478-83 [1995] (Trichoderma harzianum), both of which are incorporated herein by reference).
Promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses and which can be used in some embodiments of the invention include SV40 promoter, E. coli lac or trp promoter, phage lambda PL promoter, tac promoter, T7 promoter, and the like. In bacterial host cells, suitable promoters include the promoters obtained from the E. coli lac operon, Streptomyces coelicolor agarase gene (dagA), Bacillus subtilis levansucranse gene (sacB), Bacillus licheniformis α-amylase gene (amyl), Bacillus stearothermophilus maltogenic amylase gene (amyM), Bacillus amyloliquefaciens α-amylase gene (amyQ), Bacillus subtilis xylA and xylB genes and prokaryotic beta-lactamase gene.
Any other promoter sequence that drives expression in a suitable host cell may be used. Suitable promoter sequences can be identified using well known methods. In one approach, a putative promoter sequence is linked 5′ to a sequence encoding a reporter protein, the construct is transfected into the host cell (e.g., M. thermophila) and the level of expression of the reporter is measured. Expression of the reporter can be determined by measuring, for example, mRNA levels of the reporter sequence, an enzymatic activity of the reporter protein, or the amount of reporter protein produced. For example, promoter activity may be determined by using the green fluorescent protein as coding sequence (See e.g., Henriksen et al, Microbiol., 145:729-34 [1999], incorporated herein by reference) or a lacZ reporter gene (Punt et al., Gene, 197:189-93 [1997], incorporated herein by reference). Functional promoters may be derived from naturally occurring promoter sequences by directed evolution methods (See, e.g, Wright et al., Human Gene Therapy, 16:881-892 [2005], incorporated herein by reference.
Additional promoters include those from M. thermophila, provided in U.S. Prov. Patent Appln. Ser. Nos. 61/375,702, 61/375,745, 61/375,753, 61/375,755, and 61/375,760, all of which were filed on Aug. 20, 2010, and are hereby incorporated by reference in their entireties, as well as WO 2010/107303.
Other Expression Elements
Cloned GH61 variants may also have a suitable transcription terminator sequence, a sequence recognized by a host cell to terminate transcription. The terminator sequence is operably linked to the 3′ terminus of the nucleic acid sequence encoding the polypeptide. Any terminator that is functional in the host cell of choice may be used in the present invention.
For example, exemplary transcription terminators for filamentous fungal host cells can be obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate synthase, Aspergillus niger alpha-glucosidase, and Fusarium oxysporum trypsin-like protease. Suitable transcription terminators are known in the art (See e.g., U.S. Pat. No. 7,399,627, incorporated herein by reference).
Exemplary terminators for yeast host cells include those obtained from the genes for Saccharomyces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C (CYC1), and Saccharomyces cerevisiae glyceraldehyde-3-phosphate dehydrogenase. Other useful terminators for yeast host cells are known in the art (See e.g., Romanos et al., Yeast 8:423-88 [1992]).
A suitable leader sequence may be part of a cloned GH61 variant sequence, which is a nontranslated region of an mRNA that is important for translation by the host cell. The leader sequence is operably linked to the 5′ terminus of the nucleic acid sequence encoding the polypeptide. Any leader sequence that is functional in the host cell of choice may be used. Exemplary leaders for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase and Aspergillus nidulans triose phosphate isomerase. Suitable leaders for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae 3-phosphoglycerate kinase, Saccharomyces cerevisiae alpha-factor, and Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP).
In some embodiments, sequences also contain a polyadenylation sequence, which is a sequence operably linked to the 3′ terminus of the nucleic acid sequence and which, when transcribed, is recognized by the host cell as a signal to add polyadenosine residues to transcribed mRNA. Any polyadenylation sequence which is functional in the host cell of choice may be used in the present invention. Exemplary polyadenylation sequences for filamentous fungal host cells can be from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate synthase, Fusarium oxysporum trypsin-like protease, and Aspergillus niger alpha-glucosidase. Useful polyadenylation sequences for yeast host cells are known in the art (See e.g., Guo and Sherman, Mol. Cell. Biol., 15:5983-5990 [1995]).
The expression vector of the present invention optionally contains one or more selectable markers, which facilitate easy selection of transformed cells. A selectable marker is a typically gene, the product of which provides for biocide or viral resistance, resistance to heavy metals, prototrophy to auxotrophs, and the like. Selectable markers for use in a filamentous fungal host cell include, but are not limited to, amdS (acetamidase), argB (ornithine carbamoyltransferase), bar (phosphinothricin acetyltransferase), hph (hygromycin phosphotransferase), niaD (nitrate reductase), pyrG (orotidine-5′-phosphate decarboxylase), sC (sulfate adenyltransferase), and trpC (anthranilate synthase), as well as equivalents thereof. Embodiments for use in an Aspergillus cell include the amdS and pyrG genes of Aspergillus nidulans or Aspergillus oryzae and the bar gene of Streptomyces hygroscopicus. Suitable markers for yeast host cells include but are not limited to ADE2, HIS3, LEU2, LYS2, MET3, TRP1, and URA3.
Host Cells
In some embodiments, at least one GH61 variant protein of the present invention is expressed from a nucleic acid that has been recombinantly introduced into a suitable host cell line. In some embodiments, the host cell also expresses other proteins of interest, particularly one or more cellulase enzymes that work in concert with at least one GH61 variant protein in the process of saccharification. The cellulase enzymes may be constitutively expressed by the parent strain of the host cell, or they may be expressed from other recombinant nucleic acids that were introduced serially or simultaneously with the GH61 variant encoding sequence.
Rather than expressing at least one GH61 variant protein and at least one additional cellulase enzyme in the same cell, in some embodiments, the invention is practiced by producing at least one GH61 variant protein in one host cell, and producing one or more cellulases together in another host cell, or in a plurality of host cells. Once such cells have been engineered, cells expressing GH61 protein and cells expressing cellulase enzymes can be combined and cultured together to produce compositions of this invention containing both GH61 variant proteins and other cellulase enzymes. Alternatively, the culture supernatant or broth from each cell line can be collected separately, optionally fractionated to enrich for the respective activities, and then mixed together to produce the desired combination.
Suitable fungal host cells include, but are not limited to Ascomycota, Basidiomycota, Deuteromycota, Zygomycota, and Fungi imperfecti. In some embodiments, preferred fungal host cells are yeast cells, and filamentous fungal cells, including all filamentous forms of the subdivision Eumycotina and Oomycota. Filamentous fungi are characterized by a vegetative mycelium with a cell wall composed of chitin, cellulose and other complex polysaccharides, and are morphologically distinct from yeast. In some embodiments, Trichoderma is a source of one or more cellulases for use in combination with GH61 variant proteins.
Any suitable host cell finds use in the present invention, including but not limited to host cells that are species of Achlya, Acremonium, Aspergillus, Aureobasidium, Azospirillum, Bjerkandera, Cellulomonas, Cephalosporium, Ceriporiopsis, Chrysosporium, Clostridium, Coccidioides, Cochliobolus, Coprinus, Coriolus, Corynascus, Cryphonectria, Cryptococcus, Dictyostelium, Diplodia, Elizabethkingia, Endothia, Erwinia, Escherichia, Fusarium, Gibberella, Gliocladium, Gluconacetobacter, Humicola, Hypocrea, Kuraishia, Mucor, Myceliophthora, Neurospora, Nicotiana, Paenibacillus, Penicillium, Periconia, Phaeosphaeria, Phlebia, Piromyces, Podospora, Prevotella, Pyricularia, Rhizobium, Rhizomucor, Rhizopus, Ruminococcus, Saccharomycopsis, Salmonella, Schizophyllum, Scytalidium, Septoria, Sporotrichum, Streptomyces, Talaromyces, Thermoanaerobacter, Thermoascus, Thermotoga, Thielavia, Tolypocladium, Trametes, Trichoderma, Tropaeolum, Uromyces, Verticillium, Volvariella, Wickerhamomyces, or corresponding teleomorphs, or anamorphs, and synonyms or taxonomic equivalents thereof.
An exemplary host cell is yeast, including but not limited to Candida, Hansenula, Saccharomyces, Schizosaccharomyces, Pichia, Kluyveromyces, or Yarrowia. In some embodiments, the yeast cell is Hansenula polymorpha, Saccharomyces cerevisiae, Saccharomyces carlsbergensis, Saccharomyces diastaticus, Saccharomyces norbensis, Saccharomyces kluyveri, Schizosaccharomyces pombe, Pichia pastoris, Pichia finlandica, Pichia trehalophila, Pichia kodamae, Pichia membranaefaciens, Pichia opuntiae, Pichia thermotolerans, Pichia salictaria, Pichia quercuum, Pichia pijperi, Pichia stipitis, Pichia methanolica, Pichia angusta, Kluyveromyces lactis, Candida albicans, or Yarrowia lipolytica. 
Another exemplary host cell is a Myceliophthora species, such as M. thermophila. As used herein, the term “C1” refers to Myceliophthora thermophila, including a fungal strain described by Garg (See, Garg, Mycopathol., 30: 3-4 [1966]). As used herein, “Chrysosporium lucknowense” includes the strains described in U.S. Pat. Nos. 6,015,707, 5,811,381 and 6,573,086; US Pat. Pub. Nos. 2007/0238155, US 2008/0194005, US 2009/0099079; International Pat. Pub. Nos., WO 2008/073914 and WO 98/15633, all of which are incorporated herein by reference, and include, without limitation, Chrysosporium lucknowense Garg 27K, VKM-F 3500 D (Accession No. VKM F-3500-D), C1 strain UV13-6 (Accession No. VKM F-3632 D), C1 strain NG7C-19 (Accession No. VKM F-3633 D), and C1 strain UV 18-25 (VKM F-3631 D), all of which have been deposited at the All-Russian Collection of Microorganisms of Russian Academy of Sciences (VKM), Bakhurhina St. 8, Moscow, Russia, 113184, and any derivatives thereof. Although initially described as Chrysosporium lucknowense, C1 may currently be considered a strain of Myceliophthora thermophila. Other C1 strains include cells deposited under accession numbers ATCC 44006, CBS (Centraalbureau voor Schimmelcultures) 122188, CBS 251.72, CBS 143.77, CBS 272,77, CBS122190, CBS122189, and VKM F-3500D. Exemplary C1 derivatives include modified organisms in which one or more endogenous genes or sequences have been deleted or modified and/or one or more heterologous genes or sequences have been introduced. Derivatives include, but are not limited to UV18#100f Δalp1, UV18#100f Δpyr5 Δalp1, UV18#1001Δalp1 Δpep4 Δalp2, UV18#1001 Δpyr5 Δalp1 Δpep4 Δalp2 and UV18#1001Δpyr4 Δpyr5 ΔaIp1 Δpep4 Δalp2, as described in WO2008073914 and WO2010107303, each of which is incorporated herein by reference.
In some embodiments, the host cell is a Trichoderma species, such as T. longibrachiatum, T. viride, Hypocrea jecorina or T. reesei, T. koningii, and T. harzianum. 
In some embodiments, the host cell is a Aspergillus species, such as A. awamori, A. funigatus, A. japonicus, A. nidulans, A. niger, A. aculeatus, A. foetidus, A. oryzae, A. sojae, and A. kawachi. 
In some additional embodiments, the host cell is a Fusarium species, such as F. bactridioides, F. cerealis, F. crookwellense, F. culmorum, F. graminearum, F. graminum. F. oxysporum, F. roseum, and F. venenatum. 
The host cell may also be a Neurospora species, such as N. crassa. Alternatively, the host cell is a Humicola species, such as H. insolens, H. grisea, and H. lanuginosa. Alternatively, the host cell is a Mucor species, such as M. miehei and M. circinelloides. Alternatively, the host cell is a Rhizopus species, such as R. oryzae and R. niveus. Alternatively, the host cell is a Penicillum species, such as P. purpurogenum, P. chrysogenum, and P. verruculosum. 
In some embodiments, the host cell is a Thielavia species, such as T. terrestris. Alternatively, the host cell is a Tolypocladium species, such as T. inflatum and T. geodes. Alternatively, the host cell is a the Trametes species, such as T. villosa and T. versicolor. 
In some embodiments, the host cell is of a Chrysosporium species, such as C. lucknowense, C. keratinophilum, C. tropicum, C. merdarium, C. mops, C. pannicola, and C. zonatum. In a particular embodiment the host is C. lucknowense. Alternatively, the host cell is an algae such as Chlamydotnonas (e.g., C. reinhardtii) or Phormidium (P. sp. ATCC29409).
In some alternative embodiments, the host cell is a prokaryotic cell. Suitable prokaryotic cells include Gram-positive, Gram-negative and Gram-variable bacterial cells. Examples of bacterial host cells include, but are not limited to Bacillus (e.g., B. subtilis, B. licheniformis, B. megaterium, B. stearothermophilus and B. amyloliquefaciens), Streptomyces (e.g., S. ambofaciens, S. achromogenes, S. avermitilis, S. coelicolor, S. aureofaciens, S. aureus, S. fungicidicus, S. griseus, and S. lividans), and Streptococcus (e.g., S. equisimiles, S. pyogenes, and S. uberis) species.
Any suitable eukaryotic or prokaryotic species finds use as host cells, including but not limited to Aspergillus aculeatus, Azospirillum irakense KBC 1, Bacillus sp. GL1, Cellulomonas biazotea, Clostridium thermocellum, Thermoanaerobacter brockii, Coccidioides posadasii, Dictyostelium discoideum, Elizabethkingia meningoseptica, Erwinia chrysanthemi, Escherichia coli, Gluconacetobacter xylinus, Hypocrea jecorina, Kuraishia capsulata, Nicotiana tabacum, Paenibacillus sp. C7, Penicillium brasilianum, Periconia sp. BCC 2871, Phaeosphaeria avenaria, Prevotella albensis, Rhizobium leguminosarum, Rhizomucor miehei, Ruminococcus albus, Saccharomycopsis fibuligera, Salmonella typhimurium, Septoria lycopersici, Streptomyces coelicolor, Talaromyces emersonii, Thermotoga maritima, Tropaeolum mains, Uromyces viciae-fabae, and Wickerhamomyces anomalus. 
Strains that may be used in the practice of the invention (both prokaryotic and eukaryotic strains) may be obtained from any suitable source, including but not limited to the American Type Culture Collection (ATCC), or other biological depositories such as Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM), Centraalbureau Voor Schimmelcultures (CBS), and the Agricultural Research Service Patent Culture Collection, Northern Regional Research Center (NRRL).
In some embodiments, host cells are genetically modified to have characteristics that improve genetic manipulation, protein secretion, protein stability or other properties desirable for expression or secretion of a protein. For example, knock-out of Alp1 function results in a cell that is protease deficient. Knock-out of pyr5 function results in a cell with a pyrimidine deficient phenotype. Host cells may be modified to delete endogenous cellulase protein-encoding sequences or otherwise eliminate expression of one or more endogenous cellulases. Expression of one or more unwanted endogenous cellulases may be inhibited to increase the proportion of cellulases of interest, for example, by chemical or UV mutagenesis and subsequent selection. Homologous recombination can be used to induce targeted gene modifications by specifically targeting a gene in vivo to suppress expression of the encoded protein.
Signal Peptides
In general, polypeptides are secreted from the host cell after being expressed as a pre-protein including a signal peptide (i.e., an amino acid sequence linked to the amino terminus of a polypeptide which directs the encoded polypeptide into the cell's secretory pathway).
In some embodiments, the secreted part of a GH61 variant is linked at the N-terminal to a heterologous signal peptide, depending on the host cell and other factors. Effective signal peptide coding regions for filamentous fungal host cells include but are not limited to signal peptide coding regions obtained from Aspergillus oryzae TAKA amylase, Aspergillus niger neutral amylase, Aspergillus niger glucoamylase, Rhizomucor miehei aspartic proteinase, Humicola insolens cellulase, Humicola lanuginosa lipase, and T. reesei cellobiohydrolase II (TrCBH2).
Effective signal peptide coding regions for bacterial host cells include but are not limited to signal peptide coding regions obtained from the genes for Bacillus NCIB 11837 maltogenic amylase, Bacillus stearothermophilus alpha-amylase, Bacillus licheniformis subtilisin, Bacillus licheniformis beta-lactamase, Bacillus stearothermophilus neutral proteases (nprT, nprS, nprM), and Bacillus subtilis prsA. Further signal peptides are known in the art (See e.g., described by Simonen and Palva, Microbiol. Rev., 57:109-137 [1993]).
Useful signal peptides for yeast host cells also include those from the genes for Saccharomyces cerevisiae alpha-factor, Saccharomyces cerevisiae SUC2 invertase (see Taussig and Carlson, Nucl. Acids Res., 11:1943-54 [1983]; SwissProt Accession No. P00724; and Romanos et al., Yeast 8:423-488 [1992]). Variants of these signal peptides and other signal peptides are suitable. In addition, the signal peptides provided herein find use in the present invention.
EXPERIMENTAL
The present invention is described in further detail in the following Examples, which are not in any way intended to limit the scope of the invention as claimed.
In the experimental disclosure below, the following abbreviations apply: ppm (parts per million); M (molar); mM (millimolar), uM and μM (micromolar); nM (nanomolar); mol (moles); gm and g (gram); mg (milligrams); ug and μg (micrograms); L and l (liter); ml and mL (milliliter); cm (centimeters); mm (millimeters); um and μm (micrometers); sec. (seconds); min(s) (minute(s)); h(s) and hr(s) (hour(s)); U (units); MW (molecular weight); rpm (rotations per minute); ° C. (degrees Centigrade); DNA (deoxyribonucleic acid); RNA (ribonucleic acid); HPLC (high pressure liquid chromatography); MES (2-N-morpholino ethanesulfonic acid); FIOPC (fold improvements over positive control); YPD (10 g/L yeast extract, 20 g/L peptone, and 20 g/L dextrose); SOE-PCR (splicing by overlapping extension PCR); PEG (polyethylene glycol); TWEEN®-20 (TWEEN® non-ionic surfactant; Sigma-Aldrich); ARS (ARS Culture Collection or NRRL Culture Collection, Peoria, Ill.); Axygen (Axygen, Inc., Union City, Calif.); Lallemand (Lallemand Ethanol Technology, Milwaukee, Wis.); Dual Biosystems (Dual Biosystems AG, Schlieven, Switzerland); US Biological (United States Biological, Swampscott, Mass.); Megazyme (Megazyme International Ireland, Ltd., Wicklow, Ireland); Genetix (Genetix USA, Inc., Beaverton, Oreg.); Sigma-Aldrich (Sigma-Aldrich, St. Louis, Mo.); Dasgip (Dasgip Biotools, LLC, Shrewsbury, Mass.); Difco (Difco Laboratories, BD Diagnostic Systems, Detroit, Mich.); PCRdiagnostics (PCRdiagnostics, by E. coli SRO, Slovak Republic); Agilent (Agilent Technologies, Inc., Santa Clara, Calif.); Molecular Devices (Molecular Devices, Sunnyvale, Calif.); Symbio (Symbio, Inc., Menlo Park, Calif.); Newport (Newport Scientific, Australia); and Bio-Rad (Bio-Rad Laboratories, Hercules, Calif.).
The M. thermophila strains included in the development of the present invention included a “Strain CF-400” (Δcdh1), which is a derivative of C1 strain (“UV18#100fΔalp1Δpyr5”), modified by deletion of cdh1, wherein cdh1 comprises the polynucleotide sequence of SEQ ID NO:5 of U.S. Pat. No. 8,236,551. “Strain CF-401” (Δcdh1 Δcdh2) (ATCC No. PTA-12255), is a derivative of the C1 strain modified by deletion of both a cdh1 and a cdh2, wherein cdh2 comprises the polynucleotide sequence of SEQ ID NO:7 of U.S. Pat. No. 8,236,551. “Strain CF-402” (+Bgl1) is a derivative of the C1 strain further modified for overexpression of an endogenous beta-glucosidase 1 enzyme (Bgl1). “Strain CF-403” is a derivative of the C1 strain modified with a deletion of cdh1 and further modified to overexpress bgl1 “Strain CF-404” is a derivative of the C1 strain further modified to overexpress bgl1 with a deletion of both cdh1 and cdh2. “Strain CF-416” is a derivative of the CF-404 strain, further modified to overexpress wild-type GH61a enzyme.
The following sequences are referred to herein and find use in the present invention








Wild-type M. thermophila C1 GH61a cDNA sequence:



(SEQ ID NO: 1)



ATGTCCAAGGCCTCTGCTCTCCTCGCTGGCCTGACGGGCGCGGCCCTCGTCGCTGCACATGG



 


CCACGTCAGCCACATCGTCGTCAACGGCGTCTACTACAGGAACTACGACCCCACGACAGACT


 


GGTACCAGCCCAACCCGCCAACAGTCATCGGCTGGACGGCAGCCGATCAGGATAATGGCTT


 


CGTTGAACCCAACAGCTTTGGCACGCCAGATATCATCTGCCACAAGAGCGCCACCCCCGGCG


 


GCGGCCACGCTACCGTTGCTGCCGGAGACAAGATCAACATCGTCTGGACCCCCGAGTGGCCC


 


GAATCCCACATCGGCCCCGTCATTGACTACCTAGCCGCCTGCAACGGTGACTGCGAGACCGT


 


CGACAAGTCGTCGCTGCGCTGGTTCAAGATTGACGGCGCCGGCTACGACAAGGCCGCCGGC


 


CGCTGGGCCGCCGACGCTCTGCGCGCCAACGGCAACAGCTGGCTCGTCCAGATCCCGTCGGA


 


TCTCAAGGCCGGCAACTACGTCCTCCGCCACGAGATCATCGCCCTCCACGGTGCTCAGAGCC


 


CCAACGGCGCCCAGGCCTACCCGCAGTGCATCAACCTCCGCGTCACCGGCGGCGGCAGCAA


 


CCTGCCCAGCGGCGTCGCCGGCACCTCGCTGTACAAGGCGACCGACCCGGGCATCCTCTTCA


 


ACCCCTACGTCTCCTCCCCGGATTACACCGTCCCCGGCCCGGCCCTCATTGCCGGCGCCGCC


 


AGCTCGATCGCCCAGAGCACGTCGGTCGCCACTGCCACCGGCACGGCCACCGTTCCCGGCGG


 


CGGCGGCGCCAACCCTACCGCCACCACCACCGCCGCCACCTCCGCCGCCCCGAGCACCACCC


 


TGAGGACGACCACTACCTCGGCCGCGCAGACTACCGCCCCGCCCTCCGGCGATGTGCAGACC


 


AAGTACGGCCAGTGTGGTGGCAACGGATGGACGGGCCCGACGGTGTGCGCCCCCGGCTCGA


 


GCTGCTCCGTCCTCAACGAGTGGTACTCCCAGTGTTTGTAA


 


Wild-type M. thermophila C1 GH61a polypeptide sequence:


(SEQ ID NO: 2)



MSKASALLAGLTGAALVAAHGHVSHIVVNGVYYRNYDPTTDWYQPNPPTVIGWTAADQDNGF



 


VEPNSEGTPDIICHKSATPGGGHATVAAGDKINIVWTPEWPESHIGPVIDYLAACNGDCETVDKSS


 


LRWFKIDGAGYDKAAGRWAADALRANGNSWLVQIPSDLKAGNYVLRHEIIALHGAQSPNGAQ


 


AYPQCINLRVTGGGSNLPSGVAGTSLYKATDPGILFNPYVSSPDYTVPGPALIAGAASSIAQSTSV


 


ATATGTATVPGGGGANPTATTTAATSAAPSTTLRTTTTSAAQTTAPPSGDVQTKYGQCGGNGW


 


TGPTVCAPGSSCSVLNEWYSQCL


 


Wild-type M. thermophila C1 GH61a polypeptide sequence


without the signal sequence:


(SEQ ID NO: 3)



HGHVSHIVVNGVYYRNYDPTTDWYQPNPPTVIGWTAADQDNGFVEPNSFGTPDIICHKSATPGG



 


GHATVAAGDKINIVWTPEWPESHIGPVIDYLAACNGDCETVDKSSERWFKIDGAGYDKAAGRW


 


AADALRANGNSWLVQIPSDLKAGNYVLRHEIIALHGAQSPNGAQAYPQCINLRVTGGGSNLPSG


 


VAGTSLYKATDPGILFNPYVSSPDYTVPGPALIAGAASSIAQSTSVATATGTATVPGGGGANPTA


 


TTTAATSAAPSTTLRTTTTSAAQTTAPPSGDVQTKYGQCGGNGWTGPTVCAPGSSCSVLNEWYS


 


QCL


 


GH61a Variant 1 cDNA sequence:


(SEQ ID NO: 4)



ATGTCCAAGGCCTCTGCTCTCCTCGCTGGCCTGACGGGCGCGGCCCTCGTCGCTGCACACGG



 


CCACGTCAGCCACATCGTCGTCAACGGCGTCTACTACAGGGGCTACGACCCCACGACAGACT


 


GGTACCAGCCCAACCCGCCAACAGTCATCGGCTGGACGGCAGCCGATCAGGATAATGGCTT


 


CGTTGAACCCAACAGCTTTGGCACGCCAGATATCATCTGCCACAAGAGCGCCACCCCCGGCG


 


GCGGCCACGCTACCGTTGCTGCCGGAGACAAGATCAACATCGTCTGGACCCCCGAGTGGCCC


 


CACTCCCACATCGGCCCCGTCATTGACTACCTAGCCGCCTGCAACGGTGACTGCGAGACCGT


 


CGACAAGTCGTCGCTGCGCTGGTTCAAGATTGACGGCGCCGGCTACGACAAGGCCGCCGGC


 


CGCTGGGCCGCCGACGCTCTGCGCGCCAACGGCAACAGCTGGCTCGTCCAGATCCCGTCGGA


 


TCTCAAGCCCGGCAACTACGTCCTCCGCCACGAGATCATCGCCCTCCACGGTGCTCAGAGCC


 


CCAACGGCGCCCAGGCGTACCCGCAGTGCATCAACCTCCGCGTCACCGGCGGCGGCAGCAA


 


CCTGCCCAGCGGCGTCGCCGGCACCTCGCTGTACAAGGCGACCGACCCGGGCATCCTCTTCA


 


ACCCCTACGTCTCCTCCCCGGATTACACCGTCCCCGGCCCGGCCCTCATTGCCGGCGCCGCC


 


AGCTCGATCGCCCAGAGCACGTCGGTCGCCACTGCCACCGGCACGGCCACCGTTCCCGGCGG


 


CGGCGGCGCCAACCCTACCGCCACCACCACCGCCGCCACCTCCGCCGCCCCGAGCACCACCC


 


TGAGGACGACCACTACCTCGGCCGCGCAGACTACCGCCCCGCCCTCCGGCGATGTGCAGACC


 


AAGTACGGCCAGTGTGGTGGCAACGGATGGACGGGCCCGACGGTGTGCGCCCCCGGCTCGA


 


GCTGCTCCGTCCTCAACGAGTGGTACTCCCAGTGTTTGTAA


 


GH61a Variant 1 polypeptide sequence:


(SEQ ID NO: 5)



MSKASALLAGLTGAALVAAHGHVSHIVVNGVYYRGYDPTTDWYQPNPPTVIGWTAADQDNGF



 


VEPNSFGTPDIICHKSATPGGGHATVAAGDKINIVWTPEWPHSHIGPVIDYLAACNGDCETVDKS


 


SLRWFKIDGAGYDKAAGRWAADALRANGNSWLVQIPSDLKPGNYVLRHEIIALHGAQSPNGAQ


 


AYPQCINLRVTGGGSNLPSGVAGTSLYKATDPGILFNPYVSSPDYTVPGPALIAGAASSIAQSTSV


 


ATATGTATVPGGGGANPTATTTAATSAAPSTTLRTTTTSAAQTTAPPSGDVQTKYGQCGGNGW


 


TGPTVCAPGSSCSVLNEWYSQCL


 


GH61a Variant 1 polypeptide sequence without the 


signal sequence:


(SEQ ID NO: 6)



HGHVSHIVVNGVYYRGYDPTTDWYQPNPPTVIGWTAADQDNGFVEPNSFGTPDIICHKSATPGG



 


GHATVAAGDKINIVWTPEWPHSHIGPVIDYLAACNGDCETVDKSSLAWFKIDGAGYDKAAGRW


 


AADALRANGNSWINQIPSDLKPGNYVLRHEIIALHGAQSPNGAQAYPQCINLRVTGGGSNLPSG


 


VAGTSLYKATDPGILFNPYYSSPDYTVPGPALIAGAASSIAQSTSVATATGTATVPGGGGANPTA


 


TTTAATSAAPSTTLRTTTTSAAQTTAPPSGDVQTKYGQCGGNGWTGPTVCAPGSSCSVLNEWYS


 


QCL


 


GH61a Variant 5 cDNA sequence


(SEQ ID NO: 7)



ACACAAATGTCCAAGGCCTCTGCTCTCCTCGCTGGCCTGACGGGCGCGGCCCTCGTCGCTGC



 


ACACGGCCACGTCAGCCACATCGTCGTCAACGGCGTCTACTACAGGAACTACGACCCCACG


 


ACAGACTGGTACCAGCCCAACCCGCCAACAGTCATCGGCTGGACGGCAGCCGATCAGGATA


 


ATGGCTTCGTTGAACCCAACAGCTTTGGCACGCCAGATATCATCTGCCACAAGAGCGCCACC


 


CCCGGCGGCGGCCACGCTACCGTTGCTGCCGGAGACAAGATCAACATCGTATGGACCCCCG


 


AGTGGCCCCACTCCCACATCGGCCCCGTCATTGACTACCTAGCCGCCTGCAACGGTGACTGC


 


GAGACCGTCGACAAGTCGTCGCTGCGCTGGTTCAAGATTGACGGCGCCGGCTACGACAAGG


 


CCGCCGGCCGCTGGGCCGCCGACGCTCTGCGCGCCAACGGCAACAGCTGGCTCGTCCAGATC


 


CCGTCGGATCTCGCGGCCGGCAACTACGTCCTCCGCCACGAGATCATCGCCCTCCACGGTGC


 


TCAGAGCCCCAACGGCGCCCAGGCGTACCCGCAGTGCATCAACCTCCGCGTCACCGGCGGC


 


GGCAGCAACCTGCCCAGCGGCGTCGCCGGCACCTCGCTGTACAAGGCGACCGACCCGGGCA


 


TCCTCTTCAACCCCTACGTCTCCTCCCCGGATTACACCGTCCCCGGCCCGGCCCTCATTGCCG


 


GCGCCGCCAGCTCGATCGCCCAGAGCACGTCGGTCGCCACTGCCACCGGCACGGCCACCGTT


 


CCCGGCGGCGGCGGCGCCAACCCTACCGCCACCACCACCGCCGCCACCTCCGCCGCCCCGA


 


GCACCACCCTGAGGACGACCACTACCTCGGCCGCGCAGACTACCGCCCCGCCCTCCGGCGAT


 


GTGCAGACCAAGTACGGCCAGTGTGGTGGCAACGGATGGACGGGCCCGACGGTGTGCGCCC


 


CCGGCTCGAGCTGCTCCGTCCTCAACGAGTGGTACTCCCAGTGTTTGTAA


 


GH61a Variant 5 polypeptide sequence:


(SEQ ID NO: 8)



MSKASALLAGLTGAALVAAHGHVSHIVVNGVYYRNYDPTTDWYQPNPPTVIGWTAADQDNGF



 


VEPNSEGTPDIICHKSATPGGGHATVAAGDKINIVWTPEWPHSHIGPVIDYLAACNGDCETVDKS


 


SLRWFKIDGAGYDKAAGRWAADALRANGNSWINQIPSDLAAGNYVLRHEIIALHGAQSPNGAQ


 


AYPQCINLRVTGGGSNLPSGVAGTSLYKATDPGILFNPYVSSPDYTVPGPALIAGAASSIAQSTSV


 


ATATGTATVPGGGGANPTATTTAATSAAPSTTLRITTTSAAQTTAPPSGDVQTKYGQCGGNGW


 


TGPTVCAPGSSCSVLNEWYSQCL


 


GH61a Variant 5 polypeptide sequence without


the signal sequence:


(SEQ ID NO: 9)



HGHVSHIVVNGVYYRNYDPTTDWYQPNPPTVIGWTAADQDNGFVEPNSEGTPDIICHKSATPGG



 


GHATVAAGDKINIVWTPEWPHSHIGPVIDYLAACNGDCETVDKSSIRWFKIDGAGYDKAAGRW


 


AADALRANGNSWLVQIPSDLAAGNYVLRHEIIALHGAQSPNGAQAYPQCINLRVTGGGSNLPSG


 


VAGTSLYKATDPGILFNPYVSSPDYTVPGPALIAGAASSIAQSTSVATATGTATVPGGGGANPTA


 


TTTAATSAAPSTTLRTTTTSAAQTTAPPSGDVQTKYGQCGGNGWTGPTVCAPGSSCSVLNEWYS


 


QCL


 


GH61a Variant 9 cDNA sequence:


(SEQ ID NO: 10)



ACAAACATGTCCAAGGCCTCTGCTCTCCTCGCTGGCCTGACGGGCGCGGCCCTCGTCGCTGC



 


ACATGGCCACGTCAGCCACATCGTCGTCAACGGCGTCTACTACAGGAACTACGACCCCACGA


 


CAGACTGGTACCAGCCCAACCCGCCAACAGTCATCGGCTGGACGGCAGCCGATCAGGATAA


 


TGGCTTCGTTGAACCCAACAGCTTTGGCACGCCAGATATCATCTGCCACAAGAGCGCCACCC


 


CCGGCGGCGGCCACGCTACCGTTGCTGCCGGAGACAAGATCAACATCCAGTGGACCCCCGA


 


GTGGCCCGAATCCCACATCGGCCCCGTCATTGACTACCTAGCCGCCTGCAACGGTGACTGCG


 


AGACCGTCGACAAGTCGTCGCTGCGCTGGTTCAAGATTGACGGCGCCGGCTACGACAAGGC


 


CGCCGGCCGCTGGGCCGCCGACGCTCTGCGCGCCAACGGCAACAGCTGGCTCGTCCAGATCC


 


CGTCGGATCTCAAGGCCGGCAACTACGTCCTCCGCCACGAGATCATCGCCCTCCACGGTGCT


 


CAGAGCCCCAACGGCGCCCAGAACTACCCGCAGTGCATCAACCTCCGCGTCACCGGCGGCG


 


GCAGCAACCTGCCCAGCGGCGTCGCCGGCACCTCGCTGTACAAGGCGACCGACCCGGGCAT


 


CCTCTTCAACCCCTACGTCTCCTCCCCGGATTACACCGTCCCCGGCCCGGCCCTCATTGCCGG


 


CGCCGCCAGCTCGATCGCCCAGAGCACGTCGGTCGCCACTGCCACCGGCACGGCCACCGTTC


 


CCGGCGGCGGCGGCGCCAACCCTACCGCCACCACCACCGCCGCCACCTCCGCCGCCCCGAG


 


CACCACCCTGAGGACGACCACTACCTCGGCCGCGCAGACTACCGCCCCGCCCTCCGGCGATG


 


TGCAGACCAAGTACGGCCAGTGTGGTGGCAACGGATGGACGGGCCCGACGGTGTGCGCCCC


 


CGGCTCGAGCTGCTCCGTCCTCAACGAGTGGTACTCCCAGTGTTTGTAA


 


GH61a Variant 9 polypeptide sequence:


(SEQ ID NO: 11)



MSKASALLAGLTGAALVAAHGHVSHIVVNGVYYRNYDPTTDWYQPNPPTVIGWTAADQDNGF



 


VEPNSEGTPDIICHKSATPGGGHATVAAGDKINIQWTPEWPESHIGPVIDYLAACNGDCETVDKSS


 


LRWFKIDGAGYDKAAGRWAADALRANGNSWLVQIPSDLKAGNYVLRHEIIALHGAQSPNGAQ


 


NYPQCINLRVTGGGSNLPSGVAGTSLYKATDPGILFNPYVSSPDYTVPGPALIAGAASSIAQSTSV


 


ATATGTATVPGGGGANPTATTTAATSAAPSTTLRTTTTSAAQTTAPPSGDVQTKYGQCGGNGW


 


TGPTVCAPGSSCSVLNEWYSQCL


 


GH6la Variant 9 polypeptide sequence without the


signal sequence:


(SEQ ID NO: 12)



MSKASALLAGLTGAALVAAHGHVSHIVVNGVYYRNYDPTTDWYQPNPPTVIGWTAADQDNGF



 


VEPNSFGTPDIICHKSATPGGGHATVAAGDKINIQWTPEWPESHIGPVIDYLAACNGDCETVDKSS


 


LRWFKIDGAGYDKAAGRWAADALRANGNSWLVQIPSDLKAGNYVLRHEIIALHGAQSPNGAQ


 


NYPQCINLRVTGGGSNLPSGVAGTSLYKATDPGILFNPYVSSPDYTVPGPALIAGAASSIAQSTSV


 


ATATGTATVPGGGGANPTATTTAATSAAPSTTLRTTTTSAAQTTAPPSGDVQTKYGQCGGNGW


 


TGPTVCAPGSSCSVLNEWYSQCL






The polynucleotide (SEQ ID NO:13) and amino acid (SEQ ID NO:14) sequences of an M. thermophila GH61b are provided below. The signal sequence is shown underlined in SEQ ID NO:14. SEQ ID NO:15 provides the sequence of this GH61b without the signal sequence.








(SEQ ID NO: 13)



ATGAAGCTCTCCCTCTTTTCCGTCCTGGCCACTGCCCTCACCGTCGAGGGGCATGCCATCTTC



 


CAGAAGGTCTCCGTCAACGGAGCGGACCAGGGCTCCCTCACCGGCCTCCGCGCTCCCAACA


 


ACAACAACCCCGTGCAGAATGTCAACAGCCAGGACATGATCTGCGGCCAGTCGGGATCGAC


 


GTCGAACACTATCATCGAGGTCAAGGCCGGCGATAGGATCGGTGCCTGGTATCAGCATGTCA


 


TCGGCGGTGCCCAGTTCCCCAACGACCCAGACAACCCGATTGCCAAGTCGCACAAGGGCCC


 


CGTCATGGCCTACCTCGCCAAGGTTGACAATGCCGCAACCGCCAGCAAGACGGGCCTGAAG


 


TGGTTCAAGATTTGGGAGGATACCTTTAATCCCAGCACCAAGACCTGGGGTGTCGACAACCT


 


CATCAACAACAACGGCTGGGTGTACTTCAACCTCCCGCAGTGCATCGCCGACGGCAACTACC


 


TCCTCCGCGTCGAGGTCCTCGCTCTGCACTCGGCCTACTCCCAGGGCCAGGCTCAGTTCTACC


 


AGTCCTGCGCCCAGATCAACGTATCCGGCGGCGGCTCCTTCACGCCGGCGTCGACTGTCAGC


 


TTCCCGGGTGCCTACAGCGCCAGCGACCCCGGTATCCTGATCAACATCTACGGCGCCACCGG


 


CCAGCCCGACAACAACGGCCAGCCGTACACTGCCCCTGGGCCCGCGCCCATCTCCTGC


 


(SEQ ID NO: 14)



MKLSLFSVLATALTVEGHAIFQKVSVNGADQGSLTGLRAPNNNNPVQNVNSQDMICGQSGSTSN



 


TIIEVKAGDRIGAWYQHVIGGAQFPNDPDNPIAKSHKGPVMAYLAKVDNAATASKTGLKWFKI


 


WEDTFNPSTKTWGVDNLINNNGWVYFNLPQCIADGNYLLRVEVLALHSAYSQGQAQFYQSCAQ


 


INVSGGGSFTPASTVSFPGAYSASDPGILINIYGATGQPDNNGQPYTAPGPAPISC


 


(SEQ ID NO: 15)



IFQKVSVNGADQGSLTGLRAPNNNNPVQNVNSQDMICGQSGSTSNTIIEVKAGDRIGAWYQHVI



 


GGAQFPNDPDNPIAKSHKGPVMAYLAKVDNAATASKTGLKWFKIWEDTFNPSTKTWGVDNLIN


 


NNGWVYFNLPQCIADGNYLLRVEVLALHSAYSQGQAQFYQSCAQINVSGGGSFTPASTVSFPGA


 


YSASDPGILINIYGATGQPDNNGQPYTAPGPAPISC






The polynucleotide (SEQ ID NO:16) and amino acid (SEQ ID NO:17) sequences of an M. thermophila GH61c are provided below. The signal sequence is shown underlined in SEQ ID NO:17. SEQ ID NO:18 provides the sequence of this GH61c without the signal sequence.








(SEQ ID NO: 16)



ATGGCCCTCCAGCTCTTGGCGAGCTTGGCCCTCCTCTCAGTGCCGGCCCTTGCCCACGGTGGC



 


TTGGCCAACTACACCGTCGGTGATACTTGGTACAGAGGCTACGACCCAAACCTGCCGCCGGA


 


GACGCAGCTCAACCAGACCTGGATGATCCAGCGGCAATGGGCCACCATCGACCCCGTCTTCA


 


CCGTGTCGGAGCCGTACCTGGCCTGCAACAACCCGGGCGCGCCGCCGCCCTCGTACATCCCC


 


ATCCGCGCCGGTGACAAGATCACGGCCGTGTACTGGTACTGGCTGCACGCCATCGGGCCCAT


 


GAGCGTCTGGCTCGCGCGGTGCGGCGACACGCCCGCGGCCGACTGCCGCGACGTCGACGTC


 


AACCGGGTCGGCTGGTTCAAGATCTGGGAGGGCGGCCTGCTGGAGGGTCCCAACCTGGCCG


 


AGGGGCTCTGGTACCAAAAGGACTTCCAGCGCTGGGACGGCTCCCCGTCCCTCTGGCCCGTC


 


ACGATCCCCAAGGGGCTCAAGAGCGGGACCTACATCATCCGGCACGAGATCCTGTCGCTTCA


 


CGTCGCCCTCAAGCCCCAGTTTTACCCGGAGTGTGCGCATCTGAATATTACTGGGGGCGGAG


 


ACTTGCTGCCACCCGAAGAGACTCTGGTGCGGTTTCCGGGGGTTTACAAAGAGGACGATCCC


 


TCTATCTTCATCGATGTCTACTCGGAGGAGAACGCGAACCGGACAGATTATACGGTTCCGGG


 


AGGGCCAATCTGGGAAGGG


 


(SEQ ID NO: 17)



MALQLLASLALLSVPALAHGGLANYTVGDTWYRGYDPNLPPETQLNQTWMIQRQWATIDPVFT



 


VSEPYLACNNPGAPPPSYIPLRAGDKITAVYWYWLHAIGPMSVWLARCGDTPAADCRDVDVNR


 


VGWFKIWEGGLLEGPNLAEGLWYQKDFQRWDGSPSLWPVTIPKGLKSGTYIIRHEILSLHVALKP


 


QFYPECAHLNITGGGDLLPPEETLVRFPGVYKEDDPSIFIDVYSEENANRTDYTVPGGPIWEG


 


(SEQ ID NO: 18)



NYTVGDTWYRGYDPNLPPETQLNQTWMIQRQWATIDPVFTVSEPYLACNNPGAPPPSYIPIRAG



 


DKITAVYWYWLHAIGPMSVWLARCGDTPAADCRDVDVNRVGWFKIWEGGLLEGPNLAEGLW


 


YQKDFQRWDGSPSLWPVTIPKGLKSGTYIIRHEILSLHVALKPQFYPECAHLNITGGGDLLPPEET


 


LVRFPGVYKEDDPSIFIDVYSEENANRTDYTVPGGPIWEG






The polynucleotide (SEQ ID NO:19) and amino acid (SEQ ID NO:20) sequences of an M. thermophila GH61d are provided below. The signal sequence is shown underlined in SEQ ID NO:20. SEQ ID NO:21 provides the sequence of this GH61d without the signal sequence.








(SEQ ID NO: 19)



ATGAAGGCCCTCTCTCTCCTTGCGGCTGCCGGGGCAGTCTCTGCGCATACCATCTTCGTCCAG



 


CTCGAAGCAGACGGCACGAGGTACCCGGTTTCGTACGGGATCCGGGACCCAACCTACGACG


 


GCCCCATCACCGACGTCACATCCAACGACGTTGCTTGCAACGGCGGTCCGAACCCGACGACC


 


CCCTCCAGCGACGTCATCACCGTCACCGCGGGCACCACCGTCAAGGCCATCTGGAGGCACAC


 


CCTCCAATCCGGCCCGGACGATGTCATGGACGCCAGCCACAAGGGCCCGACCCTGGCCTAC


 


ATCAAGAAGGTCGGCGATGCCACCAAGGACTCGGGCGTCGGCGGTGGCTGGTTCAAGATCC


 


AGGAGGACGGTTACAACAACGGCCAGTGGGGCACCAGCACCGTTATCTCCAACGGCGGCGA


 


GCACTACATTGACATCCCGGCCTGCATCCCCGAGGGTCAGTACCTCCTCCGCGCCGAGATGA


 


TCGCCCTCCACGCGGCCGGGTCCCCCGGCGGCGCTCAGCTCTACATGGAATGTGCCCAGATC


 


AACATCGTCGGCGGCTCCGGCTCGGTGCCCAGCTCGACGGTCAGCTTCCCCGGCGCGTATAG


 


CCCCAACGACCCGGGTCTCCTCATCAACATCTATTCCATGTCGCCCTCGAGCTCGTACACCAT


 


CCCGGGCCCGCCCGTTTTCAAGTGC


 


(SEQ ID NO: 20)



MKALSLLAAAGAVSAHTIFVQLEADGTRYPVSYGIRDPTYDGPITDVTSNDVACNGGPNPTTPSS



 


DVITVTAGTTVKAIWRHTLQSGPDDVMDASHKGPTLAYIKKVGDATKDSGVGGGWFKIQEDGY


 


NNGQWGTSTVISNGGEHYIDIPACIPEGQYLLRAEMIALHAAGSPGGAQLYMECAQINIVOGSGS


 


VPSSTVSFPGAYSPNDPGLLINIYSMSPSSSYTIPGPPVFKC


 


(SEQ ID NO: 21)



HTIFVQLEADGTRYPVSYGIRDPTYDGPITDVTSNDVACNGGPNPTTPSSDVITVTAGTTVKAIWR



 


HTLQSGPDDVMDASHKGPTLAYIKKVGDATKDSGVGGGWFKIQEDGYNNGQWGTSTVISNGG


 


EHYIDIPACIPEGQYLLRAEMIALHAAGSPGGAQLYMECAQINIVGGSGSVPSSTVSFPGAYSPND


 


PGLLINIYSMSPSSSYTIPGPPVFKC






The polynucleotide (SEQ ID NO:22) and amino acid (SEQ ID NO:23) sequences of an M. thermophila GH61e are provided below. The signal sequence is shown underlined in SEQ ID NO:23. SEQ ID NO:24 provides the sequence of this GH61d without the signal sequence,








(SEQ ID NO: 22)



ATGAAGTCGTCTACCCCGGCCTTGTTCGCCGCTGGGCTCCTTGCTCAGCATGCTGCGGCCCAC



 


TCCATCTTCCAGCAGGCGAGCAGCGGCTCGACCGACTTTGATACGCTGTGCACCCGGATGCC


 


GCCCAACAATAGCCCCGTCACTAGTGTGACCAGCGGCGACATGACCTGCAAAGTCGGCGGC


 


ACCAAGGGGGTGTCCGGCTTCTGCGAGGTGAACGCCGGCGACGAGTTCACGGTTGAGATGC


 


ACGCGCAGCCCGGCGACCGCTCGTGCGCCAACGAGGCCATCGGCGGGAACCACTTCGGCCC


 


GGTCCTCATCTACATGAGCAAGGTCGACGACGCCTCCACCGCCGACGGGTCCGGCGACTGGT


 


TCAAGGTGGACGAGTTCGGCTACGACGCAAGCACCAAGACCTGGGGCACCGACAAGCTCAA


 


CGAGAACTGCGGCAAGCGCACCTTCAACATCCCCAGCCACATCCCCGCGGGCGACTATCTCG


 


TCCGGGCCGAGGCTATCGCGCTACACACTGCCAACCAGCCAGGCGGCGCGCAGTTCTACATG


 


AGCTGCTATCAAGTCAGGATTTCCGGCGGCGAAGGGGGCCAGCTGCCTGCCGGAGTCAAGA


 


TCCCGGGCGCGTACAGTGCCAACGACCCCGGCATCCTTGTCGACATCTGGGGTAACGATTTC


 


AACGACCCTCCAGGACACTCGGCCCGTCACGCCATCATCATCATCAGCAGCAGCAGCAACA


 


ACAGCGGCGCCAAGATGACCAAGAAGATCCAGGAGCCCACCATCACATCGGTCACGGACCT


 


CCCCACCGACGAGGCCAAGTGGATCGCGCTCCAAAAGATCTCGTACGTGGACCAGACGGGC


 


ACGGCGCGGACATACGAGCCGGCGTCGCGCAAGACGCGGTCGCCAAGAGTCTAG


 


(SEQ ID NO: 23)



MKSSTPALFAAGLLAQHAAAHSIFQQASSGSTDFDTLCTRMPPNNSPVTSVTSGDMTCKVGGTK



 


GVSGFCEVNAGDEETVEMHAQPGDRSCANEAIGGNHFGPVLIYMSKVDDASTADGSGDWFKVD


 


EFGYDASTKTWGTDKLNENCGKRTFNIPSHIPAGDYLVRAEAIALHTANQPGGAQFYMSCYQVR


 


ISGGEGGQLPAGVKIPGAYSANDPGILVDIWGNDFNDPPGHSARHAIIIISSSSNNSGAKMTKKIQE


 


PTITSVTDLPTDEAKWIALQKISYVDQTGTARTYEPASRKTRSPRV


 


(SEQ ID NO: 24)



HSIFQQASSGSTDFDTLETRMPPNNSPVTSVTSGDMTCKVGGTKGVSGFCEVNAGDEFTVEMHA



 


QPGDRSCANEAIGGNHFGPVLIYMSKVDDASTADGSGDWFKVDEFGYDASTKTWGTDKLNENC


 


GKRTFNIPSHIPAGDYLVRAEAIALHTANQPGGAQFYMSCYQVRISGGEGGQLPAGVKIPGAYSA


 


NDPGILVDIWGNDFNDPPGHSARHAIIIISSSSNNSGAKMTKKIQEPTITSVTDEPTDEAKWIALQKI


 


SYVDQTGTARTYEPASRKTRSPRV






The polynucleotide (SEQ ID NO:25) and amino acid (SEQ ID NO:26) sequences of an alternative M. thermophila GH61e are provided below. The signal sequence is shown underlined in SEQ ID NO:26. SEQ ID NO:27 provides the sequence of this GH61e without the signal sequence.








(SEQ ID NO: 25)



ATGAAGTCGTCTACCCCGGCCTTGTTCGCCGCTGGGCTCCTTGCTCAGCATGCTGCGGCCCAC



 


TCCATCTTCCAGCAGGCGAGCAGCGGCTCGACCGACTTTGATACGCTGTGCACCCGGATGCC


 


GCCCAACAATAGCCCCGTCACTAGTGTGACCAGCGGCGACATGACCTGCAACGTCGGCGGC


 


ACCAAGGGGGTGTCGGGCTTCTGCGAGGTGAACGCCGGCGACGAGTTCACGGTTGAGATGC


 


ACGCGCAGCCCGGCGACCGCTCGTGCGCCAACGAGGCCATCGGCGGGAACCACTTCGGCCC


 


GGTCCTCATCTACATGAGCAAGGTCGACGACGCCTCCACTGCCGACGGGTCCGGCGACTGGT


 


TCAAGGTGGACGAGTTCGGCTACGACGCAAGCACCAAGACCTGGGGCACCGACAAGCTCAA


 


CGAGAACTGCGGCAAGCGCACCTTCAACATCCCCAGCCACATCCCCGCGGGCGACTATCTCG


 


TCCGGGCCGAGGCTATCGCGCTACACACTGCCAACCAGCCAGGCGGCGCGCAGTTCTACATG


 


AGCTGCTATCAAGTCAGGATTTCCGGCGGCGAAGGGGGCCAGCTGCCTGCCGGAGTCAAGA


 


TCCCGGGCGCGTACAGTGCCAACGACCCCGGCATCCTTGTCGACATCTGGGGTAACGATTTC


 


AACGAGTACGTTATTCCGGGCCCCCCGGTCATCGACAGCAGCTACTTC


 


(SEQ ID NO: 26)



MKSSTPALFAAGLLAQHAAAHSIFQQASSGSTDFDTLCTRMPPNNSPVTSVTSGDMTCNVGGTK



 


GVSGFCEVNAGDEFTVEMHAQPGDRSCANEAIGGNHFGPVLIYMSKVDDASTADGSGDWFKVD


 


EFGYDASTKTWGTDKLNENCGKRTFNIPSHIPAGDYLVRAEAIALHTANQPGGAQFYMSCYQVR


 


ISGGEGGQLPAGVKIPGAYSANDPGILVDIWGNDFNEYVIPGPPVIDSSYF


 


(SEQ ID NO: 27)



HSIFQQASSGSTDFDTLCTRMPPNNSPVTSVTSGDMTCNVGGTKGVSGFCEVNAGDEFTVEMHA



 


QPGDRSCANEAIGGNHFGPVLIYMSKVDDASTADGSGDWFKVDEFGYDASTKTWGTDKLNENC


 


GKRTFNIPSHIPAGDYLVRAEAIALHTANQPGGAQFYMSCYQVRISGGEGGQLPAGVKIPGAYSA


 


NDPGILVDIWGNDFNEYVIPGPPVIDSSYF






The polynucleotide (SEQ ID NO:28) and amino acid (SEQ ID NO:29) sequences of a M. thermophila GH61f are provided below. The signal sequence is shown underlined in SEQ ID NO:29. SEQ ID NO:30 provides the sequence of this GH61f without the signal sequence.








(SEQ ID NO: 28)



ATGAAGTCCTTCACCCTCACCACTCTGGCCGCCCTGGCTGGCAACGCCGCCGCTCACGCGAC



 


CTTCCAGGCCCTCTGGGTCGACGGCGTCGACTACGGCGCGCAGTGTGCCCGTCTGCCCGCGT


 


CCAACTCGCCGGTCACCGACGTGACCTCCAACGCGATCCGCTGCAACGCCAACCCCTCGCCC


 


GCTCGGGGCAAGTGCCCGGTCAAGGCCGGCTCGACCGTTACGGTCGAGATGCATCAGCAAC


 


CCGGTGACCGCTCGTGCAGCAGCGAGGCGATCGGCGGGGCGCACTACGGCCCCGTGATGGT


 


GTACATGTCCAAGGTGTCGGACGCGGCGTCGGCGGACGGGTCGTCGGGCTGGTTCAAGGTG


 


TTCGAGGACGGCTGGGCCAAGAACCCGTCCGGCGGGTCGGGCGACGACGACTACTGGGGCA


 


CCAAGGACCTGAACTCGTGCTGCGGGAAGATGAACGTCAAGATCCCCGCCGACCTGCCCTC


 


GGGCGACTACCTGCTCCGGGCCGAGGCCCTCGCGCTGCACACGGCCGGCAGCGCGGGCGGC


 


GCCCAGTTCTACATGACCTGCTACCAGCTCACCGTGACCGGCTCCGGCAGCGCCAGCCCGCC


 


CACCGTCTCCTTCCCGGGCGCCTACAAGGCCACCGACCCGGGCATCCTCGTCAACATCCACG


 


CCCCGCTGTCCGGCTACACCGTGCCCGGCCCGGCCGTCTACTCGGGCGGCTCCACCAAGAAG


 


GCCGGCAGCGCCTGCACCGGCTGCGAGTCCACTTGCGCCGTCGGCTCCGGCCCCACCGCCAC


 


CGTCTCCCAGTCGCCCGGTTCCACCGCCACCTCGGCCCCCGGCGGCGGCGGCGGCTGCACCG


 


TCCAGAAGTACCAGCAGTGCGGCGGCCAGGGCTACACCGGCTGCACCAACTGCGCGTCCGG


 


CTCCACCTGCAGCGCGGTCTCGCCGCCCTACTACTCGCAGTGCGTC


 


(SEQ ID NO: 29)



MKSFTLTTLAALAGNAAAHATFQALWVDGVDYGAQCARLPASNSPVTDVTSNAIRCNANPSPA



 


RGKCPVKAGSTVTVEMHQQPGDRSCSSEAIGGAHYGPVMVYMSKVSDAASADGSSGWFKVFE


 


DGWAKNPSGGSGDDDYWGTKDLNSCCGKMNVKIPADLPSGDYLLRAEALALHTAGSAGGAQF


 


YMTCYQLTVTGSGSASPPTVSFPGAYKATDPGILVNIHAPLSGYTVPGPAVYSGGSTKKAGSACT


 


GCESTCAVGSGPTATVSQSPGSTATSAPGGGGGCTVQKYQQCGGQGYTGCTNCASGSTCSAVSP


 


PYYSQCV


 


(SEQ ID NO: 30)



HATFQALWVDGVDYGAQCARLPASNSPVTDVTSNAIRCNANPSPARGKCPVKAGSTVTVEMHQ



 


QPGDRSCSSEAIGGAHYGPVMVYMSKVSDAASADGSSGWFKVFEDGWAKNPSGGSGDDDYW


 


GTKDINSCCGKMNVKIPADLPSGDYLLRAEALALHTAGSAGGAQFYMTCYQLTVTGSGSASPP


 


TVSFPGAYKATDPGILVNIHAPLSGYTVPGPAVYSGGSTKKAGSACTGCESTCAVGSGPTATVSQ


 


SPGSTATSAPGGGGGCTVQKYQQCGGQGYTGCTNCASGSTCSAVSPPYYSQCV






The polynucleotide (SEQ ID NO:31) and amino acid (SEQ ID NO:32) sequences of an M. thermophila GH61g are provided below. The signal sequence is shown underlined in SEQ ID NO:32. SEQ ID NO:33 provides the sequence of this GH61g without the signal sequence.








(SEQ ID NO: 31)



ATGAAGGGACTCCTCGGCGCCGCCGCCCTCTCGCTGGCCGTCAGCGATGTCTCGGCCCACTA



 


CATCTTTCAGCAGCTGACGACGGGCGGCGTCAAGCACGCTGTGTACCAGTACATCCGCAAGA


 


ACACCAACTATAACTCGCCCGTGACCGATCTGACGTCCAACGACCTCCGCTGCAATGTGGGT


 


GCTACCGGTGCGGGCACCGATACCGTCACGGTGCGCGCCGGCGATTCGTTCACCTTCACGAC


 


CGATACGCCCGTTTACCACCAGGGCCCGACCTCGATCTACATGTCCAAGGCCCCCGGCAGCG


 


CGTCCGACTACGACGGCAGCGGCGGCTGGTTCAAGATCAAGGACTGGGCTGACTACACCGC


 


CACGATTCCGGAATGTATTCCCCCCGGCGACTACCTGCTTCGCATCCAGCAACTCGGCATCC


 


ACAACCCTTGGCCCGCGGGCATCCCCCAGTTCTACATCTCTTGTGCCCAGATCACCGTGACT


 


GGTGGCGGCAGTGCCAACCCCGGCCCGACCGTCTCCATCCCAGGCGCCTTCAAGGAGACCG


 


ACCCGGGCTACACTGTCAACATCTACAACAACTTCCACAACTACACCGTCCCTGGCCCAGCC


 


GTCTTCACCTGCAACGGTAGCGGCGGCAACAACGGCGGCGGCTCCAACCCAGTCACCACCA


 


CCACCACCACCACCACCAGGCCGTCCACCAGCACCGCCCAGTCCCAGCCGTCGTCGAGCCCG


 


ACCAGCCCCTCCAGCTGCACCGTCGCGAAGTGGGGCCAGTGCGGAGGACAGGGTTACAGCG


 


GCTGCACCGTGTGCGCGGCCGGGTCGACCTGCCAGAAGACCAACGACTACTACAGCCAGTG


 


CTTGTAG


 


(SEQ ID NO: 32)



MKGLLGAAALSLAVSDVSAHYIFQQLTTGGVKHAVYQYIRKNTNYNSPVTDLTSNDLRCNVGA



 


TGAGTDTVTVRAGDSFTFTTDTPVYHQGPTSIYMSKAPGSASDYDGSGGWFKIKDWADYTATIP


 


ECIPPGDYLLRIQQLGIHNPWPAGIPQFYISCAQITVTGGGSANPGPTVSIPGAFKETDPGYTVNIY


 


NNFHNYTVPGPAVFTCNGSGGNNGGGSNPVTTTTTTTTRPSTSTAQSQPSSSPTSPSSCTVAKWG


 


QCGGQGYSGCTVCAAGSTCQKTNDYYSQCL


 


(SEQ ID NO: 33)



HYIFQQLTTGGVKHAVYQYIRKNTNYNSPVTDLTSNDLRCNVGATGAGTDTVTVRAGDSFTFTT



 


DTPVYHQGPTSIYMSKAPGSASDYDGSGGWFKIKDWADYTATIPECIPPGDYLLRIQQLGIHNPW


 


PAGIPQFYISCAQITVTGGGSANPGPTVSIPGAFKETDPGYTVNIYNNFHNYTVPGPAVFTCNGSG


 


GNNGGGSNPVTTTTTTTTRPSTSTAQSQPSSSPTSPSSCTVAKWGQCGGQGYSGCTVCAAGSTCQ


 


KTNDYYSQCL






The polynucleotide (SEQ ID NO:34) and amino acid (SEQ ID NO:35) sequences of an alternative M. thermophila GH61g are provided below. The signal sequence is shown underlined in SEQ ID NO:35. SEQ ID NO:36 provides the sequence of this GH61g without the signal sequence.








(SEQ ID NO: 34)



CTGACGACGGGCGGCGTCAAGCACGCTGTGTACCAGTACATCCGCAAGAACACCAACTATA



 


ACTCGCCCGTGACCGATCTGACGTCCAACGACCTCCGCTGCAATGTGGGTGCTACCGGTGCG


 


GGCACCGATACCGTCACGGTGCGCGCCGGCGATTCGTTCACCTTCACGACCGATACGCCCGT


 


TTACCACCAGGGCCCGACCTCGATCTACATGTCCAAGGCCCCCGGCAGCGCGTCCGACTACG


 


ACGGCAGCGGCGGCTGGTTCAAGATCAAGGACTGGGGTGCCGACTTTAGCAGCGGCCAGGC


 


CACCTGGACCTTGGCGTCTGACTACACCGCCACGATTCCGGAATGTATTCCCCCCGGCGACT


 


ACCTGCTTCGCATCCAGCAACTCGGCATCCACAACCCTTGGCCCGCGGGCATCCCCCAGTTC


 


TACATCTCTTGTGCCCAGATCACCGTGACTGGTGGCGGCAGTGCCAACCCCGGCCCGACCGT


 


CTCCATCCCAGGCGCCTTCAAGGAGACCGACCCGGGCTACACTGTCAACATCTACAACAACT


 


TCCACAACTACACCGTCCCTGGCCCAGCCGTCTTCACCTGCAACGGTAGCGGCGGCAACAAC


 


GGCGGCGGCTCCAACCCAGTCACCACCACCACCACCACCACCACCAGGCCGTCCACCAGCA


 


CCGCCCAGTCCCAGCCGTCGTCGAGCCCGACCAGCCCCTCCAGCTGCACCGTCGCGAAGTGG


 


GGCCAGTGCGGAGGACAGGGTTACAGCGGCTGCACCGTGTGCGCGGCCGGGTCGACCTGCC


 


AGAAGACCAACGACTACTACAGCCAGTGCTTG


 


(SEQ ID NO: 35)



MKGLLGAAALSLAVSDVSAHYTFQQLTTGGVKHAVYQYIRKNTNYNSPVTDLTSNDLRCNVGA



 


TGAGTDTVTVRAGDSFTFTTDTPVYHQGPTSIYMSKAPGSASDYDGSGGWFKIKDWGADFSSGQ


 


ATWTLASDYTATIPECIPPGDYLLRIQQLGIHNPWPAGIPQFYISCAQITVTGGGSANPGPTVSIPG


 


AFKETDPGYTVNIYNNFHNYTVPGPAVFTCNGSGGNNGGGSNPVTTTTTTTTRPSTSTAQSQPSS


 


SPTSPSSCTVAKWGQCGGQGYSGCTVCAAGSTCQKTNDYYSQCL


 


(SEQ ID NO: 36)



HYIFQQLTTGGVKHAVYQYIRKNTNYNSPVTDLTSNDLRCNVGATGAGTDTVTVRAGDSFTFTT



 


DTPVYHQGPTSIYMSKAPGSASDYDGSGGWFKIKDWGADFSSGQATWTLASDYTATIPECIPPG


 


DYLLRIQQLGIHNPWPAGIPQFYISCAQITVTGGGSANPGPTVSIPGAFKETDPGYTVNIYNNFHN


 


YTVPGPAVFTCNGSGGNNGGGSNPVTTTTTTTTRPSTSTAQSQPSSSPTSPSSCTVAKWGQCGGQ


 


GYSGCTVCAAGSTCQKTNDYYSQCL






The polynucleotide (SEQ ID NO:37) and amino acid (SEQ ID NO:38) sequences of an M. thermophila GH61h are provided below. The signal sequence is shown underlined in SEQ ID NO:38. SEQ ID NO:39 provides the sequence of this GH61h without the signal sequence.








(SEQ ID NO: 37)



ATGTCTTCCTTCACCTCCAAGGGTCTCCTTTCCGCCCTCATGGGCGCGGCAACGGTTGCCGCC



 


CACGGTCACGTCACCAACATCGTCATCAACGGCGTCTCATACCAGAACTTCGACCCATTCAC


 


GCACCCTTATATGCAGAACCCTCCGACGGTTGTCGGCTGGACCGCGAGCAACACGGACAAC


 


GGCTTCGTCGGCCCCGAGTCCTTCTCTAGCCCGGACATCATCTGCCACAAGTCCGCCACCAA


 


CGCTGGCGGCCATGCCGTCGTCGCGGCCGGCGATAAGGTCTTCATCCAGTGGGACACCTGGC


 


CCGAGTCGCACCACGGTCCGGTCATCGACTATCTCGCCGACTGCGGCGACGCGGGCTGCGAG


 


AAGGTCGACAAGACCACGCTCAAGTTCTTCAAGATCAGCGAGTCCGGCCTGCTCGACGGCA


 


CTAACGCCCCCGGCAAGTGGGCGTCCGACACGCTGATCGCCAACAACAACTCGTGGCTGGTC


 


CAGATCCCGCCCAACATCGCCCCGGGCAACTACGTCCTGCGCCACGAGATCATCGCCCTGCA


 


CAGCGCCGGCCAGCAGAACGGCGCCCAGAACTACCCTCAGTGCTTCAACCTGCAGGTCACC


 


GGCTCCGGCACTCAGAAGCCCTCCGGCGTCCTCGGCACCGAGCTCTACAAGGCCACCGACGC


 


CGGCATCCTGGCCAACATCTACACCTCGCCCGTCACCTACCAGATCCCCGGCCCGGCCATCA


 


TCTCGGGCGCCTCCGCCGTCCAGCAGACCACCTCGGCCATCACCGCCTCTGCTAGCGCCATC


 


ACCGGCTCCGCTACCGCCGCGCCCACGGCTGCCACCACCACCGCCGCCGCCGCCGCCACCAC


 


TACCACCACCGCTGGCTCCGGTGCTACCGCCACGCCCTCGACCGGCGGCTCTCCTTCTTCCGC


 


CCAGCCTGCTCCTACCACCGCTGCCGCTACCTCCAGCCCTGCTCGCCCGACCCGCTGCGCTG


 


GTCTGAAGAAGCGCCGTCGCCACGCCCGTGACGTCAAGGTTGCCCTC


 


(SEQ ID NO: 38)



MSSFTSKGLLSALMGAATVAAHGHVTNIVINGVSYQNFDPFTHPYMQNPPTVVGWTASNTDNG



 


FVGPESFSSPDIICHKSATNAGGHAVVAAGDKVFIQWDTWPESHHGPVIDYLADCGDAGCEKVD


 


KTTLKFFKISESGLLDGTNAPGKWASDTLIANNNSWVQIPPNIAPGNYVLRHEIIALHSAGQQNG


 


AQNYPQCFNLQVTGSGTQKPSGVLGTELYKATDAGILANIYTSPVTYQIPGPAIISGASAVQQTTS


 


AITASASAITGSATAAPTAATTTAAAAATTTTTAGSGATATPSTGGSPSSAQPAPTTAAATSSPAR


 


PTRCAGLKKRRRHARDVKVAL


 


(SEQ ID NO: 39)



AHGHVTNIVINGVSYQNFDPFTHPYMQNPPTVVGWTASNTDNGFVGPESFSSPDIICHKSATNAG



 


GHAVVAAGDKVFIQWDTWPESHHGPVIDYLADCGDAGCEKVDKTTLKFFKISESGLLDGTNAP


 


GKWASDTLIANNNSWLVQIPPNIAPGNYVLRHEIIALHSAGQQNGAQNYPQCFNLQVTGSGTQK


 


PSGVLGTELYKATDAGILANIYTSPVTYQIPGPAIISGASAVQQTTSAITASASAITGSATAAPTAA


 


TTTAAAAATTTTTAGSGATATPSTGGSPSSAQPAPTTAAATSSPARPTRCAGLKKRRRHARDVK


 


VAL






The polynucleotide (SEQ ID NO:40) and amino acid (SEQ ID NO:41) sequences of an M. thermophila GH61i are provided below. The signal sequence is shown underlined in SEQ ID NO:41. SEQ ID NO:42 provides the sequence of this GH61i without the signal sequence.








(SEQ ID NO: 40)



ATGAAGACGCTCGCCGCCCTCGTGGTCTCGGCCGCCCTCGTGGCCGCGCACGGCTATGTTGA



 


CCACGCCACGATCGGTGGCAAGGATTATCAGTTCTACCAGCCGTACCAGGACCCTTACATGG


 


GCGACAACAAGCCCGATAGGGTTTCCCGCTCCATCCCGGGCAACGGCCCCGTGGAGGACGT


 


CAACTCCATCGACCTCCAGTGCCACGCCGGTGCCGAACCGGCCAAGCTCCACGCCCCCGCCG


 


CCGCCGGCTCGACCGTGACGCTCTACTGGACCCTCTGGCCCGACTCCCACGTCGGCCCCGTC


 


ATCACCTACATGGCTCGCTGCCCCGACACCGGCTGCCAGGACTGGTCCCCGGGAACTAAGCC


 


CGTTTGGTTCAAGATCAAGGAAGGCGGCCGTGAGGGCACCTCCAATACCCCGCTCATGACG


 


GCCCCCTCCGCCTACACCTACACGATCCCGTCCTGCCTCAAGAGCGGCTACTACCTCGTCCG


 


CCACGAGATCATCGCCCTGCACTCGGCCTGGCAGTACCCCGGCGCCCAGTTCTACCCGGGCT


 


GCCACCAGCTCCAGGTCACCGGCGGCGGCTCCACCGTGCCCTCTACCAACCTGGTCTCCTTC


 


CCCGGCGCCTACAAGGGGAGCGACCCCGGCATCACCTACGACGCTTACAAGGCGCAACCTT


 


ACACCATCCCTGGCCCGGCCGTGTTTACCTGCTGA


 


(SEQ ID NO: 41)



MKTLAALVVSAALVAAHGYVDHATIGGKDYQFYQPYQDPYMGDNKEDRVSRSIPGNGPVEDV



 


NSIDLQCHAGAEPAKLHAPAAAGSTVTLYWTLWPDSHVGPVITYMARCPDTGCQDWSPGTKPV


 


WFKIKEGGREGTSNTPLMTAPSAYTYTIPSCLKSGYYLVRHEIIALHSAWQYPGAQFYPGCHQLQ


 


VTGGGSTVPSTNLVSFPGAYKGSDPGITYDAYKAQPYTIPGPAVFTC


 


(SEQ ID NO: 42)



YVDHATIGGKDYQFYQPYQDPYMGDNKPDRVSRSIPGNGPVEDVNSIDLQCHAGAEPAKLHAP



 


AAAGSTVTLYWTLWPDSHVGPVITYMARCPDTGCQDWSPGTKPVWFKIKEGGREGTSNTPLMT


 


APSAYTYTIPSCLKSGYYLVRHEIIALHSAWQYPGAQFYPGCHQLQVTGGGSTVPSTNLVSFPGA


 


YKGSDPGITYDAYKAQPYTIPGPAVFTC






The polynucleotide (SEQ ID NO:43) and amino acid (SEQ ID NO:44) sequences of an alternative M. thermophila GH61i are provided below. The signal sequence is shown underlined in SEQ ID NO:44. SEQ ID NO:45 provides the sequence of this GH61i without the signal sequence.








(SEQ ID NO: 43)



ATGAAGACGCTCGCCGCCCTCGTGGTCTCGGCCGCCCTCGTGGCCGCGCACGGCTATGTTGA



 


CCACGCCACGATCGGTGGCAAGGATTATCAGTTCTACCAGCCGTACCAGGACCCTTACATGG


 


GCGACAACAAGCCCGATAGGGTTTCCCGCTCCATCCCGGGCAACGGCCCCGTGGAGGACGT


 


CAACTCCATCGACCTCCAGTGCCACGCCGGTGCCGAACCGGCCAAGCTCCACGCCCCCGCCG


 


CCGCCGGCTCGACCGTGACGCTCTACTGGACCCTCTGGCCCGACTCCCACGTCGGCCCCGTC


 


ATCACCTACATGGCTCGCTGCCCCGACACCGGCTGCCAGGACTGGTCCCCGGGAACTAAGCC


 


CGTTTGGTTCAAGATCAAGGAAGGCGGCCGTGAGGGCACCTCCAATGTCTGGGCTGCTACCC


 


CGCTCATGACGGCCCCCTCCGCCTACACCTACACGATCCCGTCCTGCCTCAAGAGCGGCTAC


 


TACCTCGTCCGCCACGAGATCATCGCCCTGCACTCGGCCTGGCAGTACCCCGGCGCCCAGTT


 


CTACCCGGGCTGCCACCAGCTCCAGGTCACCGGCGGCGGCTCCACCGTGCCCTCTACCAACC


 


TGGTCTCCTTCCCCGGCGCCTACAAGGGGAGCGACCCCGGCATCACCTACGACGCTTACAAG


 


GCGCAACCTTACACCATCCCTGGCCCGGCCGTGTTTACCTGC


 


(SEQ ID NO: 44)



MKTLAALVVSAALVAAHGYVDHATIGGKDYQFYQPYQDPYMGDNKPDRVSRSIPGNGPVEDV



 


NSIDLQCHAGAEPAKLHAPAAAGSTVTLYWTLWPDSHVGPVITYMARCPDTGCQDWSPGTKPV


 


WFKIKEGGREGTSNVWAATPLMTAPSAYTYTIPSCLKSGYYLVRHEIIALHSAWQYPGAQFYPG


 


CHQLQVTGGGSTVPSTNLVSFPGAYKGSDPGITYDAYKAQPYTIPGPAVFTC


 


(SEQ ID NO: 45)



YVDHATIGGKDYQFYQPYQDPYMGDNKPDRVSRSIPGNGPVEDVNSIDLQCHAGAEPAKLHAP



 


AAAGSTVTLYWTLWPDSHVGPVITYMARCPDTGCQDWSPGTKPVWFKIKEGGREGTSNVWAA


 


TPLMTAPSAYTYTIPSCLKSGYYLVRHEIIALHSAWQYPGAQFYPGCHQLQVTGGGSTVPSTNLV


 


SFPGAYKGSDPGITYDAYKAQPYTIPGPAVFTC






The polynucleotide (SEQ ID NO:46) and amino acid (SEQ ID NO:47) sequences of an M. thermophila GH61j are provided below. The signal sequence is shown underlined in SEQ ID NO:47. SEQ ID NO:48 provides the sequence of this GH61j without the signal sequence.








(SEQ ID NO: 46)



ATGAGATACTTCCTCCAGCTCGCTGCGGCCGCGGCCTTTGCCGTGAACAGCGCGGCGGGTCA



 


CTACATCTTCCAGCAGTTCGCGACGGGCGGGTCCAAGTACCCGCCCTGGAAGTACATCCGGC


 


GCAACACCAACCCGGACTGGCTGCAGAACGGGCCGGTGACGGACCTGTCGTCGACCGACCT


 


GCGCTGCAACGTGGGCGGGCAGGTCAGCAACGGGACCGAGACCATCACCTTGAACGCCGGC


 


GACGAGTTCAGCTTCATCCTCGACACGCCCGTCTACCATGCCGGCCCCACCTCGCTCTACAT


 


GTCCAAGGCGCCCGGAGCTGTGGCCGACTACGACGGCGGCGGGGCCTGGTTCAAGATCTAC


 


GACTGGGGTCCGTCGGGGACGAGCTGGACGTTGAGTGGCACGTACACTCAGAGAATTCCCA


 


AGTGCATCCCTGACGGCGAGTACCTCCTCCGCATCCAGCAGATCGGGCTCCACAACCCCGGC


 


GCCGCGCCACAGTTCTACATCAGCTGCGCTCAAGTCAAGGTCGTCGATGGCGGCAGCACCAA


 


TCCGACCCCGACCGCCCAGATTCCGGGAGCCTTCCACAGCAACGACCCTGGCTTGACTGTCA


 


ATATCTACAACGACCCTCTCACCAACTACGTCGTCCCGGGACCTAGAGTTTCGCACTGG


 


(SEQ ID NO: 47)



MRYFLQLAAAAAFAVNSAAGHYIFQQFATGGSKYPPWKYIRRNTNPDWLQNGPVTDLSSTDLR



 


CNVGGQVSNGTETITLNAGDEFSFILDTPVYHAGPTSLYMSKAPGAVADYDGGGAWFKIYDWG


 


PSGTSWTLSGTYTQRIPKCIPDGEYLLRIQQIGLHNPGAAPQFYISCAQVKVVDGGSTNPTPTAQIP


 


GAFHSNDPGLTVNIYNDPLTNYVVPGPRVSHW


 


(SEQ ID NO: 48)



HYIFQQFATGGSKYPPWKYIRRNTNPDWLQNGPVTDLSSTDLRCNVGGQVSNGTETITLNAGDE



 


FSFILDTPVYHAGPTSLYMSKAPGAVADYDGGGAWFKIYDWGPSGTSWTLSGTYTQRIPKCIPD


 


GEYLLRIQQIGLHNPGAAPQFYISCAQVKVVDGGSTNPTPTAQIPGAFHSNDPGLTVNIYNDPLTN


 


YVVPGPRVSHW






The polynucleotide (SEQ ID NO:49) and amino acid (SEQ ID NO:50) sequences of an M. thermophila GH61k are provided below. The signal sequence is shown underlined in SEQ ID NO:50. SEQ ID NO:51 provides the sequence of this GH61k without the signal sequence.








(SEQ ID NO: 49)



ATGCACCCCTCCCTTCTTTTCACGCTTGGGCTGGCGAGCGTGCTTGTCCCCCTCTCGTCTGCA



 


CACACTACCTTCACGACCCTCTTCGTCAACGATGTCAACCAAGGTGATGGTACCTGCATTCG


 


CATGGCGAAGAAGGGCAATGTCGCCACCCATCCTCTCGCAGGCGGTCTCGACTCCGAAGAC


 


ATGGCCTGTGGTCGGGATGGTCAAGAACCCGTGGCATTTACGTGTCCGGCCCCAGCTGGTGC


 


CAAGTTGACTCTCGAGTTTCGCATGTGGGCCGATGCTTCGCAGTCCGGATCGATCGATCCAT


 


CCCACCTTGGCGTCATGGCCATCTACCTCAAGAAGGTTTCCGACATGAAATCTGACGCGGCC


 


GCTGGCCCGGGCTGGTTCAAGATTTGGGACCAAGGCTACGACTTGGCGGCCAAGAAGTGGG


 


CCACCGAGAAGCTCATCGACAACAACGGCCTCCTGAGCGTCAACCTTCCAACCGGCTTACCA


 


ACCGGCTACTACCTCGCCCGCCAGGAGATCATCACGCTCCAAAACGTTACCAATGACAGGCC


 


AGAGCCCCAGTTCTACGTCGGCTGCGCACAGCTCTACGTCGAGGGCACCTCGGACTCACCCA


 


TCCCCTCGGACAAGACGGTCTCCATTCCCGGCCACATCAGCGACCCGGCCGACCCGGGCCTG


 


ACCTTCAACGTCTACACGGGCGACGCATCCACCTACAAGCCGCCCGGCCCCGAGGTTTACTT


 


CCCCACCACCACCACCACCACCTCCTCCTCCTCCTCCGGAAGCAGCGACAACAAGGGAGCCA


 


GGCGCCAGCAAACCCCCGACGACAAGCAGGCCGACGGCCTCGTTCCAGCCGACTGCCTCGT


 


CAAGAACGCGAACTGGTGCGCCGCTGCCCTGCCGCCGTACACCGACGAGGCCGGCTGCTGG


 


GCCGCCGCCGAGGACTGCAACAAGCAGCTGGACGCGTGCTACACCAGCGCACCCCCCTCGG


 


GCAGCAAGGGGTGCAAGGTCTGGGAGGAGCAGGTGTGCACCGTCGTCTCGCAGAAGTGCGA


 


GGCCGGGGATTTCAAGGGGCCCCCGCAGCTCGGGAAGGAGCTCGGCGAGGGGATCGATGAG


 


CCTATTCCGGGGGGAAAGCTGCCCCCGGCGGTCAACGCGGGAGAGAACGGGAATCATGGCG


 


GAGGTGGTGGTGATGATGGTGATGATGATAATGATGAGGCCGGGGCTGGGGCAGCGTCGAC


 


TCCGACTTTTGCTGCTCCTGGTGCGGCCAAGACTCCCCAACCAAACTCCGAGAGGGCCCGGC


 


GCCGTGAGGCGCATTGGCGGCGACTGGAATCTGCTGAG


 


(SEQ ID NO: 50)



MHPSLLFTLGLASVLVPLSSAHTTFTTLFVNDVNQGDGTCIRMAKKGNVATHPLAGGLDSEDMA



 


CGRDGQEPVAFTCPAPAGAKLTLEFRMWADASQSGSIDPSHLGVMAIYLKKVSDMKSDAAAGP


 


GWFKIWDQGYDLAAKKWATEKLIDNNGLLSVNLPTGLPTGYYLARQEIITLQNVTNDRPEPQFY


 


VGCAQLYVEGTSDSPIPSDKTVSIPGHISDPADPGLTFNVYTGDASTYKPPGPEVYFPTTTTTSSS


 


SSGSSDNKGARRQQTPDDKQADGLVPADCLVKNANWCAAALPPYTDEAGCWAAAEDCNKQL


 


DACYTSAPPSGSKGCKVWEEQVCTVVSQKCEAGDFKGPPQLGKELGEGIDEPIPGGKLPPAVNA


 


GENGNHGGGGGDDGDDDNDEAGAGAASTPTFAAPGAAKTPQPNSERARRREAHWRRLESAE


 


(SEQ ID NO: 51)



HTTFTTLFVNDVNQGDGTCIRMAKKGNVATHPLAGGLDSEDMACGRDGQEPVAFTCPAPAGAK



 


LTLEFRMWADASQSGSIDPSHLGVMAIYLKKVSDMKSDAAAGPGWFKIWDQGYDLAAICKWAT


 


EKLIDNNGLLSVNLPTGLPTGYYLARQEIITLQNVTNDRPEPQFYVGCAQLYVEGTSDSPSDKT


 


VSIPGHISDPADPGLTFNVYTGDASTYKPPGPEVYFPTTTTTTSSSSSGSSDNKGARRQQTPDDKQ


 


ADGLVPADCLVKNANWCAAALPPYTDEAGCWAAAEDCNKQLDACYTSAPPSGSKGCKVWEE


 


QVCTVVSQKCEAGDFKGPPQLGKELGEGIDEPIPGGKLPPAVNAGENGNHGGGGGDDGDDDND


 


EAGAGAASTPTFAAPGAAKTPQPNSERARRREAHWRRLESAE






The polynucleotide (SEQ ID NO:52) and amino acid (SEQ ID NO:53) sequences of a M. thermophila GH61l are provided below. The signal sequence is shown underlined in SEQ ID NO:53. SEQ ID NO:54 provides the sequence of this GH61l without the signal sequence.








(SEQ ID NO: 52)



ATGTTTTCTCTCAAGTTCTTTATCTTGGCCGGTGGGCTTGCTGTCCTCACCGAGGCTCACATA



 


AGACTAGTGTCGCCCGCCCCTTTTACCAACCCTGACCAGGGCCCCAGCCCACTCCTAGAGGC


 


TGGCAGCGACTATCCCTGCCACAACGGCAATGGGGGCGGTTATCAGGGAACGCCAACCCAG


 


ATGGCAAAGGGTTCTAAGCAGCAGCTAGCCTTCCAGGGGTCTGCCGTTCATGGGGGTGGCTC


 


CTGCCAAGTGTCCATCACCTACGACGAAAACCCGACCGCTCAGAGCTCCTTCAAGGTCATTC


 


ACTCGATTCAAGGTGGCTGCCCCGCCAGGGCCGAGACGATCCCGGATTGCAGCGCACAAAA


 


TATCAACGCCTGCAATATAAAGCCCGATAATGCCCAGATGGACACCCCGGATAAGTATGAG


 


TTCACGATCCCGGAGGATCTCCCCAGTGGCAAGGCCACCCTCGCCTGGACATGGATCAACAC


 


TATCGGCAACCGCGAGTTTTATATGGCATGCGCCCCGGTTGAGATCACCGGCGACGGCGGTA


 


GCGAGTCGGCTCTGGCTGCGCTGCCCGACATGGTCATTGCCAACATCCCGTCCATCGGAGGA


 


ACCTGCGCGACCGAGGAGGGGAAGTACTACGAATATCCCAACCCCGGTAAGTCGGTCGAAA


 


CCATCCCGGGCTGGACCGATTTGGTTCCCCTGCAAGGCGAATGCGGTGCTGCCTCCGGTGTC


 


TCGGGCTCCGGCGGAAACGCCAGCAGTGCTACCCCTGCCGCAGGGGCCGCCCCGACTCCTGC


 


TGTCCGCGGCCGCCGTCCCACCTGGAACGCC


 


(SEQ ID NO: 53)



MFSLKFFILAGGLAVLTEAHIRLVSPAPFTNPDQGPSPLLEAGSDYPCHNGNGGGYQGTPTQMAK



 


GSKQQLAFQGSAVHGGGSCQVSITYDENPTAQSSFKVIHSIQGGCPARAETIPDCSAQNINACNIK


 


PDNAQMDTPDKYEFTIPEDLPSGKATLAWTWINTIGNREFYMACAPVEITGDGGSESALAALPD


 


MVIANIPSIGGTCATEEGKYVEYPNEGKSVETIPGWTDLVELQGECGAASGVSGSGGNASSATEA


 


AGAAPTPAVRGRRPTWNA


 


(SEQ ID NO: 54)



HIRLVSPAPFTNPDQGPSPLLEAGSDYPCHNGNGGGYQGTPTQMAKGSKQQLAFQGSAVHGGGS



 


CQVSITYDENPTAQSSEKVIESIQGGCPARAETIPDCSAQNINACNIKPDNAQMDTPDKYEFTIPED


 


LPSGKATLAWTWINTIGNREFYMACAPVEITGDGGSESALAALPDMVIANIESIGGTCATEEGKY


 


YEYPNPGKSVETIPGWTDLVPLQGECGAASGVSGSGGNASSATPAAGAAPTPAVRGRRPTWNA






The polynucleotide (SEQ ID NO:55) and amino acid (SEQ ID NO:56) sequences of a M. thermophila GH61m are provided below. The signal sequence is shown underlined in SEQ ID NO:56. SEQ ID NO:57 provides the sequence of this GH61m without the signal sequence.








(SEQ ID NO: 55)



ATGAAGCTCGCCACGCTCCTCGCCGCCCTCACCCTCGGGGTGGCCGACCAGCTCAGCGTCGG



 


GTCCAGAAAGTTTGGCGTGTACGAGCACATTCGCAAGAACACGAACTACAACTCGCCCGTTA


 


CCGACCTGTCGGACACCAACCTGCGCTGCAACGTCGGCGGGGGCTCGGGCACCAGCACCAC


 


CGTGCTCGACGTCAAGGCCGGAGACTCGTTCACCTTCTICAGCGACGTTGCCGTCTACCACC


 


AGGGGCCCATCTCGCTGTGCGTGGACCGGACCAGTGCAGAGAGCATGGATGGACGGGAACC


 


GGACATGCGCTGCCGAACTGGCTCACAAGCTGGCTACCTGGCGGTGACTGACTACGACGGG


 


TCCGGTGACTGTTTCAAGATCTATGACTGGGGACCGACGTTCAACGGGGGCCAGGCGTCGTG


 


GCCGACGAGGAATTCGTACGAGTACAGCATCCTCAAGTGCATCAGGGACGGCGAATACCTA


 


CTGCGGATTCAGTCCCTGGCCATCCATAACCCAGGTGCCCTTCCGCAGTTCTACATCAGCTGC


 


GCCCAGGTGAATGTGACGGGCGGAGGCACCGTCACCCCGAGATCAAGGCGACCGATCCTGA


 


TCTATTTCAACTTCCACTCGTATATCGTCCCTGGGCCGGCAGTGTTCAAGTGCTAG


 


(SEQ ID NO: 56)



MKLATLLAALTLGVADQLSVGSRKFGVYEHIRKNTNYNSPVTDLSDTNLRCNVGGGSGTSTTVL



 


DVKAGDSFTFFSDVAVYHQGPISLCVDRTSAESMDGREPDMRCRTGSQAGYLAVTDYDGSGDC


 


FKIYDWGPTFNGGQASWPTRNSYEYSILKCIRDGEYLLRIQSLAIHNPGALPQFYISCAQVNVTGG


 


GTVTPRSRRPILIYFNFHSYIVPGPAVFKC


 


(SEQ ID NO: 57)



DQLSVGSRKFGVYEHIRKNTNYNSPVTDLSDTNLRCNVGGGSGTSTTVLDVKAGDSFTFFSDVA



 


VYHQGPISLCVDRTSAESMDGREPDMRCRTGSQAGYLAVTDYDGSGDCFKIYDWGPTFNGGQA


 


SWPTRNSYEYSILKCIRDGEYLLRIQSLAIHNPGALPQFYISCAQVNVTGGGTVTPRSRRPILIYFNF


 


HSYIVPGPAVFKC






The polynucleotide (SEQ ID NO:58) and amino acid (SEQ ID NO:59) sequences of an alternative M. thermophila GH61m are provided below. The signal sequence is shown underlined in SEQ ID NO:59. SEQ ID NO:60 provides the sequence of this GH61m without the signal sequence.








(SEQ ID NO: 58)



ATGAAGCTCGCCACGCTCCTCGCCGCCCTCACCCTCGGGCTCAGCGTCGGGTCCAGAAAGTT



 


TGGCGTGTACGAGCACATTCGCAAGAACACGAACTACAACTCGCCCGTTACCGACCTGTCGG


 


ACACCAACCTGCGCTGCAACGTCGGCGGGGGCTCGGGCACCAGCACCACCGTGCTCGACGT


 


CAAGGCCGGAGACTCGTTCACCTTCTTCAGCGACGTTGCCGTCTACCACCAGGGGCCCATCT


 


CGCTGTGCGTGGACCGGACCAGTGCAGAGAGCATGGATGGACGGGAACCGGACATGCGCTG


 


CCGAACTGGCTCACAAGCTGGCTACCTGGCGGTGACTGTGATGACTGTGACTGACTACGACG


 


GGTCCGGTGACTGTTTCAAGATCTATGACTGGGGACCGACGTTCAACGGGGGCCAGGCGTCG


 


TGGCCGACGAGGAATTCGTACGAGTACAGCATCCTCAAGTGCATCAGGGACGGCGAATACC


 


TACTGCGGATTCAGTCCCTGGCCATCCATAACCCAGGTGCCCTTCCGCAGTTCTACATCAGCT


 


GCGCCCAGGTGAATGTGACGGGCGGAGGCACCATCTATTTCAACTTCCACTCGTATATCGTC


 


CCTGGGCCGGCAGTGTTCAAGTGC


 


(SEQ ID NO: 59)



MKLATLLAALTLGLSVGSRKFGVYEHIRKNTNYINTSPVTDESDTNERCNVGGGSGTSTTVLDVKA



 


GDSFTFFSDVAVYHQGPISLCVDRTSAESMDGREPDMRCRTGSQAGYLAVTVMTVTDYDGSGD


 


CFKIYDWGPTFNGGQASWPTRNSYEYSILKCIRDGEYLLRIQSLAIHNPGALPQFYISCAQVNVTG


 


GGTIYFNFHSYIVPGPAVFKC


 


(SEQ ID NO: 60)



RKFGVYEHIRKNTNYNSPVTDLSDTNLRCNVGGGSGTSTTVLDVKAGDSFTFFSDVAVYHQGPI



 


SLCVDRTSAESMDGREPDMRCRTGSQAGYLAVTVMTVTDYDGSGDCFKIYDWGPTENGGQAS


 


WPTRNSYEYSILKCIRDGEYLLRIQSLAIHNPGALPQFYISCAQVNVTGGGTIYENFHSYIVPGPAV


 


FKC






The polynucleotide (SEQ ID NO:61) and amino acid (SEQ ID NO:62) sequences of a M. thermophila GH61n are provided below.








(SEQ ID NO: 61)



ATGACCAAGAATGCGCAGAGCAAGCAGGGCGTTGAGAACCCAACAAGCGGCGACATCCGCT



 


GCTACACCTCGCAGACGGCGGCCAACGTCGTGACCGTGCCGGCCGGCTCGACCATTCACTAC


 


ATCTCGACCCAGCAGATCAACCACCCCGGCCCGACTCAGTACTACCTGGCCAAGGTACCCCC


 


CGGCTCGTCGGCCAAGACCTTTGACGGGTCCGGCGCCGTCTGGTTCAAGATCTCGACCACGA


 


TGCCTACCGTGGACAGCAACAAGCAGATGTTCTGGCCAGGGCAGAACACTTATGAGACCTC


 


AAACACCACCATTCCCGCCAACACCCCGGACGGCGAGTACCTCCTTCGCGTCAAGCAGATCG


 


CCCTCCACATGGCGTCTCAGCCCAACAAGGTCCAGTTCTACCTCGCCTGCACCCAGATCAAG


 


ATCACCGGTGGTCGCAACGGCACCCCCAGCCCGCTGGTCGCGCTGCCCGGAGCCTACAAGA


 


GCACCGACCCCGGCATCCTGGTCGACATCTACTCCATGAAGCCCGAATCGTACCAGCCTCCC


 


GGGCCGCCCGTCTGGCGCGGCTAA


 


(SEQ ID NO: 62)



MTKNAQSKQGVENPTSGDIRCYTSQTAANVVTVPAGSTIHYISTQQINHPGPTQYYLAKVPPGSS



 


AKTEDGSGAVWFKISTTMPTVDSNKQMFWPGQNTYETSNTTIPANTPDGEYLLRVKQIALHMAS


 


QPNKVQFYLACTQIKITGGRNGTPSPLVALPGAYKSTDPGILVDIYSMKPESYQPPGPPVWRG






The polynucleotide (SEQ ID NO:63) and amino acid (SEQ ID NO:64) sequences of an alternative M. thermophila GH61n are provided below. The signal sequence is shown underlined in SEQ ID NO:64. SEQ ID NO:65 provides the sequence of this GH61n without the signal sequence.








(SEQ ID NO: 63)



ATGAGGCTTCTCGCAAGCTTGTTGCTCGCAGCTACGGCTGTTCAAGCTCACTTTGTTAACGGA



 


CAGCCCGAAGAGAGTGACTGGTCAGCCACGCGCATGACCAAGAATGCGCAGAGCAAGCAG


 


GGCGTTGAGAACCCAACAAGCGGCGACATCCGCTGCTACACCTCGCAGACGGCGGCCAACG


 


TCGTGACCGTGCCGGCCGGCTCGACCATTCACTACATCTCGACCCAGCAGATCAACCACCCC


 


GGCCCGACTCAGTACTACCTGGCCAAGGTACCCCCCGGCTCGTCGGCCAAGACCTTTGACGG


 


GTCCGGCGCCGTCTGGTTCAAGATCTCGACCACGATGCCTACCGTGGACAGCAACAAGCAG


 


ATGTTCTGGCCAGGGCAGAACACTTATGAGACCTCAAACACCACCATTCCCGCCAACACCCC


 


GGACGGCGAGTACCTCCTTCGCGTCAAGCAGATCGCCCTCCACATGGCGTCTCAGCCCAACA


 


AGGTCCAGTTCTACCTCGCCTGCACCCAGATCAAGATCACCGGTGGTCGCAACGGCACCCCC


 


AGCCCGCTGGTCGCGCTGCCCGGAGCCTACAAGAGCACCGACCCCGGCATCCTGGTCGACAT


 


CTACTCCATGAAGCCCGAATCGTACCAGCCTCCCGGGCCGCCCGTCTGGCGCGGC


 


(SEQ ID NO: 64)



MRLLASLLLAATAVQAHFVNGQPEESDWSATRMTKNAQSKQGVENPTSGDIRCYTSQTAANVV



 


TVPAGSTIHYISTQQINHPGPTQYYLAKVPPGSSAKTFDGSGAVWFKISTTMPTVDSNKQMFWPG


 


QNTYETSNTTIPANTPDGEYLLRVKQIALHMASQPNKVQFYLACTQIKITGGRNGTPSPLVALPG


 


AYKSTDPGILVDIYSMKPESYQPPGPPVWRG


 


(SEQ ID NO: 65)



HFVNGQPEESDWSATRMTKNAQSKQGVENPTSGDIRCYTSQTAANVVTVPAGSTIHYISTQQIN



 


HPGPTQYYLAKVPPGSSAKTFDGSGAVWFKISTTMPTVDSNKQMFWPGQNTYETSNTTIPANTP


 


DGEYLLRVKQIALHMASQPNKVQFYLACTQIKITGGRNGTPSPLVALPGAYKSTDPGILVDIYSM


 


KPESYQPPGPPVWRG






The polynucleotide (SEQ ID NO:66) and amino acid (SEQ ID NO:67) sequences of an alternative M. thermophila GH61o are provided below. The signal sequence is shown underlined in SEQ ID NO:67. SEQ ID NO:68 provides the sequence of this GH61o without the signal sequence.








(SEQ ID NO: 66)



ATGAAGCCCTTTAGCCTCGTCGCCCTGGCGACTGCCGTGAGCGGCCATGCCATCTTCCAGCG



 


GGTGTCGGTCAACGGGCAGGACCAGGGCCAGCTCAAGGGGGTGCGGGCGCCGTCGAGCAAC


 


TCCCCGATCCAGAACGTCAACGATGCCAACATGGCCTGCAACGCCAACATTGTGTACCACGA


 


CAACACCATCATCAAGGTGCCCGCGGGAGCCCGCGTCGGCGCGTGGTGGCAGCACGTCATC


 


GGCGGGCCGCAGGGCGCCAACGACCCGGACAACCCGATCGCCGCCTCCCACAAGGGCCCCA


 


TCCAGGTCTACCTGGCCAAGGTGGACAACGCGGCGACGGCGTCGCCGTCGGGCCTCAAGTG


 


GTTCAAGGTGGCCGAGCGCGGCCTGAACAACGGCGTGTGGGCCTACCTGATGCGCGTCGAG


 


CTGCTCGCCCTGCACAGCGCCTCGAGCCCCGGCGGCGCCCAGTTCTACATGGGCTGTGCACA


 


GATCGAAGTCACTGGCTCCGGCACCAACTCGGGCTCCGACTTTGTCTCGTTCCCCGGCGCCT


 


ACTCGGCCAACGACCCGGGCATCTTGCTGAGCATCTACGACAGCTCGGGCAAGCCCAACAA


 


TGGCGGGCGCTCGTACCCGATCCCCGGCCCGCGCCCCATCTCCTGCTCCGGCAGCGGCGGCG


 


GCGGCAACAACGGCGGCGACGGCGGCGACGACAACAACGGTGGTGGCAACAACAACGGCG


 


GCGGCAGCGTCCCCCTGTACGGGCAGTGCGGCGGCATCGGCTACACGGGCCCGACCACCTG


 


TGCCCAGGGAACTTGCAAGGTGTCGAACGAATACTACAGCCAGTGCCTCCCC


 


(SEQ ID NO: 67)



MKPFSLVALATAVSGHAIFQRVSVNGQDQGQLKGVRAPSSNSPIQNVNDANMACNANIVYHDN



 


TIIKVPAGARVGAWWQHVIGGPQGANDPDNPIAASHKGPIQVYLAKVDNAATASPSGLKWEKV


 


AERGLNNGVWAYLMRVELLALHSASSPGGAQFYMGCAQIEVTGSGTNSGSDFVSFPGAYSAND


 


PGILLSIYDSSGKPNNGGRSYPIPGPRPISCSGSGGGGNNGGDGGDDNNGGGNNNGGGSVPLYGQ


 


CGGIGYTGPTTCAQGTCKVSNEYYSQCLP


 


(SEQ ID NO: 68)



HAIFQRVSVNGQDQGQLKGVRAPSSNSPIQNVNDANMACNANIVYHDNTIIKVPAGARVGAWW



 


QHVIGGPQGANDPDNPIAASHKGPIQVYLAKVDNAATASPSGLKWFKVAERGLNNGVWAYLM


 


RVELLALHSASSPGGAQFYMGCAQIEVTGSGTNSGSDFVSFPGAYSANDPGILLSIYDSSGKPNN


 


GGRSYPIPGPRPISCSGSGGGGNNGGDGGDDNNGGGNNNGGGSVPLYGQCGGIGYTGPTTCAQG


 


TCKVSNEYYSQCLP






The polynucleotide (SEQ ID NO:69) and amino acid (SEQ ID NO:70) sequences of a M. thermophila GH61p are provided below. The signal sequence is shown underlined in SEQ ID NO:70, SEQ ID NO:71 provides the sequence of this GH61p without the signal sequence.








(SEQ ID NO: 69)



ATGAAGCTCACCTCGTCCCTCGCTGTCCTGGCCGCTGCCGGCGCCCAGGCTCACTATACCTTC



 


CCTAGGGCCGGCACTGGTGGITCGCTCTCTGGCGAGTGGGAGGTGGTCCGCATGACCGAGA


 


ACCATTACTCGCACGGCCCGGTCACCGATGTCACCAGCCCCGAGATGACCTGCTATCAGTCC


 


GGCGTGCAGGGTGCGCCCCAGACCGTCCAGGTCAAGGCGGGCTCCCAATTCACCTTCAGCGT


 


GGATCCCTCCATCGGCCACCCCGGCCCTCTCCAGTTCTACATGGCTAAGGTGCCGTCGGGCC


 


AGACGGCCGCCACCTTTGACGGCACGGGAGCCGTGTGGTTCAAGATCTACCAAGACGGCCC


 


GAACGGCCTCGGCACCGACAGCATTACCTGGCCCAGCGCCGGCAAAACCGAGGTCTCGGTC


 


ACCATCCCCAGCTGCATCGAGGATGGCGAGTACCTGCTCCGGGTCGAGCACACCCCCCTCCC


 


TACAGCGCCAGCAGCGCAAAACCGAGCTCGCTCGTCACCATCCCCAGCTGCATACAAGGCC


 


ACCGACCCGGGCATCCTCTTCCAGCTCTACTGGCCCATCCCGACCGAGTACATCAACCCCGG


 


CCCGGCCCCCGTCTCTTGCTAA


 


(SEQ ID NO: 70)



MKLTSSLAVLAAAGAQAHYTFPRAGTGGSLSGEWEVVRMTENHYSHGPVTDVTSPEMTCYQS



 


GVQGAPQTVQVKAGSQFTFSVDPSIGHPGPLQFYMAKVPSGQTAATFDGTGAVWFKIYQDGPN


 


GLGTDSITWPSAGKTEVSVTIPSCIEDGEYLLRVEHTPLPTAPAAQNRARSSPSPAAYKATDPGILF


 


QLYWPIPTEYINPGPAPVSC


 


(SEQ ID NO: 71)



HYTFPRAGTGGSLSGEWEVVRMTENHYSHGPVTDVTSPEMTCYQSGVQGAPQTVQVKAGSQFT



 


FSVDPSIGHPGPLQFYMAKVPSGQTAATFDGTGAVWFKIYQDGPNGLGTDSITWPSAGKTEVSV


 


TIPSCIEDGEYLLRVEHTPLPTAPAAQNRARSSPSPAAYKATDPGILFQLYWPIPTEYINPGPAPVS


 


C






The polynucleotide (SEQ ID NO:72) and amino acid (SEQ ID NO:73) sequences of an alternative M. thermophila GH61p are provided below. The signal sequence is shown underlined in SEQ ID NO:73. SEQ ID NO:74 provides the sequence of this GH61p without the signal sequence.








(SEQ ID NO: 72)



ATGAAGCTCACCTCGTCCCTCGCTGTCCTGGCCGCTGCCGGCGCCCAGGCTCACTATACCTTC



 


CCTAGGGCCGGCACTGGTGGTTCGCTCTCTGGCGAGTGGGAGGTGGTCCGCATGACCGAGAC


 


CATTACTCGCACGGCCCGGTCACCGATGTCACCAGCCCCGAGATGACCTGCTATCAGTCCGG


 


CGTGCAGGGTGCGCCCCAGACCGTCCAGGTCAAGGCGGGCTCCCAATTCACCTTCAGCGTGG


 


ATCCCTCCATCGGCCACCCCGGCCCTCTCCAGTTCTACATGGCTAAGGTGCCGTCGGGCCAG


 


ACGGCCGCCACCTTTGACGGCACGGGAGCCGTGTGGTTCAAGATCTACCAAGACGGCCCGA


 


ACGGCCTCGGCACCGACAGCATTACCTGGCCCAGCGCCGGCAAAACCGAGGTCTCGGTCAC


 


CATCCCCAGCTGCATCGAGGATGGCGAGTACCTGCTCCGGGTCGAGCACATCGCGCTCCACA


 


GCGCCAGCAGCGTGGGCGGCGCCCAGTTCTACATCGCCTGCGCCCAGCTCTCCGTCACCGGC


 


GGCTCCGGCACCCTCAACACGGGCTCGCTCGTCTCCCTGCCCGGCGCCTACAAGGCCACCGA


 


CCCGGGCATCCTCTTCCAGCTCTACTGGCCCATCCCGACCGAGTACATCAACCCCGGCCCGG


 


CCCCCGTCTCTTGC


 


(SEQ ID NO: 73)



MKLTSSLAVLAAAGAQAHYTFPRAGTGGSLSGEWEVVRMTENHYSHGPVTDVTSPEMTCYQS



 


GVQGAPQTVQVKAGSQFTFSVDPSIGHPGPLQFYMAKVPSGQTAATFDGTGAVWFKIYQDGPN


 


GLGTDSITWPSAGKTEVSVTIPSCIEDGEYLLRVEHIALHSASSVGGAQFYIACAQLSVTGGSGTL


 


NTGSLVSLPGAYKATDPGILFQLYWPIPTEYINPGPAPVSC


 


(SEQ ID NO: 74)



HYTFPRAGTGGSLSGEWEVVRMTENHYSHGPVTDVTSPEMTCYQSGVQGAPQTVQVKAGSQFT



 


FSVDPSIGHPGPLQFYMAKVPSGQTAATFDGTGAVWFKIYQDGPNGLGTDSITWPSAGKTEVSV


 


TIPSCIEDGEYLLRVEHIALHSASSVGGAQFYIACAQLSVTGGSGTLNTGSLVSLPGAYKATDPGIL


 


FQLYWPIPTEYINPGPAPVSC






The polynucleotide (SEQ ID NO:75) and amino acid (SEQ ID NO:76) sequences of an alternative M. thermophila GH61q are provided below. The signal sequence is shown underlined in SEQ ID NO:76. SEQ ID NO:77 provides the sequence of this GH61q without the signal sequence.








(SEQ ID NO: 75)



ATGCCGCCACCACGACTGAGCACCCTCCTTCCCCTCCTAGCCTTAATAGCCCCCACCGCCCTG



 


GGGCACTCCCACCTCGGGTACATCATCATCAACGGCGAGGTATACCAAGGATTCGACCCGCG


 


GCCGGAGCAGGCGAACTCGCCGTTGCGCGTGGGCTGGTCGACGGGGGCAATCGACGACGGG


 


TTCGTGGCGCCGGCCAACTACTCGTCGCCCGACATCATCTGCCACATCGAGGGGGCCAGCCC


 


GCCGGCGCACGCGCCCGTCCGGGCGGGCGACCGGGTGCACGTGCAATGGAACGGCTGGCCG


 


CTCGGACACGTGGGGCCGGTGCTGTCGTACCTGGCGCCCTGCGGCGGGCTGGAGGGGTCCG


 


AGAGCGGGTGCGCCGGGGTGGACAAGCGGCAGCTGCGGTGGACCAAGGTGGACGACTCGCT


 


GCCGGCGATGGAGCTG


 


(SEQ ID NO: 76)



MPPPRLSTLLPLLALIAPTALGHSHLGYIIINGEVYQGFDPRPEQANSPLRVGWSTGAIDDGFVAP



 


ANYSSPDIICHIEGASPPAHAPVRAGDRVHVQWNGWPLGHVGPVLSYLAPCGGLEGSESGCAGV


 


DKRQLRWTKVDDSLPAMEL


 


(SEQ ID NO: 77)



HSHLGYIIINGEVYQGFDPRPEQANSPLRVGWSTGAIDDGFVAPANYSSPDIICHIEGASPPAHAPV



 


RAGDRVHVQWNGWPLGHVGPVLSYLAPCGGLEGSESGCAGVDKRQLRWTKVDDSLPAMEL






The polynucleotide (SEQ ID NO:78) and amino acid (SEQ ID NO:79) sequences of an alternative M. thermophila GH61q are provided below. The signal sequence is shown underlined in SEQ ID NO:79. SEQ ID NO:80 provides the sequence of this GH61q without the signal sequence.








(SEQ ID NO: 78)



ATGCCGCCACCACGACTGAGCACCCTCCTTCCCCTCCTAGCCTTAATAGCCCCCACCGCCCTG



 


GGGCACTCCCACCTCGGGTACATCATCATCAACGGCGAGGTATACCAAGGATTCGACCCGCG


 


GCCGGAGCAGGCGAACTCGCCGTTGCGCGTGGGCTGGTCGACGGGGGCAATCGACGACGGG


 


TTCGTGGCGCCGGCCAACTACTCGTCGCCCGACATCATCTGCCACATCGAGGGGGCCAGCCC


 


GCCGGCGCACGCGCCCGTCCGGGCGGGCGACCGGGTGCACGTGCAATGGAAACGGCTGGCC


 


GCTCGGACACGTGGGGCCGGTGCTGTCGTACCTGGCGCCCTGCGGCGGGCTGGAGGGGTCC


 


GAGAGCGGGTGGACGACTCGCTGCCGGCGATGGAGCTGGTCGGGGCCGCGGGGGGCGCGG


 


GGGGCGAGGACGACGGCAGCGGCAGCGACGGCAGCGGCAGCGGCGGCAGCGGACGCGTCG


 


GCGTGCCCGGGCAGCGCTGGGCCACCGACGTGTTGATCGCGGCCAACAACAGCTGGCAGGT


 


CGAGATCCCGCGCGGGCTGCGGGACGGGCCGTACGTGCTGCGCCACGAGATCGTCGCGCTG


 


CACTACGCGGCCGAGCCCGGCGGCGCGCAGAACTACCCGCTCTGCGTCAACCTGTGGGTCG


 


AGGGCGGCGACGGCAGCATGGAGCTGGACCACTTCGACGCCACCCAGTTCTACCGGCCCGA


 


CGACCCGGGCATCCTGCTCAACGTGACGGCCGGCCTGCGCTCATACGCCGTGCCGGGCCCGA


 


CGCTGGCCGCGGGGGCGACGCCGGTGCCGTACGCGCAGCAGAACATCAGCTCGGCGAGGGC


 


GGATGGAACCCCCGTGATTGTCACCAGGAGCACGGAGACGGTGCCCTTCACCGCGGCACCC


 


ACGCCAGCCGAGACGGCAGAAGCCAAAGGGGGGAGGTATGATGACCAAACCCGAACTAAA


 


GACCTAAATGAACGCTTCTTTTATAGTAGCCGGCCAGAACAGAAGAGGCTGACAGCGACCT


 


CAAGAAGGGAACTAGTTGATCATCGTACCCGGTACCTCTCCGTAGCTGTCTGCGCAGATTTC


 


GGCGCTCATAAGGCAGCAGAAACCAACCACGAAGCTTTGAGAGGCGGCAATAAGCACCATG


 


GCGGTGTTTCAGAG


 


(SEQ ID NO: 79)



MPPPRLSTLLPLLALIAPTALGHSHLGYIIINGEVYQGFDPRPEQANSPLRVGWSTGAIDDGEVAP



 


ANYSSPDHCHIEGASPPAHAPVRAGDRVHVQWKRLAARTRGAGAVVPGALRRAGGVRERVDD


 


SLPAMELVGAAGGAGGEDDGSGSDGSGSGGSGRVGVPGQRWATDVLIAANNSWQVEIPRGLR


 


DGPYVLRHEIVALHYAAEPGGAQNYPLCVNLWVEGGDGSMELDHFDATQFYRPDDPGILLNVT


 


AGLRSYAVPGPTLAAGATPVPYAQQNISSARADGTPVIVTRSTETVPFTAAPTPAETAEAKGGRY


 


DDQTRTKDLNERFFYSSRPEQKRLTATSRRELVDHRTRYLSVAVCADFGAHKAAETNHEALRG


 


GNKHHGGVSE


 


(SEQ ID NO: 80)



HSHLGYIIINGEVYQGFDPRPEQANSPLRVGWSTGAIDDGFVAPANYSSPDIECHIEGASPPAFIAPV



 


RAGDRVHVQWKRLAARTRGAGAVVPGALRRAGGVRERVDDSLPAMELVGAAGGAGGEDDGS


 


GSDGSGSGGSGRVGVPGQRWATDVLIAANNSWQVEIPRGLRDGPYVLRITEIVALHYAAEPGGA


 


QNYPLCVNLWVEGGDGSMELDHFDATQFYRPDDPGILLNVTAGLRSYAVPGPTLAAGATPVPY


 


AQQNISSARADGTPVIVTRSTETVPFTAAPTPAETAEAKGGRYDDQTRTKDLNERFFYSSRPEQK


 


RLTATSRRELVDHRTRYLSVAVCADFGAHKAAETNHEALRGGNKHHGGVSE






The polynucleotide (SEQ ID NO:81) and amino acid (SEQ ID NO:82) sequences of an M. thermophila GH61r are provided below. The signal sequence is shown underlined in SEQ ID NO:82. SEQ ID NO:83 provides the sequence of this GH61r without the signal sequence.








(SEQ ID NO: 81)



ATGAGGTCGACATTGGCCGGTGCCCTGGCAGCCATCGCTGCTCAGAAAGTAGCCGGCCACG



 


CCACGTTTCAGCAGCTCTGGCACGGCTCCTCCTGTGTCCGCCTTCCGGCTAGCAACTCACCCG


 


TCACCAATGTGGGAAGCAGAGACTTCGTCTGCAACGCTGGCACCCGCCCCGTCAGTGGCAA


 


GTGCCCCGTGAAGGCTGGCGGCACCGTCACCATCGAGATGCACCAGCAACCCGGCGACCGC


 


AGCTGCAACAACGAAGCCATCGGAGGGGCGCATTGGGGCCCCGTCCAGGTGTACCTGACCA


 


AGGTTCAGGACGCCGCGACGGCCGACGGCTCGACGGGCTGGTTCAAGATCTTCTCCGACTCG


 


TGGTCCAAGAAGCCCGGGGGCAACTTGGGCGACGACGACAACTGGGGCACGCGCGACCTGA


 


ACGCCTGCTGCGGGAAGATGGAC


 


(SEQ ID NO: 82)



MRSTLAGALAAIAAQKVAGHATFQQLWHGSSCVRLPASNSPVTNVGSRDFVCNAGTRPVSGKC



 


PVKAGGTVTIEMHQQPGDRSCNNEAIGGAHWGPVQVYLTKVQDAATADGSTGWFKIFSDSWSK


 


KPGGNLGDDDNWGTRDLNACCGKMD


 


(SEQ ID NO: 83)



HATFQQLWHGSSCVRLPASNSPVTNVGSRDFVCNAGTRPVSGKCPVKAGGTVTIEMIIQQPGDR



 


SCNNEAIGGAHWGPVQVYLTKVQDAATADGSTGWFKIFSDSWSKKPGGNLGDDDNWGTRDLN


 


ACCGKMD






The polynucleotide (SEQ ID NO:84) and amino acid (SEQ ID NO:85) sequences of an alternative M. thermophila GH61r are provided below. The signal sequence is shown underlined in SEQ ID NO:85. SEQ ID NO:86 provides the sequence of this GH61r without the signal sequence.








(SEQ ID NO: 84)



ATGAGGTCGACATTGGCCGGTGCCCTGGCAGCCATCGCTGCTCAGAAAGTAGCCGGCCACG



 


CCACGTTTCAGCAGCTCTGGCACGGCTCCTCCTGTGTCCGCCTTCCGGCTAGCAACTCACCCG


 


TCACCAATGTGGGAAGCAGAGACTTCGTCTGCAACGCTGGCACCCGCCCCGTCAGTGGCAA


 


GTGCCCCGTGAAGGCTGGCGGCACCGTCACCATCGAGATGCACCAGCAACCCGGCGACCGC


 


AGCTGCAACAACGAAGCCATCGGAGGGGCGCATTGGGGCCCCGTCCAGGTGTACCTGACCA


 


AGGTTCAGGACGCCGCGACGGCCGACGGCTCGACGGGCTGGTTCAAGATCTTCTCCGACTCG


 


TGGTCCAAGAAGCCCGGGGGCAACTCGGGCGACGACGACAACTGGGGCACGCGCGACCTGA


 


ACGCCTGCTGCGGGAAGATGGACGTGGCCATCCCGGCCGACATCGCGTCGGGCGACTACCT


 


GCTGCGGGCCGAGGCGCTGGCCCTGCACACGGCCGGACAGGCCGGCGGCGCCCAGTTCTAC


 


ATGAGCTGCTACCAGATGACGGTCGAGGGCGGCTCCGGGACCGCCAACCCGCCCACCGTCA


 


AGTTCCCGGGCGCCTACAGCGCCAACGACCCGGGCATCCTCGTCAACATCCACGCCCCCCTT


 


TCCAGCTACACCGCGCCCGGCCCGGCCGTCTACGCGGGCGGCACCATCCGCGAGGCCGGCTC


 


CGCCTGCACCGGCTGCGCGCAGACCTGCAAGGTCGGGTCGTCCCCGAGCGCCGTTGCCCCCG


 


GCAGCGGCGCGGGCAACGGCGGCGGGTTCCAACCCCGA


 


(SEQ ID NO: 85)



MRSTLAGALAAIAAQKVAGHATFQQLWHGSSCVRLPASNSPVTNVGSRDFVCNAGTRPVSGKC



 


PVKAGGTVTIEMHQQPGDRSCNNEAIGGAHWGPVQVYLTKVQDAATADGSTGWFKIFSDSWSK


 


KPGGNSGDDDNWGTRDLNACCGKMDVAIPADIASGDYLLRAEALALHTAGQAGGAQFYMSCY


 


QMTVEGGSGTANPPTVKFPGAYSANDPGILVNIHAPLSSYTAPGPAVYAGGTIREAGSACTGCAQ


 


TCKVGSSPSAVAPGSGAGNGGGFQPR


 


(SEQ ID NO: 86)



HATFQQLWHGSSCVRLPASNSPVTNVGSRDFVCNAGTRPVSGKCPVKAGGTVTIEMHQQPGDR



 


SCNNEAIGGAHWGPVQVYLTKVQDAATADOSTGWFKIFSDSWSKKPGGNSGDDDNWGTRDLN


 


ACCGKMDVAIPADIASGDYELRAEALALHTAGQAGGAQFYMSCYQMTVEGGSGTANPPTVKFP


 


GAYSANDPGILVNIHAPLSSYTAPGPAVYAGGTIREAGSACTGCAQTCKVGSSPSAVAPGSGAGN


 


GGGFQPR






The polynucleotide (SEQ ID NO:87) and amino acid (SEQ ID NO:88) sequences of an M. thermophila GH61s are provided below. The signal sequence is shown underlined in SEQ ID NO:88. SEQ ID NO:89 provides the sequence of this GH61s without the signal sequence.








(SEQ ID NO: 87)



ATGCTCCTCCTCACCCTAGCCACACTCGTCACCCTCCTGGCGCGCCACGTCTCGGCTCACGCC



 


CGGCTGTTCCGCGTCTCTGTCGACGGGAAAGACCAGGGCGACGGGCTGAACAAGTACATCC


 


GCTCGCCGGCGACCAACGACCCCGTGCGCGACCTCTCGAGCGCCGCCATCGTGTGCAACACC


 


CAGGGGTCCAAGGCCGCCCCGGACTTCGTCAGGGCCGCGGCCGGCGACAAGCTGACCTTCC


 


TCTGGGCGCACGACAACCCGGACGACCCGGTCGACTACGTCCTCGACCCGTCCCACAAGGG


 


CGCCATCCTGACCTACGTCGCCGCCTACCCCTCCGGGGACCCGACCGGCCCCATCTGGAGCA


 


AGCTTGCCGAGGAAGGATTCACCGGCGGGCAGTGGGCGACCATCAAGATGATCGACAACGG


 


CGGCAAGGTCGACGTGACGCTGCCCGAGGCCCTTGCGCCGGGAAAGTACCTGATCCGCCAG


 


GAGCTGCTGGCCCTGCACCGGGCCGACTTTGCCTGCGACGACCCGGCCCACCCCAACCGCGG


 


CGCCGAGTCGTACCCCAACTGCGTCCAGGTGGAGGTGTCGGGCAGCGGCGACAAGAAGCCG


 


GACCAGAACTTTGACTTCAACAAGGGCTATACCTGCGATAACAAAGGACTCCACTTTAAGAT


 


CTACATCGGTCAGGACAGCCAGTATGTGGCCCCGGGGCCGCGGCCTTGGAATGGGAGC


 


(SEQ ID NO: 88)



MLLLTLATLVTLLARHVSAHARLFRVSVDGKDQGDGLNKYIRSPATNDPVRDLSSAAIVCNTQG



 


SKAAPDEVRAAAGDKLTFLWAHDNPDDPVDYVLDPSHKGAILTYVAAYPSGDPTGPIWSKLAE


 


EGFTGGQWATIKMLDNGGKVDVTLPEALAPGKYLIRQELLALHRADFACDDPAHPNRGAESYPN


 


CVQVEVSGSGDKKPDQNFDFNKGYTCDNKGLRFKIYIGQDSQYVAPGPRPWNGS


 


(SEQ ID NO: 89)



HARLFRVSVDGKDQGDGLNKYIRSPATNDPVRDLSSAAIVCNTQGSKAAPDFVRAAAGDKLTFL



 


WAHDNPDDPVDYVLDPSHKGAILTYVAAYPSGDPTGPIWSKLAEEGFTGGQWATIKMIDNGGK


 


VDVTLPEALAPGKYLIRQELLALHRADFACDDPAHPNRGAESYPNCVQVEVSGSGDICKPDQNFD


 


FNKGYTCDNKGLHFKIYIGQDSQYVAPGPRPWNGS






The polynucleotide (SEQ ID NO:90) and amino acid (SEQ ID NO:91) sequences of an M. thermophila GH61t are provided below.








(SEQ ID NO: 90)



ATGTTCACTTCGCTTTGCATCACAGATCATTGGAGGACTCTTAGCAGCCACTCTGGGCCAGTC



 


ATGAACTATCTCGCCCATTGCACCAATGACGACTGCAAGTCTTTCAAGGGCGACAGCGGCAA


 


CGTCTGGGTCAAGATCGAGCAGCTCGCGTACAACCCGTCAGCCAACCCCCCCTGGGCGTCTG


 


ACCTCCTCCGTGAGCACGGTGCCAAGTGGAAGGTGACGATCCCGCCCAGTCTTGTCCCCGGC


 


GAATATCTGCTGCGGCACGAGATCCTGGGGTTGCACGTCGCAGGAACCGTGATGGGCGCCC


 


AGTTCTACCCCGGCTGCACCCAGATCAGGGTCACCGAAGGCGGGAGCACGCAGCTGCCCTC


 


GGGTATTGCGCTCCCAGGCGCTTACGGCCCACAAGACGAGGGTATCTTGGTCGACTTGTGGA


 


GGGTTAACCAGGGCCAGGTCAACTACACGGCGCCTGGAGGACCCGTTTGGAGCGAAGCGTG


 


GGACACCGAGTTTGGCGGGTCCAACACGACCGAGTGCGCCACCATGCTCGACGACCTGCTC


 


GACTACATGGCGGCCAACGACGAGTGGATCGGCTGGACGGCCTAG


 


(SEQ ID NO: 91)



MFTSLCITDHWRTLSSHSGPVMNYLAHCTNDDCKSFKGDSGNVWVKIEQLAYNPSANPPWASD



 


LLREHGAKWKVTIPPSLVPGEYLLRHEILGLHVAGTVMGAQFYPGCTQIRVTEGGSTQLPSGIAL


 


PGAYGPQDEGILVDLWRVNQGQVNYTAPGGPVWSEAWDTEFGGSNTTECATMLDDLLDYMA


 


ANDEWIGWTA






The polynucleotide (SEQ ID NO:92) and amino acid (SEQ ID NO:93) sequences of an alternative M. thermophila GH61t are provided below.








(SEQ ID NO: 92)



ATGAACTATCTCGCCCATTGCACCAATGACGACTGCAAGTCTTTCAAGGGCGACAGCGGCAA



 


CGTCTGGGTCAAGATCGAGCAGCTCGCGTACAACCCGTCAGCCAACCCCCCCTGGGCGTCTG


 


ACCTCCTCCGTGAGCACGGTGCCAAGTGGAAGGTGACGATCCCGCCCAGTCTTGTCCCCGGC


 


GAATATCTGCTGCGGCACGAGATCCTGGGGTTGCACGTCGCAGGAACCGTGATGGGCGCCC


 


AGTTCTACCCCGGCTGCACCCAGATCAGGGTCACCGAAGGCGGGAGCACGCAGCTGCCCTC


 


GGGTATTGCGCTCCCAGGCGCTTACGGCCCACAAGACGAGGGTATCTTGGTCGACTTGTGGA


 


GGGTTAACCAGGGCCAGGTCAACTACACGGCGCCTGGAGGACCCGTTTGGAGCGAAGCGTG


 


GGACACCGAGTTTGGCGGGTCCAACACGACCGAGTGCGCCACCATGCTCGACGACCTGCTC


 


GACTACATGGCGGCCAACGACGACCCATGCTGCACCGACCAGAACCAGTTCGGGAGTCTCG


 


AGCCGGGGAGCAAGGCGGCCGGCGGCTCGCCGAGCCTGTACGATACCGTCTTGGTCCCCGTT


 


CTCCAGAAGAAAGTGCCGACAAAGCTGCAGTGGAGCGGACCGGCGAGCGTCAACGGGGAT


 


GAGTTGACAGAGAGGCCC


 


(SEQ ID NO: 93)



MNYLAHCTNDDCKSFKGDSGNVWVKIEQLAYNPSANPPWASDLLREHGAKWKVTIPPSLVPGE



 


YLLRBEELGLHVAGTVMGAQFYPGCTQIRVTEGGSTQLPSGIALPGAYGPQDEGILVDLWRVNQ


 


GQVNYTAPGGPVWSEAWDTEFGGSNTTECATMLDDLLDYMAANDDPCCTDQNQFGSLEPGSK


 


AAGGSPSLYDTVLVPVLQKKVPTKLQWSGPASVNGDELTERP






The polynucleotide (SEQ ID NO:94) and amino acid (SEQ ID NO:95) sequences of an M. thermophila GH61u are provided below. The signal sequence is shown underlined in SEQ ID NO:95. SEQ ID NO:96 provides the sequence of this GH61u without the signal sequence.








(SEQ ID NO: 94)



ATGAAGCTGAGCGCTGCCATCGCCGTGCTCGCGGCCGCCCTTGCCGAGGGGCACTATACCTT



 


CCCCAGCATCGCCAACACGGCCGACTGGCAATATGTGCGCATCACGACCAACTTCCAGAGC


 


AACGGCCCCGTGACGGACGTCAACTCGGACCAGATCCGGTGCTACGAGCGCAACCCGGGCA


 


CCGGCGCCCCCGGCATCTACAACGTCACGGCCGGCACAACCATCAACTACAACGCCAAGTC


 


GTCCATCTCCCACCCGGGACCCATGGCCTTCTACATTGCCAAGGTTCCCGCCGGCCAGTCGG


 


CCGCCACCTGGGACGGTAAGGGCGCCGTCTGGTCCAAGATCCACCAGGAGATGCCGCACTIT


 


GGCACCAGCCTCACCTGGGACTCCAACGGCCGCACCTCCATGCCCGTCACCATCCCCCGCTG


 


TCTGCAGGACGGCGAGTATCTGCTGCGTGCAGAGCACATTGCCCTCCACAGCGCCGGCAGCC


 


CCGGCGGCGCCCAGTTCTACATTTCTTGTGCCCAGCTCTCAGTCACCGGCGGCAGCGGGACC


 


TGGAACCCCAGGAACAAGGTGTCGTTCCCCGGCGCCTACAAGGCCACTGACCCGGGCATCCT


 


GATCAACATCTACTACCCCGTCCCGACTAGCTACACTCCCGCTGGTCCCCCCGTCGACACCT


 


GC


 


(SEQ ID NO: 95)



MKLSAAIAVLAAALAEGHYTFPSIANTADWQYVRITTNFQSNGPVTDVNSDQIRCYERNPGTGA



 


PGTYNVTAGTTINYNAKSSISHPGPMAFYIAKVPAGQSAATWDGKGAVWSKIHQEMPHFGTSLT


 


WDSNGRTSMPVTIPRCLQDGEYLLRAEHIALHSAGSPGGAQFYISCAQLSVTGGSGTWNPRNKV


 


SFPGAYKATDPGILINIYYPVPTSYTPAGPPVDTC


 


(SEQ ID NO: 96)



HYTEPSIANTADWQYVRITTNFQSNGPVTDVNSDQIRCYERNPGTGAPGIYNVTAGTTINYNAKS



 


SISHPGPMAFYIAKVPAGQSAATWDGKGAVWSKIHQEMPHFGTSLTWDSNGRTSMPVTIPRCLQ


 


DGEYLLRAEHIALHSAGSPGGAQFYISCAQLSVTGGSGTWNPRNKVSFPGAYKATDPGILINIYYP


 


VPTSYTPAGPPVDTC






The polynucleotide (SEQ ID NO:97) and amino acid (SEQ ID NO:98) sequences of an M. thermophila GH61v are provided below. The signal sequence is shown underlined in SEQ ID NO:98. SEQ ID NO:99 provides the sequence of this GH61v without the signal sequence.








(SEQ ID NO: 97)



ATGTACCGCACGCTCGGTTCCATTGCCCTGCTCGCGGGGGGCGCTGCCGCCCACGGCGCCGT



 


GACCAGCTACAACATTGCGGGCAAGGACTACCCTGGATACTCGGGCTTCGCCCCTACCGGCC


 


AGGATGTCATCCAGTGGCAATGGCCCGACTATAACCCCGTGCTGTCCGCCAGCGACCCCAAG


 


CTCCGCTGCAACGGCGGCACCGGGGCGGCGCTGTATGCCGAGGCGGCCCCCGGCGACACCA


 


TCACGGCCACCTGGGCCCAGTGGACGCACTCCCAGGGCCCGATCCTGGTGTGGATGTACAAG


 


TGCCCCGGCGACTTCAGCTCCTGCGACGGCTCCGGCGCGGGTTGGTTCAAGATCGACGAGGC


 


CGGCTTCCACGGCGACGGCACGACCGTCTTCCTCGACACCGAGACCCCCTCGGGCTGGGACA


 


TTGCCAAGCTGGTCGGCGGCAACAAGTCGTGGAGCAGCAAGATCCCTGACGGCCTCGCCCC


 


GGGCAATTACCTGGTCCGCCACGAGCTCATCGCCCTGCACCAGGCCAACAACCCGCAATTCT


 


ACCCCGAGTGCGCCCAGATCAAGGTCACCGGCTCTGGCACCGCCGAGCCCGCCGCCTCCTAC


 


AAGGCCGCCATCCCCGGCTACTGCCAGCAGAGCGACCCCAACATTTCGTTCAACATCAACGA


 


CCACTCCCTCCCGCAGGAGTACAAGATCCCCGGTCCCCCGGTCTTCAAGGGCACCGCCTCCG


 


CCAAGGCTCGCGCTTTCCAGGCC


 


(SEQ ID NO: 98)



MYRTLGSIALLAGGAAAHGAVTSYNIAGKDYPGYSGFAPTGQDVIQWQWPDYNPVLSASDPKE



 


RCNGGTGAALYAEAAPGDTITATWAQWTHSQGPILVWMYKCPGDFSSCDGSGAGWFKIDEAGF


 


HGDGTTVFLDTETPSGWDIAKLVGGNKSWSSKIPDGLAPGNYLVRHELIALHQANNPQFYPECA


 


QIKVTGSGTAEPAASYKAAIPGYCQQSDPNISFNINDHSLPQEYKIPGPPVFKGTASAKARAFQA


 


(SEQ ID NO: 99)



AVTSYNIAGKDYPGYSGFAPTGQDVIQWQWPDYNPVLSASDPKIRCNGGTGAALYAEAAPGDT



 


ITATWAQWTHSQGPILVWMYKCPGDFSSCDGSGAGWFKIDEAGFHGDGTTVFLDTETPSGWDI


 


AKLVGGNKSWSSKIPDGLAPGNYLVRHELIALHQANNPQFYPECAQIKVTGSGTAEPAASYKAA


 


IPGYCQQSDPNISFNINDHSLPQEYKIPGPPVFKGTASAKARAFQA






The polynucleotide (SEQ ID NO:100) and amino acid (SEQ ID NO:101) sequences of an M. thermophila GH61w are provided below. The signal sequence is shown underlined in SEQ ID NO:101. SEQ ID NO:102 provides the sequence of this GH61w without the signal sequence.








(SEQ ID NO: 100)



ATGCTGACAACAACCTTCGCCCTCCTGACGGCCGCTCTCGGCGTCAGCGCCCATTATACCCT



 


CCCCAGGGTCGGGACCGGTTCCGACTGGCAGCACGTGCGGCGGGCTGACAACTGGCAAAAC


 


AACGGCTTCGTCGGCGACGTCAACTCGGAGCAGATCAGGTGCTTCCAGGCGACCCCTGCCGG


 


CGCCCAAGACGTCTACACTGTTCAGGCGGGATCGACCGTGACCTACCACGCCAACCCCAGTA


 


TCTACCACCCCGGCCCCATGCAGTTCTACCTGGCCCGCGTTCCGGACGGACAGGACGTCAAG


 


TCGTGGACCGGCGAGGGTGCCGTGTGGTTCAAGGTGTACGAGGAGCAGCCTCAATTTGGCG


 


CCCAGCTGACCTGGCCTAGCAACGGCAAGAGCTCGTTCGAGGTTCCTATCCCCAGCTGCATT


 


CGGGCGGGCAACTACCTCCTCCGCGCTGAGCACATCGCCCTGCACGTTGCCCAAAGCCAGGG


 


CGGCGCCCAGTTCTACATCTCGTGCGCCCAGCTCCAGGTCACTGGTGGCGGCAGCACCGAGC


 


CTTCTCAGAAGGTTTCCTTCCCGGGTGCCTACAAGTCCACCGACCCCGGCATTCTTATCAACA


 


TCAACTACCCCGTCCCTACCTCGTACCAGAATCCGGGTCCGGCTGTCTTCCGTTGC


 


(SEQ ID NO: 101)



MLTTTFALLTAALGVSAHYTLERVGTGSDWQHVRRADNWQNNGFVGDVNSEQIRCFQATPAG



 


AQDVYTVQAGSTVTYHANPSIYHPGPMQFYLARVPDGQDVKSWTGEGAVWFKVYEEQPQFGA


 


QLTWPSNGKSSFEVPIPSCIRAGNYLLRAEHIALHVAQSQGGAQFYISCAQLQVTGGGSTEPSQK


 


VSFPGAYKSTDPGILININYPVPTSYQNPGPAVFRC


 


(SEQ ID NO: 102)



HYTLPRVGTGSDWQHVRRADNWQNNGFVGDVNSEQIRCFQATPAGAQDVYTVQAGSTVTYHA



 


NPSIYHPGPMQFYLARVPDGQDVKSWTGEGAVWFKVYEEQPQFGAQLTWPSNGKSSFEVPIPSC


 


IRAGNYLLRAEHIALHVAQSQGGAQFYISCAQLQVTGGGSTEPSQKVSFPGAYKSTDPGILININY


 


PVPTSYQNPGPAVFRC






The polynucleotide (SEQ ID NO:103) and amino acid (SEQ ID NO:104) sequences of a M. thermophila GH61x are provided below. The signal sequence is shown underlined in SEQ ID NO:104. SEQ ID NO:105 provides the sequence of this GH61x without the signal sequence.








(SEQ ID NO: 103)



ATGAAGGTTCTCGCGCCCCTGATTCTGGCCGGTGCCGCCAGCGCCCACACCATCTTCTCATCC



 


CTCGAGGTGGGCGGCGTCAACCAGGGCATCGGGCAGGGTGTCCGCGTGCCGTCGTACAACG


 


GTCCGATCGAGGACGTGACGTCCAACTCGATCGCCTGCAACGGGCCCCCCAACCCGACGAC


 


GCCGACCAACAAGGTCATCACGGTCCGGGCCGGCGAGACGGTGACGGCCGTCTGGCGGTAC


 


ATGCTGAGCACCACCGGCTCGGCCCCCAACGACATCATGGACAGCAGCCACAAGGGCCCGA


 


CCATGGCCTACCTCAAGAAGGTCGACAACGCCACCACCGACTCGGGCGTCGGCGGCGGCTG


 


GTTCAAGATCCAGGAGGACGGCCTTACCAACGGCGTCTGGGGCACCGAGCGCGTCATCAAC


 


GGCCAGGGCCGCCACAACATCAAGATCCCCGAGTGCATCGCCCCCGGCCAGTACCTCCTCCG


 


CGCCGAGATGCTTGCCCTGCACGGAGCTTCCAACTACCCCGGCGCTCAGTTCTACATGGAGT


 


GCGCCCAGCTCAATATCGTCGGCGGCACCGGCAGCAAGACGCCGTCCACCGTCAGCTTCCCG


 


GGCGCTTACAAGGGTACCGACCCCGGAGTCAAGATCAACATCTACTGGCCCCCCGTCACCAG


 


CTACCAGATTCCCGGCCCCGGCGTGTTCACCTGC


 


(SEQ ID NO: 104)



MKVLAPLILAGAASAHTIFSSLEVGGVNQGIGQGVRVPSYNGPIEDVTSNSIACNGPPNPTTPTNK



 


VITVRAGETVTAVWRYMLSTTGSAPNDIMDSSHKGPTMAYLKKVDNATTDSGVGGGWFKIQED


 


GLTNGVWGTERVINGQGRHNIKIPECIAPGQYLLRAEMLALHGASNYPGAQFYMECAQLNIVGG


 


TGSKTPSTVSFPGAYKGTDPGVKINIYWPPVTSYQIPGPGVFTC


 


(SEQ ID NO: 105)



HTIFSSLEVGGVNQGIGQGVRVPSYNGPIEDVTSNSIACNGPPNPTTPTNKVITVRAGETVTAVWR



 


YMLSTTGSAPNDIMDSSHKGPTMAYLKKVDNATTDSGVGGGWFKIQEDGIANGVWGTERVIN


 


GQGRHNIKIPECIAPGQYLLRAEMLALHGASNYPGAQFYMECAQLNIVGGTGSKTPSTVSFPGAY


 


KGTDPGVKINIYWPPVTSYQIPGPGVFTC






The polynucleotide (SEQ ID NO:106) and amino acid (SEQ ID NO:107) sequences of an M. thermophila GH61y are provided below. The signal sequence is underlined in SEQ ID NO:107. SEQ ID NO:108 provides the sequence of GH61y, without the signal sequence.








(SEQ ID NO: 106)



ATGATCGACAACCTCCCTGATGACTCCCTACAACCCGCCTGCCTCCGCCCGGGCCACTACCT



 


CGTCCGCCACGAGATCATCGCGCTGCACTCGGCCTGGGCCGAGGGCGAGGCCCAGTTCTACC


 


CCTTCCCCCTTTTTCCTTTTTTTCCCTCCCTTCTTTTGTCCGGTAACTACACGATTCCCGGTCCC


 


GCGATCTGGAAGTGCCCAGAGGCACAGCAGAACGAG


 


(SEQ ID NO: 107)



MIDNLPDDSLQPACLRPGHYLVRHEIIALHSAWAEGEAQFYPFPLFPFFPSELLSGNYTIPGPAIWK



 


CPEAQQNE


 


(SEQ ID NO: 108)



HYLVRHEIIALHSAWAEGEAQFYPFPLFPFTPSLLLSGNYTIPGPAIWKCPEAQQNE







Additional enzymes (i.e., non-GH61 enzymes) that find us in the present invention include, but are not limited to the following enzymes.
Wild-type EG1b cDNA (SEQ ID NO:109) and amino acid (SEQ ID NO:110) sequences are provided below. The signal sequence is underlined in SEQ ID NO:110. SEQ ID NO:111 provides the sequence of EG1b, without the signal sequence.








(SEQ ID NO: 109)



ATGGGGCAGAAGACTCTCCAGGGGCTGGTGGCGGCGGCGGCACTGGCAGCCTCGGTGGCGA



 


ACGCGCAGCAACCGGGCACCTTCACGCCCGAGGTGCATCCGACGCTGCCGACGTGGAAGTG


 


CACGACGAGCGGCGGGTGCGTCCAGCAGGACACGTCGGTGGTGCTCGACTGGAACTACCGC


 


TGGTTCCACACCGAGGACGGTAGCAAGTCGTGCATCACCTCTAGCGGCGTCGACCGGACCCT


 


GTGCCCGGACGAGGCGACGTGCGCCAAGAACTGCTTCGTCGAGGGCGTCAACTACACGAGC


 


AGCGGGGTCGAGACGTCCGGCAGCTCCCTCACCCTCCGCCAGTTCTTCAAGGGCTCCGACGG


 


CGCCATCAACAGCGTCTCCCCGCGCGTCTACCTGCTCGGGGGAGACGGCAACTATGTCGTGC


 


TCAAGCTCCTCGGCCAGGAGCTGAGCTTCGACGTGGACGTATCGTCGCTCCCGTGCGGCGAG


 


AACGCGGCCCTGTACCTGTCCGAGATGGACGCGACGGGAGGACGGAACGAGTACAACACGG


 


GCGGGGCCGAGTACGGGTCGGGCTACTGTGACGCCCAGTGCCCCGTGCAGAACTGGAACAA


 


CGGGACGCTCAACACGGGCCGGGTGGGCTCGTGCTGCAACGAGATGGACATCCTCGAGGCC


 


AACTCCAAGGCCGAGGCCTTCACGCCGCACCCCTGCATCGGCAACTCGTGCGACAAGAGCG


 


GGTGCGGCTTCAACGCGTACGCGCGCGGTTACCACAACTACTGGGCCCCCGGCGGCACGCTC


 


GACACGTCCCGGCCTTTCACCATGATCACCCGCTTCGTCACCGACGACGGCACCACCTCGGG


 


CAAGCTCGCCCGCATCGAGCGCGTCTACGTCCAGGACGGCAAGAAGGTGCCCAGCGCGGCG


 


CCCGGGGGGGACGTCATCACGGCCGACGGGTGCACCTCCGCGCAGCCCTACGGCGGCCTTTC


 


CGGCATGGGCGACGCCCTCGGCCGCGGCATGGTCCTGGCCCTGAGCATCTGGAACGACGCG


 


TCCGGGTACATGAACTGGCTCGACGCCGGCAGCAACGGCCCCTGCAGCGACACCGAGGGTA


 


ACCCGTCCAACATCCTGGCCAACCACCCGGACGCCCACGTCGTGCTCTCCAACATCCGCTGG


 


GGCGACATCGGCTCCACCGTCGACACCGGCGATGGCGACAACAACGGCGGCGGCCCCAACC


 


CGTCATCCACCACCACCGCTACCGCTACCACCACCTCCTCCGGCCCGGCCGAGCCTACCCAG


 


ACCCACTACGGCCAGTGTGGAGGGAAAGGATGGACGGGCCCTACCCGCTGCGAGACGCCCT


 


ACACCTGCAAGTACCAGAACGACTGGTACTCGCAGTGCCTGTAG


 


(SEQ ID NO: 110)



MGQKTLQGLVAAAALAASVANAQQPGTFTPEVHPTLPTWKCTTSGGCVQQDTSVVLDWNYR



 


WFHTEDGSKSCITSSGVDRTLCPDEATCAKNCFVEGVNYTSSGVETSGSSLTLRQFFKGSDGAIN


 


SVSPRVYLLGGDGNYVVLKLLGQELSFDVDVSSLPCGENAALYLSEMDATGGRNEYNTGGAEY


 


GSGYCDAQCPVQNWNNGTLNTGRVGSCCNEMDILEANSKAEAFTPITPCIGNSCDKSGCGENAY


 


ARGYHNYWAPGGTLDTSRPFTMITRFVTDDGTTSGKLARIERVYVQDGKKVPSAAPGGDVITAD


 


GCTSAQPYGGLSGMGDALGRGMVLALSIWNDASGYMNWLDAGSNGPCSDTEGNPSNILANHP


 


DAHVVLSNIRWGDIGSTVDTGDGDNNGGGPNPSSTTTATATTTSSGPAEPTQTHYGQCGGKGW


 


TGPTRCETPYTCKYQNDWYSQCL


 


(SEQ ID NO: 111)



QQPGTFTPEVHPTLPTWKCTTSGGCVQQDTSVVLDWNYRWFHTEDGSKSCITSSGVDRTLCPDE



 


ATCAKNCFVEGVNYTSSGVETSGSSLTLRQFFKGSDGAINSVSPRVYLLGGDGNYVVLKLLGQE


 


LSFDVDVSSLPCGENAALYLSEMDATGGRNEYNTGGAEYGSGYCDAQCPVQNWNNGTLNTGR


 


VGSCCNEMDILEANSKAEAFTPHPCIGNSCDKSGCGENAYARGYHNYWAPGGTLDTSRPFTMIT


 


REVTDDGTTSGKLARIERVYVQDGKKVPSAAPGGDVITADGCTSAQPYGGLSGMGDALGRGMV


 


LALSIWNDASGYMNWLDAGSNGPCSDTEGNPSNILANHPDAHVVLSNIRWGDIGSTVDTGDGD


 


NNGGGPNPSSTTTATATTTSSGPAEPTQTHYGQCGGKGWTGPTRCETPYTCKYQNDWYSQCL






Wild-type M. thermophila EG2 polynucleotide (SEQ ID NO:112) and amino acid (SEQ ID NO:113) sequences are provided below. The signal sequence is underlined in SEQ ID NO:113. SEQ ID NO:114 provides the sequence of EG2, without the signal sequence.








(SEQ ID NO: 112)



ATGAAGTCCTCCATCCTCGCCAGCGTCTTCGCCACGGGCGCCGTGGCTCAAAGTGGTCCGTG



 


GCAGCAATGTGGTGGCATCGGATGGCAAGGATCGACCGACTGTGTGTCGGGTTACCACTGC


 


GTCTACCAGAACGATTGGTACAGCCAGTGCGTGCCTGGCGCGGCGTCGACAACGCTCCAGA


 


CATCTACCACGTCCAGGCCCACCGCCACCAGCACCGCCCCTCCGTCGTCCACCACCTCGCCT


 


AGCAAGGGCAAGCTCAAGTGGCTCGGCAGCAACGAGTCGGGCGCCGAGTTCGGGGAGGGC


 


AACTACCCCGGCCTCTGGGGCAAGCACTTCATCTTCCCGTCGACTTCGGCGATTCAGACGCT


 


CATCAATGATGGATACAACATCTTCCGGATCGACTTCTCGATGGAGCGTCTGGTGCCCAACC


 


AGTTGACGTCGTCCTTCGACGAGGGCTACCTCCGCAACCTGACCGAGGTGGTCAACTTCGTG


 


ACGAACGCGGGCAAGTACGCCGTCCTGGACCCGCACAACTACGGCCGGTACTACGGCAACG


 


TCATCACGGACACGAACGCGTTCCGGACCTTCTGGACCAACCTGGCCAAGCAGTTCGCCTCC


 


AACTCGCTCGTCATCTTCGACACCAACAACGAGTACAACACGATGGACCAGACCCTGGTGCT


 


CAACCTCAACCAGGCCGCCATCGACGGCATCCGGGCCGCCGGCGCGACCTCGCAGTACATCT


 


TCGTCGAGGGCAACGCGTGGAGCGGGGCCTGGAGCTGGAACACGACCAACACCAACATGGC


 


CGCCCTGACGGACCCGCAGAACAAGATCGTGTACGAGATGCACCAGTACCTCGACTCGGAC


 


AGCTCGGGCACCCACGCCGAGTGCGTCAGCAGCAACATCGGCGCCCAGCGCGTCGTCGGAG


 


CCACCCAGTGGCTCCGCGCCAACGGCAAGCTCGGCGTCCTCGGCGAGTTCGCCGGCGGCGCC


 


AACGCCGTCTGCCAGCAGGCCGTCACCGGCCTCCTCGACCACCTCCAGGACAACAGCGACGT


 


CTGGCTGGGTGCCCTCTGGTGGGCCGCCGGTCCCTGGTGGGGCGACTACATGTACTCGTTCG


 


AGCCTCCTTCGGGCACCGGCTATGTCAACTACAACTCGATCCTAAAGAAGTACTTGCCGTAA


 


(SEQ ID NO: 113)



MKSSILASVFATGAVAQSGPWQQCGGIGWQGSTDCVSGYHCVYQNDWYSQCVPGAASTTLQT



 


STTSRPTATSTAPPSSTTSPSKGKLKWLGSNESGAEFGEGNYPGLWGKHFIFPSTSAIQTLINDGYN


 


IFRIDFSMERLVPNQLTSSFDEGYLRNLTEVVNFVTNAGKYAVLDPHNYGRYYGNVITDINAFRT


 


FWTNLAKQFASNSLVIFDTNNEYNTMDQTLVLNLNQAAIDGIRAAGATSQYIFVEGNAWSGAW


 


SWNTTNTNMAALTDPQNKIVYEMHQYLDSDSSGTHAECVSSNIGAQRVVGATQWLRANGKLG


 


VLGEFAGGANAVCQQAVTGLLDHLQDNSEVWLGALWWAAGPWWGDYMYSFEPPSGTGYVN


 


YNSILKKYLP


 


(SEQ ID NO: 114)



QSGPWQQCGGIGWQGSTDCVSGYHCVYQNDWYSQCVPGAASTTLQTSTTSRPTATSTAPPSSTT



 


SPSKGKLKWLGSNESGAEFGEGNYPGLWGKHFIFPSTSAIQTLINDGYNIFRIDFSMERLVPNQLT


 


SSFDEGYLRNLTEVVNFVINAGKYAVLDPHNYGRYYGNVITDTNAFRTFWTNLAKQFASNSLVI


 


FDTNNEYNTMDQTLVLNLNQAAIDGIRAAGATSQYIFVEGNAWSGAWSWNTTNTNMAALTDP


 


QNKIVYEMHQYLDSDSSGTHAECVSSNIGAQRVVGATQWLRANGKLGVLGEFAGGANAVCQQ


 


AVTGLLDHLQDNSEVWLGALWWAAGPWWGDYMYSFEPPSGTGYVNYNSILKKYLP






The polynucleotide (SEQ ID NO:115) and amino acid (SEQ ID NO:116) sequences of a wild-type BGL are provided below. The signal sequence is underlined in SEQ ID NO:116. SEQ ID NO:117provides the polypeptide sequence without the signal sequence.








(SEQ ID NO: 115)



ATGAAGGCTGCTGCGCTTTCCTGCCTCTTCGGCAGTACCCTTGCCGTTGCAGGCGCCATTGAA



 


TCGAGAAAGGTTCACCAGAAGCCCCTCGCGAGATCTGAACCTTTTTACCCGTCGCCATGGAT


 


GAATCCCAACGCCGACGGCTGGGCGGAGGCCTATGCCCAGGCCAAGTCCTTTGTCTCCCAAA


 


TGACTCTGCTAGAGAAGGTCAACTTGACCACGGGAGTCGGCTGGGGGGCTGAGCAGTGCGT


 


CGGCCAAGTGGGCGCGATCCCTCGCCTTGGACTTCGCAGTCTGTGCATGCATGACTCCCCTC


 


TCGGCATCCGAGGAGCCGACTACAACTCAGCGTTCCCCTCTGGCCAGACCGTTGCTGCTACC


 


TGGGATCGCGGTCTGATGTACCGTCGCGGCTACGCAATGGGCCAGGAGGCCAAAGGCAAGG


 


GCATCAATGTCCTTCTCGGACCAGTCGCCGGCCCCCTTGGCCGCATGCCCGAGGGCGGTCGT


 


AACTGGGAAGGCTTCGCTCCGGATCCCGTCCTTACCGGCATCGGCATGTCCGAGACGATCAA


 


GGGCATTCAGGATGCTGGCGTCATCGCTTGTGCGAAGCACTTTATTGGAAACGAGCAGGAGC


 


ACTTCAGACAGGTGCCAGAAGCCCAGGGATACGGTTACAACATCAGCGAAACCCTCTCCTCC


 


AACATTGACGACAAGACCATGCACGAGCTCTACCTTTGGCCGTTTGCCGATGCCGTCCGGGC


 


CGGCGTCGGCTCTGTCATGTGCTCGTACCAGCAGGTCAACAACTCGTACGCCTGCCAGAACT


 


CGAAGCTGCTGAACGACCTCCTCAAGAACGAGCTTGGGTTTCAGGGCTTCGTCATGAGCGAC


 


TGGCAGGCACAGCACACTGGCGCAGCAAGCGCCGTGGCTGGTCTCGATATGTCCATGCCGG


 


GCGACACCCAGTTCAACACTGGCGTCAGTTTCTGGGGCGCCAATCTCACCCTCGCCGTCCTC


 


AACGGCACAGTCCCTGCCTACCGTCTCGACGACATGGCCATGCGCATCATGGCCGCCCTCTT


 


CAAGGTCACCAAGACCACCGACCTGGAACCGATCAACTTCTCCTTCTGGACCGACGACACTT


 


ATGGCCCGATCCACTGGGCCGCCAAGCAGGGCTACCAGGAGATTAATTCCCACGTTGACGTC


 


CGCGCCGACCACGGCAACCTCATCCGGGAGATTGCCGCCAAGGGTACGGTGCTGCTGAAGA


 


ATACCGGCTCTCTACCCCTGAACAAGCCAAAGTTCGTGGCCGTCATCGGCGAGGATGCTGGG


 


TCGAGCCCCAACGGGCCCAACGGCTGCAGCGACCGCGGCTGTAACGAAGGCACGCTCGCCA


 


TGGGCTGGGGATCCGGCACAGCCAACTATCCGTACCTCGTTTCCCCCGACGCCGCGCTCCAG


 


GCCCGGGCCATCCAGGACGGCACGAGGTACGAGAGCGTCCTGTCCAACTACGCCGAGGAAA


 


AGACAAAGGCTCTGGTCTCGCAGGCCAATGCAACCGCCATCGTCTTCGTCAATGCCGACTCA


 


GGCGAGGGCTACATCAACGTGGACGGTAACGAGGGCGACCGTAAGAACCTGACTCTCTGGA


 


ACAACGGTGATACTCTGGTCAAGAACGTCTCGAGCTGGTGCAGCAACACCATCGTCGTCATC


 


CACTCGGTCGGCCCGGTCCTCCTGACCGATTGGTACGACAACCCCAACATCACGGCCATTCT


 


CTGGGCTGGTCTTCCGGGCCAGGAGTCGGGCAACTCCATCACCGACGTGCTTTACGGCAAGG


 


TCAACCCCGCCGCCCGCTCGCCCTTCACTTGOGGCAAGACCCGCGAAAGCTATGGCGCGGAC


 


GTCCTGTACAAGCCGAATAATGGCAATGGTGCGCCCCAACAGGACTTCACCGAGGGCGTCTT


 


CATCGACTACCGCTACTTCGACAAGGTTGACGATGACTCGGTCATCTACGAGTTCGGCCACG


 


GCCTGAGCTACACCACCTTCGAGTACAGCAACATCCGCGTCGTCAAGTCCAACGTCAGCGAG


 


TACCGGCCCACGACGGGCACCACGGCCCAGGCCCCGACGTTTGGCAACTTCTCCACCGACCT


 


CGAGGACTATCTCTTCCCCAAGGACGAGTTCCCCTACATCTACCAGTACATCTACCCGTACCT


 


CAACACGACCGACCCCCGGAGGGCCTCGGCCGATCCCCACTACGGCCAGACCGCCGAGGAG


 


TTCCTCCCGCCCCACGCCACCGATGACGACCCCCAGCCGCTCCTCCGGTCCTCGGGCGGAAA


 


CTCCCCCGGCGGCAACCGCCAGCTGTACGACATTGTCTACACAATCACGGCCGACATCACGA


 


ATACGGGCTCCGTTGTAGGCGAGGAGGTACCGCAGCTCTACGTCTCGCTGGGCGGTCCCGAG


 


GATCCCAAGGTGCAGCTGCGCGACTTTGACAGGATGCGGATCGAACCCGGCGAGACGAGGC


 


AGTTCACCGGCCGCCTGACGCGCAGAGATCTGAGCAACTGGGACGTCACGGTGCAGGACTG


 


GGTCATCAGCAGGTATCCCAAGACGGCATATGTTGGGAGGAGCAGCCGGAAGTTGGATCTC


 


AAGATTGAGCTTCCTTGA


 


(SEQ ID NO: 116)



MKAAALSCLFGSTLAVAGAIESRKVHQKPLARSEPFYPSPWMNPNADGWAEAYAQAKSEVSQM



 


TELEKVNLTTGVGWGAEQCVGQVGAIPRLGLRSLCMHDSPLGIRGADYNSAFPSGQTVAATWD


 


RGLMYRRGYAMGQEAKGKGINVLLGPVAGPLGRMPEGGRNWEGFAPDPVLTGIGMSETIKGIQ


 


DAGVIACAKHEIGNEQEFIMVPEAQGYGYNISETLSSNIDDKTMHELYLWPFADAVRAGVGSV


 


MCSYQQVNNSYACQNSKLLNDLLKNELGFQGFVMSDWQAQHTGAASAVAGLDMSMPGDTQF


 


NTGVSFWGANLTLAVINGTVPAYRLDDMAMRIMAALFKVTKTTDLEPINFSFWTDDTYGPIHW


 


AAKQGYQEINSHVDVRADHGNLIREIAAKGTVLLKNTGSLPLNKPKFVAVIGEDAGSSPNGPNG


 


CSDRGCNEGTLAMGWGSGTANYPYLVSPDAALQARAIQDGTRYESVLSNYAEEKTKALVSQAN


 


ATAIVFVNADSGEGYINVDGNEGDRKNETEWNNGDTLVKNVSSWCSNTIVVIHSVGPVELTDW


 


YDNPNITAILWAGLPGQESGNSITDVLYGKVNPAARSPFTWGKTRESYGADVLYKPNNGNGAPQ


 


QDFTEGVFIDYRYFDKVDDDSVIYEFGHGLSYTTFEYSNIRVVKSNVSEYRPTTGTTAQAPTEGN


 


FSTDLEDYLFPKDEFPYIYQYIYPYLNTTDPRRASADPHYGQTAEEFLPPHATDDDPQPLLRSSGG


 


NSPGGNRQLYDIVYTITADITNTGSVVGEEVPQLYVSLGGPEDPKVQLRDFDRMRIEPGETRQFT


 


GRLTRRDLSNWDVTVQDWVISRYPKTAYVGRSSRKLDLKIELP


 


(SEQ ID NO: 117)



IESRKVHQKPLARSEPFYPSPWMNPNADGWAEAYAQAKSFVSQMTLLEKVNLTTGVGWGAEQ



 


CVGQVGAIPRLGLRSLCMHDSPLGIRGADYNSAFPSGQTVAATWDRGLMYRRGYAMGQEAKG


 


KGINVLLGPVAGPLGRMPEGGRNWEGFAPDPVLTGIGMSETIKGIQDAGVIACAKHFIGNEQEHF


 


RQVPEAQGYGYNISETLSSNIDDKTMBELYEWPFADAVRAGVGSVMCSYQQVNNSYACQNSKL


 


LNDLLKNELGFQGFVMSDWQAQHTGAASAVAGLDMSMPGDTQFNTGVSFWGANLTLAVLNG


 


TVPAYRLDDMAMRIMAALFKVTKTTDLEPINFSFWTDDTYGPIHWAAKQGYQEINSHVDVRAD


 


HGNLIREIAAKGTVLLKNTGSLPLNKPKFVAVIGEDAGSSPNGPNGCSDRGCNEGTLAMGWGSG


 


TANYPYLVSPDAALQARAIQDGTRYESVLSNYAEEKTKALVSQANATAIVEVNADSGEGYINVD


 


GNEGDRKNLTLWNNGDTLVKNVSSWCSNTIVVIHSVGPVLLTDWYDNPNITAILWAGLPGQES


 


GNSITDVLYGKVNPAARSPFTWGKTRESYGADVLYKPNNGNGAPQQDFTEGVFIDYRYFDKVD


 


DDSVIYEFGHGLSYTTFEYSNIRVVKSNVSEYRPTTGTTAQAPTFGNFSTDLEDYLFPKDEFPYIY


 


QYIYPYLNTTDPRRASADPHYGQTAEEFLPPHATDDDPQPLLRSSGGNSPGGNRQLYDIVYTITA


 


DITNTGSVVGEEVPQLYVSLGGPEDPKVQLRDFDRMRIEPGETRQFTGRLTRRDLSNWDVTVQD


 


WVISRYPKTAYVGRSSRKLDLKIELP






The polynucleotide (SEQ ID NO:118) and amino acid (SEQ ID NO:119) sequences of a BGL variant (“Variant 883”) are provided below. The signal sequence is underlined in SEQ ID NO:119. SEQ ID NO:120 provides the sequence of this BGL variant, without the signal sequence.








(SEQ ID NO: 118)



ATGAAGGCTGCTGCGCTTTCCTGCCTCTTCGGCAGTACCCTTGCCGTTGCAGGCGCCATTGAA



 


TCGAGAAAGGTTCACCAGAAGCCCCTCGCGAGATCTGAACCTTTTTACCCGTCGCCATGGAT


 


GAATCCCAACGCCGACGGCTGGGCGGAGGCCTATGCCCAGGCCAAGTCCTTTGTCTCCCAAA


 


TGACTCTGCTAGAGAAGGTCAACTTGACCACGGGAGTCGGCTGGGGGGCTGAGCAGTGCGT


 


CGGCCAAGTGGGCGCGATCCCTCGCCTTGGACTTCGCAGTCTGTGCATGCATGACTCCCCTC


 


TCGGCATCCGAGGAGCCGACTACAACTCAGCGTTCCCCTCTGGCCAGACCGTTGCTGCTACC


 


TGGGATCGCGGTCTGATGTACCGTCGCGGCTACGCAATGGGCCAGGAGGCCAAAGGCAAGG


 


GCATCAATGTCCTTCTCGGACCAGTCGCCGGCCCCCTTGGCCGCATGCCCGAGGGCGGTCGT


 


AACTGGGAAGGCTTCGCTCCGGATCCCGTCCTTACCGGCATCGGCATGTCCGAGACGATCAA


 


GGGCATTCAGGATGCTGGCGTCATCGCTTGTGCGAAGCACTTTATTGGAAACGAGCAGGAGC


 


ACTTCAGACAGGTGCCAGAAGCCCAGGGATACGGTTACAACATCAGCGAAACCCTCTCCTCC


 


AACATTGACGACAAGACCATGCACGAGCTCTACCTTTGGCCGTTTGCCGATGCCGTCCGGGC


 


CGGCGTCGGCTCTGTCATGTGCTCGTACAACCAGGTCAACAACTCGTACGCCTGCCAGAACT


 


CGAAGCTGCTGAACGACCTCCTCAAGAACGAGCTTGGGTTTCAGGGCTTCGTCATGAGCGAC


 


TGGTGGGCACAGCACACTGGCGCAGCAAGCGCCGTGGCTGGTCTCGATATGTCCATGCCGG


 


GCGACACCATGTTCAACACTGGCGTCAGTTTCTGGGGCGCCAATCTCACCCTCGCCGTCCTC


 


AACGGCACAGTCCCTGCCTACCGTCTCGACGACATGGCCATGCGCATCATGGCCGCCCTCTT


 


CAAGGTCACCAAGACCACCGACCTGGAACCGATCAACTTCTCCTTCTGGACCCGCGACACTT


 


ATGGCCCGATCCACTGGGCCGCCAAGCAGGGCTACCAGGAGATTAATT'CCCACGTTGACGTC


 


CGCGCCGACCACGGCAACCTCATCCGGAACATTGCCGCCAAGGGTACGGTGCTGCTGAAGA


 


ATACCGGCTCTCTACCCCTGAACAAGCCAAAGTTCGTGGCCGTCATCGGCGAGGATGCTGGG


 


CCGAGCCCCAACGGGCCCAACGGCTGCAGCGACCGCGGCTGTAACGAAGGCACGCTCGCCA


 


TGGGCTGGGGATCCGGCACAGCCAACTATCCGTACCTCGTTTCCCCCGACGCCGCGCTCCAG


 


TTGCGGGCCATCCAGGACGGCACGAGGTACGAGAGCGTCCTGTCCAACTACGCCGAGGAAA


 


ATACAAAGGCTCTGGTCTCGCAGGCCAATGCAACCGCCATCGTCTTCGTCAATGCCGACTCA


 


GGCGAGGGCTACATCAACGTGGACGGTAACGAGGGCGACCGTAAGAACCTGACTCTCTGGA


 


ACAACGGTGATACTCTGGTCAAGAACGTCTCGAGCTGGTGCAGCAACACCATCGTCGTCATC


 


CACTCGGTCGGCCCGGTCCTCCTGACCGATTGGTACGACAACCCCAACATCACGGCCATTCT


 


CTGGGCTGGTCTTCCGGGCCAGGAGTCGGGCAACTCCATCACCGACGTGCTTTACGGCAAGG


 


TCAACCCCGCCGCCCGCTCGCCCTTCACTTGGGGCAAGACCCGCGAAAGCTATGGCGCGGAC


 


GTCCTGTACAAGCCGAATAATGGCAATTGGGCGCCCCAACAGGACTTCACCGAGGGCGTCTT


 


CATCGACTACCGCTACTTCGACAAGGTTGACGATGACTCGGTCATCTACGAGTTCGGCCACG


 


GCCTGAGCTACACCACCTTCGAGTACAGCAACATCCGCGTCGTCAAGTCCAACGTCAGCGAG


 


TACCGGCCCACGACGGGCACCACGATTCAGGCCCCGACGTTTGGCAACTTCTCCACCGACCT


 


CGAGGACTATCTCTTCCCCAAGGACGAGTTCCCCTACATCCCGCAGTACATCTACCCGTACC


 


TCAACACGACCGACCCCCGGAGGGCCTCGGCCGATCCCCACTACGGCCAGACCGCCGAGGA


 


GTTCCTCCCGCCCCACGCCACCGATGACGACCCCCAGCCGCTCCTCCGGTCCTCGGGCGGAA


 


ACTCCCCCGGCGGCAACCGCCAGCTGTACGACATTGTCTACACAATCACGGCCGACATCACG


 


AATACGGGCTCCGTTGTAGGCGAGGAGGTACCGCAGCTCTACGTCTCGCTGGGCGGTCCCGA


 


GGATCCCAAGGTGCAGCTGCGCGACTTTGACAGGATGCGGATCGAACCCGGCGAGACGAGG


 


CAGTTCACCGGCCGCCTGACGCGCAGAGATCTGAGCAACTGGGACGTCACGGTGCAGGACT


 


GGGTCATCAGCAGGTATCCCAAGACGGCATATGTTGGGAGGAGCAGCCGGAAGTTGGATCT


 


CAAGATTGAGCTTCCTTGA


 


(SEQ ID NO: 119)



MKAAALSCLFGSTLAVAGAIESRKVHQKPLARSEPFYPSPWMNPNADGWAEAYAQAKSFVSQM



 


TLLEKVNLTTGVGWGAEQCVGQVGAIPRLGLRSLCMHDSPLGIRGADYNSAFPSGQTVAATWD


 


RGLMYRRGYAMGQEAKGKGINVLLGPVAGPLGRMPEGGRNWEGFAPDPVLTGIGMSETIKGIQ


 


DAGVIACAKHFIGNEQEHFRQVPEAQGYGYNISETLSSNIDDKTMHELYLWPFADAVRAGVGSV


 


MCSYNQVNNSYACQNSKLLNDLLKNELGFQGFVMSDWWAQHTGAASAVAGLDMSMPGDTM


 


FNTGVSFWGANLTLAVLNGTVPAYRLDDMAMRIMAALFKVTKTTDLEPINFSFWTRDTYGPIH


 


WAAKQGYQEINSHVDVRADHGNLJRNIAAKGTVLLKNTGSLPLNKPKFVAVIGEDAGPSPNGPN


 


GCSDRGCNEGTLAMGWGSGTANYPYLVSPDAALQLRAIQDGTRYESVLSNYAEENTKALVSQA


 


NATAIVEVNADSGEGYINVDGNEGDRKNLTLWNNGDTLVKNVSSWCSNTIVVIHSVGPVLLTD


 


WYDNPNITAILWAGLPGQESGNSITDVLYGKVNPAARSPFTWGKTRESYGADVLYKPNNGNWA


 


PQQDFTEGVFIDYRYEDKVDDDSVIYEFGHGLSYTTFEYSNIRVVKSNVSEYRPTTGTTIQAPTEG


 


NFSTDLEDYLFPKDEFPYIPQYIYPYLNTTDPRRASADPHYGQTAEEFLPPHATDDDPQPLLRSSG


 


GNSPGGNRQLYDIVYTITADITNTGSVVGEEVPQLYVSLGGPEDPKVQLRDFDRMRIEPGETRQF


 


TGRLTRRDLSNWDVTVQDWVISRYPKTAYVGRSSRKLDLKIELP


 


(SEQ ID NO: 120)



IESRKVHQKPLARSEPFYPSPWMNPNADGWAEAYAQAKSFVSQMTLLEKVNLTTGVGWGAEQ



 


CVGQVGAIPRLGIRSLCMHDSPLGIRGADYNSAFPSGQTVAATWDRGLMYRRGYAMGQEAKG


 


KGINVLLGPVAGPLGRMPEGGRNWEGFAPDPVLTGIGMSETIKGIQDAGVIACAKHFIGNEQEHF


 


RQVPEAQGYGYNISETLSSNIDDKTMHELYLWPFADAVRAGVGSVMCSYNQVNNSYACQNSKL


 


LNDLLKNELGFQGFVMSDWWAQHTGAASAVAGLDMSMPGDTMFNTGVSFWGANLTLAVLNG


 


TVPAYRLDDMAMRIMAALFKVTKTTDLEPINFSFWTRDTYGPIHWAAKQGYQEINSHVDVRAD


 


HGNLIRNIAAKGTVLLKNTGSLPLNKPKFVAVIGEDAGPSPNGPNGCSDRGCNEGTLAMGWGSG


 


TANYPYLVSPDAALQLRAIQDGTRYESVLSNYAEENTKALVSQANATAIVEVNADSGEGYINVD


 


GNEGDRKNLTLWNNGDTLVKNVSSWCSNTIVVIHSVGPVLLTDWYDNPNITAILWAGLPGQES


 


GNSITDVLYGKVNPAARSPFTWGKTRESYGADVLYKPNNGNWAPQQDFTEGVFIDYRYFDKVD


 


DDSVIYEFGHGLSYTTFEYSNIRVVKSNVSEYRPTTGTTIQAPTFGNFSTDLEDYLFPKDEFPYIPQ


 


YIYPYLNTTDPRRASADPHYGQTAEEFLPPHATDDDPQPLLRSSGGNSPGGNRQLYDIVYTITADI


 


TNTGSVVGEEVPQLYVSLGGPEDPKVQLRDFDRMRIEPGETRQFTGRLTRRDLSNWDVTVQDW


 


VISRYPKTAYVGRSSRKLDLKIELP






The polynucleotide (SEQ ID NO:121) and amino acid (SEQ ID NO:122) sequences of a BGL variant (“Variant 900”) are provided below. The signal sequence is underlined in SEQ ID NO:122. SEQ ID NO:123 provides the sequence of this BGL variant, without the signal sequence.








(SEQ ID NO: 121)



ATGAAGGCTGCTGCGCTTTCCTGCCTCTTCGGCAGTACCCTTGCCGTTGCAGGCGCCATTGAA



 


TCGAGAAAGGTTCACCAGAAGCCCCTCGCGAGATCTGAACCTTTTTACCCGTCGCCATGGAT


 


GAATCCCAACGCCATCGGCTGGGCGGAGGCCTATGCCCAGGCCAAGTCCTTTGTCTCCCAAA


 


TGACTCTGCTAGAGAAGGTCAACTTGACCACGGGAGTCGGCTGGGGGGAGGAGCAGTGCGT


 


CGGCAACGTGGGCGCGATCCCTCGCCTTGGACTTCGCAGTCTGTGCATGCATGACTCCCCTC


 


TCGGCGTGCGAGGAACCGACTACAACTCAGCGTTCCCCTCTGGCCAGACCGTTGCTGCTACC


 


TGGGATCGCGGTCTGATGTACCGTCGCGGCTACGCAATGGGCCAGGAGGCCAAAGGCAAGG


 


GCATCAATGTCCTTCTCGGACCAGTCGCCGGCCCCCTTGGCCGCATGCCCGAGGGCGGTCGT


 


AACTGGGAAGGCTTCGCTCCGGATCCCGTCCTTACCGGCATCGGCATGTCCGAGACGATCAA


 


GGGCATTCAGGATGCTGGCGTCATCGCTTGTGCGAAGCACTTTATTGGAAACGAGCAGGAGC


 


ACTTCAGACAGGTGCCAGAAGCCCAGGGATACGGTTACAACATCAGCGAAACCCTCTCCTCC


 


AACATTGACGACAAGACCATGCACGAGCTCTACCTTTGGCCGTTTGCCGATGCCGTCCGGGC


 


CGGCGTCGGCTCTGTCATGTGCTCGTACAACCAGGGCAACAACTCGTACGCCTGCCAGAACT


 


CGAAGCTGCTGAACGACCTCCTCAAGAACGAGCTTGGGTTTCAGGGCTTCGTCATGAGCGAC


 


TGGTGGGCACAGCACACTGGCGCAGCAAGCGCCGTGGCTGGTCTCGATATGTCCATGCCGG


 


GCGACACCATGGTCAACACTGGCGTCAGTTTCTGGGGCGCCAATCTCACCCTCGCCGTCCTC


 


AACGGCACAGTCCCTGCCTACCGTCTCGACGACATGTGCATGCGCATCATGGCCGCCCTCTT


 


CAAGGTCACCAAGACCACCGACCTGGAACCGATCAACTTCTCCTTCTGGACCCGCGACACTT


 


ATGGCCCGATCCACTGGGCCGCCAAGCAGGGCTACCAGGAGATTAATTCCCACGTTGACGTC


 


CGCGCCGACCACGGCAACCTCATCCGGAACATTGCCGCCAAGGGTACGGTGCTGCTGAAGA


 


ATACCGGCTCTCTACCCCTGAACAAGCCAAAGTTCGTGGCCGTCATCGGCGAGGATGCTGGG


 


CCGAGCCCCAACGGGCCCAACGGCTGCAGCGACCGCGGCTGTAACGAAGGCACGCTCGCCA


 


TGGGCTGGGGATCCGGCACAGCCAACTATCCGTACCTCGTTTCCCCCGACGCCGCGCTCCAG


 


GCGCGGGCCATCCAGGACGGCACGAGGTACGAGAGCGTCCTGTCCAACTACGCCGAGGAAA


 


ATACAAAGGCTCTGGTCTCGCAGGCCAATGCAACCGCCATCGTCTTCGTCAATGCCGACTCA


 


GGCGAGGGCTACATCAACGTGGACGGTAACGAGGGCGACCGTAAGAACCTGACTCTCTGGA


 


ACAACGGTGATACTCTGGTCAAGAACGTCTCGAGCTGGTGCAGCAACACCATCGTCGTCATC


 


CACTCGGTCGGCCCGGTCCTCCTGACCGATTGGTACGACAACCCCAACATCACGGCCATTCT


 


CTGGGCTGGTCTTCCGGGCCAGGAGTCGGGCAACTCCATCACCGACGTGCTTTACGGCAAGG


 


TCAACCCCGCCGCCCGCTCGCCCTTCACTTGGGGCAAGACCCGCGAAAGCTATGGCGCGGAC


 


GTCCTGTACAAGCCGAATAATGGCAATTGGGCGCCCCAACAGGACTTCACCGAGGGCGTCTT


 


CATCGACTACCGCTACTTCGACAAGGTTGACGATGACTCGGTCATCTACGAGTTCGGCCACG


 


GCCTGAGCTACACCACCTTCGAGTACAGCAACATCCGCGTCGTCAAGTCCAACGTCAGCGAG


 


TACCGGCCCACGACGGGCACCACGATTCAGGCCCCGACGTTTGGCAACTTCTCCACCGACCT


 


CGAGGACTATCTCTTCCCCAAGGACGAGTTCCCCTACATCCCGCAGTACATCTACCCGTACC


 


TCAACACGACCGACCCCCGGAGGGCCTCGGGCGATCCCCACTACGGCCAGACCGCCGAGGA


 


GTTCCTCCCGCCCCACGCCACCGATGACGACCCCCAGCCGCTCCTCCGGTCCTCGGGCGGAA


 


ACTCCCCCGGCGGCAACCGCCAGCTGTACGACATTGTCTACACAATCACGGCCGACATCACG


 


AATACGGGCTCCGTTGTAGGCGAGGAGGTACCGCAGCTCTACGTCTCGCTGGGCGGTCCCGA


 


GGATCCCAAGGTGCAGCTGCGCGACTTTGACAGGATGCGGATCGAACCCGGCGAGACGAGG


 


CAGTTCACCGGCCGCCTGACGCGCAGAGATCTGAGCAACTGGGACGTCACGGTGCAGGACT


 


GGGTCATCAGCAGGTATCCCAAGACGGCATATGTTGGGAGGAGCAGCCGGAAGTTGGATCT


 


CAAGATTGAGCTTCCTTGA


 


(SEQ ID NO: 122)



MKAAALSCLFGSTLAVAGAIESRKVHQKPLARSEPFYPSPWMNPNAIGWAEAYAQAKSFVSQM



 


TLLEKVNLTTGVGWGEEQCVGNVGAIPRLGLRSLCMHDSPLGVRGTDYNSAFPSGQTVAATWD


 


RGLMYRRGYAMGQEAKGKGINVLLGPVAGPLGRMPEGGRNWEGFAPDPVLTGIGMSETIKGIQ


 


DAGVIACAKITFIGNEQEHFRQVPEAQGYGYNISETLSSNIDDKTMHELYLWPFADAVRAGVGSV


 


MCSYNQGNNSYACQNSKLLNDLLKNELGFQGFVMSDWWAQHTGAASAVAGLDMSMPGDTM


 


VNTGVSFWGANLTLAVLNGTVPAYRLDDMCMRIMAALFKVTKTTDLEPINFSFWTRDTYGPIH


 


WAAKQGYQEINSHVDVRADHGNLIRNIAAKGTVLLKNTGSLPLNKPKEVAVIGEDAGPSPNGPN


 


GCSDRGCNEGTLAMGWGSGTANYPYLVSPDAALQARAIQDGTRYESVLSNYAEENTKALVSQA


 


NATAIVFVNADSGEGYINVDGNEGDRKNLTLWNNGDTLVKNVSSWCSNTIVVIHSVGPVLLTD


 


WYDNPNITAILWAGLPGQESGNSITDVLYGKVNPAARSPFTWGKTRESYGADVLYKPNNGNWA


 


PQQDFTEGVFIDYRYFDKVDDDSVIYEFGHGLSYTTFEYSNIRVVKSNVSEYRPTTGTTIQAPTFG


 


NFSTDLEDYLFPKDEFPYIPQYIYPYLNTTDPRRASGDPHYGQTAEEFLPPHATDDDPQPLLASSG


 


GNSPGGNRQLYDIVYTITADITNTGSVVGEEVPQLYVSLGGPEDPKVQLRDFDRMRIEPGETRQF


 


TGRLTRRDLSNWDVTVQDWVISRYPKTAYVGRSSRKLDLKIELP


 


(SEQ ID NO: 123)



IESRKVHQKPLARSEPFYPSPWMNPNAIGWAEAYAQAKSFVSQMTLLEKVNLTTGVGWGEEQC



 


VGNVGAIPRLGLRSLCMHDSPLGVRGTDYNSAFPSGQTVAATWDRGLMYRRGYAMGQEAKGK


 


GINVLLGPVAGPLGRMPEGGRNWEGFAPDPVLTGIGMSETIKGIQDAGVIACAKHFIGNEQEHFR


 


QVPEAQGYGYNISETLSSNIDDKTMHELYLWPFADAVRAGVGSVMCSYNQGNNSYACQNSKLL


 


NDLLKNELGFQGFVMSDWWAQHTGAASAVAGLDMSMPGDTMVNTGVSFWGANLTLAVLNG


 


TVPAYRLDDMCMRIMAALFKVTKTTDLEPINFSFWTRDTYGPIHWAAKQGYQEINSHVDVRAD


 


HGNLIRNIAAKGTVLLKNTGSLPLNKPKFVAVIGEDAGPSPNGPNGCSDRGCNEGTLAMGWGSG


 


TANYPYLVSPDAALQARAIQDGTRYESVLSNYAEENTKALVSQANATAIVFVNADSGEGYINVD


 


GNEGDRKNLTLWNNGDTLVKNVSSWCSNTIVVIHSVGPVLLTDWYDNPNITAILWAGLPGQES


 


GNSITDVLYGKVNPAARSPFTWGKTRESYGADVLYICPNNGNWAPQQDFTEGVFIDYRYFDKVD


 


DDSVIYEFGHGLSYTTFEYSNIRVVKSNVSEYRPTTGTTIQAPTFGNFSTDLEDYLFPKDEFPYIPQ


 


YIYPYLNTTDPRRASGDPHYGQTAEEFLPPHATDDDPQPLLRSSGGNSPGGNRQTYDIVYTITADI


 


TNTGSVVGEEVPQLYVSLGGPEDPKVQLRDTDRMRIEPGETRQFTGRLTRRDLSNWDVTVQDW


 


VISRYPKTAYVGRSSRKLDLKIELP






The polynucleotide (SEQ ID NO:124) and amino acid (SEQ ID NO:125) sequences of wild-type Talaromyces emersonii CBH1 are provided below. The signal sequence is shown underlined in SEQ ID NO:125. SEQ ID NO:126 provides the sequence of this CBH1, without the signal sequence.








(SEQ ID NO: 124)



ATGCTTCGACGGGCTCTTCTTCTATCCTCTTCCGCCATCCTTGCTGTCAAGGCACAGCAGGCC



 


GGCACGGCGACGGCAGAGAACCACCCGCCCCTGACATGGCAGGAATGCACCGCCCCTGGGA


 


GCTGCACCACCCAGAACGGGGCGGTCGTTCTTGATGCGAACTGGCGTTGGGTGCACGATGTG


 


AACGGATACACCAACTGCTACACGGGCAATACCTGGGACCCCACGTACTGCCCTGACGACG


 


AAACCTGCGCCCAGAACTGTGCGCTGGACGGCGCGGATTACGAGGGCACCTACGGCGTGAC


 


TTCGTCGGGCAGCTCCTTGAAACTCAATTTCGTCACCGGGTCGAACGTCGGATCCCGTCTCTA


 


CCTGCTGCAGGACGACTCGACCTATCAGATCTTCAAGCTTCTGAACCGCGAGTTCAGCTTTG


 


ACGTCGATGTCTCCAATCTTCCGTGCGGATTGAACGGCGCTCTGTACTTTGTCGCCATGGACG


 


CCGACGGCGGCGTGTCCAAGTACCCGAACAACAAGGCTGGTGCCAAGTACGGAACCGGGTA


 


TTGCGACTCCCAATGCCCACGGGACCTCAAGTTCATCGACGGCGAGGCCAACGTCGAGGGCT


 


GGCAGCCGTCTTCGAACAACGCCAACACCGGAATTGGCGACCACGGCTCCTGCTGTGCGGA


 


GATGGATGTCTGGGAAGCAAACAGCATCTCCAATGCGGTCACTCCGCACCCGTGCGACACG


 


CCAGGCCAGACGATGTGCTCTGGAGATGACTGCGGTGGCACATACTCTAACGATCGCTACGC


 


GGGAACCTGCGATCCTGACGGCTGTGACTTCAACCCTTACCGCATGGGCAACACTTCTTTCT


 


ACGGGCCTGGCAAGATCATCGATACCACCAAGCCCTTCACTGTCGTGACGCAGTTCCTCACT


 


GATGATGGTACGGATACTGGAACTCTCAGCGAGATCAAGCGCTTCTACATCCAGAACAGCA


 


ACGTCATTCCGCAGCCCAACTCGGACATCAGTGGCGTGACCGGCAACTCGATCACGACGGA


 


GTTCTGCACTGCTCAGAAGCAGGCCTTTGGCGACACGGACGACTTCTCTCAGCACGGTGGCC


 


TGGCCAAGATGGGAGCGGCCATGCAGCAGGGTATGGTCCTGGTGATGAGTTTGTGGGACGA


 


CTACGCCGCGCAGATGCTGTGGTTGGATTCCGACTACCCGACGGATGCGGACCCCACGACCC


 


CTGGTATTGCCCGTGGAACGTGTCCGACGGACTCGGGCGTCCCATCGGATGTCGAGTCGCAG


 


AGCCCCAACTCCTACGTGACCTACTCGAACATTAAGTTTGGTCCGATCAACTCGACCTTCAC


 


CGCTTCGTGA


 


(SEQ ID NO: 125)



MLRRALLLSSSAILAVKAQQAGTATAENHPPLTWQECTAPGSCTTQNGAVVLDANWRWVHDV



 


NGYTNCYTGNTWDPTYCPDDETCAQNCALDGADYEGTYGVTSSGSSLKLNEVTGSNVGSRLYL


 


LQDDSTYQIFKLLNREFSEDVDVSNLPCGENGALYFVAMDADGGVSKYPNNKAGAKYGTGYCD


 


SQCPRDLKFIDGEANVEGWQPSSNNANTGIGDHGSCCAEMDVWEANSISNAVTPHPCDTPGQT


 


MCSGDDCGGTYSNDRYAGTCDPDGCDFNPYRMGNTSFYGPGKIIDTTKPFTVVTQFLTDDGTDT


 


GTLSEIKRFYIQNSNVIPQPNSDISGVTGNSITTEFCTAQKQAFGDTDDFSQHGGLAKMGAAMQQ


 


GMVLVMSLWDDYAAQMLWLDSDYPTDADPTTPGIARGTCPTDSGVPSDVESQSPNSYVTYSNI


 


KFGPINSTFTAS


 


(SEQ ID NO: 126)



QQAGTATAENHPPLTWQECTAPGSCTTQNGAVVLDANWRWVHDVNGYTNCYTGNTWDPTYC



 


PDDETCAQNCALDGADYEGTYGVTSSGSSLKLNFVTGSNVGSRLYLLQDDSTYQIFKLLNREFSF


 


DVDVSNLPCGLNGALYFVAMDADGGVSKYPNNKAGAKYGTGYCDSQCPRDLKFIDGEANVEG


 


WQPSSNNANTGIGDHGSCCAEMDVWEANSISNAVTPHPCDTPGQTMCSGDDCGGTYSNDRYA


 


GTCDPDGCDFNPYRMGNTSFYGPGKIIDTTKPFTVVTQFLTDDGTDTGTLSEIKRFYIQNSNVIPQ


 


PNSDISGVIGNSITTEFCTAQKQAFGDTDDESQHGGLAKMGAAMQQGMVLVMSLWDDYAAQM


 


LWLDSDYPTDADPTTPGIARGTCPTDSGVPSDVESQSPNSYVTYSNIKFGPINSTFTAS






The polynucleotide (SEQ ID NO:127) and amino acid (SEQ ID NO:128) sequences of wild-type M. thermophila CBH1a are provided below. The signal sequence is shown underlined in SEQ ID NO:128. SEQ ID NO:129 provides the sequence of this CBH1a, without the signal sequence.








(SEQ ID NO: 127)



ATGTACGCCAAGTTCGCGACCCTCGCCGCCCTTGTGGCTGGCGCCGCTGCTCAGAACGCCTG



 


CACTCTGACCGCTGAGAACCACCCCTCGCTGACGTGGTCCAAGTGCACGTCTGGCGGCAGCT


 


GCACCAGCGTCCAGGGTTCCATCACCATCGACGCCAACTGGCGGTGGACTCACCGGACCGAT


 


AGCGCCACCAACTGCTACGAGGGCAACAAGTGGGATACTTCGTACTGCAGCGATGGTCCTTC


 


TTGCGCCTCCAAGTGCTGCATCGACGGCGCTGACTACTCGAGCACCTATGGCATCACCACGA


 


GCGGTAACTCCCTGAACCTCAAGTTCGTCACCAAGGGCCAGTACTCGACCAACATCGGCTCG


 


CGTACCTACCTGATGGAGAGCGACACCAAGTACCAGATGTTCCAGCTCCTCGGCAACGAGTT


 


CACCTTCGATGTCGACGTCTCCAACCTCGGCTGCGGCCTCAATGGCGCCCTCTACTTCGTGTC


 


CATGGATGCCGATGGTGGCATGTCCAAGTACTCGGGCAACAAGGCAGGTGCCAAGTACGGT


 


ACCGGCTACTGTGATTCTCAGTGCCCCCGCGACCTCAAGTTCATCAACGGCGAGGCCAACGT


 


AGAGAACTGGCAGAGCTCGACCAACGATGCCAACGCCGGCACGGGCAAGTACGGCAGCTGC


 


TGCTCCGAGATGGACGTCTGGGAGGCCAACAACATGGCCGCCGCCTTCACTCCCCACCCTTG


 


CACCGTGATCGGCCAGTCGCGCTGCGAGGGCGACTCGTGCGGCGGTACCTACAGCACCGAC


 


CGCTATGCCGGCATCTGCGACCCCGACGGATGCGACTTCAACTCGTACCGCCAGGGCAACAA


 


GACCTTCTACGGCAAGGGCATGACGGTCGACACGACCAAGAAGATCACGGTCGTCACCCAG


 


TTCCTCAAGAACTCGGCCGGCGAGCTCTCCGAGATCAAGCGGTTCTACGTCCAGAACGGCAA


 


GGTCATCCCCAACTCCGAGTCCACCATCCCGGGCGTCGAGGGCAACTCCATCACCCAGGACT


 


GGTGCGACCGCCAGAAGGCCGCCTTCGGCGACGTGACCGACTTCCAGGACAAGGGCGGCAT


 


GGTCCAGATGGGCAAGGCCCTCGCGGGGCCCATGGTCCTCGTCATGTCCATCTGGGACGACC


 


ACGCCGTCAACATGCTCTGGCTCGACTCCACCTGGCCCATCGACGGCGCCGGCAAGCCGGGC


 


GCCGAGCGCGGTGCCTGCCCCACCACCTCGGGCGTCCCCGCTGAGGTCGAGGCCGAGGCCC


 


CCAACTCCAACGTCATCTTCTCCAACATCCGCTTCGGCCCCATCGGCTCCACCGTCTCCGGCC


 


TGCCCGACGGCGGCAGCGGCAACCCCAACCCGCCCGTCAGCTCGTCCACCCCGGTCCCCTCC


 


TCGTCCACCACATCCTCCGGTTCCTCCGGCCCGACTGGCGGCACGGGTGTCGCTAAGCACTA


 


TGAGCAATGCGGAGGAATCGGGTTCACTGGCCCTACCCAGTGCGAGAGCCCCTACACTTGCA


 


CCAAGCTGAATGACTGGTACTCGCAGTGCCTGTAA


 


(SEQ ID NO: 128)



MYAKFATLAALVAGAAAQNACTLTAENHPSLTYSKCTSGGSCTSVQGSITIDANWRWTHRTDS



 


ATNCYEGNKWDTSWCSDGPSCASKCCIDGADYSSTYGITTSGNSLNLKFVTKGQYSTNIGSRTY


 


LMESDTKYQMFQLLGNEFTFDVDVSNLGCGLNGALYFVSMDADGGMSKYSGNKAGAKYGTG


 


YCDSQCPRDLKFINGEANVENWQSSINDANAGTGKYGSCCSEMDVWEANNMAAAFTPFIPCTVI


 


GQSRCEGDSCGGTYSTDRYAGICDPDGCDFNSYRQGNKTFYGKGMTVDTTKKITVVTQFLKNS


 


AGELSELECRFYVQNGKVIPNSESTIPGVEGNSITQDWCDRQKAAFGDVTDFQDKGGMVQMGICA


 


LAGPMVLVMSIWDDHAVNMLWLDSTWPIDGAGKPGAERGACPTTSGVPAEVEAEAPNSNVIFS


 


NIRFGPIGSTVSGLPDGGSGNPNPPVSSSTPVPSSSTTSSGSSGPTGGTGVAKHYEQCGGIGFTGPT


 


QCESPYTCTKLNDWYSQCL


 


(SEQ ID NO: 129)



QNACTLTAENHPSLTYSKCTSGGSCTSVQGSITIDANWRWTHRTDSAINCYEGNKWDTSWCSD



 


GPSCASKCCIDGADYSSTYGITTSGNSLNLKFVTKGQYSTNIGSRTYLMESDTKYQMFQLLGNEF


 


TFDVDVSNLGCGLNGALYFVSMDADGGMSKYSGNKAGAKYGTGYCDSQCPRDLKFINGEANV


 


ENWQSSTNDANAGTGKYGSCCSEMDVWEANNMAAAFTPHPCTVIGQSRCEGDSCGGTYSTDR


 


YAGICDPDGCDFNSYRQGNKTFYGKGMTVDTTKKITVVTQFLKNSAGELSEIKRFYVQNGKVIP


 


NSESTIPGVEGNSITQDWCDRQKAAFGDVTDFQDKGGMVQMGKALAGPMVLVMSIWDDHAVN


 


MLWLDSTWPIDGAGKPGAERGACPTTSGVPAEVEALAPNSNVITSNIRFGPIGSTVSGLPDGGSG


 


NPNPPVSSSTPVPSSSTTSSGSSGPTGGTGVAKHYEQCGGIGFTGPTQCESPYTCTKLNDWYSQCL






The polynucleotide (SEQ ID NO:130) and amino acid (SEQ ID NO:131) sequences of a M. thermophila CBH1a variant (“Variant 145”) are provided below. The signal sequence is shown underlined in SEQ ID NO:131. SEQ ID NO:132 provides the sequence of this CBH1a, without the signal sequence.








(SEQ ID NO: 130)



ATGTACGCCAAGTTCGCGACCCTCGCCGCCCTTGTGGCTGGCGCCGCTGCTCAGAACGCCTG



 


CACTCTGACCGCTGAGAACCACCCCTCGCTGACGTGGTCCAAGTGCACGTCTGGCGGCAGCT


 


GCACCAGCGTCCAGGGTTCCATCACCATCGACGCCAACTGGCGGTGGACTCACCGGACCGAT


 


AGCGCCACCAACTGCTACGAGGGCAACAAGTGGGATACTTCGTGGTGCAGCGATGGTCCTTC


 


TTGCGCCTCCAAGTGCTGCATCGACGGCGCTGACTACTCGAGCACCTATGGCATCACCACGA


 


GCGGTAACTCCCTGAACCTCAAGTTCGTCACCAAGGGCCAGTACTCGACCAACATCGGCTCG


 


CGTACCTACCTGATGGAGAGCGACACCAAGTACCAGATGTTCCAGCTCCTCGGCAACGAGTT


 


CACCTTCGATGTCGACGTCTCCAACCTCGGCTGCGGCCTCAATGGCGCCCTCTACTTCGTGTC


 


CATGGATGCCGATGGTGGCATGTCCAAGTACTCGGGCAACAAGGCAGGTGCCAAGTACGGT


 


ACCGGCTACTGTGATTCTCAGTGCCCCCGCGACCTCAAGTTCATCAACGGCGAGGCCAACGT


 


AGAGAACTGGCAGAGCTCGACCAACGATGCCAACGCCGGCACGGGCAAGTACGGCAGCTGC


 


TGCTCCGAGATGGACGTCTGGGAGGCCAACAACATGGCCGCCGCCTTCACTCCCCACCCTTG


 


CACCGTGATCGGCCAGTCGCGCTGCGAGGGCGACTCGTGCGGCGGTACCTACAGCACCGAC


 


CGCTATGCCGGCATCTGCGACCCCGACGGATGCGACTTCAACTCGTACCGCCAGGGCAACAA


 


GACCTTCTACGGCAAGGGCATGACGGTCGACACGACCAAGAAGATCACGGTCGTCACCCAG


 


TTCCTCAAGAACTCGGCCGGCGAGCTCTCCGAGATCAAGCGGTTCTACGTCCAGAACGGCAA


 


GGTCATCCCCAACTCCGAGTCCACCATCCCGGGCGTCGAGGGCAACTCCATCACCCAGGACT


 


GGTGCGACCGCCAGAAGGCCGCCTTCGGCGACGTGACCGACTTCCAGGACAAGGGCGGCAT


 


GGTCCAGATGGGCAAGGCCCTCGCGGGGCCCATGGTCCTCGTCATGTCCATCTGGGACGACC


 


ACGCCGTCAACATGCTCTGGCTCGACTCCACCTGGCCCATCGACGGCGCCGGCAAGCCGGGC


 


GCCGAGCGCGGTGCCTGCCCCACCACCTCGGGCGTCCCCGCTGAGGTCGAGGCCGAGGCCC


 


CCAACTCCAACGTCATCTTCTCCAACATCCGCTTCGGCCCCATCGGCTCCACCGTCTCCGGCC


 


TGCCCGACGGCGGCAGCGGCAACCCCAACCCGCCCGTCAGCTCGTCCACCCCGGTCCCCTCC


 


TCGTCCACCACATCCTCCGGTTCCTCCGGCCCGACTGGCGGCACGGGTGTCGCTAAGCACTA


 


TGAGCAATGCGGAGGAATCGGGTTCACTGGCCCTACCCAGTGCGAGAGCCCCTACACTTGCA


 


CCAAGCTGAATGACTGGTACTCGCAGTGCCTGTAA


 


(SEQ ID NO: 131)



MYAKFATLAALVAGAAAQNACTLTAENHPSLTWSKCTSGGSCTSVQGSITIDANWRWTHRTDS



 


ATNCYEGNKWDTSWCSDGPSCASKCCIDGADYSSTYGITTSGNSLNLKFVTKGQYSTNIGSRTY


 


LMESDTKYQMFQLLGNEFTFDVDVSNLGCGLNGALYFVSMDADGGMSKYSGNKAGAKYGTG


 


YCDSQCPRDLKFINGEANVENWQSSTNDANAGTGKYGSCCSEMDVWEANNMAAAFTPFIPCTVI


 


GQSRCEGDSCGGTYSTDRYAGICDPDGCDFNSYRQGNKTFYGKGMTVDTTKKITVVTQFLKNS


 


AGELSEIKRFYVQNGKVIPNSESTIPGVEGNSITQDWCDRQKAAFGDVTDFQDKGGMVQMGKA


 


LAGPMVLVMSIWDDHAVNMLWLDSTWPIDGAGKPGAERGACPTTSGVPAEVEAEAPNSNVIFS


 


NIRFGPIGSTVSGLPDGGSGNPNPPVSSSTPVPSSSTTSSGSSGPTGGTGVAKHYEQCGGIGFTGPT


 


QCESPYTCTKLNDWYSQCL


 


(SEQ ID NO:  132)



QNACTLTAENHPSLTWSKCTSGGSCTSVQGSITIDANWRWTHRTDSATNCYEGNKWDTSWCSD



 


GPSCASKCCIDGADYSSTYGITTSGNSLNLKFVTKGQYSTNIGSRTYLMESDTKYQMFQLLGNEF


 


TFDVDVSNLGCGLNGALYFVSMDADGGMSKYSGNKAGAKYGTGYCDSQCPRDLKFINGEANV


 


ENWQSSTNDANAGTGKYGSCCSEMDVWEANNMAAAFTPHPCTVIGQSRCEGDSCGGTYSTDR


 


YAGICDPDGCDFNSYRQGNKTFYGKGMTVDTTKKITVVTQFLKNSAGELSEIKRFYVQNGKVIP


 


NSESTIPGVEGNSITQDWCDRQKAAFGDVTDFQDKGGMVQMGICALAGPMVLVMSIWDDHAVN


 


MLWLDSTWPIDGAGKPGAERGACPTTSGVPAEVEAEAPNSNVIHNERFGPIGSTVSGLPDGGSG


 


NPNPPVSSSTPVPSSSTTSSGSSGPTGGTGVAKHYEQCGGIGFTGPTQCESPYTCTKLNDWYSQCL






The polynucleotide (SEQ ID NO:133) and amino acid (SEQ ID NO:134) sequences of a M. thermophila CBH1a variant (“Variant 983”) are provided below. The signal sequence is shown underlined in SEQ ID NO:134. SEQ ID NO:135 provides the sequence of this CBH1a variant, without the signal sequence.








(SEQ ID NO: 133)



ATGTACGCCAAGTTCGCGACCCTCGCCGCCCTTGTGGCTGGCGCCGCTGCTCAGAACGCCTG



 


CACTCTGAACGCTGAGAACCACCCCTCGCTGACGTGGTCCAAGTGCACGTCTGGCGGCAGCT


 


GCACCAGCGTCCAGGGITCCATCACCATCGACGCCAACTGGCGGTGGACTCACCGGACCGAT


 


AGCGCCACCAACTGCTACGAGGGCAACAAGTGGGATACTTCGTACTGCAGCGATGGTCCTTC


 


TTGCGCCTCCAAGTGCTGCATCGACGGCGCTGACTACTCGAGCACCTATGGCATCACCACGA


 


GCGGTAACTCCCTGAACCTCAAGTTCGTCACCAAGGGCCAGTACTCGACCAACATCGGCTCG


 


CGTACCTACCTGATGGAGAGCGACACCAAGTACCAGATGTTCCAGCTCCTCGGCAACGAGTT


 


CACCTTCGATGTCGACGTCTCCAACCTCGGCTGCGGCCTCAATGGCGCCCTCTACTTCGTGTC


 


CATGGATGCCGATGGTGGCATGTCCAAGTACTCGGGCAACAAGGCAGGTGCCAAGTACGGT


 


ACCGGCTACTGTGATTCTCAGTGCCCCCGCGACCTCAAGTTCATCAACGGCGAGGCCAACGT


 


AGAGAACTGGCAGAGCTCGACCAACGATGCCAACGCCGGCACGGGCAAGTACGGCAGCTGC


 


TGCTCCGAGATGGACGTCTGGGAGGCCAACAACATGGCCGCCGCCTTCACTCCCCACCCTTG


 


CACCGTGATCGGCCAGTCGCGCTGCGAGGGCGACTCGTGCGGCGGTACCTACAGCACCGAC


 


CGCTATGCCGGCATCTGCGACCCCGACGGATGCGACTTCAACTCGTACCGCCAGGGCAACAA


 


GACCTTCTACGGCAAGGGCATGACGGTCGACACGACCAAGAAGATCACGGTCGTCACCCAG


 


TTCCTCAAGAACTCGGCCGGCGAGCTCTCCGAGATCAAGCGOTTCTACGTCCAGAACGGCAA


 


GGTCATCCCCAACTCCGAGTCCACCATCCCGGGCGTCGAGGGCAACTCCATCACCCAGGAGT


 


ACTGCGACCGCCAGAAGGCCGCCTTCGGCGACGTGACCGACTTCCAGGACAAGGGCGGCAT


 


GGTCCAGATGGGCAAGGCCCTCGCGGGGCCCATGGTCCTCGTCATGTCCATCTGGGACGACC


 


ACGCCGACAACATGCTCTGGCTCGACTCCACCTGGCCCATCGACGGCGCCGGCAAGCCGGG


 


CGCCGAGCGCGGTGCCTGCCCCACCACCTCGGGCGTCCCCGCTGAGGTCGAGGCCGAGGCC


 


CCCAACTCCAACGTCATCTTCTCCAACATCCGCTTCGGCCCCATCGGCTCCACCGTCTCCGGC


 


CTGCCCGACGGCGGCAGCGGCAACCCCAACCCGCCCGTCAGCTCGTCCACCCCGGTCCCCTC


 


CTCGTCCACCACATCCTCCGGTTCCTCCGGCCCGACTGGCGGCACGGGTGTCGCTAAGCACT


 


ATGAGCAATGCGGAGGAATCGGGTTCACTGGCCCTACCCAGTGCGAGAGCCCCTACACTTGC


 


ACCAAGCTGAATGACTGGTACTCGCAGTGCCTGTAA


 


(SEQ ID NO: 134)



MYAKFATLAALVAGAAAQNACTLNAENHPSLTWSKCTSGGSCTSVQGSITIDANWRWTHRTDS



 


ATNCYEGNKWDTSYCSDGPSCASKCCIDGADYSSTYGITTSGNSLNLKEVTKGQYSTNIGSRTYL


 


MESDTKYQMFQLLGNEFTFDVDVSNLGCGLNGALYFVSMDADGGMSKYSGNKAGAKYGTGY


 


CDSQCPRDLKENGEANVENWQSSTNDANAGTGKYGSCCSEMDVWEANNMAAAFTPHPCTVIG


 


QSRCEGDSCGGTYSTDRYAGICDPDGCDENSYRQGNKTFYGKGMTVDTTKKITVVTQFLKNSA


 


GELSETKREYVQNGKVIPNSESTIPGVEGNSITQEYCDRQKAAFGDVTDFQDKGGMVQMGKALA


 


GPMVLVMSIWDDHADNMLWLDSTWPIDGAGKPGAERGACPTTSGVPAEVEAEAPNSNVIFSNI


 


RFGPIGSTVSGLPDGGSGNPNPPVSSSTPVPSSSTTSSGSSGPTGGTGVAKHYEQCGGIGFTGPTQC


 


ESPYTCTKLNDWYSQCL


 


(SEQ ID NO: 135)



QNACTLNAENHPSLTWSKCTSGGSCTSVQGSITEDANWRWTHRTDSATNCYEGNKWDTSYCSD



 


GPSCASKCCIDGADYSSTYGITTSGNSLNLKFVIKGQYSTNIGSRTYLMESDTKYQMFQLLGNEF


 


TEDVDVSNLGCGLNGALYFVSMDADGGMSKYSGNKAGAKYGTGYCDSQCPRDLKEINGEANV


 


ENWQSSTNDANAGTGKYGSCCSEMDVWEANNMAAAFTPLIPCTVIGQSRCEGDSCGGTYSTDR


 


YAGICDPDGCDFNSYRQGNKTFYGKGMTVDTTKKITVVTQFLKNSAGELSEIKRFYVQNGKVIP


 


NSESTIPGVEGNSITQEYCDRQKAAFGDVTDFQDKGGMVQMGKALAGPMVLVMSIWDDHADN


 


MLWLDSTWPIDGAGKPGAERGACPTTSGVPAEVEALAPNSNVIFSNIREGPIGSTVSGLPDGGSG


 


NPNPPVSSSTPVPSSSTTSSGSSGPTGGTGVAKHYEQCGGIGFTGPTQCESPYTCTKLNDWYSQCL






The polynucleotide (SEQ ID NO:136) and amino acid (SEQ ID NO:137) sequences of wild-type M. thermophila CBH2b are provided below. The signal sequence is shown underlined in SEQ ID NO:137. SEQ ID NO:138 provides the sequence of this CBH2b, without the signal sequence.








(SEQ ID NO: 136)



ATGGCCAAGAAGCTTTTCATCACCGCCGCGCTTGCGGCTGCCGTGTTGGCGGCCCCCGTCAT



 


TGAGGAGCGCCAGAACTGCGGCGCTGTGTGGACTCAATGCGGCGGTAACGGGTGGCAAGGT


 


CCCACATGCTGCGCCTCGGGCTCGACCTGCGTTGCGCAGAACGAGTGGTACTCTCAGTGCCT


 


GCCCAACAGCCAGGTGACGAGTTCCACCACTCCGTCGTCGACTTCCACCTCGCAGCGCAGCA


 


CCAGCACCTCCAGCAGCACCACCAGGAGCGGCAGCTCCTCCTCCTCCTCCACCACGCCCCCG


 


CCCGTCTCCAGCCCCGTGACCAGCATTCCCGGCGGTGCGACCTCCACGGCGAGCTACTCTGG


 


CAACCCCTTCTCGGGCGTCCGGCTCTTCGCCAACGACTACTACAGGTCCGAGGTCCACAATC


 


TCGCCATTCCTAGCATGACTGGTACTCTGGCGGCCAAGGCTTCCGCCGTCGCCGAAGTCCCT


 


AGCTTCCAGTGGCTCGACCGGAACGTCACCATCGACACCCTGATGGTCCAGACTCTGTCCCA


 


GGTCCGGGCTCTCAATAAGGCCGGTGCCAATCCTCCCTATGCTGCCCAACTCGTCGTCTACG


 


ACCTCCCCGACCGTGACTGTGCCGCCGCTGCGTCCAACGGCGAGTTTTCGATTGCAAACGGC


 


GGCGCCGCCAACTACAGGAGCTACATCGACGCTATCCGCAAGCACATCATTGAGTACTCGG


 


ACATCCGGATCATCCTGGTTATCGAGCCCGACTCGATGGCCAACATGGTGACCAACATGAAC


 


GTGGCCAAGTGCAGCAACGCCGCGTCGACGTACCACGAGTTGACCGTGTACGCGCTCAAGC


 


AGCTGAACCTGCCCAACGTCGCCATGTATCTCGACGCCGGCCACGCCGGCTGGCTCGGCTGG


 


CCCGCCAACATCCAGCCCGCCGCCGAGCTGTTTGCCGGCATCTACAATGATGCCGGCAAGCC


 


GGCTGCCGTCCGCGGCCTGGCCACTAACGTCGCCAACTACAACGCCTGGAGCATCGCTTCGG


 


CCCCGTCGTACACGTCGCCTAACCCTAACTACGACGAGAAGCACTACATCGAGGCCTTCAGC


 


CCGCTCTTGAACTCGGCCGGCTTCCCCGCACGCTTCATTGTCGACACTGGCCGCAACGGCAA


 


ACAACCTACCGGCCAACAACAGTGGGGTGACTGGTGCAATGTCAAGGGCACCGGCTTTGGC


 


GTGCGCCCGACGGCCAACACGGGCCACGAGCTGGTCGATGCCTTTGTCTGGGTCAAGCCCGG


 


CGGCGAGTCCGACGGCACAAGCGACACCAGCGCCGCCCGCTACGACTACCACTGCGGCCTG


 


TCCGATGCCCTGCAGCCTGCCCCCGAGGCTGGACAGTGGTTCCAGGCCTACTTCGAGCAGCT


 


GCTCACCAACGCCAACCCGCCCTTCTAA


 


(SEQ ID NO: 137)



MAKKEFITAALAAAVLAAPVIEERQNCGAVWTQCGGNGWQGPTCCASGSTCVAQNEWYSQCL



 


PNSQVTSSTTPSSTSTSQRSTSTSSSTTRSGSSSSSSTTPPPVSSPVTSIPGGATSTASYSGNPFSGVRL


 


FANDYYRSEVHNLAIPSMTGTLAAKASAVAEVPSFQWLDRNVTIDTLMVQTESQVRALNKAGA


 


NPPYAAQLVVYDLPDRDCAAAASNGEFSIANGGAANYRSYIDAIRKHIIEYSDIRIILVIEPDSMAN


 


MVTNMNVAKCSNAASTYHELTVYALKQENLPNVAMYLDAGHAGWEGWPANIQPAAELFAGI


 


YNDAGKPAAVRGLATNVANYNAWSIASAPSYTSPNPNYDEKHYIEAFSPLLNSAGFPARFIVDTG


 


RNGKQPTGQQQWGDWCNVKGTGEGVRPTANTGHELVDAFVWVKPGGESDGTSDTSAARYDY


 


HCGLSDALQPAPEAGQWFQAYFEQLLTNANPPF


 


(SEQ ID NO: 138)



APVIEERQNCGAVWTQCGGNGWQGPTCCASGSTCVAQNEWYSQCLPNSQVTSSTTPSSTSTSQR



 


STSTSSSTTRSGSSSSSSTTPPPVSSPVTSIPGGATSTASYSGNPFSGVRLFANDYYRSEVHNLAIPS


 


MTGTLAAKASAVAEVPSFQWLDRNVTIDTLMVQTLSQVRALNKAGANPPYAAQLVVYDLPDR


 


DCAAAASNGEFSIANGGAANYRSYIDAIRKHIIEYSDIRIILVIEPDSMANMVTNMNVAKCSNAAS


 


TYHELTVYALKQLNLPNVAMYLDAGHAGWLGWPANIQPAAELFAGIYNDAGKPAAVRGLATN


 


VANYNAWSIASAPSYTSPNPNYDEKHYIEAFSPLLNSAGFPARFIVDTGRNGKQPTGQQQWGDW


 


CNVKGTGEGVRPTANTGHELVDAFVWVKPGGESDGTSDTSAARYDYHCGLSDALQPAPEAGQ


 


WFQAYFEQLLTNANPPF






The polynucleotide (SEQ ID NO:139) and amino acid (SEQ ID NO:140) sequences of a M. thermophila CBH2b variant (“Variant 196”) are provided below. The signal sequence is shown underlined in SEQ ID NO:140. SEQ ID NO:141 provides the sequence of this CBH2b variant, without the signal sequence.








(SEQ ID NO: 139)



ATGGCCAAGAAGCTTTTCATCACCGCCGCGCTTGCGGCTGCCGTGTTGGCGGCCCCCGTCAT



 


TGAGGAGCGCCAGAACTGCGGCGCTGTGTGGACTCAATGCGGCGGTAACGGGTGGCAAGGT


 


CCCACATGCTGCGCCTCGGGCTCGACCTGCGTTGCGCAGAACGAGTGGTACTCTCAGTGCCT


 


GCCCAACAGCCAGGTGACGAGTTCCACCACTCCGTCGTCGACTTCCACCTCGCAGCGCAGCA


 


CCAGCACCTCCAGCAGCACCACCAGGAGCGGCAGCTCCTCCTCCTCCTCCACCACGCCCACC


 


CCCGTCTCCAGCCCCGTGACCAGCATTCCCGGCGGTGCGACCTCCACGGCGAGCTACTCTGG


 


CAACCCCTTCTCGGGCGTCCGGCTCTTCGCCAACGACTACTACAGGTCCGAGGTCCACAATC


 


TCGCCATTCCTAGCATGACTGGTACTCTGGCGGCCAAGGCTTCCGCCGTCGCCGAAGTCCCT


 


AGCTTCCAGTGGCTCGACCGGAACGTCACCATCGACACCCTGATGGTCCCGACTCTGTCCCG


 


CGTCCGGGCTCTCAATAAGGCCGGTGCCAATCCTCCCTATGCTGCCCAACTCGTCGTCTACG


 


ACCTCCCCGACCGTGACTGTGCCGCCGCTGCGTCCAACGGCGAGTTTTCGATTGCAAACGGC


 


GGCGCCGCCAACTACAGGAGCTACATCGACGCTATCCGCAAGCACATCATTGAGTACTCGG


 


ACATCCGGATCATCCTGGTTATCGAGCCCGACTCGATGGCCAACATGGTGACCAACATGAAC


 


GTGGCCAAGTGCAGCAACGCCGCGTCGACGTACCACGAGTTGACCGTGTACGCGCTCAAGC


 


AGCTGAACCTGCCCAACGTCGCCATGTATCTCGACGCCGGCCACGCCGGCTGGCTCGGCTGG


 


CCCGCCAACATCCAGCCCGCCGCCGAGCTGTTTGCCGGCATCTACAATGATGCCGGCAAGCC


 


GGCTGCCGTCCGCGGCCTGGCCACTAACGTCGCCAACTACAACGCCTGGAGCATCGCTTCGG


 


CCCCGTCGTACACGTCGCCTAACCCTAACTACGACGAGAAGCACTACATCGAGGCCTTCAGC


 


CCGCTCTTGAACTCGGCCGGCTTCCCCGCACGCTTCATTGTCGACACTGGCCGCAACGGCAA


 


ACAACCTACCGGCCAACAACAGTGGGGTGACTGGTGCAATGTCAAGGGCACCGGCTTTGGC


 


GTGCGCCCGACGGCCAACACGGGCCACGAGCTGGTCGATGCCTTTGTCTGGGTCAAGCCCGG


 


CGGCGAGTCCGACGGCACAAGCGACACCAGCGCCGCCCGCTACGACTACCACTGCGGCCTG


 


TCCGATGCCCTGCAGCCTGCCCCCGAGGCTGGACAGTGGTTCCAGGCCTACTTCGAGCAGCT


 


GCTCACCAACGCCAACCCGCCCTTCTAA


 


(SEQ ID NO: 140)



MAKKLFITAALAAAVLAAPVIEERQNCGAVWTQCGGNGWQGPTCCASGSTCVAQNEWYSQCL



 


PNSQVTSSTTPSSTSTSQRSTSTSSSTTRSGSSSSSSTTPTPVSSPVTSIPGGATSTASYSGNPFSGVR


 


LFANDYYRSEVHNLAIPSMTGTLAAKASAVAEVPSFQWLDRNVTIDTLMVPTLSRVRALNKAG


 


ANPPYAAQLVVYDLPDRDCAAAASNGEFSIANGGAANYRSYIDAIRKHIIEYSDIRIILVIEPDSMA


 


NMVTNMNVAKCSNAASTYHELTVYALKQLNLPNVAMYLDAGHAGWLGWPANIQPAAELFAG


 


IYNDAGKPAAVRGLATNVANYNAWSIASAPSYTSPNPNYDEKHYIEAFSPLLNSAGFPARFIVDT


 


GRNGKQPTGQQQWGDWCNVKGTGFGVRPTANTGHELVDAFVWVKPGGESDGTSDTSAARYD


 


YHCGLSDALQPAPEAGQWFQAYFEQLLTNANPPF


 


(SEQ ID NO: 141)



APVIEERQNCGAVWTQCGGNGWQGPTCCASGSTCVAQNEWYSQCLPNSQVTSSTTPSSTSTSQR



 


STSTSSSTTRSGSSSSSSTTPTPVSSPVTSIPGGATSTASYSGNPFSGVRLFANDYYRSEVHNLAIPS


 


MTGTLAAKASAVAEVPSFQWLDRNVTIDTLMVPTLSRVRALNKAGANPPYAAQLVVYDLPDRD


 


CAAAASNGEFSIANGGAANYRSYIDAIRKHIIEYSDIRIILVIEPDSMANMVTNMNVAKCSNAAST


 


YHELTVYALKQLNLPNVAMYLDAGHAGWEGWPANIQPAAELFAGIYNDAGKPAAVRGLATNV


 


ANYNAWSIASAPSYTSPNPNYDEKHYIEAFSPLLNSAGFPARFIVDTGRNGKQPTGQQQWGDWC


 


NVKGTGFGVRPTANTGHELVDAFVWVKPGGESDGTSDTSAARYDYHCGLSDALQPAPEAGQW


 


FQAYFEQLLTNANPPF






The polynucleotide (SEQ ID NO:142) and amino acid (SEQ ID NO:143) sequences of a M. thermophila CBH2b variant (“Variant 287”) are provided below. The signal sequence is shown underlined in SEQ ID NO:143. SEQ ID NO:144 provides the sequence of this CBH2b variant, without the signal sequence.








(SEQ ID NO: 142)



ATGGCCAAGAAGCTTTTCATCACCGCCGCGCTTGCGGCTGCCGTGTTGGCGGCCCCCGTCAT



 


TGAGGAGCGCCAGAACTGCGGCGCTGTGTGGACTCAATGCGGCGGTAACGGGTGGCAAGGT


 


CCCACATGCTGCGCCTCGGGCTCGACCTGCGTTGCGCAGAACGAGTGGTACTCTCAGTGCCT


 


GCCCAACAGCCAGGTGACGAGTTCCACCACTCCGTCGTCGACTTCCACCTCGCAGCGCAGCA


 


CCAGCACCTCCAGCAGCACCACCAGGAGCGGCAGCTCCTCCTCCTCCTCCACCACGCCCCCG


 


CCCGTCTCCAGCCCCGTGACCAGCATTCCCGGCGGTGCGACCTCCACGGCGAGCTACTCTGG


 


CAACCCCTTCTCGGGCGTCCGGCTCTTCGCCAACGACTACTACAGGTCCGAGGTCCACAATC


 


TCGCCATTCCTAGCATGACTGGTACTCTGGCGGCCAAGGCTTCCGCCGTCGCCGAAGTCCCT


 


AGCTTCCAGTGGCTCGACCGGAACGTCACCATCGACACCCTGATGGTCCCGACTCTGTCCCG


 


CGTCCGGGCTCTCAATAAGGCCGGTGCCAATCCTCCCTATGCTGCCCAACTCGTCGTCTACG


 


ACCTCCCCGACCGTGACTGTGCCGCCGCTGCGTCCAACGGCGAGTTTTCGATTGCAAACGGC


 


GGCGCCGCCAACTACAGGAGCTACATCGACGCTATCCGCAAGCACATCAAGGAGTACTCGG


 


ACATCCGGATCATCCTGGTTATCGAGCCCGACTCGATGGCCAACATGGTGACCAACATGAAC


 


GTGGCCAAGTGCAGCAACGCCGCGTCGACGTACCACGAGTTGACCGTGTACGCGCTCAAGC


 


AGCTGAACCTGCCCAACGTCGCCATGTATCTCGACGCCGGCCACGCCGGCTGGCTCGGCTGG


 


CCCGCCAACATCCAGCCCGCCGCCGAGCTGTTTGCCGGCATCTACAATGATGCCGGCAAGCC


 


GGCTGCCGTCCGCGGCCTGGCCACTAACGTCGCCAACTACAACGCCTGGAGCATCGCTTCGG


 


CCCCGTCGTACACGTCGCCTAACCCTAACTACGACGAGAAGCACTACATCGAGGCCTTCAGC


 


CCGCTCTTGAACGACGCCGGCTTCCCCGCACGCTTCATTGTCGACACTGGCCGCAACGGCAA


 


ACAACCTACCGGCCAACAACAGTGGGGTGACTGGTGCAATGTCAAGGGCACCGGCTTTGGC


 


GTGCGCCCGACGGCCAACACGGGCCACGAGCTGGTCGATGCCTTTGTCTGGGTCAAGCCCGG


 


CGGCGAGTCCGACGGCACAAGCGACACCAGCGCCGCCCGCTACGACTACCACTGCGGCCTG


 


TCCGATGCCCTGCAGCCTGCCCCCGAGGCTGGACAGTGGTTCCAGGCCTACTTCGAGCAGCT


 


GCTCACCAACGCCAACCCGCCCTTCTAA


 


(SEQ ID NO: 143)



MAKKLFITAALAAAVLAAPVIEERQNCGAVWTQCGGNGWQGPTCCASGSTCVAQNEWYSQCL



 


PNSQVTSSTTPSSTSTSQRSTSTSSSTTRSGSSSSSSTTPPPVSSPVTSIPGGATSTASYSGNPFSGVRL


 


FANDYYRSEVHNLAIPSMTGTLAAKASAVAEVPSFQWLDRNVTIDTLMVPTLSRVRALNKAGA


 


NPPYAAQLVVYDLPDRDCAAAASNGEFSIANGGAANYRSYIDAIRKHIKEYSDIRIILVIEPDSMA


 


NMVTNMNVAKCSNAASTYHELTVYALKQLNLPNVAMYLDAGHAGWLGWPANIQPAAELFAG


 


IYNDAGKPAAVRGLATNVANYNAWSIASAPSYTSPNPNYDEKHYIEAFSPLLNDAGFPARFIVDT


 


GRNGKQPTGQQQWGDWCNVKGTGFGVRPTANTGHELVDAFVWVKPGGESDGTSDTSAARYD


 


YHCGLSDALQPAPEAGQWFQAYFEQLLTNANPPF


 


(SEQ ID NO: 144)



APVIEERQNCGAVWTQCGGNGWQGPTCCASGSTCVAQNEWYSQCLPNSQVTSSTTPSSTSTSQR



 


STSTSSSTTRSGSSSSSSTTPPPVSSPVTSIPGGATSTASYSGNPFSGVRLFANDYYRSEVHNLAIPS


 


MTGTLAAKASAVAEVPSFQWLDRNVTIDTLMVPTLSRVRALNKAGANPPYAAQLVVYDLPDRD


 


CAAAASNGEFSIANGGAANYRSYIDAERKHIKEYSDIRIILVIEPDSMANMVTNMNVAKCSNAAS


 


TYHELTVYALKQLNLPNVAMYLDAGHAGWLGWPANIQPAAELFAGIYNDAGKPAAVRGLATN


 


VANYNAWSIASAPSYTSPNPNYDEKHYIEAFSPLLNDAGFPARFIVDTGRNGKQPTGQQQWGDW


 


CNVKGTGFGVRPTANTGHELVDAFVWVKPGGESDGTSDTSAARYDYHCGLSDALQPAPEAGQ


 


WFQAYFEQLLTNANPPF






The polynucleotide (SEQ ID NO:145) and amino acid (SEQ ID NO:146) sequences of a M. thermophila CBH2b variant (“Variant 962”) are provided below. The signal sequence is shown underlined in SEQ ID NO:146. SEQ ID NO:147 provides the sequence of this CBH2b variant, without the signal sequence.








(SEQ ID NO: 145)



ATGGCCAAGAAGCTTTTCATCACCGCCGCGCTTGCGGCTGCCGTGTTGGCGGCCCCCGTCAT



 


TGAGGAGCGCCAGAACTGCGGCGCTGTGTGGACTCAATGCGGCGGTAACGGGTGGCAAGGT


 


CCCACATGCTGCGCCTCGGGCTCGACCTGCGTTGCGCAGAACGAGTGGTACTCTCAGTGCCT


 


GCCCAACAGCCAGGTGACGAGTTCCACCACTCCGTCGTCGACTTCCACCTCGCAGCGCAGCA


 


CCAGCACCTCCAGCAGCACCACCAGGAGCGGCAGCTCCTCCTCCTCCTCCACCACGCCCACC


 


CCCGTCTCCAGCCCCGTGACCAGCATTCCCGGCGGTGCGACCTCCACGGCGAGCTACTCTGG


 


CAACCCCTTCTCGGGCGTCCGGCTCTTCGCCAACGACTACTACAGGTCCGAGGTCATGAATC


 


TCGCCATTCCTAGCATGACTGGTACTCTGGCGGCCAAGGCTTCCGCCGTCGCCGAAGTCCCT


 


AGCTTCCAGTGGCTCGACCGGAACGTCACCATCGACACCCTGATGGTCACCACTCTGTCCCA


 


GGTCCGGGCTCTCAATAAGGCCGGTGCCAATCCTCCCTATGCTGCCCAACTCGTCGTCTACG


 


ACCTCCCCGACCGTGACTGTGCCGCCGCTGCGTCCAACGGCGAGTTTTCGATTGCAAACGGC


 


GGCAGCGCCAACTACAGGAGCTACATCGACGCTATCCGCAAGCACATCATTGAGTACTCGG


 


ACATCCGGATCATCCTGGTTATCGAGCCCGACTCGATGGCCAACATGGTGACCAACATGAAC


 


GTGGCCAAGTGCAGCAACGCCGCGTCGACGTACCACGAGTTGACCGTGTACGCGCTCAAGC


 


AGCTGAACCTGCCCAACGTCGCCATGTATCTCGACGCCGGCCACGCCGGCTGGCTCGGCTGG


 


CCCGCCAACATCCAGCCCGCCGCCGAGCTGTTTGCCGGCATCTACAATGATGCCGGCAAGCC


 


GGCTGCCGTCCGCGGCCTGGCCACTAACGTCGCCAACTACAACGCCTGGAGCATCGCTTCGG


 


CCCCGTCGTACACGCAGCCTAACCCTAACTACGACGAGAAGCACTACATCGAGGCCTTCAGC


 


CCGCTCTTGAACTCGGCCGGCTTCCCCGCACGCTTCATTGTCGACACTGGCCGCAACGGCAA


 


ACAACCTACCGGCCAACAACAGTGGGGTGACTGGTGCAATGTCAAGGGCACCGGCTTTGGC


 


GTGCGCCCGACGGCCAACACGGGCCACGAGCTGGTCGATGCCTTTGTCTGGGTCAAGCCCGG


 


CGGCGAGTCCGACGGCACAAGCGACACCAGCGCCGCCCGCTACGACTACCACTGCGGCCTG


 


TCCGATGCCCTGCAGCCTGCCCCCGAGGCTGGACAGTGGTTCCAGGCCTACTTCGAGCAGCT


 


GCTCACCAACGCCAACCCGCCCTTCTAA


 


(SEQ ID NO: 146)



MAKKLFITAALAAAVLAAPVIEERQNCGAVWTQCGGNGWQGPTCCASGSTCVAQNEWYSQCL



 


PNSQVTSSTTPSSTSTSQRSTSTSSSTTRSGSSSSSSTTPTPVSSPVTSIPGGATSTASYSGNPFSGVR


 


LFANDYYRSEVMNLAIPSMTGTLAAKASAVAEVPSFQWLDRNVTIDTLMVTTLSQVRALNKAG


 


ANPPYAAQLVVYDLPDRDCAAAASNGEFSIANGGSANYRSYIDAIRKHIIEYSDIRIILVIEPDSMA


 


NMVTNMNVAKCSNAASTYHELTVYALKQLNLPNVAMYLDAGHAGWLGWPANIQPAAELFAG


 


IYNDAGKPAAVRGLATNVANYNAWSIASAPSYTQPNPNYDEKHYIEAFSPLINSAGFPARFIVDT


 


GRNGKQPTGQQQWGDWCNVKGTGFGVRPTANTGHELVDAFVWVKPGGESDGTSDTSAARYD


 


YHCGLSDALQPAPEAGQWFQAYFEQLLTNANPPF


 


(SEQ ID NO: 147)



APVIEERQNCGAVWTQCGGNGWQGPTCCASGSTCVAQNEWYSQCLPNSQVTSSTTPSSTS



 


TSQRSTSTSSSTTRSGSSSSSSTTPTPVSSPVTSIPGGATSTASYSGNPFSGVRLFANDY


 


YRSEVMNLAIPSMTGTLAAKASAVAEVPSFQWLDRNVTIDTLMVTTLSQVRALNKAGANP


 


PYAAQLVVYDLPDRDCAAAASNGEFSIANGGSANYRSYIDAIRKHUIEYSDIRIILVIEP


 


DSMANMVTNMNVAKCSNAASTYHELTVYALKQLNLPNVAMYLDAGHAGWLGWPANIQPAA


 


ELFAGIYNDAGKPAAVRGLATNVANYNAWSIASAPSYTQPNPNYDEKHYIEAFSPLLNSA


 


GFPARFIVDTGRNGKQPTGQQQWGDWCNVKGTGFGVRPTANTGHELVDAFVWVKPGGESD


 


GTSDTSAARYDYHCGLSDALQPAPEAGQWFQAYFEQLLTNANPPF






The polynucleotide (SEQ ID NO:148) and amino acid (SEQ ID NO:149) sequences of another wild-type M. thermophila xylanase (“Xyl3”) are provided below. The signal sequence is shown underlined in SEQ ID NO:149. SEQ ID NO:150 provides the sequence of this xylanase without the signal sequence.








(SEQ ID NO: 148)



ATGCACTCCAAAGCTTTCTTGGCAGCGCTTCTTGCGCCTGCCGTCTCAGGGCAACTGAACGA



 


CCTCGCCGTCAGGGCTGGACTCAAGTACTTTGGTACTGCTCTTAGCGAGAGCGTCATCAACA


 


GTGATACTCGGTATGCTGCCATCCTCAGCGACAAGAGCATGTTCGGCCAGCTCGTCCCCGAG


 


AATGGCATGAAGTGGGATGCTACTGAGCCGTCCCGTGGCCAGTTCAACTACGCCTCGGGCGA


 


CATCACGGCCAACACGGCCAAGAAGAATGGCCAGGGCATGCGTTGCCACACCATGGTCTGG


 


TACAGCCAGCTCCCGAGCTGGGTCTCCTCGGGCTCGTGGACCAGGGACTCGCTCACCTCGGT


 


CATCGAGACGCACATGAACAACGTCATGGGCCACTACAAGGGCCAATGCTACGCCTGGGAT


 


GTCATCAACGAGGCCATCAATGACGACGGCAACTCCTGGCGCGACAACGTCTTTCTCCGGAC


 


CTTTGGGACCGACTACTTCGCCCTGTCCTTCAACCTAGCCAAGAAGGCCGATCCCGATACCA


 


AGCTGTACTACAACGACTACAACCTCGAGTACAACCAGGCCAAGACGGACCGCGCTGTTGA


 


GCTCGTCAAGATGGTCCAGGCCGCCGGCGCGCCCATCGACGGTGTCGGCTTCCAGGGCCACC


 


TCATTGTCGGCTCGACCCCGACGCGCTCGCAGCTGGCCACCGCCCTCCAGCGCTTCACCGCG


 


CTCGGCCTCGAGGTCGCCTACACCGAGCTCGACATCCGCCACTCGAGCCTGCCGGCCTCTTC


 


GTCGGCGCTCGCGACCCAGGGCAACGACTTCGCCAACGTGGTCGGCTCTTGCCTCGACACCG


 


CCGGCTGCGTCGGCGTCACCGTCTGGGGCTTCACCGATGCGCACTCGTGGATCCCGAACACG


 


TTCCCCGGCCAGGGCGACGCCCTGATCTACGACAGCAACTACAACAAGAAGCCCGCGTGGA


 


CCTCGATCTCGTCCGTCCTGGCCGCCAAGGCCACCGGCGCCCCGCCCGCCTCGTCCTCCACC


 


ACCCTCGTCACCATCACCACCCCTCCGCCGGCATCCACCACCGCCTCCTCCTCCTCCAGTGCC


 


ACGCCCACGAGCGTCCCGACGCAGACGAGGTGGGGACAGTGCGGCGGCATCGGATGGACGG


 


GGCCGACCCAGTGCGAGAGCCCATGGACCTGCCAGAAGCTGAACGACTGGTACTGGCAGTG


 


CCTG


 


(SEQ ID NO: 149)



MHSKAFLAALLAPAVSGQLNDLAVRAGLKYFGTALSESVINSDTRYAAILSDKSMFGQLVPENG



 


MKWDATEPSRGQFNYASGDITANTAKKNGQGMRCHTMVWYSQLPSWVSSGSWTRDSLTSVIE


 


THMNNVMGHYKGQCYAWDVINEAINDDGNSWRDNVFLRTFGTDYFALSFNLAKKADPDTKLY


 


YNDYNLEYNQAKTDRAVELVKMVQAAGAPIDGVGFQGHLIVGSTPTRSQLATALQRFTALGLE


 


VAYTELDIRHSSLPASSSALATQGNDFANVVGSCLDTAGCVGVTVWGFTDAHSWIPNTFPGQGD


 


ALIYDSNYNKKPAWTSISSVLAAKATGAPPASSSTTLVTITTPPPASTTASSSSSATPTSVPTQTRW


 


GQCGGIGWTGPTQCESPWTCQKLNDWYWQCL


 


(SEQ ID NO: 150)



QLNDLAVRAGLKYFGTALSESVINSDTRYAAILSDKSMFGQLVPENGMKWDATEPSRGQFNYAS



 


GDITANTAKKNGQGMRCHTMVWYSQLPSWVSSGSWTRDSLTSVIETHMNNVMGHYKGQCYA


 


WDVINEAINDDGNSWRDNVFLRTFGTDYFALSFNLAKKADPDTKLYYNDYNLEYNQAKTDRA


 


VELVKMVQAAGAPIDGVGFQGHLIVGSTPTRSQLATALQRFTALGLEVAYTELDIRHSSLPASSS


 


ALATQGNDFANVVGSCLDTAGCVGVTVWGFTDAHSWIPNTFPGQGDALIYDSNYNKKPAWTSI


 


SSVLAAKATGAPPASSSTTLVTITTPPPASTTASSSSSATPTSVPTQTRWGQCGGIGWTGPTQCESP


 


WTCQKLNDWYWQCL






The polynucleotide (SEQ ID NO:151) and amino acid (SEQ ID NO:152) sequences of a wild-type M. thermophila xylanase (“Xyl 2”) are provided below. The signal sequence is shown underlined in SEQ ID NO:152. SEQ ID NO:153 provides the sequence of this xylanase without the signal sequence.








(SEQ ID NO: 151)



ATGGTCTCGTTCACTCTCCTCCTCACGGTCATCGCCGCTGCGGTGACGACGGCCAGCCCTCTC



 


GAGGTGGTCAAGCGCGGCATCCAGCCGGGCACGGGCACCCACGAGGGGTACTTCTACTCGT


 


TCTGGACCGACGGCCGTGGCTCGGTCGACTTCAACCCCGGGCCCCGCGGCTCGTACAGCGTC


 


ACCTGGAACAACGTCAACAACTGGGTTGGCGGCAAGGGCTGGAACCCGGGCCCGCCGCGCA


 


AGATTGCGTACAACGGCACCTGGAACAACTACAACGTGAACAGCTACCTCGCCCTGTACGG


 


CTGGACTCGCAACCCGCTGGTCGAGTATTACATCGTGGAGGCATACGGCACGTACAACCCCT


 


CGTCGGGCACGGCGCGGCTGGGCACCATCGAGGACGACGGCGGCGTGTACGACATCTACAA


 


GACGACGCGGTACAACCAGCCGTCCATCGAGGGGACCTCCACCTTCGACCAGTACTGGTCCG


 


TCCGCCGCCAGAAGCGCGTCGGCGGCACTATCGACACGGGCAAGCACTTTGACGAGTGGAA


 


GCGCCAGGGCAACCTCCAGCTCGGCACCTGGAACTACATGATCATGGCCACCGAGGGCTAC


 


CAGAGCTCTGGTTCGGCCACTATCGAGGTCCGGGAGGCC


 


(SEQ ID NO: 152)



MVSFTLLLTVIAAAVTTASPLEVVKRGIQPGTGTHEGYFYSFWTDGRGSVDFNPGPRGSYSVTW



 


NNVNNWVGGKGWNPGPPRKIAYNGTWNNYNVNSYLALYGWTRNPLVEYYIVEAYGTYNPSS


 


GTARLGTIEDDGGVYDIYKTTRYNQPSIEGTSTFDQYWSVRRQKRVGGTIDTGKHFDEWKRQGN


 


LQLGTWNYMIMATEGYQSSGSATIEVREA


 


(SEQ ID NO: 153)



MVSFTLLLTVIAAAVTTASPLEVVKRGIQPGTGTHEGYFYSFWTDGRGSVDFNPGPRGSYSVTW



 


NNVNNWVGGKGWNPGPPRKIAYNGTWNNYNVNSYLALYGWTRNPLVEYYIVEAYGTYNPSS


 


GTARLGTIEDDGGVYDIYKTTRYNQPSIEGTSTFDQYWSVRRQKRVGGTIDTGKHFDEWKRQGN


 


LQLGTWNYMIMATEGYQSSGSATIEVREA






The polynucleotide (SEQ ID NO:154) and amino acid (SEQ ID NO:155) sequences of another wild-type M. thermophila xylanase (“Xyl1”) are provided below. The signal sequence is shown underlined in SEQ ID NO:155. SEQ ID NO:156 provides the sequence of this xylanase without the signal sequence.








(SEQ ID NO: 154)



ATGCGTACTCTTACGTTCGTGCTGGCAGCCGCCCCGGTGGCTGTGCTTGCCCAATCTCCTCTG



 


TGGGGCCAGTGCGGCGGTCAAGGCTGGACAGGTCCCACGACCTGCGTTTCTGGCGCAGTATG


 


CCAATTCGTCAATGACTGGTACTCCCAATGCGTGCCCGGATCGAGCAACCCTCCTACGGGCA


 


CCACCAGCAGCACCACTGGAAGCACCCCGGCTCCTACTGGCGGCGGCGGCAGCGGAACCGG


 


CCTCCACGACAAATTCAAGGCCAAGGGCAAGCTCTACTTCGGAACCGAGATCGATCACTACC


 


ATCTCAACAACAATGCCTTGACCAACATTGTCAAGAAAGACTTTGGTCAAGTCACTCACGAG


 


AACAGCTTGAAGTGGGATGCTACTGAGCCGAGCCGCAATCAATTCAACTTTGCCAACGCCGA


 


CGCGGTTGTCAACTTTGCCCAGGCCAACGGCAAGCTCATCCGCGGCCACACCCTCCTCTGGC


 


ACTCTCAGCTGCCGCAGTGGGTGCAGAACATCAACGACCGCAACACCTTGACCCAGGTCATC


 


GAGAACCACGTCACCACCCTTGTCACTCGCTACAAGGGCAAGATCCTCCACTGGGACGTCGT


 


TAACGAGATCTTTGCCGAGGACGGCTCGCTCCGCGACAGCGTCTTCAGCCGCGTCCTCGGCG


 


AGGACTTTGTCGGCATCGCCTTCCGCGCCGCCCGCGCCGCCGATCCCAACGCCAAGCTCTAC


 


ATCAACGACTACAACCTCGACATTGCCAACTACGCCAAGGTGACCCGGGGCATGGTCGAGA


 


AGGTCAACAAGTGGATCGCCCAGGGCATCCCGATCGACGGCATCGGCACCCAGTGCCACCT


 


GGCCGGGCCCGGCGGGTGGAACACGGCCGCCGGCGTCCCCGACGCCCTCAAGGCCCTCGCC


 


GCGGCCAACGTCAAGGAGATCGCCATCACCGAGCTCGACATCGCCGGCGCCTCCGCCAACG


 


ACTACCTCACCGTCATGAACGCCTGCCTCCAGGTCTCCAAGTGCGTCGGCATCACCGTCTGG


 


GGCGTCTCTGACAAGGACAGCTGGAGGTCGAGCAGCAACCCGCTCCTCTTCGACAGCAACT


 


ACCAGCCAAAGGCGGCATACAATGCTCTGATTAATGCCTTGTAA


 


(SEQ ID NO: 155)



MRTLTFVLAAAPVAVLAQSPLWGQCGGQGWTGPTTCVSGAVCQFVNDWYSQCVPGSSNPPTG



 


TTSSTTGSTPAPTGGGGSGTGLHDKFKAKGKLYFGTEIDHYHLNNNALTNIVKKDFGQVTHENS


 


LKWDATEPSRNQFNFANADAVVNFAQANGKLIRGHTLLWHSQLPQWVQNINDRNTLTQVIENH


 


VTTLVTRYKGKILHWDVVNEIFAEDGSLRDSVFSRVLGEDFVGIAFRAARAADPNAKLYINDYN


 


LDIANYAKVTRGMVEKVNKWIAQGIPIDGIGTQCHLAGPGGWNTAAGVPDALKALAAANVKEI


 


AITELDIAGASANDYLTVMNACLQVSKCVGITVWGVSDKDSWRSSSNPLLFDSNYQPKAAYNA


 


LINAL


 


(SEQ ID NO: 156)



QSPLWGQCGGQGWTGPTTCVSGAVCQFVNDWYSQCVPGSSNPPTGTTSSTTGSTPAPTGGGGS



 


GTGLHDKFKAKGKLYEGTEIDHYHLNNNALTNIVKKDFGQVTHENSLKWDATEPSRNQFNFAN


 


ADAVVNFAQANGKLIRGHTLLWHSQLPQWVQNINDRNTLTQVIENHVTTLVTRYKGKILHWDV


 


VNEIFAEDGSLRDSVFSRVLGEDFVGIAFRAARAADPNAKLYINDYNLDIANYAKVTRGMVEKV


 


NKWIAQGIPIDGIGTQCHLAGPGGWNTAAGVPDALKALAAANVKEIAITELDIAGASANDYLTV


 


MNACLQVSKCVGITVWGVSDKDSWRSSSNPLLFDSNYQPKAAYNALINAL






The polynucleotide (SEQ ID NO:157) and amino acid (SEQ ID NO:158) sequences of another wild-type M. thermophila xylanase (“Xyl6”) are provided below. The signal sequence is shown underlined in SEQ ID NO:158. SEQ ID NO:159 provides the sequence of this xylanase without the signal sequence.








(SEQ ID NO: 157)



ATGGTCTCGCTCAAGTCCCTCCTCCTCGCCGCGGCGGCGACGTTGACGGCGGTGACGGCGCG



 


CCCGTTCGACTTTGACGACGGCAACTCGACCGAGGCGCTGGCCAAGCGCCAGGTCACGCCC


 


AACGCGCAGGGCTACCACTCGGGCTACTTCTACTCGTGGTGGTCCGACGGCGGCGGCCAGGC


 


CACCTTCACCCTGCTCGAGGGCAGCCACTACCAGGTCAACTGGAGGAACACGGGCAACTTTG


 


TCGGTGGCAAGGGCTGGAACCCGGGTACCGGCCGGACCATCAACTACGGCGGCTCGTTCAA


 


CCCGAGCGGCAACGGCTACCTGGCCGTCTACGGCTGGACGCACAACCCGCTGATCGAGTACT


 


ACGTGGTCGAGTCGTACGGGACCTACAACCCGGGCAGCCAGGCCCAGTACAAGGGCAGCTT


 


CCAGAGCGACGGCGGCACCTACAACATCTACGTCTCGACCCGCTACAACGCGCCCTCGATCG


 


AGGGCACCCGCACCTTCCAGCAGTACTGGTCCATCCGCACCTCCAAGCGCGTCGGCGGCTCC


 


GTCACCATGCAGAACCACTTCAACGCCTGGGCCCAGCACGGCATGCCCCTCGGCTCCCACGA


 


CTACCAGATCGTCGCCACCGAGGGCTACCAGAGCAGCGGCTCCTCCGACATCTACGTCCAGA


 


CTCACTAG


 


(SEQ ID NO: 158)



MVSLKSLLLAAAATLTAVTARPFDFDDGNSTEALAKRQVTPNAQGYHSGYFYSWWSDGGGQA



 


TFTLLEGSHYQVNWRNTGNFVGGKGWNPGTGRTINYGGSFNPSGNGYLAVYGWTHNPLIEYYV


 


VESYGTYNPGSQAQYKGSFQSDGGTYNIYVSTRYNAPSIEGTRTFQQYWSIRTSKRVGGSVTMQ


 


NHFNAWAQHGMPLGSHDYQIVATEGYQSSGSSDIYVQTH


 


(SEQ ID NO: 159)



RPFDFDDGNSTEALAKRQVTPNAQGYHSGYFYSWWSDGGGQATFTLLEGSHYQVNWRNTGNF



 


VGGKGWNPGTGRTINYGGSFNPSGNGYLAVYGWTHNPLIEYYVVESYGTYNPGSQAQYKGSFQ


 


SDGGTYNIYVSTRYNAPSIEGTRTFQQYWSIRTSKRVGGSVTMQNHFNAWAQHGMPLGSHDYQI


 


VATEGYQSSGSSDIYVQTH






The polynucleotide (SEQ ID NO:160) and amino acid (SEQ ID NO:161) sequences of another wild-type M. thermophila xylanase (“Xyl5”) are provided below. The signal sequence is shown underlined in SEQ ID NO:161. SEQ ID NO:162 provides the sequence of this xylanase, without the signal sequence.








(SEQ ID NO: 160)



ATGGTTACCCTCACTCGCCTGGCGGTCGCCGCGGCGGCCATGATCTCCAGCACTGGCCTGGC



 


TGCCCCGACGCCCGAAGCTGGCCCCGACCTTCCCGACTTTGAGCTCGGGGTCAACAACCTCG


 


CCCGCCGCGCGCTGGACTACAACCAGAACTACAGGACCAGCGGCAACGTCAACTACTCGCC


 


CACCGACAACGGCTACTCGGTCAGCTTCTCCAACGCGGGAGATTTTGTCGTCGGGAAGGGCT


 


GGAGGACGGGAGCCACCAGAAACATCACCTTCTCGGGATCGACACAGCATACCTCGGGCAC


 


CGTGCTCGTCTCCGTCTACGGCTGGACCCGGAACCCGCTGATCGAGTACTACGTGCAGGAGT


 


ACACGTCCAACGGGGCCGGCTCCGCTCAGGGCGAGAAGCTGGGCACGGTCGAGAGCGACGG


 


GGGCACGTACGAGATCTGGCGGCACCAGCAGGTCAACCAGCCGTCGATCGAGGGCACCTCG


 


ACCTTCTGGCAGTACATCTCGAACCGCGTGTCCGGCCAGCGGCCCAACGGCGGCACCGTCAC


 


CCTCGCCAACCACTTCGCCGCCTGGCAGAAGCTCGGCCTGAACCTGGGCCAGCACGACTACC


 


AGGTCCTGGCCACCGAGGGCTGGGGCAACGCCGGCGGCAGCTCCCAGTACACCGTCAGCGG


 


CTGA


 


(SEQ ID NO: 161)



MVTLTRLAVAAAAMESSTGLAAPTPEAGPDLPDFELGVNNLARRALDYNQNYRTSGNVNYSPT



 


DNGYSVSFSNAGDFVVGKGWRTGATRNITFSGSTQHTSGTVLVSVYGWTRNPLIEYYVQEYTSN


 


GAGSAQGEKLGTVESDGGTYEIWRHQQVNQPSIEGTSTFWQYISNRVSGQRPNGGTVTLANHFA


 


AWQKLGLNLGQHDYQVLATEGWGNAGGSSQYTVSG


 


(SEQ ID NO: 162)



APTPEAGPDLPDFELGVNNLARRALDYNQNYRTSGNVNYSPTDNGYSVSFSNAGDFVVGKGWR



 


TGATRNIFFSGSTQHTSGTVLVSVYGWTRNPLIEYYVQEYTSNGAGSAQGEKLGTVESDGGTYEI


 


WRHQQVNQPSIEGTSTFWQYISNRVSGQRPNGGTVTLANHFAAWQKLGLNLGQHDYQVLATE


 


GWGNAGGSSQYTVSG






The polynucleotide (SEQ ID NO:163) and amino acid (SEQ ID NO:164) sequences of a wild-type M. thermophila beta-xylosidase are provided below. The signal sequence is shown underlined in SEQ ID NO:164. SEQ ID NO:165 provides the sequence of this xylanase without the signal sequence.








(SEQ ID NO: 163)



ATGTTCTTCGCTTCTCTGCTGCTCGGTCTCCTGGCGGGCGTGTCCGCTTCACCGGGACACGGG



 


CGGAATTCCACCTTCTACAACCCCATCTTCCCCGGCTTCTACCCCGATCCGAGCTGCATCTAC


 


GTGCCCGAGCGTGACCACACCTTCTTCTGTGCCTCGTCGAGCTTCAACGCCTTCCCGGGCATC


 


CCGATTCATGCCAGCAAGGACCTGCAGAACTGGAAGTTGATCGGCCATGTGCTGAATCGCA


 


AGGAACAGCTTCCCCGGCTCGCTGAGACCAACCGGTCGACCAGCGGCATCTGGGCACCCAC


 


CCTCCGGTTCCATGACGACACCTTCTGGTTGGTCACCACACTAGTGGACGACGACCGGCCGC


 


AGGAGGACGCTTCCAGATGGGACAATATTATCTTCAAGGCAAAGAATCCGTATGATCCGAG


 


GTCCTGGTCCAAGGCCGTCCACTTCAACTTCACTGGCTACGACACGGAGCCTTTCTGGGACG


 


AAGATGGAAAGGTGTACATCACCGGCGCCCATGCTTGGCATGTTGGCCCATACATCCAGCAG


 


GCCGAAGTCGATCTCGACACGGGGGCCGTCGGCGAGTGGCGCATCATCTGGAACGGAACGG


 


GCGGCATGGCTCCTGAAGGGCCGCACATCTACCGCAAAGATGGOTGGTACTACTTGCTGGCT


 


GCTGAAGGGGGGACCGGCATCGACCATATGGTGACCATGGCCCGGTCGAGAAAAATCTCCA


 


GTCCTTACGAGTCCAACCCAAACAACCCCGTGTTGACCAACGCCAACACGACCAGTTACTTT


 


CAAACCGTCGGGCATTCAGACCTGTTCCATGACAGACATGGGAACTGGTGGGCAGTCGCCCT


 


CTCCACCCGCTCCGGTCCAGAATATCTTCACTACCCCATGGGCCGCGAGACCGTCATGACAG


 


CCGTGAGCTGGCCGAAGGACGAGTGGCCAACCTTCACCCCCATATCTGGCAAGATGAGCGG


 


CTGGCCGATGCCTCCTTCGCAGAAGGACATTCGCGGAGTCGGCCCCTACGTCAACTCCCCCG


 


ACCCGGAACACCTGACCTTCCCCCGCTCGGCGCCCCTGCCGGCCCACCTCACCTACTGGCGA


 


TACCCGAACCCGTCCTCCTACACGCCGTCCCCGCCCGGGCACCCCAACACCCTCCGCCTGAC


 


CCCGTCCCGCCTGAACCTGACCGCCCTCAACGGCAACTACGCGGGGGCCGACCAGACCTTCG


 


TCTCGCGCCGGCAGCAGCACACCCTCTTCACCTACAGCGTCACGCTCGACTACGCGCCGCGG


 


ACCGCCGGGGAGGAGGCCGGCGTGACCGCCTTCCTGACGCAGAACCACCACCTCGACCTGG


 


GCGTCGTCCTGCTCCCTCGCGGCTCCGCCACCGCGCCCTCGCTGCCGGGCCTGAGTAGTAGT


 


ACAACTACTACTAGTAGTAGTAGTAGTCGTCCGGACGAGGAGGAGGAGCGCGAGGCGGGCG


 


AAGAGGAAGAAGAGGGCGGACAAGACTTGATGATCCCGCATGTGCGGTTCAGGGGCGAGTC


 


GTACGTGCCCGTCCCGGCGCCCGTCGTGTACCCGATACCCCGGGCCTGGAGAGGCGGGAAG


 


CTTGTGTTAGAGATCCGGGCTTGTAATTCGACTCACTTCTCGTTCCGTGTCGGGCCGGACGGG


 


AGACGGTCTGAGCGGACGGTGGTCATGGAGGCTTCGAACGAGGCCGTTAGCTGGGGCTTTA


 


CTGGAACGCTGCTGGGCATCTATGCGACCAGTAATGGTGGCAACGGAACCACGCCGGCGTA


 


TTTTTCGGATTGGAGGTACACACCATTGGAGCAGTTTAGGGAT


 


(SEQ ID NO: 164)



MFFASLLLGLLAGVSASPGHGRNSTFYNPIFPGFYPDPSCIYVPERDHTFFCASSSFNAFPGIPIHAS



 


KDLQNWKLIGHVLNRKEQLPRLAETNRSTSGIWAPTLRFHDDTFWLVTTLVDDDRPQEDASRW


 


DNIIFKAKNPYDPRSWSKAVHFNFTGYDTEPFWDEDGKVYTTGAHAWHVGPYIQQAEVDLDTG


 


AVGEWRIIWNGTGGMAPEGPHIYRKDGWYYLLAAEGGTGIDHMVTMARSRKISSPYESNPNNP


 


VLTNANTTSYFQTVGHSDLFHDRHGNWWAVALSTRSGPEYLHYPMGRETVMTAVSWPKDEWP


 


TFTPISGKMSGWPMPPSQKDIRGVGPYVNSPDPEHLTFPRSAPLPAHLTYWRYPNPSSYTPSPPGH


 


PNTLRLTPSRLNLTALNGNYAGADQTFVSRRQQHTLFTYSVTLDYAPRTAGEEAGVTAFLTQNH


 


HLDLGVVLLPRGSATAPSLPGLSSSTTTTSSSSSRPDEEEEREAGEEEEEGGQDLMIPHVRFRGESY


 


VPVPAPVVYPIPRAWRGGKLVLEIRACNSTHFSFRVGPDGRRSERTVVMEASNEAVSWGFTGTL


 


LGIYATSNGGNGTTPAYFSDWRYTPLEQFRD


 


(SEQ ID NO: 165)



SPGHGRNSTFYNPIFPGFYPDPSCIYVPERDHTFECASSSFNAFPGIPIHASKDLQNWKLIGHVLNR



 


KEQLPRLAETNRSTSGIWAPTLRFHDDTFWLVTTLVDDDRPQEDASRWDNIIFKAKNPYDPRSW


 


SKAVHFNFTGYDTEPFWDEDGKVYITGAHAWHVGPYIQQAEVDLDTGAVGEWRIIWNGTGGM


 


APEGPHIYRKDGWYYLLAAEGGTGIDHMVTMARSRKISSPYESNPNNPVLTNANTTSYFQTVGH


 


SDLFHDRHGNWWAVALSTRSGPEYLHYPMGRETVMTAVSWPKDEWPTFTPISGKMSGWPMPP


 


SQKDIRGVGPYVNSPDPEHLTFPRSAPLPAHLTYWRYPNPSSYTPSPPGHPNTLRLTPSRLNLTAL


 


NGNYAGADQTFVSRRQQHTLFTYSVTLDYAPRTAGEEAGVTAFLTQNHHLDLGVVLLPRGSAT


 


APSLPGLSSSTTTTSSSSSRPDEEEEREAGEEEEEGGQDLMIPHVRFRGESYVPVPAPVVYPIPRAW


 


RGGKLVLEIRACNSTHFSFRVGPDGRRSERTVVMEASNEAVSWGFTGTLLGIYATSNGGNGTTP


 


AYFSDWRYTPLEQFRD






The polynucleotide (SEQ ID NO:166) and amino acid (SEQ ID NO:167) sequences of a wild-type M. thermophila acetylxylan esterase (“Axe3”) are provided below. The signal sequence is shown underlined in SEQ ID NO:167. SEQ ID NO:168 provides the sequence of this acetylxylan esterase without the signal sequence.








(SEQ ID NO: 166)



ATGAAGCTCCTGGGCAAACTCTCGGCGGCACTCGCCCTCGCGGGCAGCAGGCTGGCTGCCGC



 


GCACCCGGTCTTCGACGAGCTGATGCGGCCGACGGCGCCGCTGGTGCGCCCGCGGGCGGCC


 


CTGCAGCAGGTGACCAACTTTGGCAGCAACCCGTCCAACACGAAGATGTTCATCTACGTGCC


 


CGACAAGCTGGCCCCCAACCCGCCCATCATAGTGGCCATCCACTACTGCACCGGCACCGCCC


 


AGGCCTACTACTCGGGCTCCCCTTACGCCCGCCTCGCCGACCAGAAGGGCTTCATCGTCATC


 


TACCCGGAGTCCCCCTACAGCGGCACCTGTTGGGACGTCTCGTCGCGCGCCGCCCTGACCCA


 


CAACGGCGGCGGCGACAGCAACTCGATCGCCAACATGGTCACCTACACCCTCGAAAAGTAC


 


AATGGCGACGCCAGCAAGGTCTTTGTCACCGGCTCCTCGTCCGGCGCCATGATGACGAACGT


 


GATGGCCGCCGCGTACCCGGAACTGTTCGCGGCAGGAATCGCCTACTCGGGCGTGCCCGCCG


 


GCTGCTTCTACAGCCAGTCCGGAGGCACCAACGCGTGGAACAGCTCGTGCGCCAACGGGCA


 


GATCAACTCGACGCCCCAGGTGTGGGCCAAGATGGTCTTCGACATGTACCCGGAATACGAC


 


GGCCCGCGCCCCAAGATGCAGATCTACCACGGCTCGGCCGACGGCACGCTCAGACCCAGCA


 


ACTACAACGAGACCATCAAGCAGTGGTGCGGCGTCTTCGGCTTCGACTACACCCGCCCCGAC


 


ACCACCCAGGCCAACTCCCCGCAGGCCGGCTACACCACCTACACCTGGGGCGAGCAGCAGC


 


TCGTCGGCATCTACGCCCAGGGCGTCGGACACACGGTCCCCATCCGCGGCAGCGACGACAT


 


GGCCTTCTTTGGCCTGTGA


 


(SEQ ID NO: 167)



MKLLGKLSAALALAGSRLAAAHPVFDELMRPTAPLVRPRAALQQVTNFGSNPSNTKMFIYVPDK



 


LAPNPPIIVAIHYCTGTAQAYYSGSPYARLADQKGFIVIYPESPYSGTCWDVSSRAALTHNGGGDS


 


NSIANMVTYTLEKYNGDASKVFVTGSSSGAMMTNVMAAAYPELFAAGIAYSGVPAGCFYSQSG


 


GTNAWNSSCANGQINSTPQVWAKMVFDMYPEYDGPRPKMQIYHGSADGTLRPSNYNETIKQW


 


CGVFGFDYTRPDTTQANSPQAGYTTYTWGEQQLVGIYAQGVGHTVPIRGSDDMAFFGL


 


(SEQ ID NO: 168)



HPVFDELMRPTAPLVRPRAALQQVTNFGSNPSNTKMFIYVPDKLAPNPPIIVAIHYCTGTAQAYY



 


SGSPYARLADQKGFIVIYPESPYSGTCWDVSSRAALTHNGGGDSNSIANMVTYTLEKYNGDASK


 


VFVTGSSSGAMMTNVMAAAYPELFAAGIAYSGVPAGCFYSQSGGTNAWNSSCANGQINSTPQV


 


WAKMVFDMYPEYDGPRPKMQIYHGSADGTLRPSNYNETIKQWCGVFGFDYTRPDTTQANSPQ


 


AGYTTYTWGEQQLVGIYAQGVGHTVPIRGSDDMAFFGL






The polynucleotide (SEQ ID NO:169) and amino acid (SEQ ID NO:170) sequences of a wild-type M. thermophila ferulic acid esterase (“FAE”) are provided below. The signal sequence is shown underlined in SEQ ID NO:170. SEQ ID NO:171 provides the sequence of this xylanase without the signal sequence








(SEQ ID NO: 169)



ATGATCTCGGTTCCTGCTCTCGCTCTGGCCCTTCTGGCCGCCGTCCAGGTCGTCGAGTCTGCC



 


TCGGCTGGCTGTGGCAAGGCGCCCCCTTCCTCGGGCACCAAGTCGATGACGGTCAACGGCAA


 


GCAGCGCCAGTACATTCTCCAGCTGCCCAACAACTACGACGCCAACAAGGCCCACAGGGTG


 


GTGATCGGGTACCACTGGCGCGACGGATCCATGAACGACGTGGCCAACGGCGGCTTCTACG


 


ATCTGCGGTCCCGGGCGGGCGACAGCACCATCTTCGTTGCCCCCAACGGCCTCAATGCCGGA


 


TGGGCCAACGTGGGCGGCGAGGACATCACCTTTACGGACCAGATCGTAGACATGCTCAAGA


 


ACGACCTCTGCGTGGACGAGACCCAGTTCTTTGCTACGGGCTGGAGCTATGGCGGTGCCATG


 


AGCCATAGCGTGGCTTGTTCTCGGCCAGACGTCTTCAAGGCCGTCGCGGTCATCGCCGGGGC


 


CCAGCTGTCCGGCTGCGCCGGCGGCACGACGCCCGTGGCGTACCTAGGCATCCACGGAGCC


 


GCCGACAACGTCCTGCCCATCGACCTCGGCCGCCAGCTGCGCGACAAGTGGCTGCAGACCA


 


ACGGCTGCAACTACCAGGGCGCCCAGGACCCCGCGCCGGGCCAGCAGGCCCACATCAAGAC


 


CACCTACAGCTGCTCCCGCGCGCCCGTCACCTGGATCGGCCACGGGGGCGGCCACGTCCCCG


 


ACCCCACGGGCAACAACGGCGTCAAGTTTGCGCCCCAGGAGACCTGGGACTTCTTTGATGCC


 


GCCGTCGGAGCGGCCGGCGCGCAGAGCCCGATGACATAA


 


(SEQ ID NO: 170)



MISVPALALALLAAVQVVESASAGCGKAPPSSGTKSMTVNGKQRQYILQLPNNYDANKAHRVV



 


IGYHWRDGSMNDVANGGFYDLRSRAGDSTIFVAPNGLNAGWANVGGEDITFTDQIVDMLKNDL


 


CVDETQFFATGWSYGGAMSHSVACSRPDVFKAVAVIAGAQLSGCAGGTTPVAYLGIHGAADNV


 


LPIDLGRQLRDKWLQTNGCNYQGAQDPAPGQQAHIKTTYSCSRAPVTWIGHGGGHVPDPTGNN


 


GVKFAPQETWDFFDAAVGAAGAQSPMT


 


(SEQ ID NO: 171)



ASAGCGKAPPSSGTKSMTVNGKQRQYILQLPNNYDANKAHRVVIGYHWRDGSMNDVANGGFY



 


DLRSRAGDSTIFVAPNGLNAGWANVGGEDITFTDQIVDMLKNDLCVDETQFFATGWSYGGAMS


 


HSVACSRPDVFKAVAVIAGAQLSGCAGGTTPVAYLGIHGAADNVLPIDLGRQLRDKWLQTNGC


 


NYQGAQDPAPGQQAHIKTTYSCSRAPVTWIGHGGGHVPDPTGNNGVKFAPQETWDFFDAAVG


 


AAGAQSPMT






Example 1
Gene Acquisition and Construction of Expression Vectors
A protein from a strain of M. thermophila having the amino acid sequence provided in SEQ ID NO:2 was previously identified as having GH61 activity. It was designated “GH61a”. FIG. 1 shows the improvement in glucose yield resulting from having GH61a present in a reaction where crystalline cellulose undergoes saccharification by cellulase enzymes that are contained in culture broth from M. thermophila cells.
In this Example, the wild type GH61a gene from M. thermophila was isolated from the genome and the DNA sequence verified. The gene was cloned into a Saccharomyces cerevisiae/M. thermophila shuttle vector pYTDX60 using Pml1 cloning sites, using standard methods known in the art. The signal peptide and gene were under the control of a yeast transcription elongation factor 1 promoter (pTEF1). The vector contained the REP2, rep1 and protein D (partial) origin of replication for S. cerevisiae and a URA3 resistance marker.
The resulting plasmid (pYTDX60-GH61a) was transformed into S. cerevisiae INVSC1 strain and the transformed host cells were grown in Costar 96 deep well plates for GH61a protein production. The GH61a sequence from the transformants were verified as the wild type GH61a DNA sequence (SEQ ID NO:1) and the encoded polypeptide (SEQ ID NO:2).
Example 2
Shake Flask Procedure
A single colony of S. cerevisiae containing a plasmid with the GH61a gene was inoculated into 3 mL synthetic defined-uracil (SD-ura) broth (2 g/L synthetic drop-out minus uracil without yeast nitrogen base (US Biological), 5 g/L ammonium sulfate, 0.1 g/L calcium chloride, 2 mg/L inositol, 0.5 g/L magnesium sulfate, 1 g/L potassium phosphate monobasic (KH.2PO4), 0.1 g/L sodium chloride) containing 6% glucose. Cells were grown overnight (at least 21 hrs) in an incubator at 30° C. with shaking at 250 rpm. Then, 500 μL of the overnight culture was diluted into either 50 mL SD-ura medium or modified galactose expression medium (30 g/L galactose, 6.7 g/L yeast nitrogen base without amino acids, 5 g/L ammonium sulfate, 24 g/L amino acid mix minus uracil, 10 g/L potassium phosphate monobasic (KH2PO4) and 0.38% vitamin mix) containing 2% glucose in a 250 mL baffled sterile shake flask and incubated at 37° C. (for SD-ura medium) or 30° C. (for modified galactose expression medium) for 48 hours. Cells were pelleted by centrifugation (4000 rpm, 15 min, 4° C.). The clear media supernatant containing the secreted GH61a enzyme was collected and stored at 4° C. until used.
Example 3
GH61 Activity Assays
In some experiments, GH61 activity was determined using a biomass assay. The substrate was wheat straw that had been pretreated under acidic conditions (hereinafter referred to as “pretreated wheat straw”). The reaction was carried out in a total volume of 77 μL in the presence of 10 mg of pre-treated wheat straw, with 62 μL of 1× ̃20× concentrated clear media supernatant (“broth”) containing S. cerevisiae-produced M. thermophila GH61a enzyme and 15 μL of sodium acetate buffer (pH 5.0), M. thermophila-produced cellobiohydrolase 1a (CBH1a), cellobiohydrolase 2b (CBH2b) and beta-glucosidase. The final concentration of sodium acetate was 150 mM and the enzyme loads of CBHs and beta-glucosidase were approximately 0.0025% ̃0.0125% (CBH1a and CBH2b in 1:1 ratio) and 0.01 to 0.02% with respect to substrate glucan mass in the biomass substrate, respectively.
Some experiments were also performed in the presence of inhibitors that may arise through the routine preparation or pre-treatment of a cellulose substrate. In this way, GH61 protein variants can be identified that are more resistant to the presence of such inhibitors, and therefore find use with a wider range of feedstocks and have wider applicability in the processing of biomass from different sources.
In some experiments, the pretreatment filtrate was obtained by washing pretreated substrate solids with water. The GH61 activity assay was carried out with 50 μL of GH61a containing supernatant, 12 μL of pretreatment filtrate, and 15 μL of sodium acetate buffer mixed with CBH1a, CBH2b and beta-glucosidase isolated from M. thermophila. Background negative controls were obtained by using media supernatant from cultures of cells without the GH61a gene in the plasmid. Thus, the negative controls represent activities of CBH1a, CBH2b and beta-glucosidase in the absence of GH61a. The reaction was incubated at 50 to 60° C. for 24 to 72 hours with shaking, and then quenched by adding 130 μL H2O at room temperature.
Some experiments were carried out in a total volume of 360 μL in the presence of 10 mg of pre-treated wheat straw and 40 μL filtrate (11% total volume), with 262 μL of clear media supernatant containing S. cerevisiae-produced M. thermophila GH61a enzyme and 48 μL of sodium acetate buffer (pH 5; supplemented with CuSO4) mixed with M. thermophila-produced CBH1a, CBH2b and β-glucosidase. The final concentrations of sodium acetate and CuSO4 were 128 mM and 15 μM, respectively, and the enzyme loads of CBH's and beta-glucosidase were 0.01% (CBH1a and CBH2b in 1:1 ratio) and 0.02% with respect to substrate glucan mass in the biomass substrate, respectively. Background negative controls were obtained by using media supernatant from cultures of S. cerevisiae cells without the GH61a gene in the plasmid. Thus, the negative controls represent glucose production by CBH1a, CBH2b and beta-glucosidase in the absence of GH61a. The reaction was incubated at 55° C. for 72 hours with shaking.
The GH61 activity in the reaction mixture was measured by monitoring glucose production, as determined using an enzymatic glucose assay kit (K-GLUC, Megazyme). In a total volume of 200 μL, 20 μL of GH61a reaction mixture was added to 180 μL of 2× concentrated glucose determination reagent (GOPOD ReagentTM, supplied as part of the K-GLUC assay kit). The reaction was incubated at room temperature for 30 minutes and the absorbance of the solution was measured at 510 nm. The glucose oxidase enzyme in the GOPOD reagent reacts with glucose and produces hydrogen peroxide, which then reacts with the 4-aminoantipyrine in the reagent to produce a quinoneimine dye. The amount of quinoneimine dye was measured spectrophotometrically at 510 nm to calculate the total amount of D-glucose in the reaction mixture. The total amount of glucose in the reaction mixture was also measured using an AGILENT® HPLC 1200 equipped with an AMINEXTM HPX-87H ion exclusion column (300 mm×7.8 mm+Bio-Rad) with 5 mM sulfuric acid in water as eluent at a flow rate of 0.6 mL/min at 65° C. The retention time of glucose was 9.5 minutes.
Detectable amounts of glucose, as a measure of GH61 activity, were observed under high throughput screening conditions (pH 5, 55° C.). GH61a specific activity in the reaction mixture (which also comprised CBH1a, CBH2b and beta-glucosidase) was determined by subtracting the amount of glucose in the negative control reaction (comprising CBH1a, CBH2b and BGL, but not GH61a) from the total glucose measurement.
Example 4
High Throughput Assays to Identify Improved GH61a Variants
Plasmid libraries containing variant GH61a genes were transformed into S. cerevisiae INVSC1 strain and plated on SD-ura agar plate containing 2% glucose. After incubation for at least 48 hours at 30° C., colonies were picked using a Q-Bot® robotic colony picker (Genetix) into shallow, 96-well well microtiter plates containing 200 μL SD-ura media and 6% glucose. Cells were grown for at least 21 hours at 30° C. with shaking at 250 rpm and 85% humidity. Then, 20 μL of the overnight culture was transferred into 96-deep well microtiter plates containing 380 μL SD-ura medium with 2% glucose as described in Example 2. In some cases, 15 μL of the overnight culture was transferred into 96-deep well microtiter plates containing 285 μL modified galactose expression medium with 2% glucose as described in Example 2. The plates were incubated at 37° C. (for SD-ura medium) or 30° C. (for modified galactose expression medium) with shaking at 250 rpm and 85% humidity for 48 hours. The deep well plates were centrifuged at 4000 rpm for 15 minutes and the clear media supernatant containing the secreted GH61a enzyme was used for the high throughput biomass assay.
The GH61a libraries were screened for thermoactivity using a biomass-based high throughput method using the assays described in Example 3.
Example 5
Improved GH61 Activity of Engineered GH61a Variants
Improved GH61a variants were identified from the high throughput screening of various GH61a variant libraries as described in the previous Example. The screening was done by measuring thermoactivity of these variants compared with that of the parental GH61a enzyme (expressed from GH61a DNA; SEQ ID NO:1). The high throughput (HTP) saccharification reactions were conducted at pH 5, 55° C. for 24-72 hrs, using 50 g/L pretreated wheat straw, 0.0025-0.01% of mixture of CBH1a and CBH2b (1:1 ratio), and 0.01 to 0.02% of beta-glucosidase.
Example 6
Shake Flask Validation of Improved GH61a Variants
Improved GH61a variants identified in the high throughput screening (as described in the previous Example) were prepared using the shake flask procedure described above. GH61 activities were determined using a biomass assay as described above, in which normalized concentrations of GH61a variants were used for direct comparison of the specific activities of the GH61a variants. Reactions were quenched at different time points between 24 to 72 hours and glucose levels measured for time-course analysis. FIG. 2 shows time course results for three GH61a variants. FIG. 2 also shows specific activities observed under the following assay conditions: pH 5.0, and 55° C., utilizing 50 g/L pretreated wheat straw, 0.0025% ̃0.0125% of mixture of CBH1a and CBH2b (1:1 ratio) and 0.01 to 0.02% of beta-galactosidase. The protein concentration was normalized in reactions. In this Figure, N=3; error bars represent ±1 standard deviation. GH61 activity is shown as the increase in glucose production by the enzyme combination [CBH1a+CBH2b+BGL1] supplemented by the GH61 protein, minus the glucose production by the same enzyme combination in the absence of the GH61 protein.
The results show that Variants 5 and 9 (SEQ ID NOS:6 and 8) have a 2.0 to 2.9 fold improvement over the native GH61a (SEQ ID NO:2); and Variant 1 has a 3.0 to 3.9 fold improvement over GH61a (SEQ ID NO:2).
Substitutions improving GH61 activity are compiled in Table 6-1 below. This table shows GH61a variants derived from the native GH61a enzyme (SEQ ID NO:2) that were shown to have improved thermoactivity. Improvement in GH61 activity in relation to the parental GH61a protein (SEQ ID NO:2) is indicated with the following scale:
+=1.1 to 1.9 fold improvement compared with wild-type (SEQ ID NO:2)
++=2.0 to 2.9 fold improvement compared with wild-type
+++=3.0 to 3.9 fold improvement compared with wild-type







TABLE 6-1







GH61 Variants with Improved Activity













Improvement


Var.

Silent Nucleotide
in GH61


No.
Amino Acid Changes
Changes
Activity





 1
N35G/E104H/A168P
t60c/c573g
+++



(SEQ ID NO: 4)


 2
W42P/E104H/K167A
t60c/c573g/g1026a
++


 3
N35G/W42P/V97Q/A191N

++


 4
W42P/E104H
c573g
++


 5
E104H/K167A
t60c/c291a/c573g
++


 6
W42P/A191N
t60c/c291a
++


 7
N35G/W42P/A191N
t60c/c291a
++


 8
H20D

++


 9
V97Q/A191N

++


 10
N35G/E104H/A191N
t60c/c876t
++


 11
E104H

++


 12
E104Q

+


 13
H20D/E104D/Q190H/Y192H

+


 14
H20D/Q190E/Y192Q
a312g
+


 15
H20D/E104C

+


 16
H20D/P103H/E104C

+


 17
H20D/P103H
a312g
+


 18
N35G/E104H
t60c/c573g
+


 19
H20D/P103H/E104Q/Q190E

+


 20
H20D/P103H/E104C/Y192Q

+


 21
E104D
t60c
+


 22
N35G/W42P
t60c/c573g
+


 23
A137P

+


 24
H20D/P103H/E104Q

+


 25
P103E/E104D
t60c
+


 26
N35G/F68Y/A191N
t379a/c380g/g381c
+


 27
W42P/A168P

+


 28
H20D/E104C/Q190E/Y192Q

+


 29
A142W

+


 30
N35G

+


 31
H20C/Q190E

+


 32
W42P/A212P/T236P

+


 33
N35G/W42P/V97Q/K167A/
t60c/c573g
+



A168P


 34
V97Q/A168P
c573g
+


 35
S232A

+


 36
W42P/E104H/K167A/A168P/
c573g
+



Q190E


 37
W42P/A168P/A212P/T236P

+


 38
N35G/V97Q/K167A

+


 39
N35G/V97Q

+


 40
N35G/A191N

+


 41
S127T/K167A/A191N

+


 42
W42P

+


 43
W42P/E104C/K167A/A168P
t60c/c291a/c573g
+


 44
K167Q

+


 45
W131V

+


 46
E176C

+


 47
K167I/P273S
c300t
+


 48
W42P/T87P

+


 49
W42P/A212P

+


 50
K133H

+


 51
D165N

+


 52
D165A

+


 53
A168D

+


 54
K218T

+


 55
P45T

+


 56
Q44V

+


 57
S164W

+


 58
I177F

+


 59
A191N

+


 60
I134P

+


 61
K133F

+


 62
I134D

+


 63
N35G/K167A
t60c/c291a/c573g
+


 64
I162R

+


 65
N35G/K167A
t204c/t379a/c380g/
+




g381c/c385t


 66
D165W/A246T

+


 67
I162L

+


 68
S164M

+


 69
F132D/A244D

+


 70
H181Q

+


 71
I177G
g1026a
+


 72
L166W

+


 73
I162F

+


 74
I134V

+


 75
E176Q

+


 76
H181S

+


 77
I178A

+


 78
K167A

+


 79
V172K

+


 80
I177H

+


 81
I134N

+


 82
K133Y

+


 83
N35G/Y139L

+


 84
A168G

+


 85
T12A/I162G
c246t
+


 86
D165E

+


 87
D165M

+


 88
I134M

+


 89
A168P

+


 90
I177D

+


 91
S164P

+


 92
H175T

+


 93
N187K/S330R
c597g
+


 94
H175R

+


 95
L166H

+


 96
I178L

+


 97
L173H

+


 98
I177T

+


 99
N170Y

+


100
H175S

+


101
K167T

+


102
L166R

+


103
V172Y

+


{grave over (104)}
P163S/E176D

+


105
S164I

+


106
H175M

+


107
A168N

+


108
A179W

+


109
W131K/H175Q
g1026a
+


110
Y171A

+


111
N170H

+


112
P163R

+


113
A168C

+


114
G169T

+


115
R174F

+


116
W131Y

+


117
I134L

+


118
I177V

+


119
K167E

+


120
H175C

+


121
W131I

+


122
W42P/A143P

+


123
I178G
c72t
+


124
N170P

+


125
A179D/N317K
c732g/c843t/c882t/
+




c909t/c912g


126
I162V

+


127
I178M

+


128
V172A

+


129
K167A/A191N
t60c/c291a
+


130
F132A

+


131
P163E

+


132
F132M

+


133
A179G

+


134
I177S

+


135
K167A
g921a
+


136
K167F

+


137
A168I

+


138
A179N

+


139
I134A
c792t
+


140
K167E
g972t
+


141
R174K

+


142
S164F

+


143
V172L

+


144
A168H

+


145
I134T

+


146
K167H

+


147
L166A

+


148
S164R

+


149
R174C

+


150
A179P

+


151
G169R
g1026a
+


152
L173M

+


153
D165K

+


154
E176S

+


155
F132L

+


156
F132I/A179I

+


157
F132P

+


158
S164Q

+


159
V172Q

+


160
W131D

+


161
W131Q

+


162
A179H

+


163
I134H/G270S

+


164
N170G

+


165
A168T

+


166
A179C

+


167
K133N

+


168
K167L

+


169
L180M

+


170
W131F

+


171
I134W
g1026a
+


172
I178H

+


173
N170A

+


174
V172H

+


175
A168H/S205N

+


176
I134H
g921a
+


177
S164C

+


178
S164K

+


179
I177C

+


180
I178Q

+


181
L180W

+


182
I177M

+


183
R174D

+


184
V172M

+


185
A179M

+


186
H175Y

+


187
I178P

+


188
L173A

+


189
N170E

+


190
N170F

+


191
N35G/A191N/T258I/T323P/
t379a/c380g/g381c/
+



G328A/C341R
c454a/c456a/c732t/




c843t/c849t


192
A168R

+


193
D165I

+


194
I162M

+


195
K167V

+


196
A179S

+


197
E176N

+


198
I134L/P322L

+


199
P163L

+


200
H181D

+


201
N170S

+


202
R174G

+


203
I177R

+


204
K167C

+


205
L166Q

+


206
P163I

+


207
S164L/L166I

+


208
Y171R

+


209
F132P/Q190E/A191T

+


210
F132Q

+


211
I134C

+


212
I177A

+


213
E176R

+


214
G169A

+


215
G169K

+


216
H181A

+


217
I177L

+


218
A168G

+


219
A179R

+


220
D165T

+


221
K167R

+


222
L166V

+


223
N170C

+


224
I178R

+


225
R174H

+


226
S164H

+


227
W131R/L166I

+


228
I162A/A191T

+


229
L173F

+


230
N170Q

+


231
I177P

+


232
R174N

+


233
V172K/S215W

+


234
D165R

+


235
G239D
c520a/c522g
+


236
H175V

+


237
H181R

+


238
I134Y

+


239
V172F

+


240
V172G

+









Table 6-2 shows GH61a variants derived from the GH61a protein designated “Variant 1” in Table 6-1 with improved thermoactivity. The second-round variants usually retained the alterations of Variant 1 compared with wild-type GH61a (N35G/E104H/A168P), along with additional alterations. Improvement in GH61 activity in relation to Variant 1 (SEQ ID NO:4) is indicated in Table 6-2 according to the following scale:
*=0.5 to 1.0 fold improvement compared with Variant 1 (SEQ ID NO:4)
+=1.1 to 1.9 fold improvement compared with Variant 1;
++=2.0 to 2.9 fold improvement compared with Variant 1







TABLE 6-2







GH61 Variants with Improved Activity Compared to Variant 1












Silent



Variant

Nucleotide
GH61 Activity


Number
Amino Acid Changes
Changes
Improvement





241
N35G/T40A/E104H/A168P/P327M
t60c/c573g
++


242
N35G/P45D/E104H/A168P/N317R
t60c/c573g
++


243
N35G/E104H/A168P/N317R
t60c/c573g
+


244
N35G/E104H/A168P/N317L
t60c/c573g
+


245
N35G/T54H/E104H/A168P
t60c/c573g
+


246
N35G/E104H/A168P/N317D/S329Y
t60c/c573g
+


247
N35G/E104H/A137S/A168P/S232E
t60c/c573g
+


248
N35G/E104H/A168P/N317R/T320A
t60c/c573g
+


249
N35G/E104H/A168P/D234E
t60c/c573g
+


250
N35G/T40S/E104H/A142G/A168P
t60c/c573g
+


251
N35G/T40S/S78C/V88I/E104H/S128K/
t60c/c573g
+



A168P/D234M


252
N35G/E104H/A168P/S330V
t60c/c573g
+


253
N35G/E104H/A168P/G203E/P266S
t60c/c573g
+


254
N35G/E104H/A168P/D234N
t60c/c573g
+


255
N35G/E104H/A168P/S286N/S329H
t60c/c573g
+


256
N35G/E104H/A168P/S330H
t60c/c573g
+


257
N35G/E104H/A168P/W337R
t60c/c573g
+


258
N35G/N66D/E104H/S164E/A168P/G267T
t60c/c573g
+


259
N35G/E104H/A168P/P233V
t60c/c573g
+


260
R34E/N35G/E104H/R145T/A168P
t60c/c573g
+


261
S24Q/N35G/E104H/A168P/V237I
t60c/c573g
+


262
Y32S/N35G/E64S/E104H/A168P
t60c/c573g
+


263
N35G/E104H/A168P/V333R
t60c/c573g
+


264
N35G/E104H/G144S/A168P/V333Q
t60c/c573g
+


265
V28H/N35G/P45K/E104H/A168P
t60c/c573g
+


266
N35G/E104H/A168P/P327K
t60c/c573g
+


267
N35G/N66Q/E104H/A168P
t60c/c573g
+


268
N35G/E104H/A168P/G203E
t60c/c573g
+


269
N35G/E104H/A168P/S339W
t60c/c573g
+


270
N35G/P45K/N46E/E104H/A150Y/A168P
t60c/c573g
+


271
N35G/E104H/R130S/A168P
t60c/c573g
+


272
N35G/E104H/R145T/A168P
t60c/c573g/g891a
+


273
N35G/E104H/A168P/S231K
t60c/c573g
+


274
N35G/T40A/E104H/A168P/D234E/P327M
t60c/c573g
+


275
N35G/E104H/A168P/S231H
t60c/c573g
+


276
N35G/E104H/A168P/N317M
t60c/c573g
+


277
N35G/E104H/A168P/S330Y
t60c/c573g
+


278
N35G/E104H/A168P/S329I
t60c/c573g
+


279
N35G/E104H/A168P/S329R
t60c/c573g
+


280
N35G/N66D/E104H/A168P/P322R/S329L
t60c/c573g
+


281
N35G/E104H/A168P/P327F
t60c/c288t/c573g
+


282
N35G/P45D/E104H/A168P
t60c/c573g
+


283
N35G/E104H/A168P/S332R
t60c/c573g
+


284
N35G/E104H/A116S/A168P
t60c/c573g
+


285
N35G/T40A/E104H/A168P/V230I/P327M
t60c/c573g
+


286
N35G/T49A/E104H/A168P
t60c/c573g
+


287
N35G/E104H/A168P/N317T
t60c/c573g
+


288
N35G/N46Y/E104H/A168P
t60c/c573g
+


289
N35G/E104H/A168P/G203V
t60c/c573g
+


290
N35G/E104H/A168P/S329L
t60c/c573g
+


291
N35G/E104H/R145N/A168P/S329H
t60c/c573g
+


292
N35G/A56S/E104H/A168P
t60c/c573g
+


293
N35G/T40S/T49R/E104H/A168P/D234E/
t60c/c573g
+



P327M


294
N35G/E104H/Q161R/A168P
t60c/c573g
+


295
N35G/E104H/A168P/S332F
t60c/c573g
+


296
N35G/P45R/T49A/E104H/A168P/N317R/
t60c/c573g
+



T320A


297
N35G/E104H/A168P/V237I
t60c/c573g
+


298
N35G/Q44K/T80V/E104H/A168P
t60c/c573g
+


299
N35G/E104H/A168P/E336S
t60c/c573g
+


300
N35G/E104H/A168P/P233T
t60c/c573g
+


301
N35G/E104H/A168P/S329Y
t60c/c573g
+


302
N35G/E104H/A168P/P327L
t60c/c573g
+


303
N35G/E104H/A168P/N317I
t60c/c573g
+


304
N35G/E104H/R130H/A168P
t60c/c573g
+


305
N35G/Q44K/E104H/A168P
t60c/c573g
+


306
N35G/N66D/E104H/A168P
t60c/c573g
+


307
N35G/E104H/A168P/S329V
t60c/c573g
+


308
N35G/E104H/A168P/W337F
t60c/c573g
+


309
N35G/E104H/A168P/N317H
t60c/c573g
+


310
N35G/T40L/E104H/S128K/A168P
t60c/c573g
+


311
N35G/E104H/A168P/A326V
t60c/c573g
+


312
N35G/T80V/E104H/A168P/P303T
t60c/c573g
+


313
N35G/E104H/A168P/S231A/S295L
t60c/c573g
+


314
N35G/E104H/A116Q/A168P
t60c/c573g
+


315
N35G/E104H/A168P/S330C
t60c/c573g
+


316
N35G/T40S/E101T/E104H/A168P/P327M
t60c/c573g
+


317
N35G/E104H/A168P/A326Q
t60c/c573g
+


318
N35G/N46R/E104H/A168P
t60c/c573g
+


319
N35G/P45K/E104H/A168P/A219R/S232E
t60c/c573g
+


320
S24Q/N35G/E104H/A168P/V237I/P303T
t60c/c573g
+


321
N35G/E104H/A168P/G203E/T281A
t60c/c573g
+


322
N35G/A56N/E104H/A168P
t60c/c573g
+


323
N35G/E104H/A168P/E336G
t60c/c573g
+


324
N35G/E104H/A168P/E336R
t60c/c573g
+


325
N35G/T40S/E104H/S128K/A142G/A168P
t60c/c573g
+


326
N35G/Q44K/S67T/E104H/A168P
t60c/c198t/c573g
+


327
N35G/E104H/A168P/N317A
t60c/c573g
+


328
N35G/E104H/G155N/A168P
t60c/c573g
+


329
N35G/E104H/Q161E/A168P
t60c/c573g
+


330
N35G/E104H/N118S/A168P
t60c/c573g
+


331
N35G/P45T/V97Q/E104H/A168P/G267S
t60c/c573g
+


332
V28H/N35G/E104H/A168P
t60c/c573g
+


333
N35G/E104H/A168P/Q184L
t60c/c573g
+


334
N35G/E104H/A168P/N317V
t60c/c573g
+


335
N35G/Q44L/E104H/A168P
t60c/c573g
+


336
N35G/E104H/A168P/S330G
t60c/c573g
+


337
N35G/E104H/A168P/T320A/V333W
t60c/c573g
+


338
N35G/E104H/A168P/E336A
t60c/c573g
+


339
N35G/E104H/A168P/N335S
t60c/c573g
+


340
N35G/N66M/E104H/A168P
t60c/c573g
+


341
N35G/T54G/E104H/A168P
t60c/c573g
+


342
N35G/E104H/A168P/N317S
t60c/c573g
+


343
N35G/E64L/E104H/A168P
t60c/c573g
+


344
N35G/E104H/S164E/A168P/A271T
t60c/c573g
+


345
N35G/N66A/E104H/A168P
t60c/c573g
+


346
N35G/G83R/E104H/A168P
t60c/c573g
+


347
N35G/E104H/A168P/N317Q/T320A
t60c/c573g
+


348
N35G/E104H/K141A/A168P
t60c/c573g
+


349
N35G/P71T/E104H/A168P
t60c/c573g
+


350
N35G/P71S/E104H/A168P
t60c/c573g
+


351
N35G/E104H/R130G/A168P
t60c/c573g
+


352
N35G/E104H/R145Q/A168P
t60c/c573g
+


353
N35G/T70A/E104H/A168P
t60c/c573g
+


354
N35G/E104H/A168P/K218R
t60c/c573g
+


355
N35G/E104H/A168P/Q184E
t60c/c573g
+


356
N35G/E104H/R130K/A168P
t60c/c573g
+


357
N35G/Q58H/E104H/A168P
t60c/c573g
+


358
Y32S/N35G/E104H/A168P
t60c/c573g
+


359
N35G/E104H/A168P/S329T
t60c/c573g
+


360
N35G/E104H/A168P/S330I
t60c/c573g
+


361
Y32S/N35G/P71A/E104H/A168P
t60c/c573g
+


362
N35G/E104H/A168P/S330T
t60c/c573g
+


363
N35G/G82A/E104H/A168P
t60c/c573g
+


364
N35G/T80V/E104H/A168P
t60c/c573g
+


365
N35G/E104H/A168P/S295T
t60c/c573g
+


366
N35G/N66G/E104H/A168P
t60c/c573g
+


367
N35G/E104H/R145L/A168P
t60c/c573g
+


368
N35G/S67H/E104H/A168P/V230M
t60c/c573g
+


369
N35G/E104H/G136E/A168P
t60c/c573g
+


370
N35G/T54S/E104H/A168P
t60c/c573g
+


371
N35G/P45S/E104H/A168P
t60c/c573g
+


372
N35G/E104H/A168P/A326M
t60c/c573g/c882t
+


373
N35G/N66D/N95E/E104H/S164E/A168P/
t60c/c573g
+



G267D


374
N35G/E104H/A168P/S332C
t60c/c573g
+


375
N35G/E104H/S128L/A168P
t60c/c573g
+


376
N35G/T54W/E104H/A168P
t60c/c573g
+


377
N35G/E104H/A168P/G268A/G269A/G270A
t60c/c573g
+


378
N35G/Q44K/E104H/A168P/S231T
t60c/c573g
+


379
R34E/N35G/E104H/A168P/A280D
t60c/c573g
+


380
N35G/E104H/A168P/A297T
t60c/g399a/c573g
+


381
N35G/E104H/K141P/R145Q/A168P
t60c/c573g
+


382
N35G/P45E/E104H/K141R/A168P
t60c/c573g
+


383
N35G/N66T/E104H/A168P
t60c/c573g
+


384
N35G/E104H/S164E/A168P/S295D
t60c/c573g
+


385
N35G/E104H/A168P/N317F
t60c/c573g
+


386
N35G/E104H/A168P/N317Q
t60c/c573g
+


387
N35G/T40G/T49R/S78C/E104H/A142G/
t60c/c573g
+



A168P


388
N35G/G82S/E104H/A168P
t60c/c573g
+


389
N35G/Q58P/E104H/A168P
t60c/c573g
+


390
N35G/N46R/E104H/A168P/G203E/A263V
t60c/c573g
+


391
N35G/P45R/E104H/A168P
t60c/c573g
+


392
N35G/S67G/E104H/A168P
t60c/c573g
+


393
N35G/E104H/A168P/R199E
t60c/c573g
+


394
N35G/G69T/E104H/A168P
t60c/c573g
+


395
N35G/E104H/A168P/G203E/G268A/G269A/
t60c/c573g
+



G270A


396
N35G/E104H/A168P/P266S
t60c/c573g
+


397
N35G/E104H/A168P/V324M
t60c/c573g
+


398
N35G/E104H/A168P/G245A
t60c/c573g
+


399
N35G/N66R/E104H/A168P
t60c/c573g
+


400
N35G/E104H/A168P/T236E
t60c/c573g
+


401
S24Q/N35G/Q44K/T80H/E104H/A168P
t60c/c573g
+


402
N35G/E104H/S128D/A168P
t60c/c573g
+


403
N35G/N66D/S78D/E104H/A168P/S253D
t60c/c573g
+


404
N35G/E104H/R130Y/A168P
t60c/c573g
+


405
N35G/E104H/A168P/K310I
t60c/c573g
+


406
N35G/E104H/R145E/A168P
t60c/c573g
+


407
N35G/N66D/E104H/S164E/A168P/S282D
t60c/c573g
+


408
N35G/E104H/K141P/A168P
t60c/c573g
+


409
N35G/E104H/A168P/Q184R
t60c/c573g
+


410
N35G/E104H/A168P/S231T
t60c/c573g
+


411
N35G/N66V/E104H/A168P
t60c/c573g
+


412
N35G/E104H/A142L/A168P
t60c/c573g
+


413
N35G/E104H/R145H/A168P
t60c/c573g
+


414
N35G/E104H/A168P/K218L
t60c/c573g
+


415
N35G/E104H/K141T/A168P
t60c/c573g
+


416
N35G/E104H/A168P/P233F
t60c/c573g
+


417
N35G/T40S/E104H/A168P/P327M
t60c/c573g
+


418
N35G/T54M/E104H/A168P
t60c/c573g
+


419
S24T/N35G/E104H/S164E/A168P
t60c/c573g
+


420
N35G/P45T/E104H/A168P
t60c/c573g
+


421
N35G/N66D/E104H/S164E/A168P/S231T/
t60c/c573g
+



S253T


422
N35G/G69H/E104H/A168P
t60c/c573g
+


423
N35G/E104H/S128Y/A168P
t60c/c573g
+


424
N35G/T49Q/E104H/A168P
t60c/c573g
+


425
N35G/T49A/E104H/A168P/Q184H
t60c/c573g
+


426
N35G/E104H/A168P/G203Y
t60c/c573g
+


427
N35G/Q44K/N66V/E104H/A168P
t60c/c573g
+


428
N35G/E104H/A137M/A168P
t60c/c573g
+


429
N35G/E104H/A168P/P327C
t60c/c573g
+


430
N35G/E104H/A168P/T236R
t60c/c573g
+


431
N35G/I51A/E104H/A168P
t60c/c573g
+


432
N35G/S67H/E104H/A168P
t60c/c573g
+


433
N35G/E104H/A168P/A326C
t60c/c573g
+


434
N35G/T49A/E104H/S128N/A168P
t60c/c573g
+


435
N35G/T49R/E104H/A168P/K218L/N317Q
t60c/c573g
+


436
N35G/E104H/A168P/P266S/G267V
t60c/c573g
+


437
N35G/E104H/A168P/V237I/P303T
t60c/c573g
+


438
N35G/T49E/E104H/A168P
t60c/c573g
+


439
N35G/P45R/E104H/A168P/T320A
t60c/c573g
+


440
N35G/N66L/E104H/A168P
t60c/c573g
+


441
N35G/P45R/E104H/A168P/K218L/N317Q
t60c/c573g
+


442
N35G/E104H/R145V/A168P
t60c/c573g
+


443
N35G/N66D/E104H/A168P/R290K
t60c/c573g
+


444
N35G/T80L/E104H/A168P
t60c/c573g
+


445
N35G/A55G/E104H/A168P
t60c/c573g
+


446
N35G/E104H/A168P/S330A
t60c/c573g
+


447
N35G/E104H/K141N/A168P/P266S
t60c/c573g
+


448
N35G/E104H/A142S/A168P
t60c/c573g
+


449
N35G/E104H/A168P/Q184G
t60c/c573g
+


450
N35G/E104H/N118E/A168P
t60c/c573g
+


451
N35G/E104H/A168P/A212M
t60c/c573g
+


452
N35G/E104H/A168P/G267D
t60c/c573g
+


453
N35G/K93N/E104H/R130Y/A168P
t60c/c573g
+


454
N35G/P45R/T49Y/E104H/A168P/N317D
t60c/c573g
+


455
N35G/E104H/A168P/S329Q
t60c/c573g
+


456
N35G/E104H/A168P/V230Q
t60c/c573g
+


457
N35G/P45K/E104H/A168P/A219R
t60c/c573g
+


458
N35G/E104H/A142G/A168P
t60c/c573g
+


459
N35G/E104H/A168P/S205T
t60c/c573g
+


460
N35G/S78D/E104H/S164E/A168P
t60c/c573g
+


461
N35G/E104H/R130E/A168P
t60c/c573g
+


462
N35G/E104H/A168P/Q184H
t60c/c573g
+


463
N35G/E104H/A116P/A168P
t60c/c573g
+


464
N35G/E104H/A142D/A168P
t60c/c573g
+


465
V28H/N35G/N46E/Q58H/E104H/A168P
t60c/c573g
+


466
N35G/E104H/A168P/A280T
t60c/c573g
+


467
R34E/N35G/E104H/A168P/A280T
t60c/c573g
+


468
N35G/E104H/A168P/E336L
t60c/c573g
+


469
N35G/T49D/E104H/A168P
t60c/c573g
+


470
N35G/E104H/A168P/A219T
t60c/c573g
+


471
N35G/E104H/A142W/A168P
t60c/c573g
+


472
N35G/E104H/A168P/P303T/G305D
t60c/c573g
+


473
N35G/Q44V/E104H/A168P
t60c/c573g
+


474
N35G/E104H/A168P/N187D
t60c/c573g
+


475
N35G/E104H/G136H/A168P
t60c/c573g
+


476
S24Q/N35G/Q44K/E104H/A168P/P303T/
t60c/c573g
+



S332D


477
N35G/E104H/A168P/Q184N
t60c/c573g
+


478
N35G/E104H/A168P/S332L
t60c/c573g
+


479
S24T/N35G/N66D/S78D/E104H/A168P/
t60c/c573g
+



S205T/S253T


480
N35G/E104H/A168P/P327A
t60c/c573g
+


481
N35G/T40A/T49Q/S78C/E104H/A168P
t60c/c573g
+


482
N35G/T40L/E104H/A142G/A168P
t60c/c573g
+


483
N35G/T49Y/E104H/A168P/N317R
t60c/c573g
+


484
R34E/N35G/K93T/E104H/R130E/R145T/
t60c/c573g
+



A168P/R199E/K218T/A280D









Example 7
Selection of Further GH61 Candidates for Strain Improvement
This example illustrates the selection of potential candidates to further improve whole cellulase broth activity of M. thermophila cultures on different types of pretreated substrates like pretreated corn stover and pretreated wheat straw.
In this Example, M. thermophila-produced and purified GH61a, GH61p, GH61f, GH61n, CBH1a, CBH2b, AXE3, FAE, and Xyl3, were used to supplement the activity present in culture broths (i.e., “whole broth cellulase base”) of the M. thermophila strain CF-416 prepared using standard methods known in the art. The broth cellulase base was fixed to 0.5% protein and the single purified enzyme was added at 0.4% (wt added protein/wt glucan) to the saccharification reactions. The whole cellulase broth base and individual enzymes were characterized by standard BCA assays for total protein quantification.
The saccharification reactions were carried out at 74 g/L glucan load of pretreated wheat straw (PWS) or pretreated corn stover (PCS) at pH 5.0, 55° C. at 950 rpm in the presence of 50 μM copper in high throughput (HTP) 96 deep well plates. Glucose analysis was carried out by the glucose oxidase assay as described above. In each case, the fold improvement was calculated using the formula Fold Improvement=[Total Glucose Production with addition of 0.4% single enzyme to the whole cellulase broth base]/[glucose production from the 0.5% whole cellulase broth base]. The results are provided in Table 10-1. In this Table, the fold improvements were ranked from 0 to 3; fold improvements less than 1.2× are indicated by “0,” fold improvements of >1.2 to <1.5 are indicated by “1,” fold improvements of ≧1.5× to <1.7× improvements are indicated by “2,” and fold improvements ≧1.7 are indicated by “3.”
As indicated by the results in the Table, the greatest benefit was observed using GH61p on pre-treated corn stover (PCS), and GH61a on pre-treated wheatstraw (PWS), indicating that GH61 activity is increases the cellulolytic activity of the reaction mix. In addition to the enzymes listed in Table 10-1, EG1b, Xyl1, Xyl6, beta-xylosidase, and another xylanase were also tested, but did not show any improvement under the test conditions.







TABLE 7-1







Fold Improvement










Fold Improvement
Fold Improvement Over


Whole broth cellulases
Over Whole Cellulase
Whole Cellulase


from
Broth Tested on PCS
Broth Tested on PWS





CF-416
1
1


CBH1a
1
3


CBH2b
1
1


GH61a
2
3


GH61p
3
2


GH61f
1
1


GH61n
1
1


AXE3
0
1


FAE
1
1


Xyl3
0
1









Example 8
Improvement of GH61 Activity by Copper(II) Ions
This example illustrates the enhancement in GH61 activity with the addition of copper(II) ion to the saccharification reaction.
Purified M. thermophila-produced GH61a or S. cerevisiae supernatant containing M. thermophila-GH61a was pre-incubated with different amounts of copper(II) (CuSO4) at concentrations of 0 to 100 μM at ambient temperature for 30 min. The biomass assay was then performed in a total volume of 300 μL, in the presence of 10 mg of pre-treated wheat straw, using 2614 of copper-treated GH61 samples, 39 μL of sodium acetate buffer (pH 5), M. thermophila-produced CBH1a, CBH2b and β-glucosidase. The final concentration of sodium acetate was 120 mM and the enzyme loads of CBHs and β-glucosidase (CBH1a and CBH2b in 1:1 ratio) were 0.01% and 0.02% with respect to substrate glucan mass in the biomass substrate, respectively. Background (negative) controls were obtained by using either water or media supernatant from cultures of S. cerevisiae cells without the GH61a gene in the plasmid. Thus, the negative controls represent activities of CBH1a, CBH2b and beta-glucosidase in the absence of GH61a. The reaction was incubated at 55° C. for 72 hours with shaking. The GH61a activity in the reaction mixture was measured by monitoring glucose production using a glucose oxidase/peroxidase-based glucose assay.
Some experiments were also performed without pre-incubating GH61 with copper(II), but instead, by directly adding different amounts of copper(II) (CuSO4) to the biomass assay reactions as described herein.
FIG. 3 shows activity of M. thermophila-GH61a pre-incubated with different amounts of copper(II) ion. Biomass assays were performed with (A) S. cerevisiae-produced M. thermophila GH61a Variant 5, and (B) M. thermophila-produced wild-type GH61a. Glucose production after 72 h incubation at pH 5, 55° C. was determined by the glucose assay. The data in this Figure indicate GH61a-only activity, in which the amount of glucose produced in control reaction containing CBH and β-glucosidase was subtracted from the total amount of glucose produced in the reactions with GH61a. In this Figure, N=4; and the error bars represent ±1 standard deviation. Copper concentrations shown are with respect to the total reaction volume.
The results indicate that the activities of M. thermophila-produced GH61a and S. cerevisiae supernatant containing M. thermophila-GH61a are improved by pre-incubation with copper(II) ions under the conditions tested. Similar results were obtained when copper(II) was directly added to the biomass assay reactions.
Example 9
Further Evaluation of Copper Requirements in Saccharification Reactions
This Example describes experiments designed to determine the effects of added copper in saccharification reactions. The saccharification reactions were run in 30 g shake flasks (250 mL flasks) using 82 g/kg glucan of acid-pretreated corn stover and whole broth enzymes produced by M. thermophila strain CF-416 (produced using standard methods known in the art) at a 0.81% total enzyme load with respect to glucan. The reactions were conducted at pH 5.0 or pH 6.0, 55° C. and 250 rpm mixing, with supplementation of either 0 or 50 μM CuSO4, copper(II) with respect to the total reaction volume. A pH trim was also performed using 2M NaOH at time intervals of 1, 4, 7, 22, 24 29, 46, 52, 70, 75 and 96 hrs, to maintain the pH at the desired value of pH 5.0 or pH 6.0. Samples were removed at 72 hours and the total amount of glucose in the reaction mixture was determined using standard HPLC methods and equipment as known in the art. The results indicated that under the conditions described herein, the effect of copper is dependent on saccharification pH. As shown in FIG. 4, Panel A, at a saccharification pH of pH 5.0, the addition of copper caused an increase in glucose yields by  ̃3.5% while this effect was not observed when the saccharification was carried out at pH 6.0. Also, the addition of copper may cause a decrease in the total amounts of C5 sugars that are produced as shown in FIG. 4, Panel B.
Example 10
Effect of Reducing Agents on the Cellulolytic Activity of GH61a
This Example provides experiments conducted to determine the effect of adding reducing agents (e.g., gallic acid and ascorbic acid) to saccharification reactions. In these experiments, enhancement of GH61 activity was tested using Variant 1 (SEQ ID NO:5) in the presence of reducing agents (specifically, ascorbic acid or gallic acid) and pretreatment filtrate, which contains various reducing agents from lignin degradation. Reactions were performed on cellulosic substrates, AVICEL® PH microcrystalline cellulose and phosphoric acid swollen cellulose (PASC), with purified M. thermophila-produced GH61 Variant 1 and beta-glucosidase at 0.3% and 0.08% respectively, with respect to substrate glucan mass, and 128 mM sodium acetate buffer (pH 5) supplemented with 30 μM CuSO4. Thus, reactions were performed with 0.3% GH61a and 0.08% BGL, where % enzyme loads are with respect to substrate glucan mass (36 g/L AVICEL® cellulose and 5 g/L PASC). Background (negative) controls were beta-glucosidase-only reactions tested in the absence of GH61a. Glucose production after 48 h incubation at pH 5, 55° C. was determined by glucose oxidase/peroxidase-based or HPLC-based glucose assay glucose assay, using methods known in the art.
FIG. 5 shows the activity of M. thermophila-produced GH61a Variant 1 on cellulosic substrates in the presence of ascorbic acid, gallic acid and pretreatment filtrate. Panel A shows the results for AVICEL® PH microcrystalline cellulose and Panel B shows the results for PASC. GH61-only activity is also shown, these results were obtained by subtracting the amount of glucose produced in the beta-glucosidase-only control reaction from the total amount of glucose produced in the reaction that included GH61a. Filtrate dilutions are indicated in this Figure, where undiluted filtrate equals 72% of the total reaction volume. In this Figure, N=4; and the error bars represent ±1 standard deviation.
The results indicate that supplementing the GH61a reaction with gallic acid improved the GH61 activity in generating soluble sugars from AVICEL® cellulose and PASC, which were then hydrolyzed by beta-glucosidase to generate glucose monomers. The improvement was also observed with diluted pretreatment filtrate, which suggests that the filtrate may contain gallic acid or gallic acid-like reductants that can beneficially impact GH61 activity.
Example 11
Evaluation of Oxygen Limitation in Saccharification Reactions
This example describes experiments conducted to determine if oxygen is a limiting factor in saccharification reactions. To investigate the level of oxygen required in the overall saccharification efficiency, two shake flask reactions were performed, in which one was left closed throughout the 72 hour reaction, while the other was opened at 4 hrs and 24 hrs for 10 seconds to provide fresh air. The reactions were run in 30 g shake flasks (250 mL flasks) using 87 g/kg glucan and M. thermophila CF-416 whole broth cellulases. The total protein content in each reaction was 0.81% total enzyme load with respect to glucan. The reactions were conducted at pH 5.0, 55° C. and 250 rpm mixing, with supplementation of 50 μM CuSO4. Samples were removed at 72 hours and glucose yields were measured by monitoring glucose production using a glucose oxidase/peroxidase-based glucose assay. The results indicated that under the reaction conditions tested, oxygen was not a limiting factor as the two reactions (control vs. the reaction with air supplemented) yielded similar levels of glucose.
Example 12
Enhancement of Saccharification Efficiency by Addition of Surfactants
This example illustrates the enhancement of overall saccharification yield with the addition of surfactants such as TWEEN®-20 and PEG-4000. Experiments were designed to monitor the enhancement in cellulase activity with different concentrations of TWEEN®-20 or PEG-4000 in the biomass assay. The biomass assay was performed in a total volume of 90 μL, including 10 mg of pre-treated wheat straw, 64.8 μL (72% by volume) of filtrate (or H2O for no filtrate conditions), and 11.6 μL of a mixture of sodium acetate buffer (pH 5.0, supplemented with CuSO4), M. thermophila-produced cellobiohydrolase 1a (CBH1a), cellobiohydrolase 2b (CBH2b), beta-glucosidase (BGL), and glycoside hydrolase type 61 (GH61a). The final concentration of sodium acetate was 128 mM (with 30 μM CuSO4) and the enzyme loads of CBH1a, CBH2b, BGL and GH61a were 0.15%, 0.15%, 0.08% and 0.3% with respect to the substrate glucan mass in the biomass substrate, respectively. Water was used in place of the enzymes as a negative control. Herein, “1× filtrate” indicates 72% of filtrate (i.e., the filtered liquid portion of pre-treated substrate) in the total reaction volume. The amount of glucose in the filtrate background was subtracted from the test data (N=2; Error bars in the Figures represent ±1 standard deviation). The reaction was incubated at 55° C. for 72 hours at pH 5, with shaking at 950 rpm, then was quenched by adding 180 μL of water. The total cellulase activity in the reaction mixture was measured by monitoring glucose production using a glucose oxidase/peroxidase-based glucose assay as known in the art. The results indicate that the total glucose production in the saccharification reaction was enhanced with the addition of TWEEN®-20 or PEG-4000.
FIG. 6, Panel A, shows enzymatic hydrolysis activity of the cellulase mixture in the presence of TWEEN®-20. Data shown are total glucose produced by a mixture of GH61a, CBH1a, CBH2b, and BGL at 0.3%, 0.15%, 0.15%, and 0.08% with respect to the substrate glucan mass in the biomass substrate, respectively. In this Figure, TWEEN®-20 concentrations are expressed as % total reaction volume.
FIG. 6, Panel B, shows enzymatic hydrolysis activity of the cellulase mixture in the presence of PEG-4000. In this Figure, PEG-4000 concentrations are expressed as % total reaction volume.
While the invention has been described with reference to the specific embodiments, various changes can be made and equivalents can be substituted to adapt to a particular situation, material, composition of matter, process, process step or steps, thereby achieving benefits of the invention without departing from the scope of what is claimed.
For all purposes in the United States of America, each and every publication and patent document cited in this disclosure is incorporated herein by reference as if each such publication or document was specifically and individually indicated to be incorporated herein by reference. Citation of publications and patent documents is not intended as an indication that any such document is pertinent prior art, nor does it constitute an admission as to its contents or date.

## Claims

1. A glycoside hydrolase 61 (GH61) variant protein comprising an amino acid sequence that is at least at least 90%, identical to SEQ ID NO:2 or a fragment of SEQ ID NO:2 having GH61 activity, wherein the amino acid sequence of the variant protein has one or more amino acid substitutions with respect to SEQ ID NO:2 or said fragment.

2. The GH61 variant protein of claim 1, wherein said GH61 variant protein is at least 95% identical to SEQ ID NO:2 or a fragment of SEQ ID NO:2 having GH61 activity.

3. The GH61 variant protein of claim 1, wherein said GH61 variant protein has increased thermoactivity, thermostability, and/or activity as compared to the GH61 wild-type protein of SEQ ID NO:2.

4. The GH61 variant protein of claim 1, wherein said GH61 variant protein comprises at least one substitution(s) at one or more of the following amino acid positions: H20, N35, W42, Q44, P45, F68, T87, V97, P103, E104, S127, W131, F132, K133, I134, A137, Y139, A142, A143, I162, P163, S164, D165, L166, K167, A168, G169, N170, Y171, V172, L173, R174, H175, E176, I177, I178, A179, L180, H181, Q190, A191, Y192, Y192, S205, A212, S215, K218, S232, T236, G239, A244, A246, T258, G270, P273, N317, P322, T323, G328, S330, and/or C341, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.

5. The GH61 variant protein of claim 4, wherein said GH61 variant protein comprises at least one substitution(s) at one or more of the following amino acid positions: H20, N35, W42, E104, I134, S164, K167, A168, V172, I177, A179, and/or A191, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.

6. The GH61 variant protein of claim 1, wherein said GH61 variant protein comprises the substitution set N35/E104/A168, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.

7. The GH61 variant protein of claim 1, wherein said amino acid substitution(s) comprise one or more of the following substitutions numbered with reference to SEQ ID NO:2: N35G, E104C/D/H/Q, and A168P/X, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.

8. The GH61 variant protein of claim 1, wherein said GH61 variant protein comprises one or more of the following substitutions: N35G, E104H, and A168P, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.

9. The GH61 variant protein of claim 1, wherein said GH61 variant protein comprises the substitution set N35G/E104H/A168P, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.

10. The GH61 variant protein of claim 1, wherein said variant protein comprises the sequence set forth in any of SEQ ID NOS:4, 6, and/or 8.

11. The GH61 variant protein of claim 1, wherein said GH61 variant protein is encoded by at least one polynucleotide sequence set forth in SEQ ID NOS:3, 5, and/or 7.

12. The GH61 variant protein of claim 1, wherein said GH61 variant protein, comprises at least one substitution(s) at one or more of the following amino acid positions: S24, V28, Y32, R34, N35, T40, Q44, P45, N46, T49, I51, T54, A55, A56, Q58, E64, N66, S67, G69, T70, P71, S78, T80, G82, G83, V88, K93, N95, E101, E104, A116, N118, S128, R130, G136, A137, K141, A142, G144, R145, A150, G155, Q161, S164, A168, Q184, N187, R199, G203, S205, A212, K218, A219, V230, S231, S232, P233, D234, T236, V237, G245, S253, A263, P266, G267, G268, G269, G270, A271, A280, T281, S282, R290, S295, A297, P303, G305, K310, N317, T320, V324, A326, P327, S329, S330, S332, V333, E336, W337, and/or S339, wherein the amino acid positions are numbered with reference to SEQ ID NO:2.

13. The GH61 variant protein of claim 1, wherein said GH61 variant protein comprises a plurality of amino acid substitutions.

14. The GH61 variant protein of claim 1, wherein said GH61 variant protein comprises a polypeptide sequence that is at least 90% identical to any of SEQ ID NOS:2, 3, 5, 6, 8, and/or 9, and/or a biologically active fragment of any of SEQ ID NOS: 2, 3, 5, 6, 8, and/or 9, wherein said fragment has GH61 activity.

15. A GH61 variant protein comprising an amino acid sequence that is at least 90% identical to SEQ ID NO:5, or a fragment of SEQ ID NO:5, having GH61 activity, wherein the amino acid sequence of the variant protein has one or more amino acid substitutions with respect to SEQ ID NO:2 or said fragment, and wherein the substitution(s) in the amino acid sequence result in the variant protein having increased GH61 activity in a reaction where crystalline cellulose undergoes saccharification by cellulase enzymes that are contained in culture broth from M. thermophile cells, compared with a reference protein comprising SEQ ID NO:2, or said fragment, without any of said substitutions.

16. An enzyme composition comprising at least one GH61 variant protein as set forth in claim 1.

17. The enzyme composition of claim 16, further comprising one or more enzymes selected from wild-type GH61 enzymes, endoglucanases (EG), β-glucosidases (BGL), Type 1 cellobiohydrolases (CBH1), and/or Type 2 cellobiohydrolases (CBH2), cellulases, hemicellulases, xylanases, xylosidases, amylases, glucoamylases, proteases, esterases, and lipases.

18. The enzyme composition of claim 17, further comprising at least one adjunct material.

19. The enzyme composition of claim 18, wherein said adjunct material is selected from divalent metal cations, reductants, surfactants, buffers, culture media, and enzyme stabilizing systems.

20. The composition of claim 16, wherein the cellulosic substrate is selected from wheat grass, wheat straw, barley straw, sorghum, rice grass, sugarcane straw, bagasse, switchgrass, corn stover, corn fiber, grains, or any combination thereof.

21. A composition comprising at least one variant GH61 protein of claim 1, one or more cellulase enzymes, a cellulosic substrate, and Cu++, wherein the variant GH61 protein is at least 90% identical to SEQ ID NO:5, and/or a biologically fragment thereof with GH61 activity.

22. A composition comprising at least one GH61 protein of claim 1, one or more cellulase enzymes, a cellulosic substrate, and gallic acid, wherein the GH61 protein is at least 90% SEQ ID NO:5, and/or a biologically fragment thereof with GH61 activity.

23. A GH61 variant protein encoded by a polynucleotide, wherein the protein comprises an amino acid sequence that is at least or about 85% identical to any of SEQ ID NO:5, or a fragment of SEQ ID NO:5, having GH61 activity, wherein the amino acid sequence of the variant protein has one or more amino acid substitutions with respect to SEQ ID NO:2, or said fragment, and wherein the polynucleotide encoding the GH61 variant protein comprises at least one mutation set comprising t60c/c573g, wherein the nucleotide positions are numbered with reference to SEQ ID NO:1.