WO2012048171A2 - Variant cbh i polypeptides with reduced product inhibition - Google Patents

Variant cbh i polypeptides with reduced product inhibition Download PDF

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Publication number
WO2012048171A2
WO2012048171A2 PCT/US2011/055181 US2011055181W WO2012048171A2 WO 2012048171 A2 WO2012048171 A2 WO 2012048171A2 US 2011055181 W US2011055181 W US 2011055181W WO 2012048171 A2 WO2012048171 A2 WO 2012048171A2
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seq
positions
polypeptide
cbh
substitution
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PCT/US2011/055181
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French (fr)
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WO2012048171A3 (en
WO2012048171A9 (en
Inventor
Justin T. Stege
Alexander Varvak
John Poland
Chris S. Lyon
Shaun Healey
Peter Luginbuhl
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Bp Corporation North America Inc.
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Priority to US13/824,317 priority Critical patent/US9096871B2/en
Priority to JP2013532961A priority patent/JP2014502145A/en
Priority to BR112013008048A priority patent/BR112013008048A2/en
Priority to CA2811789A priority patent/CA2811789A1/en
Priority to EP11785509.8A priority patent/EP2625269A2/en
Publication of WO2012048171A2 publication Critical patent/WO2012048171A2/en
Publication of WO2012048171A3 publication Critical patent/WO2012048171A3/en
Publication of WO2012048171A9 publication Critical patent/WO2012048171A9/en
Priority to US14/816,992 priority patent/US20150329880A1/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/02—Preparation of oxygen-containing organic compounds containing a hydroxy group
    • C12P7/04—Preparation of oxygen-containing organic compounds containing a hydroxy group acyclic
    • C12P7/06—Ethanol, i.e. non-beverage
    • C12P7/14—Multiple stages of fermentation; Multiple types of microorganisms or re-use of microorganisms
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
    • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
    • C12Y302/01091—Cellulose 1,4-beta-cellobiosidase (3.2.1.91)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C12N9/2405—Glucanases
    • C12N9/2434—Glucanases acting on beta-1,4-glucosidic bonds
    • C12N9/2437—Cellulases (3.2.1.4; 3.2.1.74; 3.2.1.91; 3.2.1.150)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/02—Monosaccharides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/14—Preparation of compounds containing saccharide radicals produced by the action of a carbohydrase (EC 3.2.x), e.g. by alpha-amylase, e.g. by cellulase, hemicellulase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/02—Preparation of oxygen-containing organic compounds containing a hydroxy group
    • C12P7/04—Preparation of oxygen-containing organic compounds containing a hydroxy group acyclic
    • C12P7/06—Ethanol, i.e. non-beverage
    • C12P7/08—Ethanol, i.e. non-beverage produced as by-product or from waste or cellulosic material substrate
    • C12P7/10—Ethanol, i.e. non-beverage produced as by-product or from waste or cellulosic material substrate substrate containing cellulosic material
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02E—REDUCTION OF GREENHOUSE GAS [GHG] EMISSIONS, RELATED TO ENERGY GENERATION, TRANSMISSION OR DISTRIBUTION
    • Y02E50/00—Technologies for the production of fuel of non-fossil origin
    • Y02E50/10—Biofuels, e.g. bio-diesel

Definitions

  • Cellulose is an unbranched polymer of glucose linked by P(l ⁇ 4)-glycosidic bonds. Cellulose chains can interact with each other via hydrogen bonding to form a crystalline solid of high mechanical strength and chemical stability .
  • the cellulose chains are depolymerized into glucose and short oligosaccharides before organisms, such as the fermenting microbes used in ethanol production, can use them as metabolic fuel.
  • Cellulase enzymes catalyze the hydrolysis of the cellulose (hydrolysis of P-l,4-D-glucan linkages) in the biomass into products such as glucose, cellobiose, and other cellooligosaccharides.
  • Cellulase is a generic term denoting a multienzyme mixture comprising exo-acting cellobiohydrolases (CBHs), endoglucanases (EGs) and ⁇ -glucosidases (BGs) that can be produced by a number of plants and microorganisms.
  • CBHs exo-acting cellobiohydrolases
  • EGs endoglucanases
  • BGs ⁇ -glucosidases
  • Enzymes in the cellulase of Trichoderma reesei include CBH I (more generally, Cel7A), CBH2 (Cel6A), EG1 (Cel7B), EG2 (Cel5), EG3 (Cell 2), EG4 (Cel61A), EG5 (Cel45A), EG6 (Cel74A), Cipl, Cip2, ⁇ -glucosidases (including, . e.g., Cel3A), acetyl xylan esterase, ⁇ -mannanase, and swollenin.
  • Cellulase enzymes work synergistically to hydrolyze cellulose to glucose.
  • CBH I and CBH II act on opposing ends of cellulose chains (Barr et al, 1996, Biochemistry 35:586-92), while the endoglucanases act at internal locations in the cellulose.
  • the primary product of these enzymes is cellobiose, which is further hydrolyzed to glucose by one or more ⁇ - glucosidases.
  • the cellobiohydrolases are subject to inhibition by their direct product, cellobiose, which results in a slowing down of saccharification reactions as product accumulates.
  • cellobiose which results in a slowing down of saccharification reactions as product accumulates.
  • cellobiohyrolases with improved productivity that maintain their reaction rates during the course of a saccharification reaction, for use in the conversion of cellulose into fermentable sugars and for related fields of cellulosic material processing such as pulp and paper, textiles and animal feeds.
  • the present disclosure relates to variant CBH I polypeptides.
  • Most naturally occurring CBH I polypeptides have arginines at positions corresponding to R268 and R41 1 of T. reesei CBH I (SEQ ID NO:2).
  • the variant CBH I polypeptides of the present disclosure include a substitution at either or both positions resulting in a reduction or decrease in product (e.g. , cellobiose) inhibition.
  • product tolerant is sometimes referred to herein as "product tolerant.”
  • the variant CBH I polypeptides of the disclosure minimally contain at least a CBH I catalytic domain, comprising (a) a substitution at the amino acid position corresponding to R268 of T. reesei CBH I ("R268 substitution”); (b) a substitution at the amino acid position corresponding to R41 1 of T. reesei CBH I ("R41 1 substitution”); or (c) both an R268 substitution and an R41 1 substitution.
  • the amino acid positions of exemplary CBH I polypeptides into which R268 and/or R41 1 substitutions can be introduced are shown in Table 1 , and the amino acid positions corresponding to R268 and/or R41 1 in these exemplary CBH I polypeptides are shown in Table 2.
  • R268 and/or R41 1 substituents can include lysines and/or alanines.
  • the present disclosure provides a variant CBH I polypeptide comprising a CBH I catalytic domain with one of the following amino acid substitutions or pairs of R268 and/or R41 1 substitutions: (a) R268K and R41 IK; (b) R268K and R41 1 A; (c) R268A and R41 IK; (d) R268A and R41 1A; (e) R268A; (f) R268K; (g) R41 1A; and (h) R41 IK.
  • the amino acid sequence of the variant CBH I polypeptide does not comprise or consist of SEQ ID NO: 150, SEQ ID NO: 151 , SEQ ID NO: 152, or SEQ ID NO: 153.
  • the variant CBHI polypeptides of the disclosure typically include a CD comprising an amino acid sequence having at least 50% sequence identity to a CD of a reference CBH I exemplified in Table 1.
  • the CD portions of the CBH I polypeptides exemplified in Table 1 are delineated in Table 3.
  • the variant CBH I polypeptides can have a cellulose binding domain ("CBD") sequence in addition to the catalytic domain (“CD”) sequence.
  • CBD can be N- or C-terminal to the CD, and the CBD and CD are optionally connected via a linker sequence.
  • the variant CBH I polypeptides can be mature polypeptides or they may further comprise a signal sequence.
  • the variant CBH I polypeptides of the disclosure typically exhibit reduced product inhibition by cellobiose.
  • the IC50 of cellobiose towards a variant CBH I polypeptide of the disclosure is at least 1.2-fold, at least 1.5-fold, or at least 2-fold the IC50 of cellobiose towards a reference CBH I lacking the R268 substitution and/or R41 1 substitution present in the variant. Additional embodiments of the product inhibition characteristics of the variant CBH I polypeptides are provided in Section 5.1.
  • variant CBH I polypeptides of the disclosure typically retain some
  • a variant CBH I polypeptide retains at least 50% the CBH I activity of a reference CBH I lacking the R268 substitution and/or R41 1 substitution present in the variant. Additional embodiments of cellobiohydrolase activity of the variant CBH I polypeptides are provided in Section 5.1.
  • compositions including cellulase
  • compositions e.g., whole cellulase compositions, and fermentation broths
  • variant CBH I polypeptides Additional embodiments of compositions comprising variant CBH I polypeptides are provided in Section 5.3.
  • the variant CBH I polypeptides and compositions comprising them can be used, inter alia, in processes for saccharifying biomass. Additional details of saccharification reactions, and additional applications of the variant CBH I polypeptides, are provided in Section 5.4.
  • the present disclosure further provides nucleic acids (e.g., vectors) comprising nucleotide sequences encoding variant CBH I polypeptides as described herein, and recombinant cells engineered to express the variant CBH I polypeptides.
  • the recombinant cell can be a prokaryotic (e.g., bacterial) or eukaryotic (e.g., yeast or filamentous fungal) cell. Further provided are methods of producing and optionally recovering the variant CBH I polypeptides. Additional embodiments of the recombinant expression system suitable for expression and production of the variant CBH I polypeptides are provided in Section 5.2.
  • FIG. 1A-1B Cellobiose dose-response curves using a 4-MUL assay for a wild- type CBH I (BD29555; Figure 1A) and a R268K/R41 IK variant CBH I (BD29555 with the substitutions R273K/R422K; Figure IB).
  • FIGURE 2A-2B The effect of cellobiose accumulation on the activity of wild-type CBH I and a R268K/R41 IK variant CBH I, based on percent conversion of glucan after 72 hours in the bagasse assay.
  • FIGURE 3 Cellobiose dose-response curves using PASC assay for a R268K/R41 IK variant CBH I polypeptide as compared to two wild type CBH I polypeptides.
  • FIGURE 5 Characterization of cellobiose product tolerance of variant CBH I polypeptides, based on percent conversion of glucan after 72 hours in the absence and presence of ⁇ -glucosidase (BG) in the bagasse assay; tolerance is evaluated as a function of the ratio of activity in the absence vs. presence of ⁇ -glucosidase.
  • TABLE 1 Amino acid sequences of exemplary "reference" CBH I polypeptides that can be modified at positions corresponding to R268 and/or R411 in T. reesei CBH I (SEQ ID NO:2). The database accession numbers are indicated in the second column. Unless indicated otherwise, the accession numbers refer to the Genbank database.
  • SS signal sequence
  • CD catalytic domain
  • CBD cellulose binding domain
  • Table 4 shows a segment within the catalytic domain of each exemplary reference CBH I polypeptide containing the active site loop (shown in bold, underlined text) and the catalytic residues (glutamates in most CBH I polypeptides) (shown in bold, double underlined text).
  • Database descriptors are as for Table 1.
  • TABLE 6 MUL and bagasse assay results for variants of T. reesei CBH I. ND means not determined.
  • ⁇ %Activity (+/- cellobiose) [(Activity with cellobiose)/(Activity without cellobiose)] * 100.
  • ⁇ %Activity (-/+ BG) [(Activity without BG)/( Activity with BG)] * 100.
  • SEQ ID NO: l-149 correspond to the exemplary reference CBH I polypeptides.
  • SEQ ID NO: 150 corresponds to mature T. reesei CBH I (amino acids 26-529 of SEQ ID NO:2) with an R268A substitution.
  • SEQ ID NO: 151 corresponds to mature T. reesei CBH I (amino acids 26-529 of SEQ ID NO:2) with an R41 1A substitution.
  • SEQ ID NO: 152 corresponds to full length BD29555 with both an R268K substitution and an R41 IK substitution.
  • SEQ ID NO: 153 corresponds to mature BD29555 with both an R268K substitution and an R41 IK substitution.
  • the present disclosure relates to variant CBH I polypeptides.
  • Most naturally occurring CBH I polypeptides have arginines at positions corresponding to R268 and R41 1 of T. reesei CBH I (SEQ ID NO:2).
  • the variant CBH I polypeptides of the present disclosure include a substitution at either or both positions resulting in a reduction of product ⁇ e.g., cellobiose) inhibition.
  • the following subsections describe in greater detail the variant CBH I polypeptides and exemplary methods of their production, exemplary cellulase compositions comprising them, and some industrial applications of the polypeptides and cellulase compositions.
  • variant CBH I polypeptides comprising at least one amino acid substitution that results in reduced product inhibition.
  • Variant means a polypeptide which is differs in sequence from a reference polypeptide by substitution of one or more amino acids at one or a number of different sites in the amino acid sequence.
  • the variant CBH I polypeptides of the disclosure have an amino acid substitution at the amino acid position corresponding to R268 of T. reesei CBH I (SEQ ID NO:2) (an "R268 substitution"), (b) a substitution at the amino acid position corresponding to R41 1 of T. reesei CBH I ("R41 1 substitution”); or (c) both an R268 substitution and an R41 1 substitution, as compared to a reference CBH I polypeptide. It is noted that the R268 and R41 1 numbering is made by reference to the full length T. reesei CBH I, which includes a signal sequence that is generally absent from the mature enzyme. The corresponding numbering in the mature T.
  • reesei CBH I (see, e.g., SEQ ID NO:4) is R251 and R394, respectively.
  • the present disclosure provides variant CBH I polypeptides in which at least one of the amino acid positions corresponding to R268 and R41 1 of T. reesei CBH I, and optionally both the amino acid positions corresponding to R268 and R41 1 of T. reesei CBH I, is not an arginine.
  • amino acid positions in the reference polypeptides of Table 1 that correspond to R268 and R41 1 in T. reesei CBH I are shown in Table 2.
  • Amino acid positions in other CBH I polypeptides that correspond to R268 and R41 1 can be identified through alignment of their sequences with T. reesei CBH I using a sequence comparison algorithm. Optimal alignment of sequences for comparison can be conducted, e.g. , by the local homology algorithm of Smith & Waterman, 1981 , Adv. Appl. Math. 2:482-89; by the homology alignment algorithm of Needleman & Wunsch, 1970, J. Mol. Biol.
  • R268 and/or R41 1 substitutions are preferably selected from (a) R268K and R41 IK; (b) R268K and R41 1 A; (c) R268A and'R41 IK; (d) R268A and R41 1 A; (e) R268A; (f) R268K; (g) R41 1A; and (h) R41 IK.
  • CBH I polypeptides belong to the glycosyl hydrolase family 7 ("GH7").
  • the glycosyl hydrolases of this family include endoglucanases and cellobiohydrolases
  • the cellobiohydrolases act processively from the reducing ends of cellulose chains to generate cellobiose.
  • Cellulases of bacterial and fungal origin act processively from the reducing ends of cellulose chains to generate cellobiose.
  • CBD cellulose-binding domain
  • CD cellulose-binding domain
  • the CD contains the active site whereas the CBD interacts with cellulose by binding the enzyme to it (van Tilbeurgh et al, 1986, FEBS Lett. 204(2): 223- 227; Tomme et al, 1988, Eur. J. Biochem. 170:575-581).
  • the three-dimensional structure of the catalytic domain of T. reesei CBH I has been solved (Divne et al, 1994, Science
  • the CD consists of two ⁇ -sheets that pack face-to-face to form a ⁇ -sandwich. Most of the remaining amino acids in the CD are loops connecting the ⁇ -sheets. Some loops are elongated and bend around the active site, forming cellulose-binding tunnel of ( ⁇ 50 A). In contrast, endoglucanases have an open substrate binding cleft/groove rather than a tunnel. Typically, the catalytic residues are glutamic acids corresponding to E229 and E234 of T. reesei CBH I.
  • the loops characteristic of the active sites ("the active site loops") of reference CBH I polypeptides, which are absent from GH7 family endoglucanases, as well as catalytic glutamate residues of the reference CBH I polypeptides, are shown in Table 4.
  • the variant CBH I polypeptides of the disclosure preferably retain the catalytic glutamate residues or may include a glutamine instead at the position corresponding to E234, as for SEQ ID NO:4.
  • the variant CBH I polypeptides contain no substitutions or only conservative substitutions in the active site loops relative to the reference CBH I
  • polypeptides from which the variants are derived are derived.
  • CBH I polypeptides do not have a CBD, and most studies concerning the activity of cellulase domains on different substrates have been carried out with only the catalytic domains of CBH I polypeptides. Because CDs with cellobiohydrolase activity can be generated by limited proteolysis of mature CBH I by papain (see, e.g., Chen et al., 1993, Biochem. Mol. Biol. Int. 30(5):901-10), they are often referred to as "core" domains.
  • a variant CBH I can include only the CD "core" of CBH I.
  • Exemplary reference CDs comprise amino acid sequences corresponding to positions 26 to 455 of SEQ ID NO: l , positions 18 to 444 of SEQ ID NO:2, positions 26 to 455 of SEQ ID NO:3, positions 1 to 427 of SEQ ID NO:4, positions 24 to 457 of SEQ ID NO:5, positions 18 to 448 of SEQ ID NO:6, positions 27 to 460 of SEQ ID NO:7, positions 27 to 460 of SEQ ID NO:8, positions 20 to 449 of SEQ ID NO:9, positions 1 to 424 of SEQ ID NO: 10, positions 18 to 447 of SEQ ID NO: 1 1 , positions 18 to 434 of SEQ ID NO: 12, positions 18 to 445 of SEQ ID NO : 13 , positions 19 to 454 of SEQ ID NO : 14, positions 19 to 443 of SEQ ID NO : 15 , positions 2 to 426 of SEQ ID NO: 16, positions 23 to 446 of SEQ ID NO: 17, positions
  • the CBDs are particularly involved in the hydrolysis of crystalline cellulose. It has been shown that, the ability of cellobiohydrolases to degrade crystalline cellulose decreases when the CBD is absent (Under and Teeri, 1997, Journal of Biotechnol. 57: 15-28).
  • the variant CBH I polypeptides of the disclosure can further include a CBD.
  • Exemplary CBDs comprise amino acid sequences corresponding to positions 494 to 529 of SEQ ID NO: l, positions 480 to 514 of SEQ ID NO:2, positions 494 to 529 of SEQ ID NO:3, positions 491 to 526 of SEQ ID NO: 5, positions 477 to 512 of SEQ ID NO:6, positions 497 to 532 of SEQ ID NO:7, positions 504 to 539 of SEQ ID NO:8, positions 486 to 521 of SEQ ID NO: 13, positions 556 to 596 of SEQ ID NO: 15, positions 490 to 525 of SEQ ID NO: 18, positions 495 to 530 of SEQ ID NO:20, positions 471 to 506 of SEQ ID NO:23, positions 481 to 516 of SEQ ID NO:27, positions 480 to 514 of SEQ ID NO:30, positions 495 to 529 of SEQ ID NO:35, positions 493 to 528 of SEQ ID NO:36, positions 477 to 512 of SEQ ID NO:38, positions 547 to 586 of SEQ ID NO
  • the CD and CBD are often connected via a linker.
  • Exemplary linker sequences correspond to positions 456 to 493 of SEQ ID NO: 1 , positions 445 to 479 of SEQ ID NO:2, positions 456 to 493 of SEQ ID NO: 3, positions 458 to 490 of SEQ ID NO:5, positions 449 to 476 of SEQ ID NO:6, positions 461 to 496 of SEQ ID NO:7, positions 461 to 503 of SEQ ID NO:8, positions 446 to 485 of SEQ ID NO: 13, positions 444 to 555 of SEQ ID NO: 15, positions 450 to 489 of SEQ ID NO: 18, positions 450 to 494 of SEQ ID NO:20, positions
  • CBH I polypeptides are modular, the CBDs, CDs and linkers of different CBH I polypeptides, such as the exemplary CBH I polypeptides of Table 1 , can be used interchangeably. However, in a preferred embodiment, the CBDs, CDs and linkers of a variant CBH I of the disclosure originate from the same polypeptide.
  • the variant CBH I polypeptides of the disclosure preferably have at least a two-fold reduction of product inhibition, such that cellobiose has an IC50 towards the variant CBH I that is at least 2-fold the IC50 of the corresponding reference CBH I, e.g., CBH I lacking the R268 substitution and/or R41 1 substitution. More preferably the IC50 of cellobiose towards the variant CBH I is at least 3-fold, at least 5-fold, at least 8-fold, at least 10-fold, at least 12- fold or at least 15-fold the IC50 of the corresponding reference CBH I.
  • the IC50 of cellobiose towards the variant CBH I is at least 3-fold, at least 5-fold, at least 8-fold, at least 10-fold, at least 12- fold or at least 15-fold the IC50 of the corresponding reference CBH I.
  • the IC50 of cellobiose towards the variant CBH I is ranges from 2-fold to 15- fold, from 2-fold to 10-fold, from 3-fold to 10-fold, from 5-fold to 12-fold, from 4-fold to 12- fold, from 5-fold to 10-fold, from 5-fold to 12-fold, from 2-fold to 8-fold, or from 8-fold to 20-fold the IC50 of the corresponding reference CBH I.
  • MUL methylumbelliferyl lactoside
  • the variant CBH I polypeptides of the disclosure preferably have a cellobiohydrolase activity that is at least 30% the cellobiohydrolase activity of the corresponding reference CBH I, e.g., CBH I lacking the R268 substitution and/or R41 1 substitution. More preferably, the cellobiohydrolase activity of the variant CBH I is at least 40%, at least 50%, at least 60% or at least 70% the cellobiohydrolase activity of the corresponding reference CBH I.
  • the IC50 cellobiohydrolase activity of the variant CBH I is ranges from 30%) to 80%, from 40% to 70%, 30% to 60%, from 50% to 80% or from 60% to 80% of the cellobiohydrolase activity of the corresponding reference CBH I.
  • Substrates useful for assaying cellobiohydrolase activity include crystalline cellulose, filter paper, phosphoric acid swollen cellulose, cellooligosaccharides, methylumbelliferyl lactoside, methylumbelliferyl cellobioside, orthonitrophenyl lactoside, paranitrophenyl lactoside, orthonitrophenyl cellobioside, paranitrophenyl cellobioside.
  • Cellobiohydrolase activity can be measured in an assay utilizing PASC as the substrate and a calcofluor white detection method (Du et al., 2010, Applied Biochemistry and Biotechnology 161 :313-317).
  • PASC can be prepared as described by Walseth, 1952, TAPPI 35:228-235 and Wood, 1971, Biochem. J. 121 :353-362.
  • variant CBH I polypeptides of the disclosure preferably:
  • positions 18 to 447 of SEQ ID NO: 1 1 positions 18 to 434 of SEQ ID NO: 12, positions 18 to 521 of SEQ ID NO: 13, positions 19 to 454 of SEQ ID NO: 14, positions 19 to 596 of SEQ ID NO: 15, positions 2 to 426 of SEQ ID NO: 16, positions 23 to 446 of SEQ ID NO: 17, positions 19 to 525 of SEQ ID NO: 18, positions 23 to 446 of SEQ ID NO: 19, positions 19 to 530 of SEQ ID NO:20, positions 2 to 416 of SEQ ID NO:21 , positions
  • HSPs high scoring sequence pairs
  • Extension of the word hits is stopped when: the cumulative alignment score falls off by the quantity X from a maximum achieved value; the cumulative score goes to zero or below; or the end of either sequence is reached.
  • the BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment.
  • the BLAST program uses as defaults a word length (W) of 1 1, the BLOSUM62 scoring matrix (see Henikoff & Henikoff, 1992, Proc. Nat'l. Acad. Sci. USA 89:10915-10919) alignments (B) of 50, expectation (E) of 10, M'5, N'-4, and a comparison of both strands.
  • CBH I polypeptides are secreted and are therefore expressed with a signal sequence that is cleaved upon secretion of the polypeptide from the cell. Accordingly, in certain aspects, the variant CBH I polypeptides of the disclosure further include a signal sequence.
  • Exemplary signal sequences comprise amino acid sequences corresponding to positions 1 to 25 of SEQ ID NO: l, positions 1 to 17 of SEQ ID NO:2, positions 1 to 25 of SEQ ID NO:3, positions 1 to 23 of SEQ ID NO:5, positions 1 to 17 of SEQ ID NO:6, positions 1 to 26 of SEQ ID NO:7, positions 1 to 27 of SEQ ID NO:8, positions 1 to 19 of SEQ ID NO:9, positions 1 to 17 of SEQ ID NO:l 1, positions 1 to 17 of SEQ ID NO: 12, positions 1 to 17 of SEQ ID NO: 13, positions 1 to 18 of SEQ ID NO: 14, positions 1 to 18 of SEQ ID NO: 15, positions 1 to 22 of SEQ ID NO: 17, positions 1 to 18 of SEQ ID NO: 18, positions 1 to 22 of SEQ ID NO: 19, positions 1 to 18 of SEQ ID NO:20, positions 1 to 18 of SEQ ID NO:22, positions 1 to 18 of SEQ ID NO:23, positions 1 to 18 of SEQ ID NO:24, positions 1 to 19 of SEQ ID NO:25,
  • the disclosure also provides recombinant cells engineered to express variant CBH I polypeptides.
  • the variant CBH I polypeptide is encoded by a nucleic acid operably linked to a promoter.
  • the promoter can be a filamentous fungal promoter.
  • the nucleic acids can be, for example, under the control of heterologous promoters.
  • the variant CBH I polypeptides can also be expressed under the control of constitutive or inducible promoters.
  • promoters include, but are not limited to, a cellulase promoter, a xylanase promoter, the 1818 promoter (previously identified as a highly expressed protein by EST mapping Trichodermd).
  • the promoter can suitably be a cellobiohydrolase, endoglucanase, or ⁇ - glucosidase promoter.
  • a particularly suitable promoter can be, for example, a T. reesei cellobiohydrolase, endoglucanase, or ⁇ - glucosidase promoter.
  • Non-limiting examples of promoters include a cbhl, cbh2, egll, egl2, egl3, egl4, egl5, pkil, gpdl, xynl, or xyn2 promoter.
  • Suitable host cells include cells of any microorganism ⁇ e.g., cells of a bacterium, a protist, an alga, a fungus ⁇ e.g. , a yeast or filamentous fungus), or other microbe), and are preferably cells of a bacterium, a yeast, or a filamentous fungus.
  • Suitable host cells of the bacterial genera include, but are not limited to, cells of
  • Suitable cells of bacterial species include, but are not limited to, cells of Escherichia coli, Bacillus subtilis, Bacillus licheniformis, Lactobacillus brevis, Pseudomonas aeruginosa, and Streptomyces lividans.
  • Suitable host cells of the genera of yeast include, but are not limited to, cells of
  • yeast species include, but are not limited to, cells of
  • Saccharomyces cerevisiae Schizosaccharomyces pombe, Candida albicans, Hansenula polymorpha, Pichia pastoris, P. canadensis, Kluyveromyces marxianus, and Phaffia rhodozyma.
  • Suitable host cells of filamentous fungi include all filamentous forms of the subdivision Eumycotina.
  • Suitable cells of filamentous fungal genera include, but are not limited to, cells of Acremonium, Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis, Chrysoporium, Coprinus, Coriolus, Corynascus, Chaetomium, Cryptococcus, Filobasidium, Fusarium, Gibberella, Humicola, Hypocrea, Magnaporthe, Mucor, Myceliophthora, Mucor, Neocallimastix, Ne rospora, Paecilomyces, Penicillium, Phanerochaete, Phlebia,
  • the recombinant cell is a Trichoderma sp. ⁇ e.g., Trichoderma reesei), Penicillium sp., Humicola sp. ⁇ e.g. , Humicola insolens); Aspergillus sp. ⁇ e.g., Aspergillus niger), Chrysosporium sp., Fusarium sp., or Hypocrea sp.
  • Suitable cells can also include cells of various anamorph and teleomorph forms of these filamentous fungal genera.
  • Suitable cells of filamentous fungal species include, but are not limited to, cells of Aspergillus awamori, Aspergillus fumigatus, Aspergillus foetidus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Chrysosporium lucknowense, Fusarium bactridioides , Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi, Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusarium sulphureum, Fusarium torulo
  • the engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants, or amplifying the nucleic acid sequence encoding the variant CBH I polypeptide.
  • Culture conditions such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to those skilled in the art.
  • many references are available for the culture and production of many cells, including cells of bacterial and fungal origin. Cell culture media in general are set forth in Atlas and Parks (eds.), 1993, The Handbook of
  • Microbiological Media CRC Press, Boca Raton, FL, which is incorporated herein by reference.
  • the cells are cultured in a standard medium containing physiological salts and nutrients, such as described in Pourquie et al, 1988, Biochemistry and Genetics of Cellulose Degradation, eds. Aubert, et al, Academic Press, pp. 71-86; and Ilmen et al, 1997, Appl. Environ. Microbiol. 63: 1298-1306.
  • Culture conditions are also standard, e.g., cultures are incubated at 28°C in shaker cultures or fermenters until desired levels of variant CBH I expression are achieved.
  • Preferred culture conditions for a given filamentous fungus may be found in the scientific literature and/or from the source of the fungi such as the American Type Culture Collection (ATCC). After fungal growth has been established, the cells are exposed to conditions effective to cause or permit the expression of a variant CBH I.
  • ATCC American Type Culture Collection
  • the inducing agent e.g., a sugar, metal salt or antibiotics
  • the inducing agent is added to the medium at a concentration effective to induce variant CBH I expression.
  • the recombinant cell is an Aspergillus niger, which is a useful strain for obtaining overexpressed polypeptide.
  • Aspergillus niger which is a useful strain for obtaining overexpressed polypeptide.
  • A. niger var. awamori dgr246 is known to product elevated amounts of secreted cellulases (Goedegebuur et al, 2002, Curr. Genet. 41 :89-98).
  • Other strains of Aspergillus niger var awamori such as GCDAP3, GCDAP4 and GAP3-4 are known (Ward et al , 1993, Appl. Microbiol. Biotechnol. 39:738- 743).
  • the recombinant cell is a Trichoderma reesei, which is a useful strain for obtaining overexpressed polypeptide.
  • Trichoderma reesei which is a useful strain for obtaining overexpressed polypeptide.
  • RL-P37 described by Sheir-Neiss et al, 1984, Appl. Microbiol. Biotechnol. 20:46-53, is known to secrete elevated amounts of cellulase enzymes.
  • Functional equivalents of RL-P37 include Trichoderma reesei strain RUT-C30 (ATCC No. 56765) and strain QM9414 (ATCC No. 26921). It is contemplated that these strains would also be useful in overexpressing variant CBH I polypeptides.
  • Cells expressing the variant CBH I polypeptides of the disclosure can be grown under batch, fed-batch or continuous fermentations conditions.
  • Classical batch fermentation is a closed system, wherein the compositions of the medium is set at the beginning of the fermentation and is not subject to artificial alternations during the fermentation.
  • a variation of the batch system is a fed-batch fermentation in which the substrate is added in increments as the fermentation progresses.
  • Fed-batch systems are useful when catabolite repression is likely to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the medium. Batch and fed-batch fermentations are common and well known in the art.
  • Continuous fermentation is an open system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned medium is removed simultaneously for processing.
  • Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth.
  • Continuous fermentation systems strive to maintain steady state growth conditions. Methods for modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology.
  • the disclosure provides transgenic plants and seeds that recombinantly express a variant CBH I polypeptide.
  • the disclosure also provides plant products, e.g., oils, seeds, leaves, extracts and the like, comprising a variant CBH I polypeptide.
  • the transgenic plant can be dicotyledonous (a dicot) or monocotyledonous (a monocot).
  • the disclosure also provides methods of making and using these transgenic plants and seeds.
  • the transgenic plant or plant cell expressing a variant CBH I can be constructed in accordance with any method known in the art. See, for example, U.S. Patent No.
  • T. reesei CBH I has been successfully expressed in transgenic tobacco (Nicotiana tabaccum) and potato (Solanum tuberosum). See Hooker et al, 2000, in Glycosyl
  • the present disclosure provides for the expression of CBH I variants in transgenic plants or plant organs and methods for the production thereof.
  • DNA expression constructs are provided for the transformation of plants with a nucleic acid encoding the variant CBH I polypeptide, preferably under the control of regulatory sequences which are capable of directing expression of the variant CBH I polypeptide.
  • regulatory sequences include sequences capable of directing transcription in plants, either constitutively, or in stage and/or tissue specific manners.
  • variant CBH I polypeptides in plants can be achieved by a variety of means. Specifically, for example, technologies are available for transforming a large number of plant species, including dicotyledonous species (e.g. , tobacco, potato, tomato, Petunia, Brassica) and monocot species. Additionally, for example, strategies for the expression of foreign genes in plants are available. Additionally still, regulatory sequences from plant genes have been identified that are serviceable for the construction of chimeric genes that can be functionally expressed in plants and in plant cells (e.g., Klee, 1987, Ann. Rev. of Plant Phys. 38:467-486; Clark et al, 1990, Virology 179(2):640-7; Smith et al, 1990, Mol. Gen. Genet. 224(3):477-81.
  • nucleic acids into plants can be achieved using several technologies including transformation with Agrobacterium tumefaciens or Agrobacterium rhizogenes.
  • plant tissues that can be transformed include protoplasts, microspores or pollen, and explants such as leaves, stems, roots, hypocotyls, and cotyls.
  • DNA encoding a variant CBH I can be introduced directly into protoplasts and plant cells or tissues by microinjection, electroporation, particle
  • Variant CBH I polypeptides can be produced in plants by a variety of expression systems.
  • a constitutive promoter such as the 35S promoter of Cauliflower Mosaic Virus (Guilley et al, 1982, Cell 30:763-73) is serviceable for the accumulation of the expressed protein in virtually all organs of the transgenic plant.
  • promoters that are tissue-specific and/or stage-specific can be used (Higgins, 1984, Annu. Rev. Plant Physiol. 35: 191-221 ; Shotwell and Larkins, 1989, In:The Biochemistry of Plants Vol. 15 (Academic Press, San Diego: Stumpf and Conn, eds.), p. 297), permit expression of variant CBH I polypeptides in a target tissue and/or during a desired stage of development.
  • a variant CBH I polypeptide produced in cell culture is secreted into the medium and may be purified or isolated, e.g., by removing unwanted components from the cell culture medium.
  • a variant CBH I polypeptide may be produced in a cellular form necessitating recovery from a cell lysate.
  • the variant CBH I polypeptide is purified from the cells in which it was produced using techniques routinely employed by those of skill in the art. Examples include, but are not limited to, affinity chromatography (Van Tilbeurgh et al, 1984, FEBS Lett.
  • the variant CBH I polypeptides of the disclosure are suitably used in cellulase compositions.
  • Cellulases are known in the art as enzymes that hydro lyze cellulose (beta- 1 ,4- glucan or beta D-glucosidic linkages) resulting in the formation of glucose, cellobiose, cellooligosaccharides, and the like.
  • EG endoglucanases
  • CBH cellobiohydrolases
  • BG beta-glucosidases
  • Certain fungi produce complete cellulase systems which include exo- cellobiohydrolases or CBH-type cellulases, endoglucanases or EG-type cellulases and ⁇ - glucosidases or BG-type cellulases (Schulein, 1988, Methods in Enzymology 160(25):234- 243). Such cellulase compositions are referred to herein as "whole" cellulases. However, sometimes these systems lack CBH-type cellulases and bacterial cellulases also typically include little or no CBH-type cellulases. In addition, it has been shown that the EG components and CBH components synergistically interact to more efficiently degrade cellulose. See, e.g., Wood, 1985, Biochemical Society Transactions 13(2):407-410.
  • the cellulase compositions of the disclosure typically include, in addition to a variant CBH I polypeptide, one or more cellobiohydrolases, endoglucanases and/or ⁇ -glucosidases.
  • cellulase compositions contain the microorganism culture that produced the enzyme components.
  • Cellulase compositions also refers to a crude fermentation product of the microorganisms.
  • a crude fermentation is preferably a fermentation broth that has been separated from the microorganism cells and/or cellular debris (e.g., by centrifugation and/or filtration).
  • the enzymes in the broth can be optionally diluted, concentrated, partially purified or purified and/or dried.
  • the variant CBH I polypeptide can be co-expressed with one or more of the other components of the cellulase composition or it can be expressed separately, optionally purified and combined with a composition comprising one or more of the other cellulase components.
  • the variant CBH I When employed in cellulase compositions, the variant CBH I is generally present in an amount sufficient to allow release of soluble sugars from the biomass.
  • the amount of variant CBH I enzymes added depends upon the type of biomass to be saccharified which can be readily determined by the skilled artisan.
  • the weight percent of variant CBH I polypeptide is suitably at least 1, at least 5, at least 10, or at least 20 weight percent of the total polypeptides in a cellulase composition.
  • Exemplary cellulase compositions include a variant CBH I of the disclosure in an amount ranging from about 1 to about 20 weight percent, from about 1 to about 25 weight percent, from about 5 to about 20 weight percent, from about 5 to about 25 weight percent, from about 5 to about 30 weight percent, from about 5 to about 35 weight percent, from about 5 to about 40 weight percent, from about 5 to about 45 weight percent, from about 5 to about 50 weight percent, from about 10 to about 20 weight percent, from about 10 to about 25 weight percent, from about 10 to about 30 weight percent, from about 10 to about 35 weight percent, from about 10 to about 40 weight percent, from about 10 to about 45 weight percent, from about 10 to about 50 weight percent, from about 15 to about 20 weight percent, from about 15 to about 25 weight percent, from about 15 to about 30 weight percent, from about 15 to about 35 weight percent, from about 15 to about 30 weight percent, from about 15 to about 45 weight percent, or from about 15 to about 50 weight percent of the total polypeptides in the composition.
  • variant CBH I polypeptides of the disclosure and compositions comprising the variant CBH I polypeptides find utility in a wide variety applications, for example detergent compositions that exhibit enhanced cleaning ability, function as a softening agent and/or improve the feel of cotton fabrics (e.g., "stone washing” or “biopolishing"), or in cellulase compositions for degrading wood pulp into sugars (e.g., for bio-ethanol production).
  • Other applications include the treatment of mechanical pulp (Pere et al, 1996, Tappi Pulping Conference, pp. 693-696 (Nashville, TN, Oct. 27-31, 1996)), for use as a feed additive (see, e.g., WO 91/04673) and in grain wet milling.
  • Ethanol can be produced via saccharification and fermentation processes from cellulosic biomass such as trees, herbaceous plants, municipal solid waste and agricultural and forestry residues.
  • cellulosic biomass such as trees, herbaceous plants, municipal solid waste and agricultural and forestry residues.
  • the ratio of individual cellulase enzymes within a naturally occurring cellulase mixture produced by a microbe may not be the most efficient for rapid conversion of cellulose in biomass to glucose.
  • endoglucanases act to produce new cellulose chain ends which themselves are substrates for the action of cellobiohydrolases and thereby improve the efficiency of hydrolysis of the entire cellulase system.
  • the use of optimized cellobiohydrolase activity may greatly enhance the production of ethanol.
  • biomass refers to any composition comprising cellulose (optionally also hemicellulose and/or lignin).
  • biomass includes, without limitation, seeds, grains, tubers, plant waste or byproducts of food processing or industrial processing (e.g.
  • stalks including, e.g., cobs, stover, and the like
  • grasses including, e.g., Indian grass, such as Sorghastrum nutans; or, switchgrass, e.g. , Panicum species, such as Panicum virgatum
  • wood including, e.g., wood chips, processing waste
  • paper including, e.g., pulp, and recycled paper (including, e.g., newspaper, printer paper, and the like).
  • Other biomass materials include, without limitation, potatoes, soybean (e.g., rapeseed), barley, rye, oats, wheat, beets, and sugar cane bagasse.
  • the saccharified biomass e.g., lignocellulosic material processed by enzymes of the disclosure
  • the saccharified biomass can be made into a number of bio-based products, via processes such as, e.g., microbial fermentation and/or chemical synthesis.
  • microbial fermentation refers to a process of growing and harvesting fermenting microorganisms under suitable conditions.
  • the fermenting microorganism can be any microorganism suitable for use in a desired fermentation process for the production of bio-based products. Suitable fermenting microorganisms include, without limitation, filamentous fungi, yeast, and bacteria.
  • the saccharified biomass can, for ' example, be made it into a fuel (e.g., a biofuel such as a bioethanol, biobutanol, biomethanol, a biopropanol, a biodiesel, a jet fuel, or the like) via fermentation and/or chemical synthesis.
  • a fuel e.g., a biofuel such as a bioethanol, biobutanol, biomethanol, a biopropanol, a biodiesel, a jet fuel, or the like
  • the saccharified biomass can, for example, also be made into a commodity chemical (e.g., ascorbic acid, isoprene, 1 ,3-propanediol), lipids, amino acids, polypeptides, and enzymes, via fermentation and/or chemical synthesis.
  • a commodity chemical e.g., ascorbic acid, isoprene, 1 ,3-propanediol
  • lipids e.g.
  • the variant CBH I polypeptides of the disclosure find utility in the generation of ethanol from biomass in either separate or simultaneous saccharification and fermentation processes.
  • Separate saccharification and fermentation is a process whereby cellulose present in biomass is saccharified into simple sugars (e.g. , glucose) and the simple sugars subsequently fermented by microorganisms (e.g., yeast) into ethanol.
  • Simultaneous saccharification and fermentation is a process whereby cellulose present in biomass is saccharified into simple sugars (e.g., glucose) and, at the same time and in the same reactor, microorganisms (e.g., yeast) ferment the simple sugars into ethanol.
  • biomass Prior to saccharification, biomass is preferably subject to one or more pretreatment step(s) in order to render cellulose material more accessible or susceptible to enzymes and thus more amenable to hydrolysis by the variant CBH I polypeptides of the disclosure.
  • the pretreatment entails subjecting biomass material to a catalyst comprising a dilute solution of a strong acid and a metal salt in a reactor.
  • the biomass material can, e.g., be a raw material or a dried material.
  • This pretreatment can lower the activation energy, or the temperature, of cellulose hydrolysis, ultimately allowing higher yields of fermentable sugars. See, e.g., U.S. Patent Nos. 6,660,506; 6,423,145.
  • Another exemplary pretreatment method entails hydro lyzing biomass by subjecting the biomass material to a first hydrolysis step in an aqueous medium at a temperature and a pressure chosen to effectuate primarily depolymerization of hemicellulose without achieving significant depolymerization of cellulose into glucose.
  • This step yields a slurry in which the liquid aqueous phase contains dissolved monosaccharides resulting from depolymerization of hemicellulose, and a solid phase containing cellulose and lignin.
  • the slurry is then subject to a second hydrolysis step under conditions that allow a major portion of the cellulose to be depolymerized, yielding a liquid aqueous phase containing dissolved/soluble
  • a further exemplary method involves processing a biomass material by one or more stages of dilute acid hydrolysis using about 0.4% to about 2% of a strong acid; followed by treating the unreacted solid lignocellulosic component of the acid hydrolyzed material with alkaline delignification. See, e.g., U.S. Patent No. 6,409,841.
  • Another exemplary pretreatment method comprises prehydrolyzing biomass (e.g., lignocellulosic materials) in a prehydrolysis reactor; adding an acidic liquid to the solid lignocellulosic material to make a mixture; heating the mixture to reaction temperature; maintaining reaction temperature for a period of time sufficient to fractionate the lignocellulosic material into a solubilized portion containing at least about 20% of the lignin from the lignocellulosic material, and a solid fraction containing cellulose; separating the solubilized portion from the solid fraction, and removing the solubilized portion while at or near reaction temperature; and recovering the solubilized portion.
  • the cellulose in the solid fraction is rendered more amenable to enzymatic digestion. See, e.g., U.S. Patent No. 5,705,369.
  • Further pretreatment methods can involve the use of hydrogen peroxide H 2 0 2 . See Gould, 1984, Biotech, and Bioengr. 26:46-
  • Pretreatment can also comprise contacting a biomass material with stoichiometric amounts of sodium hydroxide and ammonium hydroxide at a very low concentration. See Teixeira et ah, 1999, Appl. Biochem.and Biotech. 77-79:19-34. Pretreatment can also comprise contacting a lignocellulose with a chemical (e.g., a base, such as sodium carbonate or potassium hydroxide) at a pH of about 9 to about 14 at moderate temperature, pressure, and pH. See PCT Publication WO2004/081185.
  • a chemical e.g., a base, such as sodium carbonate or potassium hydroxide
  • Ammonia pretreatment can also be used.
  • Such a pretreatment method comprises subjecting a biomass material to low ammonia concentration under conditions of high solids. See, e.g., U.S. Patent Publication No. 20070031918 and PCT publication WO 06/1 10901.
  • the present disclosure also provides detergent compositions comprising a variant CBH I polypeptide of the disclosure.
  • the detergent compositions may employ besides the variant CBH I polypeptide one or more of a surfactant, including anionic, non-ionic and ampholytic surfactants; a hydrolase; a bleaching agents; a bluing agent; a caking inhibitors; a solubilizer; and a cationic surfactant. All of these components are known in the detergent art.
  • the variant CBH I polypeptide is preferably provided as part of celkilase
  • the cellulase composition can be employed from about 0.00005 weight percent to about 5 weight percent or from about 0.0002 weight percent to about 2 weight percent of the total detergent composition.
  • the cellulase composition can be in the form of a liquid diluent, granule, emulsion, gel, paste, and the like. Such forms are known to the skilled artisan. When a solid detergent composition is employed, the cellulase composition is preferably formulated as granules. 6.
  • Protein expression was carried out in an Aspergillus niger host strain that had been transformed using PEG-mediated transformation with expression constructs for CBHI that included the hygromycin resistance gene as a selectable marker, in which the full length CBH I sequences (signal sequence, catalytic domain, linker and cellulose binding domain) were under the control of the glyceraldeyhde-3 -phosphate dehydrogenase (gpd) promoter. Transformants were selected on the regeneration medium based on resistance to hygromycin.
  • the selected transformants were cultured in Aspergillus salts medium, pH 6.2 supplemented with the antibiotics penicillin, streptomycin, and hygromycin, and 80g/L glycerol, 20g/L soytone, lOmM uridine, 20g/L MES) in baffled shake flasks at 30°C, 170 rpm. After five days of incubation, the total secreted protein supernatant was recovered, and then subjected to hollow fiber filtration to concentrate and exchange the sample into acetate buffer (50 mM NaAc, pH 5). CBH I protein represented over 90% of the total protein in these samples. Protein purity was analyzed by SDS-PAGE. Protein concentration was determined by gel densitometry and/or HPLC analysis. All CBH I protein concentrations were normalized before assay and concentrated to 1-2.5 mg/ml..
  • 4- Methyiumbelliferyl Lactoside (4-MUL) Assay This assay measures the activity of CBH I on the fluorogenic substrate 4-MUL (also known as MUL). Assays were run in a costar 96-well black bottom plate, where reactions were initiated by the addition of 4-MUL to enzyme in buffer (2mM 4-MUL in 200mM MES pH 6). Enzymatic rates were monitored by fluorescent readouts over five minutes on a SPECTRAMAXTM plate reader (ex/em 365/450 nm). Data in the linear range was used to calculate initial rates (Vo).
  • Phosphoric Acid Swollen Cellulose This assay measures the activity of CBH I using PASC as the substrate. During the assay, the concentration of PASC is monitored by a fluorescent signal derived from calcofluor binding to PASC (ex/em 365/440 nm). The assay is initiated by mixing enzyme (15 ⁇ ) and reaction buffer (85 ⁇ of 0.2% PASC, 200 mM MES, pH 6), and then incubating at 35°C while shaking at 225 RPM. After 2 hours, one reaction volume of calcofluor stop solution (100 ⁇ g/ml in 500 mM glycine pH 10) is added and fluorescence read-outs obtained (ex/em 365/440 nm).
  • reaction buffer 85 ⁇ of 0.2% PASC, 200 mM MES, pH 6
  • Bagasse Assay This assay measures the activity of CBH I on bagasse, a
  • reactions were run in 10 ml vials with 5% dilute acid pretreated bagasse (250 mg solids per 5 ml reaction). Each reaction contained 4 mg CBH I enzyme/g solids, 200 mM MES pH 6, kanamycin, and chloramphenicol. Reactions were incubated at 35°C in hybridization incubators (Robbins Scientific), rotating at 20 RPM. Time points were taken by transferring a sample of homogenous slurry (150 ⁇ ) into a 96-well deep well plate and quenching the reaction with stop buffer (450 ⁇ of 500 mM sodium carbonate, pH 10). Time point measurements were taken every 24 hours for 72 hours.
  • stop buffer 450 ⁇ of 500 mM sodium carbonate, pH 10
  • Cellobiose Tolerance Assays (or Cellobiose Inhibition Assays): Tolerance to cellobiose (or inhibition caused by cellobiose) was tested in two ways in the CBH I assays.
  • a direct-dose tolerance method can be applied to all of the CBH I assays (i.e., 4-MUL, PASC, and/or bagasse assays), and entails the exogenous addition of a known amount of cellobiose into assay mixtures.
  • a different indirect method entails the addition of an excess amount of ⁇ -glucosidase (BG) to PASC and bagasse assays (typically, 1 mg ⁇ -glucosidase/g solids loaded).
  • BG ⁇ -glucosidase
  • BG will enzymatically hydrolyze the cellobiose generated during these assays; therefore, CBH I activity in the presence of BG can be taken as a measure of activity in the absence of cellobiose. Furthermore, when activity in the presence and absence of BG are similar, this indicates tolerance to cellobiose. Notably, in cases where BG activity is undesired, but may be present in crude CBH I enzyme preparations, the BG inhibitor gluconolactone can be added into CBH I assays to prevent cellobiose breakdown.
  • the wild type CBH I polypeptide BD29555 was mutagenized to identify variants with improved product tolerance.
  • a small (60-member) library of BD29555 variants was designed to identify variant CBH I polypeptides with reduced product inhibition.
  • This product-release-site library was designed based on residues directly interacting with the cellobiose product in an attempt to identify variants with weakened interactions with cellobiose from which the product would be released more readily than the wild type enzyme.
  • the 60-member evolution library contained wild-type residues and mutations at positions R273, W405, and R422 of BD29555 (SEQ ID NO: l), and included the following substitutions: R273 (WT), R273Q, R273K, R273A, W405 (WT), W405Q, W405H, R422 (WT), R422Q, R422K, R422L, and R422E (4 variants at position 273 X 3 variants at position 405 X 5 variants at position 422 equals 60 variants in total). All members of the library were screened using the 4-MUL assay in the presence and absence of 250g/L cellobiose and using gluconolactone to inhibit any BG activity.
  • the R273A, R273Q, and R273K/R422K variants showed enhanced product tolerance.
  • the R273K/R422K variant showed greatest activity among the variants and cellobiose tolerance at 250 mg/L. Due to low expression, the R273K variant was not tested for product inhibition.
  • R273K/R422K substitutions were characterized in both a wild type BD29555 background and also in combination with the substitutions Y274Q, D281K, Y410H, P411G, which were identified in a screen of an expanded product release site evolution library.
  • R273K/R422K variant showed little inhibition in the presence of 10 g/L cellobiose.
  • bars represent tolerance to cellobiose, as represented by the ratio of activity in the presence of accumulating cellobiose (-BG) to that of activity in the absence of cellobiose (+BG); ratios close to 1 indicate greater tolerance to cellobiose.

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Abstract

The present disclosure relates to variant CBH I polypeptides that have reduced product inhibition, and compositions, e.g., cellulase compositions, comprising variant CBH I polypeptides. The variant CBH I polypeptides and related compositions can be used in variety of agricultural and industrial applications. The present disclosure further relates to nucleic acids encoding variant CBH I polypeptides and host cells that recombinantly express the variant CBH I polypeptides.

Description

VARIANT CBH I POLYPEPTIDES WITH REDUCED PRODUCT
INHIBITION
1. CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit under 35 U.S.C. § 1 19(e) of U.S. Provisional Application no. 61/390,392, filed October 6, 2010, the contents of which are incorporated herein in their entireties by reference thereto.
2. BACKGROUND
[0002] Cellulose is an unbranched polymer of glucose linked by P(l→4)-glycosidic bonds. Cellulose chains can interact with each other via hydrogen bonding to form a crystalline solid of high mechanical strength and chemical stability . The cellulose chains are depolymerized into glucose and short oligosaccharides before organisms, such as the fermenting microbes used in ethanol production, can use them as metabolic fuel. Cellulase enzymes catalyze the hydrolysis of the cellulose (hydrolysis of P-l,4-D-glucan linkages) in the biomass into products such as glucose, cellobiose, and other cellooligosaccharides. Cellulase is a generic term denoting a multienzyme mixture comprising exo-acting cellobiohydrolases (CBHs), endoglucanases (EGs) and β-glucosidases (BGs) that can be produced by a number of plants and microorganisms. Enzymes in the cellulase of Trichoderma reesei include CBH I (more generally, Cel7A), CBH2 (Cel6A), EG1 (Cel7B), EG2 (Cel5), EG3 (Cell 2), EG4 (Cel61A), EG5 (Cel45A), EG6 (Cel74A), Cipl, Cip2, β-glucosidases (including,. e.g., Cel3A), acetyl xylan esterase, β-mannanase, and swollenin.
[0003] Cellulase enzymes work synergistically to hydrolyze cellulose to glucose. CBH I and CBH II act on opposing ends of cellulose chains (Barr et al, 1996, Biochemistry 35:586-92), while the endoglucanases act at internal locations in the cellulose. The primary product of these enzymes is cellobiose, which is further hydrolyzed to glucose by one or more β- glucosidases.
[0004] The cellobiohydrolases are subject to inhibition by their direct product, cellobiose, which results in a slowing down of saccharification reactions as product accumulates. There is a need for new and improved cellobiohyrolases with improved productivity that maintain their reaction rates during the course of a saccharification reaction, for use in the conversion of cellulose into fermentable sugars and for related fields of cellulosic material processing such as pulp and paper, textiles and animal feeds.
3. SUMMARY
[0005] The present disclosure relates to variant CBH I polypeptides. Most naturally occurring CBH I polypeptides have arginines at positions corresponding to R268 and R41 1 of T. reesei CBH I (SEQ ID NO:2). The variant CBH I polypeptides of the present disclosure include a substitution at either or both positions resulting in a reduction or decrease in product (e.g. , cellobiose) inhibition. Such variants are sometimes referred to herein as "product tolerant."
[0006] The variant CBH I polypeptides of the disclosure minimally contain at least a CBH I catalytic domain, comprising (a) a substitution at the amino acid position corresponding to R268 of T. reesei CBH I ("R268 substitution"); (b) a substitution at the amino acid position corresponding to R41 1 of T. reesei CBH I ("R41 1 substitution"); or (c) both an R268 substitution and an R41 1 substitution. The amino acid positions of exemplary CBH I polypeptides into which R268 and/or R41 1 substitutions can be introduced are shown in Table 1 , and the amino acid positions corresponding to R268 and/or R41 1 in these exemplary CBH I polypeptides are shown in Table 2.
[0007] R268 and/or R41 1 substituents can include lysines and/or alanines. Accordingly, the present disclosure provides a variant CBH I polypeptide comprising a CBH I catalytic domain with one of the following amino acid substitutions or pairs of R268 and/or R41 1 substitutions: (a) R268K and R41 IK; (b) R268K and R41 1 A; (c) R268A and R41 IK; (d) R268A and R41 1A; (e) R268A; (f) R268K; (g) R41 1A; and (h) R41 IK. In some embodiments, however, the amino acid sequence of the variant CBH I polypeptide does not comprise or consist of SEQ ID NO: 150, SEQ ID NO: 151 , SEQ ID NO: 152, or SEQ ID NO: 153.
[0008] The variant CBHI polypeptides of the disclosure typically include a CD comprising an amino acid sequence having at least 50% sequence identity to a CD of a reference CBH I exemplified in Table 1. The CD portions of the CBH I polypeptides exemplified in Table 1 are delineated in Table 3. The variant CBH I polypeptides can have a cellulose binding domain ("CBD") sequence in addition to the catalytic domain ("CD") sequence. The CBD can be N- or C-terminal to the CD, and the CBD and CD are optionally connected via a linker sequence.
[0009] The variant CBH I polypeptides can be mature polypeptides or they may further comprise a signal sequence.
[0010] Additional embodiments of the variant CBH I polypeptides are provided in Section 5.1.
[0011] The variant CBH I polypeptides of the disclosure typically exhibit reduced product inhibition by cellobiose. In certain embodiments, the IC50 of cellobiose towards a variant CBH I polypeptide of the disclosure is at least 1.2-fold, at least 1.5-fold, or at least 2-fold the IC50 of cellobiose towards a reference CBH I lacking the R268 substitution and/or R41 1 substitution present in the variant. Additional embodiments of the product inhibition characteristics of the variant CBH I polypeptides are provided in Section 5.1.
[0012] The variant CBH I polypeptides of the disclosure typically retain some
cellobiohydrolase activity. In certain embodiments, a variant CBH I polypeptide retains at least 50% the CBH I activity of a reference CBH I lacking the R268 substitution and/or R41 1 substitution present in the variant. Additional embodiments of cellobiohydrolase activity of the variant CBH I polypeptides are provided in Section 5.1.
[0013] The present disclosure further provides compositions (including cellulase
compositions, e.g., whole cellulase compositions, and fermentation broths) comprising variant CBH I polypeptides. Additional embodiments of compositions comprising variant CBH I polypeptides are provided in Section 5.3. The variant CBH I polypeptides and compositions comprising them can be used, inter alia, in processes for saccharifying biomass. Additional details of saccharification reactions, and additional applications of the variant CBH I polypeptides, are provided in Section 5.4. [0014] The present disclosure further provides nucleic acids (e.g., vectors) comprising nucleotide sequences encoding variant CBH I polypeptides as described herein, and recombinant cells engineered to express the variant CBH I polypeptides. The recombinant cell can be a prokaryotic (e.g., bacterial) or eukaryotic (e.g., yeast or filamentous fungal) cell. Further provided are methods of producing and optionally recovering the variant CBH I polypeptides. Additional embodiments of the recombinant expression system suitable for expression and production of the variant CBH I polypeptides are provided in Section 5.2.
4. BRIEF DESCRIPTION OF THE FIGURES AND TABLES
[0015] .FIGURE 1A-1B: Cellobiose dose-response curves using a 4-MUL assay for a wild- type CBH I (BD29555; Figure 1A) and a R268K/R41 IK variant CBH I (BD29555 with the substitutions R273K/R422K; Figure IB).
[0016] FIGURE 2A-2B: The effect of cellobiose accumulation on the activity of wild-type CBH I and a R268K/R41 IK variant CBH I, based on percent conversion of glucan after 72 hours in the bagasse assay. Figure 2A shows relative activity in the presence (+) and absence (-) of β-glucosidase (BG), where relative activity is normalized to wild type activity with BG (WT+ = 1). Figure 2B shows tolerance to cellobiose as a function of the ratio of activity in the absence vs. presence of β-glucosidase (activity ratio = Activity -BG/Activity +BG).
[0017] FIGURE 3: Cellobiose dose-response curves using PASC assay for a R268K/R41 IK variant CBH I polypeptide as compared to two wild type CBH I polypeptides.
[0018] FIGURE 4: The effect of cellobiose accumulation on the activity of a wild-type CBH I and a R268K/R41 IK variant CBH I based on percent conversion of glucan after 72 hours in the bagasse assay in the presence (+) and absence (-) of β-glucosidase (BG). Activity is normalized to wild type activity with BG (WT+ = 1).
[0019] FIGURE 5: Characterization of cellobiose product tolerance of variant CBH I polypeptides, based on percent conversion of glucan after 72 hours in the absence and presence of β-glucosidase (BG) in the bagasse assay; tolerance is evaluated as a function of the ratio of activity in the absence vs. presence of β-glucosidase. [0020] TABLE 1: Amino acid sequences of exemplary "reference" CBH I polypeptides that can be modified at positions corresponding to R268 and/or R411 in T. reesei CBH I (SEQ ID NO:2). The database accession numbers are indicated in the second column. Unless indicated otherwise, the accession numbers refer to the Genbank database. "#" indicates that the CBH I has no signal peptide; "&" indicate that the sequence is from the PDB database and represents the catalytic domain only without signal sequence; * indicates a nonpublic database. These amino acid sequences are mostly wild type, with the exception of some sequences from the PDB database which contain mutations to facilitate protein
crystallization.
[0021] TABLE 2: Amino acid positions in the exemplary reference CBH I polypeptides that correspond to R268 and R411 in T. reesei CBH I. Database descriptors are as for Table 1.
[0022] TABLE 3: Approximate amino acid positions of CBH I polypeptide domains.
Abbreviations used: SS is signal sequence; CD is catalytic domain; and CBD is cellulose binding domain. Database descriptors are as for Table 1.
[0023] TABLE 4: Table 4 shows a segment within the catalytic domain of each exemplary reference CBH I polypeptide containing the active site loop (shown in bold, underlined text) and the catalytic residues (glutamates in most CBH I polypeptides) (shown in bold, double underlined text). Database descriptors are as for Table 1.
[0024] TABLE 5: MUL and bagasse assay results for variants of BD29555. ND means not determined. ± %Activity (+/- cellobiose) = [(Activity with cellobiose)/(Activity without cellobiose)] *100. ¥ %Activity (-/+ BG) = [(Activity without BG)/( Activity with BG)] *100]
[0025] TABLE 6: MUL and bagasse assay results for variants of T. reesei CBH I. ND means not determined. ± %Activity (+/- cellobiose) = [(Activity with cellobiose)/(Activity without cellobiose)] * 100. ¥ %Activity (-/+ BG) = [(Activity without BG)/( Activity with BG)] * 100.
[0026] TABLE 7: Informal sequence listing. SEQ ID NO: l-149 correspond to the exemplary reference CBH I polypeptides. SEQ ID NO: 150 corresponds to mature T. reesei CBH I (amino acids 26-529 of SEQ ID NO:2) with an R268A substitution. SEQ ID NO: 151 corresponds to mature T. reesei CBH I (amino acids 26-529 of SEQ ID NO:2) with an R41 1A substitution. SEQ ID NO: 152 corresponds to full length BD29555 with both an R268K substitution and an R41 IK substitution. SEQ ID NO: 153 corresponds to mature BD29555 with both an R268K substitution and an R41 IK substitution.
5. DETAILED DESCRIPTION
[0027] The present disclosure relates to variant CBH I polypeptides. Most naturally occurring CBH I polypeptides have arginines at positions corresponding to R268 and R41 1 of T. reesei CBH I (SEQ ID NO:2). The variant CBH I polypeptides of the present disclosure include a substitution at either or both positions resulting in a reduction of product {e.g., cellobiose) inhibition. The following subsections describe in greater detail the variant CBH I polypeptides and exemplary methods of their production, exemplary cellulase compositions comprising them, and some industrial applications of the polypeptides and cellulase compositions.
5.1. VARIANT CBH I POLYPEPTIDES
[0028] The present disclosure provides variant CBH I polypeptides comprising at least one amino acid substitution that results in reduced product inhibition. "Variant" means a polypeptide which is differs in sequence from a reference polypeptide by substitution of one or more amino acids at one or a number of different sites in the amino acid sequence.
Exemplary reference CBH I polypeptides are shown in Table 1.
[0029] The variant CBH I polypeptides of the disclosure have an amino acid substitution at the amino acid position corresponding to R268 of T. reesei CBH I (SEQ ID NO:2) (an "R268 substitution"), (b) a substitution at the amino acid position corresponding to R41 1 of T. reesei CBH I ("R41 1 substitution"); or (c) both an R268 substitution and an R41 1 substitution, as compared to a reference CBH I polypeptide. It is noted that the R268 and R41 1 numbering is made by reference to the full length T. reesei CBH I, which includes a signal sequence that is generally absent from the mature enzyme. The corresponding numbering in the mature T. reesei CBH I (see, e.g., SEQ ID NO:4) is R251 and R394, respectively. [0030] Accordingly, the present disclosure provides variant CBH I polypeptides in which at least one of the amino acid positions corresponding to R268 and R41 1 of T. reesei CBH I, and optionally both the amino acid positions corresponding to R268 and R41 1 of T. reesei CBH I, is not an arginine.
[0031] The amino acid positions in the reference polypeptides of Table 1 that correspond to R268 and R41 1 in T. reesei CBH I are shown in Table 2. Amino acid positions in other CBH I polypeptides that correspond to R268 and R41 1 can be identified through alignment of their sequences with T. reesei CBH I using a sequence comparison algorithm. Optimal alignment of sequences for comparison can be conducted, e.g. , by the local homology algorithm of Smith & Waterman, 1981 , Adv. Appl. Math. 2:482-89; by the homology alignment algorithm of Needleman & Wunsch, 1970, J. Mol. Biol. 48:443-53; by the search for similarity method of Pearson & Lipman, 1988, Proc. Nat'l Acad. Sci. USA 85:2444-48, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the
Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr.,
Madison, Wis.), or by visual inspection.
[0032] The R268 and/or R41 1 substitutions are preferably selected from (a) R268K and R41 IK; (b) R268K and R41 1 A; (c) R268A and'R41 IK; (d) R268A and R41 1 A; (e) R268A; (f) R268K; (g) R41 1A; and (h) R41 IK.
[0033] CBH I polypeptides belong to the glycosyl hydrolase family 7 ("GH7"). The glycosyl hydrolases of this family include endoglucanases and cellobiohydrolases
(exoglucanases). The cellobiohydrolases act processively from the reducing ends of cellulose chains to generate cellobiose. Cellulases of bacterial and fungal origin
characteristically have a small cellulose-binding domain ("CBD") connected to either the N or the C terminus of the catalytic domain ("CD") via a linker peptide (see Suumakki et al, 2000, Cellulose 7: 189-209). The CD contains the active site whereas the CBD interacts with cellulose by binding the enzyme to it (van Tilbeurgh et al, 1986, FEBS Lett. 204(2): 223- 227; Tomme et al, 1988, Eur. J. Biochem. 170:575-581). The three-dimensional structure of the catalytic domain of T. reesei CBH I has been solved (Divne et al, 1994, Science
265:524-528). The CD consists of two β-sheets that pack face-to-face to form a β-sandwich. Most of the remaining amino acids in the CD are loops connecting the β-sheets. Some loops are elongated and bend around the active site, forming cellulose-binding tunnel of (~50 A). In contrast, endoglucanases have an open substrate binding cleft/groove rather than a tunnel. Typically, the catalytic residues are glutamic acids corresponding to E229 and E234 of T. reesei CBH I.
[0034] The loops characteristic of the active sites ("the active site loops") of reference CBH I polypeptides, which are absent from GH7 family endoglucanases, as well as catalytic glutamate residues of the reference CBH I polypeptides, are shown in Table 4. The variant CBH I polypeptides of the disclosure preferably retain the catalytic glutamate residues or may include a glutamine instead at the position corresponding to E234, as for SEQ ID NO:4. In some embodiments, the variant CBH I polypeptides contain no substitutions or only conservative substitutions in the active site loops relative to the reference CBH I
polypeptides from which the variants are derived.
[0035] Many CBH I polypeptides do not have a CBD, and most studies concerning the activity of cellulase domains on different substrates have been carried out with only the catalytic domains of CBH I polypeptides. Because CDs with cellobiohydrolase activity can be generated by limited proteolysis of mature CBH I by papain (see, e.g., Chen et al., 1993, Biochem. Mol. Biol. Int. 30(5):901-10), they are often referred to as "core" domains.
Accordingly, a variant CBH I can include only the CD "core" of CBH I. Exemplary reference CDs comprise amino acid sequences corresponding to positions 26 to 455 of SEQ ID NO: l , positions 18 to 444 of SEQ ID NO:2, positions 26 to 455 of SEQ ID NO:3, positions 1 to 427 of SEQ ID NO:4, positions 24 to 457 of SEQ ID NO:5, positions 18 to 448 of SEQ ID NO:6, positions 27 to 460 of SEQ ID NO:7, positions 27 to 460 of SEQ ID NO:8, positions 20 to 449 of SEQ ID NO:9, positions 1 to 424 of SEQ ID NO: 10, positions 18 to 447 of SEQ ID NO: 1 1 , positions 18 to 434 of SEQ ID NO: 12, positions 18 to 445 of SEQ ID NO : 13 , positions 19 to 454 of SEQ ID NO : 14, positions 19 to 443 of SEQ ID NO : 15 , positions 2 to 426 of SEQ ID NO: 16, positions 23 to 446 of SEQ ID NO: 17, positions 19 to 449 of SEQ ID NO: 18, positions 23 to 446 of SEQ ID NO: 19, positions 19 to 449 of SEQ ID NO:20, positions 2 to 416 of SEQ ID NO:21 , positions 19 to 454 of SEQ ID NO:22, positions 19 to 447 of SEQ ID NO:23, positions 19 to 447 of SEQ ID NO:24, positions 20 to 443 of SEQ ID NO:25, positions 18 to 447 of SEQ ID NO:26, positions 19 to 442 of SEQ ID NO:27, positions 18 to 451 of SEQ ID NO:28, positions 23 to 446 of SEQ ID NO:29, positions 18 to 444 of SEQ ID NO:30, positions 18 to 451 of SEQ ID NO:31, positions 18 to
447 of SEQ ID NO:32, positions 19 to 449 of SEQ ID NO:33, positions 18 to 447 of SEQ ID NO:34, positions 26 to 459 of SEQ ID NO:35, positions 19 to 450 of SEQ ID NO:36, positions 19 to 453 of SEQ ID NO:37, positions 18 to 448 of SEQ ID NO:38, positions 19 to 443 of SEQ ID NO:39, positions 19 to 442 of SEQ ID NO:40, positions 18 to 444 of SEQ ID NO:41, positions 24 to 457 of SEQ ID NO:42, positions 18 to 449 of SEQ ID NO:43, positions 19 to 453 of SEQ ID NO:44, positions 26 to 456 of SEQ ID NO:45, positions 19 to 451 of SEQ ID NO:46, positions 18 to 443 of SEQ ID NO:47, positions 18 to 448 of SEQ ID NO:48, positions 19 to 4 1 of SEQ ID NO:49, positions 18 to 444 of SEQ ID NO:50, positions 2 to 419 of SEQ ID NO:51, positions 27 to 461 of SEQ ID NO:52, positions 21 to 445 of SEQ ID NO:53, positions 19 to 449 of SEQ ID NO:54, positions 19 to 448 of SEQ ID NO:55, positions 18 to 443 of SEQ ID NO:56, positions 20 to 443 of SEQ ID NO:57, positions 18 to 448 of SEQ ID NO:58, positions 18 to 447 of SEQ ID NO:59, positions 26 to 455 of SEQ ID NO:60, positions 19 to 449 of SEQ ID NO:61, positions 19 to 449 of SEQ ID NO:62, positions 26 to 460 of SEQ ID NO:63, positions 18 to 448 of SEQ ID NO:64, positions 19 to 451 of SEQ ID NO:65, positions 19 to 447 of SEQ ID NO:66, positions 1 to 424 of SEQ ID NO:67, positions 19 to 448 of SEQ ID NO:68, positions 19 to 443 of SEQ ID NO:69, positions 23 to 447 of SEQ ID NO:70, positions 17 to 448 of SEQ ID NO:71, positions 19 to 449 of SEQ ID NO:72, positions 18 to 444 of SEQ ID NO:73, positions 23 to 458 of SEQ ID NO:74, positions 20 to 452 of SEQ ID NO:75, positions 18 to 435 of SEQ ID NO:76, positions 18 to 446 of SEQ ID NO:77, positions 22 to 457 of SEQ ID NO:78, positions 18 to 448 of SEQ ID NO:79, positions 1 to 431 of SEQ ID NO:80, positions 19 to 453 of SEQ ID NO:81, positions 21 to 440 of SEQ ID NO:82, positions 19 to 442 of SEQ ID NO:83, positions 18 to 448 of SEQ ID NO:84, positions 17 to 446 of SEQ ID NO:85, positions 18 to 447 of SEQ ID NO:86, positions 18 to 443 of SEQ ID NO:87, positions 23 to
448 of SEQ ID NO:88, positions 18 to 451 of SEQ ID NO:89, positions 21 to 447 of SEQ ID NO:90, positions 18 to 444 of SEQ ID NO:91, positions 19 to 442 of SEQ ID NO:92, positions 20 to 436 of SEQ ID NO:93, positions 18 to 450 of SEQ ID NO:94, positions 22 to 453 of SEQ ID NO:95, positions 16 to 472 of SEQ ID NO:96, positions 21 to 445 of SEQ ID NO:97, positions 19 to 447 of SEQ ID NO:98, positions 19 to 450 of SEQ ID NO:99, positions 19 to 451 of SEQ ID NO: 100, positions 18 to 448 of SEQ ID NO: 101, positions 19 to 442 of SEQ ID NO: 102, positions 20 to 457 of SEQ ID NO: 103, positions 19 to 454 of SEQ ID NO: 104, positions 18 to 440 of SEQ ID NO: 105, positions 18 to 439 of SEQ ID NO: 106, positions 27 to 460 of SEQ ID NO: 107, positions 23 to 446 of SEQ ID NO: 108, positions 17 to 446 of SEQ ID NO: 109, positions 21 to 447 of SEQ ID NO: l 10, positions 19 to 447 of SEQ ID NO: 111 , positions 18 to 449 of SEQ ID NO: 112, positions 22 to 457 of SEQ ID NO: l 13, positions 18 to 445 of SEQ ID NO: l 14, positions 18 to 448 of SEQ ID NO: l 15, positions 18 to 448 of SEQ ID NO: l 16, positions 23 to 435 of SEQ ID NO: l 17, positions 21 to 442 of SEQ ID NO: l 18, positions 23 to 435 of SEQ ID NO: l 19, positions 20 to 445 of SEQ ID NO: 120, positions 21 to 443 of SEQ ID NO: 121, positions 20 to 445 of SEQ ID NO: 122, positions 23 to 443 of SEQ ID NO: 123, positions 20 to 445 of SEQ ID NO: 124, positions 21 to 435 of SEQ ID NO:125, positions 20 to 437 of SEQ ID NO: 126, positions 21 to 442 of SEQ ID NO: 127, positions 23 to 434 of SEQ ID NO: 128, positions 20 to 444 of SEQ ID NO: 129, positions 21 to 435 of SEQ ID NO: 130, positions 20 to 445 of SEQ ID NO: 131, positions 21 to 446 of SEQ ID NO: 132, positions 21 to 435 of SEQ ID NO: 133, positions 22 to 448 of SEQ ID NO: 134, positions 23 to 433 of SEQ ID NO: 135, positions 23 to 434 of SEQ ID NO: 136, positions 23 to 435 of SEQ ID NO: 137, positions 23 to 435 of SEQ ID NO: 138, positions 20 to 445 of SEQ ID NO: 139, positions 20 to 437 of SEQ ID NO: 140, positions 21 to 435 of SEQ ID NO: 141, positions 20 to 437 of SEQ ID NO: 142, positions 21 to 435 of SEQ ID NO:143, positions 26 to 435 of SEQ ID NO: 144, positions 23 to 435 of SEQ ID NO: 145, positions 24 to 443 of SEQ ID NO: 146, positions 20 to 445 of SEQ ID NO: 147, positions 21 to 441 of SEQ ID NO: 148, and positions 20 to 437 of SEQ ID NO: 149.
[0036] The CBDs are particularly involved in the hydrolysis of crystalline cellulose. It has been shown that, the ability of cellobiohydrolases to degrade crystalline cellulose decreases when the CBD is absent (Under and Teeri, 1997, Journal of Biotechnol. 57: 15-28). The variant CBH I polypeptides of the disclosure can further include a CBD. Exemplary CBDs comprise amino acid sequences corresponding to positions 494 to 529 of SEQ ID NO: l, positions 480 to 514 of SEQ ID NO:2, positions 494 to 529 of SEQ ID NO:3, positions 491 to 526 of SEQ ID NO: 5, positions 477 to 512 of SEQ ID NO:6, positions 497 to 532 of SEQ ID NO:7, positions 504 to 539 of SEQ ID NO:8, positions 486 to 521 of SEQ ID NO: 13, positions 556 to 596 of SEQ ID NO: 15, positions 490 to 525 of SEQ ID NO: 18, positions 495 to 530 of SEQ ID NO:20, positions 471 to 506 of SEQ ID NO:23, positions 481 to 516 of SEQ ID NO:27, positions 480 to 514 of SEQ ID NO:30, positions 495 to 529 of SEQ ID NO:35, positions 493 to 528 of SEQ ID NO:36, positions 477 to 512 of SEQ ID NO:38, positions 547 to 586 of SEQ ID NO:39, positions 475 to 510 of SEQ ID NO:40, positions 479 to 513 of SEQ ID NO:41, positions 506 to 541 of SEQ ID NO:42, positions 481 to 516 of SEQ ID NO:43, positions 503 to 537 of SEQ ID NO:45, positions 488 to 523 of SEQ ID NO:46, positions 476 to 511 of SEQ ID NO:48, positions 488 to 523 of SEQ ID NO:49, positions 479 to 513 of SEQ ID NO:50, positions 500 to 535 of SEQ ID NO:52, positions 493 to 528 of SEQ ID NO:55, positions 479 to 514 of SEQ ID NO:58, positions 494 to 529 of SEQ ID NO:60, positions 490 to 525 of SEQ ID NO:61, positions 497 to 532 of SEQ ID NO:62, positions 475 to 510 of SEQ ID NO:64, positions 477 to 512 of SEQ ID NO:65, positions 486 to 521 of SEQ ID NO:66, positions 470 to 505 of SEQ ID NO:67, positions 491 to 526 of SEQ ID NO:68, positions 476 to 511 of SEQ ID NO:69, positions 480 to 514 of SEQ ID NO:73, positions 506 to 540 of SEQ ID NO:74, positions 471 to 504 of SEQ ID NO:76, positions 501 to 536 of SEQ ID NO:78, positions 473 to 508 of SEQ ID NO:79, positions 481 to 516 of SEQ ID NO:83, positions 488 to 523 of SEQ ID NO:86, positions 475 to 510 of SEQ ID NO:92, positions 468 to 504 of SEQ ID NO:93, positions 501 to 536 of SEQ ID NO:96, positions 482 to 517 of SEQ ID NO:98, positions 481 to 516 of SEQ ID NO:99, positions 488 to 523 of SEQ ID NO: 100, positions 472 to 507 of SEQ ID NO: 101, positions 481 to 516 of SEQ ID NO: 102, positions 471 to 505 of SEQ ID NO: 105, positions 481 to 516 of SEQ ID NO: 106, positions 495 to 530 of SEQ ID NO: 107, positions 488 to 523 of SEQ ID NO: l 1 1, positions 478 to 513 of SEQ ID NO: l 12, positions 501 to 536 of SEQ ID NO:l 13, positions 491 to 526 of SEQ ID NO: l 15, and positions 503 to 538 of SEQ ID NO: 1 16.
[0037] The CD and CBD are often connected via a linker. Exemplary linker sequences correspond to positions 456 to 493 of SEQ ID NO: 1 , positions 445 to 479 of SEQ ID NO:2, positions 456 to 493 of SEQ ID NO: 3, positions 458 to 490 of SEQ ID NO:5, positions 449 to 476 of SEQ ID NO:6, positions 461 to 496 of SEQ ID NO:7, positions 461 to 503 of SEQ ID NO:8, positions 446 to 485 of SEQ ID NO: 13, positions 444 to 555 of SEQ ID NO: 15, positions 450 to 489 of SEQ ID NO: 18, positions 450 to 494 of SEQ ID NO:20, positions
448 to 470 of SEQ ID NO:23, positions 443 to 480 of SEQ ID NO:27, positions 445 to 479 of SEQ ID NO:30, positions 460 to 494 of SEQ ID NO:35, positions 451 to 492 of SEQ ID NO:36, positions 449 to 476 of SEQ ID NO:38, positions 444 to 546 of SEQ ID NO:39, positions 443 to 474 of SEQ ID NO:40, positions 445 to 478 of SEQ ID NO:41, positions 458 to 505 of SEQ ID NO:42, positions 450 to 480 of SEQ ID NO:43, positions 457 to 502 of SEQ ID NO:45, positions 452 to 487 of SEQ ID NO:46, positions 449 to 475 of SEQ ID NO:48, positions 452 to 487 of SEQ ID NO:49, positions 445 to 478 of SEQ ID NO:50, positions 462 to 499 of SEQ ID NO:52, positions 449 to 492 of SEQ ID NO:55, positions
449 to 478 of SEQ ID NO:58, positions 456 to 493 of SEQ ID NO:60, positions 450 to 489 of SEQ ID NO:61, positions 450 to 496 of SEQ ID NO:62, positions 449 to 474 of SEQ ID NO:64, positions 452 to 476 of SEQ ID NO:65, positions 448 to 485 of SEQ ID NO:66, positions 425 to 469 of SEQ ID NO:67, positions 449 to 490 of SEQ ID NO:68, positions 444 to 475 of SEQ ID NO:69, positions 445 to 479 of SEQ ID NO:73, positions 459 to 505 of SEQ ID NO:74, positions 436 to 470 of SEQ ID NO:76, positions 458 to 500 of SEQ ID NO:78, positions 449 to 472 of SEQ ID NO:79, positions 443 to 480 of SEQ ID NO:83, positions 448 to 487 of SEQ ID NO:86, positions 443 to 474 of SEQ ID NO:92, positions 437 to 467 of SEQ ID NO:93, positions 473 to 500 of SEQ ID NO:96, positions 448 to 481 of SEQ ID NO:98, positions 451 to 480 of SEQ ID NO:99, positions 452 to 487 of SEQ ID NO: 100, positions 449 to 471 of SEQ ID NO: 101 , positions 443 to 480 of SEQ ID NO: 102, positions 441 to 470 of SEQ ID NO: 105, positions 440 to 480 of SEQ ID NO: 106, positions 461 to 494 of SEQ ID NO: 107, positions 448 to 487 of SEQ ID NO: 11 1 , positions 450 to 478 of SEQ ID NO: l 12, positions 458 to 500 of SEQ ID NO: l 13, positions 449 to 490 of SEQ ID NO: 1 15, and positions 449 to 502 of SEQ ID NO: 1 16.
[0038] Because CBH I polypeptides are modular, the CBDs, CDs and linkers of different CBH I polypeptides, such as the exemplary CBH I polypeptides of Table 1 , can be used interchangeably. However, in a preferred embodiment, the CBDs, CDs and linkers of a variant CBH I of the disclosure originate from the same polypeptide.
[0039] The variant CBH I polypeptides of the disclosure preferably have at least a two-fold reduction of product inhibition, such that cellobiose has an IC50 towards the variant CBH I that is at least 2-fold the IC50 of the corresponding reference CBH I, e.g., CBH I lacking the R268 substitution and/or R41 1 substitution. More preferably the IC50 of cellobiose towards the variant CBH I is at least 3-fold, at least 5-fold, at least 8-fold, at least 10-fold, at least 12- fold or at least 15-fold the IC50 of the corresponding reference CBH I. In specific
embodiments the IC50 of cellobiose towards the variant CBH I is ranges from 2-fold to 15- fold, from 2-fold to 10-fold, from 3-fold to 10-fold, from 5-fold to 12-fold, from 4-fold to 12- fold, from 5-fold to 10-fold, from 5-fold to 12-fold, from 2-fold to 8-fold, or from 8-fold to 20-fold the IC50 of the corresponding reference CBH I. The IC50 can be determined in a phosphoric, acid swollen cellulose ("PASC") assay (Du et al, 2010, Applied Biochemistry and Biotechnology 161 :313-317) or a methylumbelliferyl lactoside ("MUL") assay (van Tilbeurgh and Claeyssens, 1985, FEBS Letts. 187(2):283-288), as exemplified in the
Examples below.
[0040] The variant CBH I polypeptides of the disclosure preferably have a cellobiohydrolase activity that is at least 30% the cellobiohydrolase activity of the corresponding reference CBH I, e.g., CBH I lacking the R268 substitution and/or R41 1 substitution. More preferably, the cellobiohydrolase activity of the variant CBH I is at least 40%, at least 50%, at least 60% or at least 70% the cellobiohydrolase activity of the corresponding reference CBH I. In specific embodiments the IC50 cellobiohydrolase activity of the variant CBH I is ranges from 30%) to 80%, from 40% to 70%, 30% to 60%, from 50% to 80% or from 60% to 80% of the cellobiohydrolase activity of the corresponding reference CBH I. Assays for
cellobiohydrolase activity are described, for example, in Becker et al, 201 1 , Biochem J. 356: 19-30 and Mitsuishi et al, 1990, FEBS Letts. 275: 135-138, each of which is expressly incorporated by reference herein. The ability of CBH I to hydrolyze isolated soluble and insoluble substrates can also be measured using assays described in Srisodsuk et al, 1997, J. Biotech. 57:4957 and Nidetzky and Claeyssens, 1994, Biotech. Bioeng. 44:961-966.
Substrates useful for assaying cellobiohydrolase activity include crystalline cellulose, filter paper, phosphoric acid swollen cellulose, cellooligosaccharides, methylumbelliferyl lactoside, methylumbelliferyl cellobioside, orthonitrophenyl lactoside, paranitrophenyl lactoside, orthonitrophenyl cellobioside, paranitrophenyl cellobioside. Cellobiohydrolase activity can be measured in an assay utilizing PASC as the substrate and a calcofluor white detection method (Du et al., 2010, Applied Biochemistry and Biotechnology 161 :313-317). PASC can be prepared as described by Walseth, 1952, TAPPI 35:228-235 and Wood, 1971, Biochem. J. 121 :353-362.
[0041] Other than said R268 and/or R411 substitution, the variant CBH I polypeptides of the disclosure preferably:
• comprise an amino acid sequence having at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity to a CD of a reference CBH I exemplified in Table 1 {i.e., a CD comprising an amino acid sequence corresponding to positions 26 to 455 of SEQ ID NO: l, positions 18 to 444 of SEQ ID NO:2, positions 26 to 455 of SEQ ID NO:3, positions 1 to 427 of SEQ ID NO:4, positions 24 to 457 of SEQ ID NO:5, positions 18 to 448 of SEQ ID NO: 6, positions 27 to 460 of SEQ ID NO:7, positions 27 to 460 of SEQ ID NO:8, positions 20 to 449 of SEQ ID NO:9, positions 1 to 424 of SEQ ID NO: 10, positions 18 to 447 of SEQ ID NO: l 1, positions 18 to 434 of SEQ ID NO: 12, positions 18 to 445 of SEQ ID NO : 13 , positions 19 to 454 of SEQ ID NO : 14, positions 19 to 443 of SEQ ID NO : 15 , positions 2 to 426 of SEQ ID NO: 16, positions 23 to 446 of SEQ ID NO: 17, positions 19 to 449 of SEQ ID NO: 18, positions 23 to 446 of SEQ ID NO: 19, positions 19 to 449 of SEQ ID NO:20, positions 2 to 416 of SEQ ID NO:21, positions 19 to 454 of SEQ ID NO:22, positions 19 to 447 of SEQ ID NO:23, positions 19 to 447 of SEQ ID NO:24, positions 20 to 443 of SEQ ID NO:25, positions 18 to 447 of SEQ ID NO:26, positions 19 to 442 of SEQ ID NO:27, positions 18 to 451 of SEQ ID NO 28, positions 23 to 446 of SEQ ID NO:29, positions 18 to 444 of SEQ ID NO 30, positions 18 to 451 of SEQ ID NO:31, positions 18 to 447 of SEQ ID NO 32, positions 19 to 449 of SEQ ID NO:33, positions 18 to 447 of SEQ ID NO 34, positions 26 to 459 of SEQ ID NO:35, positions 19 to 450 of SEQ ID NO 36, positions 19 to 453 of SEQ ID NO:37, positions 18 to 448 of SEQ ID NO 38, positions 19 to 443 of SEQ ID NO:39, positions 19 to 442 of SEQ ID NO 40, positions 18 to 444 of SEQ ID NO:41, positions 24 to 457 of SEQ ID NO 42, positions 18 to 449 of SEQ ID NO:43, positions 19 to 453 of SEQ ID NO 44, positions 26 to 456 of SEQ ID NO:45, positions 19 to 451 of SEQ ID NO 46, positions 18 to 443 of SEQ ID NO:47, positions 18 to 448 of SEQ ID NO 48, positions 19 to 451 of SEQ ID NO:49, positions 18 to 444 of SEQ ID NO 50, positions 2 to 419 of SEQ ID NO:51, positions 27 to 461 of SEQ ID NO:52, positions 21 to 445 of SEQ ID NO:53, positions 19 to 449 of SEQ ID NO:54, positions 19 to 448 of SEQ ID NO:55, positions 18 to 443 of SEQ ID NO:56, positions 20 to 443 of SEQ ID NO:57, positions 18 to 448 of SEQ ID NO:58, positions 18 to 447 of SEQ ID NO:59, positions 26 to 455 of SEQ ID NO:60, positions 19 to 449 of SEQ ID NO:61, positions 19 to 449 of SEQ ID NO:62, positions 26 to 460 of SEQ ID NO:63, positions 18 to 448 of SEQ ID NO:64, positions 19 to 451 of SEQ ID NO:65, positions 19 to 447 of SEQ ID NO:66, positions 1 to 424 of SEQ ID NO:67, positions 19 to 448 of SEQ ID NO:68, positions 19 to 443 of SEQ ID NO:69, positions 23 to 447 of SEQ ID NO:70, positions 17 to 448 of SEQ ID NO:71, positions 19 to 449 of SEQ ID NO:72, positions 18 to 444 of SEQ ID NO:73, positions 23 to 458 of SEQ ID NO:74, positions 20 to 452 of SEQ ID NO:75, positions 18 to 435 of SEQ ID NO:76, positions 18 to 446 of SEQ ID NO:77, positions 22 to 457 of SEQ ID NO:78, positions 18 to 448 of SEQ ID NO:79, positions 1 to 431 of SEQ ID NO: 80, positions 19 to 453 of SEQ ID NO:81, positions 21 to 440 of SEQ ID NO:82, positions 19 to 442 of SEQ ID NO:83, positions 18 to 448 of SEQ-ID NO:84, positions 17 to 446 of SEQ ID NO:85, positions 18 to 447 of SEQ ID NO:86, positions 18 to 443 of SEQ ID NO:87, positions 23 to 448 of SEQ ID NO:88, positions 18 to 451 of SEQ ID NO:89, positions 21 to 447 of SEQ ID NO:90, positions 18 to 444 of SEQ ID NO:91 , positions 19 to 442 of SEQ ID NO:92, positions 20 to 436 of SEQ ID NO:93, positions 18 to 450 of SEQ ID NO:94, positions 22 to 453 of SEQ ID NO:95, positions 16 to 472 of SEQ ID NO:96, positions 21 to 445 of SEQ ID NO:97, positions 19 to 447 of SEQ ID NO:98, positions 19 to 450 of SEQ ID NO:99, positions 19 to 451 of SEQ ID NO: 100, positions 18 to 448 of SEQ ID NO: 101 , positions 19 to 442 of SEQ ID NO: 102, positions 20 to 457 of SEQ ID NO: 103, positions 19 to 454 of SEQ ID NO: 104, positions 18 to 440 of SEQ ID NO: 105, positions 18 to 439 of SEQ ID NO: 106, positions 27 to 460 of SEQ ID NO: 107, positions 23 to 446 of SEQ ID NO: 108, positions 17 to 446 of SEQ ID NO: 109, positions 21 to 447 of SEQ ID NO : 1 10, positions 19 to 447 of SEQ ID NO : 1 1 1 , positions 18 to 449 of SEQ ID NO: l 12, positions 22 to 457 of SEQ ID NO: 1 13, ' positions 18 to 445 of SEQ ID NO : 114, positions 18 to 448 of SEQ ID NO : 1 15 , positions 18 to 448 of SEQ ID NO: 116, positions 23 to 435 of SEQ ID NO: 1 17, positions 21 to 442 of SEQ ID NO: 1 18, positions 23 to 435 of SEQ ID NO: 1 19, positions 20 to 445 of SEQ ID NO: 120, positions 21 to 443 of SEQ ID NO: 121, positions 20 to 445 of SEQ ID NO: 122, positions 23 to 443 of SEQ ID NO: 123, positions 20 to 445 of SEQ ID NO:124, positions 21 to 435 of SEQ ID NO: 125, positions 20 to 437 of SEQ ID NO: 126, positions 21 to 442 of SEQ ID NO: 127, positions 23 to 434 of SEQ ID NO: 128, positions 20 to 444 of SEQ ID NO:129, positions 21 to 435 of SEQ ID NO: 130, positions 20 to 445 of SEQ ID NO: 131, positions 21 to 446 of SEQ ID NO: 132, positions 21 to 435 of SEQ ID NO: 133, positions 22 to 448 of SEQ ID NO: 134, positions 23 to 433 of SEQ ID NO:135, positions 23 to 434 of SEQ ID NO: 136, positions 23 to 435 of SEQ ID NO: 137, positions 23 to 435 of SEQ ID NO: 138, positions 20 to 445 of SEQ ID NO: 139, positions 20 to 437 of SEQ ID NO : 140, positions 21 to 435 of SEQ ID NO : 141 , positions 20 to 437 of SEQ ID NO: 142, positions 21 to 435 of SEQ ID NO: 143, positions 26 to 435 of SEQ ID NO: 144, positions 23 to 435 of SEQ ID NO: 145, positions 24 to 443 of SEQ ID NO: 146, positions 20 to 445 of SEQ ID NO: 147, positions 21 to 441 of SEQ ID NO: 148, and positions 20 to 437 of SEQ ID NO: 149 (preferably the CD corresponding to positions 26-455 of SEQ ID NO; l or 18-444 of SEQ ID NO: 2); and/or
comprise an amino acid sequence having at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%; 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or complete (100%) sequence identity to a mature polypeptide of a reference CBH I exemplified in Table 1 (i.e., a mature protein comprising an amino acid sequence corresponding to positions 26 to 529 of SEQ ID NO: l , positions 18 to 514 of SEQ ID NO:2, positions 26 to 529 of SEQ ID NO:3, positions 1 to 427 of SEQ ID NO:4, positions 24 to 526 of SEQ ID NO:5, positions 18 to 512 of SEQ ID NO:6, positions 27 to 532 of SEQ ID NO:7, positions 27 to 539 of SEQ ID NO:8, positions 20 to 449 of SEQ ID NO:9, positions 1 to 424 of SEQ ID NO: 10, positions
18 to 447 of SEQ ID NO: 1 1 , positions 18 to 434 of SEQ ID NO: 12, positions 18 to 521 of SEQ ID NO: 13, positions 19 to 454 of SEQ ID NO: 14, positions 19 to 596 of SEQ ID NO: 15, positions 2 to 426 of SEQ ID NO: 16, positions 23 to 446 of SEQ ID NO: 17, positions 19 to 525 of SEQ ID NO: 18, positions 23 to 446 of SEQ ID NO: 19, positions 19 to 530 of SEQ ID NO:20, positions 2 to 416 of SEQ ID NO:21 , positions
19 to 454 of SEQ ID NO:22, positions 19 to 506 of SEQ ID NO:23, positions 19 to 447 of SEQ ID NO:24, positions 20 to 443 of SEQ ID NO:25, positions 18 to 447 of SEQ ID NO:26, positions 19 to 516 of SEQ ID NO:27, positions 18 to 451 of SEQ ID NO:28, positions 23 to 446 of SEQ ID NO:29, positions 18 to 514 of SEQ ID NO:30, positions 18 to 451 of SEQ ID NO:31 , positions 18 to 447 of SEQ ID NO:32, positions 19 to 449 of SEQ ID NO:33, positions 18 to 447 of SEQ ID NO:34, positions 26 to 529 of SEQ ID NO:35, positions 19 to 528 of SEQ ID NO:36, positions 19 to 453 of SEQ ID NO:37, positions 18 to 512 of SEQ ID NO:38, positions 19 to 586 of SEQ ID NO:39, positions 19 to 510 of SEQ ID NO:40, positions 18 to 513 of SEQ ID NO :41, positions 24 to 541 of SEQ ID NO:42, positions 18 to 516 of SEQ ID NO:43, positions 19 to 453 of SEQ ID NO:44, positions 26 to 537 of SEQ ID NO:45, positions 19 to 523 of SEQ ID NO:46, positions 18 to 443 of SEQ ID NO:47, positions 18 to 511 of SEQ ID NO:48, positions 19 to 523 of SEQ ID NO:49, positions 18 to 513 of SEQ ID NO:50, positions 2 to 419 of SEQ ID NO:51, positions 27 to 535 of SEQ ID NO:52, positions 21 to 445 of SEQ ID NO: 53, positions 19 to 449 of SEQ ID NO: 54, positions 19 to 528 of SEQ ID NO:55, positions 18 to 443 of SEQ ID NO:56, positions 20 to 443 of SEQ ID NO:57, positions 18 to 514 of SEQ ID NO:58, positions 18 to 447 of SEQ ID NO:59, positions 26 to 529 of SEQ ID NO:60, positions 19 to 525 of SEQ ID NO:61, positions 19 to 532 of SEQ ID NO:62, positions 26 to 460 of SEQ ID NO:63, positions 18 to 510 of SEQ ID NO: 64, positions 19 to 512 of SEQ ID NO: 65, positions 19 to 521 of SEQ ID NO:66, positions 1 to 505 of SEQ ID NO:67, positions 19 to 526 of SEQ ID NO:68, positions 19 to 511 of SEQ ID NO:69, positions 23 to 447 of SEQ ID NO:70, positions 17 to 448 of SEQ ID NO:71, positions 19 to 449 of SEQ ID NO:72, positions 18 to 514 of SEQ ID NO:73, positions 23 to 540 of SEQ ID NO:74, positions 20 to 452 of SEQ ID NO:75, positions 18 to 504 of SEQ ID NO:76, positions 18 to 446 of SEQ ID NO:77, positions 22 to 536 of SEQ ID NO:78, positions 18 to 508 of SEQ ID NO:79, positions 1 to 431 of SEQ ID NO:80, positions 19 to 453 of SEQ ID NO: 81, positions 21 to 440 of SEQ ID NO:82, positions 19 to 516 of SEQ ID NO:83, positions 18 to 448 of SEQ ID NO:84, positions 17 to 446 of SEQ ID NO:85, positions 18 to 523 of SEQ ID NO:86, positions 18 to 443 of SEQ ID NO:87, positions 23 to 448 of SEQ ID NO:88, positions 18 to 451 of SEQ ID NO:89, positions 21 to 447 of SEQ ID NO: 90, positions 18 to 444 of SEQ ID NO:91, positions 19 to 510 of SEQ ID NO:92, positions 20 to 504 of SEQ ID NO:93, positions 18 to 450 of SEQ ID NO:94, positions 22 to 453 of SEQ ID NO:95, positions 16 to 536 of SEQ ID NO:96, positions 21 to 445 of SEQ ID NO:97, positions 19 to 517 of SEQ ID NO:98, positions 19 to 516 of SEQ ID NO:99, positions 19 to 523 of SEQ ID NO: 100, positions 18 to 507 of SEQ ID NO 101 , positions 19 to 516 of SEQ ID NO: 102, positions 20 to 457 of SEQ ID NO 103, positions 19 to 454 of SEQ ID NO: 104, positions 18 to 505 of SEQ ID NO 105, positions 18 to 516 of SEQ ID NO: 106, positions 27 to 530 of SEQ ID NO 107, positions 23 to 446 of SEQ ID NO: 108, positions 17 to 446 of SEQ ID NO 109, positions 21 to 447 of SEQ ID NO: 1 10, positions 19 to 523 of SEQ ID NO H I , positions 18 to 513 of SEQ ID NO: 1 12, positions 22 to 536 of SEQ ID NO 1 13, positions 18 to 445 of SEQ ID NO: 1 14, positions 18 to 526 of SEQ ID NO 115, positions 18 to 538 of SEQ ID NO: 1 16, positions 23 to 435 of SEQ ID NO 1 17, positions 21 to 442 of SEQ ID NO: 1 18, positions 23 to 435 of SEQ ID NO 1 19, positions 20 to 445 of SEQ ID NO: 120, positions 21 to 443 of SEQ ID NO 121, positions 20 to 445 of SEQ ID NO: 122, positions 23 to 443 of SEQ ID NO 123, positions 20 to 445 of SEQ ID NO: 124, positions 21 to 435 of SEQ ID NO 125, positions 20 to 437 of SEQ ID NO: 126, positions 21 to 442 of SEQ ID NO 127, positions 23 to 434 of SEQ ID NO: 128, positions 20 to 444 of SEQ ID NO 129, positions 21 to 435 of SEQ ID NO: 130, positions 20 to 445 of SEQ ID NO 131, positions 21 to 446 of SEQ ID NO: 132, positions 21 to 435 of SEQ ID NO 133, positions 22 to 448 of SEQ ID NO: 134, positions 23 to 433 of SEQ ID NO 135, positions 23 to 434 of SEQ ID NO: 136, positions 23 to 435 of SEQ ID NO 137, positions 23 to 435 of SEQ ID NO: 138, positions 20 to 445, of SEQ ID NO: 139, positions 20 to 437 of SEQ ID NO: 140, positions 21 to 435 of SEQ ID NO: 141, positions 20 to 437 of SEQ ID NO: 142, positions 21 to 435 of SEQ ID NO: 143, positions 26 to 435 of SEQ ID NO: 144, positions 23 to 435 of SEQ ID NO: 145, positions 24 to 443 of SEQ ID NO: 146, positions 20 to 445 of SEQ ID NO: 147, positions 21 to 441 of SEQ ID NO: 148, and positions 20 to 437 of SEQ ID NO: 149, preferably the mature polypeptide corresponding to positions 26-529 of SEQ ID NO: 1 or 18-514 of SEQ ID NO:2). [0042] An example of an algorithm that is suitable for determining sequence similarity is the BLAST algorithm, which is described in Altschul et al, 1990, J. Mol. Biol. 215:403-410. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence that either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. These initial neighborhood word hits act as starting points to find longer HSPs containing them. The word hits are expanded in both directions along each of the two sequences being compared for as far as the cumulative alignment score can be increased. Extension of the word hits is stopped when: the cumulative alignment score falls off by the quantity X from a maximum achieved value; the cumulative score goes to zero or below; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLAST program uses as defaults a word length (W) of 1 1, the BLOSUM62 scoring matrix (see Henikoff & Henikoff, 1992, Proc. Nat'l. Acad. Sci. USA 89:10915-10919) alignments (B) of 50, expectation (E) of 10, M'5, N'-4, and a comparison of both strands.
[0043] Most CBH I polypeptides are secreted and are therefore expressed with a signal sequence that is cleaved upon secretion of the polypeptide from the cell. Accordingly, in certain aspects, the variant CBH I polypeptides of the disclosure further include a signal sequence. Exemplary signal sequences comprise amino acid sequences corresponding to positions 1 to 25 of SEQ ID NO: l, positions 1 to 17 of SEQ ID NO:2, positions 1 to 25 of SEQ ID NO:3, positions 1 to 23 of SEQ ID NO:5, positions 1 to 17 of SEQ ID NO:6, positions 1 to 26 of SEQ ID NO:7, positions 1 to 27 of SEQ ID NO:8, positions 1 to 19 of SEQ ID NO:9, positions 1 to 17 of SEQ ID NO:l 1, positions 1 to 17 of SEQ ID NO: 12, positions 1 to 17 of SEQ ID NO: 13, positions 1 to 18 of SEQ ID NO: 14, positions 1 to 18 of SEQ ID NO: 15, positions 1 to 22 of SEQ ID NO: 17, positions 1 to 18 of SEQ ID NO: 18, positions 1 to 22 of SEQ ID NO: 19, positions 1 to 18 of SEQ ID NO:20, positions 1 to 18 of SEQ ID NO:22, positions 1 to 18 of SEQ ID NO:23, positions 1 to 18 of SEQ ID NO:24, positions 1 to 19 of SEQ ID NO:25, positions 1 to 17 of SEQ ID,NO:26, positions 1 to 18 of SEQ ID NO:27, positions 1 to 17 of SEQ ID NO:28, positions 1 to 22 of SEQ ID NO:29, positions 1 to 18 of SEQ ID NO:30, positions 1 to 17 of SEQ ID NO:31, positions 1 to 17 of SEQ ID NO:32, positions 1 to 18 of SEQ ID NO:33, positions 1 to 17 of SEQ ID NO:34, positions 1 to 25 of SEQ ID NO:35, positions 1 to 18 of SEQ ID NO:36, positions 1 to 18 of SEQ ID NO:37, positions 1 to 17 of SEQ ID NO:38, positions 1 to 18 of SEQ ID NO:39, positions 1 to 18 of SEQ ID NO:40, positions 1 to 17 of SEQ ID NO:41, positions 1 to 23 of SEQ ID NO:42, positions 1 to 17 of SEQ ID NO:43, positions 1 to 18 of SEQ ID NO:44, positions 1 to 25 of SEQ ID NO:45, positions 1 to 18 of SEQ ID NO:46, positions 1 to 17 of SEQ ID NO:47, positions 1 to 17 of SEQ ID NO:48, positions 1 to 18 of SEQ ID NO:49, positions 1 to 17 of SEQ ID NO:50, positions 1 to 26 of SEQ ID NO:52, positions 1 to 20 of SEQ ID NO:53, positions 1 to 18 of SEQ ID NO:54, positions 1 to 18 of SEQ ID NO:55, positions 1 to 17 of SEQ ID NO:56, positions 1 to 19 of SEQ ID NO:57, positions 1 to 17 of SEQ ID NO:58, positions 1 to 17 of SEQ ID NO:59, positions 1 to 25 of SEQ ID NO:60, positions 1 to 18 of SEQ ID NO:61, positions 1 to 18 of SEQ ID NO:62, positions 1 to 25 of SEQ ID NO:63, positions 1 to 17 of SEQ ID NO:64, positions 1 to 18 of SEQ ID NO:65, positions 1 to 18 of SEQ ID NO:66, positions 1 to 18 of SEQ ID NO:68, positions 1 to 18 of SEQ ID NO:69, positions 1 to 23 of SEQ ID NO:70, positions 1 to 17 of SEQ ID NO:71, positions 1 to 18 of SEQ ID NO:72, positions 1 to 17 of SEQ ID NO:73, positions 1 to 22 of SEQ ID NO:74, positions 1 to 19 of SEQ ID NO:75, positions 1 to 17 of SEQ ID NO:76, positions 1 to 17 of SEQ ID NO:77, positions 1 to 21 of SEQ ID NO:78, positions 1 to 18 of SEQ ID NO:79, positions 1 to 18 of SEQ ID NO:81, positions 1 to 20 of SEQ ID NO:82, positions 1 to 18 of SEQ ID NO:83, positions 1 to 17 of SEQ ID NO:84, positions 1 to 16 of SEQ ID NO-.85, positions 1 to 17 of SEQ ID NO:86, positions 1 to 17 of SEQ ID NO:87, positions 1 to 22 of SEQ ID NO:88, positions 1 to 17 of SEQ ID NO:89, positions 1 to 20 of SEQ ID NO:90, positions 1 to 17 of SEQ ID NO:91, positions 1 to 18 of SEQ ID NO:92, positions 1 to 19 of SEQ ID NO:93, positions 1 to 17 of SEQ ID NO:94, positions 1 to 21 of SEQ ID NO:95, positions 1 to 15 of SEQ ID NO:96, positions 1 to 20 of SEQ ID NO:97, positions 1 to 18 of SEQ ID NO:98, positions 1 to 18 of SEQ ID NO:99, positions 1 to 18 of SEQ ID NO: 100, positions 1 to 17 of SEQ ID NO: 101 , positions 1 to 18 of SEQ ID NO: 102, positions 1 to 19 of SEQ ID NO: 103, positions 1 to 18 of SEQ ID NO: 104, positions 1 to 17 of SEQ ID NO: 105, positions 1 to 17 of SEQ ID NO: 106, positions 1 to 26 of SEQ ID NO: 107, positions 1 to 22 of SEQ ID NO: 108, positions 1 to 16 of SEQ ID NO: 109, positions 1 to 20 of SEQ ID NO: 110, positions 1 to 18 of SEQ ID NO: 11 1 , positions 1 to 17 of SEQ ID NO : 112, positions 1 to 21 of SEQ ID NO : 1 13 , positions 1 to 17 of SEQ ID NO : 1 14, positions 1 to 17 of SEQ ID NO : 1 15 , positions 1 to 18 of SEQ ID NO : 1 16, positions 1 to 22 of SEQ ID NO: 117, positions 1 to 20 of SEQ ID NO: 118, positions 1 to 22 of SEQ ID NO: 119, positions 1 to 19 of SEQ ID NO: 120, positions 1 to 20 of SEQ ID NO: 121, positions 1 to 19 of SEQ ID NO: 122, positions 1 to 22 of SEQ ID NO: 123, positions 1 to 19 of SEQ ID NO: 124, positions 1 to 20 of SEQ ID NO: 125, positions 1 to 19 of SEQ ID NO: 126, positions 1 to 21 of SEQ ID NO: 127, positions 1 to 22 of SEQ ID NO: 128, positions 1 to 19 of SEQ ID NO: 129, positions 1 to 20 of SEQ ID NO: 130, positions 1 to 19 of SEQ ID NO: 131, positions 1 to 20 of SEQ ID NO: 132, positions 1 to 20 of SEQ ID NO : 133 , positions 1 to 21 of SEQ ID NO : 134, positions 1 to 22 of SEQ ID NO: 135, positions 1 to 22 of SEQ ID NO: 136, positions 1 to 22 of SEQ ID NO: 137, positions 1 to 22 of SEQ ID NO: 138, positions 1 to 19 of SEQ ID NO: 139, positions 1 to 19 of SEQ ID NO: 140, positions 1 to 20 of SEQ ID NO: 141, positions 1 to 19 of SEQ ID NO: 142, positions 1 to 20 of SEQ ID NO: 143, positions 1 to 25 of SEQ ID NO: 144, positions 1 to 22 of SEQ ID NO: 145, positions 1 to 23 of SEQ ID NO: 146, positions 1 to 19 of SEQ ID NO: 147, positions 1 to 20 of SEQ ID NO: 148, and positions 1 to 19 of SEQ ID NO: 149.
5.2. RECOMBINANT EXPRESSION OF VARIANT CBH I
POLYPEPTIDES
5.2.1. Cell Culture Systems
[0044] The disclosure also provides recombinant cells engineered to express variant CBH I polypeptides. Suitably, the variant CBH I polypeptide is encoded by a nucleic acid operably linked to a promoter.
[0045] Where recombinant expression in a filamentous fungal host is desired, the promoter can be a filamentous fungal promoter. The nucleic acids can be, for example, under the control of heterologous promoters. The variant CBH I polypeptides can also be expressed under the control of constitutive or inducible promoters. Examples of promoters that can be used include, but are not limited to, a cellulase promoter, a xylanase promoter, the 1818 promoter (previously identified as a highly expressed protein by EST mapping Trichodermd). For example, the promoter can suitably be a cellobiohydrolase, endoglucanase, or β- glucosidase promoter. A particularly suitable promoter can be, for example, a T. reesei cellobiohydrolase, endoglucanase, or β- glucosidase promoter. Non-limiting examples of promoters include a cbhl, cbh2, egll, egl2, egl3, egl4, egl5, pkil, gpdl, xynl, or xyn2 promoter.
[0046] Suitable host cells include cells of any microorganism {e.g., cells of a bacterium, a protist, an alga, a fungus {e.g. , a yeast or filamentous fungus), or other microbe), and are preferably cells of a bacterium, a yeast, or a filamentous fungus.
[0047] Suitable host cells of the bacterial genera include, but are not limited to, cells of
Escherichia, Bacillus, Lactobacillus, Pseudomonas, and Streptomyces. Suitable cells of bacterial species include, but are not limited to, cells of Escherichia coli, Bacillus subtilis, Bacillus licheniformis, Lactobacillus brevis, Pseudomonas aeruginosa, and Streptomyces lividans.
[0048] Suitable host cells of the genera of yeast include, but are not limited to, cells of
Saccharomyces, Schizosaccharomyces, Candida, Hansenula, Pichia, Kluyveromyces, and Phaffia. Suitable cells of yeast species include, but are not limited to, cells of
Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, Hansenula polymorpha, Pichia pastoris, P. canadensis, Kluyveromyces marxianus, and Phaffia rhodozyma.
[0049] Suitable host cells of filamentous fungi include all filamentous forms of the subdivision Eumycotina. Suitable cells of filamentous fungal genera include, but are not limited to, cells of Acremonium, Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis, Chrysoporium, Coprinus, Coriolus, Corynascus, Chaetomium, Cryptococcus, Filobasidium, Fusarium, Gibberella, Humicola, Hypocrea, Magnaporthe, Mucor, Myceliophthora, Mucor, Neocallimastix, Ne rospora, Paecilomyces, Penicillium, Phanerochaete, Phlebia,
Piromyces, Pleurotus, Scytaldium, Schizophyllum, Sporotrichum, Talaromyces,
Thermoascus, Thielavia, Tolypocladium, Trametes, and Trichoderma. More preferably, the recombinant cell is a Trichoderma sp. {e.g., Trichoderma reesei), Penicillium sp., Humicola sp. {e.g. , Humicola insolens); Aspergillus sp. {e.g., Aspergillus niger), Chrysosporium sp., Fusarium sp., or Hypocrea sp. Suitable cells can also include cells of various anamorph and teleomorph forms of these filamentous fungal genera.
[0050] Suitable cells of filamentous fungal species include, but are not limited to, cells of Aspergillus awamori, Aspergillus fumigatus, Aspergillus foetidus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Chrysosporium lucknowense, Fusarium bactridioides , Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi, Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusarium sulphureum, Fusarium torulosum, Fusarium trichothecioides, Fusarium venenatum, Bjerkandera adusta,
Ceriporiopsis aneirina, Ceriporiopsis aneirina, Ceriporiopsis caregiea, Ceriporiopsis gilvescens, Ceriporiopsis pannocinta, Ceriporiopsis rivulosa, Ceriporiopsis subrufa, Ceriporiopsis subvermispora, Coprinus cinereus, Coriolus hirsutus, Humicola insolens, Humicola lanuginosa, Mucor miehei, Myceliophthora thermophila, Neurospora crassa, Neurospora intermedia, Penicillium purpurogenum, Penicillium canescens, Penicillium solitum, Penicillium funiculosum, Phanerochaete chrysosporium, Phlebia radiate, Pleurotus eryngii, Talaromyces flavus, Thielavia terrestris, Trametes villosa, Trametes versicolor, Trichoderma harzianum, Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma reesei, and Trichoderma viride.
[0051] The engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants, or amplifying the nucleic acid sequence encoding the variant CBH I polypeptide. Culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to those skilled in the art. As noted, many references are available for the culture and production of many cells, including cells of bacterial and fungal origin. Cell culture media in general are set forth in Atlas and Parks (eds.), 1993, The Handbook of
Microbiological Media, CRC Press, Boca Raton, FL, which is incorporated herein by reference. For recombinant expression in filamentous fungal cells, the cells are cultured in a standard medium containing physiological salts and nutrients, such as described in Pourquie et al, 1988, Biochemistry and Genetics of Cellulose Degradation, eds. Aubert, et al, Academic Press, pp. 71-86; and Ilmen et al, 1997, Appl. Environ. Microbiol. 63: 1298-1306. Culture conditions are also standard, e.g., cultures are incubated at 28°C in shaker cultures or fermenters until desired levels of variant CBH I expression are achieved. Preferred culture conditions for a given filamentous fungus may be found in the scientific literature and/or from the source of the fungi such as the American Type Culture Collection (ATCC). After fungal growth has been established, the cells are exposed to conditions effective to cause or permit the expression of a variant CBH I.
[0052] In cases where a variant CBH I coding sequence is under the control of an inducible promoter, the inducing agent, e.g., a sugar, metal salt or antibiotics, is added to the medium at a concentration effective to induce variant CBH I expression.
[0053] In one embodiment, the recombinant cell is an Aspergillus niger, which is a useful strain for obtaining overexpressed polypeptide. For example A. niger var. awamori dgr246 is known to product elevated amounts of secreted cellulases (Goedegebuur et al, 2002, Curr. Genet. 41 :89-98). Other strains of Aspergillus niger var awamori such as GCDAP3, GCDAP4 and GAP3-4 are known (Ward et al , 1993, Appl. Microbiol. Biotechnol. 39:738- 743).
[0054] In another embodiment, the recombinant cell is a Trichoderma reesei, which is a useful strain for obtaining overexpressed polypeptide. For example, RL-P37, described by Sheir-Neiss et al, 1984, Appl. Microbiol. Biotechnol. 20:46-53, is known to secrete elevated amounts of cellulase enzymes. Functional equivalents of RL-P37 include Trichoderma reesei strain RUT-C30 (ATCC No. 56765) and strain QM9414 (ATCC No. 26921). It is contemplated that these strains would also be useful in overexpressing variant CBH I polypeptides. [0055] Cells expressing the variant CBH I polypeptides of the disclosure can be grown under batch, fed-batch or continuous fermentations conditions. Classical batch fermentation is a closed system, wherein the compositions of the medium is set at the beginning of the fermentation and is not subject to artificial alternations during the fermentation. A variation of the batch system is a fed-batch fermentation in which the substrate is added in increments as the fermentation progresses. Fed-batch systems are useful when catabolite repression is likely to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the medium. Batch and fed-batch fermentations are common and well known in the art. Continuous fermentation is an open system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned medium is removed simultaneously for processing. Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth. Continuous fermentation systems strive to maintain steady state growth conditions. Methods for modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology.
5.2.2. Recombinant Expression in Plants
[0056] The disclosure provides transgenic plants and seeds that recombinantly express a variant CBH I polypeptide. The disclosure also provides plant products, e.g., oils, seeds, leaves, extracts and the like, comprising a variant CBH I polypeptide.
[0057] The transgenic plant can be dicotyledonous (a dicot) or monocotyledonous (a monocot). The disclosure also provides methods of making and using these transgenic plants and seeds. The transgenic plant or plant cell expressing a variant CBH I can be constructed in accordance with any method known in the art. See, for example, U.S. Patent No.
6,309,872. T. reesei CBH I has been successfully expressed in transgenic tobacco (Nicotiana tabaccum) and potato (Solanum tuberosum). See Hooker et al, 2000, in Glycosyl
Hydrolases for Biomass Conversion, ACS Symposium Series, Vol. 769, Chapter 4, pp. 55- 90. [0058] In a particular aspect, the present disclosure provides for the expression of CBH I variants in transgenic plants or plant organs and methods for the production thereof. DNA expression constructs are provided for the transformation of plants with a nucleic acid encoding the variant CBH I polypeptide, preferably under the control of regulatory sequences which are capable of directing expression of the variant CBH I polypeptide. These regulatory sequences include sequences capable of directing transcription in plants, either constitutively, or in stage and/or tissue specific manners.
[0059] The expression of variant CBH I polypeptides in plants can be achieved by a variety of means. Specifically, for example, technologies are available for transforming a large number of plant species, including dicotyledonous species (e.g. , tobacco, potato, tomato, Petunia, Brassica) and monocot species. Additionally, for example, strategies for the expression of foreign genes in plants are available. Additionally still, regulatory sequences from plant genes have been identified that are serviceable for the construction of chimeric genes that can be functionally expressed in plants and in plant cells (e.g., Klee, 1987, Ann. Rev. of Plant Phys. 38:467-486; Clark et al, 1990, Virology 179(2):640-7; Smith et al, 1990, Mol. Gen. Genet. 224(3):477-81.
[0060] The introduction of nucleic acids into plants can be achieved using several technologies including transformation with Agrobacterium tumefaciens or Agrobacterium rhizogenes. Non-limiting examples of plant tissues that can be transformed include protoplasts, microspores or pollen, and explants such as leaves, stems, roots, hypocotyls, and cotyls. Furthermore, DNA encoding a variant CBH I can be introduced directly into protoplasts and plant cells or tissues by microinjection, electroporation, particle
bombardment, and direct DNA uptake.
[0061] Variant CBH I polypeptides can be produced in plants by a variety of expression systems. For instance, the use of a constitutive promoter such as the 35S promoter of Cauliflower Mosaic Virus (Guilley et al, 1982, Cell 30:763-73) is serviceable for the accumulation of the expressed protein in virtually all organs of the transgenic plant.
Alternatively, promoters that are tissue-specific and/or stage-specific can be used (Higgins, 1984, Annu. Rev. Plant Physiol. 35: 191-221 ; Shotwell and Larkins, 1989, In:The Biochemistry of Plants Vol. 15 (Academic Press, San Diego: Stumpf and Conn, eds.), p. 297), permit expression of variant CBH I polypeptides in a target tissue and/or during a desired stage of development.
5.3. COMPOSITIONS OF VARIANT CBH I POLYPEPTIDES
[0062] In general, a variant CBH I polypeptide produced in cell culture is secreted into the medium and may be purified or isolated, e.g., by removing unwanted components from the cell culture medium. However, in some cases, a variant CBH I polypeptide may be produced in a cellular form necessitating recovery from a cell lysate. In such cases the variant CBH I polypeptide is purified from the cells in which it was produced using techniques routinely employed by those of skill in the art. Examples include, but are not limited to, affinity chromatography (Van Tilbeurgh et al, 1984, FEBS Lett. 169(2):215-218), ion-exchange chromatographic methods (Goyal et al, 1991, Bioresource Technology, 36:37-50; Fliess et al, 1983, Eur. J. Appl. Microbiol. Biotechnol.17:314-318; Bhikhabhai et al., 1984, J. Appl. Biochem. 6:336-345; Ellouz et al, 1987, Journal of Chromatography, 396:307-317), including ion-exchange using materials with high resolution power (Medve et al., 1998, J. Chromatography A, 808: 153-165), hydrophobic interaction chromatography (Tomaz and Queiroz, 1999, J. Chromatography A, 865: 123-128), and two-phase partitioning (Brumbauer et al., 1999, Bioseparation 7:287-295).
[0063] The variant CBH I polypeptides of the disclosure are suitably used in cellulase compositions. Cellulases are known in the art as enzymes that hydro lyze cellulose (beta- 1 ,4- glucan or beta D-glucosidic linkages) resulting in the formation of glucose, cellobiose, cellooligosaccharides, and the like. Cellulase enzymes have been traditionally divided into three major classes: endoglucanases ("EG"), exoglucanases or cellobiohydrolases (EC 3.2.1.91) ("CBH") and beta-glucosidases (EC 3.2.1.21) ("BG") (Knowles et al, 1987, TIBTECH 5:255-261 ; Schulein, 1988, Methods in Enzymology 160(25):234-243).
[0064] Certain fungi produce complete cellulase systems which include exo- cellobiohydrolases or CBH-type cellulases, endoglucanases or EG-type cellulases and β- glucosidases or BG-type cellulases (Schulein, 1988, Methods in Enzymology 160(25):234- 243). Such cellulase compositions are referred to herein as "whole" cellulases. However, sometimes these systems lack CBH-type cellulases and bacterial cellulases also typically include little or no CBH-type cellulases. In addition, it has been shown that the EG components and CBH components synergistically interact to more efficiently degrade cellulose. See, e.g., Wood, 1985, Biochemical Society Transactions 13(2):407-410.
[0065] The cellulase compositions of the disclosure typically include, in addition to a variant CBH I polypeptide, one or more cellobiohydrolases, endoglucanases and/or β-glucosidases. In their crudest form, cellulase compositions contain the microorganism culture that produced the enzyme components. "Cellulase compositions" also refers to a crude fermentation product of the microorganisms. A crude fermentation is preferably a fermentation broth that has been separated from the microorganism cells and/or cellular debris (e.g., by centrifugation and/or filtration). In some cases, the enzymes in the broth can be optionally diluted, concentrated, partially purified or purified and/or dried. The variant CBH I polypeptide can be co-expressed with one or more of the other components of the cellulase composition or it can be expressed separately, optionally purified and combined with a composition comprising one or more of the other cellulase components.
[0066] When employed in cellulase compositions, the variant CBH I is generally present in an amount sufficient to allow release of soluble sugars from the biomass. The amount of variant CBH I enzymes added depends upon the type of biomass to be saccharified which can be readily determined by the skilled artisan. In certain embodiments, the weight percent of variant CBH I polypeptide is suitably at least 1, at least 5, at least 10, or at least 20 weight percent of the total polypeptides in a cellulase composition. Exemplary cellulase compositions include a variant CBH I of the disclosure in an amount ranging from about 1 to about 20 weight percent, from about 1 to about 25 weight percent, from about 5 to about 20 weight percent, from about 5 to about 25 weight percent, from about 5 to about 30 weight percent, from about 5 to about 35 weight percent, from about 5 to about 40 weight percent, from about 5 to about 45 weight percent, from about 5 to about 50 weight percent, from about 10 to about 20 weight percent, from about 10 to about 25 weight percent, from about 10 to about 30 weight percent, from about 10 to about 35 weight percent, from about 10 to about 40 weight percent, from about 10 to about 45 weight percent, from about 10 to about 50 weight percent, from about 15 to about 20 weight percent, from about 15 to about 25 weight percent, from about 15 to about 30 weight percent, from about 15 to about 35 weight percent, from about 15 to about 30 weight percent, from about 15 to about 45 weight percent, or from about 15 to about 50 weight percent of the total polypeptides in the composition.
5.4. UTILITY OF VARIANT CBH I POLYPEPTIDES
[0067] It can be appreciated that the variant CBH I polypeptides of the disclosure and compositions comprising the variant CBH I polypeptides find utility in a wide variety applications, for example detergent compositions that exhibit enhanced cleaning ability, function as a softening agent and/or improve the feel of cotton fabrics (e.g., "stone washing" or "biopolishing"), or in cellulase compositions for degrading wood pulp into sugars (e.g., for bio-ethanol production). Other applications include the treatment of mechanical pulp (Pere et al, 1996, Tappi Pulping Conference, pp. 693-696 (Nashville, TN, Oct. 27-31, 1996)), for use as a feed additive (see, e.g., WO 91/04673) and in grain wet milling.
5.4.1. Saccharification Reactions
[0068] Ethanol can be produced via saccharification and fermentation processes from cellulosic biomass such as trees, herbaceous plants, municipal solid waste and agricultural and forestry residues. However, the ratio of individual cellulase enzymes within a naturally occurring cellulase mixture produced by a microbe may not be the most efficient for rapid conversion of cellulose in biomass to glucose. It is known that endoglucanases act to produce new cellulose chain ends which themselves are substrates for the action of cellobiohydrolases and thereby improve the efficiency of hydrolysis of the entire cellulase system. The use of optimized cellobiohydrolase activity may greatly enhance the production of ethanol.
[0069] Cellulase compositions comprising one or more of the variant CBH I polypeptides of the disclosure can be used in saccharification reaction to produce simple sugars for fermentation. Accordingly, the present disclosure provides methods for saccharification comprising contacting biomass with a cellulase composition comprising a variant CBH I polypeptide of the disclosure and, optionally, subjecting the resulting sugars to fermentation by a microorganism. [0070] The term "biomass," as used herein, refers to any composition comprising cellulose (optionally also hemicellulose and/or lignin). As used herein, biomass includes, without limitation, seeds, grains, tubers, plant waste or byproducts of food processing or industrial processing (e.g. , stalks), corn (including, e.g., cobs, stover, and the like), grasses (including, e.g., Indian grass, such as Sorghastrum nutans; or, switchgrass, e.g. , Panicum species, such as Panicum virgatum), wood (including, e.g., wood chips, processing waste), paper, pulp, and recycled paper (including, e.g., newspaper, printer paper, and the like). Other biomass materials include, without limitation, potatoes, soybean (e.g., rapeseed), barley, rye, oats, wheat, beets, and sugar cane bagasse.
[0071] The saccharified biomass (e.g., lignocellulosic material processed by enzymes of the disclosure) can be made into a number of bio-based products, via processes such as, e.g., microbial fermentation and/or chemical synthesis. As used herein, "microbial fermentation" refers to a process of growing and harvesting fermenting microorganisms under suitable conditions. The fermenting microorganism can be any microorganism suitable for use in a desired fermentation process for the production of bio-based products. Suitable fermenting microorganisms include, without limitation, filamentous fungi, yeast, and bacteria. The saccharified biomass can, for' example, be made it into a fuel (e.g., a biofuel such as a bioethanol, biobutanol, biomethanol, a biopropanol, a biodiesel, a jet fuel, or the like) via fermentation and/or chemical synthesis. The saccharified biomass can, for example, also be made into a commodity chemical (e.g., ascorbic acid, isoprene, 1 ,3-propanediol), lipids, amino acids, polypeptides, and enzymes, via fermentation and/or chemical synthesis.
[0072] Thus, in certain aspects, the variant CBH I polypeptides of the disclosure find utility in the generation of ethanol from biomass in either separate or simultaneous saccharification and fermentation processes. Separate saccharification and fermentation is a process whereby cellulose present in biomass is saccharified into simple sugars (e.g. , glucose) and the simple sugars subsequently fermented by microorganisms (e.g., yeast) into ethanol. Simultaneous saccharification and fermentation is a process whereby cellulose present in biomass is saccharified into simple sugars (e.g., glucose) and, at the same time and in the same reactor, microorganisms (e.g., yeast) ferment the simple sugars into ethanol. [0073] Prior to saccharification, biomass is preferably subject to one or more pretreatment step(s) in order to render cellulose material more accessible or susceptible to enzymes and thus more amenable to hydrolysis by the variant CBH I polypeptides of the disclosure.
[0074] In an exemplary embodiment, the pretreatment entails subjecting biomass material to a catalyst comprising a dilute solution of a strong acid and a metal salt in a reactor. The biomass material can, e.g., be a raw material or a dried material. This pretreatment can lower the activation energy, or the temperature, of cellulose hydrolysis, ultimately allowing higher yields of fermentable sugars. See, e.g., U.S. Patent Nos. 6,660,506; 6,423,145.
[0075] Another exemplary pretreatment method entails hydro lyzing biomass by subjecting the biomass material to a first hydrolysis step in an aqueous medium at a temperature and a pressure chosen to effectuate primarily depolymerization of hemicellulose without achieving significant depolymerization of cellulose into glucose. This step yields a slurry in which the liquid aqueous phase contains dissolved monosaccharides resulting from depolymerization of hemicellulose, and a solid phase containing cellulose and lignin. The slurry is then subject to a second hydrolysis step under conditions that allow a major portion of the cellulose to be depolymerized, yielding a liquid aqueous phase containing dissolved/soluble
depolymerization products of cellulose. See, e.g., U.S. Patent No. 5,536,325.
[0076] A further exemplary method involves processing a biomass material by one or more stages of dilute acid hydrolysis using about 0.4% to about 2% of a strong acid; followed by treating the unreacted solid lignocellulosic component of the acid hydrolyzed material with alkaline delignification. See, e.g., U.S. Patent No. 6,409,841. Another exemplary pretreatment method comprises prehydrolyzing biomass (e.g., lignocellulosic materials) in a prehydrolysis reactor; adding an acidic liquid to the solid lignocellulosic material to make a mixture; heating the mixture to reaction temperature; maintaining reaction temperature for a period of time sufficient to fractionate the lignocellulosic material into a solubilized portion containing at least about 20% of the lignin from the lignocellulosic material, and a solid fraction containing cellulose; separating the solubilized portion from the solid fraction, and removing the solubilized portion while at or near reaction temperature; and recovering the solubilized portion. The cellulose in the solid fraction is rendered more amenable to enzymatic digestion. See, e.g., U.S. Patent No. 5,705,369. Further pretreatment methods can involve the use of hydrogen peroxide H202. See Gould, 1984, Biotech, and Bioengr. 26:46- 52.
[0077] Pretreatment can also comprise contacting a biomass material with stoichiometric amounts of sodium hydroxide and ammonium hydroxide at a very low concentration. See Teixeira et ah, 1999, Appl. Biochem.and Biotech. 77-79:19-34. Pretreatment can also comprise contacting a lignocellulose with a chemical (e.g., a base, such as sodium carbonate or potassium hydroxide) at a pH of about 9 to about 14 at moderate temperature, pressure, and pH. See PCT Publication WO2004/081185.
[0078] Ammonia pretreatment can also be used. Such a pretreatment method comprises subjecting a biomass material to low ammonia concentration under conditions of high solids. See, e.g., U.S. Patent Publication No. 20070031918 and PCT publication WO 06/1 10901.
5.4.2. Detergent Compositions Comprising Variant CBH I Proteins
[0079] The present disclosure also provides detergent compositions comprising a variant CBH I polypeptide of the disclosure. The detergent compositions may employ besides the variant CBH I polypeptide one or more of a surfactant, including anionic, non-ionic and ampholytic surfactants; a hydrolase; a bleaching agents; a bluing agent; a caking inhibitors; a solubilizer; and a cationic surfactant. All of these components are known in the detergent art.
[0080] The variant CBH I polypeptide is preferably provided as part of celkilase
composition. The cellulase composition can be employed from about 0.00005 weight percent to about 5 weight percent or from about 0.0002 weight percent to about 2 weight percent of the total detergent composition. The cellulase composition can be in the form of a liquid diluent, granule, emulsion, gel, paste, and the like. Such forms are known to the skilled artisan. When a solid detergent composition is employed, the cellulase composition is preferably formulated as granules. 6. EXAMPLES
6.1. MATERIALS AND METHODS
6.1.1. Preparation Of CBH I Polypeptides For Biochemical Characterization
[0081] Protein expression was carried out in an Aspergillus niger host strain that had been transformed using PEG-mediated transformation with expression constructs for CBHI that included the hygromycin resistance gene as a selectable marker, in which the full length CBH I sequences (signal sequence, catalytic domain, linker and cellulose binding domain) were under the control of the glyceraldeyhde-3 -phosphate dehydrogenase (gpd) promoter. Transformants were selected on the regeneration medium based on resistance to hygromycin. The selected transformants were cultured in Aspergillus salts medium, pH 6.2 supplemented with the antibiotics penicillin, streptomycin, and hygromycin, and 80g/L glycerol, 20g/L soytone, lOmM uridine, 20g/L MES) in baffled shake flasks at 30°C, 170 rpm. After five days of incubation, the total secreted protein supernatant was recovered, and then subjected to hollow fiber filtration to concentrate and exchange the sample into acetate buffer (50 mM NaAc, pH 5). CBH I protein represented over 90% of the total protein in these samples. Protein purity was analyzed by SDS-PAGE. Protein concentration was determined by gel densitometry and/or HPLC analysis. All CBH I protein concentrations were normalized before assay and concentrated to 1-2.5 mg/ml..
6.1.2. CBH I Activity Assays
[0082] 4- Methyiumbelliferyl Lactoside (4-MUL) Assay: This assay measures the activity of CBH I on the fluorogenic substrate 4-MUL (also known as MUL). Assays were run in a costar 96-well black bottom plate, where reactions were initiated by the addition of 4-MUL to enzyme in buffer (2mM 4-MUL in 200mM MES pH 6). Enzymatic rates were monitored by fluorescent readouts over five minutes on a SPECTRAMAX™ plate reader (ex/em 365/450 nm). Data in the linear range was used to calculate initial rates (Vo).
[0083] Phosphoric Acid Swollen Cellulose (PASO Assay: This assay measures the activity of CBH I using PASC as the substrate. During the assay, the concentration of PASC is monitored by a fluorescent signal derived from calcofluor binding to PASC (ex/em 365/440 nm). The assay is initiated by mixing enzyme (15 μΐ) and reaction buffer (85 μΐ of 0.2% PASC, 200 mM MES, pH 6), and then incubating at 35°C while shaking at 225 RPM. After 2 hours, one reaction volume of calcofluor stop solution (100 μg/ml in 500 mM glycine pH 10) is added and fluorescence read-outs obtained (ex/em 365/440 nm).
[0084] Bagasse Assay; This assay measures the activity of CBH I on bagasse, a
lignocellulosic substrate. Reactions were run in 10 ml vials with 5% dilute acid pretreated bagasse (250 mg solids per 5 ml reaction). Each reaction contained 4 mg CBH I enzyme/g solids, 200 mM MES pH 6, kanamycin, and chloramphenicol. Reactions were incubated at 35°C in hybridization incubators (Robbins Scientific), rotating at 20 RPM. Time points were taken by transferring a sample of homogenous slurry (150 μΐ) into a 96-well deep well plate and quenching the reaction with stop buffer (450 μΐ of 500 mM sodium carbonate, pH 10). Time point measurements were taken every 24 hours for 72 hours.
[0085] Cellobiose Tolerance Assays (or Cellobiose Inhibition Assays): Tolerance to cellobiose (or inhibition caused by cellobiose) was tested in two ways in the CBH I assays. A direct-dose tolerance method can be applied to all of the CBH I assays (i.e., 4-MUL, PASC, and/or bagasse assays), and entails the exogenous addition of a known amount of cellobiose into assay mixtures. A different indirect method entails the addition of an excess amount of β-glucosidase (BG) to PASC and bagasse assays (typically, 1 mg β-glucosidase/g solids loaded). BG will enzymatically hydrolyze the cellobiose generated during these assays; therefore, CBH I activity in the presence of BG can be taken as a measure of activity in the absence of cellobiose. Furthermore, when activity in the presence and absence of BG are similar, this indicates tolerance to cellobiose. Notably, in cases where BG activity is undesired, but may be present in crude CBH I enzyme preparations, the BG inhibitor gluconolactone can be added into CBH I assays to prevent cellobiose breakdown.
6.2. LIBRARY SCREENING ASSAYS
[0086] The wild type CBH I polypeptide BD29555 was mutagenized to identify variants with improved product tolerance. A small (60-member) library of BD29555 variants was designed to identify variant CBH I polypeptides with reduced product inhibition. This product-release-site library was designed based on residues directly interacting with the cellobiose product in an attempt to identify variants with weakened interactions with cellobiose from which the product would be released more readily than the wild type enzyme. The 60-member evolution library contained wild-type residues and mutations at positions R273, W405, and R422 of BD29555 (SEQ ID NO: l), and included the following substitutions: R273 (WT), R273Q, R273K, R273A, W405 (WT), W405Q, W405H, R422 (WT), R422Q, R422K, R422L, and R422E (4 variants at position 273 X 3 variants at position 405 X 5 variants at position 422 equals 60 variants in total). All members of the library were screened using the 4-MUL assay in the presence and absence of 250g/L cellobiose and using gluconolactone to inhibit any BG activity. The R273A, R273Q, and R273K/R422K variants showed enhanced product tolerance. The R273K/R422K variant showed greatest activity among the variants and cellobiose tolerance at 250 mg/L. Due to low expression, the R273K variant was not tested for product inhibition.
6.3. CHARACTERIZATION OF PRODUCT TOLERANT VARIANTS OF BD29555
[0087] The R273K/R422K substitutions were characterized in both a wild type BD29555 background and also in combination with the substitutions Y274Q, D281K, Y410H, P411G, which were identified in a screen of an expanded product release site evolution library.
[0088] The wild type, the R273K/R422K variant and the
R273K/Y274Q/D281 K/Y410H/P411 G/R422K variants were tested for activity on 4-MUL in the presence and absence of 250mg/L cellobiose, and the R273K R422K variant was also tested in the bagasse assay in the presence and absence of BG. The results are summarized in Table 5.
[0089] The results from these activity assays were converted into the percentage of activity remaining with and without cellobiose present, where values close to 100% indicated cellobiose tolerance. The percent of activity remaining in the MUL assay in the presence cellobiose versus in the absence of cellobiose shows that the R273K/R422K variant was the most tolerant, followed by the R273K/Y274Q/D281K/Y410H/P411G/R422K variant, and then wild-type, at 95%, 78%, and 25% activity, respectively. [0090] Cellobiose dose response curves of the wild-type and R273K/R422K variant of BD29555 were obtained during the 4-MUL assay. Enzyme rates (Vo) were measured in the presence of different concentrations of cellobiose (200 mM MES pH 6, 25°C). Rates were measured in quadruplicate. The results are shown in Figure 1 A- IB. Figure 1A shows that wild type BD2955 is inhibited by cellobiose, with a half maximal inhibitory concentration (IC50 value) of 60 mg/L. Figure IB shows that the R273K/R422K variant is tolerant to cellobiose up to 250 mg/L.
[0091] The bagasse assay results shown in Table 5, which lists the percentage of activity remaining in the absence vs. presence of BG, also demonstrate that the percentage activity of the wild type BD29555 is lower than the percentage activity of the R273K/R422K variant, indicating that the R273K/R422K variant is less sensitive to the presence of cellobiose than the wild type. Figure 2A-2B shows bar graph data for the bagasse assay of BD29555 vs. the R273K R422K variant. In Figure 2A, bars represent relative activity, which has been normalized to wild type activity in the absence of cellobiose (WT +BG = uninhibited activity = 1). In Figure 2B, bars indicate tolerance to cellobiose, as represented by the ratio of activity in the presence of cellobiose (-BG) to that of activity in the absence of cellobiose (+BG); ratios close to 1 indicate greater tolerance to cellobiose. These data again demonstrate that the R273K/R422K variant of BD29555 is more tolerant to cellobiose than the wild type BD29555.
[0092] The wild type and R273K/R422K variant were also characterized in the PASC assay. Results are shown in Figure 3. The activities of both wild type BD29555 (SEQ ID NO: l) and wild type T. reesei CBH I (SEQ ID NO:2) were inhibited by cellobiose concentrations starting around 1 g L (with IC50 values of 2.2 and 3 g/L, respectively), whereas the
R273K/R422K variant showed little inhibition in the presence of 10 g/L cellobiose.
6.4. CHARACTERIZATION OF PRODUCT TOLERANT VARIANTS OF T. REESEI CBH I
[0093] Cellobiose product tolerant substitutions were introduced into T. reesei CBH I (SEQ ID NO:2). A panel of variants with single and double alanine and lysine substitutions at R268 and R41 1 were expressed and analyzed. The variants were tested for activity on 4- MUL in the presence and absence of 250mg/L cellobiose and also in the bagasse assay in the absence and prseence of BG. The results from these assays were converted into the percentage activity remaining in the presence and absence of cellobiose and BG,
respectively. Values are summarized in Table 6.
[0094] The 4-MUL assay results shown in Table 6 demonstrate that the activity of the wild type T. reesei CBH I was reduced to 23% in the presence of cellobiose, whereas the double mutants at R268 and R41 1 retained more than 90% of their activity under the same conditions.
[0095] The bagasse assay results shown in Table 6 demonstrate that the activity of the wild type T. reesei CBH I is more significantly impacted by the presence of BG than is the activity of the single or double substitution variants, indicating that the variants are less sensitive to the accumulation of cellobiose than the wild type. Figures 4 and 5 show bar graph data for the bagasse assay of wild type T. reesei CBH I vs. the variants. In Figure 4, bars represent relative activity, normalized to wild type activity in the absence of cellobiose (WT +BG = 1). In Figure 5, bars represent tolerance to cellobiose, as represented by the ratio of activity in the presence of accumulating cellobiose (-BG) to that of activity in the absence of cellobiose (+BG); ratios close to 1 indicate greater tolerance to cellobiose.
7. SPECIFIC EMBODIMENTS AND INCORPORATION BY REFERENCE
[0096] All publications, patents, patent applications and other documents cited in this application are hereby incorporated by reference in their entireties for all purposes to the same extent as if each individual publication, patent, patent application or other document were individually indicated to be incorporated by reference for all purposes.
[0097] While various specific embodiments have been illustrated and described, it will be appreciated that various changes can be made without departing from the spirit and scope of the invention(s).
Figure imgf000040_0001
Figure imgf000041_0001
Figure imgf000042_0001
Figure imgf000043_0001
Figure imgf000044_0001
Figure imgf000045_0001
Figure imgf000046_0001
Figure imgf000047_0001
Figure imgf000048_0001
Figure imgf000049_0001
Figure imgf000050_0001
Figure imgf000051_0001
Figure imgf000052_0001
Figure imgf000053_0001
Figure imgf000054_0001
Figure imgf000055_0001
Figure imgf000056_0001
Figure imgf000057_0001
Figure imgf000058_0001
Figure imgf000059_0001
Figure imgf000060_0001
Figure imgf000061_0001
Figure imgf000062_0001
Figure imgf000063_0001
Figure imgf000064_0001
Figure imgf000065_0001
Figure imgf000066_0001
Figure imgf000067_0001
Figure imgf000068_0001
Figure imgf000069_0001
Figure imgf000070_0001
Figure imgf000071_0001
Figure imgf000072_0001
Figure imgf000073_0001
Figure imgf000074_0001
Figure imgf000075_0001
7i C
I- m
Is)
Figure imgf000076_0001
Figure imgf000077_0001
Figure imgf000078_0001
Figure imgf000079_0001
Figure imgf000080_0001
Figure imgf000081_0001
Figure imgf000082_0001
Figure imgf000083_0001
Figure imgf000084_0001
Figure imgf000085_0001
t ermop ium
Figure imgf000086_0001
Figure imgf000087_0001
speratus
Figure imgf000088_0001
speratus
Figure imgf000089_0001
speratus
Figure imgf000090_0001
Figure imgf000091_0001
Figure imgf000092_0002
Figure imgf000092_0003
Figure imgf000092_0001
Figure imgf000093_0001
Figure imgf000094_0001
Figure imgf000095_0002
Figure imgf000095_0003
Figure imgf000095_0001
Figure imgf000096_0002
Figure imgf000096_0003
Figure imgf000096_0001
Figure imgf000097_0001
Figure imgf000098_0001
Figure imgf000099_0001
Figure imgf000100_0001
Figure imgf000101_0002
Figure imgf000101_0003
Figure imgf000101_0001
Figure imgf000101_0004
Figure imgf000102_0002
Figure imgf000102_0003
Figure imgf000102_0001
TABLE 4
Amino acid
Sequence Database positions of
Amino acid sequence ot fragment ot catalytic domain
Identifier Accession Species ot Origin fragment in including loop and catalytic resid ue
(SEQ II) NO:) Number sequence identifer
SEQ ID NO:287 146197095 uncultured NVDDD D D D D D D D D D D D D KLGTCC SD MD IWD GNA 197-229 symbiotic protist
of Reticulitermes
speratus
SEQ ID NO:288 146197401 uncultured NVLDD D D D D D D D D D D D D RYGACC ID MD IWD ANS 198-230 symbiotic protist
of Cryptocercus
punctulatus
SEQ ID NO:289 146197225 uncultured N SDGD D D D D D D D D D D D D KYGSCC SD MD IWD ANS 195-227 symbiotic protist
of Neotermes
koshunensis
SEQ ID NO:290 146197317 uncultured N SDGD D D D D D D D D D D D D KYGSCC SD MD IWD ANS 196-228 symbiotic protist
of Mastotermes
darwiniensis
SEQ ID O:291 146197251 uncultured N SDGD D D D D D D D D D D D D RYGSCC SD MDVWD ANS 195-227 symbiotic protist
of Neotermes
koshunensis
SEQ ID NO:292 146197319 uncultured N SDGD D D D D D D D D D D D D KYGSCC SD MD IWD ANS 196-228 symbiotic protist
of Mastotermes
darwiniensis
SEQ ID NO:293 146197071 uncultured N I LDD D D D D D D D D D D D D RYGTCCTD MD IWD ANS 200-232 symbiotic protist
of Reticulitermes
speratus
Figure imgf000104_0001
Figure imgf000105_0001
Figure imgf000105_0002
Figure imgf000106_0001
Figure imgf000107_0001
Figure imgf000108_0001
Figure imgf000109_0001
Figure imgf000110_0001
Figure imgf000111_0001
Figure imgf000112_0001
Figure imgf000113_0001
Figure imgf000114_0001
Figure imgf000115_0001
Figure imgf000116_0001
Figure imgf000117_0001
Figure imgf000118_0001
Figure imgf000119_0001
Figure imgf000120_0001
Figure imgf000121_0001
Figure imgf000122_0001
Figure imgf000123_0001
Figure imgf000124_0001
Figure imgf000125_0001
Figure imgf000126_0001
Figure imgf000127_0001
Figure imgf000128_0001
Figure imgf000129_0001
Figure imgf000130_0001

Claims

WHAT IS CLAIMED IS:
1. A polypeptide comprising a variant cellobiohydrolase I ("CBH I") catalytic domain as compared to a reference CBH I catalytic domain, comprising:
(a) a substitution at the amino acid position corresponding to R268 of T. reesei CBH I ("R268 substitution");
(b) a substitution at the amino acid position corresponding to R411 of T. reesei CBH I ("R411 substitution"); or
(c) both an R268 substitution and an R411 substitution, wherein substitution (a), (b) or (c) decreases product inhibition as compared to the reference CBH I catalytic domain.
2. The polypeptide of claim 1, which comprises an R268 substitution.
3. The polypeptide of claim 2, wherein the R268 substituent is a lysine.
4. The polypeptide of claim 2, wherein the R268 substituent is an alanine.
5. The polypeptide of any one of claims 1 to 4, which comprises an R411 substitution.
6. The polypeptide of claim 5, wherein the R411 substituent is a lysine.
7. The polypeptide of claim 5, wherein the R411 substituent is an alanine.
8. The polypeptide of any one of claims 1 to 7, wherein the variant CBH I catalytic domain comprises an amino acid sequence having at least 90% sequence identity to amino acids 18-444 of SEQ ID NO:2.
9. The polypeptide of claim 8, wherein the variant CBH I catalytic domain comprises an amino acid sequence having at least 95% sequence identity to amino acids 18-444 of SEQ ID NO :2.
10. The polypeptide of claim 9, wherein, other than said R268 and/or R411 substitutions, the variant CBH I catalytic domain comprises the sequence of amino acids 18- 444 of SEQ ID NO:2.
11. The polypeptide of any one of claims 8 to 10, wherein the variant CBH I catalytic domain comprises one of the following amino acid substitutions or pairs of amino acid substitution as compared to a protein of SEQ ID NO:2:
(a) R268K and R41 IK;
(b) R268K and R411 A;
(c) R268A and R411K;
(d) R268A and R411 A;
(e) R268A;
(f) R268K;
(g) R411A; and
(h) R411K.
12. The polypeptide of any one of claims 8 to 11, wherein the variant CBH I catalytic domain does not comprise a R268A substitution.
13. The polypeptide of claim 12 whose amino acid sequence does not comprise SEQ ID NO:150.
14. The polypeptide of claim 12 whose amino acid sequence does not consist of SEQ ID NO:150.
15. The polypeptide of any one of claims 8 to 14 wherein the variant CBH I catalytic domain does not comprise a R411A substitution.
16. The polypeptide of claim 15 whose amino acid sequence does not comprise SEQ ID NO: 152 or SEQ ID NO: 151.
17. The polypeptide of claim 15 whose amino acid sequence does not consist of SEQ ID NO: 152 or SEQ ID NO:151.
18. A polypeptide comprising an amino acid sequence having at least 95% sequence identity to the amino acid sequence corresponding to positions 18-444 of SEQ ID NO:2, which has an R268K substitution and an R411A substitution as compared to a protein of SEQ ID NO:2.
19. The polypeptide of claim 18 in which said amino acid sequence has at least 97% sequence identity to the amino acid sequence corresponding to positions 18-444 of SEQ ID NO:2.
20. The polypeptide of any one of claims 1 to 7, wherein the variant CBH I catalytic domain comprises an amino acid sequence having at least 90% sequence identity to amino acids 26-455 of SEQ ID NO:l .
21. The polypeptide of claim 20, wherein the variant CBH I catalytic domain comprises an amino acid sequence having at least 95% sequence identity to amino acids 26-455 of SEQ ID NO: 1.
22. The polypeptide of claim 21, wherein, other than said R268 and/or R411 substitutions, the variant CBH I catalytic domain comprises the sequence of amino acids 26- 455 of SEQ ID NO:l .
23. The polypeptide of any one of claims 20 to 22, wherein the variant CBH I catalytic domain comprises one of the following amino acid substitutions or pairs of amino acid substitutions as compared to a protein of SEQ ID NO: 1 :
(a) R273K and R422K;
(b) R273K and R422A;
(c) R273A and R422K;
(d) R273A and R422A;
(e) R273A;
(f) R273K;
(g) R422A; and
(h) R422K.
24. The polypeptide of any one of claims 20 to 23, wherein the variant CBH I catalytic domain comprises the amino acid substitutions R273K and R422K as compared to a protein of SEQ ID NO: 1.
25. The polypeptide of any one of claims 20 to 23, wherein the variant CBH I catalytic domain does not comprise both R273K and R422K substitutions as compared to a protein of SEQ ID NO: 1.
26. The polypeptide of claim 25 whose amino acid sequence does not comprise SEQ ID NO: 152 or SEQ ID NO: 153.
27. The polypeptide of claim 25 whose amino acid sequence does not consist of SEQ ID NO: 152 or SEQ ID NO:153.
28. The polypeptide of any one of claims 1 to 7, wherein the variant CBH I catalytic domain comprises an amino acid sequence having at least 90% or at least 95% sequence identity of the amino acid sequence of the catalytic domain of any one of SEQ ID NOs:l-149.
29. The polypeptide of any one claims 1 to 28 in which the variant CBH I catalytic domain is operably linked to a cellulose binding domain.
30. The polypeptide of claim 29 in which the catalytic domain is operably linked to a cellulose binding domain via a linker.
31. The polypeptide of claim 29 or claim 30 in which the cellulose binding domain is C -terminal to the catalytic domain.
32. The polypeptide of claim 29 or claim 30 in which the cellulose binding domain is N-terminal to the catalytic domain.
33. The polypeptide of any one of claims 1 to 32 which is a mature polypeptide.
34. The polypeptide of any one of claims 1 to 32 which further comprises a signal sequence.
35. The polypeptide of any one of claims 1 to 34 towards which cellobiose has an IC50 that is at least 2-fold the IC50 of a reference CBH I lacking said R268 substitution and/or R411 substitution.
36. The polypeptide of any one of claims 1 to 35 which CBH I activity that is at least 50% the CBH I activity of a reference CBH I lacking said R268 substitution and/or R411 substitution.
37. A composition comprising a polypeptide according to any one of claims 1 to 36.
38. The composition of claim 37 in which said polypeptide represents at least 1% of all polypeptides in said composition.
39. The composition of claim 38 in which said polypeptide represents at least 5% of all polypeptide in said composition.
40. The composition of claim 39 in which said polypeptide represents at least 25% of all polypeptide in said composition.
41. The composition of any one of claims 37 to 40 which is a whole cellulase.
42. The composition of claim 41, wherein the whole cellulase is produced by a host cell that recombinantly expresses said polypeptide.
43. The composition of any one of claims 37 to claim 42 which is filamentous fungal whole cellulase.
44. A fermentation broth comprising a polypeptide according to any one of claims
1 to 36.
45. The fermentation broth of claim 44, which is a filamentous fungal fermentation broth.
46. The fermentation broth of claim 44 or claim 45 which is a cell-free fermentation broth.
47. A method for saccharifying biomass, comprising: treating biomass with a composition according to any one of claims 37 to 43 or with a fermentation broth according to any one of claims 44 to 46.
48. The method of claim 47, further comprising recovering monosaccharides.
49. A method for producing ethanol, comprising:
(a) treating biomass with a composition according to any one of claims 37 to 43 or with a fermentation broth according to any one of claims 44 to 46, thereby producing monosaccharides; and
(b) culturing a fermenting microorganism in the presence of the monosaccharides produced in step (a) under fermentation conditions, thereby producing ethanol.
50. The method of claim 49, further comprising, prior to step (a), pretreating the biomass.
51. The method of claim 49 or claim 50, wherein said fermenting microorganism is a bacterium or a yeast.
52. The method of claim 51, wherein said fermenting microorganism is a bacterium selected from Zymomonas mobilis, Escherichia coli and Klebsiella oxytoca.
53. The method of claim 51, wherein said fermenting microorganism is a yeast selected from Saccharomyces cerevisiae, Saccharomyces uvarum, Kluyveromyces fragilis, Kluyveromyces lactis, Candida pseudotropicalis, and Pachysolen tannophilus.
54. The method of any one of claims 49 to 53, wherein said biomass is corn stover, bagasses, sorghum, giant reed, elephant grass, miscanthus, Japanese cedar, wheat straw, switchgrass, hardwood pulp, softwood pulp, crushed sugar cane, energy cane, or Napier grass.
55. A nucleic acid comprising a nucleotide sequence encoding the polypeptide of any one of claims 1 to 36.
56. A vector comprising the nucleic acid of claim 55.
57. The vector of claim 56 which further comprises an origin of replication.
58. The vector of claim 56 or claim 57 which further comprises a promoter sequence operably linked to said nucleotide sequence.
59. The vector of claim 58, wherein the promoter sequence is operable in yeast.
60. The vector of claim 58, wherein the promoter sequence is operable in filamentous fungi.
61. A recombinant cell engineered to express the nucleic acid of claim 55.
62. The recombinant cell of claim 61 which is a eukaryotic cell.
63. The recombinant cell of claim 62 which is a filamentous fungal cell.
64. The recombinant cell of claim 63, wherein the filamentous fungal cell is of the genus Aspergillus, Penicillium, Rhizopus, Chrysosporium, Myceliophthora, Trichoderma, Humicola, Acremonium or Fusarium.
65. The recombinant cell of claim 63, wherein the filamentous fungal cell is of the species Aspergillus niger, Aspergillus oryzae, Trichoderma reesei, Penicillium chrysogenum, Myceliophthora thermophila, or Rhizopus oryzae.
66. The recombinant cell of claim 62 which is a yeast cell.
67. The recombinant cell of claim 66 which is a yeast cell of the genus
Saccharomyces, Kluyveromyces, Candida, Pichia, Schizosaccharomyces, Hansenula, Klockera, Schwanniomyces or Yarrowia.
68. The recombinant cell of claim 67, wherein the yeast cell is of the species S. cerevisiae, S. bulderi, S. barnetti, S. exiguus, S. uvarum, S. diastaticus, K. lactis, K. marxianus or K. fragilis.
69. The recombinant cell of claim 68, which is a S. cerevisiae cell.
70. A host cell transformed with the vector of any one of claims 56 to 60.
71. The host cell of claim 70 which is a prokaryotic cell.
72. The host cell of claim 71 which is a bacterial cell.
73. The host cell of claim 70 which is a eukaryotic cell.
74. A method of producing a polypeptide according to any one of claims 1 to 36, comprising culturing the recombinant cell engineered to express said polypeptide under conditions in which the polypeptide is expressed.
75. The method of claim 74, wherein the polypeptide comprises a signal sequence and wherein the recombinant cell is cultured under conditions in which the polypeptide is secreted from the recombinant cell.
76. The method of claim 75, further comprising recovering the polypeptide from the cell culture.
77. The method of claim 76, wherein recovering the polypeptide comprises a step of centrifuging away cells and/or cellular debris.
78. The method of claim 76, wherein recovering the polypeptide comprises a step of filtering away cells and/or cellular debris.
79. A method for generating a product tolerant variant CBH I polypeptide, comprising
(a) modifying the nucleotide sequence of a CBH I-encoding nucleic acid so that the nucleic acid encodes a variant CBH I polypeptide, wherein said variant CBH I polypeptide comprises:
(i) an R268 substitution;
(ii) an R411 substitution; or
(iii) both an R268 substitution and an R411 substitution; and
(b) expressing said variant CBH I polypeptide, thereby generating a product tolerant variant CBH I polypeptide.
80. A method for generating a nucleic acid that encodes a product tolerant variant CBH I polypeptide, comprising modifying the nucleotide sequence of a CBH I-encoding nucleic acid so that the nucleic acid encodes a variant CBH I polypeptide, wherein said variant CBH I polypeptide comprises:
(i) an R268 substitution;
(ii) an R411 substitution; or
(iii) both an R268 substitution and an R411 substitution, thereby generating a nucleic acid that encodes a product tolerant variant CBH I polypeptide.
81. The method of claim 79 or claim 80, wherein the modification is by site directed mutagenesis.
82. The method of any one of claims 79 to 81, wherein variant CBH I polypeptide comprises an R268 substitution.
83. The method of claim 82, wherein the R268 substituent is a lysine.
84. The method of claim 82, wherein the R268 substituent is an alanine.
85. The method of any one of claims 79 to 84, which comprises an R411 substitution.
86. The method of claim 85, wherein the R411 substituent is a lysine.
87. The method of claim 85, wherein the R411 substituent is an alanine.
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JP2014502144A (en) 2014-01-30

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