WO2006012904A1 - Polypeptides of botryosphaeria rhodina - Google Patents

Polypeptides of botryosphaeria rhodina Download PDF

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WO2006012904A1
WO2006012904A1 PCT/DK2005/000519 DK2005000519W WO2006012904A1 WO 2006012904 A1 WO2006012904 A1 WO 2006012904A1 DK 2005000519 W DK2005000519 W DK 2005000519W WO 2006012904 A1 WO2006012904 A1 WO 2006012904A1
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seq
polypeptide
amino acids
nucleotides
identity
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PCT/DK2005/000519
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French (fr)
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WO2006012904B1 (en
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Kirk Matthew Schnorr
Lene Lange
Pernille Uldall Bolvig
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Novozymes A/S
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Priority to US11/573,261 priority Critical patent/US7666649B2/en
Priority to JP2007524180A priority patent/JP2008508868A/en
Priority to AU2005269084A priority patent/AU2005269084B2/en
Priority to EP05763286A priority patent/EP1789556A1/en
Priority to CA2576110A priority patent/CA2576110C/en
Publication of WO2006012904A1 publication Critical patent/WO2006012904A1/en
Publication of WO2006012904B1 publication Critical patent/WO2006012904B1/en
Priority to US12/631,477 priority patent/US8143047B2/en
Priority to US13/368,690 priority patent/US20120171189A1/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
    • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
    • C12Y302/01032—Xylan endo-1,3-beta-xylosidase (3.2.1.32), i.e. endo-1-3-beta-xylanase
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/37—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from fungi
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0012—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7)
    • C12N9/0044—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7) acting on other nitrogen compounds as donors (1.7)
    • C12N9/0046—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7) acting on other nitrogen compounds as donors (1.7) with oxygen as acceptor (1.7.3)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/18—Carboxylic ester hydrolases (3.1.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C12N9/2477—Hemicellulases not provided in a preceding group
    • C12N9/248—Xylanases
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
    • C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
    • C12N9/58—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from fungi
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
    • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
    • C12Y302/01008—Endo-1,4-beta-xylanase (3.2.1.8)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
    • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
    • C12Y302/01021—Beta-glucosidase (3.2.1.21)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
    • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
    • C12Y302/01099—Arabinan endo-1,5-alpha-L-arabinosidase (3.2.1.99)

Definitions

  • TITLE POLYPEPTIDES OF BOTRYOSPHAERIA RHODINA
  • the present invention relates to functional polypeptides encoded by polynucleotides comprised in the mRNA of Diplodia gossypina, syn. Botryospaeria rhodina deposited under deposit ac- cession number CBS 247.96.
  • the invention relates further to the polynucleotides and con ⁇ structs of such polynucleotides encoding such polypeptides or facilitating their expression as well as to method for preparing the polypeptide. Still further the invention relates to composi ⁇ tions comprising the polypeptide and to uses of the polypeptide.
  • Botryosphaeria rhodina (Berk. & M.A.Curtis) Arx, (syn. Diplodia gossypina Cooke).
  • Botryosphaeria rhodina (Berk. & M.A.Curtis) Arx, (syn. Diplodia gossypina Cooke).
  • Very few reports have been published concerning the characterization of this organism; Selbmann et al., 2003 report exopolysaccharide production from Botryosphaeria rhodina (Selbmann L, Stingele F, and Petruccioli M (2003) Exopolysaccharide production by filamentous fungi: the example of Botryosphaeria rhodina. Antonie van Leeuwenhoek, 84:2, pp.135-145.
  • whole genome sequencing is a known method to obtain the information on all genes from a given microorganism e.g. as described in Fleischmann et al.; Whole genome se- quences and assembly of Haemophilus influenzae Rd; Nature 269: 496- 512; (1995).
  • ESTs expressed sequence tags
  • EST approaches suffer two drawbacks with regard to secreted protein identification; 1) Depending on the induction condi ⁇ tions used for the cDNA library sequenced, very few, typically between 0.5%-15% or even 1 and 5% of the cDNAs encode secreted proteins. 2) The clones all come from a cDNA pool de ⁇ rived from mRNAs that are present in the organism in proportion to the induction level of each particular gene.
  • signal trapping is a method to identify genes including nucleotides encoding a signal peptide using a translational fusion to an extracellular reporter gene lacking its own signal (WO 01/77315).
  • the genome of a microorganism contains thousands of different genes; some encoding polypeptides some coding for RNAs. Only a limited number of the genes in the genome of a microorganism encode functional polypeptides which are secreted by the microorganism to the surrounding medium serving an external purpose for the microorganism.
  • polypeptides are interesting for industry from the point of view that such polypep- tides may be produced in considerable amounts in continuous processes without destroying the cells producing the polypeptides.
  • the present invention provides in a first aspect an isolated polypeptide selected from the group consisting of:
  • polypeptide which is encoded by a nucleotide sequence which hybridize under high stringency conditions with a polynucleotide probe selected from the group consisting of (i) the complementary strand to a nucleotide sequence selected from the group of regions of SEQ ID NO: 1 , 3, 5, 7, 9, 11, 13, 15, 17, 19, 21 , 23, 25, 27, 29, 31 ,
  • polypeptide has a function of the corresponding mature polypeptides comprised in the group consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 32, 34, 36, 38, 40 and 42.
  • the invention provides an isolated enzyme selected from the group consisting of:
  • an enzyme comprising an amino acid sequence which has at least 90% identity with the amino acid sequence of a mature enzyme selected from the group consisting of xy- lanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from the strain of Botryosphaeria rhodina deposited under CBS accession No. 247.96
  • polypeptide which is encoded by a nucleotide sequence which hybridize under high stringency conditions with a polynucleotide probe selected from the group consisting of (i) the complementary strand to a nucleotide sequence comprised in the strain of
  • Botryosphaeria rhodina Deposited under CBS accession No. 247.96 encoding a mature enzyme selected from the group consisting of xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from that strain;
  • the enzyme have a function selected from xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta- glucosidase, endo-arabinase and pepsin peptidase.
  • the invention provides a polynucleotide encoding the polypeptide of the invention; a nucleotide construct comprising the polynucleotide encoding the polypeptide, operably linked to one or more control sequences that direct the production of the polypeptide in a host cell; a recombinant expression vector comprising the nucleotide construct of the in- vention and to a recombinant host cell comprising the nucleotide construct of the invention.
  • the invention provides a method of preparing a polypeptide of the invention comprising:
  • the invention provide a composition comprising a polypeptide of the invention and a method for preparing such a composition comprising admixing the poly ⁇ peptide of the invention with an excipient.
  • the invention provides use of the polypeptide of the invention or a composition comprising said polypeptide in various applications.
  • the present application contains information in the form of a sequence listing, which is ap ⁇ pended to the application and also submitted on a data carrier accompanying this application.
  • the contents of the data carrier are fully incorporated herein by reference.
  • the regions of se ⁇ quences selected from the group consisting of SEQ ID NO: 1, 3, 5, 7, 9, 11 , 13, 15, 17, 19, 21 , 23, 25, 27, 29, 31 , 33, 35, 37, 39 and 41 which encode a mature polypeptide encodes the ma ⁇ ture polypeptides of sequences selected from the group consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 32, 34, 36, 38, 40 and 42 respectively.
  • the region of SEQ ID NO: 1 encoding a mature polypeptide thus encodes the mature polypeptide sequence comprised in SEQ ID NO:2, the region of SEQ ID NO:3 encoding a mature polypeptide encode the mature polypeptide comprised in SEQ ID NO:4 and so on.
  • group A DNA as used hereinafter means a group of nucleotide sequences consisting of SEQ ID NO: 1 , 3, 5, 7, 9, 11 , 13, 15, 17, 19, 21 , 23, 25, 27, 29, 31, 33, 35, 37, 39 and 41.
  • group A DNA (or just comprised in or selected from “group A D NA”). it means that the sequence is comprised in or selected from the group of nucleotide se ⁇ quences consisting of SEQ ID NO: 1 , 3, 5, 7, 9, 11 , 13, 15, 17, 19, 21 , 23, 25, 27, 29, 31 , 33, 35, 37, 39 and 41.
  • group E D N A as used hereinafter means a group of nucleotide sequences consisting of SEQ ID NO: 1 , 3, 5, 7, 9, 11 , 13, 15, 17, 33, 35, 37, 39 and 41.
  • group B pO ⁇ ypeptide as used hereinafter means a group of polypep ⁇ tide sequences consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 32, 34, 36, 38, 40 and 42.
  • group Bp o iypepti de or just comprised in or selected from “group Bp O iy P eptide”
  • sequence is comprised in or selected from the group of polypeptide sequences consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 32, 34, 36, 38, 40 and 42.
  • group D P oiyp ep tide means a group of polypep- tide sequences consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 34, 36, 38, 40 and 42.
  • group Dp O ⁇ ype ptide or just comprised in or selected from “group Dpoiyp e p t i d e”
  • group Dpoiyp e p t i d e it means that the sequence is comprised in or selected from the group of polypeptide sequences consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 34, 36, 38, 40 and 42.
  • identity is to be understood as the homology between two amino acid sequences or between two nucleotide sequences.
  • degree of identity is determined by using AlignX in the program of Vector NTI ver. 7.1 (Informax inc., 7600 Wisconsin Avenue, Suite #1100, Bethesda, MD 20814, USA).
  • Amino acid alignment is created using the Clustal W algo ⁇ rithm (Thompson, J. D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sen ⁇ sitivity of progressive multiple sequence alignment through sequence weighting, positions- specific gap penalties and weight matrix choice.
  • Gap opening penalty of 10 Gap extension penalty of 0.05
  • polypeptide as used herein in the context of the present inven- tion means a polypeptide which can be expressed and secreted by a cell and which constitutes an operational unit capable of operating in accordance with the function it is designed to fulfill by the cell.
  • co-factors may be required for the polypeptide to adopt the intended function.
  • functional polypeptides is catalytically active polypeptides or en ⁇ zymes which help the cell catalyzing reactions in the environment surrounding the cell.
  • Another example could be polypeptides which serve as signal substance.
  • polypeptides which function as sensors (receptors) for environmental parameters (chemicals in the environment surrounding the cell) or polypeptides, which are active against other organisms (antimicrobial (poly)peptides) or polypeptides, which contributes to the structural integrity of the cell.
  • matrix region as used herein about portion of an amino acid sequences or polypeptide means the portion or region or domain or section of the amino acid sequences or polypeptide which is the mature functional polypeptide.
  • region of nucleotide sequence encoding a mature polypeptide means the region of a nucleotide sequence counting from the triplet encoding the first amino acid of a mature polypeptide to the last triplet encoding the last amino acid of a mature polypeptide.
  • GH glycosyl hydrolase enzymes made by B. Hen- rissat. The number following the GH each denotes distinct families. This classification system is well known to the skilled person. See Henrissat B., A classification of glycosyl hydrolases based on amino-acid sequence similarities, Biochem. J. 280:309-316 (1991); Henrissat B., Bairoch A, New families in the classification of glycosyl hydrolases based on amino- acid se ⁇ quence similarities, Biochem. J.
  • polypeptides of the invention are all polypeptides secreted by Botryosphaeria rhodina CBS 247.96 with the purpose of serving a function for that particular cell.
  • Botryosphaeria rhodina CBS 247.96 expresses and secretes the func ⁇ tional mature polypeptides comprised in group B P ⁇ iyp ep tide, and in the genome of that particular strain, the regions of sequences of group A DNA , encoding a mature polypeptide are the genes encoding the mature polypeptides comprised in the sequences of group Bp 0 iy p8ptide . Further in a particular embodiment the genes encoding the mature polypeptides comprised in the se ⁇ quences of of group B P oiy P e Pt ide can all be expressed and their corresponding mature polypep ⁇ tides can be secreted when culturing an E.
  • the invention thus provides an isolated polypeptide selected from the group consisting of:
  • polypeptide exhibits the function of the corresponding mature polypeptides of grOUp Bpoiypeptide-
  • the polypeptide of the invention is selected among the enzymes secreted by Botryosphaeria rhodina deposited under CBS accession No. 247.96 and isolated by the present inventors, i.e. the group of enzymes consisting of xylanase, serine es ⁇ terase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase.
  • the group of enzymes consisting of xylanase, serine es ⁇ terase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase.
  • the invention also provides an isolated enzyme selected from the group consisting of: (a) an enzyme comprising an amino acid sequence which has at least 90% identity with the amino acid sequence of a mature enzyme selected from the group consisting of xy- lanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from the strain of Botryosphaeria rhodina Deposited under CBS accession No. 247.96 and
  • polypeptide which is encoded by a nucleotide sequence which hybridize under high stringency conditions with a polynucleotide probe selected from the group consisting of (i) the complementary strand to a nucleotide sequence comprised in the strain of
  • Botryosphaeria rhodina Deposited under CBS accession No. 247.96 encoding a mature enzyme selected from the group consisting of xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from that strain;
  • the enzyme have a function selected from xylanase, serine esterase, peroxidase, GH 61A polypeptide, GH 61 B polypeptide, GH 61C polypeptide, GH 61D polypeptide, beta- glucosidase, endo-arabinase and pepsin peptidase.
  • the polypeptide of the invention is an isolated polypeptide, preferably the preparation of the polypeptide of the invention contains at the most 90% by weight of other polypeptide material with which it may be natively associated (lower percentages of other polypeptide ma ⁇ terial are preferred, e.g. at the most 80% by weight, at the most 60% by weight, at the most 50% by weight, at the most 40% at the most 30% by weight, at the most 20% by weight, at the most 10% by weight, at the most 9% by weight ,at the most 8% by weight, at the most 6% by weight, at the most 5% by weight, at the most 4% at the most 3% by weight, at the most 2% by weight, at the most 1% by weight and at the most > • >% by weight).
  • lower percentages of other polypeptide ma ⁇ terial are preferred, e.g. at the most 80% by weight, at the most 60% by weight, at the most 50% by weight, at the most 40% at the most 30% by weight, at the most 20% by weight,
  • the isolated polypeptide of the invention is at least 92% pure, i.e. that the polypeptide of the inven- tion constitutes at least 92% by weight of the total polypeptide material present in the prepara ⁇ tion, and higher percentages are preferred such as at least 94% pure, at least 95% pure, at least 96% pure, at least 96% pure, at least 97% pure, at least 98% pure, at least 99%, and at the most 99.5% pure.
  • the polypeptide of the invention is in "es ⁇ sentially pure form", i.e. that the polypeptide preparation is essentially free of other polypeptide material with which it is natively associated. This can be accomplished, for example, by prepar ⁇ ing the polypeptide of the invention by means of well-known recombinant methods.
  • polypeptide of the invention of the invention may be synthetically made, naturally occurring or a combination thereof.
  • the polypeptide of the invention may be obtained from a microorganism such as a prokaryotic cell, an archaeal cell or a eu- karyotic cell.
  • the cell may further have been modified by genetic engineering
  • the polypeptide of the invention is an enzyme exhibiting op ⁇ timum enzyme activity at a temperature within the range from about 10 0 C to about 80 0 C, par ⁇ ticularly in the range from about 20 0 C to about 60 0 C.
  • polypeptide of the invention is an enzyme, which is functionally stabile at a temperature of up to 100 0 C, in particular up to 80 0 C, more particularly up to 6O 0 C.
  • the polypeptide of the invention is an enzyme exhibiting at least 20%, in particular at least 40%, such as at least 50%, in particular at least 60%, such as at least 70%, more particularly at least 80%, such as at least 90%, most particularly at least 95%, such as about or at least 100% of the enzyme activity of an enzyme selected from ma ⁇ ture enzymes comprised in group Bp o iypeptide-
  • the polypeptide of the invention comprises, contains or con ⁇ sists of an amino acid sequence which has at least 90% identity with a polypeptide sequence selected from the group consisting of mature polypeptides comprised in group B P oiyp ep tide; par ⁇ ticularly at least 95%, e.g. at least 96%, such as at least 97%, and even more particularly at least 98%, such as at least 99% or even 100% identity.
  • polypeptide of the invention comprises, contains or consists of an amino acid sequence, which has at least 50% identity with a polypeptide se ⁇ quence selected from the group consisting of mature polypeptides comprised in group B P oiy Pe p- ti d ⁇ ; particularly at least 60%, particularly at least 65%, particularly at least 70%, particularly at least 75%, particularly at least 80%, and even more particularly at least 85% identity.
  • the amino acid sequence of the polypeptide of the inven ⁇ tion differs by at the most ten amino acids (e.g. by ten amino acids), in particular by at the most five amino acids (e.g. by five amino acids), such as by at the most four amino acids (e.g. by four amino acids), e.g. by at the most three amino acids (e.g. by three amino acids), in particu- lar by at the most two amino acids (e.g. by two amino acids), such as by one amino acid from the mature polypeptides comprised in group B P ⁇
  • the polypeptide of the invention may be a wild-type polypeptide isolated from a natural source such as the strain Botryosphaeria rhodina CBS 247.96 or another wild type strain, however the present invention also encompass artificial variants, where a polypeptide of the invention has been mutated for example by adding, substituting and/or deleting one or more amino acids from said polypeptide while retaining the function of the polypeptide and/or other properties.
  • polypeptide of the invention may be an artificial variant, wherein at least one substitution, deletion and/or insertion of an amino acid has been made to an amino acid se- quence comprising or consisting of the mature polypeptide comprised in group B P ⁇
  • polypeptides of the invention also include functional fragments of the amino acid sequences described herein and nucleic acids encoding functional fragments of the amino acid sequences described herein, including fragments of the mature enzymes secreted from the strain of Botryosphaeria rhodina Deposited under CBS accession No.
  • 247.96 including fragment of an enzyme selected from the group consisting of xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from the strain of Botryosphaeria rhodina Deposited under CBS accession No. 247.96.
  • an enzyme selected from the group consisting of xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from the strain of Botryosphaeria rhodina Deposited under CBS accession No. 247
  • Artificial variants may be constructed by standard techniques known in the art usually followed by screening and/or characterization.
  • Standard techniques includes classical mutagenesis, e.g. by UV irradiation of the cells or treatment of cells with chemical mutagens as described by Gerhardt et al. (1994); in vivo gene shuffling as described in WO 97/07205; in vitro shuffling as described by Stemmer, (1994) or WO 95/17413, random mutagenesis as de ⁇ scribed by Eisenstadt E. et al., (1994); PCR techniques as described by Poulsen et al. (1991 ); family shuffling as described by J. E. Ness, et al, Nature Biotechnology, vol. 17, pp.
  • Such standard genetic engineering methods may also be used prepare a diversified li ⁇ brary of variant nucleotide sequences from the genes encoding one or more parent enzymes of the invention, expressing the enzyme variants in a suitable host cell and selecting a pre ⁇ ferred variant(s).
  • a diversified library can be established by a range of techniques known to the art (Reetz MT; Jaeger KE 1 in Biocatalysis - from Discovery to Application edited by Fessner WD, Vol. 200, pp. 31-57 (1999); Stemmer, Nature, vol. 370, p.389-391, 1994; Zhao and Ar ⁇ nold, Proc. Natl. Acad. ScL, USA, vol. 94, pp. 7997-8000, 1997; or Yano et al., Proc. Natl. Acad. ScL, USA, vol. 95, pp 5511 -5515, 1998).
  • amino acid changes are of a minor nature, that is conservative amino acid substitu ⁇ tions that do not significantly affect the folding and/or activity of the protein; small deletions, typically of one to about 30 amino acids; small amino- or carboxyl-terminal extensions, such as an amino-terminal methionine residue; a small linker peptide of up to about 20-25 residues; or a small extension that facilitates purification by changing net charge or another function, such as a poly-histidine tract, an antigenic epitope or a binding domain.
  • conservative substitutions are within the group of basic amino acids (ar- ginine, lysine and histidine), acidic amino acids (glutamic acid and aspartic acid), polar amino acids (glutamine and asparagine), hydrophobic amino acids (leucine, isoleucine, valine and methionine), aromatic amino acids (phenylalanine, tryptophan and tyrosine), and small amino acids (glycine, alanine, serine and threonine).
  • Amino acid substitutions which do not generally alter and or impair the function of a protein are known in the art and are described, for exam ⁇ ple, by H. Neurath and R. L. Hill, 1979, In, The Proteins, Academic Press, New York.
  • the most commonly occurring exchanges are Ala/Ser, Val/lle, Asp/Glu, Thr/Ser, Ala/Gly, Ala/Thr, Ser/Asn, Ala/Val, Ser/Gly, Tyr/Phe, Ala/Pro, Lys/Arg, Asp/Asn, Leu/lle, Leu/Val, Ala/Glu, and Asp/Gly as well as these in reverse.
  • the amino acid changes are of such a nature that the phys ⁇ ico-chemical properties of the polypeptides are altered.
  • amino acid changes may be performed, which improve the thermal stability of the enzyme, which alter the substrate specificity, which changes the pH optimum, and the like.
  • the number of such substitutions, deletions and/or insertions in the poly ⁇ peptide of the invention, particularly in those polypeptides selected from the group consisting of mature polypeptides comprised in group Bp O iy P epti de to produce an artificial variant is at the most 10, such as at the most 9, e.g. at the most 8, more preferably at the most 7, e.g. at the most 6, such as at the most 5, most preferably at the most 4, e.g. at the most 3, such as at the most 2, in particular at the most 1.
  • the artificial variant is a variant, which has an altered, pref ⁇ erably reduced, immunogenicity, especially allergenicity, in animals including man as com ⁇ pared to a parent enzyme.
  • immunogenicity in this context is to be understood as the artificial variant capability of invoking a an altered, in particular reduced, immunological re ⁇ sponse when administered to an animal, including intravenous, cutaneous, subcutaneous, oral and intratracheal administration.
  • immunological response in this context means that the administration of the artificial variant causes an alteration in the immunoglobulin levels in the animal body, such as in IgE, IgG and IgM or an alteration in the cytokine level in the animal body.
  • allergenicity in this context is to be understood as the artificial variant ability of invoking an altered, in particular reduced, production of IgE in an animal as well as the ability to bind IgE from said animal.
  • allergenicity arising from intratracheal administration of the polypeptide variant to the animal is particularly of interest (also known as respiratory allergenicity).
  • polypeptide of the invention is a polypeptide which is en ⁇ coded by nucleotide sequences which hybridize under at least high stringency conditions, par- ticularly under very high stringency conditions with a polynucleotide probe selected from the group consisting of
  • polypeptide of the invention is encoded by a polynucleotide comprising a nu ⁇ cleotide sequence selected from the group of regions of group A D NA sequences encoding a mature polypeptide or a sequences differing there from by virtue of the degeneracy of the ge ⁇ netic code. More particularly, the polypeptide of the invention is encoded by a polynucleotide consisting of a nucleotide sequence selected from the group of regions of group ADNA se ⁇ quences encoding a mature polypeptide or a sequence differing there from by virtue of the de ⁇ generacy of the genetic code.
  • nucleotide sequences of regions of group A DNA sequences encoding a mature polypeptide or a subsequence thereof, as well as the amino acid sequences of the mature polypeptides comprised in group Bp O
  • ypeptide or a fragment thereof may be used to design a polynucleotide probe to identify and clone DNA encoding enzymes of the invention from strains of different genera or species according to methods well known in the art.
  • probes can be used for hybridization with the genomic or cDNA of the genus or species of in ⁇ terest, following standard Southern blotting procedures, in order to identify and isolate the cor- responding gene therein.
  • Such probes can be considerably shorter than the entire sequence, but should be at least 15, preferably at least 25, more preferably at least 35 nucleotides in length, such as at least 70 nucleotides in length. It is; however, preferred that the polynucleo ⁇ tide probe is at least 100 nucleotides in length.
  • the polynucleotide probe may be at least 200 nucleotides in length, at least 300 nucleotides in length, at least 400 nucleotides in length or at least 500 nucleotides in length.
  • probes may be used, e.g., polynucleo ⁇ tide probes which are at least 600 nucleotides in length, at least 700 nucleotides in length, at least 800 nucleotides in length, or at least 900 nucleotides in length. Both DNA and RNA probes can be used.
  • the probes are typically labelled for detecting the corresponding gene (for example, with 32 P, 3 H, 35 S, biotin, or avidin).
  • a genomic DNA or cDNA library prepared from such other organisms may be screened for DNA, which hybridizes with the probes described above and which encodes en ⁇ zymes of the invention.
  • Genomic or other DNA from such other organisms may be separated by agarose or polyacrylamide gel electrophoresis, or other separation techniques.
  • DNA from the libraries or the separated DNA may be transferred to, and immobilized, on nitrocellulose or other suitable carrier materials.
  • the carrier material with the immobi ⁇ lized DNA is used in a Southern blot.
  • hybridization indicates that the nucleotide se- quence hybridizes to a labelled polynucleotide probe which again hybridizes to a nucleotide sequence selected from regions of group A D NA sequences encoding a mature polypeptide un ⁇ der high to very high stringency conditions. Molecules to which the polynucleotide probe hy- bridizes under these conditions may be detected using X-ray film or by any other method known in the art. Whenever the term "polynucleotide probe" is used in the present context, it is to be understood that such a probe contains at least 15 nucleotides.
  • the polynucleotide probe is the complementary strand of a nucleotide sequence selected from regions of group A D NA sequences encoding a mature polypeptide.
  • the polynucleotide probe is the complementary strand of a nucleotide sequence which encodes an enzyme selected from group B P oiy P eptide-
  • the polynucleotide probe is the complementary strand of a mature polypeptide coding region of a nucleotide sequence selected from regions of group A D NA sequences encoding a mature polypeptide.
  • high to very high stringency condi ⁇ tions are defined as pre-hybridization and hybridization at 42°C in 5X SSPE, 1.0% SDS, 5X Denhardt's solution, 100 microgram/ml sheared and denatured salmon sperm DNA, following standard Southern blotting procedures.
  • the long probes of at least 100 nucleotides do not contain more than 1000 nucleotides.
  • the carrier material is finally washed three times each for 15 minutes using 0.1 x SSC, 0.1% SDS at 60 0 C (high stringency), in particular washed three times each for 15 minutes us ⁇ ing 0.1 x SSC, 0.1% SDS at 68 0 C (very high stringency).
  • shorter probes e.g. probes which are from about 15 to 99 nucleotides in length, such as from about 15 to about 70 nucleo ⁇ tides in length, may be also be used.
  • stringency conditions are defined as pre-hybridization, hybridization, and washing post-hybridization at 5 0 C to 10°C below the calculated Tm using the calculation according to Bolton and McCarthy (1962, Proceedings of the National Academy of Sciences USA 48:1390) in 0.9 M NaCI, 0.09 M Tris-HCI pH 7.6, 6 mM EDTA, 0.5% NP-40, 1X Denhardt's solution, 1 mM sodium pyrophosphate, 1 mM sodium monobasic phosphate, 0.1 mM ATP, and 0.2 mg of yeast RNA per ml following standard Southern blotting procedures.
  • the carrier material is washed once in 6X SCC plus 0.1% SDS for 15 minutes and twice each for 15 min ⁇ utes using 6X SSC at 5°C to 10°C below the calculated Tm.
  • the polypeptide of the invention is a GH 10 xylanase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a GH10 xylanase obtainable from Botiyosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un ⁇ der deposit accession number CBS 247.96, more particularly the mature GH10 xylanase com ⁇ prised in SEQ ID NO: 2.
  • GH10 xylanase comprise or consists of the sequences from position 1 to 291 of SEQ ID NO: 2.
  • a GH10 xy- lanase is defined as an enzyme beloning to the EC 3.2.1.8 enzyme activity grouping. This grouping endohydrolyses 1 ,4- ⁇ -D-xylosidic linkages in xylans.
  • the glycoside hydrolase family 10 also comprises enzymes with two other known activities; endo-1 ,3-beta-xylanase (EC: 3.2.1.32); cellobiohydrolase (EC: 3.2.1.91).
  • polypeptide of the invention is a GH11 xylanase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a xylanase GH11 obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un- der deposit accession number CBS 247.96, more particularly the mature GH11 xylanase com ⁇ prised in SEQ ID NO: 4.
  • GH11 xylanase comprise or consists of the sequences from position 1 to 202 of SEQ ID NO: 4.
  • a GH11 xy ⁇ lanase is defined as an enzyme beloning to the EC 3.2.1.8 enzyme activity grouping. This grouping endohydrolyses 1 ,4- ⁇ -D-xylosidic linkages in xylans.
  • Glycoside hydrolase family 11 comprises enzymes with only one known activity; xylanase (EC: 3.2.1.8).
  • the polypeptide of the invention is a serine esterase, in particular a cutinase or a lipase or a carboxyesterase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particu- larly at least 97%, more particularly at least 98%, more particularly at least 99% or most par ⁇ ticularly 100% identity with a serine esterase obtainable from Botryosphaeria rhodina, in par ⁇ ticular that strain of Botryosphaeria rhodina deposited under deposit accession number CBS 247.96, more particularly the mature serine esterase comprised in SEQ ID NO: 6.
  • the mature serine esterase comprise or consists of the sequences from position 1 to 352 of SEQ ID NO: 6.
  • a serine esterase is defined as an enzyme capa ⁇ ble of hydrolysing soluble esters in solution (esters which are not in micelle form).
  • the serin esters are enzymes acting as cutinase (EC 3.1.1.50) or lipase (EC.3.1.1.3) or carboxyesterase capable of hydrolysing wax-esters, cutin, tracyl fats, oils and/or fatty acid chains.
  • the serine esterases contain the classical Ser, His, Asp triad of serine hydrolase, such as tri-acyl lipase/cutinase.
  • SEQ ID NO: 8 Candida B type Lipase
  • the polypeptide of the invention is a Candida B type lipase (EC 3.1.1.3) comprising or consisting of an amino acid sequence which has at least 90%, particu ⁇ larly at least 95%, more particularly at least 96%, more particularly at least 97%, more particu- larly at least 98%, more particularly at least 99% or most particularly 100% identity with a Can ⁇ dida B type Lipase obtainable from Botryosphaeria rhodina, in particular that strain of Botryos- phaeria rhodina deposited under deposit accession number CBS 247.96, more particularly the mature Candida B type Lipase comprised in SEQ ID NO: 8.
  • the mature Can ⁇ dida B type Lipase comprise or consists of the sequences from position 1 to 431 of SEQ ID NO: 8.
  • the Candida B type Lipase is defined as an enzyme capable of hydrolysing triglycerides to diacyl glycerides and fatty acid anions, in particular triacylglycerol to diacylglycerol and a fatty acid anion.
  • the polypeptide of the invention is a peroxidase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a peroxidase obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un ⁇ der deposit accession number CBS 247.96, more particularly the mature peroxidase com- prised in SEQ ID NO: 10. More specifically the mature peroxidase comprises or consists of the sequences from position 1 to 185 of SEQ ID NO: 10.
  • peroxidase is defined as an enzyme belonging to defined as a group of enzymes that catalyze oxidation- reduction reactions. As such, they are classified as oxidoreductases. They are given the official EC number 1.11.1. Peroxidases reduce H 2 O 2 to water while oxidizing a variety of substrates. Thus, peroxidases are oxidoreductases which use H 2 O 2 as electron acceptor for catalyzing different oxidative reactions.
  • the polypeptide of the invention is a GH61A polypeptide comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a GH61A polypeptide ob ⁇ tainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina depos ⁇ ited under deposit accession number CBS 247.96, more particularly the mature GH61A poly ⁇ peptide comprised in SEQ ID NO: 12.
  • GH61A polypeptide More specifically the mature GH61A polypeptide com- prises or consists of the sequences from position 1 to 218 of SEQ ID NO: 12.
  • a GH 61A polypeptide is defined as a secreted polypeptide or protein providing one or more of the group of effects selected from:
  • the polypeptide of the invention is a GH 61 B polypeptide compris- ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a GH 61 B polypeptide obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina de ⁇ posited under deposit accession number CBS 247.96, more particularly the mature GH 61 B polypeptide comprised in SEQ ID NO: 14.
  • GH 61 B polypeptide comprises or consists of the sequences from position 1 to 249 of SEQ ID NO: 14.
  • a GH 61 B polypeptide is defined as a secreted polypeptide or protein providing one or more of the group of effects selected from:
  • the polypeptide of the invention is a GH 61 C polypeptide compris- ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a GH 61 C polypeptide obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina de ⁇ posited under deposit accession number CBS 247.96, more particularly the mature GH 61 C polypeptide comprised in SEQ ID NO: 16.
  • the mature GH 61 C polypeptide comprises or consists of the sequences from position 1 to 255 of SEQ ID NO: 16.
  • a GH 61 C polypeptide is defined as a secreted polypeptide or protein providing one or more of the group of effects selected from:
  • the polypeptide of the invention is a GH 61 D polypeptide compris ⁇ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a GH 61 D polypeptide obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina de ⁇ posited under deposit accession number CBS 247.96, more particularly the mature GH 61 D polypeptide comprised in SEQ ID NO: 18.
  • GH 61 D polypeptide comprises or consists of the sequences from position 1 to 205 of SEQ ID NO: 18.
  • a GH 61 C polypeptide is defined as a secreted polypeptide or protein providing one or more of the group of effects selected from:
  • polypeptide of the invention is a functional polypeptide compris ⁇ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 20.
  • the mature functional polypeptide comprises or consists of the sequences from position 1 to 243 of SEQ ID NO: 20.
  • polypeptide of the invention is a functional polypeptide compris ⁇ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 22.
  • the mature functional polypeptide comprises or consists of the sequences from position 1 to 415 Of SEQ ID NO: 22.
  • polypeptide of the invention is a functional polypeptide compris ⁇ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 24.
  • the mature functional polypeptide comprises or consists of the sequences from position 1 to 377 of SEQ ID NO: 24.
  • polypeptide of the invention is a functional polypeptide compris ⁇ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 26.
  • the mature functional polypeptide comprises or consists of the sequences from position 1 to 259 of SEQ ID NO: 26.
  • polypeptide of the invention is a functional polypeptide compris ⁇ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 28.
  • the mature functional polypeptide comprises or consists of the sequences from position 1 to 248 of SEQ ID NO: 28.
  • polypeptide of the invention is a functional polypeptide compris ⁇ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 30.
  • the mature functional polypeptide comprises or consists of the sequences from position 1 to 149 of SEQ ID NO: 30.
  • polypeptide of the invention is a functional polypeptide compris ⁇ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 32.
  • the mature functional polypeptide comprises or consists of the sequences from position 1 to 202 of SEQ ID NO: 32.
  • the polypeptide of the invention is a beta-glucosidase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a beta-glucosidase obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un- der deposit accession number CBS 247.96, more particularly the mature beta-glucosidase comprised in SEQ ID NO: 34.
  • beta-glucosidase comprise or con ⁇ sists of the sequences from position 1 to 603 of SEQ ID NO: 34.
  • the beta-glucosidase is defined as a beta-D-glucoside glucohydrolase (E. C. 3.2.1.21) which cata ⁇ lyzes the hydrolysis of terminal non-reducing beta-D-glucose residues with the release of beta- D-glucose.
  • beta-glucosidase activity is determined ac ⁇ cording to the basic procedure described by Venturi et al., 2002, J. Basic Microbiol. 42: 55-66, except different conditions were employed as described herein.
  • beta-glucosidase activity is defined as 1.0 micromole of p-nitrophenol produced per minute at 50 0 C, pH 5 from 4 mM p-nitrophenyl-beta-D-glucopyranoside as substrate in 100 mM sodium citrate, 0.01% Tween-20.
  • the polypeptide of the invention is a endo-arabinase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a endo-arabinase obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un ⁇ der deposit accession number CBS 247.96, more particularly the mature endo-arabinase com ⁇ prised in SEQ ID NO: 36.
  • the mature endo-arabinase comprises or consists of the sequences from position 1 to 301 of SEQ ID NO: 36.
  • an endo- arabinase is defined as an enzyme capable of hydrolysing arabinan.
  • the polypeptide of the invention is a endo-arabinase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a endo-arabinase obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un ⁇ der deposit accession number CBS 247.96, more particularly the mature endo-arabinase com ⁇ prised in SEQ ID NO: 38. More specifically the mature endo-arabinase comprises or consists of the sequences from position 1 to 438 of SEQ ID NO: 38.
  • an endo- arabinase is defined as an enzyme capable of hydrolysing arabinan.
  • the polypeptide of the invention is a pepsin peptidase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a pepsin peptidase obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un ⁇ der deposit accession number CBS 247.96, more particularly the mature pepsin peptidase comprised in SEQ ID NO: 40.
  • the mature pepsin peptidase comprises or consists of the sequences from position 1 to 396 of SEQ ID NO: 40.
  • a pepsin peptidase is defined as an enzyme capable of hydrolysing proteins or peptides.
  • the polypeptide of the invention is a pepsin peptidase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a pepsin peptidase obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un ⁇ der deposit accession number CBS 247.96, more particularly the mature pepsin peptidase comprised in SEQ ID NO: 42.
  • the mature pepsin peptidase comprises or consists of the sequences from position 1 to 262 of SEQ ID NO: 42.
  • a Pepsin peptidase is defined as an enzyme capable of hydrolysing proteins or peptides.
  • the present invention also relates to polynucleotides comprising or consisting of a nu ⁇ cleotide sequence encoding a polypeptide of the invention.
  • the nu- cleotide sequence is set forth in the sequences of group A D NA including nucleotide sequences differing there from by virtue of the degeneracy of the genetic code.
  • polynucleotide of the invention is a modified nucleotide sequence which comprises or con ⁇ sists of a nucleotide sequence selected from the the regions of group A D NA sequences encod ⁇ ing a mature polypeptide and which comprises at least one modification/mutation compared with the parent nucleotide sequence comprised in the sequences of group A D NA-
  • the techniques used to isolate and/or clone a nucleotide sequence encoding an en ⁇ zyme are known in the art and include isolation from genomic DNA, preparation from cDNA, or a combination thereof.
  • the cloning of the nucleotide sequences of the present invention from such genomic DNA can be effected, e.g., by using the well known polymerase chain reaction (PCR) or antibody screening of expression libraries to detect cloned DNA fragments with shared structural features. See, e.g., lnnis et al., 1990, PCR: A Guide to Methods and Applica ⁇ tion, Academic Press, New York.
  • nucleotide sequence-based amplification may be used.
  • LCR ligase chain reaction
  • LAT ligated activated transcription
  • NASBA nucleotide sequence-based amplification
  • the nucleotide sequence may be obtained by standard cloning procedures used in ge ⁇ netic engineering to relocate the nucleotide sequence from its natural location to a different site where it will be reproduced.
  • the cloning procedures may involve excision and isolation of a desired fragment comprising the nucleotide sequence encoding the polypeptide, insertion of the fragment into a vector molecule, and incorporation of the recombinant vector into a host cell where multiple copies or clones of the nucleotide sequence will be replicated.
  • the nucleo ⁇ tide sequence may be of genomic, cDNA, RNA, semi-synthetic, synthetic origin, or any combinations thereof.
  • the polynucleotide comprises, preferably consists of, a nucleotide se ⁇ quence which has at least 50% identity with a nucleotide sequence selected from the regions of group A DNA sequences encoding a mature polypeptide.
  • the nucleotide sequence has at least 65% identity, more particularly at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with a nucleotide sequence selected from the regions of group ADNA sequences encoding a mature polypeptide.
  • the nucleotide sequence comprises a nucleotide sequence selected from the regions of group A D NA sequences encoding a mature polypeptide.
  • the nucleotide sequence consists of a nucleotide sequence se ⁇ lected from the regions of group ADN A sequences encoding a mature polypeptide.
  • the polynucleotide comprises, preferably consists of, a nucleotide se ⁇ quence encoding a mature enzyme selected from xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta- glucosidase, endo-arabinase and pepsin peptidase and which has at least 50% identity, par ⁇ ticularly at least 65% identity, more particularly at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with a nucleotide sequence encoding a mature enzyme selected from xylanase, serine es ⁇ terase, peroxidase, GH 61
  • the polynucleotide comprises, preferably consists of, a nu ⁇ cleotide sequence encoding a mature enzyme selected from xylanase, serine esterase, per ⁇ oxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase and which has at least 50% identity, particularly at least 65% identity, more particularly at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% iden ⁇ tity, more particularly at least 96% identity, more particularly at least 97% identity, more par ⁇ ticularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with a nucleotide sequence encoding a mature enzyme selected from from group D Po i y- peptide sequences.
  • the polynucleotide comprises, preferably consists of, a nu ⁇ cleotide sequence encoding a mature enzyme selected from xylanase, serine esterase, per ⁇ oxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase and which has at least 50% identity, particularly at least 65% identity, more particularly at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% iden ⁇ tity, more particularly at least 96% identity, more particularly at least 97% identity, more par ⁇ ticularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with a nucleotide sequence selected from E DNA sequences
  • the polynucleotide of the invention encodes a GH 10 xylanase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu ⁇ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 55 to 927 of SEQ ID NO: 1 SEQ ID NO: 3
  • the polynucleotide of the invention encodes a GH11 xylanase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu ⁇ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 58 to 663 of SEQ ID NO: 3
  • the polynucleotide of the invention encodes a serine esterase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu ⁇ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 55 to 1110 of SEQ ID NO: 5
  • the polynucleotide of the invention encodes a lipase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% iden ⁇ tity, more particularly at least 96% identity, more particularly at least 97% identity, more par- ticularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 55 to 1347 of SEQ ID NO: 7.
  • the polynucleotide of the invention encodes a peroxidase and com ⁇ prises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 1 to 555 of SEQ ID NO: 9.
  • the polynucleotide of the invention encodes a GH61A polypeptide and comprises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% iden- 00519 tity, more particularly at least 98% identity, more particularly at least 99% identity or most par ⁇ ticularly 100% identity with the nucleotide sequence of position 49 to 702 of SEQ ID NO: 11.
  • the polynucleotide of the invention encodes a GH 61 B polypeptide and comprises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% iden ⁇ tity, more particularly at least 98% identity, more particularly at least 99% identity or most par ⁇ ticularly 100% identity with the nucleotide sequence of position 40 to 786 of SEQ ID NO: 13.
  • the polynucleotide of the invention encodes a GH 61 C polypeptide and comprises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% iden- tity, more particularly at least 98% identity, more particularly at least 99% identity or most par ⁇ ticularly 100% identity with the nucleotide sequence of position 55 to 819 of SEQ ID NO: 15.
  • the polynucleotide of the invention encodes a GH 61 D polypeptide and comprises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% iden ⁇ tity, more particularly at least 98% identity, more particularly at least 99% identity or most par ⁇ ticularly 100% identity with the nucleotide sequence of position 61 to 675 of SEQ ID NO: 17.
  • the polynucleotide of the invention encodes a mature functional polypeptide and comprises or consists of an nucleotide sequence which has at least 70% iden ⁇ tity, more particularly at least 80% identity, more particularly at least 90% identity, more par ⁇ ticularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 1 to 729 of SEQ ID NO: 19.
  • the polynucleotide of the invention encodes a mature functional polypeptide and comprises or consists of an nucleotide sequence which has at least 70% iden ⁇ tity, more particularly at least 80% identity, more particularly at least 90% identity, more par- ticularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 55 to 1299 of SEQ ID NO: 21.
  • the polynucleotide of the invention encodes a mature functional polypeptide and comprises or consists of an nucleotide sequence which has at least 70% iden ⁇ tity, more particularly at least 80% identity, more particularly at least 90% identity, more par ⁇ ticularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 49 to 1179 of SEQ ID NO: 23.
  • the polynucleotide of the invention encodes a mature functional polypeptide and comprises or consists of an nucleotide sequence which has at least 70% iden- tity, more particularly at least 80% identity, more particularly at least 90% identity, more par ⁇ ticularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 70 to 846 of SEQ ID NO: 25.
  • the polynucleotide of the invention encodes mature functional poly ⁇ peptide and comprises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 58 to 801 of SEQ ID NO: 27. 19
  • the polynucleotide of the invention encodes a mature functional polypeptide and comprises or consists of an nucleotide sequence which has at least 70% iden ⁇ tity, more particularly at least 80% identity, more particularly at least 90% identity, more par- ticularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 157 to 603 of SEQ ID NO: 29.
  • the polynucleotide of the invention encodes a mature functional polypeptide and comprises or consists of an nucleotide sequence which has at least 70% iden ⁇ tity, more particularly at least 80% identity, more particularly at least 90% identity, more par ⁇ ticularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 55 to 660 of SEQ ID NO: 31.
  • the polynucleotide of the invention encodes a beta-glucosidase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu- larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 46 to 1854 of SEQ ID NO: 33.
  • the polynucleotide of the invention encodes a endo-arabinase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu ⁇ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 64 to 966 of SEQ ID NO: 35.
  • the polynucleotide of the invention encodes a endo-arabinase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu ⁇ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 55 to 1368 of SEQ ID NO: 37.
  • the polynucleotide of the invention encodes a pepsin protease and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu ⁇ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 61 to 1248 of SEQ ID NO: 39.
  • the polynucleotide of the invention encodes a pepsin protease and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu ⁇ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 64 to 849 of SEQ ID NO: 41.
  • Modification of a nucleotide sequence encoding a polypeptide of the present invention may be necessary for the synthesis of a polypeptide which comprises an amino acid sequence that has at least one substitution, deletion and/or insertion as compared to an amino acid se ⁇ quence selected from mature polypeptide comprised in group Bp O ⁇ yP eptjde-
  • Amino acid residues which are essential to the function are therefore preferably not sub ⁇ ject to modification, such as substitution.
  • Amino acid residues essential to the function may be identified according to procedures known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (see, e.g., Cunningham and Wells, 1989, Science 244: 1081- 1085).
  • Sites of substrate-enzyme interaction can be determined by analysis of the three- dimensional structure as determined by such techniques as nuclear magnetic resonance analysis, crystallography or photoaffinity labeling (see, e.g., de Vos et a/., 1992, Science 255: 306-312; Smith et a/., 1992, Journal of Molecular Biology 224: 899-904; Wlodaver et al., 1992, FEBS Letters 309: 59-64).
  • nucleotide sequence encoding an enzyme of the invention may be modi- fied by introduction of nucleotide substitutions which do not give rise to another amino acid se- quence of the enzyme encoded by the nucleotide sequence, but which correspond to the codon usage of the host organism intended for production of the enzyme.
  • the introduction of a mutation into the nucleotide sequence to exchange one nucleotide for another nucleotide may be accomplished by site-directed mutagenesis using any of the methods known in the art. Particularly useful is the procedure, which utilizes a super coiled, double stranded DNA vector with an insert of interest and two synthetic primers con ⁇ taining the desired mutation.
  • the oligonucleotide primers, each complementary to opposite strands of the vector, extend during temperature cycling by means of Pfu DNA polymerase. On incorporation of the primers, a mutated plasmid containing staggered nicks is generated.
  • Dpn ⁇ is specific for methylated and hemimethylated DNA to digest the parental DNA template and to select for mutation- containing synthesized DNA.
  • Other procedures known in the art may also be used.
  • nucleotide substitution one may consult with e.g., Ford et al., 1991 , Protein Expression and Purification 2: 95-107.
  • the present invention also relates to a polynucleotide comprising, preferably consisting of, a nucleotide sequence which encodes a polypeptide of the invention and which hybridizes under high stringency conditions, preferably under very high stringency conditions with a polynucleotide probe selected from the group consisting of: (i) the complementary strand to a nucleotide sequence selected from the group consisting of the regions of group A D NA sequences encoding a mature polypeptide,
  • N the complementary strand to the cDNA sequence contained in a nucleotide sequences selected from the group consisting of the regions of group A D N A sequences encoding a mature polypeptide, (iii) a fragment of (i) or (ii) encoding a secreted mature polypeptide having the function of the corresponding mature polypeptides comprised in group Bp o iyp e ptide
  • the present invention also encompasses a storage medium suitable for use in an elec ⁇ tronic device comprising information of the amino acid sequence of polypeptides of the inven- tion or the nucleotide sequences of the polynucleotide of the invention.
  • the storage medium may suitably be a magnetic or optical disk and the electronic device a computing device and the information may in particular be stored on the storage medium in a digital form.
  • the present invention also relates to nucleic acid constructs comprising a nucleotide sequence of the invention operably linked to one or more control sequences that direct the ex- pression of the coding sequence in a suitable host cell under conditions compatible with the control sequences.
  • a nucleotide sequence encoding an enzyme of the invention may be manipulated in a variety of ways to provide for expression of the enzyme. Manipulation of the nucleotide se ⁇ quence prior to its insertion into a vector may be desirable or necessary depending on the ex- pression vector. The techniques for modifying nucleotide sequences utilizing recombinant DNA methods are well known in the art.
  • the control sequence may be an appropriate promoter sequence, a nucleotide se ⁇ quence that is recognized by a host cell for expression of the nucleotide sequence.
  • the pro ⁇ moter sequence contains transcriptional control sequences, which mediate the expression of the polypeptide.
  • the promoter may be any nucleotide sequence which shows transcriptional activity in the host cell of choice including mutant, truncated, and hybrid promoters, and may be obtained from genes encoding extra cellular or intracellular polypeptides either homologous or heterologous to the host cell.
  • suitable promoters for directing the transcription of the nucleic acid con- structs of the present invention are the promoters obtained from the E. coli lac operon, Streptomyces coelicolor agarase gene (dagA), Bacillus subtilis Ie- vansucrase gene (sacB), Bacillus licheniformis alpha-amylase gene ⁇ amyL), Bacillus stearothermophilus maltogenic amylase gene ⁇ amyM), Bacillus amyloliquefaciens alpha- amylase gene (amyQ), Bacillus licheniformis penicillinase gene (jpenP), Bacillus subtilis xylA and xylB genes, and prokaryotic beta-lactamase gene (Villa-Kamaroff et al., 1978, Proceed ⁇ ings of the National Academy of Sciences USA 75: 3727-3731), as well as the tac promoter (
  • promoters obtained from the genes for Aspergillus oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, As ⁇ pergillus niger neutral alpha-amylase, Aspergillus niger acid stable alpha-amylase, Aspergillus niger or Aspergillus awamori glucoamylase (glaA), Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease, Aspergillus oryzae triose phosphate isomerase, Aspergillus nidulans acetamidase
  • useful promoters are obtained from the genes for Saccharomyces cer- evisiae enolase (ENO-1), Saccharomyces cerevisiae galactokinase (GAL1), Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP), and Saccharomyces cerevisiae 3-phosphoglycerate kinase.
  • ENO-1 Saccharomyces cer- evisiae enolase
  • GAL1 Saccharomyces cerevisiae galactokinase
  • ADH2/GAP Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase
  • Saccharomyces cerevisiae 3-phosphoglycerate kinase Other useful promoters for yeast host cells are described by Romanos et al., 1992
  • the control sequence may also be a suitable transcription terminator sequence, a se ⁇ quence recognized by a host cell to terminate transcription.
  • the terminator sequence is oper- ably linked to the 3' terminus of the nucleotide sequence encoding the enzyme. Any termina ⁇ tor which is functional in the host cell of choice may be used in the present invention.
  • Preferred terminators for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans an- thranilate synthase, Aspergillus niger alpha-glucosidase, and Fusarium oxysporum trypsin-like protease.
  • Preferred terminators for yeast host cells are obtained from the genes for Saccharomy ⁇ ces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C (CYC1 ), and Saccharomy ⁇ ces cerevisiae glyceraldehyde-3-phosphate dehydrogenase. Other useful terminators for yeast host cells are described by Romanos et al., 1992, supra.
  • the control sequence may also be a suitable leader sequence, a non-translated region of an mRNA which is important for translation by the host cell.
  • the leader sequence is opera- bly linked to the 5' terminus of the nucleotide sequence encoding the polypeptide. Any leader sequence that is functional in the host cell of choice may be used in the present invention.
  • Preferred leaders for filamentous fungal host cells are obtained from the genes for As- pergillus oryzae TAKA amylase and Aspergillus nidulans triose phosphate isomerase.
  • Suitable leaders for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae 3-phosphoglycerate kinase, Sac ⁇ charomyces cerevisiae alpha-factor, and Saccharomyces cerevisiae alcohol dehydro- genase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP).
  • the control sequence may also be a polyadenylation sequence, a sequence operably linked to the 3' terminus of the nucleotide sequence and which, when transcribed, is recog ⁇ nized by the host cell as a signal to add polyadenosine residues to transcribed mRNA.
  • Any polyadenylation sequence which is functional in the host cell of choice may be used in the present invention.
  • Preferred polyadenylation sequences for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Asper- gillus nidulans anthranilate synthase, Fusarium oxysporum trypsin-like protease, and Aspergillus niger alpha-glucosidase.
  • control sequence may also be a signal peptide coding region that codes for an amino acid sequence linked to the amino terminus of a polypeptide and directs the encoded enzyme into the cell's secretory pathway.
  • the 5' end of the coding sequence of the nucleotide sequence may inherently contain a signal peptide coding region naturally linked in translation reading frame with the segment of the coding region which encodes the secreted enzyme. Al- ternatively, the 5' end of the coding sequence may contain a signal peptide coding region which is foreign to the coding sequence.
  • the foreign signal peptide coding region may be re ⁇ quired where the coding sequence does not naturally contain a signal peptide coding region.
  • the foreign signal peptide coding region may simply replace the natural signal peptide coding region in order to enhance secretion of the enzyme.
  • any signal peptide coding region which directs the expressed enzyme into the secretory pathway of a host cell of choice may be used in the present invention.
  • Effective signal peptide coding regions for bacterial host cells are the signal peptide coding regions obtained from the genes for Bacillus NCIB 11837 maltogenic amylase, Bacillus stearothermophilus alpha-amylase, Bacillus licheniformis subtilisin, Bacillus licheniformis beta- lactamase, Bacillus stearothermophilus neutral proteases (nprT, nprS, nprM), and Bacillus subtilis prsA. Further signal peptides are described by Simonen and Palva, 1993, Microbi ⁇ ological Reviews 57: 109-137.
  • Effective signal peptide coding regions for filamentous fungal host cells are the signal peptide coding regions obtained from the genes for Aspergillus oryzae TAKA amylase, Asper- gillus niger neutral amylase, Aspergillus niger glucoamylase, Rhizomucor miehei aspartic pro ⁇ teinase, Humicola insolens cellulase, and Humicola lanuginosa lipase.
  • Useful signal peptides for yeast host cells are obtained from the genes for Saccharo- myces cerevisiae alpha-factor and Saccharomyces cerevisiae invertase. Other useful signal peptide coding regions are described by Romanos et al., 1992, supra.
  • the control sequence may also be a propeptide coding region that codes for an amino acid sequence positioned at the amino terminus of a enzyme.
  • the resultant polypeptide may be denoted a pro-enzyme or propolypeptide.
  • a propolypeptide is generally inactive and can be converted to a mature active polypeptide by catalytic or autocatalytic cleavage of the propep ⁇ tide from the propolypeptide.
  • the propeptide coding region may be obtained from the genes for Bacillus subtilis alkaline protease (aprE), Bacillus subtilis neutral protease (nprT), Sac ⁇ charomyces cerevisiae alpha-factor, Rhizomucor miehei aspartic proteinase, and My- celiophthora thermophila laccase (WO 95/33836. Where both signal peptide and propeptide regions are present at the amino terminus of a polypeptide, the propeptide region is positioned next to the amino terminus of a polypeptide and the signal peptide region is positioned next to the amino terminus of the propeptide region. In yeast, the ADH2 system or GAL1 system may be used.
  • the TAKA al- pha-amylase promoter In filamentous fungi, the TAKA al- pha-amylase promoter, Aspergillus niger glucoamylase promoter, and Aspergillus oryzae glu- coamylase promoter may be used as regulatory sequences.
  • regulatory sequences are those which allow for gene amplification. In eukaryotic systems, these include the dihydrofolate reductase gene which is amplified in the presence of methotrexate, and the metallothionein genes which are amplified with heavy met- als. In these cases, the nucleotide sequence encoding the polypeptide would be operably linked with the regulatory sequence.
  • the present invention also relates to recombinant expression vectors comprising the nucleic acid construct of the invention.
  • the various nucleotide and control sequences de ⁇ scribed above may be joined together to produce a recombinant expression vector, which may include one or more convenient restriction sites to allow for insertion or substitution of the nu ⁇ cleotide sequence encoding the polypeptide at such sites.
  • the nucleotide se ⁇ quence of the present invention may be expressed by inserting the nucleotide sequence or a nucleic acid construct comprising the sequence into an appropriate vector for expression.
  • the coding sequence is located in the vector so that the coding sequence is operably linked with the appropriate control sequences for expression.
  • the recombinant expression vector may be any vector (e.g., a plasmid or virus) that can be conveniently subjected to recombinant DNA procedures and can bring about the ex- pression of the nucleotide sequence.
  • the choice of the vector will typically depend on the compatibility of the vector with the host cell into which the vector is to be introduced.
  • the vec ⁇ tors may be linear or closed circular plasmids.
  • the vector may be an autonomously replicating vector, i.e., a vector that exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a plasmid, an extrachromosomal element, a minichromosome, or an artificial chromo ⁇ some.
  • an autonomously replicating vector i.e., a vector that exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a plasmid, an extrachromosomal element, a minichromosome, or an artificial chromo ⁇ some.
  • the vector may contain any means for assuring self-replication.
  • the vec ⁇ tor may be one which, when introduced into the host cell, is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated.
  • a single vector or plasmid or two or more vectors or plasmids which together contain the total DNA to be introduced into the genome of the host cell, or a transposon may be used.
  • the vectors of the present invention preferably contain one or more selectable markers that permit easy selection of transformed cells.
  • a selectable marker is a gene the product of which provides for biocide or viral resistance, resistance to heavy metals, prototrophy to auxotrophs, and the like.
  • bacterial selectable markers are the dal genes from Bacillus subtilis or Ba- cillus licheniformis, or markers that confer antibiotic resistance such as ampicillin, kanamycin, chloramphenicol or tetracycline resistance.
  • Suitable markers for yeast host cells are ADE2, HIS3, LEU2, LYS2, MET3, TRP1 , and URA3.
  • Selectable markers for use in a filamentous fungal host cell include, but are not limited to, amdS (acetamidase), argB (ornithine carbamoyl- transferase), bar (phosphinothricin acety transferase) , hygB (hygromycin phosphotransferase), niaD (nitrate reductase), pyrG (orotidine-5'-phosphate decarboxylase), sC (sulfate adenyltrans- ferase), trpC (anthranilate synthase), as well as equivalents thereof.
  • amdS acetamidase
  • argB ornithine carbamoyl- transferase
  • bar phosphinothricin acety transferase
  • hygB hygromycin phosphotransferase
  • niaD nitrate reductase
  • the vectors of the present invention preferably contain an element(s) that permits sta ⁇ ble integration of the vector into the host cell's genome or autonomous replication of the vector in the cell independent of the genome.
  • the vector may rely on the nucleotide se ⁇ quence encoding the polypeptide or any other element of the vector for stable integration of the vector into the genome by homologous or nonhomologous recombination.
  • the vector may contain additional nucleotide sequences for directing integration by homolo ⁇ gous recombination into the genome of the host cell.
  • the additional nucleotide sequences en ⁇ able the vector to be integrated into the host cell genome at a precise location(s) in the chro ⁇ mosome ⁇ ).
  • the integrational elements should preferably contain a sufficient number of nucleotides, such as 100 to 1,500 base pairs, preferably 400 to 1 ,500 base pairs, and most preferably 800 to 1 ,500 base pairs, which are highly homologous with the corresponding target sequence to enhance the probabil ⁇ ity of homologous recombination.
  • the integrational elements may be any sequence that is homologous with the target sequence in the genome of the host cell.
  • the integra- tional elements may be non-encoding or encoding nucleotide sequences.
  • the vector may be integrated into the genome of the host cell by non-homologous recombina ⁇ tion.
  • the vector may further comprise an origin of replication enabling the vector to replicate autonomously in the host cell in question.
  • origins of replication are the origins of replication of plasmids pBR322, pUC19, pACYC177, and pACYC184 permitting replication in E. coli, and pUB110, pE194, pTA1060, and pAM ⁇ i permitting replication in Bacillus.
  • 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.
  • the origin of replication may be one having a mutation which makes its functioning temperature-sensitive in the host cell (see, e.g., Ehrlich, 1978, Proceedings of the National Academy of Sciences USA 75: 1433).
  • More than one copy of a nucleotide sequence of the present invention may be inserted into the host cell to increase production of the gene product.
  • An increase in the copy number of the nucleotide sequence can be obtained by integrating at least one additional copy of the sequence into the host cell genome or by including an amplifiable selectable marker gene with the nucleotide sequence where cells containing amplified copies of the selectable marker gene, and thereby additional copies of the nucleotide sequence, can be selected for by culti ⁇ vating the cells in the presence of the appropriate selectable agent.
  • the present invention also relates to recombinant a host cell comprising the nucleic acid con ⁇ struct of the invention, which are advantageously used in the recombinant production of the polypeptides.
  • a vector comprising a nucleotide sequence of the present invention is intro ⁇ quizd into a host cell so that the vector is maintained as a chromosomal integrant or as a self- replicating extra-chromosomal vector as described earlier.
  • the host cell may be a unicellular microorganism, e.g., a prokaryote or a non- unicellular microorganism, e.g., a eukaryote.
  • Useful unicellular cells are bacterial cells such as gram positive bacteria including, but not limited to, a Bacillus cell, e.g., Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus stearothermophilus, Bacillus subtilis, and Bacillus thuringiensis; or a Streptomyces cell, e.g., Streptomyces lividans or Streptomyces murinus, or gram negative bacteria such as E.
  • the bacterial host cell is a Bacillus lentus, Bacillus licheniformis, Bacillus stearothermophilus, or Bacillus subtilis cell.
  • the Bacillus cell is an alkalophilic Bacillus.
  • the introduction of a vector into a bacteria! host cell may, for instance, be effected by protoplast transformation (see, e.g., Chang and Cohen, 1979, Molecular General Genetics 168: 111-115), using competent cells (see, e.g., Young and Spizizin, 1961 , Journal of Bacteri ⁇ ology 81: 823-829, or Dubnau and Davidoff-Abelson, 1971, Journal of Molecular Biology 56: 209-221), electroporation (see, e.g., Shigekawa and Dower, 1988, Biotechniques 6: 742-751), or conjugation (see, e.g., Koehler and Thorne, 1987, Journal of Bacteriology 169: 5771-5278).
  • protoplast transformation see, e.g., Chang and Cohen, 1979, Molecular General Genetics 168: 111-115
  • competent cells see, e.g., Young and Spizizin, 1961 , Journal of Bacteri ⁇ ology 81:
  • the host cell may be a eukaryote, such as a mammalian, insect, plant, or fungal cell.
  • the host cell is a fungal cell.
  • the fungal host cell is a yeast cell.
  • yeast as used herein includes ascosporogenous yeast (Endomycetales), basidiosporogenous yeast, and yeast belonging to the Fungi lmperfecti (Blastomycetes). Since the classification of yeast may change in the future, for the purposes of this invention, yeast shall be defined as described in Biology and Activities of Yeast (Skinner, F.A., Passmore, S.M., and Davenport, R.R., eds, Soc. App. Bacteriol. Symposium Series No. 9, 1980).
  • the yeast host cell is a Candida, Hansenula,
  • the yeast host cell is a Saccharomyces carlsbergensis, Sac ⁇ charomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii, Saccharomy ⁇ ces kluyveri, Saccharomyces norbensis or Saccharomyces oviformis cell.
  • the yeast host cell is a Kluyveromyces lactis cell.
  • the yeast host cell is a Yarrowia lipolytica cell.
  • the fungal host cell is a filamentous fungal cell.
  • filamentous fungi include all filamentous forms of the subdivision Eumycota and Oomycota (as defined by Hawksworth et al., 1995, supra).
  • the filamentous fungi are characterized by a mycelial wall composed of chitin, cellulose, glucan, chitosan, mannan, and other complex polysaccharides.
  • Vegetative growth is by hyphal elongation and carbon catabolism is obliga- tely aerobic.
  • vegetative growth by yeasts such as Saccharomyces cerevisiae is by budding of a unicellular thallus and carbon catabolism may be fermentative.
  • the filamentous fungal host cell is a cell of a species of, but not limited to, Acremonium, Aspergillus, Fusarium, Humicola, Mucor, My- c ⁇ liophthora, Neurospora, Penicillium, Thielavia, Tolypocladium, or Trichoderma.
  • the filamentous fungal host cell is an Aspergillus awamori, Aspergillus foetidus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger or Aspergillus oryzae cell.
  • the filamentous fungal host cell is a Fusarium bactridioides, Fusarium cerealis, Fusarium crookwellense, Fusarium cul- morum, Fusarium graminearum, Fusarium graminum, Fusarium heterosporum, Fusarium ne- gundi, Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum, Fusarium sporotrich bides, Fusarium sulphureum, Fusarium torulo- sum, Fusarium trichothecioides, or Fusarium venenatum cell.
  • Fusarium bactridioides Fusarium cerealis, Fusarium crookwellense, Fusarium cul- morum, Fusarium graminearum, Fusarium graminum, Fusarium hetero
  • the filamentous fungal parent cell is a Fusarium venenatum (Nirenberg sp. nov.) cell.
  • the filamentous fungal host cell is a Humicola In- solens, Humicola lanuginosa, Mucor miehei, Myceliophthora thermophila, Neurospora crassa, Penicillium purpurogenum, Thielavia terrestris, Trichoderma harzianum, Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma reesei, or Trichoderma viride cell.
  • Fungal cells may be transformed by a process involving protoplast formation, transfor ⁇ mation of the protoplasts, and regeneration of the cell wall in a manner known per se. Suitable procedures for transformation of Aspergillus host cells are described in EP 238 023 and Yelton et al., 1984, Proceedings of the National Academy of Sciences USA 81 : 1470-1474. Suitable methods for transforming Fusarium species are described by Malardier et al., 1989, Gene 78: 147-156 and WO 96/00787. Yeast may be transformed using the procedures described by Becker and Guarente, In Abelson, J.N.
  • the present invention also relates to methods for producing an enzyme of the invention com ⁇ prising (a) cultivating a strain comprising a nucleotide sequence encoding an enzyme of the invention which strain is capable of expressing and secreting the enzyme and (b) recovering the enzyme.
  • the strain is a wild type strain such as the Bofryospae- ria rhodina CBS 247.96, while in another embodiment the strain is a recombinant host cell as described, supra.
  • the cells are cultivated in a nutrient medium suitable for production of the enzyme using methods known in the art.
  • the cell may be cultivated by shake flask cultivation, small-scale or large-scale fermentation (including continu ⁇ ous, batch, fed-batch, or solid state fermentations) in laboratory or industrial fermentors per- formed in a suitable medium and under conditions allowing the polypeptide to be expressed and/or isolated.
  • the cultivation takes place in a suitable nutrient medium comprising carbon and nitrogen sources and inorganic salts, using procedures known in the art.
  • Suitable media are available from commercial suppliers or may be prepared according to published composi ⁇ tions (e.g., in catalogues of the American Type Culture Collection).
  • the enzyme As the enzyme is secreted into the nutrient medium, the enzyme can be recovered directly from the medium.
  • the resulting enzyme may be recovered by methods known in the art.
  • the enzyme may be recovered from the nutrient medium by conventional procedures including, but not limited to, centrifugation, filtration, extraction, spray-drying, evaporation, or precipita ⁇ tion.
  • polypeptides of the present invention may be purified by a variety of procedures known in the art including, but not limited to, chromatography ⁇ e.g., ion exchange, affinity, hydrophobic, chromatofocusing, and size exclusion), electrophoretic procedures (e.g., preparative isoelectric focusing), differential solubility (e.g., ammonium sulfate precipitation), SDS-PAGE, or extrac ⁇ tion (see, e.g., Protein Purification, J.-C. Janson and Lars Ryden, editors, VCH Publishers, New York, 1989).
  • chromatography e.g., ion exchange, affinity, hydrophobic, chromatofocusing, and size exclusion
  • electrophoretic procedures e.g., preparative isoelectric focusing
  • differential solubility e.g., ammonium sulfate precipitation
  • SDS-PAGE or extrac ⁇ tion
  • the present invention also relates to a transgenic plant, plant part, or plant cell that has been transformed with a nucleotide sequence encoding an enzyme of the invention so as to express and produce the enzyme.
  • the plant could be used as host for production of enzyme in recoverable quantities.
  • the enzyme may be recovered from the plant or plant part.
  • the plant or plant part containing the recombinant enzyme may be used as such for improving the quality of a food or feed, e.g., improving nutritional value, palatability, and rheological properties, or to destroy an antinutritive factor.
  • the transgenic plant can be dicotyledonous (a dicot) or monocotyledonous (a monocot).
  • monocot plants are grasses, such as meadow grass (blue grass, Poa), forage grass such as festuca, lolium, temperate grass, such as Agrostis, and cereals, e.g., wheat, oats, rye, barley, rice, sorghum, and maize (corn).
  • dicot plants are tobacco, legumes, such as lupins, potato, sugar beet, pea, bean and soybean, and cruciferous plants (family Brassicaceae), such as cauliflower, rape seed, and the closely related model organism Arabidopsis thaliana.
  • plant parts are stem, callus, leaves, root, fruits, seeds, and tubers. Also specific plant tissues, such as chloroplast, apoplast, mitochondria, vacuole, peroxisomes, and cytoplasm are considered to be a plant part. Furthermore, any plant cell, whatever the tissue origin, is considered to be a plant part.
  • the transgenic plant or plant cell expressing an enzyme of the invention may be constructed in accordance with methods known in the art. Briefly, the plant or plant cell is constructed by incorporating one or more expression constructs encoding an enzyme of the invention into the plant host genome and propagating the resulting modified plant or plant cell into a transgenic plant or plant cell.
  • the expression construct is a nucleic acid construct which comprises a nucleotide sequence encoding an enzyme of the present invention operably linked with appropriate regulatory sequences required for expression of the nucleotide sequence in the plant or plant part of choice.
  • the expression construct may comprise a selectable marker useful for identifying host cells into which the expression construct has been integrated and DNA sequences necessary for introduction of the construct into the plant in question (the latter depends on the DNA introduction method to be used).
  • regulatory sequences such as promoter and terminator sequences and optionally signal or transit sequences
  • the expression of the gene encoding an enzyme of the invention may be constitutive or inducible, or may be developmental, stage or tissue specific, and the gene product may 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.
  • the 35S-CaMV promoter may be used (Franck ef a/., 1980,
  • Organ-specific promoters may be, for example, a promoter from storage sink tissues such as seeds, potato tubers, and fruits (Edwards & Coruzzi, 1990, Ann. Rev. Genet. 24: 275-303), or from metabolic sink tissues such as meristems (Ito et al., 1994, Plant MoI. Biol.
  • a seed specific promoter such as the glutelin, prolamin, globulin, or albumin promoter from rice (Wu et al., 1998, Plant and Cell Physiology 39: 885-889), a Vicia faba promoter from the legumin B4 and the unknown seed protein gene from Vicia faba (Conrad et al., 1998, Journal of Plant Physiology 152: 708-711), a promoter from a seed oil body protein (Chen et al., 1998, Plant and Cell Physiology 39: 935-941), the storage protein napA promoter from Brassica napus, or any other seed specific promoter known in the art, e.g., as described in WO 91/14772.
  • a seed specific promoter such as the glutelin, prolamin, globulin, or albumin promoter from rice (Wu et al., 1998, Plant and Cell Physiology 39: 885-889)
  • the promoter may be a leaf specific promoter such as the rbcs promoter from rice or tomato (Kyozuka et al., 1993, Plant Physiology 102: 991-1000, the chlorella virus adenine methyltransferase gene promoter (Mitra and Higgins, 1994, Plant Molecular Biology 26: 85-93), or the aldP gene promoter from rice (Kagaya et al., 1995, Molecular and General Genetics 248: 668-674), or a wound inducible promoter such as the potato pin2 promoter (Xu et al., 1993, Plant Molecular Biology 22: 573- 588).
  • a promoter enhancer element may also be used to achieve higher expression of the enzyme of the invention in the plant.
  • the promoter enhancer element may be an intron which is placed between the promoter and the nucleotide sequence encoding an enzyme of the present invention.
  • 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 may 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-med ⁇ ated transformation, virus-mediated transformation, microinjection, particle bombardment, biolistic transformation, and electroporation (Gasser et al., 1990, Science 244: 1293; Potrykus, 1990, Bio/Technology
  • Agrobacterium tumefaciens-medlated gene transfer is the method of choice for generating transgenic dicots (for a review, see Hooykas and Schilperoort, 1992, Plant Molecular Biology 19: 15-38). However, it can also be used for transforming monocots, although other transformation methods are generally preferred for these plants.
  • the method of choice for generating transgenic monocots is particle bombardment (microscopic gold or tungsten particles coated with the transforming DNA) of embryonic calli or developing embryos (Christou, 1992, Plant Journal 2: 275-281 ; Shimamoto, 1994, Current Opinion Biotechnology 5: 158-162; Vasil et al., 1992, ⁇ /o/Tec ⁇ no/ogy 10: 667-674).
  • An alternative method for transformation of monocots is based on protoplast transformation as described by Omirulleh et al., 1993, Plant Molecular Biology 21: 415-428.
  • transformants having incorporated therein the expression construct are selected and regenerated into whole plants according to methods well known in the art.
  • the present invention also relates to methods for producing an enzyme of the invention comprising (a) cultivating a transgenic plant or a plant cell comprising a nucleotide sequence encoding an enzyme of the invention under conditions conducive for production of the enzyme and (b) recovering the enzyme.
  • compositions comprising enzyme polypeptides and methods for their preparation
  • the invention provide a composition comprising a polypeptide of the invention and an excipient and a method for preparing such a composition comprising admixing the polypeptide of the invention with an excipient.
  • the polypeptide of the invention is the major (polypeptide) component of the composition, e.g., a mono-component composition.
  • the excipient in this context is to be understood as any auxiliary agent or compound used to for ⁇ mulate the composition and includes solvent, carriers, stabilizers and the like.
  • composition may further comprise one or more additional enzymes, such as an aminopeptidase, amylase, carbohydrase, carboxypeptidase, catalase, cellulase, chitinase, cu- tinase, cyclodextrin glycosyltransferase, deoxyribonuclease, esterase, alpha-galactosidase, beta-galactosidase, glucoamylase, alpha-glucosidase, beta-glucosidase, haloperoxidase, in- vertase, laccase, lipase, mannosidase, oxidase, pectinolytic enzyme, peptidoglutaminase, per- oxidase, phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease, transglutaminase, or xylanase.
  • compositions may be prepared in accordance with methods known in the art and may be in the form of a liquid or a solid composition.
  • the enzyme composition may be formulated using methods known to the art of formulating polypeptides and/or pharmaceutical products, e.g. into coated or uncoated granules or micro-granules.
  • the polypeptide of the invention may thus be provided in the form of a granule, preferably a non- dusting granule, a liquid, in particular a stabilized liquid, a slurry or a protected polypeptide.
  • immobilization of the polypeptide on a solid matrix may be preferred.
  • the polypeptide to be included in the composition may be stabilized in accordance with methods known in the art e.g. by stabilizing the polypeptide in the composition by adding and antioxidant or reducing agent to limit oxidation of the polypeptide or it may be stabilized by adding polymers such as PVP, PVA, PEG or other suitable polymers known to be beneficial to the stability of polypeptides in solid or liquid compositions.
  • the composition of the invention is a detergent composition which, in addition to the polypeptide of the invention, comprises a surfactant and optionally compounds selected from the group consisting of builders such as zeolites, bleaching agents such as percarbonate, bleach enhancers such as TAED or NOBS, suds suppressors, fragrants, etc.
  • the composition of the invention is a feed composition that in addition to the polypeptide of the invention comprises a cereal or grain product.
  • composition of the invention is a food composition such as a baker's flour composition, a brewed product, a fruit juice, an oil or lard product comprising the polypeptide of the invention.
  • composition of the invention is a pulping composition, which in addition to the polypeptide of the invention, comprises pulp.
  • composition of the invention is a biocidal composition, which comprises in addition to the polypeptide of the invention, an oxidoreductase enhancer.
  • the invention provides use of the polypeptides or polynucleotides of the invention or a composition comprising said polypeptides or polynucleotides in various applications, particularly (technical) processes such as processes performed in industry or household, herein under for commercial research purposes.
  • the invention encom- passes a process comprising employing a polypeptide of the invention or a polynucleotide of the invention in a (technical) industrial, research or household process.
  • the polypeptide or the composition of the invention is used for cleaning a cellulosic fabric.
  • polypeptide or the composition of the invention is used to prepare a food or feed additive.
  • polypeptide or the composition of the invention is used for treatment of lignolosic materials and pulp.
  • the polypeptide of the invention may be added to and thus become a component of a detergent composition.
  • the detergent composition of the invention may for example be formulated as a hand or machine laundry detergent composition including a laundry additive composition suitable for pre-treatment of stained fabrics and a rinse added fabric softener composition, or be formu ⁇ lated as a detergent composition for use in general household hard surface cleaning opera ⁇ tions, or be formulated for hand or machine dishwashing operations.
  • the invention provides a detergent additive comprising the poly ⁇ peptide of the invention.
  • the detergent additive as well as the detergent composition may comprise one or more other enzymes such as a protease, a lipase, a cutinase, an amylase, a carbohydrase, a cellulase, a pectinase, a mannanase, an arabinase, a galactanase, a xy- lanase, an oxidase, e.g., a laccase, and/or a peroxidase.
  • the properties of the chosen enzyme(s) should be compatible with the se ⁇ lected detergent, (i.e. pH-optimum, compatibility with other enzymatic and non-enzymatic in ⁇ gredients, etc.), and the enzyme(s) should be present in effective amounts.
  • proteases include those of animal, vegetable or microbial origin. Microbial origin is preferred. Chemically modified or protein engineered mutants are included.
  • the protease may be a serine protease or a metallo protease, preferably an alkaline microbial protease or a trypsin-like protease.
  • alkaline proteases are subtilisins, especially those derived from Bacillus, e.g., subtilisin Novo, subtilisin Carlsberg, subtilisin 309, subtilisin 147 and subtilisin 168 (described in WO 89/06279).
  • trypsin-like proteases are trypsin (e.g. of porcine or bovine origin) and the Fusarium protease described in WO 89/06270 and WO 94/25583.
  • proteases examples include the variants described in WO 92/19729, WO 98/20115, WO 98/20116, and WO 98/34946, especially the variants with the specific position substitutions mentioned therein.
  • Preferred commercially available protease enzymes include Alcalase®, Savinase®, Primase®, Duralase®, Esperase®, and Kannase® (Novozymes A/S), Maxatase®, Maxacal®, Maxapem®, Properase®, Purafect®, Purafect OxP®, FN2®, and FN3® (Genencor Interna ⁇ tional Inc.).
  • Suitable lipases include those of bacterial or fungal origin. Chemically modi ⁇ fied or protein engineered mutants are included. Examples of useful lipases include lipases from Humicola (synonym Thermomyces), e.g. from H. lanuginosa (T. lanuginosus) as de ⁇ scribed in EP 258 068 and EP 305 216 or from H. insolens as described in WO 96/13580, a Pseudomonas lipase, e.g. from P. alcaligenes or P. pseudoalcaligenes (EP 218 272), P. ce ⁇ pacia (EP 331 376), P.
  • lipase variants such as those described in WO 92/05249, WO 94/01541 , EP 407 225, EP 260 105, WO 95/35381 , WO 96/00292, WO 95/30744, WO 94/25578, WO 95/14783, WO 95/22615, WO 97/04079 and WO 97/07202.
  • Preferred commercially available lipase enzymes include LipolaseTM, Lipolase UltraTM and LipexTM (Novozymes AJS).
  • Amylases include those of bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Amylases include, for example, alpha-amylases obtained from Bacillus, e.g. a special strain of B. licheniformis, de- scribed in more detail in GB 1 ,296,839.
  • amylases examples are the variants described in WO 94/02597, WO 94/18314, WO 96/23873, and WO 97/43424, especially the variants with the specific position substitutions mentioned therein.
  • amylases are DuramylTM, TermamylTM, FungamylTM and BANTM (Novozymes A/S), RapidaseTM and PurastarTM (from Genencor International Inc.).
  • Suitable cellulases include those of bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Suitable cellulases include cellulases from the genera Bacillus, Pseudomonas, Humicola, Fusarium, Thielavia, Acremonium, e.g. the fungal cellulases produced from Humicola insolens, Myceliophthora thermophila and Fusarium oxysporum disclosed in US 4,435,307, US 5,648,263, US 5,691 ,178, US 5,776,757 and WO 89/09259.
  • cellulases are the alkaline or neutral cellulases having colour care benefits.
  • Examples of such cellulases are cellulases described in EP 0 495 257, EP 0 531
  • cellulases include Celluzyme®, and Carezyme® (No- vozymes), Clazinase®, and Puradax HA® (Genencor International Inc.), and KAC-500(B) ⁇ (Kao Corporation).
  • Peroxidases/Oxidases include those of plant, bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Examples of useful peroxidases include peroxidases from Coprinus, e.g. from C. cinereus, and variants thereof as those described in WO 93/24618, WO 95/10602, and WO 98/15257.
  • the detergent enzyme(s) may be included in a detergent composition by adding separate additives containing one or more enzymes, or by adding a combined additive com ⁇ prising all of these enzymes.
  • a detergent additive of the invention i.e. a separate additive or a combined additive, can be formulated e.g. as a granule, a liquid, a slurry, etc.
  • Preferred deter ⁇ gent additive formulations are granulates, in particular non-dusting granulates, liquids, in par ⁇ ticular stabilized liquids, or slurries.
  • Non-dusting granulates may be produced, e.g., as disclosed in US 4,106,991 and 4,661 ,452 and may optionally be coated by methods known in the art.
  • waxy coating materials are poly(ethylene oxide) products (polyethyleneglycol, PEG) with mean mo ⁇ lar weights of 1000 to 20000; ethoxylated nonylphenols having from 16 to 50 ethylene oxide units; ethoxylated fatty alcohols in which the alcohol contains from 12 to 20 carbon atoms and in which there are 15 to 80 ethylene oxide units; fatty alcohols; fatty acids; and mono- and di- and triglycerides of fatty acids.
  • Liquid enzyme preparations may, for instance, be stabilized by adding a polyol such as propylene glycol, a sugar or sugar alcohol, lactic acid or boric acid according to established methods.
  • Protected enzymes may be pre- pared according to the method disclosed in EP 238,216.
  • the detergent composition of the invention may be in any convenient form, e.g., a bar, a tablet, a powder, a granule, a paste or a liquid.
  • a liquid detergent may be aqueous, typically containing up to 70 % water and 0-30 % organic solvent, or non-aqueous.
  • the detergent composition comprises one or more surfactants, which may be non-ionic including semi-polar and/or anionic and/or cationic and/or zwitterionic.
  • the surfac ⁇ tants are typically present at a level of from 0.1% to 60% by weight.
  • the detergent When included therein the detergent will usually contain from about 1 % to about 40% of an anionic surfactant such as linear alkylbenzenesulfonate, alpha-olefinsulfonate, alkyl sulfate (fatty alcohol sulfate), alcohol ethoxysulfate, secondary alkanesulfonate, alpha-sulfo fatty acid methyl ester, alkyl- or alkenylsuccinic acid or soap.
  • an anionic surfactant such as linear alkylbenzenesulfonate, alpha-olefinsulfonate, alkyl sulfate (fatty alcohol sulfate), alcohol ethoxysulfate, secondary alkanesulfonate, alpha-sulfo fatty acid methyl ester, alkyl- or alkenylsuccinic acid or soap.
  • the detergent When included therein the detergent will usually contain from about 0.2% to about 40% of a non-ionic surfactant such as alcohol ethoxylate, nonylphenol ethoxylate, alkyl- polyglycoside, alkyldimethylamineoxide, ethoxylated fatty acid monoethanolamide, fatty acid monoethanolamide, polyhydroxy alkyl fatty acid amide, or N-acyl N-alkyl derivatives of gluco ⁇ samine (“glucamides").
  • a non-ionic surfactant such as alcohol ethoxylate, nonylphenol ethoxylate, alkyl- polyglycoside, alkyldimethylamineoxide, ethoxylated fatty acid monoethanolamide, fatty acid monoethanolamide, polyhydroxy alkyl fatty acid amide, or N-acyl N-alkyl derivatives of gluco ⁇ samine (“glucamides”).
  • the detergent may contain 0-65 % of a detergent builder or complexing agent such as zeolite, diphosphate, triphosphate, phosphonate, carbonate, citrate, nitrilotriacetic acid, ethylenediaminetetraacetic acid, diethylenetriaminepentaacetic acid, alkyl- or alkenylsuc- cinic acid, soluble silicates or layered silicates (e.g. SKS-6 from Hoechst).
  • a detergent builder or complexing agent such as zeolite, diphosphate, triphosphate, phosphonate, carbonate, citrate, nitrilotriacetic acid, ethylenediaminetetraacetic acid, diethylenetriaminepentaacetic acid, alkyl- or alkenylsuc- cinic acid, soluble silicates or layered silicates (e.g. SKS-6 from Hoechst).
  • the detergent may comprise one or more polymers.
  • examples are carboxy- methylcellulose, poly(vinylpyrrolidone), poly (ethylene glycol), polyvinyl alcohol), poly(vinylpyridine-N-oxide), poly(vinylimidazole), polycarboxylates such as polyacrylates, maleic/acrylic acid copolymers and lauryl methacrylate/acrylic acid copolymers.
  • the detergent may contain a bleaching system which may comprise a H2O2 source such as perborate or percarbonate which may be combined with a peracid-forming bleach activator such as tetraacetylethylenediamine or nonanoyloxybenzenesulfonate.
  • a bleaching system may comprise peroxyacids of e.g. the amide, imide, or sulfone type.
  • the enzyme(s) of the detergent composition of the invention may be stabilized using conventional stabilizing agents, e.g., a polyol such as propylene glycol or glycerol, a sugar or sugar alcohol, lactic acid, boric acid, or a boric acid derivative, e.g., an aromatic bo- rate ester, or a phenyl boronic acid derivative such as 4-formylphenyl boronic acid, and the composition may be formulated as described in e.g. WO 92/19709 and WO 92/19708.
  • a polyol such as propylene glycol or glycerol
  • a sugar or sugar alcohol lactic acid, boric acid, or a boric acid derivative, e.g., an aromatic bo- rate ester, or a phenyl boronic acid derivative such as 4-formylphenyl boronic acid
  • the detergent may also contain other conventional detergent ingredients such as e.g. fabric conditioners including clays, foam boosters, suds suppressors, anti-corrosion agents, soil-suspending agents, anti-soil redeposition agents, dyes, bactericides, optical bright- eners, hydrotropes, tarnish inhibitors, or perfumes.
  • fabric conditioners including clays, foam boosters, suds suppressors, anti-corrosion agents, soil-suspending agents, anti-soil redeposition agents, dyes, bactericides, optical bright- eners, hydrotropes, tarnish inhibitors, or perfumes.
  • any enzyme in particular the enzyme of the invention, may be added in an amount corresponding to 0.01-100 mg of enzyme protein per litre of wash liquor, preferably 0.05-5 mg of enzyme protein per liter of wash liquor, in particular 0.1-1 mg of enzyme protein per litre of wash liquor.
  • the enzyme of the invention may additionally be incorporated in the detergent formulations disclosed in WO 97/07202 that is hereby incorporated as reference.
  • An enzyme activity profile was obtained by assaying the culture broth on a wide spectrum of enzyme assays.
  • 96 wells microtitre (MT) plates were prepared with substrates and stored at + 10°C until use.
  • Two different pH variaties were prepared: pH3 and pH7. Following substrates were used: 0.05% AZCL (Mazurine dyed and cross-linked substrates, Megazyme) - Amylose, Arabinan, Beta Glucan (Barley), Casein, Collagen, Curdlan, Dextran, Galactan (potato), Galactomannan (Carob), He-Cellulose, Pullulan, Xylan (oat), and Xyloglucan (AZCL-casein could not be used at pH3, and was therefore left out from these plates).
  • Preparation ofpH3 substrates 0.1 g of each AZCL substrate was dissolved in 100 ml 0.2M Succinic acid pH3 + 10 microlitres TritonX-100 (0.01%), to give a final concentration of 0,1% AZCL.
  • each AZCL substrate was dissolved in 50 ml sterile H20 plus 10 microlitres TritonX- 100 (0.01%). 50 ml 0.4M MOPS pH 7 was added to each 50 ml AZCL substrate, to give a final volume of 100 ml and a final concentration of 0.2M buffer, 0,1% AZCL.
  • Laccase and lipase activity assays were included and substrates were prepared as follows: Preparation ofLaccase substrate:
  • a polyvinyl alcohol (PVA)/soy bean oil emulsion was prepared by mixing a 2% PVA solution with soy bean oil 3:1.
  • the oil was emulsified using ULTRA-TURRAX mixer and 12 ml of the emulsion was mixed with 500 ml 0.2M sodium-acetate buffer including 1OmM CaCI 2 pH 5.5 and 5 ml 0.2% Crystal Violet solution.
  • cDNA library construction cDNA from Botryosphaeria rhodina CBS 247.96 was prepared by using standard molecular biology techniques (Ausuble et al. 1995 "Current protocols in molecular biology” Publ.:John Wiley and sons).
  • Fermentation of the biomass used in the cDNA library production was initiated from an inocu ⁇ lated PDA plate that had been incubated for 7 days at 28 degrees.
  • Several mycelia-PDA agar plugs were inoculated in shake flasks with Mex1 media containing (per litre): 20 g of soy bean, 15 g of wheat bran, 10 g of cellulose Avicel, 5 g of maltodextrin 01 , 3 g of bacto peptone, 0.2 g of pluronic PE6100, and 1 gram Olive oil.
  • the flasks were shaken at 150 RPM at 26 degrees. After 7 days the mycelium was harvested by filtration through Miracloth and frozen in liquid ni ⁇ trogen and stored at -80 0 C until use.
  • RNA isolation The total RNA was prepared from frozen, powdered mycelium of Botryospaeria rhodina by extraction with guanidium thiocyanate followed by ultracentrifugation though a 5.7M CsCI cushion (Chirgwin, J. M., Przbyla, A.E., Macdonlad, RJ. , and Ruttwer W.J., Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease, Biochemistry 18, 5294-5299, 1979).
  • the polyA enriched RNA was isolated by oligo (dT)-cellulose affinity chro- matography (Aviv, H., and Leder, P., Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose, Proc. Natl. Acad. Sci. USA 69 (6), 1408- 1412, 1972).
  • Double stranded cDNA was synthesized according to the general methods of Gubler U. and Hoffman, B.J., A simple and very efficient method for gen- erating cDNA libraries, Gene 25(2-3), 263-269, (1983); Sambrook, J., Fritsch, E.F., and Mani- antis, T. Molecular cloning: A laboratory Manual, 2 nd ed., 1989, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York and Kofod et al. (1994) using a polyA-Not1 primer (Promega, USA).
  • the cDNA was treated with mung bean nuclease, blunt ended with T4 DNA polymerase, and ligated to a 50 fold molar excess of EcoRI adaptors (Invitrogen, USA).
  • the cDNA was cleaved with Notl restriction enzyme (New England Biolabs, USA) according to the manufacturer's instructions and the cDNA size fractionated by agarose gel electrophoresis.
  • cDNA corresponding to 700bp and larger were excised from the gel and purified using the GFX DNA isolation kit (AP Biotech). The prepared cDNA was then directionally cloned by liga- tion into EcoRI-Notl cleaved pMHas ⁇ .
  • the ligation mixture was electroporated into DH 1OB cells (Invitrogen) and plated on LB agar with 50mgs/liter kanamycin.
  • a cDNA plasmid pool was prepared from 30,000 total transformants of the original cDNA-pMHas5 vector ligation.
  • Plasmid DNA was prepared directly from a pool of colonies recovered from solid LB kanamycin selec ⁇ tive media according to the Qiagen protocol for plasmid DNA isolation (Qiagen Inc. GMBH).
  • Vector used for cloning was pMhas ⁇ , which is described in patent WO 03/044049 and has the following features:
  • This plasmid Notable features of this plasmid are the EcoRI-Notl restriction sites proximal to the Shine DaI- garno region of the Lac promoter. This allows EcoRI-Notl adapted cDNAs to be cloned into the vector and the resulting constructs to be actively transcribed and translated in the E. coli host.
  • TAST Transposon Assisted Signal Trapping
  • a SigA4 transposon containing the ⁇ -lactamase reporter gene Following the instructions of WO 01/77315 A1, the construction of a transposon containing a signal-less ⁇ -lactamase gene was carried out using standard molecular biology techniques.
  • the signal-less ⁇ -lactamase gene was initially PCR amplified from the vector pUC19) using a proofreading polymerase (Pfu Turbo, Stratagene, USA).
  • the resulting PCR fragment con ⁇ tained the restriction sites Not ⁇ and EcoRI in order to aid cloning.
  • the plasmid pEntrancepo- son(Cam r ) containing the Entranceposon and the antibiotic resistance markers CAT was obtained from Finnzymes, OY (Espoo Finland).
  • the plasmid was digested with the restriction enzymes Not ⁇ and EcoRI, gel purified and ligated with the signal-less ⁇ -lactamase containing fragment.
  • the ligation was transformed into electro-competent DH 1OB cells and the E.coli clone containing the recombinant plasmid with the signal-less ⁇ -lactamase was identified by restriction analysis and named SigA2.
  • SigA2NotU-P 5'- TCG CGA TCC GTT TTC GCA TTT ATC GTG AAA CGC T-3' (SEQ ID NO: 43) and SigA2NotD-P 5'-CCG CAA ACG CTG GTG AAA GTA AAA GAT GCT GAA-3' (SEQ ID NO: 44), which bind to the start and stop of the bla gene of SigA2 directing outwards were used PCR amplify SigA2 without the bla gene.
  • 3.6 kb generated in the this PCR reaction was relegated and transformed in to a suitable E.coli strain.
  • a plasmid of 3.6 kb was isolated from a transformant which was able to grow on LB chloramphenicol but not on LB ampicillin. This plasmid maintained both BgIII sites and lacks the active bla gene and was called pSig4.
  • Apali CAM a plasmid of 3.6 kb generated in the this PCR reaction was relegated and transformed in to a suitable E.coli strain.
  • a plasmid of 3.6 kb was isolated from a transformant which was able to grow on LB chloramphenicol but not on LB ampicillin. This plasmid maintained both BgIII sites and lacks the active bla gene and was called pSig4.
  • Apali CAM Apali CAM
  • SigA2 transposon DNA band of 2 kb was eluted and purified by using the "GFXTMPCR, DNA and Gel Band Purification Kit” (Amer- sham Pharmacia Biotech Inc.USA) according to the instructions of the vendor and eluted in 200 microlitres EB buffer.
  • SigA2 prepared in this manner could be be used for transposon as- sisted signal trapping (TAST vide infra).
  • the transposon prepared from pSigA4 carries a 5'-truncated bla-gene encoding a ⁇ -lactamase from which the secretion signal was removed.
  • the ⁇ -lactamase conveys ampicillin resistance on E.coli only when the protein is secreted to the periplasm, whereas cytoplasmic expression of ⁇ -lactamase does not confer ampicillin resistance. Without a signal sequence, the ⁇ - lactamase enzyme will not be transported to the periplasm and therefore the clone will not grow on media containing ampicillin.
  • the signal-less ⁇ -lactamase gene was contained within the transposon in such a way that there was a continuous open reading frame between the transposon border and the ⁇ -lactamase coding region.
  • the modified transposon when it transposes into a gene encoding a protein that is secreted, could cause an in-frame fusion with the target gene. This resulted in a fusion gene product that is secreted to the perip ⁇ lasm of E. coli and conveys resistance to the ampicillin. If the transposon integrated even in- frame into a gene encoding a non-secreted protein, the respective host will not become am ⁇ picillin resistance.
  • transposon assisted signal trapping can be found in WO 01/77315.
  • a cDNA plasmid pool was prepared from 30,000 total transformants of the original cDNA-pMHas5 vector ligation. Plasmid DNA was prepared directly from a pool of colonies re- covered from solid LB selective media according to the Qiagen protocol for plasmid DNA isola ⁇ tion (Qiagen Inc.). The plasmid pool was treated with transposon SigA2 and MuA transposase according to the transposase manufacturer's instructions (Finnizyme, Finland).
  • the DNA was precipitated by addition of 5 microlitres 3M Na- acetate pH 5 and 110 microlitres 96% ethanol and centrifugation for 30 min at 20000 rpm. The pellet was washed and dried and resuspended in 10 microlitres TE buffer.
  • Primer A AGCGT TTGCG GCCGC GATCC (SEQ ID NO: 45)
  • Primer B TTATT CGGTC GAAAA GGATC C (SEQ ID NO: 46)
  • DNA sequence was obtained for the reactions on an AB3700 capillary sequencer. Sequences were trimmed to remove vector and transposon sequence and the A and B primer reads for each plasmid. This resulted in 225 assembled sequences which were grouped into 148 contigs by using the program PhredPhrap (Brent Ewing, LaDeana Hillier, Michael C. Wendl, and Phil Green; Base-calling of automated sequencer traces using phred I. Accuracy assessment; Ge ⁇ nome Research; 8:175-185; 1998; Brent Ewing and Phil Green; Base-calling of automated se- quencer traces using phred II. Error probabilities; Genome Research 8:186-194; 1998).
  • sonication buffer 100 mM Tris-HCI, 2 mM EDTA, pH 8.0
  • Table IX ⁇ -lactamase activity of clones with different distances between the Shine DaI- garno (SD) sequence and the ATG translation initiation codon and transposon landing site.
  • Beta-lactamase activity can be detected in all ten clones. It should be emphasized that cor- responding plasmid containing E. coli transformants are resistant to 50 mg/liter ampicillin se ⁇ lection. Combining these two facts, indicates that all ten clones produce an hybrid protein consisting of part of the transposon tagged cDNA fused to the beta lactamase gene in such a manner as to provide an peptide with beta lactamase activity.
  • untranslated upstream (5' UTR) leaders can vary in length from 1 bp to several hundred base pairs.
  • an optimal distance of between 4 and 11 base pairs before the ATG start codon is optimal.
  • 5'UTRs much longer than optimal still allow for some expression of the cDNA hybrid-beta lactamase fusion protein because beta lactamase activity is observed from the transformed E.coli in the example.
  • the obtained nucleotide sequences of the invention are functional genes which encode intact and functional polypeptides, not only for the reasons above, but because they were ob- tained from ampicillin resistant clone.
  • the clones obtained herein were ampicillin resistant, be ⁇ cause after transposon tagging, the genes were fused with the signalless beta-lactamase gene, which is only expressed when fused to a gene with an intact promoter and ribosome- binding site, which can be recognized in the host strain, and translated and transported across the cytoplasm membrane and folded correctly. Therefore is could be concluded that the genes of the invention actually do encode ac ⁇ tive secreted polypeptides.
  • For the 16 genes sequence analysis revealed that in-frame fusion with the signalless beta-lactamase gene was obtained.
  • the intactness of the genes ' open reading frame was confirmed by determining the entire nucleotide sequence.
  • the function of a gene or the encoded polypeptide can be predicted by sequences comparison with genes or polypeptides of known function. Similarities between group A DNA and group B pO ⁇ y- pept i de sequences and sequences from public and internal databases were analysed, to deter ⁇ mine the functionality of the group A DNA and group Bpoiyp e ptide sequences. The sequence com- parison was carried out using the program BLASTX 2.0a19MP-WashU [14-Jul-1998]. A careful manual analysis of sequence alignments of group A D NA and group B P oiy P eptide sequences to their closest related sequences with known function made it possible to predict the function of these genes and the encoded polypeptides.
  • nidulans amdS gene as selection marker in Aspergillus
  • yeast URA3 gene interrupted by the ampicillin resistance gene for selection in E. coli
  • the following primers were used in the PCR reaction:
  • Primer #166 CGCGGATCCACCATGGTCTCCTTCAAGTCGATTC (SEQ ID NO: 47)
  • Primer #167 CCGCTCGAGTTACTGCACGGTAATCGTAGC (SEQ ID NO: 47)
  • coli DH10B or TOP10 could be used as cloning hosts in construction of the ex ⁇ pression vector) and plated on LB ampicillin media. Ten transformants were selected for plas- mid DNA purification and were sequenced to confirm the sequence integrity of the insert. One PCR error free clone pPFJo147 was selected for further studies.
  • Aspergillus oryzae strain BECh2 which was constructed as described in WO 00/39322 (BECh2 is derived from strain Aspergillus oryzae JaL228, which is constructed on the basis of the deposited strain Aspergillus oryzae IFO 4177 as described in WO 98/12300). Transformation and culture conditions were performed according to Christiansen et al., 1988, Biotechnology 6, 1419-1422 and as described in WO 01/12794-A page 63. After one round of reisolation, 10 ml YPglucose or YPmaltose medium in Nunc tubes were inoculated with spores from the transformants and the cultures were inoculated for 3 days at 30°C.
  • the culture fluid or a cell lysate of a host strain synthesising and secreting a xylanase in a suitable buffer is used for measuring the activity.
  • a suitable volume of such a sample is spotted on agarose plates which contain the insoluble chromogenic substrate AZCL-Birch xylan (Megazyme TM) and a suitable buffer at pH, e.g. pH is 4.5-7.5.
  • the plate is incubated for an appropriate time, e.g. one day, at an appropriate temperature, e.g. 37DC.
  • the activity is visible as blue halos around the spots.
  • Example 5 Determining peroxidase activity
  • Peroxidase can be determined spectrophotmetricly using the 2,4 dichlorophenol method of lshida et al., 1987: Ishida, A., N. Futamura, and T. Matsusaka. 1987. Detection of peroxidase activity and its localisation in the forespore envelopes of Bacillus cereus. J. Gen. Appl. Micro- biol. 33:27-32.
  • a mixture of 1.0 mM 2,4 Dichlorophenol and 82 mM 4- aminoantipyrene in 10OmM potassium phosphate buffer (pH 7.0) can be used while a sub ⁇ strate of hydrogen peroxide (Sigma), 5OmM in 10OmM potassium phosphate buffer (pH7.0) is suitable.
  • 200 microlitre of appropriately diluted culture fluid supernatant is added to a 1 ml plastic cuvette.
  • 200 microlitre of the indicator mixture is added. Reactions are initiated by the addition of 200 microlitre hydrogen peroxide substrate. Changes in absorbance are observed in a stan ⁇ dard spectorophotometer measuring at a wavelength of 510 nm.
  • Example 6 Determining cellulose degradation boosting effect on cellulose degrading enzymes or enzyme mixtures
  • secreted proteins demonstrate synergistic action in degradation of cellose in the pres ⁇ ence of cellulose degrading enzymes or mixtures thereof. Such secreted proteins may or may not have, in themselves, hydrolase activity. Examples of such secreted proteins and how one detects their cellulose degradation boosting effect can be found in patent application no. US 11/046,124 and corresponding PCT application PCT/US2005/003525 published 30-07-2005, in particular using the examples 24 and anyone from examples 25 to 28, hereby incorporated by reference.
  • Corn stover is pretreated at the U.S. Department of Energy National Renewable Energy Laboratory (NREL) using dilute sulfuric acid. The following conditions are used for the pretreatment: 1.4 wt % sulfuric acid at 165 0 C and 107 psi for 8 minutes.
  • NREL National Renewable Energy Laboratory
  • the water-insoluble solids in the pretreated corn stover (PCS) contain 56.5% cellulose, 4.6% hemicellulose and 28.4% lignin.
  • Cellulose and hemicellulose are determined by a two-stage sulfuric acid hydrolysis with subsequent analysis of sugars by high performance liquid chromatography using NREL Standard Analytical Procedure #002.
  • Lignin is determined gravimetrically after hydrolyzing the cellulose and hemicellulose fractions with sulfuric acid using NREL Standard Analytical Procedure #003.
  • the PCS Prior to enzymatic hydrolysis, the PCS is ished with a large volume of DDI water on a glass filter; finding the dry weight of the water- ished PCS.
  • Milled PCS is prepared from the water-ished PCS by milling in a coffee-grinder and subsequent ishing with deionized water on a 22 ⁇ m Millipore Filter (6P Express Membrane, Stericup, Millipore, Bedford, MA).
  • a 90 ⁇ l aliquot of an appropriately diluted sample is placed in a 96 well conical bottomed microplate. Reactions are initiated by adding 60 ⁇ l of 1.5% (w/v) PHBAH in 2% NaOH to each well. Plates are heated uncovered at 95 0 C for 10 minutes. Plates are allowed to cool to room temperature (RT) and 50 ⁇ l of distilled H 2 O added to each well. A 100 ⁇ l aliquot from each well is transferred to a flat bottomed 96 well plate and the absorbance at A ⁇ o nm measured using a SpectraMax Microplate Reader (Molecular Devices, Sunnyvale, CA).
  • Glucose standards (0.1-0.0125 mg/ml diluted with 0.4% sodium hydroxide) are used to prepare a standard curve to translate the obtained A 410n , ! values into glucose equivalents. The resultant equivalents are used to calculate the percentage of PCS cellulose conversion for each reaction.
  • RS is the concentration of reducing sugar in solution measured in glucose equivalents (mg/ml)
  • the factor 1.111 reflects the weight gain in converting cellulose to glucose.
  • the culture fluid or a cell lysate of a host strain synthesising and secreting a lipase in a suit ⁇ able buffer is used for measuring the activity.
  • Lipase assay 20 microlitres of dilution buffer is pipetted into each well of a 96 well microtiter plate. 5 microlitres of sample (supernatant) is added to the dilution buffer. At the start of the assay 200 microlitres of substrate is added to each well and the plate is mounted into an ELISA reader (a programmable spectrophotometer that can read 96 well plates). Absorbance is measured at 405 nm every 30 seconds for 10 minutes. The slope of the time vs. abs 405 curve is used as an arbitrary activity unit.
  • Dilution buffer 25 ml 2M Tris/HCl pH 7.5, 0.50 ml 2M CaCI2, 2.5 ml 15% Brij 35, H2O ad 500 ml.
  • Substrate stock solution 0.1295 g (117 microlitres)
  • p-Nitrophenyl valerate SIGMA N 4377 (density 1.11 g/ml) is dissolved in 10 ml methanol.
  • Store in freezer Substrate: IOOmicrolitres substrate stock solution is mixed with 10 ml dilution buffer.
  • Example 8 Determining protease and peptidase activity
  • the culture fluid or a cell lysate of a host strain synthesising and secreting a peptidase and/or protease, in a suitable buffer having a pH chosen for optimal activity of the peptidase may be assayed for that activity by spotting a suitable sample volume (for example 20 microliter) on an agarose plate which contain the insoluble chromogenic substrate AZCL-casein (Megazyme TM) or AZCL-collagen (Megazyme TM) OR Azocoll (Sigma-Aldrich) - e.g at a level of 0.1% w/w. The plate is incubated for an appropriate time, e.g.
  • non-labelled casein or non-labelled collagene can be used. On non-labelled collagen or non-labelled casein spotted on agarose plates, clearing zones form in the presence of peptidase and/or protease.
  • the culture fluid or a cell lysate of a host strain synthesising and secreting an arabinase in a suitable buffer having a pH chosen for optimal activity of the arabinase may be assayed for that activity by spotting a suitable sample volume (for example 20 microliter) on an agarose plate which contain the insoluble chromogenic substrate AZCL-arabinan - e.g at a level of 0.1% w/w.
  • the plate is incubated for an appropriate time, e.g. one day, at a temperature suit ⁇ able for the function of the arabinase, e.g. 37°C.
  • the activity is visible as blue halos around the spots.
  • the assay may be performed at different pH.
  • the AZCL-arabinan may be pre ⁇ pared by dissolving 0.1 g of AZCL arabinan (Mazurine dyed and cross-linked substrate, Megazyme, Ireland) in 100 ml 0.2M Succinic acid pH3 + 10 microlitres TritonX-100 (0.01%), to give a final concentration of 0,1% AZCL.
  • the AZCL-arabinan may be prepared by dissolving 0.1 g of AZCL arabinan (Mazurine dyed and cross-linked substrate, Megazyme, Ire- land) in 50 ml sterile H 2 O plus 10 microlitres TritonX-100 (0.01%). 50 ml 0.4M MOPS pH 7 is then added to the 50 ml AZCL substrate, to give a final volume of 100 ml and a final concentra ⁇ tion of 0.2M buffer, 0.1% AZCL.
  • Example 10 Determining beta-glucosidase activity Many betaglucosidases are likely to have at least some activity on 4-nitrophenyl ⁇ -D- glucopyranoside or cellobiose even though that may not be their natural substrates. Activity may also be found using methyl-umbiliferyl beta-D-glucoside which is very sensitive. Generally any (1 ,4)- ⁇ - and (1 ,3)- ⁇ -oligoglucosides can be used as substrate to assess activity of beta- glucosidase by measuring released glucose by using the Trinder assay (The Sigma Diagnos- tic Glucose (Trinder) Assay, Sigma, St. Louis, MO).
  • beta-glucosidase activity is to make a preparation of the culture fluid or a cell lysate of a host strain synthesising and secreting a beta-glucosidase so that the preparation contains approximately 6.9 X 10 "6 mg/ml of total protein, 100 mM sodium citrate pH 5.0, 0.01% Tween-20 and 4 mM p-nitrophenyl-beta-D-glucopyranoside.
  • the preparation is in ⁇ cubated at 50 0 C and aliquots are taken at 0.5, 1 , 2, 3, 3.75, and 24 hours. To each aliquot is added 1 M sodium carbonate pH 10.0, and the p-nitrophenyl anion concentration is determined from the absorbance at 405 nm.
  • beta-glucosidase Another way of determining beta-glucosidase is make a preparation of the culture fluid or a cell lysate of a host strain synthesising and secreting a beta-glucosidase by first desalting (BioRad Econo-Pac 10DG column) and then concentrating (Centricon Plus-20, Biomax-5, 5 kD cut-off), to a concentration of 0.92 mg/ml (BCA assay). Then the preparation is incubated at 0.037 and 0.0092 ⁇ g/ml total protein with 10 mM cellobiose in 100 mM sodium citrate pH 5.0 plus 0.01% Tween-20 at 65 0 C. Aliquots are taken at 0.5, 1 , 2, 3, 4, 6, and 19 hours. Aliquots are boiled 6 minutes to terminate the reaction, and the glucose concentration is determined using the Trinder assay (Sigma Chemical Co., St. Louis, MO) and external glucose standards.
  • Trinder assay Sigma Chemical Co
  • the culture fluid or a cell lysate of a host strain synthesising and secreting an esterase in a suitable buffer is used for measuring the activity.
  • a substrate for detecting ac- tivity of the serine esterase one should preferably choose one which does not form micelles at the concentrations at which the esterase is saturated with substrate, to gain optimal conversion of substrate.
  • esterase activity is to measure the hydrolysis of triacetin in a concentration below CMC for triacetin by the enzyme, by the alkali consumption registered as a function of time under standard conditions such as 30.0 0 C; pH 7.0. Hydrolysis of triacetin by esterase will liberate acetic acid which will requires addition of alkali to maintain a a constant pH of 7.0 (pH- stat method) thus the amount of alkali (usually in the form of sodium hydroxide) required to maintain the pH at 7.0 is a measure of triacetin ester bonds hydrolysed.
  • Another way of testing esterase activity is to measure the hydrolysis by the esterase of PNP- acetat (para-nitrophenyl-acetate) releasing the coloured PNP.
  • 20 microlitres of dilution buffer is pipetted into each well of a 96 well microtiter plate.
  • 5 microlitres of sample (culture fluid super ⁇ natant or filtered cell lysate) is added to the dilution buffer.
  • ELISA reader a pro- grammable spectrophotometer that can read 96 well plates.
  • Absorbance is measured at 405 nm every 30 seconds for 10 minutes. The slope of the time vs. abs 4 os curve is used as an arbi ⁇ trary activity unit.
  • Dilution buffer 25 ml 2M Tris/HCI pH 7.5, 0.50 ml 2M CaCI 2 , 2.5 ml 15% Brij 35, H 2 O ad 500 ml.
  • Substrate stock solution a suitable amount of p-Nitrophenyl acetate (analytical grade) is dis ⁇ solved in 10 ml methanol and stored in a freezer
  • Substrate 100 microlitres substrate stock solution is mixed with 10 ml dilution buffer.

Abstract

The invention relates to functional polypeptides secreted from Botryospaeria rhodina CBS 247.96.

Description

TITLE: POLYPEPTIDES OF BOTRYOSPHAERIA RHODINA
FIELD OF THE INVENTION
The present invention relates to functional polypeptides encoded by polynucleotides comprised in the mRNA of Diplodia gossypina, syn. Botryospaeria rhodina deposited under deposit ac- cession number CBS 247.96. The invention relates further to the polynucleotides and con¬ structs of such polynucleotides encoding such polypeptides or facilitating their expression as well as to method for preparing the polypeptide. Still further the invention relates to composi¬ tions comprising the polypeptide and to uses of the polypeptide.
BACKGROUND OF THE INVENTION Botryosphaeria rhodina (Berk. & M.A.Curtis) Arx, (syn. Diplodia gossypina Cooke). Very few reports have been published concerning the characterization of this organism; Selbmann et al., 2003 report exopolysaccharide production from Botryosphaeria rhodina (Selbmann L, Stingele F, and Petruccioli M (2003) Exopolysaccharide production by filamentous fungi: the example of Botryosphaeria rhodina. Antonie van Leeuwenhoek, 84:2, pp.135-145. A single patent ex- ists on the use of Botryosphaeria rhodina to hydroxylate beta Damascone as a flavouring agent for tobacco (CH654567-A). Jasmonic acid can also be produced by fermenting the or¬ ganism (EP1118672-A). The presence of cellobiohydrolases (WO 03/000941 -A2) and lactase (WO 01/49878-A) have been previously reported.
In the pursuit of novel enzymes it is also known to screen for such new enzymes by subjecting potential candidates to specific enzyme assays. This approach is limited to the availability of enzyme assays and does not allow the identification of functional enzymes or polypeptides for which the activity is still unknown.
Further, whole genome sequencing is a known method to obtain the information on all genes from a given microorganism e.g. as described in Fleischmann et al.; Whole genome se- quences and assembly of Haemophilus influenzae Rd; Nature 269: 496- 512; (1995).
Most enzymes for industrial use are enzymes which are secreted to the medium by a microorganism. However, only a few percent of a microorganisms' genome encodes secreted proteins. For example only approx. 4% of the Bacillus subtilis genome or its closest relatives encode secreted proteins (Van Dijl et al.: Protein transport pathways in Bacillus subtilis: a ge- nome-based road map; in "Basillus subtilis and it's closest relatives" - From genes to cells; p.337-355; A. L. Sonenshein (ed.); ASM Press 2002).
One disadvantage of genome sequencing is that the vast majority of the obtained se¬ quences encode non secreted proteins. An additional disadvantage of gemomic sequencing particular to eukaryotes such as fungi is that the genome size is many times larger than a bacterial genome making gene dis¬ covery by this method more costly and time consuming.
The random sequencing of cDNAs (Expressed sequence tags or ESTs) is another ap- proach that allows for discovery of secreted proteins. In general, EST approaches suffer two drawbacks with regard to secreted protein identification; 1) Depending on the induction condi¬ tions used for the cDNA library sequenced, very few, typically between 0.5%-15% or even 1 and 5% of the cDNAs encode secreted proteins. 2) The clones all come from a cDNA pool de¬ rived from mRNAs that are present in the organism in proportion to the induction level of each particular gene.
Also known is signal trapping which is a method to identify genes including nucleotides encoding a signal peptide using a translational fusion to an extracellular reporter gene lacking its own signal (WO 01/77315).
SUMMARY OF THE INVENTION The genome of a microorganism contains thousands of different genes; some encoding polypeptides some coding for RNAs. Only a limited number of the genes in the genome of a microorganism encode functional polypeptides which are secreted by the microorganism to the surrounding medium serving an external purpose for the microorganism.
Such polypeptides are interesting for industry from the point of view that such polypep- tides may be produced in considerable amounts in continuous processes without destroying the cells producing the polypeptides.
It is an object of the present invention to identify and provide polypeptides secreted from Botryosphaeria rhodina deposited under deposit accession number CBS 247.96 which have functional purpose for the Botryosphaeria rhodina because such polypeptides may not only be used for industrial purposes but they may also be produced in industrially relevant processes and amounts.
The present invention provides in a first aspect an isolated polypeptide selected from the group consisting of:
(a) a polypeptide comprising an amino acid sequence which has at least 90% identity with a sequence of a mature polypeptide comprised in the group consisting of SEQ ID NO:
2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 32, 34, 36, 38, 40 and 42; and
(b) a polypeptide which is encoded by a nucleotide sequence which hybridize under high stringency conditions with a polynucleotide probe selected from the group consisting of (i) the complementary strand to a nucleotide sequence selected from the group of regions of SEQ ID NO: 1 , 3, 5, 7, 9, 11, 13, 15, 17, 19, 21 , 23, 25, 27, 29, 31 ,
33, 35, 37, 39 and 41 encoding a mature polypeptide. (ii) the complementary strand to the cDNA sequence contained in a nucleotide se¬ quences selected from the group of regions of SEQ ID NO: 1, 3, 5, 7, 9, 11 , 13, 15, 17, 19, 21 , 23, 25, 27, 29, 31 , 33, 35, 37, 39 and 41 encoding a mature polypeptide
wherein the polypeptide has a function of the corresponding mature polypeptides comprised in the group consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 32, 34, 36, 38, 40 and 42.
In a further aspect the invention provides an isolated enzyme selected from the group consisting of:
(a) an enzyme comprising an amino acid sequence which has at least 90% identity with the amino acid sequence of a mature enzyme selected from the group consisting of xy- lanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from the strain of Botryosphaeria rhodina deposited under CBS accession No. 247.96
(b) a polypeptide which is encoded by a nucleotide sequence which hybridize under high stringency conditions with a polynucleotide probe selected from the group consisting of (i) the complementary strand to a nucleotide sequence comprised in the strain of
Botryosphaeria rhodina Deposited under CBS accession No. 247.96 encoding a mature enzyme selected from the group consisting of xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from that strain;
ii) the complementary strand to the cDNA sequence contained in a nucleotide se¬ quences comprised in the strain of Botryosphaeria rhodina Deposited under CBS accession No. 247.96 encoding a mature enzyme selected from the group consisting of xylanase, serine esterase, peroxidase, GH 61A polypeptide, GH
61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from that strain;
wherein the enzyme have a function selected from xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta- glucosidase, endo-arabinase and pepsin peptidase. In further aspects the invention provides a polynucleotide encoding the polypeptide of the invention; a nucleotide construct comprising the polynucleotide encoding the polypeptide, operably linked to one or more control sequences that direct the production of the polypeptide in a host cell; a recombinant expression vector comprising the nucleotide construct of the in- vention and to a recombinant host cell comprising the nucleotide construct of the invention.
In still further aspects the invention provides a method of preparing a polypeptide of the invention comprising:
(a) cultivating a strain comprising a nucleotide sequence encoding a polypeptide of the in¬ vention which strain is capable of expressing and secreting the polypeptide and (b) recovering the polypeptide.
In still further aspects the invention provide a composition comprising a polypeptide of the invention and a method for preparing such a composition comprising admixing the poly¬ peptide of the invention with an excipient. In still further aspects the invention provides use of the polypeptide of the invention or a composition comprising said polypeptide in various applications.
SEQUENCE LISTING
The present application contains information in the form of a sequence listing, which is ap¬ pended to the application and also submitted on a data carrier accompanying this application. The contents of the data carrier are fully incorporated herein by reference. The regions of se¬ quences selected from the group consisting of SEQ ID NO: 1, 3, 5, 7, 9, 11 , 13, 15, 17, 19, 21 , 23, 25, 27, 29, 31 , 33, 35, 37, 39 and 41 which encode a mature polypeptide, encodes the ma¬ ture polypeptides of sequences selected from the group consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 32, 34, 36, 38, 40 and 42 respectively. The region of SEQ ID NO: 1 encoding a mature polypeptide thus encodes the mature polypeptide sequence comprised in SEQ ID NO:2, the region of SEQ ID NO:3 encoding a mature polypeptide encode the mature polypeptide comprised in SEQ ID NO:4 and so on.
BRIEF DESCRIPTION OF DRAWINGS
No drawings.
DETAILED DESCRIPTION OF THE INVENTION
Definitions
The term "group ADNA" as used hereinafter means a group of nucleotide sequences consisting of SEQ ID NO: 1 , 3, 5, 7, 9, 11 , 13, 15, 17, 19, 21 , 23, 25, 27, 29, 31, 33, 35, 37, 39 and 41. Hence when referral is made to a nucleotide sequence comprised in or selected from group of sequences consisiting of "group ADNA "(or just comprised in or selected from "group ADNA"). it means that the sequence is comprised in or selected from the group of nucleotide se¬ quences consisting of SEQ ID NO: 1 , 3, 5, 7, 9, 11 , 13, 15, 17, 19, 21 , 23, 25, 27, 29, 31 , 33, 35, 37, 39 and 41.
The term "group EDNA" as used hereinafter means a group of nucleotide sequences consisting of SEQ ID NO: 1 , 3, 5, 7, 9, 11 , 13, 15, 17, 33, 35, 37, 39 and 41. Hence when re¬ ferral is made to a nucleotide sequence comprised in or selected from group of sequences consisiting of "group EDNA "(or just comprised in or selected from "group EDNA"), it means that the sequence is comprised in or selected from the group of nucleotide sequences consisting of SEQ ID NO: 1, 3, 5, 7, 9, 11 , 13, 15, 17, 33, 35, 37, 39 and 41.
Like wise the term "group BpOιypeptide" as used hereinafter means a group of polypep¬ tide sequences consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 32, 34, 36, 38, 40 and 42. Hence when referral is made to a polypetide sequence comprised in or selected from the group of sequences consisiting of "group Bpoiypeptide" (or just comprised in or selected from "group BpOiyPeptide") it means that the sequence is comprised in or selected from the group of polypeptide sequences consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30 32, 34, 36, 38, 40 and 42.
Like wise the term "group DPoiypeptide" as used hereinafter means a group of polypep- tide sequences consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 34, 36, 38, 40 and 42. Hence when referral is made to a polypetide sequence comprised in or selected from the group of sequences consisiting of "group DpOιypeptide" (or just comprised in or selected from "group Dpoiypeptide") it means that the sequence is comprised in or selected from the group of polypeptide sequences consisting of SEQ ID NO: 2, 4, 6, 8, 10, 12, 14, 16, 18, 34, 36, 38, 40 and 42.
The term "identity" as used herein, is to be understood as the homology between two amino acid sequences or between two nucleotide sequences. For purposes of the present in¬ vention, the degree of identity between two amino acid sequences is determined by using AlignX in the program of Vector NTI ver. 7.1 (Informax inc., 7600 Wisconsin Avenue, Suite #1100, Bethesda, MD 20814, USA). Amino acid alignment is created using the Clustal W algo¬ rithm (Thompson, J. D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sen¬ sitivity of progressive multiple sequence alignment through sequence weighting, positions- specific gap penalties and weight matrix choice. Nucleic Acids Research, 22:4673-4680). The following additional parameters are used: Gap opening penalty of 10, Gap extension penalty of 0.05, Gap separation penalty range of 8. Pain/vise alignment parameters were Ktuple = 1, gap penalty = 3, gap length opening penalty = 10, gap extension penalty = 0.1 , window size = 5 and diagonals = 5. The degree of identity between two nucleotide sequences is determined using the same algorithm and software package as described above for example with the fol¬ lowing settings: Gap penalty of 10, and gap length penalty of 10. Pairwise alignment parame¬ ters is Ktuple=3, gap penalty=3 and windows=20.
The term "functional polypeptide" as used herein in the context of the present inven- tion means a polypeptide which can be expressed and secreted by a cell and which constitutes an operational unit capable of operating in accordance with the function it is designed to fulfill by the cell. Optionally, co-factors may be required for the polypeptide to adopt the intended function. One example of functional polypeptides is catalytically active polypeptides or en¬ zymes which help the cell catalyzing reactions in the environment surrounding the cell. Another example could be polypeptides which serve as signal substance. Further examples are polypeptides which function as sensors (receptors) for environmental parameters (chemicals in the environment surrounding the cell) or polypeptides, which are active against other organisms (antimicrobial (poly)peptides) or polypeptides, which contributes to the structural integrity of the cell. The term "mature region" as used herein about portion of an amino acid sequences or polypeptide means the portion or region or domain or section of the amino acid sequences or polypeptide which is the mature functional polypeptide.
The term "region of nucleotide sequence encoding a mature polypeptide" as used herein means the region of a nucleotide sequence counting from the triplet encoding the first amino acid of a mature polypeptide to the last triplet encoding the last amino acid of a mature polypeptide.
The term "GH" as used about certain enzymes of the present invention, as for exam¬ ple "GH10", is a family classification system for glycosyl hydrolase enzymes made by B. Hen- rissat. The number following the GH each denotes distinct families. This classification system is well known to the skilled person. See Henrissat B., A classification of glycosyl hydrolases based on amino-acid sequence similarities, Biochem. J. 280:309-316 (1991); Henrissat B., Bairoch A, New families in the classification of glycosyl hydrolases based on amino- acid se¬ quence similarities, Biochem. J. 293:781-788 (1993); Henrissat B., Bairoch A., Updating the sequence-based classification of glycosyl hydrolases, Biochem. J. 316:695-696 (1996); Davies G., Henrissat B., Structures and mechanisms of glycosyl hydrolases, Structure 3:853-859 (1995).
Polypeptides of the invention
The polypeptides of the invention are all polypeptides secreted by Botryosphaeria rhodina CBS 247.96 with the purpose of serving a function for that particular cell.
Among the thousands of potential genes in the genome of Botryosphaeria rhodina CBS 247.96 the polynucleotides of this genome encoded 21 secreted functional mature polypep- tides comprised in group BPoiypeptjde, which were determined to be functional, that is translated into functional polypeptides and secreted by the chosen host cell.
Accordingly, Botryosphaeria rhodina CBS 247.96 expresses and secretes the func¬ tional mature polypeptides comprised in group BPθiypeptide, and in the genome of that particular strain, the regions of sequences of group ADNA, encoding a mature polypeptide are the genes encoding the mature polypeptides comprised in the sequences of group Bp0iyp8ptide. Further in a particular embodiment the genes encoding the mature polypeptides comprised in the se¬ quences of of group BPoiyPePtide can all be expressed and their corresponding mature polypep¬ tides can be secreted when culturing an E. coli host transformed with polynucleotides compris- ing those regions of the sequences of group ADNA encoding a mature polypeptide. By compar¬ ing homology or identity of the sequences of the 21 polypeptide sequences to known se¬ quences the particular function of the polypeptides were annotated. At least 14 of the 21 se¬ creted functional polypeptides were determined to be enzymes and/or enzyme like.
The invention thus provides an isolated polypeptide selected from the group consisting of:
(a) a polypeptide having an amino acid sequence which has at least 90% identity with an amino acid sequence selected from the group consisting of the mature polypeptides comprised in group BpOiypΘptide ^nd
(b) a polypeptide which is encoded by a nucleotide sequence which hybridize under high stringency conditions with a polynucleotide probe selected from the group consisting of (i) the complementary strand to a nucleotide sequence selected from the group consisting of the regions of group ADNA sequences encoding a mature polypep¬ tide, (ii) the complementary strand to the cDNA sequence contained in a nucleotide se¬ quences selected from the group consisting of the regions of group ADNA se¬ quences encoding a mature polypeptide;
wherein the polypeptide exhibits the function of the corresponding mature polypeptides of grOUp Bpoiypeptide-
In one particular embodiment the polypeptide of the invention is selected among the enzymes secreted by Botryosphaeria rhodina deposited under CBS accession No. 247.96 and isolated by the present inventors, i.e. the group of enzymes consisting of xylanase, serine es¬ terase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase.
The invention also provides an isolated enzyme selected from the group consisting of: (a) an enzyme comprising an amino acid sequence which has at least 90% identity with the amino acid sequence of a mature enzyme selected from the group consisting of xy- lanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from the strain of Botryosphaeria rhodina Deposited under CBS accession No. 247.96 and
(b) a polypeptide which is encoded by a nucleotide sequence which hybridize under high stringency conditions with a polynucleotide probe selected from the group consisting of (i) the complementary strand to a nucleotide sequence comprised in the strain of
Botryosphaeria rhodina Deposited under CBS accession No. 247.96 encoding a mature enzyme selected from the group consisting of xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from that strain;
ii) the complementary strand to the cDNA sequence contained in a nucleotide se¬ quences comprised in the strain of Botryosphaeria rhodina Deposited under CBS accession No. 247.96 encoding a mature enzyme selected from the group consisting of xylanase, serine esterase, peroxidase, GH 61A polypeptide, GH
61 B polypeptide, GH 61C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from that strain and
wherein the enzyme have a function selected from xylanase, serine esterase, peroxidase, GH 61A polypeptide, GH 61 B polypeptide, GH 61C polypeptide, GH 61D polypeptide, beta- glucosidase, endo-arabinase and pepsin peptidase.
In a particular embodiment the enzyme is an isolated enzyme selected from the group consisting of:
(a) an enzyme having an amino acid sequence which has at least 90% identity with an amino acid sequence selected from mature enzymes comprised in the sequences of group Dpoiypepnde and
(b) an enzyme which is encoded by a nucleotide sequence which hybridize under high stringency conditions with a polynucleotide probe selected from the group consisting of (i) the complementary strand to a nucleotide sequence selected from the group consisting of the regions of group EDNA sequences encoding a mature enzyme, (ii) the complementary strand to the cDNA sequence contained in a nucleotide se¬ quences selected from the group consisting of the regions of group EDNA se¬ quences encoding a mature enzyme; wherein the enzyme exhibits the function of the corresponding mature enzyme of group DPoly- peptide-
The polypeptide of the invention is an isolated polypeptide, preferably the preparation of the polypeptide of the invention contains at the most 90% by weight of other polypeptide material with which it may be natively associated (lower percentages of other polypeptide ma¬ terial are preferred, e.g. at the most 80% by weight, at the most 60% by weight, at the most 50% by weight, at the most 40% at the most 30% by weight, at the most 20% by weight, at the most 10% by weight, at the most 9% by weight ,at the most 8% by weight, at the most 6% by weight, at the most 5% by weight, at the most 4% at the most 3% by weight, at the most 2% by weight, at the most 1% by weight and at the most >•>% by weight). Thus, it is preferred that the isolated polypeptide of the invention is at least 92% pure, i.e. that the polypeptide of the inven- tion constitutes at least 92% by weight of the total polypeptide material present in the prepara¬ tion, and higher percentages are preferred such as at least 94% pure, at least 95% pure, at least 96% pure, at least 96% pure, at least 97% pure, at least 98% pure, at least 99%, and at the most 99.5% pure. In particular, it is preferred that the polypeptide of the invention is in "es¬ sentially pure form", i.e. that the polypeptide preparation is essentially free of other polypeptide material with which it is natively associated. This can be accomplished, for example, by prepar¬ ing the polypeptide of the invention by means of well-known recombinant methods.
The polypeptide of the invention of the invention may be synthetically made, naturally occurring or a combination thereof. In a particular embodiment the polypeptide of the invention may be obtained from a microorganism such as a prokaryotic cell, an archaeal cell or a eu- karyotic cell. The cell may further have been modified by genetic engineering
In a particular embodiment, the polypeptide of the invention is an enzyme exhibiting op¬ timum enzyme activity at a temperature within the range from about 100C to about 80 0C, par¬ ticularly in the range from about 200C to about 600C.
In a particular embodiment the polypeptide of the invention is an enzyme, which is functionally stabile at a temperature of up to 100 0C, in particular up to 80 0C, more particularly up to 6O0C.
In a particular embodiment the polypeptide of the invention is an enzyme exhibiting at least 20%, in particular at least 40%, such as at least 50%, in particular at least 60%, such as at least 70%, more particularly at least 80%, such as at least 90%, most particularly at least 95%, such as about or at least 100% of the enzyme activity of an enzyme selected from ma¬ ture enzymes comprised in group Bpoiypeptide- In a particular embodiment the polypeptide of the invention comprises, contains or con¬ sists of an amino acid sequence which has at least 90% identity with a polypeptide sequence selected from the group consisting of mature polypeptides comprised in group BPoiypeptide; par¬ ticularly at least 95%, e.g. at least 96%, such as at least 97%, and even more particularly at least 98%, such as at least 99% or even 100% identity.
In another particular embodiment the polypeptide of the invention comprises, contains or consists of an amino acid sequence, which has at least 50% identity with a polypeptide se¬ quence selected from the group consisting of mature polypeptides comprised in group BPoiyPep- tidβ; particularly at least 60%, particularly at least 65%, particularly at least 70%, particularly at least 75%, particularly at least 80%, and even more particularly at least 85% identity.
In a particular embodiment, the amino acid sequence of the polypeptide of the inven¬ tion differs by at the most ten amino acids (e.g. by ten amino acids), in particular by at the most five amino acids (e.g. by five amino acids), such as by at the most four amino acids (e.g. by four amino acids), e.g. by at the most three amino acids (e.g. by three amino acids), in particu- lar by at the most two amino acids (e.g. by two amino acids), such as by one amino acid from the mature polypeptides comprised in group BPθ|yp8ptide.
The polypeptide of the invention may be a wild-type polypeptide isolated from a natural source such as the strain Botryosphaeria rhodina CBS 247.96 or another wild type strain, however the present invention also encompass artificial variants, where a polypeptide of the invention has been mutated for example by adding, substituting and/or deleting one or more amino acids from said polypeptide while retaining the function of the polypeptide and/or other properties.
Hence, the polypeptide of the invention may be an artificial variant, wherein at least one substitution, deletion and/or insertion of an amino acid has been made to an amino acid se- quence comprising or consisting of the mature polypeptide comprised in group BPθ|ypeptide-
The polypeptides of the invention also include functional fragments of the amino acid sequences described herein and nucleic acids encoding functional fragments of the amino acid sequences described herein, including fragments of the mature enzymes secreted from the strain of Botryosphaeria rhodina Deposited under CBS accession No. 247.96, as described herein, including fragment of an enzyme selected from the group consisting of xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from the strain of Botryosphaeria rhodina Deposited under CBS accession No. 247.96.
Artificial variants may be constructed by standard techniques known in the art usually followed by screening and/or characterization. Standard techniques includes classical mutagenesis, e.g. by UV irradiation of the cells or treatment of cells with chemical mutagens as described by Gerhardt et al. (1994); in vivo gene shuffling as described in WO 97/07205; in vitro shuffling as described by Stemmer, (1994) or WO 95/17413, random mutagenesis as de¬ scribed by Eisenstadt E. et al., (1994); PCR techniques as described by Poulsen et al. (1991 ); family shuffling as described by J. E. Ness, et al, Nature Biotechnology, vol. 17, pp. 893-896 (1999); site-directed mutagenesis as described by Sambrook et al. (1989), Sambrook et al., Molecular Cloning, A Laboratory Manual, Cold Spring Harbor, NY. A general description of nu¬ cleotide substitution can be found in e.g. Ford et al., 1991 , Protein Expression and Purification 2, p. 95-107.
Such standard genetic engineering methods may also be used prepare a diversified li¬ brary of variant nucleotide sequences from the genes encoding one or more parent enzymes of the invention, expressing the enzyme variants in a suitable host cell and selecting a pre¬ ferred variant(s). A diversified library can be established by a range of techniques known to the art (Reetz MT; Jaeger KE1 in Biocatalysis - from Discovery to Application edited by Fessner WD, Vol. 200, pp. 31-57 (1999); Stemmer, Nature, vol. 370, p.389-391, 1994; Zhao and Ar¬ nold, Proc. Natl. Acad. ScL, USA, vol. 94, pp. 7997-8000, 1997; or Yano et al., Proc. Natl. Acad. ScL, USA, vol. 95, pp 5511 -5515, 1998).
In a particular embodiment of the invention, amino acid changes (in the artificial variant as well as in wild-type enzyme) are of a minor nature, that is conservative amino acid substitu¬ tions that do not significantly affect the folding and/or activity of the protein; small deletions, typically of one to about 30 amino acids; small amino- or carboxyl-terminal extensions, such as an amino-terminal methionine residue; a small linker peptide of up to about 20-25 residues; or a small extension that facilitates purification by changing net charge or another function, such as a poly-histidine tract, an antigenic epitope or a binding domain.
Examples of conservative substitutions are within the group of basic amino acids (ar- ginine, lysine and histidine), acidic amino acids (glutamic acid and aspartic acid), polar amino acids (glutamine and asparagine), hydrophobic amino acids (leucine, isoleucine, valine and methionine), aromatic amino acids (phenylalanine, tryptophan and tyrosine), and small amino acids (glycine, alanine, serine and threonine). Amino acid substitutions which do not generally alter and or impair the function of a protein are known in the art and are described, for exam¬ ple, by H. Neurath and R. L. Hill, 1979, In, The Proteins, Academic Press, New York. The most commonly occurring exchanges are Ala/Ser, Val/lle, Asp/Glu, Thr/Ser, Ala/Gly, Ala/Thr, Ser/Asn, Ala/Val, Ser/Gly, Tyr/Phe, Ala/Pro, Lys/Arg, Asp/Asn, Leu/lle, Leu/Val, Ala/Glu, and Asp/Gly as well as these in reverse.
In a particular embodiment the amino acid changes are of such a nature that the phys¬ ico-chemical properties of the polypeptides are altered. For example, amino acid changes may be performed, which improve the thermal stability of the enzyme, which alter the substrate specificity, which changes the pH optimum, and the like. Particularly, the number of such substitutions, deletions and/or insertions in the poly¬ peptide of the invention, particularly in those polypeptides selected from the group consisting of mature polypeptides comprised in group BpOiyPeptide to produce an artificial variant is at the most 10, such as at the most 9, e.g. at the most 8, more preferably at the most 7, e.g. at the most 6, such as at the most 5, most preferably at the most 4, e.g. at the most 3, such as at the most 2, in particular at the most 1.
In a particular embodiment the artificial variant is a variant, which has an altered, pref¬ erably reduced, immunogenicity, especially allergenicity, in animals including man as com¬ pared to a parent enzyme. The term "immunogenicity" in this context is to be understood as the artificial variant capability of invoking a an altered, in particular reduced, immunological re¬ sponse when administered to an animal, including intravenous, cutaneous, subcutaneous, oral and intratracheal administration. The term "immunological response" in this context means that the administration of the artificial variant causes an alteration in the immunoglobulin levels in the animal body, such as in IgE, IgG and IgM or an alteration in the cytokine level in the animal body. Methods for mapping immunogenic/antigenic epitopes of a protein, preparing variants with altered immunogenicity and methods for measuring an immunological response is well known to the art and are described e.g. in WO 92/10755, WO 00/26230, WO 00/26354 and WO 01/31989. The term "allergenicity" in this context is to be understood as the artificial variant ability of invoking an altered, in particular reduced, production of IgE in an animal as well as the ability to bind IgE from said animal. Particularly allergenicity arising from intratracheal administration of the polypeptide variant to the animal is particularly of interest (also known as respiratory allergenicity).
In a further embodiment, the polypeptide of the invention is a polypeptide which is en¬ coded by nucleotide sequences which hybridize under at least high stringency conditions, par- ticularly under very high stringency conditions with a polynucleotide probe selected from the group consisting of
(i) the complementary strand to a nucleotide sequence selected from the group consisting of the regions of group ADNA sequences encoding a mature polypeptide, (ii) the complementary strand to the cDNA sequence contained in a nucleotide sequences selected from the group consisting of the regions of group ADNA sequences encoding a mature polypeptide;
(iii) a fragment of (i) or (ii) encoding a secreted polypeptide having the function of the corre¬ sponding mature polypeptide comprised in group BPo,ypeptide.
(J. Sambrook, E.F. Fritsch, and T. Maniatus, 1989, Molecular Cloning, A Laboratory Manual,
2d edition, Cold Spring Harbor, New York). In particular, the polypeptide of the invention is encoded by a polynucleotide comprising a nu¬ cleotide sequence selected from the group of regions of group ADNA sequences encoding a mature polypeptide or a sequences differing there from by virtue of the degeneracy of the ge¬ netic code. More particularly, the polypeptide of the invention is encoded by a polynucleotide consisting of a nucleotide sequence selected from the group of regions of group ADNA se¬ quences encoding a mature polypeptide or a sequence differing there from by virtue of the de¬ generacy of the genetic code.
The nucleotide sequences of regions of group ADNA sequences encoding a mature polypeptide or a subsequence thereof, as well as the amino acid sequences of the mature polypeptides comprised in group BpO|ypeptide or a fragment thereof, may be used to design a polynucleotide probe to identify and clone DNA encoding enzymes of the invention from 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 or cDNA of the genus or species of in¬ terest, following standard Southern blotting procedures, in order to identify and isolate the cor- responding gene therein. Such probes can be considerably shorter than the entire sequence, but should be at least 15, preferably at least 25, more preferably at least 35 nucleotides in length, such as at least 70 nucleotides in length. It is; however, preferred that the polynucleo¬ tide probe is at least 100 nucleotides in length. For example, the polynucleotide probe may be at least 200 nucleotides in length, at least 300 nucleotides in length, at least 400 nucleotides in length or at least 500 nucleotides in length. Even longer probes may be used, e.g., polynucleo¬ tide probes which are at least 600 nucleotides in length, at least 700 nucleotides in length, at least 800 nucleotides in length, or at least 900 nucleotides in length. Both DNA and RNA probes can be used. The probes are typically labelled for detecting the corresponding gene (for example, with 32P, 3H, 35S, biotin, or avidin). Thus, a genomic DNA or cDNA library prepared from such other organisms may be screened for DNA, which hybridizes with the probes described above and which encodes en¬ zymes of the invention. Genomic or other DNA from such other organisms may be separated by agarose or polyacrylamide gel electrophoresis, or other separation techniques. DNA from the libraries or the separated DNA may be transferred to, and immobilized, on nitrocellulose or other suitable carrier materials. In order to identify a clone or DNA which has the required ho¬ mology and/or identity or is homologous and/or identical with nucleotides selected from regions of group ADNA sequences encoding a mature polypeptide, the carrier material with the immobi¬ lized DNA is used in a Southern blot.
For purposes of the present invention, hybridization indicates that the nucleotide se- quence hybridizes to a labelled polynucleotide probe which again hybridizes to a nucleotide sequence selected from regions of group ADNA sequences encoding a mature polypeptide un¬ der high to very high stringency conditions. Molecules to which the polynucleotide probe hy- bridizes under these conditions may be detected using X-ray film or by any other method known in the art. Whenever the term "polynucleotide probe" is used in the present context, it is to be understood that such a probe contains at least 15 nucleotides.
In an interesting embodiment, the polynucleotide probe is the complementary strand of a nucleotide sequence selected from regions of group ADNA sequences encoding a mature polypeptide.
In another interesting embodiment, the polynucleotide probe is the complementary strand of a nucleotide sequence which encodes an enzyme selected from group BPoiyPeptide- In a further interesting embodiment, the polynucleotide probe is the complementary strand of a mature polypeptide coding region of a nucleotide sequence selected from regions of group ADNA sequences encoding a mature polypeptide.
For long probes of at least 100 nucleotides in length, high to very high stringency condi¬ tions are defined as pre-hybridization and hybridization at 42°C in 5X SSPE, 1.0% SDS, 5X Denhardt's solution, 100 microgram/ml sheared and denatured salmon sperm DNA, following standard Southern blotting procedures. Preferably, the long probes of at least 100 nucleotides do not contain more than 1000 nucleotides. For long probes of at least 100 nucleotides in length, the carrier material is finally washed three times each for 15 minutes using 0.1 x SSC, 0.1% SDS at 600C (high stringency), in particular washed three times each for 15 minutes us¬ ing 0.1 x SSC, 0.1% SDS at 680C (very high stringency). Although not particularly preferred, it is contemplated that shorter probes, e.g. probes which are from about 15 to 99 nucleotides in length, such as from about 15 to about 70 nucleo¬ tides in length, may be also be used. For such short probes, stringency conditions are defined as pre-hybridization, hybridization, and washing post-hybridization at 50C to 10°C below the calculated Tm using the calculation according to Bolton and McCarthy (1962, Proceedings of the National Academy of Sciences USA 48:1390) in 0.9 M NaCI, 0.09 M Tris-HCI pH 7.6, 6 mM EDTA, 0.5% NP-40, 1X Denhardt's solution, 1 mM sodium pyrophosphate, 1 mM sodium monobasic phosphate, 0.1 mM ATP, and 0.2 mg of yeast RNA per ml following standard Southern blotting procedures.
For short probes which are about 15 nucleotides to 99 nucleotides in length, the carrier material is washed once in 6X SCC plus 0.1% SDS for 15 minutes and twice each for 15 min¬ utes using 6X SSC at 5°C to 10°C below the calculated Tm.
SEQ ID NO: 2 xylanase GH10
In a particular embodiment the polypeptide of the invention is a GH 10 xylanase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a GH10 xylanase obtainable from Botiyosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un¬ der deposit accession number CBS 247.96, more particularly the mature GH10 xylanase com¬ prised in SEQ ID NO: 2. More specifically the mature GH10 xylanase comprise or consists of the sequences from position 1 to 291 of SEQ ID NO: 2. In the present context a GH10 xy- lanase is defined as an enzyme beloning to the EC 3.2.1.8 enzyme activity grouping. This grouping endohydrolyses 1 ,4-β-D-xylosidic linkages in xylans. The glycoside hydrolase family 10 (GH10) also comprises enzymes with two other known activities; endo-1 ,3-beta-xylanase (EC: 3.2.1.32); cellobiohydrolase (EC: 3.2.1.91).
SEQ ID NO: 4 xylanase GH11 In a particular embodiment the polypeptide of the invention is a GH11 xylanase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a xylanase GH11 obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un- der deposit accession number CBS 247.96, more particularly the mature GH11 xylanase com¬ prised in SEQ ID NO: 4. More specifically the mature GH11 xylanase comprise or consists of the sequences from position 1 to 202 of SEQ ID NO: 4. In the present context a GH11 xy¬ lanase is defined as an enzyme beloning to the EC 3.2.1.8 enzyme activity grouping. This grouping endohydrolyses 1 ,4-β-D-xylosidic linkages in xylans. Glycoside hydrolase family 11 (GH11) comprises enzymes with only one known activity; xylanase (EC: 3.2.1.8).
SEQ ID NO: 6 Serine esterase
In a particular embodiment the polypeptide of the invention is a serine esterase, in particular a cutinase or a lipase or a carboxyesterase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particu- larly at least 97%, more particularly at least 98%, more particularly at least 99% or most par¬ ticularly 100% identity with a serine esterase obtainable from Botryosphaeria rhodina, in par¬ ticular that strain of Botryosphaeria rhodina deposited under deposit accession number CBS 247.96, more particularly the mature serine esterase comprised in SEQ ID NO: 6. More spe¬ cifically the mature serine esterase comprise or consists of the sequences from position 1 to 352 of SEQ ID NO: 6. In the present context a serine esterase is defined as an enzyme capa¬ ble of hydrolysing soluble esters in solution (esters which are not in micelle form). More spe¬ cifically the serin esters are enzymes acting as cutinase (EC 3.1.1.50) or lipase (EC.3.1.1.3) or carboxyesterase capable of hydrolysing wax-esters, cutin, tracyl fats, oils and/or fatty acid chains. In particulare the serine esterases contain the classical Ser, His, Asp triad of serine hydrolase, such as tri-acyl lipase/cutinase. SEQ ID NO: 8 Candida B type Lipase
In a particular embodiment the polypeptide of the invention is a Candida B type lipase (EC 3.1.1.3) comprising or consisting of an amino acid sequence which has at least 90%, particu¬ larly at least 95%, more particularly at least 96%, more particularly at least 97%, more particu- larly at least 98%, more particularly at least 99% or most particularly 100% identity with a Can¬ dida B type Lipase obtainable from Botryosphaeria rhodina, in particular that strain of Botryos- phaeria rhodina deposited under deposit accession number CBS 247.96, more particularly the mature Candida B type Lipase comprised in SEQ ID NO: 8. More specifically the mature Can¬ dida B type Lipase comprise or consists of the sequences from position 1 to 431 of SEQ ID NO: 8. In the present context the Candida B type Lipase is defined as an enzyme capable of hydrolysing triglycerides to diacyl glycerides and fatty acid anions, in particular triacylglycerol to diacylglycerol and a fatty acid anion.
SEQ ID NO: 10 Peroxidase
In a particular embodiment the polypeptide of the invention is a peroxidase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a peroxidase obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un¬ der deposit accession number CBS 247.96, more particularly the mature peroxidase com- prised in SEQ ID NO: 10. More specifically the mature peroxidase comprises or consists of the sequences from position 1 to 185 of SEQ ID NO: 10. In the present context a peroxidase is defined as an enzyme belonging to defined as a group of enzymes that catalyze oxidation- reduction reactions. As such, they are classified as oxidoreductases. They are given the official EC number 1.11.1. Peroxidases reduce H2O2 to water while oxidizing a variety of substrates. Thus, peroxidases are oxidoreductases which use H2O2 as electron acceptor for catalyzing different oxidative reactions.
SEQ ID NO: 12 GH61A polypeptide
In a particular embodiment the polypeptide of the invention is a GH61A polypeptide comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a GH61A polypeptide ob¬ tainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina depos¬ ited under deposit accession number CBS 247.96, more particularly the mature GH61A poly¬ peptide comprised in SEQ ID NO: 12. More specifically the mature GH61A polypeptide com- prises or consists of the sequences from position 1 to 218 of SEQ ID NO: 12. In the present context a GH 61A polypeptide is defined as a secreted polypeptide or protein providing one or more of the group of effects selected from:
1) Enhancing degradation of cellulosic materials when used in conjunction with a cellulase or a mixture of cellulases. 2) Increasing solubility of enzymes.
3) Increasing the stability of enzymes
4) Reducing enzyme inhibition.
SEQ ID NO: 14 GH 61 B polypeptide
In a particular embodiment the polypeptide of the invention is a GH 61 B polypeptide compris- ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a GH 61 B polypeptide obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina de¬ posited under deposit accession number CBS 247.96, more particularly the mature GH 61 B polypeptide comprised in SEQ ID NO: 14. More specifically the mature GH 61 B polypeptide comprises or consists of the sequences from position 1 to 249 of SEQ ID NO: 14. In the present context a GH 61 B polypeptide is defined as a secreted polypeptide or protein providing one or more of the group of effects selected from:
1 ) Enhancing degradation of cellulosic materials when used in conjunction with a cellulase or a mixture of cellulases.
2) Increasing solubility of enzymes.
3) Increasing the stability of enzymes
SEQ ID NO: 16 GH 61 C polypeptide
In a particular embodiment the polypeptide of the invention is a GH 61 C polypeptide compris- ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a GH 61 C polypeptide obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina de¬ posited under deposit accession number CBS 247.96, more particularly the mature GH 61 C polypeptide comprised in SEQ ID NO: 16. More specifically the mature GH 61 C polypeptide comprises or consists of the sequences from position 1 to 255 of SEQ ID NO: 16. In the present context a GH 61 C polypeptide is defined as a secreted polypeptide or protein providing one or more of the group of effects selected from:
1 ) Enhancing degradation of cellulosic materials when used in conjunction with a cellulase or a mixture of cellulases.
2) Increasing solubility of enzymes. 3) Increasing the stability of enzymes
SEQ ID NO: 18 GH 61 D polypeptide
In a particular embodiment the polypeptide of the invention is a GH 61 D polypeptide compris¬ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a GH 61 D polypeptide obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina de¬ posited under deposit accession number CBS 247.96, more particularly the mature GH 61 D polypeptide comprised in SEQ ID NO: 18. More specifically the mature GH 61 D polypeptide comprises or consists of the sequences from position 1 to 205 of SEQ ID NO: 18. In the present context a GH 61 C polypeptide is defined as a secreted polypeptide or protein providing one or more of the group of effects selected from:
1) Enhancing degradation of cellulosic materials when used in conjunction with a cellulase or a mixture of cellulases. 2) Increasing solubility of enzymes. 3) Increasing the stability of enzymes
SEQ ID NO:20 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional polypeptide compris¬ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 20. In par¬ ticular with the mature functional polypeptide comprised in SEQ ID NO: 20. More specifically the mature functional polypeptide comprises or consists of the sequences from position 1 to 243 of SEQ ID NO: 20.
SEQ ID NO: 22 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional polypeptide compris¬ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 22. In par- ticular with the mature functional polypeptide comprised in SEQ ID NO: 22. More specifically the mature functional polypeptide comprises or consists of the sequences from position 1 to 415 Of SEQ ID NO: 22. SEQ ID NO: 24 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional polypeptide compris¬ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 24. In par¬ ticular with the mature functional polypeptide comprised in SEQ ID NO: 24. More specifically the mature functional polypeptide comprises or consists of the sequences from position 1 to 377 of SEQ ID NO: 24.
SEQ ID NO: 26 functional polypeptide In a particular embodiment the polypeptide of the invention is a functional polypeptide compris¬ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 26. In par¬ ticular with the mature functional polypeptide comprised in SEQ ID NO: 26. More specifically the mature functional polypeptide comprises or consists of the sequences from position 1 to 259 of SEQ ID NO: 26.
SEQ ID NO: 28 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional polypeptide compris¬ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 28. In par¬ ticular with the mature functional polypeptide comprised in SEQ ID NO: 28. More specifically the mature functional polypeptide comprises or consists of the sequences from position 1 to 248 of SEQ ID NO: 28.
SEQ ID NO: 30 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional polypeptide compris¬ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 30. In par- ticular with the mature functional polypeptide comprised in SEQ ID NO: 30. More specifically the mature functional polypeptide comprises or consists of the sequences from position 1 to 149 of SEQ ID NO: 30. SEQ ID NO: 32 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional polypeptide compris¬ ing or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 32. In par¬ ticular with the mature functional polypeptide comprised in SEQ ID NO: 32. More specifically the mature functional polypeptide comprises or consists of the sequences from position 1 to 202 of SEQ ID NO: 32.
SEQ ID NO: 34 beta-αlucosidase In a particular embodiment the polypeptide of the invention is a beta-glucosidase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a beta-glucosidase obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un- der deposit accession number CBS 247.96, more particularly the mature beta-glucosidase comprised in SEQ ID NO: 34. More specifically the mature beta-glucosidase comprise or con¬ sists of the sequences from position 1 to 603 of SEQ ID NO: 34. In the present context the beta-glucosidase is defined as a beta-D-glucoside glucohydrolase (E. C. 3.2.1.21) which cata¬ lyzes the hydrolysis of terminal non-reducing beta-D-glucose residues with the release of beta- D-glucose. For purposes of the present invention, beta-glucosidase activity is determined ac¬ cording to the basic procedure described by Venturi et al., 2002, J. Basic Microbiol. 42: 55-66, except different conditions were employed as described herein. One unit of beta-glucosidase activity is defined as 1.0 micromole of p-nitrophenol produced per minute at 500C, pH 5 from 4 mM p-nitrophenyl-beta-D-glucopyranoside as substrate in 100 mM sodium citrate, 0.01% Tween-20.
SEQ ID NO: 36 endo-arabinase
In a particular embodiment the polypeptide of the invention is a endo-arabinase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a endo-arabinase obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un¬ der deposit accession number CBS 247.96, more particularly the mature endo-arabinase com¬ prised in SEQ ID NO: 36. More specifically the mature endo-arabinase comprises or consists of the sequences from position 1 to 301 of SEQ ID NO: 36. In the present context an endo- arabinase is defined as an enzyme capable of hydrolysing arabinan. SEQ ID NO: 38 endo-arabinase
In a particular embodiment the polypeptide of the invention is a endo-arabinase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a endo-arabinase obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un¬ der deposit accession number CBS 247.96, more particularly the mature endo-arabinase com¬ prised in SEQ ID NO: 38. More specifically the mature endo-arabinase comprises or consists of the sequences from position 1 to 438 of SEQ ID NO: 38. In the present context an endo- arabinase is defined as an enzyme capable of hydrolysing arabinan.
SEQ ID NO: 40 A1 pepsin peptidase
In a particular embodiment the polypeptide of the invention is a pepsin peptidase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a pepsin peptidase obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un¬ der deposit accession number CBS 247.96, more particularly the mature pepsin peptidase comprised in SEQ ID NO: 40. More specifically the mature pepsin peptidase comprises or consists of the sequences from position 1 to 396 of SEQ ID NO: 40. In the present context a pepsin peptidase is defined as an enzyme capable of hydrolysing proteins or peptides.
SEQ ID NO: 42 M43 Pepsin peptidase
In a particular embodiment the polypeptide of the invention is a pepsin peptidase comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 96%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with a pepsin peptidase obtainable from Botryosphaeria rhodina, in particular that strain of Botryosphaeria rhodina deposited un¬ der deposit accession number CBS 247.96, more particularly the mature pepsin peptidase comprised in SEQ ID NO: 42. More specifically the mature pepsin peptidase comprises or consists of the sequences from position 1 to 262 of SEQ ID NO: 42. In the present context a Pepsin peptidase is defined as an enzyme capable of hydrolysing proteins or peptides.
Polynucleotides
The present invention also relates to polynucleotides comprising or consisting of a nu¬ cleotide sequence encoding a polypeptide of the invention. In a particular embodiment, the nu- cleotide sequence is set forth in the sequences of group ADNA including nucleotide sequences differing there from by virtue of the degeneracy of the genetic code. In a further embodiment the polynucleotide of the invention is a modified nucleotide sequence which comprises or con¬ sists of a nucleotide sequence selected from the the regions of group ADNA sequences encod¬ ing a mature polypeptide and which comprises at least one modification/mutation compared with the parent nucleotide sequence comprised in the sequences of group ADNA-
The techniques used to isolate and/or clone a nucleotide sequence encoding an en¬ zyme are known in the art and include isolation from genomic DNA, preparation from cDNA, or a combination thereof. The cloning of the nucleotide sequences of the present invention from such genomic DNA can be effected, e.g., by using the well known polymerase chain reaction (PCR) or antibody screening of expression libraries to detect cloned DNA fragments with shared structural features. See, e.g., lnnis et al., 1990, PCR: A Guide to Methods and Applica¬ tion, Academic Press, New York. Other amplification procedures such as ligase chain reaction (LCR), ligated activated transcription (LAT) and nucleotide sequence-based amplification (NASBA) may be used. The nucleotide sequence may be obtained by standard cloning procedures used in ge¬ netic engineering to relocate the nucleotide sequence from its natural location to a different site where it will be reproduced. The cloning procedures may involve excision and isolation of a desired fragment comprising the nucleotide sequence encoding the polypeptide, insertion of the fragment into a vector molecule, and incorporation of the recombinant vector into a host cell where multiple copies or clones of the nucleotide sequence will be replicated. The nucleo¬ tide sequence may be of genomic, cDNA, RNA, semi-synthetic, synthetic origin, or any combinations thereof.
In particular the polynucleotide comprises, preferably consists of, a nucleotide se¬ quence which has at least 50% identity with a nucleotide sequence selected from the regions of group ADNA sequences encoding a mature polypeptide. Particularly, the nucleotide sequence has at least 65% identity, more particularly at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with a nucleotide sequence selected from the regions of group ADNA sequences encoding a mature polypeptide. Particularly, the nucleotide sequence comprises a nucleotide sequence selected from the regions of group ADNA sequences encoding a mature polypeptide. In an even more particular embodiment, the nucleotide sequence consists of a nucleotide sequence se¬ lected from the regions of group ADNA sequences encoding a mature polypeptide. In particular the polynucleotide comprises, preferably consists of, a nucleotide se¬ quence encoding a mature enzyme selected from xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta- glucosidase, endo-arabinase and pepsin peptidase and which has at least 50% identity, par¬ ticularly at least 65% identity, more particularly at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with a nucleotide sequence encoding a mature enzyme selected from xylanase, serine es¬ terase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from Botryos- phaeria rhodina deposited under CBS accession No. 247.96 and isolated by the present inven- tors.
In a particular embodiment the polynucleotide comprises, preferably consists of, a nu¬ cleotide sequence encoding a mature enzyme selected from xylanase, serine esterase, per¬ oxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase and which has at least 50% identity, particularly at least 65% identity, more particularly at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% iden¬ tity, more particularly at least 96% identity, more particularly at least 97% identity, more par¬ ticularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with a nucleotide sequence encoding a mature enzyme selected from from group DPoiy- peptide sequences.
In a particular embodiment the polynucleotide comprises, preferably consists of, a nu¬ cleotide sequence encoding a mature enzyme selected from xylanase, serine esterase, per¬ oxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase and which has at least 50% identity, particularly at least 65% identity, more particularly at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% iden¬ tity, more particularly at least 96% identity, more particularly at least 97% identity, more par¬ ticularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with a nucleotide sequence selected from EDNA sequences
SEQ ID NO: 1
In a particular embodiment the polynucleotide of the invention encodes a GH 10 xylanase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu¬ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 55 to 927 of SEQ ID NO: 1 SEQ ID NO: 3
In a particular embodiment the polynucleotide of the invention encodes a GH11 xylanase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu¬ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 58 to 663 of SEQ ID NO: 3
SEQ ID NO: 5
In a particular embodiment the polynucleotide of the invention encodes a serine esterase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu¬ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 55 to 1110 of SEQ ID NO: 5
SEQ ID NO: 7
In a particular embodiment the polynucleotide of the invention encodes a lipase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% iden¬ tity, more particularly at least 96% identity, more particularly at least 97% identity, more par- ticularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 55 to 1347 of SEQ ID NO: 7.
SEQ ID NO: 9
In a particular embodiment the polynucleotide of the invention encodes a peroxidase and com¬ prises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 1 to 555 of SEQ ID NO: 9.
SEQ ID NO: 11 In a particular embodiment the polynucleotide of the invention encodes a GH61A polypeptide and comprises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% iden- 00519 tity, more particularly at least 98% identity, more particularly at least 99% identity or most par¬ ticularly 100% identity with the nucleotide sequence of position 49 to 702 of SEQ ID NO: 11.
SEQ ID NO: 13
In a particular embodiment the polynucleotide of the invention encodes a GH 61 B polypeptide and comprises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% iden¬ tity, more particularly at least 98% identity, more particularly at least 99% identity or most par¬ ticularly 100% identity with the nucleotide sequence of position 40 to 786 of SEQ ID NO: 13.
SEQ ID NO: 15
In a particular embodiment the polynucleotide of the invention encodes a GH 61 C polypeptide and comprises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% iden- tity, more particularly at least 98% identity, more particularly at least 99% identity or most par¬ ticularly 100% identity with the nucleotide sequence of position 55 to 819 of SEQ ID NO: 15.
SEQ ID NO: 17
In a particular embodiment the polynucleotide of the invention encodes a GH 61 D polypeptide and comprises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% iden¬ tity, more particularly at least 98% identity, more particularly at least 99% identity or most par¬ ticularly 100% identity with the nucleotide sequence of position 61 to 675 of SEQ ID NO: 17.
SEQ ID NO: 19 In a particular embodiment the polynucleotide of the invention encodes a mature functional polypeptide and comprises or consists of an nucleotide sequence which has at least 70% iden¬ tity, more particularly at least 80% identity, more particularly at least 90% identity, more par¬ ticularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 1 to 729 of SEQ ID NO: 19. SEQ ID NO: 21
In a particular embodiment the polynucleotide of the invention encodes a mature functional polypeptide and comprises or consists of an nucleotide sequence which has at least 70% iden¬ tity, more particularly at least 80% identity, more particularly at least 90% identity, more par- ticularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 55 to 1299 of SEQ ID NO: 21.
SEQ ID NO: 23 In a particular embodiment the polynucleotide of the invention encodes a mature functional polypeptide and comprises or consists of an nucleotide sequence which has at least 70% iden¬ tity, more particularly at least 80% identity, more particularly at least 90% identity, more par¬ ticularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 49 to 1179 of SEQ ID NO: 23.
SEQ ID NO: 25
In a particular embodiment the polynucleotide of the invention encodes a mature functional polypeptide and comprises or consists of an nucleotide sequence which has at least 70% iden- tity, more particularly at least 80% identity, more particularly at least 90% identity, more par¬ ticularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 70 to 846 of SEQ ID NO: 25.
SEQ ID NO: 27
In a particular embodiment the polynucleotide of the invention encodes mature functional poly¬ peptide and comprises or consists of an nucleotide sequence which has at least 70% identity, more particularly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 58 to 801 of SEQ ID NO: 27. 19
SEQ ID NO: 29
In a particular embodiment the polynucleotide of the invention encodes a mature functional polypeptide and comprises or consists of an nucleotide sequence which has at least 70% iden¬ tity, more particularly at least 80% identity, more particularly at least 90% identity, more par- ticularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 157 to 603 of SEQ ID NO: 29.
SEQ ID NO: 31 In a particular embodiment the polynucleotide of the invention encodes a mature functional polypeptide and comprises or consists of an nucleotide sequence which has at least 70% iden¬ tity, more particularly at least 80% identity, more particularly at least 90% identity, more par¬ ticularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 55 to 660 of SEQ ID NO: 31.
SEQ ID NO: 33
In a particular embodiment the polynucleotide of the invention encodes a beta-glucosidase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu- larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 46 to 1854 of SEQ ID NO: 33.
SEQ ID NO: 35 In a particular embodiment the polynucleotide of the invention encodes a endo-arabinase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu¬ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 64 to 966 of SEQ ID NO: 35.
SEQ ID NO: 37
In a particular embodiment the polynucleotide of the invention encodes a endo-arabinase and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu¬ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 55 to 1368 of SEQ ID NO: 37.
SEQ ID NO: 39 In a particular embodiment the polynucleotide of the invention encodes a pepsin protease and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu¬ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 61 to 1248 of SEQ ID NO: 39.
SEQ ID NO: 41
In a particular embodiment the polynucleotide of the invention encodes a pepsin protease and comprises or consists of an nucleotide sequence which has at least 70% identity, more particu¬ larly at least 80% identity, more particularly at least 90% identity, more particularly at least 95% identity, more particularly at least 96% identity, more particularly at least 97% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 64 to 849 of SEQ ID NO: 41.
Modification of a nucleotide sequence encoding a polypeptide of the present invention may be necessary for the synthesis of a polypeptide which comprises an amino acid sequence that has at least one substitution, deletion and/or insertion as compared to an amino acid se¬ quence selected from mature polypeptide comprised in group BpOιyPeptjde-
It will be apparent to those skilled in the art that such modifications can be made to preserve the function of the enzyme i.e. made outside regions critical to the function of the en- zyme. Amino acid residues which are essential to the function are therefore preferably not sub¬ ject to modification, such as substitution. Amino acid residues essential to the function may be identified according to procedures known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (see, e.g., Cunningham and Wells, 1989, Science 244: 1081- 1085). Sites of substrate-enzyme interaction can be determined by analysis of the three- dimensional structure as determined by such techniques as nuclear magnetic resonance analysis, crystallography or photoaffinity labeling (see, e.g., de Vos et a/., 1992, Science 255: 306-312; Smith et a/., 1992, Journal of Molecular Biology 224: 899-904; Wlodaver et al., 1992, FEBS Letters 309: 59-64).
Moreover, a nucleotide sequence encoding an enzyme of the invention may be modi- fied by introduction of nucleotide substitutions which do not give rise to another amino acid se- quence of the enzyme encoded by the nucleotide sequence, but which correspond to the codon usage of the host organism intended for production of the enzyme.
The introduction of a mutation into the nucleotide sequence to exchange one nucleotide for another nucleotide may be accomplished by site-directed mutagenesis using any of the methods known in the art. Particularly useful is the procedure, which utilizes a super coiled, double stranded DNA vector with an insert of interest and two synthetic primers con¬ taining the desired mutation. The oligonucleotide primers, each complementary to opposite strands of the vector, extend during temperature cycling by means of Pfu DNA polymerase. On incorporation of the primers, a mutated plasmid containing staggered nicks is generated. Following temperature cycling, the product is treated with Dpn\, which is specific for methylated and hemimethylated DNA to digest the parental DNA template and to select for mutation- containing synthesized DNA. Other procedures known in the art may also be used. For a general description of nucleotide substitution, one may consult with e.g., Ford et al., 1991 , Protein Expression and Purification 2: 95-107. The present invention also relates to a polynucleotide comprising, preferably consisting of, a nucleotide sequence which encodes a polypeptide of the invention and which hybridizes under high stringency conditions, preferably under very high stringency conditions with a polynucleotide probe selected from the group consisting of: (i) the complementary strand to a nucleotide sequence selected from the group consisting of the regions of group ADNA sequences encoding a mature polypeptide,
(N) the complementary strand to the cDNA sequence contained in a nucleotide sequences selected from the group consisting of the regions of group ADNA sequences encoding a mature polypeptide, (iii) a fragment of (i) or (ii) encoding a secreted mature polypeptide having the function of the corresponding mature polypeptides comprised in group Bpoiypeptide
(J. Sambrook, E.F. Fritsch, and T. Maniatus, 1989, Molecular Cloning, A Laboratory Manual, 2d edition, Cold Spring Harbor, New York).
As will be understood, details and particulars concerning hybridization of the nucleotide se¬ quences will be the same or analogous to the hybridization aspects discussed in the section titled "polypeptides of the invention" herein.
The present invention also encompasses a storage medium suitable for use in an elec¬ tronic device comprising information of the amino acid sequence of polypeptides of the inven- tion or the nucleotide sequences of the polynucleotide of the invention. The storage medium may suitably be a magnetic or optical disk and the electronic device a computing device and the information may in particular be stored on the storage medium in a digital form. Nucleotide constructs
The present invention also relates to nucleic acid constructs comprising a nucleotide sequence of the invention operably linked to one or more control sequences that direct the ex- pression of the coding sequence in a suitable host cell under conditions compatible with the control sequences.
A nucleotide sequence encoding an enzyme of the invention may be manipulated in a variety of ways to provide for expression of the enzyme. Manipulation of the nucleotide se¬ quence prior to its insertion into a vector may be desirable or necessary depending on the ex- pression vector. The techniques for modifying nucleotide sequences utilizing recombinant DNA methods are well known in the art.
The control sequence may be an appropriate promoter sequence, a nucleotide se¬ quence that is recognized by a host cell for expression of the nucleotide sequence. The pro¬ moter sequence contains transcriptional control sequences, which mediate the expression of the polypeptide. The promoter may be any nucleotide sequence which shows transcriptional activity in the host cell of choice including mutant, truncated, and hybrid promoters, and may be obtained from genes encoding extra cellular or intracellular polypeptides either homologous or heterologous to the host cell.
Examples of suitable promoters for directing the transcription of the nucleic acid con- structs of the present invention, especially in a bacterial host cell, are the promoters obtained from the E. coli lac operon, Streptomyces coelicolor agarase gene (dagA), Bacillus subtilis Ie- vansucrase gene (sacB), Bacillus licheniformis alpha-amylase gene {amyL), Bacillus stearothermophilus maltogenic amylase gene {amyM), Bacillus amyloliquefaciens alpha- amylase gene (amyQ), Bacillus licheniformis penicillinase gene (jpenP), Bacillus subtilis xylA and xylB genes, and prokaryotic beta-lactamase gene (Villa-Kamaroff et al., 1978, Proceed¬ ings of the National Academy of Sciences USA 75: 3727-3731), as well as the tac promoter (DeBoer et al., 1983, Proceedings of the National Academy of Sciences USA 80: 21-25). Further promoters are described in "Useful proteins from recombinant bacteria" in Scientific American, 1980, 242: 74-94; and in Sambrook et al., 1989, supra. Examples of suitable promoters for directing the transcription of the nucleic acid con¬ structs of the present invention in a filamentous fungal host cell are promoters obtained from the genes for Aspergillus oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, As¬ pergillus niger neutral alpha-amylase, Aspergillus niger acid stable alpha-amylase, Aspergillus niger or Aspergillus awamori glucoamylase (glaA), Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease, Aspergillus oryzae triose phosphate isomerase, Aspergillus nidulans acetamidase, and Fusarium oxysporum trypsin-like protease (WO 96/00787), as well as the NA2-tpi promoter (a hybrid of the promoters from the genes for Aspergillus niger neutral alpha- amylase and Aspergillus oryzae triose phosphate isomerase), and mutant, truncated, and hy¬ brid promoters thereof.
In a yeast host, useful promoters are obtained from the genes for Saccharomyces cer- evisiae enolase (ENO-1), Saccharomyces cerevisiae galactokinase (GAL1), Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP), 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 may also be a suitable transcription terminator sequence, a se¬ quence recognized by a host cell to terminate transcription. The terminator sequence is oper- ably linked to the 3' terminus of the nucleotide sequence encoding the enzyme. Any termina¬ tor which is functional in the host cell of choice may be used in the present invention.
Preferred terminators for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans an- thranilate synthase, Aspergillus niger alpha-glucosidase, and Fusarium oxysporum trypsin-like protease.
Preferred terminators for yeast host cells are obtained from the genes for Saccharomy¬ ces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C (CYC1 ), and Saccharomy¬ ces cerevisiae glyceraldehyde-3-phosphate dehydrogenase. Other useful terminators for yeast host cells are described by Romanos et al., 1992, supra. The control sequence may also be a suitable leader sequence, a non-translated region of an mRNA which is important for translation by the host cell. The leader sequence is opera- bly linked to the 5' terminus of the nucleotide sequence encoding the polypeptide. Any leader sequence that is functional in the host cell of choice may be used in the present invention.
Preferred leaders for filamentous fungal host cells are obtained from the genes for As- pergillus oryzae TAKA amylase and Aspergillus nidulans triose phosphate isomerase.
Suitable leaders for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae 3-phosphoglycerate kinase, Sac¬ charomyces cerevisiae alpha-factor, and Saccharomyces cerevisiae alcohol dehydro- genase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP). The control sequence may also be a polyadenylation sequence, a sequence operably linked to the 3' terminus of the nucleotide sequence and which, when transcribed, is recog¬ nized by the host cell as a signal to add polyadenosine residues to transcribed mRNA. Any polyadenylation sequence which is functional in the host cell of choice may be used in the present invention. Preferred polyadenylation sequences for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Asper- gillus nidulans anthranilate synthase, Fusarium oxysporum trypsin-like protease, and Aspergillus niger alpha-glucosidase.
Useful polyadenylation sequences for yeast host cells are described by Guo and Sherman, 1995, Molecular Cellular Biology 15: 5983-5990. The control sequence may also be a signal peptide coding region that codes for an amino acid sequence linked to the amino terminus of a polypeptide and directs the encoded enzyme into the cell's secretory pathway. The 5' end of the coding sequence of the nucleotide sequence may inherently contain a signal peptide coding region naturally linked in translation reading frame with the segment of the coding region which encodes the secreted enzyme. Al- ternatively, the 5' end of the coding sequence may contain a signal peptide coding region which is foreign to the coding sequence. The foreign signal peptide coding region may be re¬ quired where the coding sequence does not naturally contain a signal peptide coding region. Alternatively, the foreign signal peptide coding region may simply replace the natural signal peptide coding region in order to enhance secretion of the enzyme. However, any signal peptide coding region which directs the expressed enzyme into the secretory pathway of a host cell of choice may be used in the present invention.
Effective signal peptide coding regions for bacterial host cells are the signal peptide coding regions obtained from the genes for Bacillus NCIB 11837 maltogenic amylase, Bacillus stearothermophilus alpha-amylase, Bacillus licheniformis subtilisin, Bacillus licheniformis beta- lactamase, Bacillus stearothermophilus neutral proteases (nprT, nprS, nprM), and Bacillus subtilis prsA. Further signal peptides are described by Simonen and Palva, 1993, Microbi¬ ological Reviews 57: 109-137.
Effective signal peptide coding regions for filamentous fungal host cells are the signal peptide coding regions obtained from the genes for Aspergillus oryzae TAKA amylase, Asper- gillus niger neutral amylase, Aspergillus niger glucoamylase, Rhizomucor miehei aspartic pro¬ teinase, Humicola insolens cellulase, and Humicola lanuginosa lipase.
Useful signal peptides for yeast host cells are obtained from the genes for Saccharo- myces cerevisiae alpha-factor and Saccharomyces cerevisiae invertase. Other useful signal peptide coding regions are described by Romanos et al., 1992, supra. The control sequence may also be a propeptide coding region that codes for an amino acid sequence positioned at the amino terminus of a enzyme. The resultant polypeptide may be denoted a pro-enzyme or propolypeptide. A propolypeptide is generally inactive and can be converted to a mature active polypeptide by catalytic or autocatalytic cleavage of the propep¬ tide from the propolypeptide. The propeptide coding region may be obtained from the genes for Bacillus subtilis alkaline protease (aprE), Bacillus subtilis neutral protease (nprT), Sac¬ charomyces cerevisiae alpha-factor, Rhizomucor miehei aspartic proteinase, and My- celiophthora thermophila laccase (WO 95/33836. Where both signal peptide and propeptide regions are present at the amino terminus of a polypeptide, the propeptide region is positioned next to the amino terminus of a polypeptide and the signal peptide region is positioned next to the amino terminus of the propeptide region. In yeast, the ADH2 system or GAL1 system may be used. In filamentous fungi, the TAKA al- pha-amylase promoter, Aspergillus niger glucoamylase promoter, and Aspergillus oryzae glu- coamylase promoter may be used as regulatory sequences.
Other examples of regulatory sequences are those which allow for gene amplification. In eukaryotic systems, these include the dihydrofolate reductase gene which is amplified in the presence of methotrexate, and the metallothionein genes which are amplified with heavy met- als. In these cases, the nucleotide sequence encoding the polypeptide would be operably linked with the regulatory sequence.
Recombinant expression vectors
The present invention also relates to recombinant expression vectors comprising the nucleic acid construct of the invention. The various nucleotide and control sequences de¬ scribed above may be joined together to produce a recombinant expression vector, which may include one or more convenient restriction sites to allow for insertion or substitution of the nu¬ cleotide sequence encoding the polypeptide at such sites. Alternatively, the nucleotide se¬ quence of the present invention may be expressed by inserting the nucleotide sequence or a nucleic acid construct comprising 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 expression.
The recombinant expression vector may be any vector (e.g., a plasmid or virus) that can be conveniently subjected to recombinant DNA procedures and can bring about the ex- pression of the nucleotide sequence. The choice of the vector will typically depend on the compatibility of the vector with the host cell into which the vector is to be introduced. The vec¬ tors may be linear or closed circular plasmids.
The vector may be an autonomously replicating vector, i.e., a vector that exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a plasmid, an extrachromosomal element, a minichromosome, or an artificial chromo¬ some.
The vector may contain any means for assuring self-replication. Alternatively, the vec¬ tor may be one which, when introduced into the host cell, is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated. Furthermore, a single vector or plasmid or two or more vectors or plasmids which together contain the total DNA to be introduced into the genome of the host cell, or a transposon may be used. The vectors of the present invention preferably contain one or more selectable markers that permit easy selection of transformed cells. A selectable marker is a gene the product of which provides for biocide or viral resistance, resistance to heavy metals, prototrophy to auxotrophs, and the like. Examples of bacterial selectable markers are the dal genes from Bacillus subtilis or Ba- cillus licheniformis, or markers that confer antibiotic resistance such as ampicillin, kanamycin, chloramphenicol or tetracycline resistance. Suitable markers for yeast host cells are ADE2, HIS3, LEU2, LYS2, MET3, TRP1 , and URA3. Selectable markers for use in a filamentous fungal host cell include, but are not limited to, amdS (acetamidase), argB (ornithine carbamoyl- transferase), bar (phosphinothricin acety transferase) , hygB (hygromycin phosphotransferase), niaD (nitrate reductase), pyrG (orotidine-5'-phosphate decarboxylase), sC (sulfate adenyltrans- ferase), trpC (anthranilate synthase), as well as equivalents thereof.
Preferred for use in an Aspergillus cell are the amdS and pyrG genes of Aspergillus nidulans or Aspergillus oryzae and the bar gene of Streptomyces hygroscopicus. The vectors of the present invention preferably contain an element(s) that permits sta¬ ble integration of the vector into the host cell's genome 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 nucleotide se¬ quence encoding the polypeptide or any other element of the vector for stable integration of the vector into the genome by homologous or nonhomologous recombination. Alternatively, the vector may contain additional nucleotide sequences for directing integration by homolo¬ gous recombination into the genome of the host cell. The additional nucleotide sequences en¬ able the vector to be integrated into the host cell genome at a precise location(s) in the chro¬ mosome^). To increase the likelihood of integration at a precise location, the integrational elements should preferably contain a sufficient number of nucleotides, such as 100 to 1,500 base pairs, preferably 400 to 1 ,500 base pairs, and most preferably 800 to 1 ,500 base pairs, which are highly homologous with the corresponding target sequence to enhance the probabil¬ ity of homologous recombination. The integrational elements may be any sequence that is homologous with the target sequence in the genome of the host cell. Furthermore, the integra- tional elements may be non-encoding or encoding nucleotide sequences. On the other hand, the vector may be integrated into the genome of the host cell by non-homologous recombina¬ tion.
For autonomous replication, the vector may further comprise an origin of replication enabling the vector to replicate autonomously in the host cell in question. Examples of bacte- rial origins of replication are the origins of replication of plasmids pBR322, pUC19, pACYC177, and pACYC184 permitting replication in E. coli, and pUB110, pE194, pTA1060, and pAMβi permitting 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.
The origin of replication may be one having a mutation which makes its functioning temperature-sensitive in the host cell (see, e.g., Ehrlich, 1978, Proceedings of the National Academy of Sciences USA 75: 1433).
More than one copy of a nucleotide sequence of the present invention may be inserted into the host cell to increase production of the gene product. An increase in the copy number of the nucleotide sequence can be obtained by integrating at least one additional copy of the sequence into the host cell genome or by including an amplifiable selectable marker gene with the nucleotide sequence where cells containing amplified copies of the selectable marker gene, and thereby additional copies of the nucleotide sequence, can be selected for by culti¬ vating the cells in the presence of the appropriate selectable agent.
The procedures used to ligate the elements described above to construct the recombinant ex¬ pression vectors of the present invention are well known to one skilled in the art (see, e.g., Sambrook et al., 1989, supra).
Recombinant host cells
The present invention also relates to recombinant a host cell comprising the nucleic acid con¬ struct of the invention, which are advantageously used in the recombinant production of the polypeptides. A vector comprising a nucleotide sequence of the present invention is intro¬ duced into a host cell so that the vector is maintained as a chromosomal integrant or as a self- replicating extra-chromosomal vector as described earlier.
The host cell may be a unicellular microorganism, e.g., a prokaryote or a non- unicellular microorganism, e.g., a eukaryote. Useful unicellular cells are bacterial cells such as gram positive bacteria including, but not limited to, a Bacillus cell, e.g., Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus stearothermophilus, Bacillus subtilis, and Bacillus thuringiensis; or a Streptomyces cell, e.g., Streptomyces lividans or Streptomyces murinus, or gram negative bacteria such as E. coli and Pseudomonas sp. In a preferred em¬ bodiment, the bacterial host cell is a Bacillus lentus, Bacillus licheniformis, Bacillus stearothermophilus, or Bacillus subtilis cell. In another preferred embodiment, the Bacillus cell is an alkalophilic Bacillus.
The introduction of a vector into a bacteria! host cell may, for instance, be effected by protoplast transformation (see, e.g., Chang and Cohen, 1979, Molecular General Genetics 168: 111-115), using competent cells (see, e.g., Young and Spizizin, 1961 , Journal of Bacteri¬ ology 81: 823-829, or Dubnau and Davidoff-Abelson, 1971, Journal of Molecular Biology 56: 209-221), electroporation (see, e.g., Shigekawa and Dower, 1988, Biotechniques 6: 742-751), or conjugation (see, e.g., Koehler and Thorne, 1987, Journal of Bacteriology 169: 5771-5278). The host cell may be a eukaryote, such as a mammalian, insect, plant, or fungal cell. In a preferred embodiment, the host cell is a fungal cell. "Fungi" as used herein in- eludes the phyla Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota (as defined by Hawksworth et al., In, 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). In a more preferred embodiment, the fungal host cell is a yeast cell. "Yeast" as used herein includes ascosporogenous yeast (Endomycetales), basidiosporogenous yeast, and yeast belonging to the Fungi lmperfecti (Blastomycetes). Since the classification of yeast may change in the future, for the purposes of this invention, yeast shall be defined as described in Biology and Activities of Yeast (Skinner, F.A., Passmore, S.M., and Davenport, R.R., eds, Soc. App. Bacteriol. Symposium Series No. 9, 1980). In an even more preferred embodiment, the yeast host cell is a Candida, Hansenula,
Kluyveromyces, Pichia, Saccharomyces, Schizosaccharomyces, or Yarrowia cell. In a most preferred embodiment, the yeast host cell is a Saccharomyces carlsbergensis, Sac¬ charomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii, Saccharomy¬ ces kluyveri, Saccharomyces norbensis or Saccharomyces oviformis cell. In another most pre- ferred embodiment, the yeast host cell is a Kluyveromyces lactis cell. In another most pre¬ ferred embodiment, the yeast host cell is a Yarrowia lipolytica cell.
In another more preferred embodiment, the fungal host cell is a filamentous fungal cell. "Filamentous fungi" include all filamentous forms of the subdivision Eumycota and Oomycota (as defined by Hawksworth et al., 1995, supra). The filamentous fungi are characterized by a mycelial wall composed of chitin, cellulose, glucan, chitosan, mannan, and other complex polysaccharides. Vegetative growth is by hyphal elongation and carbon catabolism is obliga- tely aerobic. In contrast, vegetative growth by yeasts such as Saccharomyces cerevisiae is by budding of a unicellular thallus and carbon catabolism may be fermentative.
In an even more preferred embodiment, the filamentous fungal host cell is a cell of a species of, but not limited to, Acremonium, Aspergillus, Fusarium, Humicola, Mucor, My- cθliophthora, Neurospora, Penicillium, Thielavia, Tolypocladium, or Trichoderma.
In a most preferred embodiment, the filamentous fungal host cell is an Aspergillus awamori, Aspergillus foetidus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger or Aspergillus oryzae cell. In another most preferred embodiment, the filamentous fungal host cell is a Fusarium bactridioides, Fusarium cerealis, Fusarium crookwellense, Fusarium cul- morum, Fusarium graminearum, Fusarium graminum, Fusarium heterosporum, Fusarium ne- gundi, Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum, Fusarium sporotrich bides, Fusarium sulphureum, Fusarium torulo- sum, Fusarium trichothecioides, or Fusarium venenatum cell. In an even most preferred em¬ bodiment, the filamentous fungal parent cell is a Fusarium venenatum (Nirenberg sp. nov.) cell. In another most preferred embodiment, the filamentous fungal host cell is a Humicola In- solens, Humicola lanuginosa, Mucor miehei, Myceliophthora thermophila, Neurospora crassa, Penicillium purpurogenum, Thielavia terrestris, Trichoderma harzianum, Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma reesei, or Trichoderma viride cell.
Fungal cells may be transformed by a process involving protoplast formation, transfor¬ mation of the protoplasts, and regeneration of the cell wall in a manner known per se. Suitable procedures for transformation of Aspergillus host cells are described in EP 238 023 and Yelton et al., 1984, Proceedings of the National Academy of Sciences USA 81 : 1470-1474. Suitable methods for transforming Fusarium species are described by Malardier et al., 1989, Gene 78: 147-156 and WO 96/00787. Yeast may be transformed using the procedures described by Becker and Guarente, In Abelson, J.N. and Simon, M.I., 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, Journal of Bacteriology 153: 163; and Hinnen et al., 1978, Proceed¬ ings of the National Academy of Sciences USA 75: 1920.
Methods for preparing enzyme polypeptides The present invention also relates to methods for producing an enzyme of the invention com¬ prising (a) cultivating a strain comprising a nucleotide sequence encoding an enzyme of the invention which strain is capable of expressing and secreting the enzyme and (b) recovering the enzyme. In a particular embodiment the strain is a wild type strain such as the Bofryospae- ria rhodina CBS 247.96, while in another embodiment the strain is a recombinant host cell as described, supra.
In these methods of the invention, the cells are cultivated in a nutrient medium suitable for production of the enzyme using methods known in the art. For example, the cell may be cultivated by shake flask cultivation, small-scale or large-scale fermentation (including continu¬ ous, batch, fed-batch, or solid state fermentations) in laboratory or industrial fermentors per- formed in a suitable medium and under conditions allowing the polypeptide to be expressed and/or isolated. The cultivation takes place in a suitable nutrient medium comprising carbon and nitrogen sources and inorganic salts, using procedures known in the art. Suitable media are available from commercial suppliers or may be prepared according to published composi¬ tions (e.g., in catalogues of the American Type Culture Collection). As the enzyme is secreted into the nutrient medium, the enzyme can be recovered directly from the medium.
The resulting enzyme may be recovered by methods known in the art. For example, the enzyme may be recovered from the nutrient medium by conventional procedures including, but not limited to, centrifugation, filtration, extraction, spray-drying, evaporation, or precipita¬ tion.
The polypeptides of the present invention may be purified by a variety of procedures known in the art including, but not limited to, chromatography {e.g., ion exchange, affinity, hydrophobic, chromatofocusing, and size exclusion), electrophoretic procedures (e.g., preparative isoelectric focusing), differential solubility (e.g., ammonium sulfate precipitation), SDS-PAGE, or extrac¬ tion (see, e.g., Protein Purification, J.-C. Janson and Lars Ryden, editors, VCH Publishers, New York, 1989).
Transgenic, plants
The present invention also relates to a transgenic plant, plant part, or plant cell that has been transformed with a nucleotide sequence encoding an enzyme of the invention so as to express and produce the enzyme. In one embodiment the plant could be used as host for production of enzyme in recoverable quantities. The enzyme may be recovered from the plant or plant part. Alternatively, the plant or plant part containing the recombinant enzyme may be used as such for improving the quality of a food or feed, e.g., improving nutritional value, palatability, and rheological properties, or to destroy an antinutritive factor. In particular the plant or plant parts expressing the enzyme may be used as an improved starting material for production of fuel-alcohols or bio-ethanol 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 festuca, lolium, temperate grass, such as Agrostis, and cereals, e.g., wheat, oats, rye, barley, rice, sorghum, and maize (corn).
Examples of dicot plants are tobacco, legumes, such as lupins, potato, sugar beet, pea, bean and soybean, and cruciferous plants (family Brassicaceae), such as cauliflower, rape seed, and the closely related model organism Arabidopsis thaliana.
Examples of plant parts are stem, callus, leaves, root, fruits, seeds, and tubers. Also specific plant tissues, such as chloroplast, apoplast, mitochondria, vacuole, peroxisomes, and cytoplasm are considered to be a plant part. Furthermore, any plant cell, whatever the tissue origin, is considered to be a plant part.
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 an enzyme of the invention may be constructed in accordance with methods known in the art. Briefly, the plant or plant cell is constructed by incorporating one or more expression constructs encoding an enzyme of the invention into the plant host genome and propagating the resulting modified plant or plant cell into a transgenic plant or plant cell. Conveniently, the expression construct is a nucleic acid construct which comprises a nucleotide sequence encoding an enzyme of the present invention operably linked with appropriate regulatory sequences required for expression of the nucleotide sequence in the plant or plant part of choice. Furthermore, the expression construct may comprise a selectable marker useful for identifying host cells into which the expression construct has been integrated and DNA sequences necessary for introduction of the construct into the plant in question (the latter depends on the DNA introduction method 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 enzyme is desired to be expressed. For instance, the expression of the gene encoding an enzyme of the invention may be constitutive or inducible, or may be developmental, stage or tissue specific, and the gene product may 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, the 35S-CaMV promoter may be used (Franck ef a/., 1980,
Cell 21 : 285-294). Organ-specific promoters may be, for example, a promoter from storage sink tissues such as seeds, potato tubers, and fruits (Edwards & Coruzzi, 1990, Ann. Rev. Genet. 24: 275-303), or from metabolic sink tissues such as meristems (Ito et al., 1994, Plant MoI. Biol. 24: 863-878), a seed specific promoter such as the glutelin, prolamin, globulin, or albumin promoter from rice (Wu et al., 1998, Plant and Cell Physiology 39: 885-889), a Vicia faba promoter from the legumin B4 and the unknown seed protein gene from Vicia faba (Conrad et al., 1998, Journal of Plant Physiology 152: 708-711), a promoter from a seed oil body protein (Chen et al., 1998, Plant and Cell Physiology 39: 935-941), the storage protein napA promoter from Brassica napus, or any other seed specific promoter known in the art, e.g., as described in WO 91/14772. Furthermore, the promoter may be a leaf specific promoter such as the rbcs promoter from rice or tomato (Kyozuka et al., 1993, Plant Physiology 102: 991-1000, the chlorella virus adenine methyltransferase gene promoter (Mitra and Higgins, 1994, Plant Molecular Biology 26: 85-93), or the aldP gene promoter from rice (Kagaya et al., 1995, Molecular and General Genetics 248: 668-674), or a wound inducible promoter such as the potato pin2 promoter (Xu et al., 1993, Plant Molecular Biology 22: 573- 588).
A promoter enhancer element may also be used to achieve higher expression of the enzyme of the invention in the plant. For instance, the promoter enhancer element may be an intron which is placed between the promoter and the nucleotide sequence encoding an enzyme of the present invention. For instance, 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 may 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-med\ated transformation, virus-mediated transformation, microinjection, particle bombardment, biolistic transformation, and electroporation (Gasser et al., 1990, Science 244: 1293; Potrykus, 1990, Bio/Technology
8: 535; Shimamoto et al., 1989, Nature 338: 274).
Presently, Agrobacterium tumefaciens-medlated gene transfer is the method of choice for generating transgenic dicots (for a review, see Hooykas and Schilperoort, 1992, Plant Molecular Biology 19: 15-38). However, it can also be used for transforming monocots, although other transformation methods are generally preferred for these plants. Presently, the method of choice for generating transgenic monocots is particle bombardment (microscopic gold or tungsten particles coated with the transforming DNA) of embryonic calli or developing embryos (Christou, 1992, Plant Journal 2: 275-281 ; Shimamoto, 1994, Current Opinion Biotechnology 5: 158-162; Vasil et al., 1992, β/o/Tecήno/ogy 10: 667-674). An alternative method for transformation of monocots is based on protoplast transformation as described by Omirulleh et al., 1993, Plant Molecular Biology 21: 415-428.
Following transformation, the transformants having incorporated therein the expression construct are selected and regenerated into whole plants according to methods well known in the art.
The present invention also relates to methods for producing an enzyme of the invention comprising (a) cultivating a transgenic plant or a plant cell comprising a nucleotide sequence encoding an enzyme of the invention under conditions conducive for production of the enzyme and (b) recovering the enzyme.
Compositions comprising enzyme polypeptides and methods for their preparation The invention provide a composition comprising a polypeptide of the invention and an excipient and a method for preparing such a composition comprising admixing the polypeptide of the invention with an excipient. In a particular embodiment the polypeptide of the invention is the major (polypeptide) component of the composition, e.g., a mono-component composition. The excipient in this context is to be understood as any auxiliary agent or compound used to for¬ mulate the composition and includes solvent, carriers, stabilizers and the like.
The composition may further comprise one or more additional enzymes, such as an aminopeptidase, amylase, carbohydrase, carboxypeptidase, catalase, cellulase, chitinase, cu- tinase, cyclodextrin glycosyltransferase, deoxyribonuclease, esterase, alpha-galactosidase, beta-galactosidase, glucoamylase, alpha-glucosidase, beta-glucosidase, haloperoxidase, in- vertase, laccase, lipase, mannosidase, oxidase, pectinolytic enzyme, peptidoglutaminase, per- oxidase, phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease, transglutaminase, or xylanase.
The compositions may be prepared in accordance with methods known in the art and may be in the form of a liquid or a solid composition. For instance, the enzyme composition may be formulated using methods known to the art of formulating polypeptides and/or pharmaceutical products, e.g. into coated or uncoated granules or micro-granules. The polypeptide of the invention may thus be provided in the form of a granule, preferably a non- dusting granule, a liquid, in particular a stabilized liquid, a slurry or a protected polypeptide. For certain applications, immobilization of the polypeptide on a solid matrix may be preferred. The polypeptide to be included in the composition may be stabilized in accordance with methods known in the art e.g. by stabilizing the polypeptide in the composition by adding and antioxidant or reducing agent to limit oxidation of the polypeptide or it may be stabilized by adding polymers such as PVP, PVA, PEG or other suitable polymers known to be beneficial to the stability of polypeptides in solid or liquid compositions. In a further embodiment the composition of the invention is a detergent composition which, in addition to the polypeptide of the invention, comprises a surfactant and optionally compounds selected from the group consisting of builders such as zeolites, bleaching agents such as percarbonate, bleach enhancers such as TAED or NOBS, suds suppressors, fragrants, etc. In a further embodiment the composition of the invention is a feed composition that in addition to the polypeptide of the invention comprises a cereal or grain product.
In a further embodiment the composition of the invention is a food composition such as a baker's flour composition, a brewed product, a fruit juice, an oil or lard product comprising the polypeptide of the invention. In a further embodiment the composition of the invention is a pulping composition, which in addition to the polypeptide of the invention, comprises pulp.
In a further embodiment the composition of the invention is a biocidal composition, which comprises in addition to the polypeptide of the invention, an oxidoreductase enhancer.
Use of enzyme polypeptides or compositions comprising them
In still further aspects the invention provides use of the polypeptides or polynucleotides of the invention or a composition comprising said polypeptides or polynucleotides in various applications, particularly (technical) processes such as processes performed in industry or household, herein under for commercial research purposes. Hence the invention encom- passes a process comprising employing a polypeptide of the invention or a polynucleotide of the invention in a (technical) industrial, research or household process. In one embodiment the polypeptide or the composition of the invention is used for cleaning a cellulosic fabric.
In another embodiment the polypeptide or the composition of the invention is used to prepare a food or feed additive. In yet another embodiment the polypeptide or the composition of the invention is used for treatment of lignolosic materials and pulp.
DETERGENT DISCLOSURE
The polypeptide of the invention may be added to and thus become a component of a detergent composition. The detergent composition of the invention may for example be formulated as a hand or machine laundry detergent composition including a laundry additive composition suitable for pre-treatment of stained fabrics and a rinse added fabric softener composition, or be formu¬ lated as a detergent composition for use in general household hard surface cleaning opera¬ tions, or be formulated for hand or machine dishwashing operations. In a specific aspect, the invention provides a detergent additive comprising the poly¬ peptide of the invention. The detergent additive as well as the detergent composition may comprise one or more other enzymes such as a protease, a lipase, a cutinase, an amylase, a carbohydrase, a cellulase, a pectinase, a mannanase, an arabinase, a galactanase, a xy- lanase, an oxidase, e.g., a laccase, and/or a peroxidase. In general the properties of the chosen enzyme(s) should be compatible with the se¬ lected detergent, (i.e. pH-optimum, compatibility with other enzymatic and non-enzymatic in¬ gredients, etc.), and the enzyme(s) should be present in effective amounts.
Proteases: Suitable proteases include those of animal, vegetable or microbial origin. Microbial origin is preferred. Chemically modified or protein engineered mutants are included. The protease may be a serine protease or a metallo protease, preferably an alkaline microbial protease or a trypsin-like protease. Examples of alkaline proteases are subtilisins, especially those derived from Bacillus, e.g., subtilisin Novo, subtilisin Carlsberg, subtilisin 309, subtilisin 147 and subtilisin 168 (described in WO 89/06279). Examples of trypsin-like proteases are trypsin (e.g. of porcine or bovine origin) and the Fusarium protease described in WO 89/06270 and WO 94/25583.
Examples of useful proteases are the variants described in WO 92/19729, WO 98/20115, WO 98/20116, and WO 98/34946, especially the variants with the specific position substitutions mentioned therein.
Preferred commercially available protease enzymes include Alcalase®, Savinase®, Primase®, Duralase®, Esperase®, and Kannase® (Novozymes A/S), Maxatase®, Maxacal®, Maxapem®, Properase®, Purafect®, Purafect OxP®, FN2®, and FN3® (Genencor Interna¬ tional Inc.).
Lipases: Suitable lipases include those of bacterial or fungal origin. Chemically modi¬ fied or protein engineered mutants are included. Examples of useful lipases include lipases from Humicola (synonym Thermomyces), e.g. from H. lanuginosa (T. lanuginosus) as de¬ scribed in EP 258 068 and EP 305 216 or from H. insolens as described in WO 96/13580, a Pseudomonas lipase, e.g. from P. alcaligenes or P. pseudoalcaligenes (EP 218 272), P. ce¬ pacia (EP 331 376), P. stutzeri (GB 1 ,372,034), P. fluorescens, Pseudomonas sp. strain SD 705 (WO 95/06720 and WO 96/27002), P. wisconsinensis (WO 96/12012), a Bacillus lipase, e.g. from B. subtilis (Dartois et al. (1993), Biochemica et Biophysica Acta, 1131, 253-360), B. stearothermophilus (JP 64/744992) or B. pumilus (WO 91/16422).
Other examples are lipase variants such as those described in WO 92/05249, WO 94/01541 , EP 407 225, EP 260 105, WO 95/35381 , WO 96/00292, WO 95/30744, WO 94/25578, WO 95/14783, WO 95/22615, WO 97/04079 and WO 97/07202. Preferred commercially available lipase enzymes include Lipolase™, Lipolase Ultra™ and Lipex™ (Novozymes AJS).
Amylases: Suitable amylases (alpha and/or beta) include those of bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Amylases include, for example, alpha-amylases obtained from Bacillus, e.g. a special strain of B. licheniformis, de- scribed in more detail in GB 1 ,296,839.
Examples of useful amylases are the variants described in WO 94/02597, WO 94/18314, WO 96/23873, and WO 97/43424, especially the variants with the specific position substitutions mentioned therein.
Commercially available amylases are Duramyl™, Termamyl™, Fungamyl™ and BAN™ (Novozymes A/S), Rapidase™ and Purastar™ (from Genencor International Inc.).
Cellulases: Suitable cellulases include those of bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Suitable cellulases include cellulases from the genera Bacillus, Pseudomonas, Humicola, Fusarium, Thielavia, Acremonium, e.g. the fungal cellulases produced from Humicola insolens, Myceliophthora thermophila and Fusarium oxysporum disclosed in US 4,435,307, US 5,648,263, US 5,691 ,178, US 5,776,757 and WO 89/09259.
Especially suitable cellulases are the alkaline or neutral cellulases having colour care benefits. Examples of such cellulases are cellulases described in EP 0 495 257, EP 0 531
372, WO 96/11262, WO 96/29397, WO 98/08940. Other examples are cellulase variants such as those described in WO 94/07998, EP 0 531 315, US 5,457,046, US 5,686,593, US
5,763,254, WO 95/24471 , WO 98/12307 and PCT/DK98/00299. Commercially available cellulases include Celluzyme®, and Carezyme® (No- vozymes), Clazinase®, and Puradax HA® (Genencor International Inc.), and KAC-500(B) © (Kao Corporation).
Peroxidases/Oxidases: Suitable peroxidases/oxidases include those of plant, bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Examples of useful peroxidases include peroxidases from Coprinus, e.g. from C. cinereus, and variants thereof as those described in WO 93/24618, WO 95/10602, and WO 98/15257.
Commercially available peroxidases include Guardzyme® (Novozymes A/S). The detergent enzyme(s) may be included in a detergent composition by adding separate additives containing one or more enzymes, or by adding a combined additive com¬ prising all of these enzymes. A detergent additive of the invention, i.e. a separate additive or a combined additive, can be formulated e.g. as a granule, a liquid, a slurry, etc. Preferred deter¬ gent additive formulations are granulates, in particular non-dusting granulates, liquids, in par¬ ticular stabilized liquids, or slurries. Non-dusting granulates may be produced, e.g., as disclosed in US 4,106,991 and 4,661 ,452 and may optionally be coated by methods known in the art. Examples of waxy coating materials are poly(ethylene oxide) products (polyethyleneglycol, PEG) with mean mo¬ lar weights of 1000 to 20000; ethoxylated nonylphenols having from 16 to 50 ethylene oxide units; ethoxylated fatty alcohols in which the alcohol contains from 12 to 20 carbon atoms and in which there are 15 to 80 ethylene oxide units; fatty alcohols; fatty acids; and mono- and di- and triglycerides of fatty acids. Examples of film-forming coating materials suitable for applica¬ tion by fluid bed techniques are given in GB 1483591. Liquid enzyme preparations may, for instance, be stabilized by adding a polyol such as propylene glycol, a sugar or sugar alcohol, lactic acid or boric acid according to established methods. Protected enzymes may be pre- pared according to the method disclosed in EP 238,216.
The detergent composition of the invention may be in any convenient form, e.g., a bar, a tablet, a powder, a granule, a paste or a liquid. A liquid detergent may be aqueous, typically containing up to 70 % water and 0-30 % organic solvent, or non-aqueous.
The detergent composition comprises one or more surfactants, which may be non-ionic including semi-polar and/or anionic and/or cationic and/or zwitterionic. The surfac¬ tants are typically present at a level of from 0.1% to 60% by weight.
When included therein the detergent will usually contain from about 1 % to about 40% of an anionic surfactant such as linear alkylbenzenesulfonate, alpha-olefinsulfonate, alkyl sulfate (fatty alcohol sulfate), alcohol ethoxysulfate, secondary alkanesulfonate, alpha-sulfo fatty acid methyl ester, alkyl- or alkenylsuccinic acid or soap.
When included therein the detergent will usually contain from about 0.2% to about 40% of a non-ionic surfactant such as alcohol ethoxylate, nonylphenol ethoxylate, alkyl- polyglycoside, alkyldimethylamineoxide, ethoxylated fatty acid monoethanolamide, fatty acid monoethanolamide, polyhydroxy alkyl fatty acid amide, or N-acyl N-alkyl derivatives of gluco¬ samine ("glucamides").
The detergent may contain 0-65 % of a detergent builder or complexing agent such as zeolite, diphosphate, triphosphate, phosphonate, carbonate, citrate, nitrilotriacetic acid, ethylenediaminetetraacetic acid, diethylenetriaminepentaacetic acid, alkyl- or alkenylsuc- cinic acid, soluble silicates or layered silicates (e.g. SKS-6 from Hoechst).
The detergent may comprise one or more polymers. Examples are carboxy- methylcellulose, poly(vinylpyrrolidone), poly (ethylene glycol), polyvinyl alcohol), poly(vinylpyridine-N-oxide), poly(vinylimidazole), polycarboxylates such as polyacrylates, maleic/acrylic acid copolymers and lauryl methacrylate/acrylic acid copolymers.
The detergent may contain a bleaching system which may comprise a H2O2 source such as perborate or percarbonate which may be combined with a peracid-forming bleach activator such as tetraacetylethylenediamine or nonanoyloxybenzenesulfonate. Alterna- tively, the bleaching system may comprise peroxyacids of e.g. the amide, imide, or sulfone type.
The enzyme(s) of the detergent composition of the invention may be stabilized using conventional stabilizing agents, e.g., a polyol such as propylene glycol or glycerol, a sugar or sugar alcohol, lactic acid, boric acid, or a boric acid derivative, e.g., an aromatic bo- rate ester, or a phenyl boronic acid derivative such as 4-formylphenyl boronic acid, and the composition may be formulated as described in e.g. WO 92/19709 and WO 92/19708.
The detergent may also contain other conventional detergent ingredients such as e.g. fabric conditioners including clays, foam boosters, suds suppressors, anti-corrosion agents, soil-suspending agents, anti-soil redeposition agents, dyes, bactericides, optical bright- eners, hydrotropes, tarnish inhibitors, or perfumes.
It is at present contemplated that in the detergent compositions any enzyme, in particular the enzyme of the invention, may be added in an amount corresponding to 0.01-100 mg of enzyme protein per litre of wash liquor, preferably 0.05-5 mg of enzyme protein per liter of wash liquor, in particular 0.1-1 mg of enzyme protein per litre of wash liquor. The enzyme of the invention may additionally be incorporated in the detergent formulations disclosed in WO 97/07202 that is hereby incorporated as reference.
DEPOSITED MICROORGANISM
The following microorganism was deposited by the applicant according to the Budapest Treaty on the International Recognition of the Deposits of Microorganisms for the Purpose of Patent Procedures at Centraalbureau voor Schimmelcultures, Fungal and Yeast Collection, Uppsala- laan 8, 3584 CT Utrecht, P.O.Box 85167, 3508 AD Utrecht, The Netherlands: Name: Botryosphaeria rhodina
Synonym: Diplodia gossypina (SBL 274) (Berkeley & M.A. Curtis) von Arx
Protolog Arx, J.A. von 1970, "The genera of fungi sporulating in pure culture": 143
Classification: Dothideaceae, Dothideales, Dothidemycetes; Ascomycota
Deposit accession number: CBS 247.96 Date of deposit: 12-Mar-1996
EXAMPLES
Example 1 Identifying functional polypeptides secreted by Botryosphaeria rhodina CBS 247.96
Enzyme finger printing of culture fluids
An enzyme activity profile was obtained by assaying the culture broth on a wide spectrum of enzyme assays. 96 wells microtitre (MT) plates were prepared with substrates and stored at + 10°C until use. Two different pH variaties were prepared: pH3 and pH7. Following substrates were used: 0.05% AZCL (Mazurine dyed and cross-linked substrates, Megazyme) - Amylose, Arabinan, Beta Glucan (Barley), Casein, Collagen, Curdlan, Dextran, Galactan (potato), Galactomannan (Carob), He-Cellulose, Pullulan, Xylan (oat), and Xyloglucan (AZCL-casein could not be used at pH3, and was therefore left out from these plates).
Preparation ofpH3 substrates: 0.1 g of each AZCL substrate was dissolved in 100 ml 0.2M Succinic acid pH3 + 10 microlitres TritonX-100 (0.01%), to give a final concentration of 0,1% AZCL.
Preparation ofpH7 substrates:
0.1 g of each AZCL substrate was dissolved in 50 ml sterile H20 plus 10 microlitres TritonX- 100 (0.01%). 50 ml 0.4M MOPS pH 7 was added to each 50 ml AZCL substrate, to give a final volume of 100 ml and a final concentration of 0.2M buffer, 0,1% AZCL.
Laccase and lipase activity assays were included and substrates were prepared as follows: Preparation ofLaccase substrate:
35 ml 0.08 mg/ml Chicago Sky Blue in 0.2 M phosphate/borate-buffer, pH 9, was prepared
Preparation of Lipase substrate: A polyvinyl alcohol (PVA)/soy bean oil emulsion was prepared by mixing a 2% PVA solution with soy bean oil 3:1. The oil was emulsified using ULTRA-TURRAX mixer and 12 ml of the emulsion was mixed with 500 ml 0.2M sodium-acetate buffer including 1OmM CaCI2 pH 5.5 and 5 ml 0.2% Crystal Violet solution.
US Sterilin 96-wells MT plates were used with a Multidrop S20 Stacker, Titertek Instruments, Inc., Alabama. 200 microlitres of each AZCL-substrate and of the lipase substrate and 150 mi- crolitres of the laccase substrate were dispensed into MT wells and 30-50 μl culture broth were added to each substrate and incubated over night at 26 degree celcius. Result scores were made the assays as follows: 0: no activity, 1 : weak activity, 2: strong activity.
Result tablel: Fingerprinting of D. gossypina culture broth
Substrate Enzyme activity pH 3 pH7
AZCL-Amylose α-amylase 0a 1
AZCL-Arabinan enαfo-1 ,5-α-L- 0 2
(Debranched) arabinanase
AZCL-Beta-Glucan β-glucanase, 2 1
(Barley) Iichenase and cellu- lases
AZCL-Casein proteases Ntb 2
AZCL-Collagen proteases 0 1
AZCL-Curdlan endoΛ ,3-β-D- 1 0 glucanase
AZCL-Dextran endoΛ ,6-α-D- 0 0 glucanase
(dextranase)
AZCL-Galactan (Po¬ endoA ,4-β-D- 0 2 tato) galactanase
AZCL- endo-λ ,4-β-D- 2 2
Galactomannan mannanase
(Carob)
AZCL-HE-Cellulose encto-cellulase 2 2 AZCL-Pullulan limit-dextrinase (pul- 0 0 lulanase)
AZCL-Xylan (Oat endo-1 ,4-β-D- 2 2 Spelts) xylanase
AZCL-Xyloglucan encto-cellulases 0 2
Chicago Sky Blue Laccase 0 0
PVA/soyabean oil Lipase 0 0 a result score for the activity assays: 0= no activity, 1 = weak reaction and 2 = strong reaction b nt = not tested
A. cDNA library construction cDNA from Botryosphaeria rhodina CBS 247.96 was prepared by using standard molecular biology techniques (Ausuble et al. 1995 "Current protocols in molecular biology" Publ.:John Wiley and sons).
Fermentation of the biomass used in the cDNA library production was initiated from an inocu¬ lated PDA plate that had been incubated for 7 days at 28 degrees. Several mycelia-PDA agar plugs were inoculated in shake flasks with Mex1 media containing (per litre): 20 g of soy bean, 15 g of wheat bran, 10 g of cellulose Avicel, 5 g of maltodextrin 01 , 3 g of bacto peptone, 0.2 g of pluronic PE6100, and 1 gram Olive oil. The flasks were shaken at 150 RPM at 26 degrees. After 7 days the mycelium was harvested by filtration through Miracloth and frozen in liquid ni¬ trogen and stored at -800C until use.
RNA isolation: The total RNA was prepared from frozen, powdered mycelium of Botryospaeria rhodina by extraction with guanidium thiocyanate followed by ultracentrifugation though a 5.7M CsCI cushion (Chirgwin, J. M., Przbyla, A.E., Macdonlad, RJ. , and Ruttwer W.J., Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease, Biochemistry 18, 5294-5299, 1979). The polyA enriched RNA was isolated by oligo (dT)-cellulose affinity chro- matography (Aviv, H., and Leder, P., Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose, Proc. Natl. Acad. Sci. USA 69 (6), 1408- 1412, 1972).
Construction of the cDNA library: Double stranded cDNA was synthesized according to the general methods of Gubler U. and Hoffman, B.J., A simple and very efficient method for gen- erating cDNA libraries, Gene 25(2-3), 263-269, (1983); Sambrook, J., Fritsch, E.F., and Mani- antis, T. Molecular cloning: A laboratory Manual, 2nd ed., 1989, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York and Kofod et al. (1994) using a polyA-Not1 primer (Promega, USA). After synthesis, the cDNA was treated with mung bean nuclease, blunt ended with T4 DNA polymerase, and ligated to a 50 fold molar excess of EcoRI adaptors (Invitrogen, USA). The cDNA was cleaved with Notl restriction enzyme (New England Biolabs, USA) according to the manufacturer's instructions and the cDNA size fractionated by agarose gel electrophoresis. cDNA corresponding to 700bp and larger were excised from the gel and purified using the GFX DNA isolation kit (AP Biotech). The prepared cDNA was then directionally cloned by liga- tion into EcoRI-Notl cleaved pMHasδ. The ligation mixture was electroporated into DH 1OB cells (Invitrogen) and plated on LB agar with 50mgs/liter kanamycin. A cDNA plasmid pool was prepared from 30,000 total transformants of the original cDNA-pMHas5 vector ligation. Plasmid DNA was prepared directly from a pool of colonies recovered from solid LB kanamycin selec¬ tive media according to the Qiagen protocol for plasmid DNA isolation (Qiagen Inc. GMBH). Vector used for cloning was pMhasδ, which is described in patent WO 03/044049 and has the following features:
Feature Location Description
CDS 365-1156 Kanamycin resistance
CDS 2232-2387 Beta galactosidase alpha peptide
-10 signal 2189-2192 Shine Dalgamo promotor 2101-2189 Lac promotor misc feature 626-650 KanP1 primer for BACE system
Notable features of this plasmid are the EcoRI-Notl restriction sites proximal to the Shine DaI- garno region of the Lac promoter. This allows EcoRI-Notl adapted cDNAs to be cloned into the vector and the resulting constructs to be actively transcribed and translated in the E. coli host.
B. Transposon construction and preparation
The rationale behind the methology of Transposon Assisted Signal Trapping (TAST) as described in WO 01/77315 A1 is to fuse all genes within a selected genome with a gene en¬ coding a signalless beta-lactamase via a transposon tag. Hence when growing host cell clones comprising the genes of a genome fused with a gene encoding a signalless beta-lactamase via a transposon tag in an ampicillin containg medium only those clones expressing and secreting a beta-lactamase will survive. However the beta-lactamase will only be secreted if the gene to which the beta-lactamase gene is fused has an intact promotor and ribosome binding site (i.e. a gene which is expressed by the cell to produce a polypeptide in real life), which can be rec¬ ognized in the host strain, and if the beta-lactamase is translated so that the synthesized poly¬ peptide is transported across the cytoplasma membrane and folded correctly. Hence, when inserting the fused gene into a selected host cell, those clones, which are ampicillin resistant contains a gene which encodes a functional secreted polypeptide. Usually, when employing the TAST methodology it is even not necessary to express the entire gene. When tagging the genes with a transposon, expression of the N-terminal part of the genes as protein fusion shows that the genes contain intact transcription, translation and secretion sequences. Hence expression of the N-terminal part of the genes as protein fusion is usually regarded as sufficient for assuring expression and secretion of the entire gene.
Thus it can be concluded that the genes obtained by the TAST method actually do encode secreted functional polypeptides.
Construction of a SigA4 transposon containing the β-lactamase reporter gene: Following the instructions of WO 01/77315 A1, the construction of a transposon containing a signal-less β-lactamase gene was carried out using standard molecular biology techniques. The signal-less β-lactamase gene was initially PCR amplified from the vector pUC19) using a proofreading polymerase (Pfu Turbo, Stratagene, USA). The resulting PCR fragment con¬ tained the restriction sites Not\ and EcoRI in order to aid cloning. The plasmid pEntrancepo- son(Camr) containing the Entranceposon and the antibiotic resistance markers CAT (encoding chloramphencol resistance in the transposon) was obtained from Finnzymes, OY (Espoo Finland). The plasmid was digested with the restriction enzymes Not\ and EcoRI, gel purified and ligated with the signal-less β-lactamase containing fragment. The ligation was transformed into electro-competent DH 1OB cells and the E.coli clone containing the recombinant plasmid with the signal-less β-lactamase was identified by restriction analysis and named SigA2.
For transposon preparation, a smaller derivative of SigA2 was constructed, which lacked the bla gene encoding beta-lactamase: Two oligonucleotide primers SigA2NotU-P 5'- TCG CGA TCC GTT TTC GCA TTT ATC GTG AAA CGC T-3' (SEQ ID NO: 43) and SigA2NotD-P 5'-CCG CAA ACG CTG GTG AAA GTA AAA GAT GCT GAA-3' (SEQ ID NO: 44), which bind to the start and stop of the bla gene of SigA2 directing outwards were used PCR amplify SigA2 without the bla gene. A amplificate of approx. 3.6 kb generated in the this PCR reaction was relegated and transformed in to a suitable E.coli strain. A plasmid of 3.6 kb was isolated from a transformant which was able to grow on LB chloramphenicol but not on LB ampicillin. This plasmid maintained both BgIII sites and lacks the active bla gene and was called pSig4. Apali CAM
Figure imgf000052_0001
60 microlitres of pSigA4 plasmid DNA preparation with a concentration of 0.3 μg/μl was di¬ gested with BgIII and separated on an agarose gel. The SigA2 transposon DNA band of 2 kb was eluted and purified by using the "GFX™PCR, DNA and Gel Band Purification Kit" (Amer- sham Pharmacia Biotech Inc.USA) according to the instructions of the vendor and eluted in 200 microlitres EB buffer. SigA2 prepared in this manner could be be used for transposon as- sisted signal trapping (TAST vide infra).
C. Transposon tagging
The transposon prepared from pSigA4 carries a 5'-truncated bla-gene encoding a β-lactamase from which the secretion signal was removed. The β-lactamase conveys ampicillin resistance on E.coli only when the protein is secreted to the periplasm, whereas cytoplasmic expression of β-lactamase does not confer ampicillin resistance. Without a signal sequence, the β- lactamase enzyme will not be transported to the periplasm and therefore the clone will not grow on media containing ampicillin. The signal-less β-lactamase gene was contained within the transposon in such a way that there was a continuous open reading frame between the transposon border and the β-lactamase coding region. In this way the modified transposon, when it transposes into a gene encoding a protein that is secreted, could cause an in-frame fusion with the target gene. This resulted in a fusion gene product that is secreted to the perip¬ lasm of E. coli and conveys resistance to the ampicillin. If the transposon integrated even in- frame into a gene encoding a non-secreted protein, the respective host will not become am¬ picillin resistance. D. Transposon Assisted Signal Trapping of Botrvosphaeria rhodina
A complete description of transposon assisted signal trapping can be found in WO 01/77315. A cDNA plasmid pool was prepared from 30,000 total transformants of the original cDNA-pMHas5 vector ligation. Plasmid DNA was prepared directly from a pool of colonies re- covered from solid LB selective media according to the Qiagen protocol for plasmid DNA isola¬ tion (Qiagen Inc.). The plasmid pool was treated with transposon SigA2 and MuA transposase according to the transposase manufacturer's instructions (Finnizyme, Finland).
For the in vitro transposon tagging of the Botryosphaeria rhodina CBS 247.96 cDNA li¬ brary, 4 or 8 microlitres of SigA2 transposon containing approx. 2,6 micrograms DNA were mixed with 1 microlitres of the DNA concentration of the plasmid pool DNA of the Botryos¬ phaeria rhodina CBS 247.96 cDNA library, 2 microlitres of Finnzymes MuA Transposase (0,22 micrograms/microlitre) and 5 microlitres of 5x buffer from Finnzymes OY, Espoo, Finland) in a total volume of 50 microlitres and incubated at 30 0C for 3.5 hours and followed by heat inactivation at 75 °C for 10 min. The DNA was precipitated by addition of 5 microlitres 3M Na- acetate pH 5 and 110 microlitres 96% ethanol and centrifugation for 30 min at 20000 rpm. The pellet was washed and dried and resuspended in 10 microlitres TE buffer.
1.5 microliter of the transposon tagged plasmid pool were electroporated into 20 micro¬ liter DH 10B ultra-competent cells according to the standard protocol provided with the cells (Gibco-BRL) in a Biorad Gene Pulse device (5OuF, 25mAmp, 1.8 kV) Electroporated cells were incubated in SOC media with shaking (28 degrees celcius, 2 hours, 250 rpm) before being plated on selective media. Three agar media were used:
LB + 50 microgram pr. ml kanamycin,
LB + kanamycin + 15 microgram pr. ml chloramphencol, and/or LB + kanamycin + chloramphenicol + 12.5 microgram pr. ml ampicillin.
From dilution plating of the electroporation onto LB+kanamycin+chloramphenicol media, it was determined that approximately 72.000 colonies were present containing a cDNA library plas¬ mid with a SigA2 transposition per electroporation and that approximately 69 colonies were recovered under triple selection (LB, kanamycin, chorlamphenicol, ampicillin). Further electro¬ poration and plating experiments were performed until 445 colonies, in all, were recovered from the experiment under triple selection. The colonies were miniprepped according to the Qiagen Qiaturbo96 protocol (Qiagen Inc. - USA). Plasmids were sequenced with the transpo¬ son forward and reverse primers (primers A and B) according to the procedure disclosed in the examples of international patent application WO 01/77315 (page 28)
Primer A: AGCGT TTGCG GCCGC GATCC (SEQ ID NO: 45) Primer B: TTATT CGGTC GAAAA GGATC C (SEQ ID NO: 46)
E. Sequence assembly and annotation
DNA sequence was obtained for the reactions on an AB3700 capillary sequencer. Sequences were trimmed to remove vector and transposon sequence and the A and B primer reads for each plasmid. This resulted in 225 assembled sequences which were grouped into 148 contigs by using the program PhredPhrap (Brent Ewing, LaDeana Hillier, Michael C. Wendl, and Phil Green; Base-calling of automated sequencer traces using phred I. Accuracy assessment; Ge¬ nome Research; 8:175-185; 1998; Brent Ewing and Phil Green; Base-calling of automated se- quencer traces using phred II. Error probabilities; Genome Research 8:186-194; 1998). All 148 contigs were subsequently compared to sequences available in standard public DNA and pro¬ tein sequences databases (TrEMBL, SWALL, PDB, EnsemblPep, GeneSeqP) by using the program BLASTX 2.0a19MP-WashU [14-Jul-1998] [Build Iinux-x86 18:51 :44 30-Jul-1998] (Gish, Warren 1994-1997- Unpublished; Gish, Warren and David J. States; Identification of protein coding regions by database similarity search; Nat. Genet. 3:266-72; 1993).
The obtained sequences being, the majority of which were functional genes encoding intact and functional polypeptides, by being obtained from ampicillin resistant clones as ex¬ plained supra, were used as a basis for the manual analysis. In order to verify that ampicillin resistance of the colonies were from increased beta lac¬ tamase activity, beta-lactamase activity was tested in ten different signal trapped clones with different transposon landing sites on the cDNA. Plasmid DNA was re-transformed into One Shot TOP10 chemically competent E. coli cells according to the protocol of Invitrogen Life Technologies and the transformation mixture spread on LB agar with kanamycin (50 μg/ml) and chloramphenicol (10 μg/ml). Colonies were replica plated on LB kanamycin, chloram¬ phenicol with 15 (10 μg/ml) ampicillin after 2 days at 28 degrees C. After 3 days at 28 degrees C, the true growers were inoculated into 10 ml LB medium with Kanamycin (50 μg/ml) and chloramphenicol (10 μg/ml), and incubated over night at 37 degrees C, 275 rpm. The overnight culture were diluted 1 :100 in fresh LB Kan/CAM medium and grown to OD600 = 0.5. The cells were harvested by centrifugation and washed once in 0.9% NaCI. Pellet were suspended in sonication buffer (100 mM Tris-HCI, 2 mM EDTA, pH 8.0), the number of cells adjusted to an optical density of OD600 = 0.5 and sonicated at an of amplitude 1.5 microns using a Soniprep 150, (MSE). The samples were centrifuged at 15.000 rpm for 10 min. and the supernatant used for beta-lactamase assay. The supernatant was mixed with 50 μl nitrocefin chromogenic beta-lactamase substrate. (1 mg/ml in 50% DMSO; 0.05 M PO4 buffer) and 0.1 M PO4 buffer, pH 7.0 up to 1 ml in a plastic cuvette and the change in AbS482 was measured in an Ultrospec 3300 pro spectrophotometer (O'Callahan, 1972). The results were as follows:
Table IX: β-lactamase activity of clones with different distances between the Shine DaI- garno (SD) sequence and the ATG translation initiation codon and transposon landing site.
Clones Transposon landing Distances between SD β-lactamase activ- site on the cDNA sequence and the ATG ity (bp) initiation codon (bp) (Normalized to trappant
ZY063807) __
ZY063832 806 102
ZY063832 650 102 11.5
ZY063836 991 35 35.5
ZY063836 991 35 4.0
ZY063807 851 256 1.0
ZY063827 568 8 202.0
ZY063816 476 126 16.0
ZY063816 634 126 3.0
ZY065171 469 9 106.5
ZY065171 684 9 52.0
The table above illustrates three main points:
1) Beta-lactamase activity can be detected in all ten clones. It should be emphasized that cor- responding plasmid containing E. coli transformants are resistant to 50 mg/liter ampicillin se¬ lection. Combining these two facts, indicates that all ten clones produce an hybrid protein consisting of part of the transposon tagged cDNA fused to the beta lactamase gene in such a manner as to provide an peptide with beta lactamase activity.
2) Because the cDNA of the ten clones were completely sequenced, the landing site of the SigA2 transposon in each clone was established. The 10 clones all had a SigA2 transposon in the correct orientation and in the correct reading frame to promote a hybrid fusion between the N terminal of the native encoded protein and the transposon encoded beta lactamase.
3) In Eukaryotic cDNAs, untranslated upstream (5' UTR) leaders can vary in length from 1 bp to several hundred base pairs. For the cDNA to be optimally translated from the E. coli translation elements such as the Shine-Dalgarno region, an optimal distance of between 4 and 11 base pairs before the ATG start codon is optimal. In the table, we can see that 5'UTRs much longer than optimal still allow for some expression of the cDNA hybrid-beta lactamase fusion protein because beta lactamase activity is observed from the transformed E.coli in the example.
The obtained nucleotide sequences of the invention are functional genes which encode intact and functional polypeptides, not only for the reasons above, but because they were ob- tained from ampicillin resistant clone. The clones obtained herein were ampicillin resistant, be¬ cause after transposon tagging, the genes were fused with the signalless beta-lactamase gene, which is only expressed when fused to a gene with an intact promoter and ribosome- binding site, which can be recognized in the host strain, and translated and transported across the cytoplasm membrane and folded correctly. Therefore is could be concluded that the genes of the invention actually do encode ac¬ tive secreted polypeptides. For the 16 genes sequence analysis revealed, that in-frame fusion with the signalless beta-lactamase gene was obtained. In addition, the intactness of the genes' open reading frame was confirmed by determining the entire nucleotide sequence.
Example 2 Determining enzyme function by homology
The function of a gene or the encoded polypeptide can be predicted by sequences comparison with genes or polypeptides of known function. Similarities between group ADNA and group BpOιy- peptide sequences and sequences from public and internal databases were analysed, to deter¬ mine the functionality of the group ADNA and group Bpoiypeptide sequences. The sequence com- parison was carried out using the program BLASTX 2.0a19MP-WashU [14-Jul-1998]. A careful manual analysis of sequence alignments of group ADNA and group BPoiyPeptide sequences to their closest related sequences with known function made it possible to predict the function of these genes and the encoded polypeptides. Even when the overall amino acid identity was below 40%, which can make it difficult to make reliable predictions, it was possible to predict the function of group ADNA and group Bpoiypeptide sequences by carefully analysing and interpreting the amino acid residues in the catalytic sites and/or in important regions of the polypeptide se¬ quences. If the amino acids of the catalytic site of known sequences were also present in the polypeptide of the invention, combined with a sufficient overall amino acid identity, it was con¬ cluded that the polypeptide from Botryosphaeria rhodina CBS 247.96 had the same function as the known sequence.
Example 3 Preparing group Bp0ιyPeptide polypeptides
To prepare polypeptides from cDNA sequences of a filamentous fungus such as Botryosphae¬ ria rhodina CBS 247.96, it was feasible to express the cDNA in yeast or another filamentous fungus. A good choice, serving as a non-exhaustive example, is expression in Aspergillus oryzae. The example given below is how a cDNA encoding a xylanase (SEQ ID No: 3) was expressed in A. oryzae. An expression plasmid pDaU71 was used. This plasmid contained (1) the A. nidulans amdS gene as selection marker in Aspergillus, (2) the yeast URA3 gene, interrupted by the ampicillin resistance gene for selection in E. coli, (3) a duplication of the A. niger NA2 promoter (neutral amylase) with 3 extra amyR-sites + the 5' untranslated part of the A. nidulans TPI promoter for heterologous expression and (4) the A. niger AMG terminator. As template for amplication of the relevant portion of the Botryosphaeria rhodina cDNA library pool, the following primers were used in the PCR reaction:
Primer #166: CGCGGATCCACCATGGTCTCCTTCAAGTCGATTC (SEQ ID NO: 47) Primer #167: CCGCTCGAGTTACTGCACGGTAATCGTAGC (SEQ ID NO: 47)
The following conditions were used:
Extensor Hi Fidelity Reddy Load DNA polymerase PCR mix was used according to the manu- facturer's instructions (ABGene, Great Britain). cDNA plasmid pool (1 nanogram/microlitre): 5 microlitre
Primer #166 1 microlitre
Primer #167 1 microlitre
PCR master mix 12.5 microlitre Deionised water 7.5 microlitre
Total volume 25 microlitre
The reation was transferred to an MJ Research DNA engine prewarmed to 94 °C and the fol¬ lowing cycle was performed: 94 0C 2 minutes then 25 cycles of
94 0C 30 seconds
53 0C 30 seconds
72 0C 1 minute then
72 0C 10 minutes.
Five microlitre of product was analyzed on a 1% agarose gel to confirm the correct size and quantify the amount of PCR product produced. The remaining 20 microlitre mixture was GFX purified according to the manufacturer's instructions (AP Pharma). 20 microlitre of the 40 microlitre purified product was used for a standard BamHI-Xhol restriction digest in a 30 microlitre standard overnight digestion reaction. The restricted product was once again purified by GFX and used in a standard ligation recation with BamHI-Xhol restricted and purifed pDau71. The ligation product was transformed into DH10B E. coli cells (E. coli DH10B or TOP10 (available from Invitrogen) could be used as cloning hosts in construction of the ex¬ pression vector) and plated on LB ampicillin media. Ten transformants were selected for plas- mid DNA purification and were sequenced to confirm the sequence integrity of the insert. One PCR error free clone pPFJo147 was selected for further studies.
Aspergillus oryzae strain BECh2, which was constructed as described in WO 00/39322 (BECh2 is derived from strain Aspergillus oryzae JaL228, which is constructed on the basis of the deposited strain Aspergillus oryzae IFO 4177 as described in WO 98/12300). Transformation and culture conditions were performed according to Christiansen et al., 1988, Biotechnology 6, 1419-1422 and as described in WO 01/12794-A page 63. After one round of reisolation, 10 ml YPglucose or YPmaltose medium in Nunc tubes were inoculated with spores from the transformants and the cultures were inoculated for 3 days at 30°C.
10 microlitre supernatant samples from the above described 10 ml cultures were sub¬ jected to SDS-gel electrophoresis. The gel was stained with SYPRO Orange Protein Gel Stain (Molecular Probes). Several Aspergillus transformants had a prominent band on the SDS gel. These positives were further analyzed for xylanase activity by performing an AZCL-wheat ara- binoxylan assay at pH 6.0. The substrate, AZCL-Arabinoxylan from wheat (Megazyme), was prepared as a 0.2% w/v suspension in 0.2 M Na-phosphate buffer pH 6.0 + 0.01% Triton-X 100. 900 microlitre substrate was preheated to 37 °C in an Eppendorf thermomixer. 100 micro- litre crude culture fluid supernatant from the recombinant host strain Bech2 or the different samples was added to the substrate and incubated for 15 min at 37 0C at maximum speed. The reaction mixture was then placed on ice for 2 minutes and then centrifuged for 1 min 20.000 x G. 2 x 200 microlitre supernatant was transferred to a microtitter plate and measured at OD 590. Activity was determined as an increase in absorbance.
Example 4 Determining xylanase activity
The culture fluid or a cell lysate of a host strain synthesising and secreting a xylanase in a suitable buffer is used for measuring the activity. A suitable volume of such a sample is spotted on agarose plates which contain the insoluble chromogenic substrate AZCL-Birch xylan (Megazyme ™) and a suitable buffer at pH, e.g. pH is 4.5-7.5. The plate is incubated for an appropriate time, e.g. one day, at an appropriate temperature, e.g. 37DC. The activity is visible as blue halos around the spots.
Example 5 Determining peroxidase activity Peroxidase can be determined spectrophotmetricly using the 2,4 dichlorophenol method of lshida et al., 1987: Ishida, A., N. Futamura, and T. Matsusaka. 1987. Detection of peroxidase activity and its localisation in the forespore envelopes of Bacillus cereus. J. Gen. Appl. Micro- biol. 33:27-32. As indicator a mixture of 1.0 mM 2,4 Dichlorophenol and 82 mM 4- aminoantipyrene in 10OmM potassium phosphate buffer (pH 7.0) can be used while a sub¬ strate of hydrogen peroxide (Sigma), 5OmM in 10OmM potassium phosphate buffer (pH7.0) is suitable. 200 microlitre of appropriately diluted culture fluid supernatant is added to a 1 ml plastic cuvette. 200 microlitre of the indicator mixture is added. Reactions are initiated by the addition of 200 microlitre hydrogen peroxide substrate. Changes in absorbance are observed in a stan¬ dard spectorophotometer measuring at a wavelength of 510 nm.
Example 6 Determining cellulose degradation boosting effect on cellulose degrading enzymes or enzyme mixtures
Some secreted proteins demonstrate synergistic action in degradation of cellose in the pres¬ ence of cellulose degrading enzymes or mixtures thereof. Such secreted proteins may or may not have, in themselves, hydrolase activity. Examples of such secreted proteins and how one detects their cellulose degradation boosting effect can be found in patent application no. US 11/046,124 and corresponding PCT application PCT/US2005/003525 published 30-07-2005, in particular using the examples 24 and anyone from examples 25 to 28, hereby incorporated by reference.
One way of determining this boosting effect is as follows: Culture fluid or a cell lysate of a host strain synthesising and secreting a cellulase boosting polypeptide are concentrated us¬ ing an Amicon stirred cell equipped with a PM10 membrane, 10 kDa cutoff (Millipore, Billerica, MA), and desalted using an Econo-Pac 10DG column (BioRad Laboratories, Hercules, CA). After assay of the protein concentration by BCA (bicinchoninic acid, P. K. Smith et a/., 1985, Anal. Biochem. 150: 76) Protein Assay Kit (Pierce, Rockford, IL) using BSA as standard these polypeptide stocks are stored at -2O0C. The polypeptides are not further purified, and stocks are added to reaction mixtures based on total protein measured.
Corn stover is pretreated at the U.S. Department of Energy National Renewable Energy Laboratory (NREL) using dilute sulfuric acid. The following conditions are used for the pretreatment: 1.4 wt % sulfuric acid at 1650C and 107 psi for 8 minutes. According to NREL, the water-insoluble solids in the pretreated corn stover (PCS) contain 56.5% cellulose, 4.6% hemicellulose and 28.4% lignin. Cellulose and hemicellulose are determined by a two-stage sulfuric acid hydrolysis with subsequent analysis of sugars by high performance liquid chromatography using NREL Standard Analytical Procedure #002. Lignin is determined gravimetrically after hydrolyzing the cellulose and hemicellulose fractions with sulfuric acid using NREL Standard Analytical Procedure #003. Prior to enzymatic hydrolysis, the PCS is ished with a large volume of DDI water on a glass filter; finding the dry weight of the water- ished PCS. Milled PCS is prepared from the water-ished PCS by milling in a coffee-grinder and subsequent ishing with deionized water on a 22 μm Millipore Filter (6P Express Membrane, Stericup, Millipore, Bedford, MA).
Hydrolysis of PCS is conducted using 1.1 ml Immunoware microtubes (Pierce, Rockford, IL) using a total reaction volume of 1.0 ml. In this protocol hydrolysis of PCS (10 mg/ml in 50 mM sodium acetate pH 5.0 buffer) is performed using different protein loadings (expressed as mg of enzyme per gram of PCS) of a test polypeptide of the invention or Celluclast® 1.5L sample (Novozymes A/S, Bagsvaerd, Denmark) in the presence of 3% Aspergillus oryzae beta-glucosidase (recombinantly produced in Aspergillus oryzae according to WO 02/095014) of the cellulase protein loading. Screening of polypeptides of the invention for PCS hydrolyzing capability is performed at 5O0C (Isotemp 102S water baths or TS Autoflow CO2 Jacketed Incubator). Typically, reactions are run in quadruplicate and aliquots taken during the course of hydrolysis. PCS hydrolysis reactions are stopped by mixing a 20 μl aliquot of each hydrolyzate with 180 μl of 0.11 M NaOH (stop reagent). Appropriate serial dilutions are generated for each sample and the reducing sugar content determined using a para-hydroxybenzoic acid hydrazide (PHBAH, Sigma, St. Louis, MO) assay adapted to a 96 well microplate format as described below. Briefly, a 90 μl aliquot of an appropriately diluted sample is placed in a 96 well conical bottomed microplate. Reactions are initiated by adding 60 μl of 1.5% (w/v) PHBAH in 2% NaOH to each well. Plates are heated uncovered at 950C for 10 minutes. Plates are allowed to cool to room temperature (RT) and 50 μl of distilled H2O added to each well. A 100 μl aliquot from each well is transferred to a flat bottomed 96 well plate and the absorbance at A^onm measured using a SpectraMax Microplate Reader (Molecular Devices, Sunnyvale, CA). Glucose standards (0.1-0.0125 mg/ml diluted with 0.4% sodium hydroxide) are used to prepare a standard curve to translate the obtained A410n,!! values into glucose equivalents. The resultant equivalents are used to calculate the percentage of PCS cellulose conversion for each reaction.
The degree of cellulose conversion to reducing sugar (conversion, %) is calculated us¬ ing the following equation:
Conversion m = RS (mg/ml) * 100 * 162 / (Cellulose (maΛtll) * 180) = = RS (mg/mi) * 100 / (Cellulose {mgM) * 1.111 ) In this equation, RS is the concentration of reducing sugar in solution measured in glucose equivalents (mg/ml), and the factor 1.111 reflects the weight gain in converting cellulose to glucose.
To screen for polypeptides of the invention which can enhance Celluclast® 1.5L performance, PCS hydrolysis reactions (1.0 ml protocol, 10 g of PCS per liter, 500C, supplemented by addition of 3% of total loading of Aspergillus oryzae beta-glucosidase) are performed in which 2.5 mg enzyme loading Celluclast® 1.5L is mixed with 2.5 mg polypeptide loading of each sample (5 mg enzyme loading Total protein per reaction). Celluclast® 1.5L control reactions consisting of 10 mg enzyme loading, 5 mg enzyme loading and 2.5 mg enzyme loading are measured and their PCS cellulose conversion values recorded for comparison.
Example 7 Determining lipase activity
The culture fluid or a cell lysate of a host strain synthesising and secreting a lipase in a suit¬ able buffer is used for measuring the activity.
Lipase assay (PNV assay): 20 microlitres of dilution buffer is pipetted into each well of a 96 well microtiter plate. 5 microlitres of sample (supernatant) is added to the dilution buffer. At the start of the assay 200 microlitres of substrate is added to each well and the plate is mounted into an ELISA reader (a programmable spectrophotometer that can read 96 well plates). Absorbance is measured at 405 nm every 30 seconds for 10 minutes. The slope of the time vs. abs405 curve is used as an arbitrary activity unit. Dilution buffer: 25 ml 2M Tris/HCl pH 7.5, 0.50 ml 2M CaCI2, 2.5 ml 15% Brij 35, H2O ad 500 ml.
Substrate stock solution: 0.1295 g (117 microlitres) p-Nitrophenyl valerate SIGMA N 4377 (density 1.11 g/ml) is dissolved in 10 ml methanol. Store in freezer Substrate: IOOmicrolitres substrate stock solution is mixed with 10 ml dilution buffer.
Example 8 Determining protease and peptidase activity
The culture fluid or a cell lysate of a host strain synthesising and secreting a peptidase and/or protease, in a suitable buffer having a pH chosen for optimal activity of the peptidase, may be assayed for that activity by spotting a suitable sample volume (for example 20 microliter) on an agarose plate which contain the insoluble chromogenic substrate AZCL-casein (Megazyme ™) or AZCL-collagen (Megazyme ™) OR Azocoll (Sigma-Aldrich) - e.g at a level of 0.1% w/w. The plate is incubated for an appropriate time, e.g. one day, at a temperature suitable for the func¬ tion of the peptidase, e.g. 37°C. The activity is visible as blue halos around the spots. As an alternative to AZCL-casein and AZCL-collagen (Megazyme ™) non-labelled casein or non- labelled collagene can be used. On non-labelled collagen or non-labelled casein spotted on agarose plates, clearing zones form in the presence of peptidase and/or protease.
Example 9 Determining endo-arabinase activity
The culture fluid or a cell lysate of a host strain synthesising and secreting an arabinase in a suitable buffer having a pH chosen for optimal activity of the arabinase, may be assayed for that activity by spotting a suitable sample volume (for example 20 microliter) on an agarose plate which contain the insoluble chromogenic substrate AZCL-arabinan - e.g at a level of 0.1% w/w. The plate is incubated for an appropriate time, e.g. one day, at a temperature suit¬ able for the function of the arabinase, e.g. 37°C. The activity is visible as blue halos around the spots.
The assay may be performed at different pH. At acidic pH the AZCL-arabinan may be pre¬ pared by dissolving 0.1 g of AZCL arabinan (Mazurine dyed and cross-linked substrate, Megazyme, Ireland) in 100 ml 0.2M Succinic acid pH3 + 10 microlitres TritonX-100 (0.01%), to give a final concentration of 0,1% AZCL. At neutral pH the AZCL-arabinan may be prepared by dissolving 0.1 g of AZCL arabinan (Mazurine dyed and cross-linked substrate, Megazyme, Ire- land) in 50 ml sterile H2O plus 10 microlitres TritonX-100 (0.01%). 50 ml 0.4M MOPS pH 7 is then added to the 50 ml AZCL substrate, to give a final volume of 100 ml and a final concentra¬ tion of 0.2M buffer, 0.1% AZCL.
Example 10 Determining beta-glucosidase activity Many betaglucosidases are likely to have at least some activity on 4-nitrophenyl β-D- glucopyranoside or cellobiose even though that may not be their natural substrates. Activity may also be found using methyl-umbiliferyl beta-D-glucoside which is very sensitive. Generally any (1 ,4)-β- and (1 ,3)-β-oligoglucosides can be used as substrate to assess activity of beta- glucosidase by measuring released glucose by using the Trinder assay (The Sigma Diagnos- tic Glucose (Trinder) Assay, Sigma, St. Louis, MO).
One way of determining beta-glucosidase activity is to make a preparation of the culture fluid or a cell lysate of a host strain synthesising and secreting a beta-glucosidase so that the preparation contains approximately 6.9 X 10"6 mg/ml of total protein, 100 mM sodium citrate pH 5.0, 0.01% Tween-20 and 4 mM p-nitrophenyl-beta-D-glucopyranoside. The preparation is in¬ cubated at 50 0C and aliquots are taken at 0.5, 1 , 2, 3, 3.75, and 24 hours. To each aliquot is added 1 M sodium carbonate pH 10.0, and the p-nitrophenyl anion concentration is determined from the absorbance at 405 nm.
Another way of determining beta-glucosidase is make a preparation of the culture fluid or a cell lysate of a host strain synthesising and secreting a beta-glucosidase by first desalting (BioRad Econo-Pac 10DG column) and then concentrating (Centricon Plus-20, Biomax-5, 5 kD cut-off), to a concentration of 0.92 mg/ml (BCA assay). Then the preparation is incubated at 0.037 and 0.0092 μg/ml total protein with 10 mM cellobiose in 100 mM sodium citrate pH 5.0 plus 0.01% Tween-20 at 650C. Aliquots are taken at 0.5, 1 , 2, 3, 4, 6, and 19 hours. Aliquots are boiled 6 minutes to terminate the reaction, and the glucose concentration is determined using the Trinder assay (Sigma Chemical Co., St. Louis, MO) and external glucose standards. Example 11 Determining esterase activity
The culture fluid or a cell lysate of a host strain synthesising and secreting an esterase in a suitable buffer is used for measuring the activity. When choosing a substrate for detecting ac- tivity of the serine esterase one should preferably choose one which does not form micelles at the concentrations at which the esterase is saturated with substrate, to gain optimal conversion of substrate.
One way of testing esterase activity is to measure the hydrolysis of triacetin in a concentration below CMC for triacetin by the enzyme, by the alkali consumption registered as a function of time under standard conditions such as 30.00C; pH 7.0. Hydrolysis of triacetin by esterase will liberate acetic acid which will requires addition of alkali to maintain a a constant pH of 7.0 (pH- stat method) thus the amount of alkali (usually in the form of sodium hydroxide) required to maintain the pH at 7.0 is a measure of triacetin ester bonds hydrolysed.
Another way of testing esterase activity is to measure the hydrolysis by the esterase of PNP- acetat (para-nitrophenyl-acetate) releasing the coloured PNP. 20 microlitres of dilution buffer is pipetted into each well of a 96 well microtiter plate. 5 microlitres of sample (culture fluid super¬ natant or filtered cell lysate) is added to the dilution buffer. At the start of the assay 200 micro- litres of substrate is added to each well and the plate is mounted into an ELISA reader (a pro- grammable spectrophotometer that can read 96 well plates). Absorbance is measured at 405 nm every 30 seconds for 10 minutes. The slope of the time vs. abs4os curve is used as an arbi¬ trary activity unit.
Dilution buffer. 25 ml 2M Tris/HCI pH 7.5, 0.50 ml 2M CaCI2, 2.5 ml 15% Brij 35, H2O ad 500 ml. Substrate stock solution: a suitable amount of p-Nitrophenyl acetate (analytical grade) is dis¬ solved in 10 ml methanol and stored in a freezer Substrate: 100 microlitres substrate stock solution is mixed with 10 ml dilution buffer.

Claims

1. An isolated polypeptide selected from the group consisting of:
(a) a polypeptide comprising an amino acid sequence which has at least 90% identity with a sequence of a mature polypeptide comprised in the group consisting of SEQ ID NO:
2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO:36, SEQ ID NO: 38, SEQ ID NO: 40 and SEQ ID NO: 42; and
(b) a polypeptide which is encoded by a nucleotide sequence which hybridize under high stringency conditions with a polynucleotide probe selected from the group consisting of (i) the complementary strand to a nucleotide sequence selected from the group of regions of SEQ ID NO: 1 , SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11 , SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ
ID NO: 19, SEQ ID NO: 21 , SEQ ID NO:23, SEQ ID NO: 25, SEQ ID NO: 27,
SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO:
37, SEQ ID NO: 39 and SEQ ID NO: 41 encoding a mature polypeptide,
(ii) the complementary strand to the cDNA sequence contained in a nucleotide se- quences selected from the group of regions of SEQ ID NO: 1 , SEQ ID NO: 3,
SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13,
SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21 , SEQ ID
NO:23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31 , SEQ
ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39 and SEQ ID NO: 41 encoding a mature polypeptide,
wherein the polypeptide has a function of the corresponding mature polypeptides comprised in the group consisting of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO:36, SEQ ID NO: 38, SEQ ID NO: 40 and SEQ ID NO: 42.
2. An isolated enzyme selected from the group consisting of: (a) an enzyme comprising an amino acid sequence which has at least 90% identity with the amino acid sequence of a mature enzyme selected from the group consisting of xy- lanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from the strain of Botryosphaeria rhodina deposited under CBS ac¬ cession No. 247.96,
(b) a polypeptide which is encoded by a nucleotide sequence which hybridizes under high stringency conditions with a polynucleotide probe selected from the group consisting of (i) the complementary strand to a nucleotide sequence comprised in the strain of Botryosphaeria rhodina Deposited under CBS accession No. 247.96 encoding a mature enzyme selected from the group consisting of xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from that strain;
ii) the complementary strand to the cDNA sequence contained in a nucleotide se¬ quences comprised in the strain of Botryosphaeria rhodina Deposited under CBS accession No. 247.96 encoding a mature enzyme selected from the group consisting of xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61C polypeptide, GH 61 D polypeptide, beta-glucosidase, endo-arabinase and pepsin peptidase secreted from that strain;
wherein the enzyme has a function selected from xylanase, serine esterase, peroxidase, GH 61 A polypeptide, GH 61 B polypeptide, GH 61 C polypeptide, GH 61 D polypeptide, beta- glucosidase, endo-arabinase and pepsin peptidase.
3. The polypeptide of claim 1 or 2 selected from the group consisting of: a) a polypeptide comprising an amino acid sequence which has at least 90% identity with a sequence selected from the group consisting of amino acids 1-291 of SEQ ID NO:2;
1-202 of SEQ ID NO:4; amino acids 1-352 of SEQ ID NO:6; amino acids 1-431 of SEQ ID NO:8; amino acids 1-185 of SEQ ID NO:10; amino acids 1-218 of SEQ ID NO:12; amino acids 1-249 of SEQ ID NO:14; amino acids 1-255 of SEQ ID NO:16; amino acids
1-205 of SEQ ID NO:18; amino acids 1-243 of SEQ ID NO:20; amino acids 1-415 of
SEQ ID NO:22; amino acids 1-377 of SEQ ID NO:24; amino acids 1-259 of SEQ ID
NO:26; amino acids 1-248 of SEQ ID NO:28; amino acids 1-149 of SEQ ID NO:30, amino acids 1-202 of SEQ ID NO:32; amino acids 1 to 603 of SEQ ID NO: 34; amino acids 1 to 301 of SEQ ID NO: 36; amino acids 1 to 438 of SEQ ID NO: 38; amino acids
1 to 396 of SEQ ID NO: 40 and amino acids 1 to 262 of SEQ ID NO: 42; b) a polypeptide which is encoded by a nucleotide sequence which hybridizes under high stringency conditions with a polynucleotide selected from the group consisting of: i) the complementary strand of a nucleotide sequence selected from the group consisting of nucleotides 55-927 of SEQ ID NO:1 ; nucleotides 58-663 of SEQ ID
NO:3; nucleotides 55-1110 of SEQ ID NO:5; nucleotides 55-1347 of SEQ ID
NO:7; nucleotides 1-555 of SEQ ID NO:9; nucleotides 49-702 of SEQ ID NO:11; nucleotides 40-786 of SEQ ID NO: 13; nucleotides 55-819 of SEQ ID NO: 15; nucleotides 61-675 of SEQ ID NO:17; nucleotides 1-729 of SEQ ID NO:19; nu- cleotides 55-1299 of SEQ ID NO:21; nucleotides 49-1179 of SEQ ID NO:23; nucleotides 70-846 of SEQ ID NO:25; nucleotides 58-810 of SEQ ID NO:27; nucleotides 55-660 of SEQ ID NO:31 ; nucleotides 46 to 1854 of SEQ ID NO:
33; nucleotides 64 to 966 of SEQ ID NO: 35; nucleotides 55 to 1368 of SEQ ID
NO: 37; nucleotides 61 to 1248 of SEQ ID NO: 39 and nucleotides 64 to 849 of SEQ ID NO: 41;
H) the complementary strand to the cDNA sequence contained in a nucleotide se¬ quences selected from the group of regions consisting of nucleotides 55-927 of SEQ ID NO:1 ; nucleotides 58-663 of SEQ ID NO:3; nucleotides 55-1110 of SEQ ID NO:5; nucleotides 55-1347 of SEQ ID NO:7; nucleotides 1-555 of SEQ ID
NO:9; nucleotides 49-702 of SEQ ID NO:11 ; nucleotides 40-786 of SEQ ID NO: 13; nucleotides 55-819 of SEQ ID NO: 15; nucleotides 61-675 of SEQ ID NO:17; nucleotides 1-729 of SEQ ID NO:19; nucleotides 55-1299 of SEQ ID NO:21; nucleotides 49-1179 of SEQ ID NO:23; nucleotides 70-846 of SEQ ID NO:25; nucleotides 58-810 of SEQ ID NO:27; nucleotides 55-660 of SEQ ID
NO:31; nucleotides 46 to 1854 of SEQ ID NO: 33; nucleotides 64 to 966 of SEQ ID NO: 35; nucleotides 55 to 1368 of SEQ ID NO: 37; nucleotides 61 to 1248 of SEQ ID NO: 39 and nucleotides 64 to 849 of SEQ ID NO: 41.
4. The polypeptide of claim 3, wherein the polypeptide is an enzyme selected from the group consisting of a polypeptide having an amino acid sequence which has at least 95% iden¬ tity with an amino acid sequence selected from the group consisting of amino acids 1-291 of SEQ ID NO:2; 1-202 of SEQ ID NO:4; amino acids 1-352 of SEQ ID NO:6; amino acids 1-431 of SEQ ID NO:8; amino acids 1-185 of SEQ ID NO:10; amino acids 1-218 of SEQ ID NO:12; amino acids 1-249 of SEQ ID NO:14; amino acids 1-255 of SEQ ID NO:16; amino acids 1-205 of SEQ ID NO:18; amino acids 1-243 of SEQ ID NO:20; amino acids 1-415 of SEQ ID NO:22; amino acids 1-377 of SEQ ID NO:24; amino acids 1-259 of SEQ ID NO:26; amino acids 1-248 of SEQ ID NO:28; amino acids 1-149 of SEQ ID NO:30; amino acids 1-202 of SEQ ID NO:32; amino acids 1 to 603 of SEQ ID NO: 34; amino acids 1 to 301 of SEQ ID NO: 36; amino acids 1 to 438 of SEQ ID NO: 38; amino acids 1 to 396 of SEQ ID NO: 40 and amino acids 1 to 262 of SEQ ID NO: 42.
5. The polypeptide of claim 4, wherein the polypeptide is an enzyme selected from the group consisting of a polypeptide which is encoded by a nucleotide sequence which hybridize under very high stringency conditions with a polynucleotide selected from the group consisting of
i) the complementary strand to a nucleotide sequence selected from the group of regions consisting of nucleotides 55-927 of SEQ ID NO:1 ; nucleotides 58-663 of SEQ ID NO:3; nucleotides 55-1110 of SEQ ID NO:5; nucleotides 55-1347 of SEQ ID NO:7; nucleotides 1-555 of SEQ ID NO:9; nucleotides 49-702 of SEQ ID NO:11 ; nucleotides 40-786 of SEQ ID NO:13; nucleotides 55-819 of SEQ ID
NO: 15; nucleotides 61-675 of SEQ ID NO: 17; nucleotides 1-729 of SEQ ID NO: 19; nucleotides 55-1299 of SEQ ID NO:21 ; nucleotides 49-1179 of SEQ ID NO:23; nucleotides 70-846 of SEQ ID NO:25; nucleotides 58-810 of SEQ ID NO:27; nucleotides 55-660 of SEQ ID NO:31; nucleotides 46 to 1854 of SEQ ID NO: 33; nucleotides 64 to 966 of SEQ ID NO: 35; nucleotides 55 to 1368 of
SEQ ID NO: 37; nucleotides 61 to 1248 of SEQ ID NO: 39 and nucleotides 64 to 849 of SEQ ID NO: 41 and
ii) the complementary strand to the cDNA sequence contained in a nucleotide se- quences selected from the group of regions consisting of nucleotides 55-927 of
SEQ ID NO:1; nucleotides 58-663 of SEQ ID NO:3; nucleotides 55-1110 of SEQ
ID NO:5; nucleotides 55-1347 of SEQ ID NO:7; nucleotides 1-555 of SEQ ID
NO:9; nucleotides 49-702 of SEQ ID NO:11 ; nucleotides 40-786 of SEQ ID
NO:13; nucleotides 55-819 of SEQ ID NO:15; nucleotides 61-675 of SEQ ID NO: 17; nucleotides 1-729 of SEQ ID NO: 19; nucleotides 55-1299 of SEQ ID
NO:21; nucleotides 49-1179 of SEQ ID NO.23; nucleotides 70-846 of SEQ ID
NO:25; nucleotides 58-810 of SEQ ID NO:27; nucleotides 55-660 of SEQ ID
NO:31 nucleotides 46 to 1854 of SEQ ID NO: 33; nucleotides 64 to 966 of SEQ
ID NO: 35; nucleotides 55 to 1368 of SEQ ID NO: 37; nucleotides 61 to 1248 of SEQ ID NO: 39 and nucleotides 64 to 849 of SEQ ID NO: 41.
6. The polypeptide of claim 3, wherein the polynucleotide encoding the polypeptide consists of a polypeptide selected from the group consisting of amino acids 1-291 of SEQ ID NO:2; 1- 202 of SEQ ID NO:4; amino acids 1-352 of SEQ ID NO:6; amino acids 1-431 of SEQ ID NO:8; amino acids 1-185 of SEQ ID NO: 10; amino acids 1-218 of SEQ ID NO: 12; amino acids 1-249 of SEQ ID NO: 14; amino acids 1-255 of SEQ ID NO: 16; amino acids 1-205 of SEQ ID NO: 18; amino acids 1-243 of SEQ ID NO:20; amino acids 1-415 of SEQ ID NO:22; amino acids 1-377 of SEQ ID NO:24; amino acids 1-259 of SEQ ID NO:26; amino acids 1-248 of SEQ ID NO:28; amino acids 1-149 of SEQ ID NO:30; amino acids 1-202 of SEQ ID NO:32; amino acids 1 to 603 of SEQ ID NO: 34; amino acids 1 to 301 of SEQ ID NO: 36; amino acids 1 to 438 of SEQ ID NO: 38; amino acids 1 to 396 of SEQ ID NO: 40 and amino acids 1 to 262 of SEQ ID NO: 42.
7. The polypeptide of claim 3, wherein the polypeptide is a GH10 xylanase comprising an amino acid sequence which has at least 90% identity with a GH10 xylanase obtainable from Botryosphaeria rhodina deposited under deposit accession number CBS 247.96.
8. The polypeptide of claim 3, wherein the polypeptide is a GH10 xylanase comprising amino acids 1-291 of SEQ ID NO:2.
9. The polypeptide of claim 3, wherein the polypeptide is a GH10 xylanase consisting of amino acids 1-291 of SEQ ID NO:2.
10. The polypeptide of claim 3, wherein the polypeptide is a GH11 xylanase comprising an amino acid sequence which has at least 90% identity with a GH11 xylanase obtainable from Botryosphaeria rhodina deposited under deposit accession number CBS 247.96.
11. The polypeptide of claim 3, wherein the polypeptides is a GH11 xylanase comprising amino acids 1-202 of SEQ ID NO:4.
12. The polypeptide of claim 3, wherein the polypeptides is a GH11 xylanase consisting of amino acids 1-202 of SEQ ID NO:4.
13. The polypeptide of claim 3, wherein the polypeptide is a serine esterase comprising an amino acid sequence which has at least 90% identity with a serine esterase obtainable from Botryosphaeria rhodina deposited under deposit accession number CBS 247.96.
14. The polypeptide of claim 3, wherein the polypeptide is a serine esterase comprising amino acids 1-352 of SEQ ID NO:6.
15. The polypeptide of claim 3, wherein the polypeptide is a serine esterase consisting of amino acids 1-352 of SEQ ID NO:6.
16. The polypeptide of claim 3, wherein the polypeptide is a Lipase comprising an amino acid sequence which has at least 90% identity with a serine esterase obtainable from Botryosphae- ria rhodina deposited under deposit accession number CBS 247.96.
17. The polypeptide of claim 3, wherein the polypeptide is a Lipase comprising amino acids 1-431 of SEQ ID NO:8.
18. The polypeptide of claim 3, wherein the polypeptide is a Lipase consisting of amino acids 1-431 of SEQ ID NO:8.
19. The polypeptide of claim 3, wherein the polypeptide is a peroxidase comprising an amino acid sequence which has at least 90% identity with a peroxidase obtainable from Botryosphae- ria rhodina deposited under deposit accession number CBS 247.96.
20. The polypeptide of claim 3, wherein the polypeptide is a peroxidase comprising amino acids 1-185 of SEQ ID NO: 10.
21. The polypeptide of claim 3, wherein the polypeptide is a peroxidase consisting of amino acids 1-185 of SEQ ID NO:10.
22. The polypeptide of claim 3, wherein the polypeptide is a GH 61A polypeptide comprising an amino acid sequence which has at least 90% identity with a GH 61 A polypeptide obtainable from Botryosphaeria rhodina deposited under deposit accession number CBS 247.96.
23. The polypeptide of claim 3, wherein the polypeptide is a GH 61 A polypeptide comprising amino acids 1 -218 of SEQ ID NO: 12.
24. The polypeptide of claim 3, wherein the polypeptide is a GH 61 A polypeptide consisting of amino acids 1-218 of SEQ ID NO: 12.
25. The polypeptide of claim 3, wherein the polypeptide is a GH 61 B polypeptide comprising an amino acid sequence which has at least 90% identity with a GH 61 B polypeptide obtainable from Botryosphaeria rhodina deposited under deposit accession number CBS 247.96.
26. The polypeptide of claim 3, wherein the polypeptide is a GH 61 B polypeptide comprising amino acids 1-249 of SEQ ID NO:14.
27. The polypeptide of claim 3, wherein the polypeptide is a GH 61 B polypeptide consisting of amino acids 1-249 of SEQ ID NO:14.
28. The polypeptide of claim 3, wherein the polypeptide is a GH 61 C polypeptide comprising an amino acid sequence which has at least 90% identity with a GH 61 C polypeptide obtainable from Botryosphaeria rhodina deposited under deposit accession number CBS 247.96.
29. The polypeptide of claim 3, wherein the polypeptide is a GH 61 C polypeptide comprising amino acids 1-255 of SEQ ID NO: 16.
30. The polypeptide of claim 3, wherein the polypeptide is a GH 61 C polypeptide consisting of amino acids 1-255 of SEQ ID NO: 16.
31. The polypeptide of claim 3, wherein the polypeptide is a GH 61 D polypeptide comprising an amino acid sequence which has at least 90% identity with a GH 61 D polypeptide obtainable from Botryosphaeria rhodina deposited under deposit accession number CBS 247.96.
32. The polypeptide of claim 3, wherein the polypeptide is a GH 61 D polypeptide comprising amino acids 1-205 of SEQ ID NO: 18.
33. The polypeptide of claim 3, wherein the polypeptide is a GH 61 D polypeptide consisting of amino acids 1-205 of SEQ ID NO: 18.
34. The polypeptide of claim 3, wherein the polypeptide is a beta-glucosidase comprising an amino acid sequence which has at least 90% identity with a beta-glucosidase obtainable from Botryosphaeria rhodina deposited under deposit accession number CBS 247.96.
35. The polypeptide of claim 3, wherein the polypeptide is a beta-glucosidase comprising amino acids 1 to 603 of SEQ ID NO: 34.
36. The polypeptide of claim 3, wherein the polypeptide is a beta-glucosidase consisting of amino acids 1 to 603 of SEQ ID NO: 34.
37. The polypeptide of claim 3, wherein the polypeptide is an endo-arabinase comprising an amino acid sequence which has at least 90% identity with a endo-arabinase obtainable from
Botryosphaeria rhodina deposited under deposit accession number CBS 247.96.
38. The polypeptide of claim 3, wherein the polypeptide is an endo-arabinase comprising amino acids 1 to 301 of SEQ ID NO: 36.
39. The polypeptide of claim 3, wherein the polypeptide is an endo-arabinase consisting of amino acids 1 to 301 of SEQ ID NO: 36.
40. The polypeptide of claim 3, wherein the polypeptide is an endo-arabinase comprising an amino acid sequence which has at least 90% identity with a endo-arabinase obtainable from
Botryosphaeria rhodina deposited under deposit accession number CBS 247.96.
41. The polypeptide of claim 3, wherein the polypeptide is an endo-arabinase comprising amino acids 1 to 438 of SEQ ID NO: 38.
42. The polypeptide of claim 3, wherein the polypeptide is an endo-arabinase consisting of amino acids 1 to 438 of SEQ ID NO: 38.
43. The polypeptide of claim 3, wherein the polypeptide is a pepsin peptidase comprising an amino acid sequence which has at least 90% identity with a pepsin peptidase obtainable from
Botryosphaeria rhodina deposited under deposit accession number CBS 247.96.
44. The polypeptide of claim 3, wherein the polypeptide is a pepsin peptidase comprising amino acids 1 to 396 of SEQ ID NO: 40.
45. The polypeptide of claim 3, wherein the polypeptide is a pepsin peptidase consisting of amino acids 1 to 396 of SEQ ID NO: 40.
46. The polypeptide of claim 3, wherein the polypeptide is a pepsin peptidase comprising an amino acid sequence which has at least 90% identity with a pepsin peptidase obtainable from
Botryosphaeria rhodina deposited under deposit accession number CBS 247.96.
47. The polypeptide of claim 3, wherein the polypeptide is a pepsin peptidase comprising amino acids 1 to 262 of SEQ ID NO: 42.
48. The polypeptide of claim 3, wherein the polypeptide is a pepsin peptidase consisting of amino acids 1 to 262 of SEQ ID NO: 42.
49. A polynucleotide comprising a nucleotide sequence which encodes for the polypeptide defined in claim 3.
50. A nucleic acid construct comprising the nucleotide sequence defined in claim 49 operably linked to one or more control sequences that direct the production of the polypeptide in a host cell.
51. A recombinant expression vector comprising the nucleic acid construct of claim 50.
52. A recombinant host cell comprising the nucleic acid construct of claim 50.
53. A method for producing the polypeptide of claim 3 comprising: a. cultivating a strain, which in its wild-type form is capable of producing the polypeptide, to produce the polypeptide; and b. recovering the polypeptide.
54. A method for producing a polypeptide of claim 3 comprising: c. cultivating a recombinant host cell as defined in claim 52 under conditions conducive for production of the polypeptide; and d. recovering the polypeptide.
55. A composition comprising the polypeptide of claim 3 and an excipient.
56. A method for preparing a composition of claim 55 comprising admixing the polypeptide of claim 1 with the excipient.
57. A storage medium suitable for use in an electronic device comprising information of the amino acid sequence of the polypeptide of claim 3.
58. A storage medium suitable for use in an electronic device comprising information of the nucleic acid sequence of the polynucleotide of claim 49.
PCT/DK2005/000519 2004-08-06 2005-08-06 Polypeptides of botryosphaeria rhodina WO2006012904A1 (en)

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US11/573,261 US7666649B2 (en) 2004-08-06 2005-08-06 Polypeptides of Botryospaeria rhodina
JP2007524180A JP2008508868A (en) 2004-08-06 2005-08-06 Botryosfa area rosina polypeptide
AU2005269084A AU2005269084B2 (en) 2004-08-06 2005-08-06 Polypeptides of Botryosphaeria rhodina
EP05763286A EP1789556A1 (en) 2004-08-06 2005-08-06 Polypeptides of botryosphaeria rhodina
CA2576110A CA2576110C (en) 2004-08-06 2005-08-06 Polypeptides of botryosphaeria rhodina
US12/631,477 US8143047B2 (en) 2004-08-06 2009-12-04 Polypeptides of botryosphaeria rhodina
US13/368,690 US20120171189A1 (en) 2004-08-06 2012-02-08 Polypeptides of Botryosphaeria Rhodina

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