transgenic microbial host cell, methods to produce a polypeptide, to produce a mutant of a precursor

专利摘要:
TRANSGENIC MICROBIAL HOSTED CELL, METHODS TO PRODUCE IN A POLYPEPTIDE, TO PRODUCE A MUTANT OF A PRECURSING CELL, TO INHIBIT THE EXPRESSION OF A POLYPEPIDE, TO PRODUCE A PROTEIN TO DEGRAD OR CONVERTELL A MATERIAL MATERIAL MATERIAL , NUCLEIC ACID CONSTRUCTIONS, EXPRESSION VECTOR, ISOLATED POLYPEPTIDE HAVING CELLULOLYTIC INTENSIFICATION ACTIVITY AND, ISOLATED POLYNUCLEOTIDE THAT CODES THE SAME. The present invention relates to isolated polypeptide having cellulolytic enhancing activity and isolated polynucleotides that encode the polypeptides. The invention also relates to nucleic acid constructs, vectors and host cells that comprise polynucleotides as well as methods of producing and using polypeptides.
公开号:BR112012000260B1
申请号:R112012000260-0
申请日:2010-07-07
公开日:2020-11-17
发明作者:Ye Liu；Lan Tang；Wenping Wu；Jason Quinlan；Randall Kramer
申请人:Novozymes A/S；Novozymes, Inc.；
IPC主号:

专利说明:

Declaration of the Rights to Inventions Made Under Research and Development Sponsored by the Federal Government
This invention was made partially with the support of the Government under Cooperative Agreement DE-FC36-08GO18080 granted by the Department of Energy. The government has certain rights in this invention. Reference to a sequence listing
This order contains a Sequence Listing in computer readable form, which is incorporated by reference. Reference to a Biological Material Deposit
This order contains a reference to a deposit of Biological Material, which deposit is incorporated by reference. Fundamentals of the Invention Field of the Invention
The present invention relates to polypeptides having cellulolytic enhancing activity and polynucleotides that encode the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells that comprise polynucleotides as well as methods of producing and using the polypeptides. Description of the Related Art
Cellulose is a simple sugar-glucose polymer linked by beta-1,4 bonds. Many microorganisms produce enzymes that hydrolyze beta-linked glycans. These enzymes include endoglycanases, cellobiohydrolases, and beta-glycosidases. Endoglycanases digest the cellulose polymer at random locations, opening them up to attack by cellobiohydrolases. Cellobiohydrolases sequentially release cellobiose molecules from the ends of the polymeric cellulose. Cellobiosis is a water-soluble beta-1,4 linked dimer of glucose. Beta-glycosidases hydrolyze cellobiose to glucose.
The conversion of lignocellulosic feed stocks into ethanol has the advantages of the prompt availability of large quantities of feed stock, the desirability of avoiding burning or disposing of materials in landfills, and the cleaning of ethanol fuel. Wood, agricultural residues, herbaceous crops, and municipal solid residues have been considered as food stocks for the production of ethanol. These materials primarily consist of cellulose, hemicellulose, and lignin. Once cellulose is converted to glucose, glucose is easily fermented by yeast into ethanol. It would be advantageous in the art to improve the ability to enzymatically degrade lignocellulosic feed stocks.
WO 2005/074647 discloses isolated polypeptides having cellulolytic intensification activity and polynucleotides from these from Thielavia terrestris. WO 2005/074656 discloses an isolated polypeptide having cellulolytic enhancing activity and its polynucleotide from Thermoascus aurantiacus. WO 2007/089290 discloses an isolated polypeptide having cellulolytic intensification activity and its polynucleotide from Trichoderma reesei.
The present invention provides polypeptides having cellulolytic enhancing activity and polynucleotides that encode the polypeptides. Summary of the invention
The present invention concerns isolated polypeptides having cellulolytic intensification activity selected from the group consisting of:
(a) a polypeptide having at least 80% sequence identity with the mature polypeptide of SEQ ID NO: 2;
(b) a polypeptide encoded by a polynucleotide that hybridizes under high stringency conditions to (i) the sequence encoding mature polypeptide of SEQ ID NO: 1, (ii) the cDNA sequence contained in the sequence encoding mature SEQ ID polypeptide NO: 1, or (iii) the complementary filament of total length of (i) or (ii);
(c) a polypeptide encoded by a polynucleotide having at least 80% sequence identity with the sequence encoding mature polypeptide of SEQ ID NO: 1 or its cDNA sequence;
(d) a variant comprising a replacement, deletion, and / or insertion of one or more (several) amino acids from the mature polypeptide of SEQ ID NO: 2; and
(e) a fragment of the polypeptide of (a), (b), (c), or (d) that has cellulolytic enhancing activity.
The present invention also relates to isolated polynucleotides that encode the polypeptides of the present invention; nucleic acid constructs, recombinant expression vectors, and recombinant host cells that comprise polynucleotides; and methods of producing the polypeptides.
The present invention also relates to methods for degrading or converting a cellulosic material, which comprise: treating the cellulosic material with an enzyme composition in the presence of a polypeptide having cellulolytic enhancing activity of the present invention. In a preferred aspect, the method further comprises recovering the degraded or converted cellulosic material.
The present invention also relates to methods of producing a fermentation product, which comprise: (a) saccharifying a cellulosic material with an enzyme composition in the presence of a polypeptide having cellulolytic enhancing activity of the present invention; (b) fermenting the saccharified cellulosic material with one or more fermenting microorganisms to produce the fermentation product; and (c) recovering the fermentation product from the fermentation.
The present invention also concerns methods of fermenting a cellulosic material, which comprise: fermenting the cellulosic material with one or more fermenting microorganisms, wherein the cellulosic material is saccharified with an enzyme composition in the presence of a polypeptide having activity of cellulolytic enhancement of the present invention. In one aspect, the fermentation of the cellulosic material produces a fermentation product. In another aspect, the method further comprises recovering the fermentation product from the fermentation.
The present invention also relates to a polynucleotide that encodes a signal peptide that comprises or consists of amino acids 1 to 21 of SEQ ID NO: 2, which is operably linked to a gene that encodes a protein; nucleic acid constructs, expression vectors, and recombinant host cells that comprise the polynucleotide; and methods of producing a protein. Brief Description of the Figures
Figure 1 shows the genomic DNA sequence and the deduced amino acid sequence of a gene from the Penicillium pinophilum strain NN046877 that encodes a GH61A polypeptide having cellulolytic intensification activity (SEQ ID NOs: 1 and 2, respectively).
Figure 2 shows a restriction map of pPFJO355.
Figure 3 shows a restriction map of pPpin7.
Figure 4 shows a restriction map of pGEM-T-Ppin7.
Figure 5 shows hydrolysis vs. concentration of the GH61A polypeptide from Penicillium pinophilumaded having cellulolytic intensification activity. Open circles: degree of hydrolysis of 3 days; closed circles: degree of hydrolysis of 7 days. Uncorrected data for sugars present in the PCS liquid. The data are adjusted using a modified, non-cooperative, saturation-agglutination model. Definitions
Cellulolytic intensification activity: The term "cellulolytic intensification activity" means a biological activity catalyzed by a GH61 polypeptide that intensifies the hydrolysis of a cellulosic material by the enzyme having cellulolytic activity. For the purposes of the present invention, cellulolytic intensification activity is determined by measuring the increase in reducing sugars or the increase in the total cellobiose and glucose in the hydrolysis of a cellulosic material by the cellulolytic enzyme under the following conditions: 1 to 50 mg of total protein / g cellulose in PCS, where the total protein is comprised of 50 to 99.5% w / w cellulolytic enzyme protein and 0.5 to 50% w / w protein of a GH61 polypeptide having intensification activity cellulolytic for 1 to 7 days at 50 ° C compared to a control hydrolysis with equal total protein load without cellulolytic intensification activity (1 to 50 mg cellulolytic protein / g cellulose in PCS). In a preferred aspect, a mixture of CELLUCLAST® 1.5L (Novozymes A / S, Bagsvaerd, Denmark) in the presence of 2 to 3% by weight of total beta-glycoside protein from Aspergillus oryzae (recombinantly produced in Aspergillus oryzae according to with WO 02/095014) or 2 to 3% by weight of total beta-glycoside protein from Aspergillus fumigatus (recombinantly produced in Aspergillus oryzae as described in WO 2002/095014) of cellulase protein charge are used as the source of cellulolytic activity.
GH61 polypeptides having cellulolytic enhancing activity enhance the hydrolysis of a cellulosic material catalyzed by the enzyme having cellulolytic activity by reducing the amount of cellulolytic enzyme required to achieve the same degree of hydrolysis preferably at least 1.01 times, more preferably at least 1, 05 times, more preferably at least 1.10 times, more preferably at least 1.25 times, more preferably at least 1.5 times, more preferably at least 2 times, more preferably at least 3 times, more preferably at least 4 times , more preferably at least 5 times, even more preferably at least 10 times, and most preferably at least 20 times.
The polypeptides of the present invention are at least 20%, for example at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, and at least minus 100% of the cellulolytic intensification activity of the mature polypeptide of SEQ ID NO: 2.
Glycoside hydrolase family 61: The term "Glycoside hydrolase family 61" or "GH61 family" or "GH61" means a polypeptide that falls within Glycoside hydrolase family 61 according to Henrissat B., 1991, A classification of glycosil hydrolases based on amino-acid sequence similarities, Biochem. J. 280: 309-316, and Henrissat B., and Bairoch A., 1996, Updating the sequence-based classification of glycosil hydrolases, Biochem. J. 316: 695-696.
Cellulolytic enzyme or cellulase: The term "cellulolytic enzyme" or "cellulase" means one or more (several) enzymes that hydrolyze a cellulosic material. Such enzymes include endoglycanase (s), cellobiohydrolase (s), beta-glycosity (s), or combinations thereof. The two basic methods for measuring cellulolytic activity include: (1) measuring total cellulolytic activity, and (2) measuring individual cellulolytic activities (endoglycanases, cellobiohydrolases, and beta-glycosides) as reviewed in Zhang et al., Outlook for cellulase improves: Screening and selection strategies, 2006, Biotechnology Advances 24: 452-481. Total cellulolytic activity is usually measured using insoluble substrates, including Whatman Nθ 1 filter paper, microcrystalline cellulose, bacterial cellulose, algal cellulose, cotton, pretreated lignocellulose, etc. The most common total cellulolytic activity test is the filter paper test using Whatman No. 1 filter paper as the substrate. The assay was established by the International Union of Pure and Applied Chemistry (IUPAC) (Ghose, 1987, Measurement of cellulase activities, Pure Appl. Chem. 59: 257-68). For the purposes of the present invention, cellulolytic enzyme activity is determined by measuring the increase in hydrolysis of a cellulosic material by the cellulolytic enzyme (s) under the following conditions: 1 to 20 mg of cellulolytic enzyme protein / g of cellulose in PCS for 3 to 7 days at 50 ° C compared to a control hydrolysis without the addition of cellulolytic enzyme protein. Typical conditions are 1 ml reactions, PCS washed or not washed, 5% insoluble solids, 50 mM sodium acetate pH 5, 1 mM MnSO4, 50 ° C, 72 hours, sugar analysis by AMINAX® HPX column -87H (Bio-Rad Laboratories, Inc., Hercules, CA, USA).
Endoglycanase: The term “endoglycanase” means an endo-, 4- (1,3, 1,4) -beta-D-glycan 4-glycanhydrolase (EC 3,2,1,4), which catalyzes endohydrolysis of 1,4-beta-D-glycosidic bonds in cellulose, cellulose derivatives (such as carboxymethyl cellulose and hydroxyethyl cellulose), lichenine, beta-1,4 bonds in mixed beta-1,3 glycans such as beta-D-glycans or cereal xyloglycans, and other plant materials containing cellulosic components. Endoglycanase activity can be determined by measuring the reduction in substrate viscosity or increase in reducing ends determined by a reducing sugar assay (Zhang et al., 2006, Biotechnology Advances 24: 452-481). For the purposes of the present invention, endoglycanase activity is determined using carboxymethyl cellulose (CMC) as a substrate according to the procedure of Ghose, 1987, Pure and Appl. Chem. 59: 257-268, at pH 5, 40 ° C.
Cellobiohydrolase: The term “cellobiohydrolase” means a 1,4-beta-D-glycan cellobiohydrolase (EC 3,2,1,91), which catalyzes the hydrolysis of 1,4-beta-D- bonds cellulose glycosides, celooligosaccharides, or any polymer containing glucose bound in 1,4-beta, which releases cellobiosis from the reducing and non-reducing ends of the chain (Teeri, 1997, Crystalline cellulose degradation: New insight into the function of cellobiohydrolases, Trends in Biotechnology 15: 160-167; Teeri et al., 1998, Trichoderma reesei cellobiohydrolases: why so efficient on crystalline cellulose , Biochem. Soc. Trans. 26: 173-178). For the purposes of the present invention, cellobiohydrolase activity is determined according to the procedures described by Lever et al., 1972, Anal. Biochem. 47: 273-279; van Tilbeurgh et al., 1982, FEBS Letters, 149: 152-156; van Tilbeurgh and Claeyssens, 1985, FEBS Letters, 187: 283-288; and Tomme et al., 1988, Eur. J. Biochem. 170: 575-581. In the present invention, the method of Lever et al.can be used to evaluate cellulose hydrolysis in corn fodder, whereas the methods of van Tilbeurgh et al. and Tomme et al.can be used to determine cellobiohydrolase activity in a fluorescent disaccharide derivative, 4-methylumbelliferyl-β-D-lactoside.
Beta-glycosity: The term "beta-glycosity" means a beta-D-glycoside glycohydrolase (EC 3,2,1,21), which catalyzes the hydrolysis of non-terminal reducing beta-D-glucose residues with the release of beta -D- glucose. For the purposes of the present invention, beta-glycosity activity is determined according to the basic procedure described by Venturi et al., 2002, Extracellular beta-D-glucosity from Chaetomium thermophilum var. coprophilum ', production, purification and some biochemical properties, J. Basic Microbiol. 42: 55-66. One unit of beta-glycosity is defined as 1.0 pmol of p-nitrophenolate anion produced per minute at 25 ° C, pH 4.8 of 1 mM p-nitrophenyl-beta-D-glycopyranoside as a substrate in 50 mM citrate sodium containing 0.01% TWEEN® 20.
Hemicellulolytic enzyme on hemicellulase: The terms "hemicellulolytic enzyme" or "hemicellulase" mean one or more (several) enzymes that hydrolyze a hemicellulosic material. See, for example, Shallom, D. and Shoham, Y. Microbial hemicellulases. Current Opinion In Microbiology, 2003, 6 (3): 219-228). Hemicellulases are key components in the degradation of plant biomass. Examples of hemicellulases include, but are not limited to, an acetylmannan esterase, an acetylxylan esterase, an arabinanase, an arabinofuranosidase, a coumaric acid esterase, a feruloyl esterase, a galactosidase, a glucuronidase, a glucuronoyl esterase, a mannanase, a mannose , a xylanase, and a xylosidase. The substrates of these enzymes, hemicelluloses, are a heterogeneous group of branched and linear polysaccharides that are linked by means of hydrogen bonds to cellulose microfibrils on the plant cell wall, cross-linking them in a robust network. Hemicelluloses are also covalently linked to lignin, forming together with cellulose a highly complex structure. The variable structure and organization of hemicelluloses requires the combined action of many enzymes for their complete degradation. The catalytic modules of hemicellulases are glycoside hydrolases (GHs) that hydrolyze glycosidic bonds, or carbohydrate esterases (CEs), which hydrolyze the bonds of side groups of acetate ester or ferulic acid. These catalytic modules, based on the homology of their primary sequence, can be designated within the GH and CE families marked by the numbers. Some families, with similar global fold, can be grouped into clans, alphabetically marked (for example, GH-A). A more informative and updated classification of these and other active carbohydrate enzymes is available in the Carbohydrate-Active Enzymes (CAZy) database. The activities of hemicellulolytic enzymes can be measured according to Ghose and Bisaria, 1987, Pure & Appl. Chem. 59: 1739-1752.Activity that degrades xylan or xylanolitic activity: The term "activity that degrades xylan" or "xylanolitic activity" means a biological activity that hydrolyzes material containing xylan. The two basic methods for measuring xylanolitic activity include: (1) measuring total xylanolitic activity, and (2) measuring individual xylanolitic activities (for example, endoxylanases, beta-xylosidases, arabinofuranosidases, alpha-glucuronidases, acetylxylan esterases, feruloyl esterases , and alpha-glucuronyl esterases). Recent progress in the testing of xylanolitic enzymes has been summarized in several publications including Biely and Puchard, Recent progress in the assays of xylanolytic enzymes, 2006, Journal of the Science of Food and Agriculture 86 (11): 1636-1647; Spanikova and Biely, 2006, Glucuronoil esterase - Novel carbohydrate esterase produced by Schizophillum commune, FEBS Letters 580 (19): 4597-4601; Herrmann, Vrsanska, Jurickova, Hirsch, Biely, and Kubicek, 1997, The beta-D-xylosydase of Trichoderma reesei is a multifunctional beta-D-xylan xylohydrolase, Biochemical Journal 321: 375-381.
The activity that degrades total xylan can be measured by determining the reducing sugars formed from various types of xylan, including, for example, oat fodder xylans, beech wood, and larch wood, or by photometric determination of xylan fragments dyes released from various covalently dyed xylans. The most common total xylanolitic activity test is based on the production of polymeric 4-O-methyl glucuronoxylane reducing sugars as described in Bailey, Biely, Poutanen, 1992, Interlaboratory testing of methods for assay of xylanase activity, Journal of Biotechnology 23 (3 ): 257-270. Xylanase activity can also be determined with 0.2% AZCL-arabinoxylan as a substrate in 0.01% Triton X-100 and 200 mM sodium phosphate buffer pH 6 at 37 ° C. A unit of xylanase activity is defined as 1.0 pmol of azurine produced per minute at 37 ° C, pH 6 of 0.2% AZCL-arabinoxylan as a substrate in 200 mM sodium phosphate buffer pH 6. For purposes of the present invention, the activity that degrades xylan is determined by measuring the increase in xylan hydrolysis of birch wood (Sigma Chemical Co., Inc., St. Louis, MO, USA) by the enzyme (s) which degrade xylan under the following typical conditions: reactions of 1 ml, 5 mg / ml of substrate (total solids), 5 mg of xylanolitic protein / g of substrate, 50 mM sodium acetate pH 5, 50 ° C, 24 hours , sugar analysis using the p-hydroxybenzoic acid hydrazide (PHBAH) assay as described by Lever, 1972, A new reaction for colorimetric determination of carbohydrates, Anal. Biochem 47: 273-279.
Xylanase: The term "xylanase" means a 1,4-beta-D-xylan-xylohydrolase (E.C. 3,2,1,8) that catalyzes the endo-hydrolysis of 1,4-beta-D-xylosidic bonds in xylans. For the purposes of the present invention, xylanase activity is determined with 0.2% AZCL-arabinoxylan as a substrate in 0.01% Triton X-100 and 200 mM sodium phosphate buffer pH 6 at 37 ° C. One unit of xylanase activity is defined as 1.0 µmol of azurine produced per minute at 37 ° C, pH 6 from 0.2% AZCL-arabinoxylan as a substrate in 200 mM sodium phosphate buffer pH 6.
Beta-xylosidase: The term “beta-xylosidase” means a beta-D-xyloside xylohydrolase (EC 3,2,1,37) that catalyzes the exohydrolysis of short beta (1— »4) -xylooligosaccharides, to remove residues of successive D-xylose from non-reducing terminals. For the purposes of the present invention, a beta-xylosidase unit is defined as 1.0 pmol of the p-nitrophenolate anion produced per minute at 40 ° C, pH 5 from 1 mM of p-nitrophenyl-beta-D- xyloside as substrate in 100 mM sodium citrate containing 0.01% TWEEN® 20.
Acetylxylan esterase: The term "acetylxylan esterase" means a carboxylesterase (EC 3,1,1,72) that catalyzes the hydrolysis of polymeric xylan acetyl groups, acetylated xylose, acetylated glucose, alpha-naphthyl acetate, and p- acetate nitrophenyl. For the purposes of the present invention, acetylxylan esterase activity is determined using 0.5 mM p-nitrophenyl acetate as a substrate in 50 mM sodium acetate pH 5.0 containing 0.01% TWEEN® 20. One unit acetylxylan esterase is defined as the amount of enzyme capable of releasing 1 pmol of p-nitrophenolate anion per minute at pH 5, 25 ° C.
Feruloyl esterase: The term "feruloyl esterase" means a 4-hydroxy-3-methoxy-aminoyl-sugar hydrolase (EC 3,1,1,73) that catalyzes the hydrolysis of the 4-hydroxy-3-methoxy-aminoyl (feruloyl) group of a sugar esterified, which is usually arabinose on “natural” substrates, to produce ferulate (4-hydroxy-3-methoxycinnamate). Feruloyl esterase is also known as ferulic acid esterase, hydroxycinnamyl esterase, FAE-III, cinnamyl ester hydrolase, FAEA, cinAE, FAE-I, or FAE-II. For the purposes of the present invention, feruloyl esterase activity is determined using 0.5 mM p-nitrophenylferulate as a substrate in 50 mM sodium acetate pH 5.0. One unit of feruloyl esterase is equal to the amount of enzyme capable of releasing 1 pmol of p-nitrophenolate anion per minute at pH 5, 25 ° C.
Alpha-glucuronidase: The term "alpha-glucuronidase" means an alpha-D-glycosiduronate glucuronhydrolase (EC 3,2,1,139) that catalyzes the hydrolysis of an alpha-D-glucuronoside to D-glucuronate and an alcohol. For the purposes of the present invention, alpha-glucuronidase activity is determined according to de Vries, 1998, J. Bacteriol. 180: 243-249. One unit of alpha-glucuronidase is equal to the amount of enzyme capable of releasing 1 pmol of glucuronic acid or 4-O-methylglycuronic per minute at pH 5, 40 ° C.
Alpha-L-arabinofuranosidase: The term "alpha-L-arabino-furanosidase" means an alpha-L-arabinofuranoside arabinofuran hydrolase (EC 3,2,1,55) that catalyzes the hydrolysis of non-alpha-L-arabinofuranoside residues terminal reducers in alpha-L-arabinosides. The enzyme acts on alpha-L-arabinofuranosides, alpha-L-arabinans containing (1,3) and / or (1,5) bonds, arabinoxylans, and arabinogalactans. Alpha-L-arabinofuranosidase is also known as arabinosidase, alpha-arabinosidase, alpha-L-arabinosidase, alpha-arabinofuranosidase, alpha-L-arabinofuranosidase polysaccharide, alpha-L-arabinofuranoside hydrolase, L-arabinosidase, or alpha-L-arabinanase . For the purposes of the present invention, alpha-L-arabinofuranosidase activity is determined using 5 mg of medium viscosity wheat arabinoxylan (Megazyme International Ireland, Ltd., Bray, Co. Wicklow, Ireland) per ml of sodium acetate a 100 mM pH 5 in a total volume of 200 pl for 30 minutes at 40 ° C followed by the analysis of arabinose by AMINAX® HPX-87H column chromatography (Bio-Rad Laboratories, Inc., Hercules, CA, USA). Cellulosic material : The cellulosic material can be any material containing cellulose. The predominant polysaccharide in the primary cell wall of the biomass is cellulose, the second most abundant is hemicellulose, and the third is pectin. The secondary cell wall, produced after the cell has stopped growing, also contains polysaccharides and is reinforced by polymeric lignin covalently cross-linked to hemicellulose. Cellulose is an anhydrocelobiose homopolymer and thus a linear beta- (1-4) -D- glycan, while hemicelluloses include a variety of compounds, such as xylans, xyloglycans, arabinoxylans, and mannans in complex branched structures with a spectrum substituents. Although generally polymorphic, cellulose is found in plant tissue primarily as an insoluble crystalline matrix of parallel glycan chains. Hemicelluloses usually bind hydrogen to cellulose, as well as other hemicelluloses, which helps to stabilize the cell wall matrix.
Cellulose is generally found, for example, in the stems, leaves, straw, bark, and cobs of plants or leaves, branches, and tree wood. Cellulosic material can be, but is not limited to, herbaceous material, agricultural waste, forest waste, municipal solid waste, waste paper, and pulp and paper mill waste (see, for example, Wiselogel et al., 1995, in Handbook on Bioethanol (Charles E. Wyman, editor), pp. 105-118, Tailor & Francis, Washington DC; Wyman, 1994, Bioresource Technology 50: 3-16; Lynd, 1990, Applied Biochemistry and Biotechnology 24/25: 695- 719; Mosier et al., 1999, Recent Progress in Bioconversion of Lignocellulosics, in Advances in Biochemical Engineering / Biotechnology, T. Scheper, general editor, Volume 65, pp. 23-40, Springer-Verlag, New York). It is understood here that cellulose may be in the form of lignocellulose, a plant cell wall material containing lignin, cellulose, and hemicellulose in a mixed matrix. In a preferred aspect, the cellulosic material is lignocellulose, which comprises cellulose, hemicellulose and lignin.
In one aspect, the cellulosic material is herbaceous material. In another aspect, the cellulosic material is agricultural waste. In another aspect, the cellulosic material is forest waste. In another aspect, cellulosic material is municipal solid waste. In another aspect, the cellulosic material is waste paper. In another aspect, the cellulosic material is pulp and paper mill residue.
In another aspect, the cellulosic material is corn forage. In another aspect, the cellulosic material is corn fiber. In another aspect, the cellulosic material is corncob. In another aspect, the cellulosic material is orange peel. In another aspect, the cellulose material is rice straw. In another aspect, the cellulosic material is wheat straw. In another aspect, the cellulosic material is yellow millet. In another aspect, the cellulosic material is eulalia. In another aspect, the cellulosic material is bagasse.
In another aspect, the cellulosic material is microcrystalline cellulose. In another aspect, the cellulosic material is bacterial cellulose. In another aspect, the cellulosic material is algal cellulose. In another aspect, the cellulosic material is cotton lint. In another aspect, the cellulosic material is cellulose treated with amorphous phosphoric acid. In another aspect, the cellulosic material is filter paper.
The cellulosic material can be used as such or can be subjected to pretreatment, using conventional methods known in the art, as described herein. In a preferred aspect, the cellulosic material is pre-treated.
Pre-treated maize fodder: The terms “PCS” or “Pre-treated maize fodder” mean cellulosic material derived from maize forage by treatment with heat and dilute sulfuric acid.
Xylan-containing material: The term "xylan-containing material" means any material that comprises a plant cell wall polysaccharide containing a main chain of beta- (1-4) linked xylose residues. Terrestrial plant xylans are heteropolymers that have a beta- (1-4) -D-xylopyranose backbone, which is branched by short carbohydrate chains. They comprise D-glucuronic acid or its 4-O-methyl ester, L-arabinose, and / or various oligosaccharides, compounds of D-xylose, L-arabinose, D- or L-galactose, and D-glucose. Xylan-like polysaccharides can be divided into homoxylans and heteroxylans, which include glucuronoxylans, (arabino) glucuronoxylans, (glucuron) arabinoxylans, arabinoxylans, and complex heteroxylans. See, for example, Ebringerova et al., 2005, Adv. Polim. Know. 186: 1-67.
In the methods of the present invention, any material containing xylan can be used. In a preferred aspect, the material containing xylan is lignocellulose.
Isolated or Purified: The terms "isolated" or "purified" mean a polypeptide or polynucleotide that is removed from at least one component with which it is naturally associated. For example, a polypeptide can be at least 1% pure, for example, at least 5% pure, at least 10% pure, at least 20% pure, at least 40% pure, at least 60% pure, at least 80% pure, at least 90% pure, or at least 95% pure, as determined by the SDS-PAGE and a polynucleotide can be at least 1% pure, for example, at least 5% pure, at least 10% pure, at least 20 % pure, at least 40% pure, at least 60% pure, at least 80% pure, at least 90% pure, or at least 95% pure, as determined by agarose electrophoresis.
Mature polypeptide: The term "mature polypeptide" means a polypeptide in its final form following translation and any post-translational modifications, such as N-terminal processing, C-terminal truncation, glycosylation, phosphorylation, etc. In one aspect, the mature polypeptide is amino acids 22 to 322 of SEQ ID NO: 2 based on the SignalP program (Nielsen et al., 1997, Protein Engineering 10: 1-6) that predicts amino acids 1 to 21 of SEQ ID NO: 2 are a signal peptide. It is known in the art that a host cell can produce a mixture of two or more different mature polypeptides (i.e., with a different C-terminal and / or N-terminal amino acid) expressed by the same polynucleotide.
Sequence encoding mature polypeptide: The term "sequence encoding mature polypeptide" means a polynucleotide that encodes a mature polypeptide having cellulolytic enhancing activity. In one aspect, the sequence encoding mature polypeptide is the nucleotides 64 to 1018 of SEQ ID NO: 1 based on the SignalP program (Nielsen et al., 1997, supra) that predicts nucleotides from 1 to 63 of SEQ ID NO: 1 encode a signal peptide. In another aspect, the sequence encoding mature polypeptide is the cDNA sequence contained in nucleotides 64 to 1018 of SEQ ID NO: 1.
Sequence identity: The relationship between two amino acid sequences or between two nucleotide sequences is described by the parameters "sequence identity".
For the purposes of the present invention, the degree of sequence identity between two amino acid sequences is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, J. Mol. Biol. 48: 443-453) as implemented in the program Needle of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000, Trends Genet. 16: 276-277), preferably version 3.0.0 or later. The optional parameters used are a gap opening penalty of 10, a gap extension penalty of 0.5, and the replacement matrix EBLOSUM62 (EMBOSS version of BLOSUM62). The output of the Needle labeled “longest identity” (obtained using the -nobrief option) is used as the percentage identity and is calculated as follows: (Identical Residues x 100) / (Alignment Length - Total Number of Intervals in Alignment)
For the purposes of the present invention, the degree of sequence identity between two deoxyribonucleotide sequences is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, supra) as implemented in the Needle program of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000, supra), preferably version 3.0.0 or later. The optional parameters used are gap opening penalty of 10, gap extension penalty of 0.5, and EDNAFULL (EMBOSS version of NCBINUC4.4). The Needle output labeled “longest identity” (obtained using the -nobrief option) is used as the percentage identity and is calculated as follows: (Identical deoxyribonucleotides x 100) / (Alignment Length - Total Number of Intervals in Alignment)
Fragment: The term "fragment" means a polypeptide having one or more (several) amino acids deleted from the amino and / or carboxyl terminus of a mature polypeptide; in which the fragment has cellulolytic intensification activity. In one aspect, a fragment contains at least 255 amino acid residues, for example, at least 270 amino acid residues or at least 285 amino acid residues of the mature polypeptide of SEQ ID NO: 2.
Subsequence: The term "subsequence" means a polynucleotide having one or more (several) deleted nucleotides from the 5 'and / or 3' end of a sequence that encodes mature polypeptide; wherein the subsequence encodes a fragment having cellulolytic intensification activity. In one aspect, a subsequence contains at least 765 nucleotides, for example, at least 810 nucleotides or at least 855 nucleotides of the sequence encoding mature polypeptide of SEQ ID NO: 1.
Allelic variant: The term "allelic variant" means any one of two or more alternative forms of a gene that occupies the same chromosomal site. Allelic variation occurs naturally through mutation, and can result in polymorphism within populations. Gene mutations can be silent (no change in the encoded polypeptide) or can encode polypeptides having altered amino acid sequences. An allele variant of a polypeptide is a polypeptide encoded by an allele variant of a gene.
Coding sequence: The term "coding sequence" means a polynucleotide, which directly specifies the amino acid sequence of a polypeptide. The encoding sequence limits are generally determined by an open reading matrix, which usually starts with the ATG start codon or alternative start codons such as GTG and TTG and ends with a stop codon such as TAA, TAG, and TGA. The coding sequence can be a DNA, cDNA, synthetic or recombinant polynucleotide.
cDNA: The term "cDNA" means a DNA molecule that can be prepared by the reverse transcription of a mature, joined mRNA molecule, obtained from a eukaryotic cell. The cDNA lacks intron sequences that may be present in the corresponding genomic DNA. The initial, primary RNA transcript is a precursor to mRNA that is processed through a series of steps, including splicing, before appearing as mature spliced mRNA.
Nucleic acid construction: The term "nucleic acid construction" means a single or double-stranded nucleic acid molecule that is isolated from a naturally occurring gene or is modified to contain nucleic acid segments in a way that otherwise way would not exist in nature or that are synthetic. The term nucleic acid construction is synonymous with the term "expression cassette" when the nucleic acid construction contains the control sequences required for the expression of a coding sequence of the present invention.
Control sequences: The term "control sequences" means all components necessary for the expression of a polynucleotide that encodes a polypeptide of the present invention. Each control sequence can be native or foreign to the polynucleotide encoding the polypeptide or native or foreign to each other. Such control sequences include, but are not limited to, a leader sequence, polyadenylation sequence, pro-peptide sequence, promoter, peptide signal sequence, and transcription terminator. At a minimum, control sequences include a promoter, and transcriptional and translational stop signals. Control sequences can be provided with linkers for the purpose of introducing specific restriction sites that facilitate the binding of control sequences to the polynucleotide coding region that encodes a polypeptide.
Operably linked: The term "operably linked" means a configuration in which a control sequence is placed in an appropriate position with respect to the coding sequence of a polynucleotide such that the control sequence directs the expression of the coding sequence.
Expression: The term "expression" includes any step involved in the production of the polypeptide including, but not limited to, transcription, post-transcriptional modification, translation, post-translational modification and secretion.
Expression vector: The term "expression vector" means a linear or circular DNA molecule that comprises a polynucleotide that encodes a polypeptide and is operably linked to the additional nucleotides that provide its expression.
Host cell: The term "host cell" means any cell type that is susceptible to transformation, transfection, transduction, and the like with a nucleic acid construct or expression vector that comprises a polynucleotide of the present invention. The term "host cell" encompasses any progeny of a precursor cell that is not identical to the precursor cell due to mutations that occur during replication.
Variant: The term "variant" means a polypeptide having cellulolytic intensification activity that comprises an alteration, that is, a substitution, insertion, and / or deletion of one or more (several) amino acid residues in one or more (several) positions . A substitution means a substitution for an amino acid that occupies a position with a different amino acid; a deletion means the removal of an amino acid that occupies a position; and an insertion means adding one or more (several) amino acids, for example, from 1 to 5 amino acids, adjacent to an amino acid that occupies a position. Detailed Description of the Invention Polypeptides Having Cellulolytic Intensification Activity
The present invention concerns isolated polypeptides having cellulolytic intensification activity selected from the group consisting of
(a) a polypeptide having at least 80% sequence identity with the mature polypeptide of SEQ ID NO: 2;
(b) a polypeptide encoded by a polynucleotide that hybridizes under high stringency conditions to (i) the sequence encoding mature polypeptide of SEQ ID NO: 1, (ii) the cDNA sequence contained in the sequence encoding mature SEQ ID polypeptide NO: 1, or (iii) the complementary filament of total length of (i) or (ii);
(c) a polypeptide encoded by a polynucleotide having at least 80% sequence identity with the sequence encoding mature polypeptide of SEQ ID NO: 1 or its cDNA sequence;
(d) a variant comprising a replacement, deletion, and / or insertion of one or more (several) amino acids from the mature polypeptide of SEQ ID NO: 2; and
(e) a fragment of a polypeptide from (a), (b), (c), or (d) that has cellulolytic enhancing activity.
The present invention relates to isolated polypeptides having a sequence identity with the mature polypeptide of SEQ ID NO: 2 of at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 100%, which have cellulolytic intensification activity. In one aspect, the polypeptide differs by no more than ten amino acids, for example, in five amino acids, in four amino acids, in three amino acids, in two amino acids, and in an amino acid of the mature polypeptide of SEQ ID NO: 2.
A polypeptide of the present invention preferably comprises or consists of an amino acid sequence of SEQ ID NO: 2 or an allelic variant thereof; or it is a fragment of it having cellulolytic intensification activity. In another aspect, the polypeptide comprises or consists of the mature polypeptide of SEQ ID NO: 2. In another preferred aspect, the polypeptide comprises or consists of amino acids 22 to 322 of SEQ ID NO: 2.
The present invention also relates to isolated polypeptides having cellulolytic enhancing activity that are encoded by polynucleotides that hybridize under conditions of high stringency or very high stringency conditions with (i) the sequence encoding mature polypeptide of SEQ ID NO: 1, ( ii) the cDNA sequence contained in the sequence encoding mature polypeptide of SEQ ID NO: 1, or (iii) the complementary full length strand of (i) or (ii) (J. Sambrook, EF Fritsch, and T. Maniatis , 1989, Molecular Cloning, A Laboratory Manual, 2nd edition, Cold Spring Harbor, New York).
The SEQ ID NO: 1 polynucleotide or a subsequence thereof, as well as the amino acid sequence of SEQ ID NO: 2 or a fragment thereof, can be used to design nucleic acid probes to identify and clone DNA-encoding polypeptides having DNA activity. cellulolytic intensification of strains of different genera or species according to methods well known in the art, in particular, such probes can be used for hybridization with the genomic DNA or cDNA of the genus or species of interest, following standard Southern blotting procedures, to identify and isolate the corresponding gene at that point. Such probes can be considerably shorter than the entire sequence, but must be at least 14, for example, at least 25, at least 35, or at least 70 nucleotides in length. Preferably, the nucleic acid probe is at least 100 nucleotides in length, for example, at least 200 nucleotides, at least 300 nucleotides, at least 400 nucleotides, at least 500 nucleotides, at least 600 nucleotides, at least 700 nucleotides, at least 800 nucleotides, or at least 900 nucleotides in length. Both the DNA probe and the RNA probe can be used. The probes are typically labeled to detect the corresponding gene (for example, with P, H, S, biotin, or avidin). Such probes are encompassed by the present invention.
A library of genomic DNA or cDNA prepared from such other strains can be screened for DNA that hybridizes to the probes described above and encodes a polypeptide having cellulolytic enhancing activity. Genomic DNA or other DNA from such other strains can be separated by agarose or polyacrylamide gel electrophoresis, or other separation techniques. The DNA from the libraries or the separated DNA can be transferred to and immobilized on nitrocellulose or other suitable carrier material. In order to identify a clone or DNA that is homologous to SEQ ID NO: 1 or a subsequence thereof, the carrier material is preferably used in a Southern blot.
For the purposes of the present invention, hybridization indicates that the polynucleotide hybridizes to a labeled nucleic acid probe that corresponds to SEQ ID NO: 1; the sequence encoding mature polypeptide of SEQ ID NO: 1; the cDNA sequence contained in the sequence encoding mature polypeptide of SEQ ID NO: 1; its complementary full-length filament; or a subsequence thereof; under very low to very high stringency conditions. The molecules to which the nucleic acid probe hybridizes under these conditions can be detected using, for example, X-ray film.
In one aspect, the nucleic acid probe is the sequence encoding mature polypeptide of SEQ ID NO: 1 or its cDNA sequence. In another aspect, the nucleic acid probe is a polynucleotide that encodes the polypeptide of SEQ ID NO: 2 or the mature polypeptide thereof; or a fragment of it. In another preferred aspect, the nucleic acid probe is SEQ ID NO: 1 or its cDNA sequence. In another aspect, the nucleic acid probe is the polynucleotide contained in plasmid pGEM-T-Ppin7 which is contained in E. coli DSM 22711, in which the polynucleotide encodes a polypeptide having cellulolytic enhancing activity. In another aspect, the nucleic acid probe is the mature polypeptide that encodes the region contained in plasmid pGEM-T-Ppin7 that is contained in E. coli DSM 22711.
For long probes of at least 100 nucleotides in length, very low to very high stringency conditions are defined as prehybridization and hybridization at 42 ° C in 5X SSPE, 0.3% SDS, 200 micrograms / ml DNA cut and denatured salmon sperm, and 25% formamide for very low and low stringency, 35% formamide for medium and medium-high stringency, or 50% formamide for high and very high stringency, following standard Southern blotting procedures ideally for 12 to 24 hours. The carrier material is finally washed three times each for 15 minutes using 2X SSC, 0.2% SDS at 45 ° C (very low stringency), 50 ° C (low stringency), 5 5 ° C (medium stringency) , at 60 ° C (medium-high stringency), 65 ° C (high stringency), and 70 ° C (very high stringency).
For short probes of about 15 nucleotides to about 70 nucleotides in length, stringency conditions are defined as prehybridization and hybridization at about 5 ° C to about 10 ° C below the Tm calculated using the calculation according to Bolton and McCarthy (1962, Proc. Natl. Acad. Sci. USA 48: 1390) in 0.9 M NaCl, 0.09 M Tris-HCl pH 7.6, 6 mM EDTA, 0.5% NP- 40, IX Denhardt's solution, 1 mM sodium pyrophosphate, 1 mM sodium monobasic phosphate, 0.1 mM ATP, and 0.2 mg yeast RNA per ml following the standard Southern blotting procedures for 12 to 24 ideally. The carrier material is finally washed once in 6X SCC plus 0.1% SDS for 15 minutes and twice each for 15 minutes using 6X SSC from 5 ° C to 10 ° C below the calculated Tm.
The present invention also concerns isolated polypeptides having cellulolytic enhancing activity encoded by polynucleotides having a sequence identity to the sequence encoding mature polypeptide of SEQ ID NO: 1 or its cDNA sequence of at least 80%, at least 85% at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% , or 100%.
The present invention relates to variants comprising a substitution, deletion, and / or insertion of one or more (or more) amino acids of the mature polypeptide of SEQ ID NO: 2, or a sequence homologous thereto. Preferably, the amino acid changes are of a minor nature, i.e. conservative amino acid substitutions or insertions that do not significantly affect protein fold and / or activity; small deletions, typically from one to about 30 amino acids; small amino or carboxyl terminal extensions, such as a methionine residue at the amino terminal; a small binding peptide of up to about 20 to 25 residues; or a small extension that facilitates purification by changing the net charge or another function, such as a polyhistidine tract, an antigenic epitope or a binding domain.
Examples of conservative substitutions are within the group of basic amino acids (arginine, lysine and histidine), acidic amino acids (glutamic acid and aspartic acid), polar amino acids (glutamine and asparagine), hydrophobic amino acids (leucine, isoleucine and valine), aromatic amino acids (phenylalanine, tryptophan and tyrosine), and small amino acids (glycine, alanine, serine, threonine and methionine). Amino acid substitutions that generally do not alter specific activity are known in the art and are described, for example, by H. Neurath and R. L. Hill, 1979, Em, The proteins, Academic Press, New York. The most common changes are Ala / Ser, Val / Ile, Asp / Glu, Thr / Ser, Ala / Gly, Ala / Thr, Ser / Asn, Ala / Val, Ser / Gly, Tyr / Phe, Ala / Pro , Lys / Arg, Asp / Asn, Leu / Ile, Leu / Val, Ala / Glu, and Asp / Gly.
Alternatively, the amino acid changes are of such a nature that the physical and chemical properties of the polypeptides are altered. For example, amino acid changes can improve the thermal stability of the polypeptide, change the substrate specificity, change the ideal pH, and others.
The essential amino acids in a precursor polypeptide can be identified according to procedures known in the art, such as loco-directed mutagenesis or alanine scan mutagenesis (Cunningham and Wells, 1989, Science 244: 1081-1085). In the latter technique, single alanine mutations are introduced into each residue in the molecule, and the resulting mutant molecules are tested for cellulolytic enhancing activity to identify amino acid residues that are critical to the molecule's activity. See also, Hilton et al., 1996, J. Biol. Chem. 271: 4699-4708. The active site of the enzyme or other biological interaction can also be determined by physical analysis of the structure, such as
TI determined by techniques such as nuclear magnetic resonance, crystallography, electron diffraction, or photoafmity labeling, in conjunction with a putative contact site amino acid mutation. See, for example, de Vos et al., 1992, Science 255: 306-312; Smith et al., 1992, J. Mol. Biol. 224: 899-904; Wlodaver et al., 1992, FEBS Lett. 309: 59-64. The identities of essential amino acids can also be deduced from the analysis of identities with polypeptides that are related to the precursor polypeptide.
Single or multiple amino acid substitutions, deletions, and / or insertions can be made and tested using known methods of mutagenesis, recombination, and / or shuffling, followed by a relevant screening procedure, such as that disclosed by Reidhaar- Olson and Sauer , 1988, Science 241: 53-57; Bowie and Sauer, 1989, Proc. Natl. Acad. Sci. USA 86: 2152-2156; WO 95/17413; or WO 95/22625. Other methods that can be used include error-prone PCR, phage demonstration (for example, Lowman et al., 1991, Biochemistry 30: 10832-10837; US Patent No. 5,223,409; WO 92/06204), and targeted mutagenesis to the region (Derbyshire et al., 1986, Gene 46: 145; Ner et al., 1988, DNA 7: 127).
Mutagenesis / shuffling methods can be combined with high-throughput screening methods, automated to detect cloned, mutagenized polypeptide activity expressed by host cells (Ness et al., 1999, Nature Biotechnology 17: 893- 896). Mutagenized DNA molecules encoding active polypeptides can be recovered from host cells and quickly sequenced using standard methods in the art. These methods allow rapid determination of the importance of individual amino acid residues in a polypeptide. The total number of amino acid substitutions, deletions and / or insertions of the mature polypeptide of SEQ ID NO: 2 is not greater than 10, for example 1 , 2, 3, 4, 5, 6, 7, 8 or 9.
The polypeptide can be a hybrid polypeptide in which a portion of a polypeptide is fused at the N-terminus or at the C-terminus of a portion of another polypeptide.
The polypeptide can be a fused polypeptide or cleavable fusion polypeptide in which another polypeptide is fused at the N-terminus or the C-terminus of the polypeptide of the present invention. A fused polypeptide is produced by fusing a polynucleotide that encodes another polypeptide to a polynucleotide of the present invention. Techniques for producing fusion polypeptides are known in the art, and include linking the coding sequences that encode the polypeptides so that they are in the matrix and that the expression of the fused polypeptide is under the control of the same promoter (s) ) and terminator. Fusion proteins can also be built using intein technology in which fusions are created post-translationally (Cooper et al., 1993, EMBO J. 12: 2575-2583; Dawson et al., 1994, Science 266: 776 -779).
A fusion polypeptide can further comprise a dividing site between the two polypeptides. In the secretion of the fusion protein, the site is cleaved which releases the two polypeptides. Examples of cleavage sites include, but are not limited to, the sites disclosed in Martin et al., 2003, J. Ind. Microbiol. Biotechnol. 3: 568-576; Svetina et al., 2000, J. Biotechnol. 76: 245-251; Rasmussen-Wilson et al., 1997, Appl. Environ. Microbiol. 63: 3488-3493; Ward et al., 1995, Biotechnology 13: 498-503; and Contreras et al., 1991, Biotechnology 9: 378-381; Eaton et al., 1986, Biochemistry 25: 505-512; Collins-Racie et al., 1995, Biotechnology 13: 982-987; Carter et al., 1989, Proteins: Structure, Function, and Genetics 6: 240-248; and Stevens, 2003, Drug Discovery World 4: 35-48. Polypeptide Sources Having Cellulolytic Enhancing Activity A polypeptide having cellulolytic enhancing activity of the present invention can be obtained from microorganisms of any genus. For the purposes of the present invention, the term "obtained from" as used herein in connection with a given source must mean that the polypeptide encoded by a polynucleotide is produced by the source or by a strain into which the polynucleotide from the source has been inserted. In one aspect, the polypeptide obtained from a given source is secreted extracellularly.
The polypeptide can be a bacterial polypeptide. For example, the polypeptide may be a gram-positive bacterial polypeptide such as a polypeptide from Bacillus, Clostridium, Enterococcus, Geobacillus, Lactobacillus, Lactococcus, Oceanobacillus, Staphilococcus, Streptococcus, or Streptomycest negative polypeptide-intensifying cellulolytic activity. such as a polypeptide from Campylobacter, E. coli, Flavobacterium, Fusobacterium, Helicobacter, Ilyobacter, Neisseria, Pseudomonas, Salmonella, or Ureaplasma.
In one aspect, the polypeptide is a polypeptide from Bacillus alkalophilus, Bacillus amiloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megillus, Bacillus megillus, Bacillus michillus subtilis, or Bacillus thuringiensis.
In another aspect, the polypeptide is a polypeptide from Streptococcus equisimilis, Streptococcus pyogenes, Streptococcus uberis, or Streptococcus equi subsp. Zooepidemicus.
In another aspect, the polypeptide is a polypeptide from Streptomyces achromogenes, Streptomyces avermitilis, Streptomyces coelicolor, Streptomyces griseus, or Streptomyces lividans.
The polypeptide can also be a fungal polypeptide. For example, the polypeptide can be a yeast polypeptide such as a polypeptide from Candida, Kluyveromyces, Pichia, Saccharomyces,
Schizosaccharomyces, or Yarrowia; or a filamentous fungal polypeptide such as an Acremonium polypeptide, Agaricus, Alternaria, Aspergillus, Aureobasidium, Botryospaeria, Ceriporiopsis, Chaetomidium,
Chrysosporium, Claviceps, Cochliobolus, Coprinopsis, Coptotermes, Corynascus, Cryphonectria, Cryptococcus, Diplodia, Exidia, Filibasidium, Fusarium, Gibberella, Holomastigotoides, Humicola, Irpex, Lentinula, Leptospaer, Merpiloc, Melapore, Melapore, Magnumortan, Melone, Paecilomyces, Phanerochaete, Piromyces, Poitrasia, Pseudoplectania, Pseudotrichonympha, Rhizomucor, Schizophillum, Scytalidium, Talaromyces, Thermoascus, Thielavia, Tolypocladium, Trichoderma, Trichophaea, Verticillium, Volvariella, or Xolvariella.
In another aspect, the polypeptide is a Penicillium polypeptide.
In another aspect, the polypeptide is a polypeptide from Saccharomyces carlsbergensis, Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomyces norbensis, or Saccharomyces oviformis.
In another aspect, the polypeptide is a polypeptide from Acremonium cellulolyticus, Aspergillus aculeatus, Aspergillus awamori, Aspergillus foetidus, Aspergillus fumigatus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus nidulans, Aspergillus niger, Aspergillus niger, Aspergilluspornus, Chrysosporium pannicola, Chrysosporium queenslandicum, Chrysosporium tropicum, Chrysosporium zonatum, Fusarium bactridioides, Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusarium graminaarum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi, Fusarium siberumum, fusarium oxisporum , Fusarium sporotrichioides, Fusarium sulphureum, Fusarium torulosum, Fusarium trichothecioides, Fusarium venenatum, Humicola grisea, Humicola insolens, Humicola lanuginosa, Irpex lacteus, Mucor miehei, Myceliophthora thermophila, Neurospora crassa, Penicillium funicillium funicillium sum, Penicillium purpurogenum, Phanerochaete chrysosporium, Thielavia achromatica, Thielavia albomyces, Thielavia albopilosa, Thielavia australeinsis, Thielavia fimeti, Thielavia microspora, Thielavia ovispora, Thielavia peruviana, Thielavia setosa, Thielavia spiedon, Thielavia spedonon, Thielavia spedonon Trichoderma longibrachiatum, Trichoderma reesei, or Trichoderma viride.
In another aspect, the polypeptide is a polypeptide from Penicillium pinophilum.
It will be understood that for the aforementioned species the invention encompasses both the perfect and the imperfect state, and other taxonomic equivalents, for example, anamorphic, regardless of the species name for which they are known. Those skilled in the art will easily recognize the identity of appropriate equivalents.
Strains of these species are easily accessible to the public in various culture collections, such as the American Type Culture Collection (ATCC), Deutsche Sammlung von Mikroorganismoen und Zellkulturen GmbH (DSMZ), Centraalbureau Voor Schimmelcultures (CBS), and Agricultural Research Service Patent Culture Collection, Northern Regional Research Center (NRRL).
The polypeptide can be identified and obtained from other sources including microorganisms isolated from nature (eg soil, compounds, water, etc.), using the probes mentioned above. Techniques for isolating microorganisms from natural habitats are well known in the art. The polynucleotide encoding the polypeptide can then be obtained by similarly screening a genomic or cDNA library from another mixed microorganism or DNA sample. Once a polynucleotide encoding a polypeptide has been detected with the probe (s), the polynucleotide can be isolated or cloned using techniques that are well known to those of ordinary skill in the art (see, for example, Sambrook et al., 1989, supra). Polynucleotides
The present invention also concerns isolated polynucleotides that encode a polypeptide of the present invention.
Techniques used to isolate or clone a polynucleotide that encodes a polypeptide are known in the art and include isolation of genomic DNA, cDNA preparation, or a combination thereof. The cloning of polynucleotides from such genomic DNA can be performed, for example, using the well-known polymerase chain reaction (PCR) or antibody screening of expression libraries to detect cloned DNA fragments with shared structural characteristics. See, for example, Innis et al., 1990, PCR: A Guide to methods and Application, Academic Press, New York. Other nucleic acid amplification procedures such as ligase chain reaction (LCR), ligation-activated transcription (LAT) and polynucleotide-based amplification (NASBA) can be used. Polynucleotides can be cloned from a strain of Penicillium, or another or related organism, and so, for example, it can be an allelic species or variant of the region that encodes the polynucleotide polypeptide.
The present invention also relates to isolated polynucleotides that comprise or consist of polynucleotides having a degree of sequence identity to the sequence encoding mature polypeptide of SEQ ID NO: 1 or its cDNA sequence of at least 80% 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%, that encodes a polypeptide having cellulolytic intensification activity.
Modification of a polynucleotide encoding a polypeptide of the present invention may be necessary for the synthesis of polypeptides substantially similar to the polypeptide. The term "substantially similar" to the polypeptide refers to the non-naturally occurring forms of the polypeptide. These polypeptides may differ in some way engineered from the polypeptide isolated from its native source, for example, variants that differ in specific activity, thermostability, ideal pH, or the like. The variant can be constructed based on the polynucleotide shown as the sequence encoding mature polypeptide of SEQ ID NO: 1 or its cDNA sequence, for example, a subsequence thereof, and / or by introducing nucleotide substitutions that do not result in a change in the amino acid sequence of the polypeptide, but which corresponds to the use of the codon of the intended host organism for the production of the enzyme, or by the introduction of nucleotide substitutions that may give rise to a different amino acid sequence. For a general description of nucleotide substitution, see, for example, Ford et al., 1991, Protein Expression and Purification 2: 95-107.
The present invention also relates to isolated polynucleotides that encode the polypeptides of the present invention, which hybridize under conditions of high stringency, or conditions of very high stringency with (i) the sequence encoding mature polypeptide of SEQ ID NO: 1, (ii ) the cDNA sequence contained in the sequence encoding mature polypeptide of SEQ ID NO: 1, or (iii) the full length complementary strand of (i) or (ii); or allelic variants and subsequences thereof (Sambrook et al., 1989, supra), as defined herein.
In one aspect, the polynucleotide comprises or consists of SEQ ID NO: 1, the sequence encoding mature polypeptide of SEQ ID NO: 1, or the sequence contained in plasmid pGEM-T-Ppin7 which is contained in E. coli DSM 22711; or a subsequence of SEQ ID NO: 1 which encodes a fragment of SEQ ID NO: 2 having cellulolytic enhancing activity. Nucleic Acid Constructions
The present invention also relates to nucleic acid constructs comprising a polynucleotide of the present invention operably linked to one or more (several) control sequences that direct the expression of coding sequence in a suitable host cell under conditions compatible with the control sequences .
A polynucleotide can be manipulated in a variety of ways to provide expression of the polypeptide. The manipulation of the polynucleotide before insertion into a vector may be desirable or necessary depending on the expression vector. Techniques for modifying polynucleotides using recombinant DNA methods are well known in the art.
The control sequence can be a promoter sequence, a polynucleotide that is recognized by a host cell for the expression of a polynucleotide that encodes a polypeptide of the present invention. The promoter sequence contains transcriptional control sequences that mediate polypeptide expression. The promoter can be any polynucleotide that shows transcriptional activity in the host cell of choice including mutant, truncated, and hybrid promoters, and can be obtained from genes encoding homologous or heterologous extracellular or intracellular polypeptides for the host cell.
Examples of promoters suitable for directing the transcription of the nucleic acid constructs of the present invention into a bacterial host cell are promoters obtained from the Bacillus amyloliquefaciens alpha-amylase gene (amyQ), the alpha-amylase gene of
Bacillus licheniformis (amyl), Bacillus licheniformis penicillinase (penP) gene, Bacillus stearothermophilus (amyM) maltogenic amylase gene, Bacillus subtilis (sacB) levansucrase gene, xylA and xilB genes of bacillus subtilis, operil agarase gene Streptomyces coelicolor (dagA), and prokaryotic beta-lactamase gene (Villa-Kamaroff et al., 1978, Proc. Natl. Acad. Sci. USA 75: 3727-3731), as well as the tac promoter (DeBoer et al. , 1983, Proc. Natl. Acad. Sci. USA 80: 21-25). Other promoters are described in “Useful proteins from recombinant bacteria” in Gilbert et al., 1980, Scientific American, 242: 74-94; and in Sambrook et al., 1989, supra.
Examples of promoters suitable for directing the transcription of the nucleic acid constructs of the present invention in a filamentous fungal host cell are promoters obtained from the genes for Aspergillus nidulans acetamidase, Aspergillus niger neutral alpha-amylase, Aspergillus acid-stable alpha-amylase niger, Aspergillus niger glycoamylase or Aspergillus awamori (glaA), Aspergillus oryzae TAKA amylase, Aspergillus oryzae alkaline protease, Aspergillus oryzae isomerase phosphate triose, Fusarium oxenporum7 amyloid 7 proteases (WO 00/56900), Daria de Fusarium venenatum (WO 00/56900), Quinn de Fusarium venenatum (WO 00/56900), Rhizomucor miehei lipase, Rhizomucor miehei aspartic proteinase, Trichoderma reesei beta-glycosity, celobiohydrolase I of Trichoderma reesei, cellobiohydrolase II of Trichoderma reesei, endoglycanase I of Trichoderma reesei, endoglycanase II of Trichoder ma reesei, endoglycanase III of Trichoderma reesei, endoglycanase IV of Trichoderma reesei, endoglycanase V of Trichoderma reesei, xylanase I of Trichoderma reesei, xylanase II of Trichoderma reesei, beta-xylidasidase of Trichoderma reesei, as well as the promoter NA, as well as promoter NA-2 modified from a gene encoding an Aspergillus-neutral alpha-amylase in which the untranslated leader has been replaced by an untranslated leader from a gene encoding Aspergillus triose phosphate isomerase; non-limiting examples include modified promoters of the gene encoding neutral alpha-amylase in Aspergillus niger in which the untranslated leader has been replaced by an untranslated leader of the gene encoding the triose phosphate isomerase in Aspergillus nidulans or Aspergillus oryzae) ', and its mutant, truncated, and hybrid promoters.
In a yeast host, useful promoters are obtained from the genes for Saccharomyces cerevisiae (ENO-1) enolase, Saccharomyces cerevisiae galactocinase (GAL1), alcohol dehydrogenase / glyceraldehyde-3-phosphate dehydrogenase de Saccharomyces cerevisiae (ADH1, ADH1, ADH1, ADH1, ADH1, ADH1, ADH1, , Saccharomyces cerevisiae triose phosphate isomerase (TPI), Saccharomyces cerevisiae metallothionein (CUP1), and Saccharomyces cerevisiae 3-phosphoglycerate kinase. Other useful promoters for yeast host cells are described by Romanos et al., 1992, Yeast 8: 423-488.
The control sequence can also be a suitable transcription terminator sequence, which is recognized by a host cell to terminate transcription. The terminator sequence is operably linked to the 3 'terminal of the polynucleotide that encodes the polypeptide. Any terminator that is functional in the host cell of choice can be used in the present invention.
Preferred terminators for filamentous fungal host cells are obtained from genes for Aspergillus nidulans anthranilate synthase, Aspergillus niger glycoamylase, Aspergillus niger alpha-glycosity, TAKA amylase from Aspergillus oryzae, and protease equivalent to Fusarium trypsin oxide protease.
Preferred terminators for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C (CYC1), and Saccharomyces cerevisiae glyceraldehyde-3-phosphate dehydrogenase. Other useful terminators for yeast host cells are described. Romanos et al., 1992, supra.
The control sequence can also be a suitable leader sequence, when transcribed is an untranslated region of an mRNA that is important for translation by the host cell. The leader sequence is operably linked to the 5 'end of the polynucleotide that encodes the polypeptide. Any leader sequence that is functional in the host cell of choice can be used.
The preferred leaders for filamentous fungal host cells are obtained from the Aspergillus oryzae TAKA amylase genes and Aspergillus nidulans phosphate isomerase triose.
The leaders suitable for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae 3-phosphoglycerate kinase, Saccharomyces cerevisiae alpha factor, and dehydrogenase / glyceraldehyde-3-phosphate alcohol Saccharomyces cerevisiae dehydrogenase (ADH2 / GAP).
The control sequence can also be a polyadenylation sequence, a sequence operably linked to the 3 'terminal of the polynucleotide and, when transcribed, is recognized by the host cell as a signal to add polyadenosine residues to the transcribed mRNA. Any polyadenylation sequence that is functional in the host cell of choice can be used.
The preferred polyadenylation sequences for filamentous fungal host cells are obtained from the genes for TAKA amylase from Aspergillus oryzae, glycoamylase from Aspergillus niger, anthranilate synthase from Aspergillus nidulans, protease equivalent to trypsin from Fusarium oxisporum, and alpha-glycosides .
Polyadenylation sequences useful for yeast host cells are described by Guo and Sherman, 1995, Mol. Cellular Biol. 15: 5983-5990.
The control sequence can also be a coding signal peptide region that encodes a signal peptide attached to the N-terminus of a polypeptide and directs the polypeptide in the cell's secretory path. The 5 'end of the polynucleotide coding sequence can inherently contain a naturally occurring signal peptide coding sequence in the translation reading matrix with the coding sequence segment encoding the polypeptide. Alternatively, the 5 'end of the coding sequence may contain a signal peptide coding sequence that is foreign to the coding sequence. The foreign signal peptide coding sequence may be required where the coding sequence does not naturally contain a signal peptide coding sequence. Alternatively, the foreign signal peptide coding sequence can simply replace the natural signal peptide coding sequence in order to enhance secretion of the polypeptide. However, any signal peptide coding sequence that directs the expressed polypeptide in the secretory path of a host cell of choice can be used.
The effective signal peptide coding sequences for bacterial host cells are the signal peptide coding sequences obtained from the genes for Bacillus licheniformis maltogenic amylase NCIB 11837, Bacillus licheniformis subtilisin, Bacillus licheniformis beta-lactamase, Bacillus alpha-amylase stearothermophilus, neutral proteases from Bacillus stearothermophilus (nprT, nprS, nprM), and prsA from Bacillus subtilis. Other signal peptides are described by Simonen and Paiva, 1993, Microbiological Reviews 57: 109-137.
The signal peptide coding sequences effective for filamentous fungal host cells are the signal peptide coding sequences obtained from the genes for the neutral amylase of
Aspergillus niger, Aspergillus niger glycoamylase, Aspergillus oryzae TAKA amylase, Humicola insolens cellulase, Humicola insolens endoglycanase V, Humicola lanuginosa lipase, and Rhizomucor miehei aspartic proteinase.
Signal peptides useful for yeast host cells are obtained from the Saccharomyces cerevisiae alpha factor and Saccharomyces cerevisiae invertase genes. Other useful signal peptide coding sequences are described by Romanos et al., 1992, supra.
The control sequence can also be a propeptide coding sequence that encodes a propeptide positioned at the N-terminus of a polypeptide. The resulting polypeptide is known as a proenzyme or propolypeptide (or a zymogen in some cases). A propolipeptide is generally inactive and can be converted to an active polypeptide by catalytic or autocatalytic cleavage of the propolipeptide propeptide. The propeptide coding sequence can be obtained from the genes for Bacillus subtilis alkaline protease (aprE), Bacillus subtilis neutral protease (nprT), Myceliophthora thermophila laccase (WO 95/33836), Rhizomucor miehei aspartic proteinase, and alpha factor of Saccharomyces cerevisiae.
Where both the signal peptide and the propeptide sequence are present at the N-terminus of a polypeptide, the propeptide sequence is positioned after the N-terminus of a polypeptide and the signal peptide sequence is positioned after the N-terminus of propeptide sequence.
It may also be desirable to add regulatory sequences that allow regulation of polypeptide expression in relation to host cell growth. Examples of regulatory systems are those that cause gene expression to turn on or off in response to a chemical or physical stimulus, including the presence of a regulatory compound. Regulatory systems in prokaryotic systems include lac, tac, and trp operator systems. In yeast, the ADH2 system or GAL1 system can be used. In filamentous fungi, the Aspergillus niger glycoamylase promoter, the Aspergillus oryzae TAKA alpha-amylase promoter, and the Aspergillus oryzae glycoamylase promoter can be used. Other examples of regulatory sequences are those that enable gene amplification in eukaryotic systems. These regulatory sequences include the dihydrofoliate reductase gene that is amplified in the presence of methotrexate, and metallothionein genes that are amplified with heavy metals. In these cases, the polynucleotide encoding the polypeptide would be operably linked with the regulatory sequence. Expression Vectors
The present invention also relates to recombinant expression vectors that comprise a polynucleotide of the present invention, a promoter, and transcriptional and translational stop signals. The various nucleotides and control sequences can be joined together to produce a recombinant expression vector that can include one or more (several) restriction sites convenient to enable the insertion or replacement of the polynucleotide encoding at such sites. Alternatively, the polynucleotide can be expressed by inserting the polynucleotide or a nucleic acid construct that comprises the sequence into an appropriate vector for expression. In creating the expression vector, the coding sequence is located in the vector so that the coding sequence is operably linked with the appropriate control sequences for the expression.
The recombinant expression vector can be any vector (for example, a plasmid or virus) that can be conveniently subjected to recombinant DNA procedures and can perform polynucleotide expression. The choice of the vector will typically depend on the vector's compatibility with the host cell into which the vector is to be introduced. The vector can be a closed linear or circular plasmid.
The vector can be a vector that replicates autonomously, that is, a vector that exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, for example, a plasmid, an extrachromosomal element, a minichromosome, or an artificial chromosome. The vector can contain any means to guarantee self-replication. Alternatively, the vector can be one that, when introduced into the host cell, is integrated into the genome and replicated along with the chromosome (s) into which it has been integrated. In addition, a single vector or plasmid or two or more vectors or plasmids that together contain the total DNA to be introduced into the host cell's genome, or a transposon, can be used.
The vector preferably contains one or more (several) selectable markers that allow easy selection of transformed, transfected, transduced, or similar cells. A selectable marker is a gene, the product of which provides resistance to biocide or viral, resistance to heavy metals, prototrophy to auxotrophs, and others.
Examples of selectable bacterial markers are the Bacillus subtilis or Bacillus licheniformis genes, or markers that confer antibiotic resistance such as resistance to ampicillin, chloramphenicol, kanamycin, or tetracycline. Suitable markers for yeast host cells are ADE2, HIS3, LEU2, LYS2, MET3, TRP1, and URA3. Selectable markers for use in a fungal filamentous host cell include, but are not limited to, amdS (acetamidase), argB (omitine carbamoyl transferase), bar (phosphinothricin acetyltransferase), hph (hygromycin phosphotransferase), niaD (nitrate reductase), pirG (orotidine-5'-phosphate decarboxylase), sC (adenyltransferase sulfate), and trpC (anthranylate synthase), as well as equivalents thereof. Preferred for use in an Aspergillus cell are the amdS and pirG genes of Aspergillus nidulans or Aspergillus oryzae and the bar gene of Streptomyces hygroscopicus.
The vector preferably contains an element (s) that allows integration of the vector into the genome of the host cell or autonomous replication of the vector in the cell independent of the genome.
For integration into the host cell genome, the vector may rely on the polynucleotide sequence encoding the polypeptide or any other element of the vector for integration into the genome by homologous or non-homologous recombination. Alternatively, the vector may contain additional polynucleotides to direct integration by homologous recombination into the host cell genome at a precise location (s) on the chromosome (s). To increase the likelihood of integration at a precise location, the integrational elements must contain a sufficient number of nucleic acids, such as from 100 to 10,000 base pairs, from 400 to 10,000 base pairs, and from 800 to 10,000 base pairs, which have a high degree of sequence identity with the corresponding target sequence to enhance the likelihood of homologous recombination. The integrational elements can be any sequence that is homologous to the target sequence in the host cell genome. In addition, the integrational elements can be non-coding or coding polynucleotides. On the other hand, the vector can be integrated into the host cell genome by non-homologous recombination.
For autonomous replication, the vector can also comprise an origin of replication that allows the vector to replicate autonomously in the host cell in question. The origin of replication can be any plasmid replicator that mediates autonomous replication that works in a cell. The terms "origin of replication" or "plasmid replicator" mean a polynucleotide that enables a plasmid or vector to replicate in vivo.
Examples of bacterial origin of replication are the origins of replication of plasmids pBR322, pUC19, pACYC177, and pACYC184 that allow replication in E. coli, and pUBl 10, pE194, pTA1060, and pAMBl that allow replication in Bacillus.
Examples of origins of replication for use in a yeast host cell are the 2 micron origin of replication, ARS1, ARS4, the combination of ARS1 and CEN3, and the combination of ARS4 and CEN6.
Examples of useful origins of replication in a filamentous fungal cell are AMAI and ANSI (Gems et al., 1991, Gene 98: 61-67; Cullen et al., 1987, Nucleic Acids Research 15: 9163-9175; WO 00 / 24883). Isolation of the AMAI gene and the construction of plasmids or vectors that comprise the gene can be performed according to the methods disclosed in WO 00/24883.
More than one copy of a polynucleotide of the present invention can be inserted into a host cell to increase production of a polypeptide. An increase in the copy number of the polynucleotide can be obtained by integrating at least one additional copy of the sequence into the host cell genome or by including a selectable marker gene amplifiable with the polynucleotide where cells containing amplified copies of the selectable marker gene, and thus, additional copies of the polynucleotide can be selected by culturing the cells in the presence of the appropriate selectable agent.
The procedures used to link the elements described above to construct the recombinant expression vectors of the present invention are well known to a person skilled in the art (see, for example, Sambrook et al., 1989, supra). Host Cells
The present invention also relates to recombinant host cells that comprise a polynucleotide of the present invention operably linked to one or more (several) control sequences that direct the production of a polypeptide of the present invention. A construct or vector comprising a polynucleotide is introduced into a host cell so that the construct or vector is maintained as a chromosomal integral or as a self-replicating extra-chromosomal vector as described earlier. The term "host cell" encompasses any progeny of a precursor cell that is not identical to the precursor cell due to mutations that occur during replication. The choice of a host cell will depend to a large degree depends on the gene that encodes the polypeptide and its source.
The host cell can be any cell useful in recombinant production of a polypeptide of the present invention, for example, a prokaryote or a eukaryote.
The prokaryotic host cell can be any Gram positive or Gram negative bacterium. Gram positive bacteria include, but are not limited to, Bacillus, Clostridium, Enterococcus, Geobacillus, Lactobacillus, Lactococcus, Oceanobacillus, Staphilococcus, Streptococcus, and Streptomyces. Gram-negative bacteria include, but are not limited to, Campilobacter, E. coli, Flavobacterium, Fusobacterium, Helicobacter, Ilyobacter, Neisseria, Pseudomonas, Salmonella, and Ureaplasma.
The bacterial host cell can be any Bacillus cell including, but not limited to, Bacillus alkalophilus, Bacillus amiloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus lentus, Bacillus lentus, Bacillus lentus, Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, Bacillus subtilis, and Bacillus thuringiensis.
The bacterial host cell can also be any Streptococcus cell including, but not limited to, Streptococcus equisimilis cells, Streptococcus pyogenes, Streptococcus uberis, and Streptococcus equi subsp. Zooepidemicus.
The bacterial host cell can also be any Streptomyces cell including, but not limited to, Streptomyces achromogenes cells, Streptomyces avermitilis, Streptomyces coelicolor, Streptomyces griseus, and Streptomyces lividans.
The introduction of DNA into a Bacillus cell, for example, can be carried out by the transformation of protoplasts (see, for example, Chang and Cohen, 1979, Mol. Gen. Genet. 168: 111-115), by the use of competent cells (see, for example, Young and Spizizen, 1961, J. Bacteriol. 81: 823-829, or Dubnau and Davidoff-Abelson, 1971, J. Mol. Biol. 56: 209- 221), by electroporation (see, for example, Shigekawa and Dower, 1988, Biotechniques 6: 742-751), or by conjugation (see, for example, Koehler and Thome, 1987, J. Bacteriol. 169: 5271-5278). The introduction of DNA into an E. coli cell, for example, can be effected by the transformation of protoplasts (see, for example, Hanahan, 1983, J. Mol. Biol. 166: 557-580) or electroporation (see, for example, Dower et al., 1988, Nucleic Acids Res. 16: 6127-6145). The introduction of DNA into a Streptomyces cell, for example, can be effected by the transformation of protoplasts and electroporation (see, for example, Gong et al., 2004, Folia Microbiol. (Praha) 49: 399-405), by conjugation (see, for example, Mazodier et al., 1989, J. Bacteriol. 171: 3583-3585), or by transduction (see, for example, Burke et al., 2001, Proc. Natl. Acad. Sci. USA 98 : 6289-6294). The introduction of DNA into a Pseudomonas cell, for example, can be carried out by electroporation (see, for example, Choi et al., 2006, J. Microbiol. Methods 64: 391-397) or by conjugation (see, for example , Pinedo and Smets, 2005, Appl. Environ. Microbiol. 71: 51-57). The introduction of DNA into a Streptococcus cell, for example, can be effected by natural competence (see, for example, Perry and Kuramitsu, 1981, Infect. Immun. 32: 1295-1297), by the transformation of protoplasts (see, for example, example, Catt and Jollick, 1991, Microbios. 68: 189-207), by electroporation (see, for example, Buckley et al., 1999, Appl. Environ. Microbiol. 65: 3800-3804) or by conjugation (see, for example, Clewell, 1981, Microbiol. Rev. 45: 409-436). However, any method known in the art to introduce DNA into a host cell can be used.
The host cell can also be a eukaryote, such as a mammalian, insect, plant, or fungus cell.
The host cell can be a fungal cell. “Fungi” as used herein includes the philosophers Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota (as defined by Hawksworth et al., Em, Ainsworth and Bisby's Dictionary of The Fungi, 8th edition, 1995, CAB International, University Press, Cambridge, UK ) as well as the Oomycota (as cited in Hawksworth et al., 1995, supra, page 171) and all mitosporic fungi (Hawksworth et al., 1995, supra).
The fungal host cell can be a yeast cell. "Yeast" as used herein includes ascosporogenous yeast (Endomycetales), basidiosporogenous yeast, and yeast belonging to Imperfect Fungi (Blastomycetes). Since the classification of yeast may change in the future, for the purposes of this invention, yeast should be defined as described in Biology and Activities of Yeast (Skinner, FA, Passmore, SM, and Davenport, RR, eds, Soc. App. Bacteriol, Symposium Series N2 9, 1980).
The yeast host cell may be a Candida, Hansenula, Kluyveromyces, Pichia, Saccharomyces, Schizosaccharomyces, or Yarrowia cell, such as a Kluyveromyces lactis cell, Saccharomyces carlsbergensis, Saccharomyces cerevisiae, Saccharomycesychaysychaisychaysychaysychaysychasty , Saccharomyces oviformis or Yarrowia lipolytic.
The fungal host cell can be a filamentous fungal cell. "Filamentous Fungi" include all filamentous forms in the subdivision Eumycota and Oomycota (as defined by Hawks worth et al., 1995, supra). Filamentous fungi are generally characterized by a mycelial wall compound of chitin, cellulose, glycan, chitosan, mannan, and other complex polysaccharides. Vegetative growth is due to hyphal elongation and carbon catabolism is mandatory aerobic. In contrast, vegetative growth by yeasts such as Saccharomyces cerevisiae is by the budding of a single-celled stalk and carbon catabolism can be fermentative.
The filamentous fungal host cell can be an Acremonium cell, Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis, Chrysosporium, Coprinus, Coriolus, Cryptococcus, Filibasidium, Fusarium, Humicola, Magnaporthe, Mucor, Necelioporch, Myceliophillora, Phlebia, Piromyces, Pleurotus, Schizophillum, Talaromyces, Thermoascus, Thielavia, Tolypocladium, Trametes, or Trichoderma.
For example, the filamentous fungal host cell can be a cell of Aspergillus awamori, Aspergillus foetidus, Aspergillus fumigatus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Bjerkandisioisisisiporisio, Ceriporisio, Ceri rivulosa, Ceriporiopsis subrufa, Ceriporiopsis subvermispora, Chrysosporium inops, Chrysosporium keratinophilum, Chrysosporium lucknowense, Chrysosporium merdarium, Chrysosporium pannicola, Chrysosporium pannicola, Chrysosporium queenslandicum, Chrysosporium queensland, Chromsosporium tropicum, Chrysosporium tropicumum, Chrysosporium tropicumum Fusarium graminaarum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi, Fusarium oxisporum, Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusarium sulphureum, Fusarium torulosu m, Fusarium trichothecioides, Fusarium venenatum, Humicola insolens, Humicola lanuginosa, Mucor miehei, Myceliophthora thermophila, Neurospora crassa, Penicillium purpurogenum, Phanerochaete chrysosporium, Phlebia radiata, Pleurotus eryichichis, Trichoderma trichoderma, Thiel, terrien, Thiel Trichoderma longibrachiatum, Trichoderma reesei, or Trichoderma viride.
Fungal cells can be transformed by a process that involves the formation of protoplasts, transformation of protoplasts, and regeneration of the cell wall in a manner known to itself. Suitable procedures for transforming Aspergilluse Trichoderma host cells are described in EP 238023 and Yelton et al., 1984, Proc. Natl. Acad. Know. USA 81: 1470-1474 and Christensen et al., 1988, Bio / Technology 6: 1419-1422. Suitable methods for transforming Fusarium species are described by Malardier et al., 1989, Gene 78: 147-156, and WO 96/00787. Yeast can be transformed using the procedures described by Becker and Guarente, In Abelson, JN and Simon, MI, editors, Guide to Yeast Genetics and Molecular Biology, Methods in Enzymology, Volume 194, pp 182-187, Academic Press, Inc. , New York; Ito et al., 1983, J. Bacteriol. 153: 163; and Hinnen et al., 1978, Proc. Natl. Acad. Sci. USA 75: 1920. Production Methods
The present invention also relates to methods of producing a polypeptide of the present invention, which comprise: (a) cultivating a cell, which in its wild type produces the polypeptide, under conductive conditions for the production of the polypeptide; and (b) recovering the polypeptide. In a preferred aspect, the cell is of the genus Penicillium. In a more preferred aspect, the cell is Penicillium pinophilum. In a more preferred aspect, the cell is Penicilliumpinophilum NN46877.
The present invention also relates to methods of producing a polypeptide of the present invention, which comprise: (a) culturing a recombinant host cell of the present invention under conductive conditions for the production of the polypeptide and (b) recovering the polypeptide.
Host cells are cultured in a nutrient medium suitable for the production of the polypeptide using methods well known in the art. For example, the cell can be grown by shaking flask cultivation, and small or large scale fermentation (including continuous, batch, fed batch, or solid state fermentations) in laboratory or industrial fermenters carried out in a suitable medium and under conditions that allow the polypeptide to be expressed and / or isolated. Cultivation takes place in a suitable nutrient medium that comprises sources of carbon and nitrogen and inorganic salts, using procedures known in the art. Suitable media are available from commercial suppliers or can be prepared according to published compositions (for example, in catalogs of the American Type Culture Collection). If the polypeptide is secreted into the nutrient medium, the polypeptide can be recovered directly from the medium. If the polypeptide is not secreted, it can be recovered from cell lysates.
Polypeptides can be detected using methods known in the art that are specific to polypeptides. These detection methods can include the use of specific antibodies, formation of an enzyme product, or disappearance of an enzyme substrate. For example, an enzyme assay can be used to determine the activity of the polypeptide.
The polypeptide can be recovered using methods known in the art. For example, the polypeptide can be recovered from the nutrient medium by conventional procedures including, but not limited to, centrifugation, filtration, extraction, spray drying, evaporation, or precipitation.
Polypeptides can be purified by a variety of procedures known in the art including, but not limited to, chromatography (eg, ion exchange, affinity, hydrophobic, chromato-focusing, size-exclusion), electrophoretic procedures (eg, focusing preparative isoelectric), differential solubility (eg ammonium sulfate precipitation), SDS-PAGE, or extraction (see, for example, Protein Purification, JC Janson and Lars Ryden, editors, VCH Publishers, New York, 1989) obtain substantially pure polypeptides.
In an alternative aspect, the polypeptide is not recovered, but instead a host cell of the present invention that expresses the polypeptide used as a source of the polypeptide. Plants
The present invention also concerns isolated plants, for example, a transgenic plant, plant part, or plant cell, which comprise a polynucleotide isolated from the present invention as well as expressing and producing the polypeptide in recoverable amounts. The polypeptide can be recovered from the plant or part of a plant. Alternatively, the plant or plant part containing the polypeptide can be used as such to improve the quality of a food or feed, for example, to improve nutritional value, palatability, and rheological properties, or to destroy an anti-nutritive factor.
The transgenic plant can be dicotyledonous (a dicot) or monocotyledonous (a monocot). Examples of monocot plants are grasses, such as meadow grass (blue grass, Poa), forage grass such as Fescue, Lolium, temperate grass, such as Agrostis, and cereals, for example, wheat, oats, rye, barley, rice , sorghum, and corn (maize).
Examples of dicot plants are tobacco, vegetables such as lupine, potato, sugar beet, peas, beans and soybeans, and cruciferous plants (Brassicaceae family), such as cauliflower, rapeseed, and the closely related model organism Arabidopsis thaliana.
Examples of plant parts are stem, callus, leaves, root, fruit, seeds, and tubers as well as the individual tissues comprising these parts, for example, epidermis, mesophile, parenchyma, vascular tissues, meristems. Specific plant cell compartments, such as chloroplasts, apoplasts, mitochondria, vacuoles, peroxisomes and cytoplasm are also considered to be a plant part. In addition, any plant cell, regardless of tissue origin, is considered to be a plant part. Likewise, plant parts such as specific tissues and cells isolated to facilitate the use of the invention are also considered plant parts, for example, embryos, endosperm, aleurone and seed coatings.
Also included within the scope of the present invention are the progeny of such plants, plant parts, and plant cells.
The transgenic plant or plant cell expressing a polypeptide can be constructed according to methods known in the art. In summary, the plant or plant cell is constructed by incorporating one or more (several) expression constructs that encode a polypeptide into the host genome of the plant or chloroplast genome and propagating the modified plant or plant cell resulting in a transgenic plant or plant cell.
The expression construct is conveniently a nucleic acid construct that comprises a polynucleotide that encodes an operably linked polypeptide with appropriate regulatory sequences required for the expression of the polynucleotide in the plant or plant part of choice. In addition, the expression construct may comprise a selectable marker useful for identifying host cells into which the expression construct has been integrated and the DNA sequences necessary for the introduction of the construct into the plant in question (the latter depends on the method of introducing DNA to be used).
The choice of regulatory sequences, such as promoter and terminator sequences and optionally signal or transit sequences, is determined, for example, on the basis of when, where, and how the polypeptide is desired to be expressed. For example, the expression of the gene encoding a polypeptide can be constitutive or inducible, or it can be developmentally, stage or tissue specific, and the gene product can be targeted to a specific tissue or plant part such as seeds or leaves. Regulatory sequences are, for example, described by Tague et al., 1988, Plant Physiology 86: 506.
For constitutive expression, 35S-CaMV, the corn ubiquitin 1 promoter, and the rice actin 1 promoter can be used (Franck et al., 1980, Cell 21: 285-294; Christensen et al., 1992 , Plant Mol. Biol. 18: 675-689; Zhang et al., 1991, Plant Cell 3: 1155-1165). Organ-specific promoters can be, for example, a promoter of storage depot tissues such as seeds, potato tubers, and fruits (Edwards and Coruzzi, 1990, Ann. Rev. Genet. 24: 275-303), or of metabolic deposit tissues such as meristems (Ito et al., 1994, Plant Mol. Biol. 24: 863-878), a specific seed promoter such as the glutelin, prolamine, globulin, or rice albumin (Wu et al., 1998, Plant Cell Physiol. 39: 885-889), a Vicia faba promoter of legumin B4 and the unknown Vicia faba seed protein gene (Conrad et al., 1998, J. Plant Physiol. 152 : 708-711), a promoter of a seed oil body protein (Chen et al., 1998, Plant Cell Physiol. 39: 935-941), the napA promoter of Brassica napus storage protein, or any other promoter specific seed known in the art, for example, as described in WO 91/14772. In addition, the promoter can be a leaf-specific promoter such as the rice or tomato rbcs promoter (Kyozuka et al., 1993, Plant Physiol. 102: 991-1000), the chlorella viral adenine methyltransferase gene promoter (Mitra and Higgins, 1994, Plant Mol. Biol. 26: 85-93), the promoter of the rice aldP gene (Kagaya et al., 1995, Mol. Gen. Genet. 248: 668-674), or a promoter pin2 inducible by potato injury (Xu et al., 1993, Plant Mol. Biol. 22: 573-588). Likewise, the promoter may be inducible by abiotic treatments such as temperature, drought, or changes in salinity or induced by exogenously applied substances that activate the promoter, for example, ethanol, estrogens, plant hormones such as ethylene, abscisic acid, and gibberellic acid, and heavy metals.
A promoter-enhancing element can also be used to obtain higher expression of a polypeptide in the plant. For example, the promoter enhancing element can be an intron that is placed between the promoter and the polynucleotide that encodes a polypeptide. For example, Xu et al., 1993, supra, disclose the use of the first intron of the rice actin 1 gene to enhance expression.
The selectable marker gene and any other parts of the expression construct can be chosen from those available in the art.
The nucleic acid construct is incorporated into the plant genome according to conventional techniques known in the art, including Agrobacterium-mediated transformation, virus-mediated transformation, microinjection, particle bombardment, biological transformation and electroporation (Gasser et al., 1990, Science 244 : 1293; Potrykus, 1990, Bio / Technology 8: 535; Shimamoto et al., 1989, Nature 338: 274).
Currently, gene transfer mediated by Agrobacterium tumefaciens is the method of choice for generating transgenic dicots (for a review, see Hooykas and Schilperoort, 1992, Plant Mol. Biol. 19: 15-38) and can also be used to transform monocots, although other transformation methods are often used for these plants. Currently, the method of choice for generating transgenic monocots is the particle bombardment (microscopic gold or tungsten particles coated with transforming DNA) from embryonic calluses or developing embryos (Christou, 1992, Plant J. 2: 275-281; Shimamoto , 1994, Curr. Opin. Biotechnol. 5: 158-162; Vasil et al., 1992, Bio / Technology 10: 667-674). An alternative method for the transformation of monocots is based on the transformation of protoplasts as described by Omirulleh et al., 1993, Plant Mol. Biol. 21: 415-428. Additional transformation methods for use in accordance with the present disclosure include those described in U.S. Patents No. 6,395,966 and 7,151,204 (both of which are incorporated herein by reference in their entirety).
Following transformation, transformants having incorporated the expression construct are selected and regenerated in whole plants according to methods well known in the art. Often the transformation procedure is designed for the selective elimination of selection genes during regeneration or in the following generations using, for example, co-transformation with two separate T-DNA constructs or site-specific excision of the selection gene by specific recombinase.
In addition to the direct transformation of a particular plant genotype with a construction prepared in accordance with the present invention, transgenic plants can be manufactured by crossing a plant having the construction with a second plant that lacks the construction. For example, a construction that encodes a polypeptide can be introduced into a particular plant variety by crossing, without the need to always directly transform a plant of that given variety. Therefore, the present invention encompasses not only a plant directly regenerated from cells that have been transformed in accordance with the present invention, but also the progeny of such plants. As used herein, progeny can refer to the offspring of any generation of a precursor plant prepared in accordance with the present invention. Such a progeny can include a DNA construct prepared in accordance with the present invention, or a portion of a DNA construct prepared in accordance with the present invention. Cross results on the introduction of a transgene into a plant strain by cross-pollinating a starting strain with a donor plant strain. Non-limiting examples of such steps are further articulated in U.S. Patent Nos. 7,151,204.
Plants can be generated through a backcross conversion process. For example, plants include plants referred to as a backcross, lineage, congenital, or hybrid genotype.
Genetic markers can be used to assist in the introgression of one or more transgenes of the invention from one genetic background to another. Marker-assisted selection offers advantages over conventional crossover in that it can be used to avoid errors caused by phenotypic variations. In addition, genetic markers can provide data regarding the relative degree of elite germplasm in the individual progeny of a particular cross. For example, when a plant with a desired trait that would otherwise have a non-agronomically desirable genetic background is crossed with an elite precursor, genetic markers can be used to select the progeny that not only have the trait of interest, but also have a relatively large proportion of the desired germplasm. In this way, the number of generations required to introgress one or more traits in a particular genetic background is minimized.
The present invention also relates to methods of producing a polypeptide of the present invention which comprise: (a) cultivating a transgenic plant or a plant cell comprising a polynucleotide that encodes the polypeptide under conditions conducive to the production of the polypeptide; and (b) recovering the polypeptide. Removal or Reduction of Cellulolytic Intensification Activity
The present invention also concerns methods of producing a precursor cell mutant, which comprises disrupting or deleting a polynucleotide, or a portion thereof, which encodes a polypeptide of the present invention, which results in the mutant cell producing less of the polypeptide than precursor cell when grown under the same conditions.
The mutant cell can be constructed by reducing or eliminating polynucleotide expression using methods well known in the art, for example, insertions, disruptions, substitutions, or deletions. In a preferred aspect, the polynucleotide is inactivated. The polynucleotide to be modified or inactivated can be, for example, the coding region or a part of it essential for the activity, or a regulatory element required for the expression of the coding region. An example of such a regulatory or control sequence may be a promoter sequence or a functional part thereof, that is, a part that is sufficient to affect the expression of the polynucleotide. Other control sequences for possible modification include, but are not limited to, a leader, polyadenylation sequence, propeptide sequence, signal peptide sequence, transcription terminator, and transcriptional activator.
The modification or inactivation of the polynucleotide can be performed by submitting the precursor cell to mutagenesis and selecting for mutant cells in which the expression of the polynucleotide has been reduced or eliminated. Mutagenesis, which can be specific or random, can be performed, for example, by using a suitable physical or chemical mutagenizing agent, by using a suitable oligonucleotide, or by subjecting the DNA sequence to mutagenesis generated by PCR. In addition, mutagenesis can be performed using any combination of these mutagenic agents.
Examples of a physical or chemical mutagenizing agent suitable for the present purpose include ultraviolet (UV) irradiation, hydroxylamine, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), O-methyl hydroxylamine, nitrous acid, methane sulfonate ethyl (EMS), sodium bisulfite, formic acid, and nucleotide analogs.
When such agents are used, mutagenesis is typically performed by incubating the precursor cell to be mutagenized in the presence of the mutagenizing agent of choice under suitable conditions, and screening and / or selecting for mutant cells that exhibit reduced or none of the gene.
The modification or inactivation of the polynucleotide can be carried out by the introduction, replacement, or removal of one or more (several) nucleotides in the gene or a regulatory element required for its transcription or translation. For example, nucleotides can be inserted or removed to result in the introduction of a stop codon, the removal of the start codon, or a change in an open reading array. Such modification or inactivation can be performed by loco-directed mutagenesis or mutagenesis generated by PCR according to methods known in the art. Although, in principle, the modification can be carried out in vivo, that is, directly in the cell expressing the polynucleotide to be modified, it is preferred that the modification is carried out in vitro as exemplified below.
An example of a convenient way to eliminate or reduce the expression of a polynucleotide is based on techniques of gene replacement, gene deletion, or gene disruption. For example, in the gene disruption method, a nucleic acid sequence that corresponds to the endogenous polynucleotide is mutagenized in vitro to produce a defective nucleic acid sequence that is then transformed into the precursor cell to produce a defective gene. By homologous recombination, the defective nucleic acid sequence replaces the endogenous polynucleotide. It may be desirable that the defective polynucleotide also encodes a marker that can be used for the selection of transformants in which the polynucleotide has been modified or destroyed. In a particularly preferred aspect, the polynucleotide is disrupted with a selectable marker such as that described herein.
The present invention also concerns methods of inhibiting the expression of a polypeptide having cellulolytic enhancing activity in a cell, which comprises administering to the cell or expressing in the cell a double-stranded RNA (dsRNA) molecule, wherein the dsRNA comprises a subsequence of a polynucleotide of the present invention. In a preferred aspect, the dsRNA is about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplex nucleotides in length.
The dsRNA is preferably a small interfering RNA (siRNA) or a micro RNA (miRNA). In a preferred aspect, dsRNA is small interfering RNA (siRNAs) to inhibit transcription. In another preferred aspect, dsRNA is micro RNA (miRNAs) to inhibit translation.
The present invention also relates to such double-stranded RNA (dsRNA) molecules, which comprises a portion of the sequence encoding mature polypeptide of SEQ ID NO: 1 to inhibit expression of the polypeptide in a cell. Although the present invention is not limited by any particular mechanism of action, dsRNA can enter a cell and cause degradation of a single-stranded RNA (ssRNA) of similar or identical sequences, including endogenous mRNAs. When a cell is exposed to dsRNA, the homologous gene's mRNA is selectively degraded by a process called RNA interference (RNAi).
The dsRNAs of the present invention can be used in gene silencing. In one aspect, the invention provides methods for selectively degrading RNA using a dsRNAi of the present invention. The process can be practiced in vitro, ex vivo or in vivo. In one aspect, dsRNA molecules can be used to generate a loss of function mutation in a cell, an organ or an animal. Methods for making and using dsRNA molecules to selectively degrade RNA are well known in the art; see, for example, U.S. Patent Nos. 6,489,127, 6,506,559, 6,511,824 and 6,515,109.
The present invention also relates to a precursor cell mutant cell comprising a disruption or deletion of a polynucleotide encoding the polypeptide or a control sequence thereof or a muted gene encoding the polypeptide, which results in the mutant cell producing less than polypeptide or no polypeptide compared to the precursor cell.
Polypeptide-deficient mutant cells are particularly useful as host cells for the expression of native and heterologous polypeptides. Therefore, the present invention also relates to methods of producing a native or heterologous polypeptide, which comprises: (a) cultivating the mutant cell under conductive conditions for the production of the polypeptide; and (b) recovering the polypeptide. The term "heterologous polypeptides" means polypeptides that are not native to the host cell, for example, a variant of a native protein. The host cell can comprise more than one copy of a polynucleotide that encodes the native or heterologous polypeptide.
The methods used for cultivating and purifying the product of interest can be carried out by methods known in the art.
The methods of the present invention for producing a product essentially free of cellulolytic enhancer is of particular interest in the production of eukaryotic polypeptides, in particular fungal proteins such as enzymes. Cells deficient in cellulolytic enhancer can also be used to express heterologous proteins of pharmaceutical interest such as hormones, growth factors, receptors, and the like. The term "eukaryotic polypeptides" includes not only native polypeptides, but also those polypeptides, for example, enzymes, which have been modified by amino acid substitutions, deletions or additions, or other such modifications to enhance activity, thermostability, pH tolerance and your peers.
In another aspect, the present invention relates to a protein product essentially free of cellulolytic enhancing activity that is produced by a method of the present invention. Compositions
The present invention also relates to compositions that comprise a polypeptide of the present invention. Preferably, the compositions are enriched in such a polypeptide. The term “enriched” indicates that the cellulolytic intensification activity of the composition has been increased, for example, with an enrichment factor of at least 1.1.
The composition can comprise a polypeptide of the present invention as the main enzyme component, for example, a mono-component composition. Alternatively, the composition may also comprise one or more (several) additional enzymes, such as an acetylxylan esterase, amylase, alpha-L-arabinofuranosidase, catalase, cellobiohydrolase, cellulase, alpha-galactosidase, beta-galactosidase, endoglycanase, alpha- glucuronidase, esterase, feruloyl esterase, glycoamylase, alpha-glucosidase, beta-glucosidase, laccase, lipase, mannosidase, peroxidase, polyphenoloxidase, xylanoase, or beta-xylosidase.
Polypeptide compositions can be prepared according to methods known in the art and can be in the form of a liquid or a dry composition. For example, the polypeptide composition can be in the form of a granulate or a microgranulate. The polypeptide to be included in the composition can be stabilized according to methods known in the art.
Examples are given below of preferred uses of the polypeptide compositions of the invention. The dosage of the polypeptide composition of the invention and other conditions under which the composition is used can be determined based on methods known in the art. Uses
The present invention is also directed to the following methods for using polypeptides having cellulolytic enhancing activity, or compositions thereof.
The present invention also relates to methods for degrading or converting a cellulosic material, which comprise: treating the cellulosic material with an enzyme composition in the presence of a polypeptide having cellulolytic enhancing activity of the present invention. In a preferred aspect, the method further comprises recovering the degraded or converted cellulosic material.
The present invention also concerns methods of producing a fermentation product, which comprise: (a) saccharifying a cellulosic material with an enzyme composition in the presence of a polypeptide having cellulolytic enhancing activity of the present invention; (b) fermenting the saccharified cellulosic material with one or more (several) fermenting microorganisms to produce the fermentation product; and (c) recovering the fermentation product from the fermentation.
The present invention also concerns methods of fermenting a cellulosic material, which comprise: fermenting the cellulosic material with one or more (several) fermenting microorganisms, wherein the cellulosic material is saccharified with an enzyme composition in the presence of a polypeptide having cellulolytic intensification activity of the present invention. In a preferred aspect, the fermentation of the cellulosic material produces a fermentation product. In another preferred aspect, the method further comprises recovering the fermentation product from the fermentation.
The methods of the present invention can be used to saccharate a cellulosic material to fermentable sugars and convert fermentable sugars to many useful substances, for example, fuels, potable ethanol, and / or fermentation products (for example, acids, alcohols, ketones, gases and others). The production of a desired fermentation product from cellulosic material typically involves pretreatment, enzymatic hydrolysis (saccharification) and fermentation.
The processing of cellulosic material according to the present invention can be carried out using conventional processes in the art. In addition, the methods of the present invention can be implemented using any conventional biomass processing apparatus configured to operate in accordance with the invention.
Hydrolysis (saccharification) and fermentation, separate or simultaneous, include, but are not limited to, separate hydrolysis and fermentation (SHF); simultaneous saccharification and fermentation (SSF); simultaneous saccharification and co-fermentation (SSCF); hybrid hydrolysis and fermentation (HHF); separate hydrolysis and co-fermentation (SHCF), hybrid hydrolysis and fermentation (HHCF) and direct microbial conversion (DMC). SHF uses the separate process steps to first enzymatically hydrolyse cellulosic material to fermentable sugars, for example, glucose, cellobiose, cellotriose and pentose sugars and then ferment fermentable sugars to ethanol. In SSF, the enzymatic hydrolysis of cellulosic material and the fermentation of sugars to ethanol are combined in one step (Philippidis, GP, 1996, Cellulose bioconversion technology, in the Handbook on Bioethanol: Prodution and Utilization, Wyman, CE, ed., Taylor & Francis, Washington, DC, 179-212). SSCF involves the co-fermentation of multiple sugars (Sheehan, J. and Himmel, M., 1999, Enzymes, energy and the environment: A strategic perspective on the US Department of Energy's research and development activities for bioethanol, Biotechnol. Prog. 15: 817-827). HHF involves a separate hydrolysis step and in addition, a simultaneous saccharification and hydrolysis step, which can be carried out in the same reactor. The steps in an HHF process can be carried out at different temperatures, that is, high temperature enzymatic saccharification followed by SSF at a lower temperature than the fermentation strain can tolerate. DMC combines all three processes (enzyme production, hydrolysis and fermentation) in one or more (several) steps where the same organisms are used to produce the enzymes for converting cellulosic material to fermentable sugars and to convert fermentable sugars into a final product (Lynd, LR, Weimer, PJ, van Zil, WH and Pretorius, IS, 2002, Microbial cellulose utilization: Fundamentals and biotechnology, Microbiol. Mol. Biol. Reviews 66: 506-577). It is understood herein that any method known in the art which comprises pretreatment, enzymatic hydrolysis (saccharification), fermentation or a combination thereof can be used in the practice of the methods of the present invention.
A conventional apparatus may include a batch fed agitated reactor, a batch agitated reactor, a continuous flow agitated reactor with ultrafiltration, and / or a continuous buffered flow column reactor (Fernanda de Castilhos Corazza, Flávio Faria de Moraes, Gisella Maria Zanin and Ivo Neitzel, 2003, Optimal control in fed-batch reactor for a cellobiose hydrolysis, Acta Scientiarum. Technology 25: 33-38; Gusakov, AV and Sinitsyn, AP, 1985, Kinetics of the enzymatic hydrolysis of cellulose: 1. A mathematical model for a batch reactor process, Enz. Microb. Technol. 7: 346-352), a friction reactor (Ryu, SK and Lee, JM, 1983, Bioconversion of waste cellulose by using a attrition bioreactor, Biotechnol. Bioeng 25: 53- 65) or an intensively agitated reactor induced by an electromagnetic field (Gusakov, AV, Sinitsyn, AP, Davydkin, IY, Davydkin, VY, Protas, OV, 1996, Enhancement of enzymatic cellulose hydrolysis using a novel type of bioreactor with intensive stirring induced by electromagnetic field, Appl. Biochem. Biotechnol. 56: 141-153). Additional types of reactor include: fluidized bed, upstream flow, immobilized and extruder type reactors for hydrolysis and / or fermentation.
Pre-treatment. In the practice of the methods of the present invention, any pretreatment process known in the art can be used to disrupt the cellulosic material components of the plant cell wall (Chandra et al., 2007, Substrate pretreatment: The key to effective enzymatic hydrolysis of lignocellulosics Adv. Biochem. Engin./Biotechnol. 108: 67-93; Galbe and Zacchi, 2007, Pretreatment of lignocellulosic materials for efficient bioethanol prodution, Adv. Biochem. Engin./Biotechnol. 108: 41-65; Hendriks and Zeeman , 2009, Pretreatments to enhance the digestibility of lignocellulosic biomass, Bioresource Technol. 100: 10-18; Mosier et al., 2005, Features of promising technologies for pretreatment of lignocellulosic biomass, Bioresource Technol. 96: 673-686; Taherzadeh and Karimi , 2008, Pretreatment of lignocellulosic wastes to improve ethanol and biogas prodution: A review, Int. J. of Mol. Sci. 9: 1621-1651; Yang and Wyman, 2008, Pretreatment: the key to unlocking low-cost cellulosic ethanol, Biofu els Bioprodutos and Biorefining-Biofpr. two'. 26-40).
Cellulosic material can also be subjected to particle size reduction, pre-soaking, wetting, washing or conditioning before pretreatment using methods known in the art.
Conventional pretreatments include, but are not limited to, steam pretreatment (with or without explosion), dilute acid pretreatment, hot water pretreatment, alkaline pretreatment, lime pretreatment, wet oxidation, wet explosion, fiber explosion with ammonia, pretreatment with organosolv and biological pretreatment. Additional pretreatments include pretreatments with percolation with ammonia, ultrasound, electroporation, microwave, supercritical CO2, supercritical H2O, ozone and gamma irradiation.
The cellulosic material can be pretreated before hydrolysis and / or fermentation. Pre-treatment is preferably carried out before hydrolysis. Alternatively, pretreatment can be carried out simultaneously with enzymatic hydrolysis to release fermentable sugars, such as glucose, xylose or cellobiosis. In most cases, the pre-treatment step itself results in some conversion of biomass to fermentable sugars (even in the absence of enzymes).
Pre-treatment with steam. In the steam pretreatment, the cellulosic material is heated to break up the components of the plant cell wall, which include lignin, hemicellulose and cellulose to take the cellulose and other fractions, for example, hemicellulose, accessible to enzymes. The cellulosic material is passed to or through a reaction vessel where steam is injected to increase the temperature to the required temperature and pressure and are retained at that point for the desired reaction time. The steam pretreatment is preferably done at 140 to 230 ° C, more preferably from 160 to 200 ° C and most preferably from 170 to 190 ° C, where the ideal temperature range depends on any addition of a chemical catalyst. The residence time for pre-treatment with steam is preferably 1 to 15 minutes, more preferably 3 to 12 minutes and most preferably 4 to 10 minutes, where the ideal residence time depends on the temperature range and any addition of a chemical catalyst. Steam pretreatment allows for relatively high solids loads, so that cellulosic material is generally only moist during pretreatment. Steam pretreatment is often combined with an explosive discharge of material after pretreatment, which is known as a steam explosion, that is, rapid discharge to atmospheric pressure and turbulent flow of the material to increase the accessible surface area. by fragmentation (Duff and Murray, 1996, Bioresource Technology 855: 1-33; Galbe and Zacchi, 2002, Appl. Microbiol. Biotechnol. 59: 618-628; US Patent Application No. 20020164730). During the steam pretreatment, the acetyl hemicellulose groups are cleaved and the resulting acid autocatalyzes the partial hydrolysis of the hemicellulose to monosaccharides and oligosaccharides. Lignin is removed only to a limited degree.
A catalyst such as H2SO4 or SO2 (typically 0.3 to 3% w / w) is often added before pre-treatment with steam, which decreases time and temperature, increases recovery and improves enzymatic hydrolysis (Ballesteros et al., 2006, Appl. Biochem. Biotechnol. 129-132: 496-508; Varga et al., 2004, Appl. Biochem. Biotechnol. 113-116: 509-523; Sassner et al., 2006, Enzyme Microb Technol 39: 756-762).
Chemical pretreatment: The term "chemical treatment" refers to any chemical pretreatment that promotes the separation and / or release of cellulose, hemicellulose, and / or lignin. Examples of suitable chemical pretreatment processes include, for example, pretreatment with dilute acid, pretreatment with lime, wet oxidation, ammonia fiber / freeze burst (AFEX), percolation with ammonia (APR) and pre-treatments with organosolv.
In the pre-treatment with diluted acid, the cellulosic material is mixed with diluted acid, typically H2SO4 and water to form a slurry, heated by steam to the desired temperature and after a residence time discharged to atmospheric pressure. Pretreatment with dilute acid can be performed with various reactor designs, for example, plug flow reactor, countercurrent reactors or backflow reactors in continuous countercurrent (Duff and Murray, 1996, supra; Schell et al., 2004, Bioresource Technol. 91: 179-188; Lee et al., 1999, Adv. Biochem. Eng. Biotechnol. 65: 93-115).
Various pretreatment methods under alkaline conditions can also be used. These alkaline pretreatments include, but are not limited to, pretreatment with lime, wet oxidation, percolation with ammonia (APR) and ammonia fiber / freeze burst (AFEX).
Pre-treatment with lime is carried out with calcium carbonate, sodium hydroxide or ammonia at low temperatures of 85 to 150 ° C and residence times from 1 hour to several days (Wyman et al., 2005, Bioresource Technol. 96: 1959 -1966; Mosier et al., 2005, Bioresource Technol. 96: 673-686). WO 2006/110891, WO 2006/11899, WO 2006/11900 and WO 2006/110901 disclose pretreatment methods using ammonia.
Wet oxidation is a thermal pretreatment typically carried out at 180 to 200 ° C for 5 to 15 minutes with the addition of an oxidizing agent such as hydrogen peroxide or excessive oxygen pressure (Schmidt and Thomsen, 1998, Bioresource Technol. 64: 139-151; Palonen et al., 2004, Appl. Biochem. Biotechnol. 117: 1-17; Varga et al., 2004, Biotechnol. Bioeng. 88: 567-574; Martin et al., 2006, J Chem, Technol, Biotechnol, 81: 1669-1677). Pre-treatment is preferably carried out on 1 to 40% dry matter, more preferably from 2 to 30% dry matter and most preferably from 5 to 20% dry matter and often the initial pH is increased by the addition of alkali such like soda ash.
A modification of the wet oxidation pretreatment method, known as a wet burst (combination of wet oxidation and steam burst), can move dry matter up to 30%. In the wet blast, the oxidizing agent is introduced during the pre-treatment after a certain residence time. The pre-treatment is then completed by the discharge to atmospheric pressure (WO 2006/032282).
The explosion with ammonia fiber (AFEX) involves treating the cellulosic material with liquid or gaseous ammonia at moderate temperatures such as 90 to 100 ° C and high pressure such as 17 to 20 bar for 5 to 10 minutes, where the dry matter content can be as high as 60% (Gollapalli et al., 2002, Appl. Biochem. Biotechnol. 98: 23-35; Chundawat et al., 2007, Biotechnol. Bioeng. 96: 219-231; Alizadeh et al., 2005 , Appl. Biochem. Biotechnol. 121: 1133-1141; Teymouri et al., 2005, Bioresource Technol. 96: 2014-2018). The AFEX pretreatment results in nonpolymerization of cellulose and partial hydrolysis of hemicellulose. Lignin-carbohydrate complexes are cleaved. Pretreatment with organosolv delignifies cellulosic material by extraction using aqueous ethanol (40 to 60% ethanol) at 160 to 200 ° C for 30 to 60 minutes (Pan et al., 2005 , Biotechnol. Bioeng. 90: 473- 481; Pan et al., 2006, Biotechnol. Bioeng. 94: 851-861; Kurabi et al., 2005, Appl. Biochem. Biotechnol. 121: 219-230). Sulfuric acid is usually added as a catalyst. In pretreatment with organosolv, most of the hemicellulose is removed.
Other examples of suitable pretreatment methods are described by Schell et al., 2003, Appl. Biochem. and Biotechnol. 105-108, p. 69-85 and Mosier et al., 2005, Bioresource Technology 96: 673-686 and Published Order US 2002/0164730. In one aspect, chemical pretreatment is preferably performed as an acid treatment and more preferably as a dilute acid treatment and / or continuous soft. The acid is typically sulfuric acid, but other acids can also be used, such as acetic acid, citric acid, nitric acid, phosphoric acid, tartaric acid, succinic acid, hydrogen chloride or mixtures thereof. The mild acid treatment is carried out in the pH range preferably from 1 to 5, more preferably from 1 to 4 and most preferably from 1 to 3. In one aspect, the acid concentration is preferably in the range of 0.01 to 20 % by weight of acid, more preferably from 0.05 to 10% by weight of acid, still more preferably from 0.1 to 5% by weight of acid and most preferably from 0.2 to 2.0% by weight of acid. The acid is contacted with cellulosic material and maintained at a temperature in the range of preferably 160 to 220 ° C and more preferably 165 to 195 ° C, for periods ranging from seconds to minutes, for example, from 1 second to 60 minutes.
In another aspect, the pretreatment is carried out as an ammonia fiber blast stage (AFEX pretreatment stage).
In another aspect, pretreatment takes place in an aqueous slurry. In preferred aspects, the cellulosic material is present during pretreatment in amounts preferably between 10 and 80% by weight, more preferably between 20 and 70% by weight and most preferably between 30 and 60% by weight, such as in bulk 50% by weight. The pre-treated cellulosic material can be unwashed or washed using any method known in the art, for example, washed with water.
Mechanical pretreatment: The term "mechanical pretreatment" refers to various types of crushing or grinding (for example, dry grinding, wet grinding or vibrating ball grinding).
Physical pretreatment: The term "physical pretreatment" refers to any pretreatment that promotes the separation and / or release of cellulose, hemicellulose, and / or lignin from cellulosic material. For example, physical pretreatment may involve irradiation (for example, microwave irradiation), steam vaporization / explosion, hydrothermolysis and combinations thereof.
Physical pretreatment may involve high pressure and / or high temperature (steam explosion). In one aspect, high pressure means pressure in the range preferably from about 300 to about 600 psi (2070 to 4140 kPa), more preferably from about 350 to about 550 psi (2415 to 3795 kPa) and most preferably about from 400 to about 500 psi (2760 to 3450 kPa), as well as around 450 psi (3105 kPa). In another aspect, high temperature means temperatures in the range of about 100 to about 300 ° C, preferably from about 140 to about 235 ° C. In a preferred aspect, mechanical pretreatment is carried out in a batch process, a steam gun hydrolyzer system that uses high pressure and high temperature as defined above, for example, a Sunds Hydrolyzer available from Sunds Defibrator AB, Sweden.
Combined Physical and Chemical Pretreatment: Cellulosic material can be pretreated both physically and chemically. For example, the pre-treatment step may involve treatment with dilute or mild acid and treatment with high temperature and / or pressure. Physical and chemical pretreatments can be carried out sequentially or simultaneously, as desired. A mechanical pretreatment can also be included.
Consequently, in a preferred aspect, the cellulosic material is subjected to mechanical, chemical or physical pretreatment or any combination thereof to promote the separation and / or release of cellulose, hemicellulose and / or lignin.
Biological pretreatment: The term "biological pretreatment" refers to any biological pretreatment that promotes the separation and / or release of cellulose, hemicellulose, and / or lignin from cellulosic material. Biological pretreatment techniques may involve applying microorganisms that solubilize lignin (see, for example, Hsu, T.-A., 1996, Pre-treatment of biomass, in the Handbook on Bioethanol: Prodution and Utilization, Wyman, CE , ed., Taylor & Francis, Washington, DC, 179-212; Ghosh and Singh, 1993, Physicochemical and biological treataments for enzymatic / microbial conversion of cellulosic biomass, Adv. Appl. Microbiol. 39: 295-333; McMillan, JD , 1994, Pretreating lignocellulosical biomass: a review, in Enzymatic Conversion of Biomass for Fuels Prodution, Himmel, ME, Baker, JO and Overend, RP, eds., ACS Symposium Series 566, American Chemical Society, Washington, DC, chapter 15; Gong, CS, Cao, NJ, Du, J. and Tsao, GT, 1999, Ethanol prodution from renewable resource, in Advances in Biochemical Engineering / Biotechnology, Scheper, T., ed., Springer-Verlag Berlin Heidelberg, Germany, 65 : 207-241; Olsson and Hahn-Hagerdal, 1996, Fermentation of lignocellulosic hydrolysat es for ethanol prodution, Enz. Microb. Tech. 18: 312-331; and Vallander and Eriksson, 1990, Prodution of ethanol from lignocellulosic materials: State of the art, Adv. Biochem. Eng./ Biotechnol. 42: 63-95).
Saccharification. In the hydrolysis stage, also known as saccharification, cellulosic material, for example pre-treated, is hydrolyzed to break down cellulose and alternatively also hemicellulose to fermentable sugars, such as glucose, cellobiose, xylose, xylulose, arabinose, mannose, galactose and / or soluble oligosaccharides. Hydrolysis is carried out enzymatically by an enzyme composition in the presence of a polypeptide having cellulolytic enhancing activity of the present invention. The enzymes in the compositions can also be added sequentially.
Enzymatic hydrolysis is preferably carried out in a suitable aqueous environment under conditions that can be easily determined by a person skilled in the art. In a preferred aspect, hydrolysis is carried out under conditions suitable for the activity of the enzyme (s), i.e., ideal for the enzyme (s). Hydrolysis can be carried out as a fed or continuous batch process where the pre-treated cellulosic material (substrate) is fed gradually, for example, to an enzyme-containing hydrolysis solution.
Saccharification is generally performed in stirred tank reactors or fermenters under controlled pH, temperature and mixing conditions. The appropriate process time, temperature and pH conditions can be easily determined by a person skilled in the art. For example, saccharification can last up to 200 hours, but is typically performed preferably for about 12 to about 96 hours, more preferably about 16 to about 72 hours and most preferably about 24 to about 48 hours . The temperature is preferably in the range of about 25 ° C to about 70 ° C, more preferably from about 30 ° C to about 65 ° C and more preferably from about 40 ° C to 60 ° C, in particular from about 50 ° C. The pH is preferably in the range of about 3 to about 8, more preferably about 3.5 to about 7 and most preferably about 4 to about 6, in particular around pH 5. The content of dry solids is preferably in the range of about 5 to about 50% by weight, more preferably from about 10 to about 40% by weight, most preferably from about 20 to about 30% by weight.
In one aspect, the enzyme composition comprises or further comprises one or more (several) proteins selected from the group consisting of a cellulase, a hemicellulase, an expansin, an esterase, a ligninolytic enzyme, a pectinase, a peroxidase, a protease, and a swolenin. In another aspect, cellulase is preferably one or more (several) enzymes selected from the group consisting of an endoglycanase, a cellobiohydrolase, and a beta-glucosidase. In another aspect, hemicellulase is preferably one or more (several) enzymes selected from the group consisting of acetylmannan esterase, acetylxylan esterase, arabinanase, arabinofuranosidase, coumaric acid esterase, feruloyl esterase, galactosidase, glucuronidase , a glucuronoyl esterase, a mannanase, a mannosidase, a xylanoase, and a xylosidase.
In another aspect, the enzyme composition comprises one or more (several) cellulolytic enzymes. In another aspect, the enzyme composition comprises or further comprises one or more (several) hemicellulolytic enzymes. In another aspect, the enzyme composition comprises one or more (several) cellulolytic enzymes and one or more (several) hemicellulolytic enzymes. In another aspect, the enzyme composition comprises one or more (several) enzymes selected from the group of cellulolytic enzymes and hemicellulolytic enzymes. In another aspect, the enzyme composition comprises an endoglycanase. In another aspect, the enzyme composition comprises a cellobiohydrolase. In another aspect, the enzyme composition comprises a beta-glycosidase. In another aspect, the enzyme composition comprises an acetylmannan esterase. In another aspect, the enzyme composition comprises an acetylxylane esterase. In another aspect, the enzyme composition comprises an arabinanase (for example, alpha-L-arabinanase). In another aspect, the enzyme composition comprises an arabinofuranosidase (for example, alpha-L-arabinofuranosidase). In another aspect, the enzyme composition comprises coumaric acid esterase. In another aspect, the enzyme composition comprises feruloyl esterase. In another aspect, the enzyme composition comprises a galactosidase (for example, alpha-galactosidase and / or beta-galactosidase). In another aspect, the enzyme composition comprises a glucuronidase (for example, alpha-D-glucuronidase). In another aspect, the enzyme composition comprises a glucuronoyl esterase. In another aspect, the enzyme composition comprises mannanase. In another aspect, the enzyme composition comprises a mannosidase (for example, beta-mannosidase). In another aspect, the enzyme composition comprises a xylanoase. In a preferred aspect, the xylanoase is a Family 10 xylanoase. In another aspect, the enzyme composition comprises a xylosidase.
In another aspect, the enzyme composition comprises an expansin. In another aspect, the enzyme composition comprises an esterase. In another aspect, the enzyme composition comprises a ligninolytic enzyme. In a preferred aspect, the ligninolytic enzyme is a laccase. In another preferred aspect, the ligninolytic enzyme is a manganese peroxidase. In another preferred aspect, the ligninolytic enzyme is a lignin peroxidase. In another preferred aspect, the ligninolytic enzyme is an enzyme that produces H2C> 2. In another aspect, the enzyme composition comprises a pectinase. In another aspect, the enzyme composition comprises a peroxidase. In another aspect, the enzyme composition comprises a protease. In another aspect, the enzyme composition comprises a swolenin.
In the methods of the present invention, the enzyme (s) can be added before or during fermentation, for example, during saccharification or during or after the propagation of the fermenting microorganism (s) ( es).
One or more (several) components of the enzyme composition may well be wild-type proteins, recombinant proteins, or a combination of wild-type proteins and recombinant proteins. For example, one or more (several) components can be proteins native to a cell, which is used as a host cell to recombinantly express one or more (several) other components of the enzyme composition. One or more (several) components of the enzyme composition can be produced as monocomponents, which are then combined to form the enzyme composition. The enzyme composition can be a combination of multicomponent and monocomponent protein preparations.
The enzymes used in the methods of the present invention can be in any form suitable for use in the processes described herein, such as, for example, a crude fermentation broth with or without removed cells, a cell lysate with or without cell fragments, a preparation of semi-purified or purified enzyme, or a host cell as a source of enzymes. The enzyme composition can be a dry or granulated powder, a non-sprayable granulate, a liquid, a stabilized liquid, or a stabilized protected enzyme. Liquid enzyme preparations, for example, can be stabilized by the addition of stabilizers such as a sugar, a sugar alcohol or another polyol, and / or lactic acid or another organic acid according to established procedures.
The ideal amounts of enzymes and polypeptides having cellulolytic enhancing activity depend on several factors including, but not limited to the mixture of component cellulolytic enzymes, the cellulosic substrate, the concentration of cellulosic substrate, the substrate pretreatment (s) cellulosic, temperature, time, pH, and inclusion of fermenting organism (for example, yeast for simultaneous saccharification and fermentation).
In a preferred aspect, an effective amount of cellulolytic enzyme (s) for cellulosic material is about 0.5 to about 50 mg, preferably about 0.5 to about 40 mg, more preferably about from 0.5 to about 25 mg, more preferably from about 0.75 to about 20 mg, more preferably from about 0.75 to about 15 mg, even more preferably 76 from about 0.5 to about 10 mg, and most preferably about 2.5 to about 10 mg per g of cellulosic material.
In another preferred aspect, an effective amount of polypeptide (s) having cellulolytic enhancing activity for cellulosic material is from about 0.01 to about 50.0 mg, preferably from about 0.01 to about 40 mg, more preferably from about 0.01 to about 30 mg, more preferably from about 0.01 to about 20 mg, more preferably from about 0.01 to about 10 mg, most preferably from about 0.01 to about 5 mg, more preferably from about 0.025 to about 1.5 mg, more preferably from about 0.05 to about 1.25 mg, more preferably from about 0.075 to about 1.25 mg, more preferably from about 0.1 to about 1.25 mg, even more preferably from about 0.15 to about 1.25 mg, and most preferably from about 0.25 to about 1.0 mg per g of cellulosic material.
In another preferred aspect, an effective amount of polypeptide (s) having cellulolytic enhancing activity for cellulolytic enzyme (s) is from about 0.005 to about 1.0 g, preferably from about 0.01 to about from 1.0 g, more preferably from about 0.15 to about 0.75 g, more preferably from about 0.15 to about 0.5 g, more preferably from about 0.1 to about 0 , 5 g, even more preferably from about 0.1 to about 0.25 g, and most preferably from about 0.05 to about 0.2 g per g of cellulolytic enzyme (s).
Enzymes can be derived or obtained from any suitable source, including, bacterial, fungal, yeast, vegetable, or mammalian origin. The term "obtained" here means that the enzyme may have been isolated from an organism that naturally produces the enzyme as a native enzyme. The term "obtained" also means here that the enzyme may have been produced recombinantly in a host organism using methods described herein, in which the enzyme that is naturally produced is native or foreign to the host organism or has a modified amino acid sequence, for example, having one or more (several) amino acids that are deleted, inserted and / or substituted, that is, a recombinantly produced enzyme that is a mutant and / or a fragment of a native amino acid sequence or an enzyme produced by the nucleic acid shuffling processes known in the art. Covered within the meaning of a native enzyme are natural variants and within the meaning of a foreign enzyme are variants obtained recombinantly, such as by loco-directed mutagenesis or shuffling.
A polypeptide having enzyme activity can be a bacterial polypeptide. For example, the polypeptide can be a gram positive bacterial polypeptide such as a Bacillus, Streptococcus, Streptomyces, Staphylococcus, Enterococcus, Lactobacillus, Lactococcus, Clostridium, Geobacillus, or Oceanobacillustendo enzyme activity, or a negative polypeptide as a gram-negative polypeptide E. coli polypeptide, Pseudomonas, Salmonella, Campylobacter, Helicobacter, Flavobacterium, Fusobacterium, Ilyobacter, Neisseria, or Ureaplasmatendo enzyme activity.
In a preferred aspect, the polypeptide is a Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus stateris, Bacillus megaterum, Bacillus stateris, , or Bacillus thuringiensis polypeptide having enzyme activity.
In another preferred aspect, the polypeptide is a polypeptide from Streptococcus equisimilis, Streptococcus pyogenes, Streptococcus uberis, or Streptococcus equi subsp. Zooepidemicus having enzyme activity.
In another preferred aspect, the polypeptide is a polypeptide from Streptomyces achromogenes, Streptomyces avermitilis, Streptomyces coelicolor, Streptomyces griseus, or Streptomyces lividans having enzyme activity.
The polypeptide having enzyme activity can also be a fungal polypeptide, and more preferably a yeast polypeptide such as a polypeptide from Candida, Kluyveromyces, Pichia, Saccharomyces, Schizosaccharomyces, or Yarrowia having enzyme activity; or more preferably a filamentous fungus polypeptide such as an Acremonium, Agaricus, Alternaria, Aspergillus, Aureobasidium, Botryospaeria, Ceriporiopsis, Chaetomidium polypeptide,
Chrysosporium, Claviceps, Cochliobolus, Coprinopsis, Coptotermes, Corynascus, Cryphonectria, Cryptococcus, Diplodia, Exidia, Filibasidium, Fusarium, Gibberella, Holomastigotoides, Humicola, Irpex, Lentinula, Leptospaer, Merpiloc, Melapore, Melapore, Magnumortan, Melone, Paecilomyces, Penicillium, Phanerochaete, Piromyces, Poitrasia, Pseudoplectania,
Pseudotrichonympha, Rhizomucor, Schizophyllum, Scytalidium, Talaromyces, Thermoascus, Thielavia, Tolypocladium, Trichoderma, Trichophaea, Verticillium, Volvariella, or Xilaria having enzyme activity.
In a preferred aspect, the polypeptide is a polypeptide from Saccharomyces carlsbergensis, Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomyces norbensis, or Saccharomyces oviformistendo enzyme activity.
In another preferred aspect, the polypeptide is a polypeptide from Acremonium cellulolyticus, Aspergillus aculeatus, Aspergillus awamori, Aspergillus fumigatus, Aspergillus foetidus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger, epery, Chilean, porpornillispor Chrysosporium merdarium, Chrysosporium inops, Chrysosporium pannicola, Chrysosporium queenslandicum, Chrysosporium zonatum, Fusarium bactridioides, Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum, Fusarium graminum, Fusarium heterosporic, Fusarium, Fusarium, Fusarium, Fusarium, Fusarium, Fusarium, Fusarium, Fusarium, Fusarium, Fusarium, Fusarium, Fusarium, Fusarium , Fusarium sarcochroum, Fusarium sporotrichioides, Fusarium sulphureum, Fusarium tòrulosum, Fusarium trichothecioides, Fusarium venenatum, Humicola grisea, Humicola insolens, Humicola lanuginosa, Irpex lacteus, Mucor miehei, Myceliophthora thermophila, Nephilla thermophila, Neuras ium funiculosum, Penicillium purpurogenum, Phanerochaete chrysosporium, Thielavia achromatica, Thielavia albomyces, Thielavia albopilosa, Thielavia australeinsis, Thielavia fimeti, Thielavia microspora, Thielavia ovispora, Thielavia peruviana, Thielavia triadichia, Thielavia spedich , Trichoderma longibrachiatum, Trichoderma reesei, Trichoderma viride, or Trichophaea saccatatando enzyme activity.
Chemically modified or engineered polypeptide protein mutants having enzyme activity can also be used.
One or more (several) components of the enzyme composition can be a recombinant component, that is, produced by cloning a DNA sequence that encodes the single component and subsequent cell transformed with the DNA sequence and expressed in a host (see, for example, WO 91/17243 and WO 91/17244). The host is preferably a heterologous host (the enzyme is foreign to the host), but the host may under certain conditions also be a homologous host (the enzyme is native to the host). Monocomponent cellulolytic proteins can also be prepared by purifying such a protein from a fermentation broth.
In one aspect, the one or more (several) cellulolytic enzymes comprise a commercial cellulolytic enzyme preparation. Examples of commercial cellulolytic enzyme preparations suitable for use in the present invention include, for example, CELLIC® Ctec (Novozymes A / S), CELLUCLAST® (Novozymes A / S), NOVOZYM® 188 (Novozymes A / S), CELLUZYME ® (Novozymes A / S), CEREFLO® (Novozymes A / S), and ULTRAFLO® (Novozymes A / S), ACCELERASE® (Genencor Int), LAMINEX® (Genencor Int.), SPEZYME® CP (Genencor Int.) , ROHAMENT® 7069 W (Rohm GmbH), FIBREZYME® LDI (Dyadic International, Inc.), FIBREZYME® LBR (Dyadic International, Inc.), or VISCOSTAR® 150L (Dyadic International, Inc.). Cellulase enzymes are added in effective amounts of about 0.001 to about 5.0% by weight of solids, more preferably from about 0.025 to about 4.0% by weight of solids, and most preferably about 0.005 to about 2.0% by weight of solids. Cellulase enzymes are added in effective amounts of about 0.001 to about 5.0% by weight of solids, more preferably from about 0.025 to about 4.0% by weight of solids, and most preferably about 0.005 to about 2.0% by weight of solids.
Examples of bacterial endoglycanases that can be used in the methods of the present invention include, but are not limited to, an endoglycanase from Acidothermus cellulolyticus (WO 91/05039; WO 93/15186; US Patent No. 5,275,944; WO 96 / 02551; US Patent No. 5,536,655, WO 00/70031, WO 05/093050); endoglycanase III from Thermobifida fusca (WO 05/093050); and endoglycanase V from Thermobifida fusca (WO 05/093050).
Examples of fungal endoglycanases that can be used in the methods of the present invention, include, but are not limited to, an endoglycanase I from Trichoderma reesei (Penttila et al., 1986, Gene 45: 253-263; access in GENBANK® No. M15665); endoglycanase II from Trichoderma reesei (Saloheimo, et al., 1988, Gene 63: 11-22; access in GENBANK® No. M19373); endoglycanase III from Trichoderma reesei (Okada et al., 1988, Appl. Environ. Microbiol. 64: 555-563; access in GENBANK® no. AB003694); and Trichoderma reesei endoglycanase V (Saloheimo et al., 1994, Molecular Microbiology 13: 219-228; access to GENBANK® No. Z33381); endoglycanase from Aspergillus aculeatus (Ooi et al., 1990, Nucleic Acids Research 18: 5884); endoglycanase from Aspergillus kawachii (Sakamoto et al., 1995, Current Genetics 27: 435-439); endoglycanase from Erwinia carotovara (Saarilahti et al., 1990, Gene 90: 9-14); Fusarium oxysporum endoglycanase (accessed from GENBANK® no. L29381); endoglycanase from Humicola grisea var. thermoidea (access to GENBANK® no. AB003107); endoglycanase of Melanocarpus albomyces (access in GENBANK® no. MAL515703); endoglycanase of Neurospora crassa (access in GENBANK® no. XM_324477); endoglycanase V from Humicola insolens; endoglycanase Myceliophthora thermophila CBS 117.65; basidiomycete endoglycanase CBS 495.95; basidiomycete endoglycanase CBS 494.95; endoglycanase from Thielavia terrestris NRRL 8126 CEL6B; endoglycanase from Thielavia terrestris NRRL 8126 CEL6C); endoglycanase from Thielavia terrestris NRRL 8126 CEL7C; endoglycanase from Thielavia terrestris NRRL 8126 CEL7E; endoglycanase from Thielavia terrestris NRRL 8126 CEL7F; Cladorrhinum foecundissimum endoglycanase ATCC 62373 CEL7A; and Trichoderma reesei strain No. VTT-D-80133 endoglycanase (accessed from GENBANK® No. Ml5665).
Examples of cellobiohydrolases useful in the methods of the present invention include, but are not limited to, Trichoderma reesei cellobiohydrolase I; cellobiohydrolase II from Trichoderma reesei; cellobiohydrolase I of Humicola insolens, cellobiohydrolase II of Myceliophthora thermophila, cellobiohydrolase II of Thielavia terrestris (CEL6A), cellobiohydrolase I of Chaetomium thermophilum, and cellobiohydrolase II of Chaetomium thermophilum.
Examples of beta-glycosidases useful in the methods of the present invention include, but are not limited to, beta-glycosidase from Aspergillus oryzae ', beta-glycosidase from Aspergillus fumigatus', beta-glucosidase from Penicillium brasilianum IBT 20888; beta-glycosidase from Aspergillus niger, and beta-glycosidase from Aspergillus aculeatus.
The Aspergillus oryza polypeptide having beta-glucosidase activity can be obtained according to WO 2002/095014. The Aspergillus fumigate polypeptide supporting beta-glycosidase activity can be obtained according to WO 2005/047499. The Penicillium brasilian polypeptide having beta-glycosidase activity can be obtained according to WO 2007/019442. The Aspergillus polypeptide nigerting beta-glycosidase activity can be obtained according to Dan et al., 2000, J. Biol. Chem. 275: 4973-4980. The Aspergillus aculeatus polypeptide having beta-glycosidase activity can be obtained according to Kawaguchi etal., 1996, Gene 173: 287-288.
Beta-glycosidase can be a fusion protein. In one aspect, beta-glycosidase is the fusion protein of the Bg variant of Aspergillus oryzae beta-glucosidase or the beta-glycosidase fusion protein of Aspergillus oryzaeobtained according to WO 2008/057637.
Other endoglycanases, cellobiohydrolases, and beta-glycosidases are disclosed in numerous families of the Glycosyl Hydrolase using the classification according to Henrissat B., 1991, A classification of glycosyl hydrolases based on amino-acid sequence similarities, Biochem. J. 280: 309-31, and Henrissat B., and Bairoch A., 1996, Updating the sequence-based classification of glycosyl hydrolases, Biochem. J. 316: 695-696.
Other cellulolytic enzymes that can be used in the present invention are described in EP 495.257, EP 531.315, EP 531.372, WO 89/09259, WO 94/07998, WO 95/24471, WO 96/11262, WO 96/29397, WO 96 / 034108, WO 97/14804, WO 98/08940, WO 98/012307, WO 98/13465, WO 98/015619, WO 98/015633, WO 98/028411, WO 99/06574, WO 99/10481, WO 99 / 025846, WO 99/025847, WO 99/031255, WO 2000/009707, WO 2002/050245, WO 2002/0076792, WO 2002/101078, WO 2003/027306, WO 2003/052054, WO 2003/052055, WO 2003 / 052056, WO 2003/052057, WO 2003/052118, WO 2004/016760, WO 2004/043980, WO 2004/048592, WO 2005/001065, WO 2005/028636, WO 2005/093050, WO 2005/093073, WO 2006 / 074005, WO 2006/117432, WO 2007/071818, WO 2007/071820, WO 2008/008070, WO 2008/008793, US Patent No. 4,435,307, US Patent No. 5,457,046, US Patent No. 5,648,263, US Patent No. 5,686,593, US Patent No. 5,691,178, US Patent No. 5,763,254, and US Patent No. 5,776,757.
In one aspect, one or more (more) hemicellulolytic enzymes comprise a commercial hemicellulolytic enzyme preparation. Examples of commercial hemicellulolytic enzyme preparations suitable for use in the present invention include, for example, SHEARZYME® (Novozymes A / S), CELLIC® Htec (Novozymes A / S), VISCOZYME® (Novozymes A / S), ULTRAFLO® (Novozymes A / S), PULPZYME® HC (Novozymes A / S), MULTIFECT® Xylanoase (Genencor), ECOPULP® TX-200A (AB Enzymes), HSP 6000 Xylanoase (DSM), DEPOL® 333P (Biocatalysts Limit, Wales, UK), DEPOL® 740L. (Biocatalysts Limit, Wales, UK), and DEPOL® 762P (Biocatalysts Limit, Wales, UK).
Examples of xylanoases useful in the methods of the present invention include, but are not limited to, Aspergillus aculeatus xylanoase (GeneSeqP: AAR63790; WO 94/21785), Aspergillus fumigatus xylanoases (WO 2006/078256), and Thielavia terrestris NRRL xylanoases 8126 (WO 2009/079210).
Examples of beta-xylosidases useful in the methods of the present invention include, but are not limited to, Trichoderma reesei beta-xylosidase (accession number on UniProtKB / TrEMBL Q92458), Talaromyces emersonii (accession number on SwissProt Q8X212), and Neurospora crassa (SwissProt Q7SOW4 access number).
Examples of acetylxylan esterases useful in the methods of the present invention include, but are not limited to, Hypocrea jecorina acetylxylan esterase (WO 2005/001036), Neurospora crassa acetylxylan esterase (UniProt access number q7s259), Thielavia terrestris acetylxylan ester NRRL 8126 (WO 2009/042846), acetylxylan esterase from Chaetomium globosum (accession number Uniprot Q2GWX4), acetylxylan esterase from Chaetomium gracile (accession number GeneSeqP AAB82124), acetylxylan esterase from Phaeosphaeria nodorum (accession number) Humicola insolens DSM 1800 (WO 2009/073709).
Examples of ferulic acid esterases useful in the methods of the present invention include, but are not limited to, ferricyl esterase from Humicola insolens DSM 1800 (WO 2009/076122), Neurospora crassa feruloyl esterase (UniProt access number Q9HGR3), and feruloyl esterase de Neosartoryafischeri (UniProt access number A1D9T4).
Examples of arabinofuranosidases useful in the methods of the present invention include, but are not limited to, Humicola insolens DSM 1800 arabinofuranosidase (WO 2009/073383) and Aspergillus niger arabinofuranosidase (GeneSeqP accession number AAR94170).
Examples of alpha-glucuronidases useful in the methods of the present invention include, but are not limited to, Aspergillus clavatus alpha-glucuronidase (UniProt access number alccl2), Trichoderma reesei alpha-glucuronidase (UniProt access number Q99024), alpha- glucuronidase from Talaromyces emersonii (accession number UniProt Q8X211), alpha-glucuronidase from Aspergillus niger (accession number UniProt Q96WX9), alpha-glucuronidase from Aspergillus terreus (accession number in SwissProt Q0CJP9), and alpha-glucuronide number SwissProt Q4WW45).
The enzymes and proteins used in the methods of the present invention can be produced by fermenting the microbial strains mentioned above in a nutrient medium containing carbon and nitrogen sources and suitable inorganic salts, using procedures known in the art (see, for example, Bennett, JW and LaSure, L. (eds.), More Gene Manipulations in Fungi, Academic Press, CA, 1991). Suitable media are available from commercial suppliers or can be prepared according to published compositions (for example, in catalogs of the American Type Culture Collection). Temperature ranges and other conditions suitable for enzyme cultivation and production are known in the art (see, for example, Bailey, J. E., and Ollis, D. F., Biochemical Engineering Fundamentals, McGraw-Hill Book Company, NY, 1986).
Fermentation can be any method of culturing a cell that results in the expression or isolation of an enzyme. Fermentation, therefore, can be understood as comprising shaking jar cultivation, or small or large scale fermentation (including continuous, batch, fed batch, or solid fermentation) in laboratory or industrial fermenters carried out in a suitable medium and under conditions that enable the enzyme to be expressed or isolated. The resulting enzymes produced by the methods described above can be recovered from the fermentation medium and purified by conventional procedures. The fermentable sugars obtained from the hydrolyzed cellulosic material can be fermented by one or more (several) fermenting microorganisms capable of fermenting the sugars directly or indirectly in a desired fermentation product. "Fermentation" or "fermentation process" refers to any fermentation process or any process that comprises a fermentation step. Fermentation processes also include fermentation processes used in the consumable alcohol industry (for example, beer and wine), the dairy industry (for example, fermented dairy products), the leather industry and the tobacco industry. The fermentation conditions depend on the desired fermentation product and the fermenting organism and can be easily determined by a person skilled in the art.In the fermentation stage, sugars, released from the cellulosic material as a result of the pre-treatment and enzymatic hydrolysis steps, they are fermented to a product, for example, ethanol, by a fermenting organism, such as yeast. Hydrolysis (saccharification) and fermentation can be separated or simultaneous, as described herein.
Any suitable hydrolyzed cellulosic material can be used in the fermentation step in the practice of the present invention. The material is generally selected on the basis of the desired fermentation product, that is, the substance to be obtained from the fermentation and the process used, as is well known in the art.
The term "fermentation medium" is understood here to refer to a medium before the fermenting micro-organism (s) is (are) added, such as, a medium resulting from a process of fermentation. saccharification, as well as a medium used in a simultaneous saccharification and fermentation process (SSF). “Fermenting micro-organism” refers to any micro-organism, which includes bacterial and fungal organisms, suitable for use in a fermentation process desired to produce a fermentation product. The fermenting organism can be Cg and / or C5 fermenting organisms or a combination thereof. Both the C6 and C5 fermenting organisms are well known in the art. Suitable fermenting microorganisms are capable of fermenting, that is, converting, sugars such as glucose, xylose, xylulose, arabinose, maltose, mannose, galactose or oligosaccharides, directly or indirectly into the desired fermentation product.
Examples of bacterial and fungal fermenting organisms that produce ethanol are described by Lin et al., 2006, Appl. Microbiol. Biotechnol. 69: 627-642.
Examples of fermenting microorganisms that can ferment C6 sugars include bacterial and fungal organisms, such as yeast. The preferred yeast includes strains of Saccharomyces spp., Preferably Saccharomyces cerevisiae.
Examples of fermenting organisms that can ferment C5 sugars include bacterial and fungal organisms, such as yeast. The preferred C5 fermenting yeast includes strains of Pichia, preferably Pichia stipitis, such as Pichia stipitis CBS 5773; strains of Candida, preferably Candida boidinii, Candida brassicae, Candida sheatae, Candida diddensii, Candida pseudotropicalis or Candida utilis.
Other fermenting organisms include strains of Zymomonas, such as Zymomonas mobilis ', Hansenula, such as Hansenula anomalous', Kluyveromyces, such as K. fragilis ', Schizosaccharomyces, such as S. pombe', and E. coli, especially strains of E coli that have been genetically modified to improve ethanol yield.
In a preferred aspect, the yeast is Saccharomyces spp. In a more preferred aspect, the yeast is Saccharomyces cerevisiae. In another more preferred aspect, the yeast is Saccharomyces distaticus. In another more preferred aspect, the yeast is Saccharomyces uvarum. In another preferred aspect, the yeast is a Kluyveromyces. In another more preferred aspect, the yeast is Kluyveromyces marxianus. In another more preferred aspect, the yeast is Kluyveromyces fragilis. In another preferred aspect, the yeast is a Candida. In another more preferred aspect, the yeast is Candida boidinii. In another more preferred aspect, the yeast is Candida brassicae. In another more preferred aspect, the yeast is Candida diddensii. In another more preferred aspect, the yeast is Candida pseudotropicalis. In another more preferred aspect, the yeast is Candida utilis. In another preferred aspect, the yeast is a Clavispora. In another more preferred aspect, the yeast is Clavispora lusitaniae. In another more preferred aspect, the yeast is Clavispora opuntiae. In another preferred aspect, the yeast is a Pachysolen. In another more preferred aspect, the yeast is Pachysolen tannophilus. In another preferred aspect, the yeast is a Pichia. In another more preferred aspect, the yeast is a Pichia stipitis. In another preferred aspect, the yeast is a Bretannomyces. In another more preferred aspect, the yeast is Bretannomyces clausenii (Philippidis, GP, 1996, Cellulose bioconversion technology, in the Handbook on Bioethanol: Prodution and Utilization, Wyman, CE, ed., Taylor & Francis, Washington, DC, 179-212 ).
Bacteria that can efficiently ferment hexose and pentose to ethanol include, for example, Zymomonas mobilis and Clostridium thermocellum (Philippidis, 1996, supra).
In a preferred aspect, the bacterium is a Zymomonas. In a more preferred aspect, the bacterium is Zymomonas mobilis. In another preferred aspect, the bacterium is a Clostridium. In another more preferred aspect, the bacterium is Clostridium thermocellum.
Commercially available yeasts suitable for ethanol production include, for example, yeast ETANOL RED® (available from Fermentis / Lesaffre, USA), FALI® (available from Fleischmann's Yeast, USA), SUPERSTART® and fresh yeast THERMOSACC® (available from Ethanol Technology, WI, USA), BIOFERM® AFT and XR (available from NABC - North American Bioproducts Corporation, GA, USA), GERT STRAND® (available from Gert Strand AB, Sweden) and FERMIOL® (available from DSM Specialties) .
In a preferred aspect, the fermenting microorganism has been genetically modified to provide the ability to ferment pentose sugars, such as xylose using, arabinose using and xylose and arabinose co-using microorganisms.
The cloning of heterologous genes in various microorganism fermenters has led to the construction of organisms capable of converting hexoses and pentoses to ethanol (co-fermentation) ((Chen and Ho, 1993, Cloning and improving the expression of Pichia stipitis xylose reductase gene in Saccharomyces cerevisiae, Appl. Biochem. Biotechnol. 39-40: 135-147; Ho et al., 1998, Genetically engineered Saccharomyces yeast capable of effectively cofermenting glucose and xylose, Appl. Environ. Microbiol. 64: 1852-1859; Kotter and Ciriacy, 1993, Xylose fermentation by Saccharomyces cerevisiae, Appl. Microbiol. Biotechnol. 38: 776-783; Walffidsson et al., 1995, Xylose-metabolizing Saccharomyces cerevisiae strains overexpressing the TKL1 and TALI genes encoding the pentose phosphakette pathway enzymes and transaldolase, Appl. Environ. Microbiol. 61: 4184-4190; Kuyper et al., 2004, Minimal metabolic engineering of Saccharomyces cerevisiae for efficient anaerobic xylose fermentation: a proof of p rinciple, FEMS Yeast Research 4: 655-664; Beall et al., 1991, Parametric studies of ethanol prodution from xylose and other sugars by recombinant Escherichia coli, Biotech. Bioeng. 38: 296-303; Ingram et al., 1998, Metabolic engineering of bacteria for ethanol prodution, Biotechnol. Bioeng. 58: 204-204; Zhang et al., 1995, Metabolic engineering of a pentose metabolism pathway in ethanologenic Zymomonas mobilis, Science 267: 240-243; Deanda et al., 1996, Development of an arabinose-fermenting Zymomonas mobilis strain by metabolic pathway engineering, Appl. Environ. Microbiol. 62: 4465-4470; WO 2003/062430, xylose isomerase).
In a preferred aspect, the genetically modified fermenting microorganism is Saccharomyces cerevisiae. In another preferred aspect, the genetically modified fermenting microorganism is Zymomonas mobilis. In another preferred aspect, the genetically modified fermenting microorganism is Escherichia coli. In another preferred aspect, the genetically modified fermenting microorganism is Klebsiella oxytoca. In another preferred aspect, the genetically modified fermentation microorganism is Kluyveromyces sp.
It is well known in the art that the organisms described above can also be used to produce other substances, as described herein.
The fermenting microorganism is typically added to the degraded or hydrolyzed lignocellulose and fermentation is carried out for about 8 to about 96 hours, such as about 24 to about 60 hours. The temperature is typically between about 26 ° C to about 60 ° C, in particular about 32 ° C or 50 ° C and about pH 3 to about pEl 8, such as around pH 4 to 5 , 6 or 7.
In a preferred aspect, yeast and / or another micro-organism are applied to the degraded cellulosic material and fermentation is carried out for about 12 to about 96 hours, as is typically 24 to 60 hours. In a preferred aspect, the temperature is preferably between about 20 ° C to about 60 ° C, more preferably from about 25 ° C to about 50 ° C and most preferably from about 32 ° C to about 50 ° C, in particular about 32 ° C or 50 ° C and the pH is generally about pH 3 to about pH 7, preferably around pH 4 to 7. However, some fermentation organisms, for example, bacteria, have a higher ideal fermentation temperature. Yeast or another microorganism is
preferably applied in amounts of approximately 10 to 10, preferably approximately 10 to 10, special and approximately 2 x 108 viable cell counts per ml of fermentation broth. Additional guidance regarding the use of yeast for fermentation can be found, for example, in “The Alcohol Textbook” (Editors K. Jacques, TP Lyons and DR Kelsall, Nottingham University Press, United Kingdom 1999), which is hereby incorporated by reference.
For the production of ethanol, after fermentation, the fermented slurry is distilled to extract the ethanol. Ethanol obtained according to the methods of the invention can be used, for example, fuel ethanol, drinking ethanol, i.e., potable neutral alcohols or industrial ethanol.
A fermentation stimulator can be used in combination with any of the processes described herein to further improve the fermentation process and in particular, the performance of the fermenting micro-organism, such as the rate of intensification and ethanol yield. A "fermentation stimulator" refers to stimulators for the growth of fermenting microorganisms, in particular, yeast. Preferred fermentation stimulators for growth include vitamins and minerals. Examples of vitamins include multivitamins, biotin, pantothenate, nicotinic acid, meso-inositol, thiamine, pyridoxine, para-aminobenzoic acid, folic acid, riboflavin and Vitamins A, B, C, D and E. See, for example, Alfenore et al., Improving ethanol prodution and viability of Saccharomyces cerevisiae by a vitamin feeding strategy during fed-batch process, Springer-Verlag (2002), which is hereby incorporated by reference. Examples of minerals include minerals and mineral salts that can provide nutrients that comprise P, K, Mg, S, Ca, Fe, Zn, Mn and Cu.are any substance derived from fermentation. The fermentation product can be, without limitation, an alcohol (for example, arabinitol, butanol, ethanol, glycerol, methanol, 1,3-propanediol, sorbitol and xylitol); an organic acid (for example, acetic acid, acetonic acid, adipic acid, ascorbic acid, citric acid, 2,5-diceto-D-glyconic acid, formic acid, fumaric acid, glucaric acid, glyconic acid, glucuronic acid, glutaric acid , 3-hydroxypropionic acid, itaconic acid, lactic acid, malic acid, malonic acid, oxalic acid, oxaloacetic acid, propionic acid, succinic acid and xylonic acid); a ketone (for example, acetone); an amino acid (for example, aspartic acid, glutamic acid, glycine, lysine, serine and threonine); and a gas (for example, methane, hydrogen (H2), carbon dioxide (CO2) and carbon monoxide (CO)). The fermentation product can also be protein as a high-value product.
In a preferred aspect, the fermentation product is an alcohol. It should be understood that the term "alcohol" includes a substance that contains one or more portions of hydroxyl. In a more preferred aspect, the alcohol is arabinitol. In another more preferred aspect, the alcohol is butanol. In another more preferred aspect, the alcohol is ethanol. In another more preferred aspect, the alcohol is glycerol. In another more preferred aspect, the alcohol is methanol. In another more preferred aspect, the alcohol is 1,3-propanediol. In another more preferred aspect, the alcohol is sorbitol. In another more preferred aspect, the alcohol is xylitol. See, for example, Gong, CS, Cao, NJ, Du, J., and Tsao, GT, 1999, Ethanol prodution from renewable resources, in Advances in Biochemical Engineering / Biotechnology, Scheper, T., ed., Springer-Verlag Berlin Heidelberg, Germany, 65: 207-241; Silveira, M. M., and Jonas, R., 2002, The biotechnological prodution of sorbitol, Appl. Microbiol. Biotechnol. 59: 400-408; Nigam, P., and Singh, D., 1995, Processes for fermentative prodution of xylitol - a sugar substitute, Process Biochemistry 30 (2): 117-124; Ezeji, T. C., Qureshi, N. and Blaschek, H. P., 2003, Prodution of acetone, butanol and ethanol by Clostridium beijerinckii BAI 01 and in situ recovery by gas stripping, World Journal of Microbiology and Biotechnology 19 (6): 595-603.
In another preferred aspect, the fermentation product is an organic acid. In another more preferred aspect, the organic acid is acetic acid. In another more preferred aspect, the organic acid is acetonic acid. In another more preferred aspect, the organic acid is adipic acid. In another more preferred aspect, the organic acid is ascorbic acid. In another more preferred aspect, the organic acid is citric acid. In another more preferred aspect, the organic acid is 2,5-diceto-D-glyconic acid. In another more preferred aspect, the organic acid is formic acid. In another more preferred aspect, organic acid is fumaric acid. In another more preferred aspect, organic acid is glucaric acid. In another more preferred aspect, organic acid is glyconic acid. In another more preferred aspect, organic acid is glycuronic acid. In another more preferred aspect, the organic acid is glutaric acid. In another preferred aspect, the organic acid is 3-hydroxypropionic acid. In another more preferred aspect, organic acid is itaconic acid. In another more preferred aspect, the organic acid is lactic acid. In another more preferred aspect, organic acid is malic acid. In another more preferred aspect, organic acid is malonic acid. In another more preferred aspect, the organic acid is oxalic acid. In another more preferred aspect, organic acid is propionic acid. In another more preferred aspect, the organic acid is succinic acid. In another more preferred aspect, organic acid is xylonic acid. See, for example, Chen, R. and Lee, Y. Y., 1997, Membrane-mediated extractive fermentation for lactic acid prodution from cellulosic biomass, Appl. Biochem. Biotechnol. 63-65: 435-448. a ketone. It should be understood that the term "ketone" includes a substance that contains one or more portions of ketone. In another more preferred aspect, the ketone is acetone. See, for example, Qureshi and Blaschek, 2003, supra.
In another preferred aspect, the fermentation product is an amino acid. In another more preferred aspect, the organic acid is aspartic acid. In another more preferred aspect, the amino acid is glutamic acid. In another more preferred aspect, the amino acid is glycine. In another more preferred aspect, the amino acid is lysine. In another more preferred aspect, the amino acid is serine. In another more preferred aspect, the amino acid is threonine. See, for example, Richard, A. and Margaritis, A., 2004, Empirical modeling of batch fermentation kinetics for poli (glutamic acid) prodution and other microbial biopolymers, Biotechnology and Bioengineering 87 (4): 501-515.
In another preferred aspect, the fermentation product is a gas. In another more preferred aspect, the gas is methane. In another more preferred aspect, the gas is H2. In another more preferred aspect, the gas is CO2. In another more preferred aspect, the gas is CO. See, for example, Kataoka, N., A. Miya and K. Kiriyama, 1997, Studies on hydrogen prodution by continuous culture system of hydrogen-producing anaerobic bacteria, Water Science and Technology 36 (6-7): 41-47; and Gunaseelan V.N. in Biomass and Bioenergy, Vol. 13 (1-2), pp. 83-114, 1997, Anaerobic digestion of biomass for metane prodution: A review.Recovery. The fermentation product (s) can optionally be recovered from the fermentation medium using any method known in the art which includes, but is not limited to, chromatography, electrophoretic procedures, differential solubility, distillation or extraction . For example, the alcohol is separated from the fermented cellulosic material and purified by conventional distillation methods. Ethanol with a purity of up to about 96 vol%. can be obtained, which can be used as, for example, fuel ethanol, drinking ethanol, i.e., potable neutral alcohols or industrial ethanol. Signal peptide
The present invention also relates to an isolated polynucleotide that encodes a signal peptide that comprises or consists of amino acids 1 to 21 of SEQ ID NO: 2. The polynucleotide may further comprise a gene that encodes a protein, which is operably linked to the signal peptide. The protein is preferably foreign to the signal peptide and / or propeptide.
The present invention also concerns the nucleic acid constructs, expression vectors and recombinant host cells that comprise such a polynucleotide.
The present invention also relates to methods of producing a protein, which comprise: (a) culturing a recombinant host cell that comprises such a polynucleotide; and (b) recovering the protein.
The protein can be native or heterologous to a host cell. The term "protein" is not intended here to refer to a specific length of the encoded product and therefore encompasses peptides, oligopeptides, and polypeptides. The term "protein" also encompasses two or more polypeptides combined to form the encoded product. Proteins also include hybrid polypeptides and fused polypeptides. Preferably, the protein is a hormone or variant of this, enzyme, receptor or portion of it, antibody or portion of it, or reporter. For example, the protein can be an oxidoreductase, transferase, hydrolase, lyase, isomerase, or ligase such as an aminopeptidase, amylase, carbohydrase, carboxypeptidase, catalase, cellulase, chitinase, cutinase, cyclodextrin glycosyltransferase, deoxyribonidase, esteroxidase, galoxase, galoxase, beta-galactosidase, glycoamylase, alpha-glycosidase, beta-glucosidase, invertase, laccase, another lipase, mannosidase, mutanase, oxidase, pectinolytic enzyme, peroxidase, phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease or transglutaminase.
The gene can be obtained from any prokaryotic, eukaryotic, or other source.
The present invention is further described by the following examples which are not to be construed as limiting the scope of the invention. Examples Means
The PDA plates were composed of 39.0 grams of potato dextrose agar and distilled water up to 1 liter.
The YG agar plates were composed of 5.0 g of yeast extract, 10.0 g of glucose, 20.0 g of agar, and distilled water up to 1 liter.
The NNCYP-PCS medium was composed of 5.0 g of NaNO3, 3.0 g of NH4CI, 2.0 g of MES, 2.5 g of citric acid, 0.2 g of CaCl2 2H2O, 1.0 g of Peptone Bacto, 5.0 g yeast extract, 0.2 g MgSCC 7H2O, 4.0 g K2HPO4, 1.0 ml COVE trace element solution, 2.5 g glucose, 25.0 g PCS, and distilled water up to 1 liter.
The COVE trace element solution was composed of 0.04 g of Na2B4O7-10H2O, 0.4 g of CuSO4-5H2O, 1.2 g of FeSO4-7H2O, 0.7 g of MnSO4-H2O, 0.8 g of Na2MoO2-2H2O, 10 g of ZnSO4-7H2O, and distilled water to 1 liter.
The LB agar plates were composed of 10 g tryptone, 5 g yeast extract, 10 g sodium chloride, 15 g agar, and 1 liter distilled water.
The SOC medium was composed of 2% tryptone, 0.5% yeast extract, 10 mM NaCl, 2.5 mM KC1, 10 mM MgCl2, 10 mM MgSÜ4, and 20 mM glucose. YPM was composed of 1% yeast extract, 2% peptone, and 2% maltose.
The minimum medium plates were composed of 6 g of NaNO3, 0.52 g of KC1, 1.52 g of KH2PO4, 1 ml of COVE trace element solution, 20 g of Noble agar, 20 ml of 50% glucose, 2.5 ml of 20% MgSO4'7H2O, 20 ml of a 0.02% biotin solution, and distilled water to 1 liter. Example 1: Isolation of strain NN046877 of Penicillium pinophilum from soil sample
Penicillium pinophilum NN046877 was isolated from a soil in Hunan, China by directly plating the soil sample on a PDA plate followed by incubation at 37 ° C for 5 days. The strain was then purified by transferring the mycelia on a YG agar plate. The strain NN046877 was identified as Penicillium pinophilum based on both morphological and molecular characterization (ITS sequencing). Example 2: Isolation of RNA from strain NN046877 of Penicillium pinophilum
The NN46877 strain of Penicillium pinophilum was inoculated on a PDA plate and incubated for 4 days at 37 ° C in the dark. Several mycelial-PDA buffers were inoculated into 500 ml shaken flasks each containing 100 ml of NNCYP-PCS medium. The flasks were incubated for 5 days at 37 ° C with shaking at 160 rpm. The mycelia were collected on day 4 and day 5. Then the mycelia of each day were frozen in liquid nitrogen and stored in a freezer at -80 ° C until use.
The frozen mycelia were transferred in a pre-frozen mortar and pistil in liquid nitrogen and crushed to a fine powder. Total RNA was prepared from the mycelia sprayed on day 4 and day 5 by extraction with TRIZOL® reagent (Invitrogen, Carlsbad, CA, USA). Poly A enriched RNA was isolated using an mTRAP® Total Kit (Active Motif, Carlsbad, CA, USA). Example 3: Construction of a cDNA library for the Penicillium pinophilum strain
The double stranded cDNA for day 4 and day 5 was synthesized using a SMART® cDNA Library Construction Kit (Takara Bio Inc., Otsu, Shiga, Japan). The cDNA was cleaved with Sfi I using standard methods and the cDNA was fractionated in size by electrophoresis on 0.8% agarose gel using 44 mM Tris base, 44 mM boric acid, 0.5 mM EDTA buffer ( TBE). A 500 base pair and larger cDNA fraction was excised from the gel and purified using a GFX® PCR DNA Kit and Gel Band Purification (GE Healthcare, Buckinghamshire, UK) according to the manufacturer's instructions. Then equal amounts of cDNA from day 4 and day 5 were pooled for the construction of the library.
The cDNA was then directionally cloned by binding in pMHas7 cleaved with Sfi I (WO 2009/037253) using T4 ligase (New England Biolabs, Ipswich, MA, USA) according to the manufacturer's instructions. The ligation mixture was electroporated into E. coli DH10B® ELECTROMAX® cells (Invitrogen, Carlsbad, CA, USA) using a GENE PULSER® and Pulse Controller (Bio-Rad Laboratories, Inc., Hercules, CA, USA ) at 25 pF, 25 mAmp, 1.8 kV with a 1 mm bucket in accordance with the manufacturer's procedure.
The cells submitted to electroporation were plated on LB agar plates supplemented with 50 mg kanamycin per liter. A cDNA plasmid pool was prepared from 60,000 transformants in total binding to the original pMHas7 vector. Plasmid DNA was prepared directly from the colony pool using a QIAGEN® Plasmid Kit (QIAGEN Inc., Valencia, CA, USA). Example 4: Construction of a SigA4 transposon containing the β-lactamase reporter gene
A transposon containing the plasmid designated pSigA4 was constructed from the pSigA2 transposon containing the plasmid described in WO 01/77315 in order to create an enhanced version of the pSigA2 signal capture transposon with decreased selection background. The pSigA2 transposon contains a signal minus the beta-lactamase construct encoded in the transposon itself. PCR was used to create a deletion of the intact beta-lactamase gene found in the plasmid backbone using PROOFSTART® DNA polymerase (QIAGEN GmbH Corporation, Hilden, Germany) and the following 5 'phosphorylated primers (TAG Copenhagen, Denmark) : SigA2NotU-P: 5'-TCGCGATCCGTTTTCGCATTTATCGTGAAACGCT-3 '(SEQ ID NO: 3) SigA2NotD-P: 5'-CCGCAAACGCTGGTGAAAGTAAAAGATGCTGAA-3' (SEQ ID NO: 4)
The amplification reaction was composed of 1 pl of pSigA2 (10 ng per pl), 5 pl of 10X PROOFSTART® Buffer (QIAGEN GmbH Corporation, Hilden, Germany), 2.5 pl of dNTP mixture (20 mM), 0, 5 pl of SigA2NotU-P (10 mM), 0.5 pl of SigA2NotD-P (10 mM), 10 pl of Q solution (QIAGEN GmbH Corporation, Hilden, Germany), and 31.25 pl of deionized water. A DNA ENGINE® Thermal Cycler (MJ Research Inc., Waltham, MA, USA) was used for amplification programmed for a cycle at 95 ° C for 5 minutes; and 20 cycles each at 94 ° C for 30 seconds, 62 ° C for 30 seconds, and 72 ° C for 4 minutes.
A 3.9 kb PCR reaction product was isolated by electrophoresis on 0.8% agarose gel using 40 mM Tris base-20 mM sodium acetate-1 mM disodium EDTA (TAE) buffer and 0 , 1 pg of ethidium bromide per ml. The DNA strip was visualized with the help of an EAGLE EYE® Image Formation System (Stratagene, La Jolla, CA, USA) at 360 nm. The 3.9 kb DNA strand was excised from the gel and purified using a GFX® PCR DNA Kit and Gel Band Purification according to the manufacturer's instructions.
The 3.9 kb fragment was self-ligated at 16 ° C overnight with 10 units of T4 DNA ligase (New England Biolabs, Inc., Ipwich, MA, USA), 9 µl of the 3.9 PCR fragment kb, and 1 pl of 1 OX binding buffer (New England Biolabs, Inc., Ipwich, MA, USA). The binding was inactivated by heat for 10 minutes at 65 ° C and then digested with Dpn I at 37 ° C for 2 hours. After incubation, digestion was purified using a GFX® PCR DNA Kit and Gel Band Purification.
The purified material was then transformed into competent E. coli TOP 10® cells (TIANGEN Biotech (Beijing) Co. Ltd., Pequin, China) according to the manufacturer's instructions. The transformation mixture was grown on LB agar plates supplemented with 25 pg of chloramphenicol per ml. Mini plasmid preparations were prepared from various transformants and digested with Bgl II. A plasmid with the correct construction was chosen. The plasmid was designated pSigA4. Plasmid pSigA4 contains the transposon flanked by Bgl II SigA2 identical to that disclosed in WO 01/77315.
A 60 pl sample of plasmid pSigA4 DNA (0.3 pg / pl) was digested with Bgl II and separated by electrophoresis on 0.8% agarose gel using TBE buffer. A 2 kb SigA2 transposon DNA strand was eluted with 200 pl of EB buffer (QIAGEN GmbH Corporation, Hilden, Germany) and purified using a GFX® PCR DNA Kit and Gel Band Purification according to the manufacturer's instructions and eluted at 200 pl of EB buffer. SigA2 was used for transposon-assisted signal capture. Example 5: Transposon Assisted Signal Capture of the Penicillium pinophilum strain
A complete description of transposon-assisted signal pickup can be found in WO 01/77315. The plasmid pool was treated with transposon SigA2 and HYPERMU® MuA transposase (Epicenter Biotechnologies, Inc., Madison, WI, USA) according to the manufacturer's instructions.
For in-vitro transposon labeling of the Penicillium pinophilum cDNA library, 2 µg of SigA2 transposon containing approximately 100 ng of DNA was mixed with 1 µl of the plasmid DNA pool of the Penicillium pinophilum cDNA library containing 1 µg of DNA, 1 µg of DNA HYPERMU® MuA transposase, and 2 pl of 1 OX buffer (Epicenter Biotechnologies, Inc., Madison, WI, USA) in a total volume of 20 pl and incubated at 30 ° C for 3 hours followed by the addition of 2 pl of buffer stop (Epicenter Biotechnologies, Inc., Madison, WI, USA) and heat inactivation at 75 ° C for 10 minutes. The DNA was precipitated by the addition of 2 pl of 3 M sodium acetate pH 5 and 55 pl of 96% ethanol and centrifuged at 10,000 x g for 30 minutes at 4 ° C. The pellet was washed in 70% ethanol, air-dried at room temperature, and resuspended in 10 pl of deionized water.
A 2 pl volume of the plasmid assembly labeled with transposon was electroporated into 50 pl of E. DH10B® ELECTROMAX® cells by colliding a GENE PULSER® and Pulse Controller at 25 pF, 25 mAmp, 1.8 kV with a cuvette 1 mm apart according to the manufacturer's procedure.
The cells submitted to electroporation were incubated in SOC medium for 1 hour at 37 ° C with agitation at 225 rpm before being plated in the following selective medium: LB agar medium supplemented with 50 pg of kanamycin per ml; LB agar medium supplemented with 50 pg of kanamycin per ml and 15 pg of chloramphenicol per ml; and LB agar medium supplemented with 50 pg of kanamycin per ml, 15 pg of chloramphenicol per ml, and 30 pg of ampicillin per ml.
From the electroporation plate culture on LB agar medium supplemented with kanamycin, chloramphenol and ampicillin, approximately 200 colonies per 50 pl were observed after 3 days at 30 ° C. All colonies were plated in replicate on LB agar supplemented with 50 pg of kanamycin per ml, 15 pg of chloramphenicol per ml, and 100 pg of ampicillin per ml. Five hundred colonies were recovered under this selection condition. Plasmid DNA from the colonies was sequenced with forward and reverse transposon primers (primers A and B), shown below, according to the procedure disclosed in WO 01/77315. Initiator A: 5'-agcgtttgcggccgcgatcc-3 '(SEQ ID NO: 5) Initiator B: 5'-ttattcggtcgaaaaggatcc-3 '(SEQ ID NO: 6) Example 6: Assembly and sequence annotation
DNA sequences were obtained from SinoGenoMax Co., Ltd., Pequin, China. Sequence readings of primer A and primer B for each plasmid were cut to remove the vector and transposon sequences. The assembled sequences were grouped into contiguous ones using the PhredPhrap program (Ewing et al., 1998, Genome Research 8: 175-185; Ewing and Green, 1998, Genome Research 8: 186-194). All contiguous were subsequently compared with the sequences available in the public DNA and protein sequence databases (TrEMBL, SWALL, PDB, EnsemblPep, GeneSeqP) using the BLASTX 2.0al9MP-WashU program [14-Jul-1998] [Build linux-x86 18:51:44 30-Jul-1998] (Gish et al., 1993, Nat. Genet. 3: 266-72). The GH61 Family protein was identified directly by analyzing the BlastX results. Example 7: Cloning of the GH61A polypeptide gene from Penicillium pinophilum from genomic DNA
Penicillium pinophilumNN046877 was grown on a PDA plate at 37 ° C for 4 to 5 days. The mycelia were collected directly from the agar plate in a sterile mortar and frozen in liquid nitrogen. The frozen mycelia were crushed, by mortar and pistil, to a fine powder, and the genomic DNA was isolated using a DNEASY® Plant Mini Kit (QIAGEN Inc., Valencia, CA, USA).
Based on the cDNA sequence obtained in Example 6, the oligonucleotide primers, shown below, were designed to amplify the gene for the genomic DNA of Penicillium pinophilum NN046877. An IN-FUSION® CF Dry-down Cloning Kit (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to clone the fragment directly into the pPFJO355 expression vector (Figure 2), without the need for restriction digestion. and connection. Sense initiator: 5 '-ACACAACTGGGGATCCACCATGCCTTCTACTAAAGTCGCTG-3' (SEQ ID NO: 7) Antisense primer: 5 '-GTCACCCTCTAGATCTTCAAAGGACAGTAGTGGTGATGAC-3' (SEQ ID NO: 8)
The bold letters represented the coding sequence and the remaining sequence was homologous for the pPFJO355 insertion sites.
The pPFJO355 expression vector contains the TAKA-amylase promoter derived from Aspergillus oryzae, the Aspergillus niger glycoamylase terminator elements, sequences derived from pUC19 for selection and propagation in E. coli, and a pirG gene from Aspergillus nidulans, which encodes an orotidine decarboxylase for the selection of transformants from a mutant AspergilluspirG strain. Twenty picomoles of each of the above primers were
used in a PCR reaction composed of genomic DNA from Penicillium pinophilum NN046877, 10 pl of 5X GC Buffer (Finnzymes Oy, Espoo, Finland), 1.5 pl of DMSO, 2.5 mM each of dATP, dTTP, dGTP, and dCTP, and 0.6 unit of PHUSION® High-Fidelity DNA Polymerase (Finnzymes Oy, Espoo, Finland) in a final volume of 50 pl. Amplification was performed using a Peltier Thermal Cycler (MJ Research Inc., South San Francisco, CA, USA) programmed to denature at 98 ° C for 1 minute; 5 cycles each of denaturation at 98 ° C for 15 seconds, annealing at 56 ° C for 30 seconds, with an increase of 1 ° C per cycle and elongation at 72 ° C for 75 seconds; 25 cycles each at 98 ° C for 15 seconds, 65 ° C for 30 seconds, and 72 ° C for 75 seconds; and a final extension at 72 ° C for 10 minutes. The thermal block then went to a 4 ° C soak cycle.
The reaction products were isolated by electrophoresis on 1.0% agarose gel using TBE buffer where a product band of approximately 1.0 kb was excised from the gel, and purified using a Kit illustrating GFX® PCR DNA and Gel Band Purification (GE Healthcare, Buckinghamshire, UK) according to the manufacturer's instructions.
Plasmid pPFJO355 was digested with Bam HI and Bgl II, isolated by 1.0% agarose gel electrophoresis using TBE buffer, and purified using a Kit illustrating GFX® PCR DNA and Gel Band Purification.
The gene fragment and the digested vector were linked together using a IN-FUSION® CF Dry-down PCR Cloning Kit resulting in pPpin7 (Figure 3) in which the transcription of the Penicillium pinophilum GH61A polypeptide gene was under control of a promoter of the gene for Aspergillus oryzae alpha-amylase. The cloning operation was performed according to the manufacturer's instructions. In summary, 30 ng of pPFJO355 digested with Bam HI and Bgl II, and 60 ng of the purified Penicillium pinophilum polypeptide GH61A PCR product were added to a reaction flask and resuspended in a final volume of 10 pl by adding water deionized. The reaction was incubated at 37 ° C for 15 minutes and then 50 ° C for 15 minutes. Three pls of the reaction were used to transform competent E. colL TOP 10® cells. An E. coli transformant containing pPpin7 was detected by colony PCR and plasmid DNA was prepared using a QIAPREP® Spin Miniprep Kit (QIAGEN Inc., Valencia , CAUSE). The Penicillium pinophilum GH61A polypeptide gene inserted in pPpin7 was confirmed by DNA sequencing using a 3730XL DNA Analyzer (Applied Biosystems Inc, Foster City, CA, USA).
The same PCR fragment was cloned into pGEM-T (Promega Corporation, Madison, WI, USA) using a pGEM-T Vector System to generate pGEM-T-Ppin7 (Figure 4). The gene for the Penicillium pinophilum GH61A polypeptide inserted in pGEM-T-Ppin7 was confirmed by DNA sequencing using a 3730XL DNA Analyzer. The E. coli T-Ppin7 strain, containing pGEM-T-Ppin7, was deposited with the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM), Braunschweig, Germany, on June 24, 2009 and designated under the DSM accession number 22711. Example 8: Characterization of the Penicillium pinophilum GH61A polypeptide gene
The nucleotide sequence data were examined for quality and all sequences were compared with the assistance of the PHRED / PHRAP software (University of Washington, Seattle, WA, USA).
The nucleotide sequence (SEQ ID NO: 1) and the deduced amino acid sequence (SEQ ID NO: 2) of the genomic sequence of the Penicillium pinophilum GH61A polypeptide are shown in Figures IA and 1B. The genomic fragment encodes a polypeptide of 322 amino acids, interrupted by 1 intron of 52 base pairs (nucleotides of 102 to 153). The% G + C content of full length coding sequence and mature coding sequence are 53.42% and 53.38%, respectively. Using the SignalP software program (Nielsen et al., 1997, Protein Engineering 10: 1-6), a 21-residue signal peptide was predicted. The predicted mature protein contains 301 amino acids with a predicted molecular mass of 32.68 kDa.
A global alignment to the comparative pairs of amino acid sequences was determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, J. Mol. Biol. 48: 443-453) as implemented in the EMBOSS Needle program with opening penalty. 10 range, 0.5 range extension penalty, and the EBLOSUM62 matrix. The alignment showed that the deduced amino acid sequence of the mature polypeptide from the Penicillium pinophilum GH61A polypeptide gene shared 75% identity (excluding the intervals) with the deduced amino acid sequence of a Thermoascus aurantiacus GH61A polypeptide gene (accession number in GeneSeq AUP68836). Example 9: Expression of the Penicillium pinophilum GH61A polypeptide having cellulolytic intensification activity in Aspergillus oryzae
Protoplasts of Aspergillus oryzae HowBlOl (WO 95/35385) were prepared according to the method of Christensen et al., 1988, Bio / Technology 6: 1419-1422 and transformed with three pg of pPpin7. The transformation produced about 50 transformants. Four transformants were isolated on individual Minimum Medium plates.
The four transformants were separately inoculated in 3 ml of YPM medium in a 24-well plate and incubated at 30 ° C with shaking at 150 rpm. After 3 days of incubation, 20 pl of the supernatant from each culture was analyzed by SDS-PAGE using a NUPAGE®NOVEX® 4 Gel 12% Bis-Tris with MES (Invitrogen Corporation, Carlsbad, CA, USA) according to manufacturer's instructions. The resulting gel was stained with INSTANT BLUE® (Expedeon Ltd., Babraham Cambridge, UK). SDS-PAGE showed that most transformants had a larger range of approximately 64 kDa. The expression strain was designated A. oryzae EXP02769.
Slopes of A. oryzae EXP02769 were washed with 10 ml of YPM medium and inoculated in 2 liter flasks each containing 400 ml of YPM medium to generate broth for the characterization of the enzyme. Cultures were harvested on day 3 and filtered using a 0.45 pm membrane of DURAPORE® (Millipore, Bedford, MA, USA). Example 10: Purification of recombinant Penicillium pinophilum GH61A polypeptide having cellulolytic intensification activity
A 1 liter volume of Aspergillus oryzae Exp02769 supernatant was precipitated with ammonium sulfate (80% saturation) and redissolved in 100 ml of 25 mM Bis-Tris buffer at pH 6.0, and then dialyzed against the same buffer and filtered through a 0.45 mm filter; the final volume was 200 ml. The solution was applied to a 40 ml Q SEPAHROSE® Fast Flow column (GE Healthcare, Buckinghamshire, UK) equilibrated in 25 mM Bis-Tris buffer at pH 6.0, and the recombinant GH61A protein was eluted with a gradient of Linear NaCl (0 to 0.25 M). Column fractions were analyzed by SDS-PAGE as described in Example 9. Fractions containing a range of approximately 64 kDa were pooled. Then the combined solution was concentrated by ultrafiltration. Example 11: Concentration and quantification of Penicillium pinophilum GH61A polypeptide having cellulolytic intensification activity
The purified sample from Example 10 was further concentrated using a 10 kDa MWCO Amicon Ultracentrifugal Concentrator (Millipore, Bedford, MA, USA) to approximately 10 times smaller volume. The concentrated filtrate was exchanged in buffer in 20 mM Tris- (hydroxymethyl) aminomethane pH 8.0 and desalted using a BIO-GEL® P-6 desalination column (Bio-Rad Laboratories, Inc., Hercules, CA, USA) pre-equilibrated with 20 ml of 20 mM Tris- (hydroxymethyl) aminomethane pH 8.0 (Sigma Chemical Co., Inc., St. Louis, MO, USA), by adding 3 ml of sample and eluting with 3 ml of the same buffer. The concentrated, desalted Penicillium pinophilum GH61A protein was quantified using a BCA® Microplate Protein Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA) with bovine serum albumin (Pierce, Rockford, IL, USA) as a standard at concentrations between 0 and 0.8 mg per ml. Quantification was performed in triplicate. The purity of the enzyme was confirmed using a gradient of 8 to 16% SDS-PAGE at 200 V for 1 hour, and staining with Coomassie BIO-SAFE® dye (Bio-Rad Laboratories, Inc., Hercules, CA, USA). Example 12: Pre-treatment of maize fodder
Corn fodder was pretreated at the U.S. Department of Energy National Renewable Energy Laboratory (NREL) using diluted sulfuric acid. The following conditions were used for the pre-treatment: 1.4% by weight of sulfuric acid at 165 ° C and 107 psi for 8 minutes. The water-insoluble solids in the pre-treated corn forage contained 57.5% cellulose, 4.6% hemicellulose and 28.4% lignin. Cellulose and hemicellulose were determined by a two-stage sulfuric acid hydrolysis with subsequent analysis of sugars by high performance liquid chromatography using NREL Standard Analytical Procedure # 002. The lignin was determined gravimetrically after hydrolyzing the cellulose and hemicellulose fractions with sulfuric acid using the Standard Analytical Procedure NREL # 003.
The pre-treated corn forage was ground and washed with water before use. The pre-treated and washed maize forage (initial dry weight of 32.35%) was prepared by grinding in a Cosmos ICMG 40 wet multi-utility crusher (EssEmm Corporation, Tamil Nadu, India), and subsequent washing repeatedly with deionized water and separating the supernatant fraction by decantation. The dry weight of the pre-treated milled forage, washed with water was found to be 7.114%. Example 13: Effect of the Penicillium pinophilum GH61A polypeptide having cellulolytic intensification activity on the enzymatic hydrolysis of pre-treated corn forage
The hydrolysis of pretreated corn fodder was conducted using 96-well plates of 2.2 ml deep (Axygen, Union City, CA, USA) containing a total reaction mass of 1 g. Hydrolysis was carried out with 5% total solids of pre-treated, washed corn forage, equivalent to 28.75 mg of cellulose per ml, in 50 mM sodium acetate buffer pH 5.0 containing 1 mM sulfate manganese and a cellulase composition from Trichoderma reesei (CELLUCLAST® supplemented with beta-glycoside from Aspergillus oryzae available from Novozymes A / S, Bagsvaerd, Denmark; the cellulase composition is referred to here in the Examples as “Trichoderma reesei cellulase composition”) to 4 mg per g of cellulose. The GH61A polypeptide from Penicillium pinophilum having cellulolytic intensification activity was added in concentrations between 0 and 93% (w / w) of total protein. The plates were sealed using an ALPS-300® plate heat sealer (Abgene, Epsom, UK) and incubated at 50 ° C for 0 to 168 hours with shaking at 150 rpm. All experiments were carried out in duplicate or triplicate.
At various time points between 24 and 168 hours of incubation, 100 pl aliquots were removed and the degree of hydrolysis was tested by high performance liquid chromatography (HPLC) using the protocol described below. For HPLC analysis, samples were filtered with a 96-well 0.45 pm MULTISCREEN® filter plate (Millipore, Bedford, MA, USA) and the filtrates analyzed for sugar content as described below. Sugar concentrations of samples diluted in 0.005 M H2SO4 were measured using a 4.6 x 250 mm AMINAX® HPX-87H column (Bio-Rad Laboratories, Inc., Hercules, CA, USA) by elution with 0.5% w / w of 5 mM benzoic acid-H2SO4 at a flow rate of 0.6 ml per minute at 65 ° C for 11 minutes, and quantification by the integration of glucose and cellobiose signals from refractive index detection (CHEMSTATION®, AGILENT® 1100 HPLC, Agilent Technologies, Santa Clara, CA, USA) calibrated by pure sugar samples. The resulting equivalents were used to calculate the percentage of cellulose conversion for each reaction. The degree of each hydrolysis was determined as the fraction of total cellulose converted to cellobiose + glucose, and was not corrected for the soluble sugars present in the pre-treated corn forage liquid.
All HPLC data processing was performed using the Kaleidagraph software (Synergy software, Reading, PA, USA). The measured sugar concentrations were adjusted for the appropriate dilution factor. Glucose and cellobiose were chromatographically separated and integrated and their respective concentrations determined independently. However, to calculate the total conversion of glucose and cellobiose the values were combined. Fractional hydrolysis is reported as the overall mass conversion to [glucose + cellobiose] / [total cellulose]. The triplicate data points were averaged and the standard deviation was calculated.
Fractional hydrolysis was plotted as a function of the concentration of the GH61A protein from Penicillium pinophilum and adjusted with a modified saturation-agglutination model using Kaleidagraph. The data as shown in Figure 5 demonstrated the intensification of hydrolysis by the composition of Trichoderma reesei cellulase by the addition of the Penicillium pinophilum polypeptide GH61A having cellulolytic intensification activity. The addition of the GH61A polypeptide from 0 to 93% (w / w) intensified hydrolysis by the cellulase composition of Trichoderma reesei by 23.4 ± 1.6%, from 60.0 ± 1.3% to 73.3 ± 2 , 1% glycan conversion after 3 days of hydrolysis, and intensified hydrolysis by 27.7 +1.9%, from 71.3 ± 1.3% to 99.0 ± 2.3% glycan conversion after 7 days of hydrolysis. Biological Material Deposit
The following Biological Material was deposited under the terms of the Budapest Treaty with the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM), Mascheroder Weg 1 B, D-38124 Braunschweig, Germany, and given the following accession number:
Deposit Access number Deposit DateE. coli (pGEM-T-Ppin7) DSM 22711 June 24, 2009
The strain was deposited under conditions that guarantee that access to the crop will be available pending this patent application to a person determined by the foreign patent laws to be designated for that purpose. The deposit represents a substantially pure culture of the deposited strain. The deposit is available as required by patent laws in countries where the counterparties to the subject application, or their progeny, are deposited. However, it must be understood that the availability of a deposit does not constitute a license to practice the object invention to the detriment of the patent rights guaranteed by government action.
The present invention is further described by the following numbered paragraphs:
[1] An isolated polypeptide having cellulolytic enhancing activity, selected from the group consisting of: (a) a polypeptide having at least 80% sequence identity with the mature polypeptide of SEQ ID NO: 2; (b) a polypeptide encoded by a polynucleotide that hybridizes under high stringency conditions to (i) the sequence encoding mature polypeptide of SEQ ID NO: 1, (ii) the cDNA sequence contained in the sequence encoding mature SEQ ID polypeptide NO: 1, or (iii) the complementary filament of total length of (i) or (ii); (c) a polypeptide encoded by a polynucleotide having at least 80% sequence identity with the sequence encoding mature polypeptide of SEQ ID NO: 1; (d) a variant comprising a replacement, deletion, and / or insertion of one or more (several) amino acids from the mature polypeptide of SEQ ID NO: 2; and (e) a fragment of a polypeptide of (a), (b), (c), or (d) that has cellulolytic enhancing activity.
[2] The polypeptide of paragraph 1, which comprises an amino acid sequence having at least 80% identity with the mature polypeptide of SEQ ID NO: 2.
[3] The polypeptide of paragraph 2, which comprises an amino acid sequence having at least 85% identity with the mature polypeptide of SEQ ID NO: 2.
[4] The polypeptide of paragraph 3, which comprises an amino acid sequence having at least 90% identity with the mature polypeptide of SEQ ID NO: 2.
[5] The polypeptide of paragraph 4, which comprises an amino acid sequence having at least 95% identity with the mature polypeptide of SEQ ID NO: 2.
[6] The polypeptide of paragraph 5, which comprises an amino acid sequence having at least 97% identity with the mature polypeptide of SEQ ID NO: 2.
[7] The polypeptide of paragraph 1, which comprises or consists of an amino acid sequence of SEQ ID NO: 2; or a fragment of it having cellulolytic intensification activity.
[8] The polypeptide of paragraph 7, which comprises or consists of an amino acid sequence of SEQ ID NO: 2.
[9] The polypeptide of paragraph 7, which comprises or consists of the mature polypeptide of SEQ ID NO: 2.
[10] The polypeptide of paragraph 1, which is encoded by a polynucleotide that hybridizes under high stringency conditions to (i) the sequence encoding mature polypeptide of SEQ ID NO: 1, (ii) the cDNA sequence contained in the sequence that encodes mature polypeptide of SEQ ID NO: 1, or (iii) a complementary strand of full length of (i) or (ii).
[11] The polypeptide of paragraph 10, which is encoded by a polynucleotide that hybridizes under very high stringency conditions to (i) the sequence encoding mature polypeptide of SEQ ID NO: 1, (ii) the cDNA sequence contained in the sequence encoding mature polypeptide of SEQ ID NO: 1, or (iii) a full length complementary strand of (i) or (ii).
[12] The polypeptide of paragraph 1, which is encoded by a polynucleotide comprising a nucleotide sequence having at least 80% identity with the sequence encoding mature polypeptide of SEQ ID NO: 1.
[13] The polypeptide of paragraph 12, which is encoded by a polynucleotide comprising a nucleotide sequence having at least 85% identity with the sequence encoding mature polypeptide of SEQ ID NO: 1.
[14] The polypeptide of paragraph 13, which is encoded by a polynucleotide comprising a nucleotide sequence having at least 90% identity with the sequence encoding mature polypeptide of SEQ ID NO: 1.
[15] The polypeptide of paragraph 14, which is encoded by a polynucleotide comprising a nucleotide sequence having at least 95% identity with the sequence encoding mature polypeptide of SEQ ID NO: 1.
[16] The polypeptide of paragraph 15, which is encoded by a polynucleotide comprising a nucleotide sequence having at least 97% identity with the sequence encoding mature polypeptide of SEQ ID NO: 1.
[17] The polypeptide of paragraph 1, which is encoded by a polynucleotide that comprises or consists of a nucleotide sequence of SEQ ID NO: 1; or a subsequence thereof that encodes a fragment having cellulolytic intensification activity.
[18] The polypeptide of paragraph 17, which is encoded by a polynucleotide that comprises or consists of a nucleotide sequence of SEQ ID NO: 1.
[19] The polypeptide of paragraph 17, which is encoded by a polynucleotide that comprises or consists of the sequence encoding mature polypeptide of SEQ ID NO: 1.
[20] The polypeptide of paragraph 1, wherein the polypeptide is a variant comprising a substitution, deletion, and / or insertion of one or more (several) amino acids from the mature polypeptide of SEQ ID NO: 2.
[21] The polypeptide of paragraph 1, which is encoded by the polynucleotide contained in plasmid pGEM-T-Ppin7 which is contained in E. coli DSM 22711.
[22] The polypeptide of any one of paragraphs 1 to 21, wherein the mature polypeptide is formed from amino acids 22 to 322 of SEQ ID NO: 2.
[23] The polypeptide of any one of paragraphs 1 through 22, wherein the sequence encoding mature polypeptide is formed from nucleotides 64 to 1018 of SEQ ID NO: 1.
[24] A composition comprising the polypeptide of any one of paragraphs 1 through 23.
[25] An isolated polynucleotide that encodes the polypeptide in any of paragraphs 1 through 23.
[26] A nucleic acid construct or expression vector that comprises the polynucleotide of paragraph 25 operably linked to one or more (several) control sequences that direct the production of the polypeptide in an expression host.
[27] A recombinant host cell comprising the polynucleotide of paragraph 25 operably linked to one or more control sequences that direct the production of the polypeptide.
[28] A method for producing the polypeptide of any one of paragraphs 1 to 23, comprising: (a) cultivating a cell, which in its wild type produces the polypeptide, under conditions conducive to the production of the polypeptide; and (b) recovering the polypeptide.
[29] A method for producing a polypeptide having cellulolytic intensification activity, which comprises: (a) cultivating the host cell of paragraph 27 under conductive conditions for the production of the polypeptide; and (b) recovering the polypeptide.
[30] A transgenic plant, part of a plant or plant cell transformed with a polynucleotide that encodes the polypeptide in any of paragraphs 1 through 23.
[31] A method for producing a polypeptide having cellulolytic intensification activity, which comprises: (a) cultivating the transgenic plant or paragraph 30 plant cell under conductive conditions for the production of the polypeptide; and (b) recovering the polypeptide.
[32] A method for producing a precursor cell mutant, which comprises inactivating a polynucleotide that encodes the polypeptide in any of paragraphs 1 through 23, which results in the production of the mutant less of the polypeptide than the precursor cell.
[33] A mutant cell produced by the method of paragraph 32.
[34] The mutant cell in paragraph 33, further comprising a gene that encodes a native or heterologous protein.
[35] A method for producing a protein, which comprises: (a) cultivating the mutant cell of paragraphs 33 or 34 under conductive conditions for the production of the protein; and (b) recovering the protein.
[36] A double-stranded inhibitor RNA (dsRNA) molecule comprising a subsequence of the polynucleotide of paragraph 25, where the dsRNA is optionally a siRNA or a miRNA molecule.
[37] The double-stranded inhibitor RNA (dsRNA) molecule of paragraph 36, which is about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplex nucleotides in length .
[38] A method for inhibiting the expression of a polypeptide having cellulolytic enhancing activity in a cell, which comprises administering to the cell or expressing in the cell the paragraph 36 double-stranded inhibitory RNA (dsRNA) molecule.
[39] A cell produced by the method of paragraph 38.
[40] The paragraph 39 cell, which further comprises a gene encoding a native or heterologous protein.
[41] A method for producing a protein, which comprises: (a) cultivating the paragraph 39 or 40 cell under conductive conditions for the production of the protein; and (b) recovering the protein.
[42] An isolated polynucleotide encoding a signal peptide comprising or consisting of amino acids 1 to 21 of SEQ ID NO: 2.
[43] A nucleic acid construct or expression vector comprising a gene encoding a protein operably linked to the polynucleotide of paragraph 42, wherein the gene is foreign to the polynucleotide encoding the signal peptide.
[44] A recombinant host cell comprising the polynucleotide of paragraph 42, where the gene is foreign to the polynucleotide that encodes the signal peptide.
[45] A method for producing a protein, comprising: (a) culturing a recombinant host cell comprising the polynucleotide of paragraph 42, where the gene is foreign to the polynucleotide encoding the signal peptide, under conditions conducive to protein production; and (b) recovering the protein.
[46] A method for degrading or converting a cellulosic material, which comprises: treating the cellulosic material with an enzyme composition in the presence of the polypeptide having cellulolytic enhancing activity in any of paragraphs 1 through 23.
[47] The method of paragraph 46, in which the cellulosic material is pre-treated.
[48] The method of paragraphs 46 or 47, wherein the enzyme composition comprises one or more enzymes selected from the group consisting of a cellulase, a hemicellulase, an expansin, an esterase, a ligninolytic enzyme, an apectinase, a peroxidase, a protease, and a swolenin.
[49] The method of paragraph 48, in which cellulase is one or more enzymes selected from the group consisting of an endoglycanase, a cellobiohydrolase, and a beta-glucosidase.
[50] The method in paragraph 48, in which hemicellulase is one or more enzymes selected from the group consisting of acetylmannan esterase, acetylxylan esterase, arabinanase, arabinofuranosidase, coumaric acid esterase, feruloyl esterase, galactosidase, a glucuronidase, a glucuronoyl esterase, a mannanase, a mannosidase, a xylanoase, and a xylosidase.
[51] The method of any of paragraphs 46 to 50, which further comprises recovering the degraded cellulosic material.
[52] The method of paragraph 51, wherein the degraded cellulosic material is sugar.
[53] The method of paragraph 52, in which sugar is selected from the group consisting of glucose, xylose, mannose, galactose, and arabinose.
[54] A method for producing a fermentation product, which comprises: (a) saccharifying a cellulosic material with an enzyme composition in the presence of the polypeptide having cellulolytic intensification activity of any of paragraphs 1 through 23; (b) fermenting the saccharified cellulosic material with one or more fermenting microorganisms to produce the fermentation product; and (c) recovering the fermentation product from the fermentation.
[55] The method of paragraph 54, in which the cellulosic material is pre-treated.
[56] The method of paragraphs 54 or 55, wherein the enzyme composition comprises one or more enzymes selected from the group consisting of a cellulase, a hemicellulase, an expansin, an esterase, a ligninolytic enzyme, a pectinase, a peroxidase, a protease, and a swolenin.
[57] The method of paragraph 56, in which cellulase is one or more enzymes selected from the group consisting of an endoglycanase, a cellobiohydrolase, and a beta-glucosidase.
[58] The method of paragraph 56, wherein hemicellulase is one or more enzymes selected from the group consisting of an acetylmannan esterase, an acetylxylan esterase, an arabinanase, an arabinofuranosidase, a coumaric acid esterase, a feruloyl esterase, a galactosidase, a glucuronidase, a glucuronoyl esterase, a mannanase, a mannosidase, a xylanoase, and a xylosidase.
[59] The method of any of paragraphs 54 to 58, in which steps (a) and (b) are performed simultaneously in simultaneous saccharification and fermentation.
[60] The method of any of paragraphs 54 to 59, wherein the fermentation product is an alcohol, an organic acid, a ketone, an amino acid, or a gas.
[61] A method of fermenting a cellulosic material, which comprises: fermenting the cellulosic material with one or more fermenting microorganisms, in which the cellulosic material is saccharified with an enzyme composition in the presence of the polypeptide having cellulolytic intensification activity of any of the paragraphs 1 through 23.
[62] The method of paragraph 61, in which the fermentation of the cellulosic material produces a fermentation product.
[63] The method of paragraph 62, which further comprises recovering the fermentation product from fermentation.
[64] The method of any of paragraphs 61 to 63, in which the cellulosic material is pre-treated before saccharification.
[65] The method of any of paragraphs 61 to 64, wherein the enzyme composition comprises one or more enzymes selected from the group consisting of a cellulase, a hemicellulase, an expansin, an esterase, a ligninolytic enzyme, a pectinase , a peroxidase, a protease, and a swolenin.
[66] The method of paragraph 65, in which cellulase is one or more enzymes selected from the group consisting of an endoglycanase, a cellobiohydrolase, and a beta-glucosidase.
[67] The method of paragraph 65, in which hemicellulase is one or more enzymes selected from the group consisting of an acetylmannan esterase, an acetylxylan esterase, an arabinanase, an arabinofuranosidase, a coumaric acid esterase, a feruloyl esterase, a galactosidase, an glucuronidase, a glucuronoyl esterase, a mannanase, a mannosidase, a xylanoase, and a xylosidase.
[68] The method of any of paragraphs 62 to 67, wherein the fermentation product is an alcohol, an organic acid, a ketone, an amino acid, or a gas. The invention described and claimed herein should not be limited in scope by the aspects disclosed herein, since these aspects are intended as illustrations of various aspects of the invention. Any of the equivalent aspects are intended to be within the scope of this invention. In fact, various modifications of the invention in addition to those shown and described herein will become evident to those skilled in the art from the preceding description. Such modifications are also intended to fall within the scope of the attached claims. In the event of conflict, submit disclosure including the definitions they will control.

权利要求:
Claims (10)
[0001]
1. Transgenic microbial host cell, characterized by the fact that it comprises a heterologous polynucleotide encoding a GH61 polypeptide having cellulolytic intensification activity, in which the polynucleotide consists of SEQ ID NO: 1 or its degenerate sequences that encode the same GH61 polypeptide of SEQ ID NO: 2, or osnucleotides 64 to 1018 of SEQ ID NO: 1 or their degenerate sequences that encode the same GH61 polypeptide as amino acids 22 to 322 of SEQ IDNO: 2.
[0002]
2. Method for producing a GH61 polypeptide having cellulolytic intensification activity, characterized by the fact that it comprises: (a) cultivating the transgenic microbial host cell as defined in claim 1 for the production of the GH61 polypeptide; and (b) recovering the GH61 polypeptide.
[0003]
3. Method for producing a precursor cell mutant, characterized by the fact that it comprises disrupting or deleting a polynucleotide consisting of SEQ ID NO: 1 or its degenerate sequences that encode the same GH61 polypeptide of SEQ ID NO: 2, which results in the mutant cell producing less polypeptide than the precursor cell.
[0004]
4. Nucleic acid construction, characterized by the fact that it comprises a gene encoding a protein operably linked to a nucleotide sequence that encodes a signal peptide comprising or consisting of nucleotides 1 to 63 of SEQ ID NO: 1 or its degenerate sequences that encode the same signal polypeptide of amino acids 1 to 21 of SEQ ID NO: 2, where the gene is of another origin to the denucleotide sequence encoding the signal peptide.
[0005]
5. Method for producing a protein, characterized by the fact that it comprises: (a) cultivating a transgenic microbial host cell for the production of the protein, wherein the transgenic microbial host cell comprises the nucleic acid construct as defined in claim 4, and (b) recovering the protein.
[0006]
6. Method for degrading a cellulosic material, characterized by the fact that it comprises: treating the cellulosic material with an enzyme composition comprising the GH61 polypeptide having cellulolytic intensification activity consisting of SEQ ID NO: 2 or amino acids 22 to 322 of SEQ ID NO: 2.
[0007]
Method according to claim 6, characterized by the fact that it further comprises recovering the degraded cellulosic material.
[0008]
8. Method for producing a fermentation product, characterized by the fact that it comprises: (a) saccharifying a cellulosic material with an enzyme composition comprising the GH61 polypeptide having cellulolytic intensifying activity consisting of SEQ ID NO: 2 or amino acids 22 to 322 of SEQ ID NO: 2; (b) fermenting the cellulosic material saccharified with one or more fermenting microorganisms to produce the fermentation product; and (c) recovering the fermentation product from fermentation.
[0009]
9. Nucleic acid construction, characterized by the fact that it comprises a polynucleotide consisting of SEQ ID NO: 1 or its degenerate sequences encoding the same GH61 polypeptide as SEQID NO: 2, or nucleotides 64 to 1018 of SEQ ID NO: 1 or its degenerate sequences which encode the same GH61 polypeptide as amino acids 22 to 322 of SEQ ID NO: 2, operably linked to one or more heterologous control sequences that direct the production of the polypeptide in an expression host.
[0010]
10. Expression vector, characterized in that it comprises the nucleic acid construct as defined in claim 9.

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法律状态:
2019-06-18| B07A| Application suspended after technical examination (opinion) [chapter 7.1 patent gazette]|

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2020-06-09| B09A| Decision: intention to grant [chapter 9.1 patent gazette]|

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2020-11-17| B16A| Patent or certificate of addition of invention granted [chapter 16.1 patent gazette]|Free format text: PRAZO DE VALIDADE: 10 (DEZ) ANOS CONTADOS A PARTIR DE 17/11/2020, OBSERVADAS AS CONDICOES LEGAIS. |

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申请号 | 申请日 | 专利标题

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US22353309P| true| 2009-07-07|2009-07-07|

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US61/223,533|2009-07-07|

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PCT/US2010/041222|WO2011005867A1|2009-07-07|2010-07-07|Polypeptides having cellulolytic enhancing activity activity and polynucleotides encoding same|

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