Title of Invention

POLYPEPTIDES OF ALICYCLOBACILLUS SP

Abstract Isolated mature functional polypeptide which is at least 90 % identical to and exhibits the same function of a corresponding secreted polypeptide obtainable from the bacterium Alicyclobacillus sp. deposited under accession number DSM 15716 are disclosed.
Full Text

TITLE: POLYPEPTIDES OF ALICYCLOBACILLUS SP.
FIELD OF THE INVENTION
The present invention relates to functional and operational polypeptides encoded by polynucleotides comprised in the genome of Alicyclobacillus sp. deposited under deposit accession number DSM 15716. The invention relates further to the polynucleotides and constructs of such polynucleotides encoding such polypeptides or facilitatog their expression as well as to method for preparing the polypeptide. Still further like invention relates to compositions comprising the polypeptides and polynucleotides and to uses of the polypeptide. Still further the invention relates to a bacterium Alicyclobacillus sp. as deposited under accession number DSM 15716.
BACKGROUND OF THE INVENTION
Some enzymes from the genus of Alicyclobacillus species are known such as described in Matzke et al.; Gene cloning, nucleotide sequence and biochemical properties of a cytoplasmic cyclomaltodextrinase (neopullulanase) from Alicyclobacillus addocaldarius ATCC 2700; reclassffication of a group of enzymes; Submitted (MAR1999) to the EMBL/GenBank/DDBJ databases or Koivula et ah; Cloning and sequencing of a gene encoding acidophilic amylase from
Bacillus addocaldarius. J. Gen. Microbiol. 139:2399 (1993) or Bartolucci et al.; Thioredoxin
*
from Bacillus addocaldarius: characterization, highlevel expression in Escherichia coli and molecular modeling; Biochem. J. 328:277 (1997) or Tsuruoka et al.; Collagenolytic SerineCarboxyl Proteinase from Alicyclobacillus sendainensis Strati NTAP1: Purification, Characterization, Gene Cloning, and Heterologous Expression; Submitted (MAY2002) to the EMBL/GenBank/DDBJ databases; Eckert K. & Schneider E., A thermoaddophilic endoglucanase (celB) from Alicyclobacillus addocaldarius displays high sequence similarity to arabinofuranosidases belonging to family 51 ofglycosyl hydrolases; Eur. J. Biochem., 270: 35933602, 2003.
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 1he idenffication of functional enzymes or polypeptides for which the activity is still unknown.
Further, whole genome sequencing is a known method to obtasi the information on all genes from a given microorganism e.g. as described in Fleischmann et al; Whole genome sequences and assembly of Haemophilus influenzae et al; 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 genomebased road map; in "Bacillus subtilis and its closest relatives" From genes to cells; p.337355; A. L. Sonenshein (ed.); ASM Press 2002).
One disadvantage of genome sequencing is that the vast majority of the obtained sequences encode non secreted proteins.
Also known is signal trapping which is a method to identify genes including nucleotides encoding a signal peptide using a translations fusion to an extra cellular reporter gene lacking its own signal (WO 01/77315).
SUMMARY OF THE INVENTION
The present Inventors have found a strain of Alicyclobacillus namely Aiicyclobacillus sp. DSM 15716 which grows at low pH (approx 45) and at high temperature (5060 °C). This strain is interesting because the phylogenetic distance between the public known strains and strain DSM 15716 is significant and because the growth conditions are similar to conditions for several applications for industrial enzymes.
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 polypeptides 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 Aiicyclobacillus sp. deposited under deposit accession number DSM 15716 which have functional purpose for the Aiicyclobacillus sp. because such polypepSdes may not only be used for industrial purposes but they may also be produced in industrially relevant processes and amounts.
In a first aspect the invention provides an isolated mature functional polypeptide which is at least 90 % identical to and exhibits the same function of a corresponding secreted polypeptide obtainable from the bacterium Alicyclobacillius sp. deposited under accession number DSM 15716.
In a further aspect the invention provides a bacterial gtutamic peptidase (EC 3.4.23.19).
In further aspects the invention provides a polynuclectide 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 invention 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
(b) invention which strain is capable of expressing and secreting the polypeptide and
(c) recovering the polypeptide.
In a further aspect the invention provides a composition comprising a polypeptide of the invention and a method for preparing such a compostion comprising admixing the polypeptide of the invention with an excipient.
In a further aspect the invention provides a composer, comprising a polynucleotide of the invention and a method for preparing such a composition comprising admixing the polynucleotide of the invention with an excipient.
In further aspects the invention provides use of the polypeptide of the invention or a composition comprising said polypeptide in various applications.
In a further aspect the invention relates to a bacterium Alicyclobacillus sp. as deposited under accession number DSM 15716.
In a final aspect the invention provides an electronic storage medium comprising information of the amino acid sequence of polypeptides of the invention or the nucleotide sequences of the polynucleotide of the invention.
SEQUENCE LISTING
The present application contains information in the form of a sequence Fisting, which is appended 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 SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide encodes the mature polypeptides of SEQ ID NO: 26 to SEQ ID NO: 50. The region of SEQ ID NO: 1 encoding a mature polypeptide thus encodes the mature polypeptide sequence comprised in SEQ D NO: 26, the region of SEQ ID NO: 2 encoding a mature polypeptide encode the mature polypeptide comprised in SEQ ID NO: 27 and so on.
DETAILED DESCRIPTION OF THE INVENTION Definitions
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 invention, the degree of identity between two amino acid sequences was determined by using AlignX in the program of Vector NTI ver. 7.1 (Infdrtnax inc., 7600 Wisconsin Avenue, Suite

#1100, Bethesda, MD 20814, USA). Amino acid alignment was created using the Clustal W algorithm (Nucleic Acid Research, 22 (22): 46734680,1994). The following additional parameters are used: Gap opening penalty of 10, Gap extension penalty of 0.05, Gap separation penalty range of 8. Pairwise 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 following settings: Gap penalty of 10, and gap length penalty of 10. Pairwise alignment parameters is Ktuple=3f gap penalty^ and windows=20.
The term "functional polypeptide" as used hereto in the context of the present invention 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 fulfil by the cell. Optionally, cofactors may be required for the polypeptide to adopt the intended function. One example of functional polypeptides is catalytically active polypeptides or enzymes 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 add 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 test amino add of a mature polypeptide.
The term "secreted polypeptide" as used herein is to be understood as a polypeptide which after expression in a cell is either transported to and released to the surrounding extracellular medium or is associated/embedded in the cellular menixane so that at least a part of the polypeptide is exposed to the surrounding extracellular rnedium.

Polypeptides of the invention
The present invention relates to polypeptides similar to those secreted polypeptides obtainable from Alicyciobacillus sp. deposited under accession number DSM 15716. In particular the invention provides an isolated mature functional polypeptide which is at least 90 % identical to and exhibits the same function of a corresponding secreted polypeptide obtainable from the bacterium Alicyciobacillus sp. deposited under accession number DSM 15716.
Moreover, surprisingly the glutamic peptidase of SEQ ID NO: 27 expressed by the Alicyclobacillus sp. DSM 15716, is the first glutamic peptidase ever to have been isolated from a bacterium. Hence, the invention also provides a bacterial glutamic peptidase (EC 3.4.23.19)
Polypeptides of the invention are, in particular, secreted by Alicydobacillus sp. DSM 15716 with the purpose of serving a function for that particular cell.
Among the thousands of potential genes in the genome of Alicyciobacillus sp. DSM 15716 the polynucleotide of this genome encoded 25 secreted functional mature polypeptides comprised in SEQ ID NO: 26 to SEQ ID NO: 50, which were determined to be functional, that is translated into functional polypeptides by the chosen host cell.
Accordingly, Alicyciobacillus sp. DSM 15716 expresses and secretes the functional mature polypeptides comprised in SEQ ID NO: 26 to SEQ NO: 50 and in the genome of that particular strain, the regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide are the genes encoding the mature polypeptides comprised in SEQ ID NO: 26 to SEQ NO: 50. Further in a particular embodiment the genes encoding the mature polypeptides comprised in of SEQ ID NO: 26 to SEQ NO: 50 can all be expressed and their corresponding mature polypeptides can be secreted when culturing an E. coli host transformed with polynucleotide comprising those regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide. By comparing homology or identity of the sequences of the 25 polypeptide sequences to known sequences the particular function of the polypeptkies were annotated. At least 15 of the 25 secreted functional polypeptides were determined to be enzymes.
In particular the isolated polypeptide is selected from the group consisting of:
(a) a polypeptide having an amino add sequence which has at least 90% identity with an
(b) amino acid sequence selected from the group consisting of the mature polypeptides
(c) comprised in SEQ ID NO: 26 to SEQ ID NO: 50 and
(d) a polypeptide which is encoded by a nucletide sequence which hybridize under high
(e) stringency conditions with a polynucleotide probe selected from the group consisting of
(f) (i) the complementary strand to a nucleotide sequence selected from the group
consisting of regions of SEQ ID NO: 1 to SEQ D NO: 3 encoding a mature polypeptide,

the complementary strand to the cDNA sequence contained in a nucleotide sequences selected from regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide;
wherein the polypeptide exhibits the function of the corresponding mature polypeptide of SEQ ID NO: 26 to SEQ ID NO: 50.
In one particular embodiment the polypeptide of the invention is selected among the enzymes secreted by Alicyclobacillus sp. deposited under DSM accession No. 15716 and isolated by the present inventors, i.e. the group of enzjymes consisting of acid endoglucanase, acid cellulose, glutamic peptidase, multi copper oxidase, serinecarboxy! protease, serine protease, HtrAIike serine protease, disulfide isomerase, gammaDglutamylLdiamino acid endopeptidase, endobetaNacetylglucosaminidase, peptidylprolyiisomerase, acid phosphatase, phytase, phosphoiipase C, polysaccharide deacetylase, xylan deacetylase and sulfite oxidase.
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
(b) the amino acid sequence of a mature enzyme selected from the group consisting of
(c) acid endoglucanase or acid cellulose, glutamic peptidase, multi copper oxidase, serine
(d) carboxyl protease, serine protease or HtrAIike serine protease, disulfide isomerase,
(e) gammaDglutamylLdiarnino acid endopeptidase, endobetaN
(f) acetyiglucosaminidase, peptidylprolylisomerase, acid phosphatase or phytase or
(g) phosphoiipase C, polysaccharide deacetyiase or xylan deacetylase and sulfite oxidase
(h) secreted from the strain of Alicyclobacillus sp. Deposited under DSM accession No.
(i) 15716 and
(j) an enzyme which is encoded by a nucleotide sequence which hybridize under high
(k) stringency conditions with a polynucleotide probe selected from the group consisting of
(l) (i) the complementary strand to a nucleotide sequence comprised in the strain of
Alicyclobacillus sp. Deposited under DSM accession No. 15716 encoding a mature enzyme selected from the group consisting of add endoglucanase or acid celluiase, glutamic peptidase, mufti copper oxidase, serinecarboxyl protease, serine protease or HtrAIike serine protease, disulfide isomerase, gammaDglutamylLdiamino acid endopeptidase, endobetaNacetylglucosaminidase, peptidylprolylisomerase, add phosphstase or phytase or phosphoiipase C, polysaccharide deacetylase or xylan deacetylase and sulfate oxidase secreted

from that strain;
the complementary strand to the cDNA sequence contained in a nucleotide sequences comprised in the strain of Alicyclobacillus sp. Deposited under DSM accession No. 15716 encoding a mature en2yme selected from the group consisting of acid endogiucanase or acid oellulase, glutamic peptidase, multi copper oxidase, serinecarboxyl protease, serine protease or HtrAlike serine protease, disulfide isomerase, gammaDglutamylLdiamino add endopeptidase, endobetaNacetylglucosamindase, pepidylprolylisisomerase, acid phosphatase or phytase or phospholipase C, polysaccharide deacetylase or xylan deacetyiase and sulfite oxidase secreted torn that strain and
wherein the enzyme have a function selected from acid endogfucanase or acid cellulose, glutamic peptidase, multi copper oxidase, serinecarboxyl protease, serine protease or HtrAfike serine protease, disulfide isomerase, gammaDglutamylLdiamino acid endopeptidase, endobetaNacetylglucosaminidase, peptidylprolylisornerase, add phosphatase or phytase or phospholipase C, polysaccharide deacetylase or xylan deacetylase and sulfrte oxidase.
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
(b) amino acid sequence selected from mature enzymes comprised in SEQ ID NO: 26 to
(c) SEQ ID NO: 40 and
(d) an enzyme which is encoded by a nucleotide sequence which hybridize under high
(e) stringency conditions with a polynucleotide probe selected from the group consisting of
(f) (i) the complementary strand to a nucleotide sequence selected from the group of
regions of SEQ ID NO: 1 to SEQ ID NO: 15 encoding the mature enzyme, (ii) the complementary strand to the cDNA sequence contained in a nucleotide sequences selected from regions of SEQ ID NO: 1 to SEQ ID NO: 15 encoding the mature enzyme and
wherein the enzyme has a function of the corresponding mature polypeptides comprised in SEQ ID NO: 26 to SEQ ID NO: 40
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 material 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 1/2% 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 invention constitutes at least 92% by weight of the total polypeptide material present in the preparation, 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 "essentially pure form", i.e. that the polypeptide preparation is essentially free of other polypeptide material with which it is natively associated TMs can be accomplished, for example, by preparing the polypeptide of the invention by means of wellknown 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 eukaryotic cell. The cell may further have been modified by genetic engineering
In a particular embodiment, the polypeptide of the invention is an enzyme exhibiting optimum enzyme activity at a temperature within the range from about 10°C to about 80°C, particularly in the range from about 20°C to about 60°C.
In a particular embodiment the polypeptide of the invention is an enzyme, which is functionally stabile at a temperature of up to 100°C, in particular up to 80°C, more particularly up to 60°C.
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%t in particular at least 60%, such as at least 70%, more particularly at least 30%, 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 mature enzymes comprised in SEQ ID NO: 26 to SEQ ID NO: 50.
In particular the isolated mature functional polypeptide is at least 90 % identical to and exhibits the same function of a corresponding secreted polypeptide obtainable from the bacterium Alicyclobacillus sp. deposited under accession number DSM 15716 and specically the polypeptide of the invention comprises, contains or consists 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 SEQ D NO: 26 to SEQ ID NO: 50. The percent identity is particularly 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 percent identity is at least 50%; particularly at least 60%, particularly at least 65%, particularly at least 70%, particularly at least 75%, particularly at least 80%, and even more particularty at least 85% identity.

In a particular embodiment, the amino acid sequence of the polypeptide of the invention 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 particular 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 SEQ ID NO: 26 to SEQ ID NO: 50.
The polypeptide of the invention may be a wildtype polypeptide isolated from a natural source such as the strain Alicyclobacillus sp, DSM 15716 or another wild type strain, however the present invention also encompass artificial variatns, 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 functional of the polypeptide and/or other properties. Hence, the polypeptide of the invention may be an arSficial variant, wherein at least one substitution, deletion and/or insertion of an amino add has been made to an amino add sequence comprising or consisting of the mature polypeptide comprised in SEQ ID NO: 26 to SEQ ID NO: 50.
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 add sequences described herein, including fragments of the mature enzymes secreted from the strain of Alicyclobadllus sp. Deposited under DSM accession No. 15716, as described herein, including fragment of an enzyme selected from the group consisting of acid endoglucanase, acid cellulose, glutamic peptidase, multi copper oxidase, serinecarboxyl protease, serine protease, HtrAlike serine protease, disulfide isomerase, gammaDglutamylLdiamino add endopeptidase, endobetaNacetylglucosaminjdase, peptidylprolylisomerase, acid phosphatase, phytase, phospholipase C, polysaccharide deacetylase, xylan deacetylase and sutfite oxidase secreted from the strain of Alicyctobacillus sp. Deposited under DSM accession No. 15716.
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 vrvo gens shutting as described in WO 97/07205; in vitro shuffling as described by Stemmer, (1994) or WO 95/17413, random mutagenesis as described by Eisenstadt E. et al., (1994); PCR techniques as described by Poulsen et ah (1991); family shuffling as described by J.E Ness, et al, Nature Biotechnology, vol. 17, pp. 893896 (1999); sitedirected mutagenesis as described by Sambrook et al. (1989), Sambrook et al., Molecular Cloning, A Laboratory Manual Cokl Spring Harbor, NY. A general description of nucleotide substitution can be found in e.g. Ford et al, 1991, Protein Expression and Purification 2, p. 95107.

Such standard genetic engineering methods may also be used prepare a diversified library 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 preferred variant(s). A diversified library can be established by a range of techniques known to the art (Reetz MT; Jaeger KE, in Biocatalysis from Discovery to Application edited by Fessner WD, Vol. 200, pp. 3157 (1999); Stemmer, Nature, vol. 370, p.389391, 1994; Zhao and Arnold, Proc. Natl. Acad. ScL, USA, vol. 94, pp. 79978000, 1997; or Yano et al, Proc. Natl. Acad Sci., USA, vol. 95, pp 55115515, 1998).
In a particular embodiment of the indention, amino acid changes (in the artificial variant as well as in wildtype enzyme) are of a minor nature, that is conservative amino acid substitutions that do not significantly affect the folding and/or activity of the protein; small deletions, typically of one to about 30 amino adds; small amino/or carboxylterminal extensions, such as an aminoterminal methionine residue; a small linker peptide of up to about 2025 residues; or a small extension that facilitates purification by changing net charge or another function, such as a polyhistidine tract, an antigenic epitope or a binding domain.
Examples of conservative substitutions are within the group of basic amino acids (arginine, lysine and histidine), acidic amino acids (glutamic acid and aspartic acid), polar amino acids (glutamine and asparagine), hydrophobic amino acids (leucine, isoleucine, 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 example, by H. Neurath and R.L. Hill, 1979, In, The Proteins, Academic Press, New York. The most commonly occurring exchanges are Ala/Ser, Va/IIe, Asp/Glu, Thr/Ser, Ala/Gly, Ala/Thr, Ser/Asn, Ala/Val, Ser/Gly, Tyr/Phe, Ala/Pro, Lys/Arg, Asp/Asn, Leu/IIe, 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 physicochemical 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 polypeptide of the invention, particularly in these polypeptides selected from the group consisting of mature polypeptides comprised in SEQ D NO; 26 to SEQ H3 NO: 50 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, preferably 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 response 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 92ttO755, WO 00/26230, WO 00/26364 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 altergenicity 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 encoded by nucleotide sequences which hybridize under at least high stringency conditions, particularly 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 of regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide, the complementary strand to the cDNA sequence contained in a nucleotide sequences selected from regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide
a fragment of (i) or (ii) encoding a secreted polypeptide having the function of the corresponding mature polypeptide comprised in SEQ ID NO: 26 to SEQ ID NO: 50
{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 nucleotide sequence selected from the group of regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide or a sequences differing there from by virtue of the degeneracy of the genetic 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 SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide or a sequence differing there from by virtue of the degeneracy of the genetic code
The nucleotide sequences of regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide or a subsequence thereof, as well as the amino add sequences of the ma

ture polypeptides comprised in SEQ ID NO: 26 to SEQ ID NO: 50 or a fragment thereof, may be used to design a polynucleotide probe to identify and done 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 interest, following standard Southern blotting procedures, in order to identify and isolate the corresponding 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 polynucleotide 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 nucteotides to length. Even longer probes may be used, e.g., polynucleotide 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 enzymes 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 homology and/or identity or is homologous and/or identical with of nucleotides selected from regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature pofypeptide, the carrier material with the immobilized DNA is used in a Southern blot
For purposes of the present invention, hybridization indicates that the nucleotide sequence hybridizes to a labelled polynuccleotide probe which again hybridizes to a nucleotide sequence selected from regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide under high to very high stringency consitions. Molecues to which the polynucleotide probe hybridizes under these conditions may be detected using Xray 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 SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide.
In another interesting embodiment, the potynucleotide probe is the complementary strand of a nucleotide sequence which encodes an enzyme selected from the group of SEQ ID NO: 26 to SEQ ID NO: 50. In a further interesting embodient, the polynucleotide probe is the

complementary strand of a mature polypeptide coding region of a nucleotide sequence selected from regions of SEQ ID NO: 1 to SEQ ID NO; 25 encoding a mature polypeptide.
For long probes of at least 100 nucleotide in length, high to very high stringency conditions are defined as prehybridization 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 nucleotide do not contain more than 1000 nucleofides. For long probes of at least 100 nucleotide in length, the carrier material is finally washed three times each for 15 minutes using 0.1 x SSC, 0.1% SDS at 60°C (high stringency), tn particular washed three times each for 15 minutes using 0.1 x SSC, 0.1% SDS at 68°C (very high stringency).
Although not particularly preferred, it is contemplated that shorter probes, e.g. probes which are from about 15 to 99 nucleotide in length, such as from about 15 to about 70 nucleotide in length, may be also be used. For such short probes, stringency conditions are defined as prehybridization, hybridization, and washing posthybridization at 5°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 TrisHCI pH 7.6, 6 mM EDTA, 0.5% NP40, 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 nucleotide to 99 nucleotide in length, the carrier material is washed once in 6X SCC plus 0.1% SDS for 15 minutes and twice each for 15 minutes using 6X SSC at 5°C to 10°C below the calculated Tm.
SEQ ID NO: 26 acid endoglucanase or add cellulose
In a particular embodiment the polypeptide of the invention is an acid endoglucanase or acid cellulose comprising or consisting of an amino acid sequence which has at least 90%, particularly at least 95%, more particularly at least 95%, more particularly at least 97%, more particularly at least 98%, more particularly at least 99% or most particularly 100% identity with an acid endogiucanase or acid cellulose obtainable from Alicydobacillus sp., in particular that strain of Alicyclobacillus sp. Deposited under DSM accession No. 15716, more particularly the mature add endogiucanase or acid cellulose comprised in SEQ ID NO: 26. More specifically the mature acid endoglucanase or acid cellulose comprise or consists of the sequences from position 25 to 959 of SEQ ID NO: 26. In the present context an add endogiucanase is defined as enzyme, which endohydrolyzes 1,4betaDglucosidic linkages in cellulose, lichenin or cereal betaDgiucans particularly at addic conditions. In the present context an add cellulose is defined as enzyme, which endohydrolyzes 1,4betaDglcosidic linkages in cellulose, particularly at acidic conditions.

SEQ >D NO: 27 glutamic peptidase
In a particular embodiment the polypeptide of the invention is an glutamic 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 an glutamic peptidase obtainable from Alicyclobacillus sp., in particular that strain of Alicyclobacillus sp. Deposited under DSM accession No. 15716, more particularly the mature glutamic peptidase comprised in SEQ ID NO: 27. More specifically the mates glutamic peptidase comprises or consists of the sequences from position 33 to 272 of SB2 ID MO; 27. In the present context a glutamic peptidase is defined as defined as an enzyme, which hydrolyses proteins or peptides, and which contains conserved active site residues Q and E.
The glutamic peptidase (PepG) (EC 3.4.23.19) was previously categorized as an aspartyl protease (A4) but was reclassified by MEROPS (http://merops.sanger.ac.uk/), which published that "As a result of the exciting paper of Fujinaga, Chemey, Oyama, Oda & James (2004), The molecular structure and catalytic mechanism of a novel carboxyl peptidase from Scytalidium lignicolum. PubMed, we now recognise a sixth catalytic type of peptidases: the glutamic peptidases. The known glutamic peptidases are all contained in the the family that was formerly A4, and now becomes G1." (Fujinaga M, Cherney MM, Oyama H, Oda K, James MN.; The molecular structure and catalytic mechanism of a novel carboxyl peptidase from Scytalidium lignicolum; Proc. Natl. Acad. ScL U, S. A.; 101(10); pp. 33649; Epub 01Mar2004; 09Mar2004.)
That the polypeptide of SEQ ID NO: 27 is a glutamic peptidase also appears from the following multiple sequence alignment confirming that active sfe residues Q and E are conserved in SEQ ID NO: 27:
r
CLUSTAL W (1.81) multiple sequence alignment
i



SWXSSPROT_P24665 V
TREMBL_Q9P8R1 V
TREMBL_Q00551 V
SWISSPROTJP15369 V
TREMBL_Q00550 VG
TREMBL_Q8X1C5
SEQ ID NO.27 GSNQPSPPAS
SWXSSPROT_P24665
Aspergillus niger) ASPERGILLOPEPSIN II; SEQ ID HO: 55
(Sclerotinia sclerotiorum) endopeptidase EapC; SEQ ID NO: 56
TREMBL__Q00551
(Cryphonectria parasitica) endopeptidasa EapC; SEQ ID NO: 57
SWISSPROT_P15369
(Scytalidium lignicoltm) scytalidoglutamic peptidase; SEQ ID NO: 58
(Cryphonectria parasitica) endopeptidase SapB; SEQ XD NO: 59
TREMBL_Q8X1C5
(Talarcmryces emersonii) Pepstatininsensitivo acid protease (Fragment); SEQ ID NO: 60
SEQ ID NO.27
sequence of this invention
o = amino acids forming the active site in Swissprot P24665
/= cysteine residues forming disulfide bonds n Swissprat P24665
Σ = propeptide removed from the Swissprat P24665 zymogene

Hence, the present inventors has identified and isolated the first (G1) glutamic peptidase from a Bacterium ever known, and in particular one that is active at low pH and high temp. The closest relatives are fungal G1 proteases (e.g. Aspergillopepsin II).
Furthermore, surprisingly this glutamic peptidase differs from most known fungal glutamic peptidases by the absence of disulphide bridges in the molecule. The glutamic peptidase comprised in SEQ ID NO: 27 contains only one Cystein and thus no disulphide bridges in the protease structure as compared to e.g. SEQ D NO: 55 disdosing a known fungal glutamic peptidase, which are composed of two petidase cross inked by 2 disulphide bridges. Hence, the glutamic peptidase of Alicyclobacillus sp, specifically that deposited under DSM accession No. 15716 a second propeptide is missing and feus requires one less maturation step less in its production. This is an advantage for the cellular production.
SEQ ID NO: 28 or SEQ ID NO:35 Multi copper oxidase
In a particular embodiment the polypeptide of the invention is a multi copper oxidase 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 multi copper oxidase obtainable from Alicyclobacillus sp., in particular that strain of Alicyclobacillus sp. Deposited under DSM accession No. 15716, more particularly the mature multi copper oxidase comprised in SEQ ID NO: 28 or 35. More specifically the mature multi copper oxidase comprises or consists of the sequences from position 26 to 315 of SEQ ID NO: 28 or position 50 to 597 of SEQ ID NO: 35. In the present context a multiCuoxidase is deiined as a protein, which possesses at least three spectroscopically different copper centers, Multicopper oxidases can be laccases that oxidizes many different types of phenols and diamines, ascorbate oxidases, ceruioplasmin, that oxidizes a great variety of inorganic and organic substances or part of proteins that have lost the ability to bind copper and thereby mediate heavy metal resistance by sequestration of the heavy metal in the periplasm of the bacterium.
SEQ ID NO: 29 or SEQ ID NO: 30 Serinecarboxyl protease
In a particular embodiment the enzyme of the invention is a serinecarboxyl protease 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 the serinecarboxyl protease obtainable from Alicyclobacillus sp., in particular that strain of Alicyclobacillus sp. Deposited under DSM accession No. 15716, more particularly the mature serinecarboxyl protease comprised in SEQ ID NO: 29 or 30. More specifically the mature serinecarboxyl protease

comprises or consists of the sequences from position 190 to 626 of SEQ ID NO: 29 or position 25 to 533 of SEQ ID NO: 30. In the present context a serinecarboxyl protease is defined as a protease belonging to the Enzyme class EC 3.4.21.100 (pseudomonapepsin) which proteolytic enzymes fold resembles that of subtilisin, with a unique catalytic triad, SerGluAsp, as well as the presence of an aspartic acid residue in the oxyanion hole. A polypeptide sequence can be classified as a serinecarboxyl peptidase, if the amino acids of the catalytic site are present in the sequence and if it shows peptide sequence similarity to peptide sequences in MEROPS serine protease family 53.
SEQ ID NO: 31 serine protease or a HtrAIike serine protease
In a particular embodiment the polypeptide of the invention is a serine protease or a HtrAIike serine protease 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 the serine protease or the HtrAIike serine protease obtainable from Alicyclobacillus sp., in particular that strain of Alicyclobacillus sp. Deposited under DSM accession No. 15716, more particularly the mature serine protease carboxyl protease comprised in SEQ ID NO: 31. More specifically the mature serine protease comprises or consists of the sequences from position 42 to 411 of SEQ ID NO: 31. In the present context a serine protease is defined as an enzyme, which hydrolyses proteins or peptides, and which contains a serine residue in the catalytic site. A HtrAIike protease is defined as an enzyme that degrades damaged proteins in the extra cellular compartment of a bacterial cell at elevated temperatures.
SEQ ID NO: 32 disulfide isomerase
In a particular embodiment the polypeptide of the invention is a dfeutfide isomerase 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 particulariy at least 99% or most particularly 100% identity with the disulfide isomerase obtainable from Alicyclobacillus sp., in particular that strain of Alicyclobacillus sp. Deposited under DSM accession No. 15716, more particularly the mature disuifide isomerase comprised in SEQ ID NO: 32. More specifically the mature dlsufide isomerase comprises or consists of the sequences from position 31 to 212 of SEQ ID NO: 32. In the present context a disulphide isomerase is defined as enzyme, which catalyses the rearrangement of both intrachain and interchain disulfide bonds in proteins to form the native strictures

SEQ ID NO: 33 qammaDglutamylLdiamino acid endopeptidase
In a particular embodiment the polypeptide of the invention is a gammaDglutamylLdiamino acid endopeptidase 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 the gammaDglutamylLdiamino acid endopeptidase obtainable from Alicyclobacillus sp., in particular that strain of Alicyclobaoillus sp. Deposited under DSM accession No. 15716, more particularly the mature gammaDglutamylLdiamino acid endopeptidase comprised in SEQ ID NO: 33. More specifically the mature gammaDglutamylLdiamino acid endopeptidase comprises or consists of the sequences from position 30 to 266 of SEQ ID NO: 33. In the present context a gammaDglutamylLdiamino add endopeptidase is defined as an enzyme that hydrolyses gammaDglutamyl bonds to (L) mesodiaminopimelic acid in LAlagammaDGlu|(L)mesodiaminopimelic acid(L)DAla. It is required that the omegaamino and omegacarboxyl groups of the (L) meso diaminopimelic acid group are unsubstituted.
SEQ ID NO: 34 endobetaNacetylalucosaminidase
In a particular embodiment the polypeptide of the invention is an endobetaNacetylglucosaminidase 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 the endobetaNacetylglucosaminidase obtainable from Alicyclobacillus sp., in particular that strain of Alicyclobacillus sp. Deposited under DSM accession No. 15716, more particularly the mature endobetaNacetylglucosaminidase comprised in SEQ ID NO: 34. More specifically the mature endobetaNacetylglucosaminidase comprises or consists of the sequences from position 27 to 768 of SEQ ID NO: 34. In the present context an endobetaNAcetylglucosaminidase is defined as enzyme that hydrolyses the 1, 4betalinkages between NacetylDglucosamine and Nacetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
SEQ ID NO: 36.peptidylprolylisomerase
In a particular embodiment the polypeptide of the invention is a peptidylprolylisomerase 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 the peptidylprolylisomerase obtainable from Alicyclobacillus sp., in particular that strain of Alicyclobacillus sp. Deposited under DSM accession No. 15716, more particularly the mature peptidylprolylisomerase comprised in SEQ ID NO: 36. More specifically the mature peptidylprolyl

isomerase comprises or consists of the sequences from position 30 to 246 of SEQ ID NO: 36. In the present context a peptidylprolylisomerase is defined as an enzyme that accelerates protein folding by catalyzing the cistrans isomerization of proline imidic peptide bonds in oligopeptides.
SEQ ID NO: 37 acid phosphatase or a phytase or a phospholipase C
In a particular embodiment the polypeptide of the invention is an acid phosphatase or a phytase or a phospholipase C comprising or consisting of an amino add 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 the acid phosphatase or phytase or phospholipase C obtamable from Alicyclobacillus sp., in particular that strain of Alicyclobacillus sp. Deposited under DSM accession No. 15716, more particularly the mature acid phosphatase or phytase or phosphofipase C comprised in SEQ ID NO: 37. More specifically the mature acid phosphatase or a phytase or a phospholipase C comprises or consists of the sequences from position 28 to 608 of SEQ ID NO: 37. An acid phosphatase is defined as enzyme hydrolyzing an orthophosphoric monoester into an alcohol and phosphate. In the present context a phytase is defined as an enzyme removing a phosphate group from phytate. A phospholipase C is defined as an enzyme hydrolyzing phosphatidylcholine into 1,2diacylglycerol and choline.
SEQ ID NO: 38 or SEQ ID NO: 39 polysaccharide deacetylase
In a particular embodiment the polypeptide of the invention is a polysaccharide deacetylase or a xylan deacetylase 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 the polysaccharide deacetylase or the xylan deacetylase obtainable from Aicyclobacillus sp., in particular that strain of Alicyclobacillus sp. Deposited under DSM accession No. 15716, more particularly the mature polysaccharide deacetylase or a xylan deacetylase comprised in SEQ ID NO: 38 or 39. More specifically the mature polysaccharide deacetytase or a xylan deacetylase comprises or consists of the sequences from position 26 to 251 of SEQ ID NO: 38 or position 22 to 324 of SEQ ID NO: 39. In the present context a polysaccharide deaoetyiase is defined as an enzyme, which removes acetyl residues from a specific acerylated polysaccharide by hydrolysis. A xyian deacetylase is defined as an enzyme removing acetyl groups from acetylated xylan.

SEQ ID NO: 40 sulfite oxidase
In a particular embodiment the polypeptide of the invention is a sulfite oxidase 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 the sulfite oxidase obtainable from Alicyclobacillus sp., in particular that strain of Alicyclobacillus sp. Deposited under DSM accession No. 15716, more particularly the mature sulfite oxidase comprised in SEQ ID NO: 40. More specifically the mature sulfite oxidase comprises or consists of the sequences from position 30 to 214 of SEQ ID NO: 40. A sulfite oxidase is defined as enzyme that oxidizes sulfite to sulfate.
SEQ ID NO: 41 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional 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 SEQ ID NO: 41. In particular with the mature functional polypeptide comprised in SEQ ID NO: 41. More specifically the mature functional polypeptide comprises or consists of the sequences from position 22 to 257 of SEQ ID NO: 41.
SEQ ID NO: 42 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional 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 al least 98%T more particularly at least 99% or most particularly 100% identity with SEQ ID NO: 42. In particular with the mature functional polypeptide comprised in SEQ ID NO: 42. More specifically the mature functional polypeptide comprises or consists of the sequences from position 25 to 1130 of SEQ ID NO: 42.
SEQ ID NO: 43 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional 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 SEQ ID NO: 43. In particular with the mature functional polypeptide comprised in SEQ ID NO: 43. More spedfically the mature functional polypeptide comprises or consists of the sequences from position 42 to 248 of SEQ ID NO: 43.

SEQ ID NO: 44 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional 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 SEQ ID NO: 44. In particular with the mature functional polypeptide comprised in SEQ ID NO: 44. More specifically the mature functional polypeptide comprises or consists of the sequences from position 26 to 172 of SEQ ID NO: 44.
SEQ ID NO: 45 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional 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 SEQ ID NO: 45. In particular with the mature functional polypeptide comprised in SEQ ID NO: 45. More specifically the mature functional polypeptide comprises or consists of the sequences from position 31 to 242 of SEQ ID NO: 45.
SEQ ID NO: 46 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional 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 SEQ ID NO: 46. In particular with the mature functional polypeptide comprised in SEQ ID NO: 46. More specifically the mature functional polypeptide comprises or consists of the sequences from position 25 to 280 of SEQ ID NO: 46.
SEQ ID NO: 47 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional 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 SEQ ID NO: 47. In particular with the mature functional polypeptide comprised in SEQ ID NC: 47. More specifically the mature functional polypeptide comprises or consists of the sequences from position 26 to 478 of SEQ ID NO: 47.

SEQ ID NO: 48 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional 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 SEQ ID NO: 48. In particular with the mature functional polypeptide comprised in SEQ ID NO: 48. More specifically the mature functional polypeptide comprises or consists of the sequences from position 20 to
340 of SEQ ID NO: 48.
SEQ ID NO: 49 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional 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 SEQ ID NO: 49. In particular with the mature functional polypeptide comprised in SEQ ID NO: 49. More specifically the mature functional polypeptide comprises or consists of the sequences from position 30 to
341 of SEQ ID NO: 49.
SEQ ID NO: 50 functional polypeptide
In a particular embodiment the polypeptide of the invention is a functional 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 SEQ ID NO: 50. In particular with the mature functional polypeptide comprised in SEQ ID NO: 50. More specifically the mature functional polypeptide comprises or consists of the sequences from position 29 to 400 of SEQ ID NO: 50.
Polynucleotides
The present invention also relates to polynucleofides, particularly isolated polynucleotides, comprising or consisting of a nucleotide sequence encoding a polypeptide of the invention. In a particular embodiment, the nucleotide sequence is set forth in SEQ ID NO: 1 to SEQ ID NO: 25 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 consists of a nucleotide sequence selected from the regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide and which comprises at least one modification/mutation compared with the parent nucleotide sequence comprised in SEQ ID NO: 1 to SEQ ID NO: 25.

The techniques used to isolate and/or clone a nucleotide sequence encoding an enzyme 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., Innis et a/., 1990, PCR: A Guide to Methods and Application, Academic Press, New York. Other amplification procedures such as ligase chain reaction (LCR), ligated activated transcription (LAT) and nucleotide sequencebased amplification (IMASBA) may be used.
The nucleotide sequence may be obtained by standard cloning procedures used in genetic 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 nucleotide sequence may be of genomic, cDNA, RNA, semisynthetic, synthetic origin, or any combinations thereof.
In particular the polynucleotide comprises, preferably consists of, a nucleotide sequence which has at least 50% identity with a nucleotide sequence selected from the regions of SEQ ID NO: 1 to SEQ ID NO: 25 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 SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide. Particularly, the nucleotide sequence comprises a nucleotide sequence selected from the regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide. In an even more particular embodiment, the nucleotide sequence consists of a nucleotide sequence selected from the regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide.
In particular the polynucleotide comprises, preferably consists of, a nucleotide sequence encoding a mature enzyme selected from acid endoglucanase or add cellulose, glutamic peptidase, multi copper oxidase, serinecarboxyl protease, serine protease or HtrAlike serine protease, disulfide isomerase, gammaDglutamylLdiamino acid endopeptidase, endobetaNacetylglucosaminidase, peptidylprolylisomerase, acid phosphatase or phytase or phospholipase C, poiysaccharide deacetylase or xyian deacetylase and sulfite oxidase 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% 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 acid endoglucanase or acid cellulose, glutamic peptidase, multi copper oxidase, serinecarboxyl protease, serine protease or HtrAlike serine protease, disulfide isomerase, gammaDglutamylLdiamino acid endopeptidase, endobetaNacetylglucosaminidase, peptidylprolylisomerase, acid phosphatase or phytase or phospholipase C, polysaccharide deacetylase or xylan deacetylase and sulfite oxidase secreted from the strain of Aficyclobacillus sp. Deposited under DSM accession No. 15716.
SEQ ID NO: 1
In a particular embodiment the polynucleotide of the invention encodes an acid endogiucanase or acid cellulose 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 73 to 2877of SEQ ID NO: 1
SEQ ID NO: 2
In a particular embodiment the polynucleotide of the invention encodes an glutamic peptidase 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 97 to 816 of SEQ ID NO: 2
SEQ ID NO: 3 and 10
In a particular embodiment the polynucleotide of the invention encodes an multi copper oxidase 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 76 to 945 of SEQ ID NO: 1 or 148 to 1791 of SEQ ID NO: 10

SEQ ID NO: 4 and 5
In a particular embodiment the polynucleotide of the invention encodes a serinecarboxyl protease 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 568 to 1878 of SEQ ID NO: 4 or 73 to 1599 of SEQ ID NO: 5.
SEQ ID NO: 6
In a particular embodiment the polynucleotide of the invention encodes a serine protease or a HtrA like serine protease 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 124 to 1233ofSEQlDNO:6.
SEQ ID NO: 7
In a particular embodiment the polynucleotide of the invention encodes a disuifide isomerase 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 91 to 633 of SEQ ID NO: 7.
SEQ ID NO: 8
In a particular embodiment the polynucleotide of the invention encodes a gammaDglutamylLdiamino add endopepitidase and comprises or consists of an nucleotide sequence which has at least 70% identify, 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 88 to 798 of SEQ ID NO: 8.

SEQ ID NO: 9
In a particular embodiment the polynucleotide of the invention encodes a endobeta Nacetylglucosaminidase 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 79 to 2304 of SEQ ID NO: 9.
SEQ ID NO: 11
In a particular embodiment the polynucleotide of the invention encodes a peptidylprolylisomerase 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 88 to 735 of SEQ ID NO: 9.
SEQ ID NO: 12
In a particular embodiment the polynucleotide of the invention encodes a acid phosphatase or a phytase or a phospholipase C 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 82 to 1824 of SEQ ID NO: 12.
SEQ ID NO: 13 and 14
In a particular embodiment the polynucleotide of the invention encodes a polysaccharide deacetylase or a xylan deacetyiase 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 76 to 750 of SEQ ID NO: 13 or position 64 to 972 of SEQ ID NO: 14.

SEQ ID NO: 15
In a particular embodiment the polynucleotide of the invention encodes a sulfite oxidase 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 88 to 642 of SEQ ID NO: 15.
SEQ ID NO: 16
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% 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 64 to 771 of SEQ ID NO: 16.
SEQ ID NO: 17
In a particular embodiment the polynucleotide of the invention encodes mature functional 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% identity, more particularly at least 98% identity, more particularly at least 99% identity or most particularly 100% identity with the nucleotide sequence of position 73 to 3390 of SEQ ID NO: 17.
SEQ ID NO: 18
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% 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 124 to 744 of SEQ ID NO: 18.

SEQID1MO: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% 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 76 to 516 of SEQ ID NO: 19.
SEQ ID NO: 20
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% 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 91 to 726 of SEQ ID NO: 20.
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% 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 73 to 540 of SEQ ID NO: 21.
SEQ ID NO: 22
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% 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 76 to 1431 of SEQ ID NO: 22.

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% 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 1020 of SEQ ID NO: 23.
SEQ ID NO: 24
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% 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 88 to 1023 of SEQ ID NO: 24.
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% identity, mare 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 85 to 1197 of SEQ ID NO: 25.
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 sequence selected from mature potypeptide comprised in SEQ ID NO: 26 to SEQ ID NO: 50.
ft 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 enzyme. Amino add residues which are essential to the function are therefore preferably not subject to modification, such as substitution. Amino acid residues essential to the function may be identified according to procedures known in the art, such as sitedirected mutagenesis or alaninescanning mutagenesis (see, e.g., Cunningham and Wells, 1989, Science 244: 1081

1085). Sites of substrateenzyme interaction can be determined by analysis of the threedimensional structure as determined by such techniques as nuclear magnetic resonance analysis, crystallography or photoaffinity labeling (see, e.g., de Vos et al., 1992, Science 255: 306312; Smith et a/., 1992, Journal of Molecular Biology 224: 899904; Wlodaveref al., 1992, FEBS Letters 309: 5964).
Moreover, a nucleotide sequence encoding an enzyme of the invention may be modified by introduction of nucleotide substitutions which do not give rise to another amino acid sequence 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 far another nueleotide may be accomplished by sitedirected 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 containing 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 mutationcontaining 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 a/., 1991, Protein Expression and Purification 2: 95107.
The present invention also relates to a polynucleotide comprising, preferably consisting of, a nuxleotide sequence which encodes a polypeptide of the invention and which hybridizes under high stringency corvjitions, preferably under very high stringency conditions with a poiynucteotide probe selected from the group consisting of: (i) the complementary strand to a nucleotide sequence selected from the regions of SEQ
HD NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide , (ii) the complementary strand to the cDNA sequence contained in a nucleotide sequences
selected from the regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide and, (iii) a fragment of (i) or (ii) encoding a secreted mature polypeptide having the function of
the corresponding mature polypeptides comprised in SEQ ID NO: 26 to SEQ ID NO: 50
(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 sequences 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 electronic, preferably digital, device comprising information of the amino acid sequence of polypeptides of the invention or the nucleotide sequences of the polynucleotide of the invention, in particular any of the polypeptide or polynucleotide sequences of the invention in an electronic or digital form, such as binary code or other digital code. 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 expression 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 sequence prior to its insertion into a vector may be desirable or necessary depending on the expression 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 sequence that is recognized by a host cell for expression of the nucleotide sequence. The promoter 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 add constructs of the present invention, especially in a bacterial host cell, are the promoters obtained from the £ coli lac operon, Streptomyces coelicolor agarase gene (ofagA), Bacillus subttilis levansucrase gene (sacB), Bacillus licheniformis alphaamylase gene (amyL), Bacillus stearothermophilus maltogenic amylase gene (amyM), Bacillus amyloliquefaciens alphaamylase gene (amyQ),. Bacillus licheniformis penicillinase gene {penP), Bacillus subtitlis xylA and xylB genes, and prokaryotic betalactamase gene (VillaKamaroff et a/., 1978, Proceedings of the National Academy of Sciences USA 75: 37273731), as well as the tac promoter (DeBoer et aL, 1983, Proceedings of the National Academy of Sciences USA 80; 2125). Fur

then promoters are described in "Useful proteins from recombinant bacteria" in Scientific American, 1980, 242: 7494; and in Sambrook et al., 1989, supra.
Examples of suitable promoters for directing the transcription of the nucleic acid constructs of the present invention in a filamentous fungal host cell are promoters obtained from the genes for Aspergillus oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, Aspergillus niger neutral alphaamylase, Aspergillus niger acid stable alphaamylase, Aspergillus niger or Aspergillus awamori glucoamylase (glaA)t Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease, Aspergillus oryzae triose phosphate isomerase, Aspergilius nidulans acetamidase, and Fusarium oxysporum trypsinlike protease (WO 96/00787), as wei as the NA2tpi promoter (a hybrid of the promoters from the genes for Aspergillus niger neutral a*phaamylase and Aspergillus oryzae triose phosphate isomerase), and mutant, truncated, and hybrid promoters thereof.
In a yeast host, useful promoters are obtained from the genes for Saccharomyces cerevisiae enolase (ENO1), Saccharomyces cerevisiae galactokinase (GAL1), Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde3phosphate dehydrogenase (ADH2/GAP), and Saccharomyces cerevisiae 3phosphoglycerate kinase. Other useful promoters for yeast host cells are described by Romanes et al., 1992, Yeast 8: 423488.
The control sequence may also be a suitable transcription terminator sequence, a sequence recognized by a host cell to terminate transcription. The terminator sequence is operably linked to the 3' terminus of the nucleotide sequence encoding the enzyme. Any terminator 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 anthranilate synthase, Aspergillus niger alphaglucosidase, and Fusarium oxysporum trypsinlike protease.
Preferred terminators for yeast host cells are obtained from the genes for Sacchammyces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C (CYC1), and Saccharomyces cerevisiae glyceraldehyde3phosphate 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 nontranslated region of an mRNA which is important for translation by the host cell. The leader sequence is operably finked 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 inventionPreferred leaders for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase and Aspergillus nidulans triose phosphate isomerase.
Suitable leaders for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase (ENO1), Saccharomyces cerevisiae 3phosphoglycerate kinase. Sac

charomyces cerevisiae alphafactor, and Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde3phosphate 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 recognized by the host cell as a signal to add polyadenosine residues to transcribed mRNA. Any polyadenylation sequence which is functional in the host cell of choice may be used in the present invention.
Preferred polyadenylation sequences for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate synthase, Fusarium oxyspomm trypsinIike protease, and Aspergillus niger alphaglucosidase.
Useful polyadenylation sequences for yeast host cells are described by Guo and Sherman, 1995, Molecular Cellular Biology 15: 59835990.
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. Alternatively, the 51 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 required 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 alphaamylase, Bacillus licheniformis subtilisin, Bacillus licheniformis betalactamase, Bacillus stearothermophilus neutral proteases (nprT, nprS, nprM), and Bacillus subtilis pr$A. Further signal peptides are described by Simonen and Palva, 1993, Microbiological Reviews 57: 109137.
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, Aspergillus niger neutral amylase, Aspergillus niger glucoamylase, Rhizomucor miehei aspartic proteinase, Humicola insolens cellulose, and Hum/cola lanuginosa lipase.

Useful signal peptides for yeast host cells are obtained from the genes for Saccharomyces cerevisiae alphafactor 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 proenzyme or propolypeptide. A propolypeptide is generally inactive and can be converted to a mature active polypeptide by catalytic or autocatalytic cleavage of the propeptide from the propolypeptide. The propeptide coding region may be obtained from the genes for Bacillus subtilis alkaline protease {aprE), Bacikis subtilis neutral protease (nprT), Saccharomyces cerevisiae alphafactor, Rhizomucor miehei aspartic proteinase, and Myceliophthora thermophita 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 alphaamylase promoter, Aspergillus niger glucoamylase promoter, and Aspergillus oryzae glucoamylase 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 metals. 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 nuccleotide and. control sequences described above may be joined together to produce a recornbinant expression vector, which may include one or more convenient restriction sites to allow for insertion or substitution of the nucleotide sequence encoding the polypeptide at such sites. Alternatively, the nucleotide sequence 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 piasmid or virus) that can be conveniently subjected to recombinant DNA procedures and can bring about the expression of the nucleotide sequence. The choice of the vector wi typically depend on the

compatibility of the vector with the host cell into which the vector is to be introduced. The vectors 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 chromosome.
The vector may contain any means for assuring selfreplication. Alternatively, the vector 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 Bacillus 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 carbamoyltransferase), bar (phosphinothricin acetyltransferase), hygB (hygromycin phosphotransferase), niaD (nitrate reductase), pyrG (orotidine5'~phosphate decarboxylase), sC (sulfate adenyltransferase), 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 stable 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 sequence 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 homologous recombination into the genome of the host cell. The additional nucleotide sequences enable the vector to be integrated into the host cell genome at a precise location(s) in the chromosome(s). 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 probability 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 integrational elements may be nonencoding or encoding nucleotide sequences. On the other hand, the vector may be integrated into the genome of the host cell by nonhomologous recombination.
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 bacterial origins of replication are the origins of replication of plasmids pBR322, pUC19, pACYC177, and pACYC184 permitting replication in E coli, and pUBHO, pE194, pTA1060, and pAMB1 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 temperaturesensitive 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 nucieotide 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 nucieotide 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 nucieotide sequence where cells containing amplified copies of the selectable marker gene, and thereby additional copies of the nucieotide sequence, can be selected for by cultivating the cells in the presence of the appropriate selectable agent
The procedures used to ligate the elements described above to construct the recombinant expression 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 ceil comprising the nucleic acid construct 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 introduced into a host cell so that the vector is maintained as a chromosomal integrant or as a selfreplicating extrachromosomal vector as described earlier.
The host cell may be a unicellular microorganism, e.g., a prokaryote or a nonunicellular 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 amyloliquefacients, 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 £. colt and Pseudomonas sp. In a preferred embodiment, 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 bacterial host cell may, for instance, be effected by protoplast transformation (see, e.g., Chang and Cohen, 1879, Molecular General Genetics 168: 111115), using competent cells (see, e.g., Young and Spizsan, 1961, Journal of Bacteriology 81: 823829, or Dubnau and DavidoffAbelson, 1971, Journal of Molecular Biology 56: 209221), electroporation (see, e.g., Shigekawa and Dower, 1988, Bkstechniques 6: 742751), or conjugation (see, e.g., Koehler and Thome, 1987, Journal of Bacteriology 169: 57715278).
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 ceil. "Fungi" as used herein includes 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 a/., 1995, supra, page 171) and all mitosporic fungi (Hawksworth et ai, 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 Imperfecti (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, FA, 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 eel is a Candida, Hansenula, Kluyveromyces, Pichia, Saccharomyces, Schizosaccharomyces, or Yanvwia cell.
In a most preferred embodiment, the yeast host cell is a Saccharomyoes carisbergensis, Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomyces norbensis or SaccharumyGes oviformis cell. In another most preferred embodiment, the yeast host cell is a Kluyveromyces lactis cell . In another most preferred 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, mannaa and other complex polysaccharides. Vegetative growth is by hyphal elongation and carbon cataboliism 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, Myceliophthora, 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 or/zae cell. In another most preferred embodiment, the filamentous fungal host cell is a Fusarium badridioides, Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusazium graminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi, Fusarium axysponim, Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusarium sulphureum, Fusarium torulosum, Fusarium trichothedoides, or Fusarium venenatum cell. In an even most preferred embodiment, 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 insolens, Humicola lanuginosa, Mucor miehei, Myceliophthora thermophila, Neurospora crassa, Penicillium purpurogenum, Thielavia terrestris, Trichoderma harzianum, Trichoderma koningill Trichoderma longibrachiatum, Trichoderma reesei, or Trichoderma viride cell.
Fungal cells may be transformed by a process involving protoplast formation, transformation 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 a/., 1984, Proceedings of the National Academy of Sciences USA 81: 14701474. Suitable methods for transforming Fusarium species are described by Malardier et a/., 1989, Gene 78: 147156 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 182187, Academic Press, Inc., New York; Ito et al., 1983, Journal of Bacteriology 153:163; and Hinnen et a/., 1978, Proceedings of the National Academy of Sciences USA 75:1920.
The donor strain
The invention also provides a bacterium, Alicyclobacillus sp., as deposited under accession number DSM 15716, and compositions comprising this microorganism.
Methods for preparing enzyme polypeptides
The present invention also relates to methods for producing an enzyme of the invention comprising (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 Alicyclobacilius sp, DSM 15716, 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, smallscale or largescale fermentation (including continuous, batch, fedbatch, or solid state fermentations) in laboratory or industrial fermentors performed 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 compositions (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, spraydrying, evaporation, or precipitation.
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), SDSPAGE, or extraction (see, e.g., Protein Purification, J.C. Janson and Lars Ryden, editors, VCH Publishers, New York, 1989).
The methods of the invention also include the TAST method of WO 01/77315 A1 on a sample of the Alicyclobacillus sp. DSM 15716, i.e. by fusing genes (e.g. from a gene library) from the genome of the Alicyclobacillus sp. DSM 15716 with a gene encoding a signailess reporter, such as a betalactamase, via a transposon tag, growing host ceil clones comprising the genes of the Alicyclobacillus sp. DSM 15716 fused with a gene encoding a signailess reporter, such as a betalactamase, via a transposon tag in a medium revealing the presence of the reporter, such as an ampicillin containing medium, detetcting clones secreting the reporter and isolating gene and poiypeptide of the Alicyclobacillus sp. DSM 15716 comprised in that clone.
When growing host cell clones comprising the genes of the Alicyclobacillus sp. DSM 15716 fused with a gene encoding a signailess reporter, such as a betalactamase, via a transposon tag in a medium revealing the presence of the reporter, such as an ampicillin containing medium, only those clones expressing and secreting the reporter (e.g. betalactamase) will be detected (e.g. survive). However the reporter will only be secreted if the gene to which

the reporter 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 recognized in the host strain, and if the reporter is translated so that the synthesized polypeptide is transported across the cytoplasma membrane and folded correctly. Hence, when inserting the fused gene into a selected host cell, those clones, for which a reporter presence is detected (e.g. ampicillin resistance), will contain a gene from the Alicyclobacillus sp. DSM 15716, which encodes a functional secreted polypeptide.
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 Theological 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 fuelalcohols or bioethanol
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 35SCaMV promoter may be used (Franck et al, 1980, Cell 21: 285294). Organspecific 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: 275303), or from metabolic sink tissues such as meristems (Ito et al., 1994, Plant Mol. BioL 24: 863878), a seed specific promoter such as the glutelin, prolamin, globulin, or albumin promoter from rice (Wu et al, 1998, Plant and Cell Physiology 39: 885889), 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: 708711), a promoter from a seed oil body protein (Chen etai, 1998, Plant and Cell Physiology 39: 935941), 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: 9911000, the chlorella virus adenine methyltransferase gene promoter (Mitra and Higgins, 1994, Plant Molecular Biology 26: 8593), or the aldP gene promoter from rice (Kagaya et al., 1995, Molecular and General Genetics 248: 668674), or a wound inducible promoter such as the potato pin2 promoter (Xu et al., 1993, Plant Molecular Biology 22: 573588).
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 Agrobacteriummediated transformation, virusmediated 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 tumefaciensmediated gene transfer is the method of choice for generating transgenic dicots (for a review, see Hooykas and Schilperoort, 1992, Plant Molecular Biology 19: 1538). 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: 275281; Shimamoto, 1994, Current Opinion Biotechnology 5: 158162; Vasil et al., 1992, Bio/Technology 10: 667674). An alternative method for transformation of monocots is based on protoplast transformation as described by Omirulleh et al, 1993, Plant Molecular Biology 21:415428.
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 polypeptides and methods for their preparation
The invention provide a composition comprising a polypeptide of the invention and preferably an excipient and a method for preparing such a composition comprising admixing the polypeptide of the invention with an excipient. In particular the composition comprises at least two different polypeptides of the invention, preferably at least 3, more preferable at least 5, more preferable at least 10, more preferable at least 15, more preferable at least 20. Most the composition comprises all polypeptides secreted when fermenting a sample of Alicyclobacillus sp. DSM 15716 or a mutant thereof wherein one or more genes has been deleted or added.
In a particular embodiment the polypeptide of the invention is the major (polypeptide) component of the composition, e.g., a monocomponent composition. The excipient in this context is to be understood as any auxiliary agent or compound used to formulate the composition and includes solvent, carriers, stabilizers and the like.
The composition may further comprise one or more additional enzymes, such as an aminopeptidase, amyiase, carbohydrase, carboxypeptidase, catalase, cellulose, chitinase, cu

tinase, cyclodextrin glycosyltransferase, deoxyribonuclease, esterase, alphagalactosidase, betagalactosidase, glucoamylase, alphaglucosidase, betaglucosidase, haloperoxidase, invertase, laccase, lipase, mannosidase, oxidase, pectinolytic enzyme, peptidoglutaminase, peroxidase, 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 microgranules. The polypeptide of the invention may thus be provided in the form of a granule, preferably a nondusting granul;e, 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 additbn 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 bakers from 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 comprises a polysaccharide or a mixture of polysaccharides and comprises the polypeptide of the invention.
In a further embedment 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 biological composition, which comprises in addition to the polypeptide of the invention, an oxidoreductase enhancer.
Use of polypeptides or compositions comprising them
In still farther 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 encompasses 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 pretreatment of stained fabrics and a rinse added fabric softener composition, or be formulated as a detergent composition for use in general household hard surface cleaning operations, or be formulated for hand or machine dishwashing operations.
In a specific aspect, the invention provides a detergent additive comprising the polypeptide 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 cefiulase, a pectinase, a mannanase, an arabinase, a galactanase, a xylanase, an oxidase, e.g., a laccase, and/or a peroxidase.
In general the properties of the chosen enzyme(s) should be compatible with the selected detergent, (i.e. proptimum, compatibility with other enzymatic and nonenzymatic ingredients, etc.), and the enzyme(s) should be present in effective amounts.
Proteges: 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 trypsinlike protease. Examples of alkaline proteases are subtilisins, especially those derived from Bacillus, e.g., subtilisin Novo, subtilisin Carls berg, subtilisin 309, subtilisin 147 and subtilisin 168 (described in WO 89/06279). Examples of trypsinlike proteases are trypsir (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 98/20*15, WO 98/20116, and WO 98/34946, especially the variants with substitutions in one

or more of the following positions: 27, 36, 57, 76, 87, 97, 101, 104, 120, 123, 167, 170, 194, 206, 218, 222, 224, 235 and 274.
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 International Inc.).
Lipases: Suitable lipases include those of bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Examples of useful lipases pipdase lipases from Humicola (synonym Thermomyces), e.g. from H. lanuginosa (T. ianogfciosus} as described in EP 258 068 and EP 305 216 or from H. insolens as described m WO 96/13580, a Pseudomonas iipase, e.g. from P. alcaligenes or P. pseudoalcaligenes (EP 213 272% P. cepacia (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 BacDIus Opase, e.g. from B. subtilis (Dartois et al. (1993), Biochemica et Biophysica Acta, 1131, 253360), 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 LipolaseTM, Lipolase UItraTM and Lipex (Novozymes A/S).
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, alphaamylases obtained from Bacillus, e.g. a special strain of B. licheninformis, described 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 substitutions in one or more of the following positions: 15, 23, 105, 106, 124, 128, 133, 154, 156, 181, 188, 190, 197, 202, 208, 209, 243, 264, 304, 305, 391, 408, and 444.
Commercially available amylases are Duramyl™, Termamyl™, Fungarrryf™ and BAN™ (Novozymes A/S), Rapidase™ and Purastar™ (from Genencor International Inc.).
Celluloses: Suitable celluloses include those of bacterial or fungal Origin Chemically modified or protein engineered mutants are included. Suitable celluloses include celluloses from the genera Bacillus, Pseudomonas, Humicola, Fusarium, Thielavia, Acremonium, e.g. the fungal celluloses produced from Humicola insolens, Myceliophthora thermapnila 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 celluloses are the alkaline or neutral celluloses having colour care benefits. Examples of such ceilulases are celluloses described in EP 0 495 257, EP 0 531 372, WO 96/11262, WO 96/29397, WO 98/08940. Other examples are cellulose 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 celluloses include Celluzyme®, and Carezyme® (Novozymes), Clazinase®, and Puradax HA® (Genencor International Inc.), and KAC500(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 psroxidases 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 comprising 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 granulate, a liquid, a slurry, etc. Preferred detergent additive formulations are granulates, in particular nondusting granulates, liquids, in particular stabilized liquids, or slurries.
Nondusting 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 molar 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 ethyiene oxide units; fatty alcohols; fatty acids; and mono and di and triglycerides of fatty acids. Examples of filmforming coating materials suitable for application 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 prepared 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 030 % organic solvent, or nonaqueous.
The detergent composition comprises one or more surfactants, which may be nonionic including semipolar and/or anionic and/or cationic and/or zwitterionic. The surfactants 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, alphaolefinsulfonate, alkyl sulfate (fatty alcohol sulfate), alcohol ethoxysulfate, secondary alkanesulfonate, alphasulfo 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 nonionic surfactant such as alcohol ethoxyiate, nonylphenol ethoxylate, alkylpolyglycoside, alkyldimethylamineoxide, ethoxylated fatty acid monoethanolamide, fatty acid monoethanolamide, polyhydroxy alkyl fatty acid amide, or Nacyl NalkyI derivatives of glucosamine ("glucamides").
The detergent may contain 065 % of a detergent builder or complexing agent such as zeolite, diphosphate, triphosphate, phosphonate, carbonate, citrate, nitrilotriacetic acid, ethylenediaminetetraacetic acid, diethylenetriaminepentaacetic add, alkyl or alkenylsuccinic acid, soluble silicates or layered silicates (e.g. SKS6 from Hoechst).
The detergent may comprise one or more polymers. Examples are carboxymethylcellulose, poly(vinylpyrrolidone), poly (ethylene glycol), poly(vinyl alcohol), poly(vinylpyridineoxide), 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 peracidforming bleach activator such as tetraacetylethylenediamine or nonanoyloxybenzenesulfonate. Alternatively, 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 borate ester, or a phenyl boronic acid derivative such as 4formylphenyl 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, anticorrosion agents, soilsuspending agents, antisoil redeposition agents, dyes, bactericides, optical brighteners, 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 0.01100 mg of enzyme protein per litre of wash liquor, preferably 0.055 mg of enzyme protein per liter of wash liquor, in particular 0.11 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 MICROORGANISMS
The following microorganism were 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 Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D38124 Braunschweig, Germany:
June 30, 2003: Alicyclobacillus sp. CS81 thermoacidophile; DSM accession No. 15716.
EXAMPLES
Example 1 Identifying functional polypeptides secreted by Alicyclobacillus sp. DSM
15716
Genomic library construction
Chromosomal DNA from Alicyclobacillus sp. DSM 15716 was prepared by using standard molecular biology techniques (Ausuble et al. 1995 "Current protocols in molecular biology" Publ: John Wiley and sons). The prepared DNA was partially cleaved with Sau3A and separated on an agarose gel. Fragments of 3 to 8 kilobases were eluted and precipitated and resuspended in a suitable buffer.
A genomic library was made by using the Stratagene ZAP Express ™ predigested Vector kit and Stratagene ZAP Express ™predigested Gigapack ® cloning kit (Bam HI predigested) (Stratagene Inc., USA) following the instructions/recommendations from the vendor. The resulting lambdaZAP library comprised 38000 plu of which 10000 were collected for mass excision. The resulting 70000 E. coli colonies were pooled and plasmids were prepared by using the Qiagen Spin Mini prep kit (Qiagen, Germany). The eluate of approx. 1 ml containing the plasmid DNA was precipitated in a centrifuge with 1 volume part of Naacetate pH5 and 2 volume parts 96% ethanol at 20000 rpm at 4C, washed with 70% v/v ethanol, dried at room temperature and resuspended in 200 microl TE buffer. The DNA concentration of the plasmid pool DNA of the Alicyclobacillus sp. genomic library was 5.2 microgram/microliter.
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 encoding a signalless betalactamase via a transposon tag. Hence when growing host cell clones comprising the genes of a genome fused with a gene encoding a signalless betalactamase via a transposon tag in an ampicillin containing medium only those clones expressing and secreting a betalactamase will survive. However the betalactamase will only be secreted if the gene

to which the betalactamase 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 recognized in the host strain, and if the betalactamase is translated so that the synthesized polypeptide 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 Nterminal part of the genes as protein fusion shows that the oenes contain intact transcription, translation and secretion sequences. Hence expression of the Nterminal 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 βlactarnase reporter gene:
Following the instructions of WO 01/77315 A1, the construction of a transposon containing a signalless βlactamase gene was carried out using standard molecular biology techniques. The signalless βlactamase gene was initially PCR amplified from the vector pUC19) using a proofreading polymerase (Pfu Turbo, Stratagene, USA). The resulting PCR fragment contained the restriction sites Noti and EcoRI in order to aid cloning. The plasmid pEntranceposon(CanY) 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 Noti and EcoRI, gel purified and ligated with the signalless βlactamase containing fragment The ligation was transformed into electrocompetent DH10B cells and the E.coli done containing the recombinant plasmid with the signalless plactamase was identified by restriction analysis and named SigA2.
For transposon preparation, a smaller derivative of SlgA2 was constructed, which lacked the bla gene encoding betalactamase: Two oiigonucieoiide primers SigA2NotUP 5fTCG CGA TCC GTT TTC GCA TTT ATC GTG AAA CGC T31 (SEQ ID NO: 51) and SigA2NotDP 5'CCG CAA ACG CTG GTG AAA GTA AAA GAT GCT GAA3' (SEQ ID NO: 52), which bind to the start and stop of the bla gene of SigA2 directing outwards were used PCR amplify SigA2 without the bla gene. An amplificate of approx. 3,6 kb generated in the this PCR reaction was relegated and transformed ir 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.


60 microliter of pSigA4 plasmid DNA preparation with a concentration of 0.3 microgram/microliter was digested with Bglll 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" (Amersham Pharmacia Biotech lnc,USA) according to the instructions of the vender and eluted in 200 microliter EB buffer.
C. Transposon tagging
The transposon prepared from pSigA4 carries a 5ftruncated blagene encoding a plactamase from which the secretion signal has been removed. The (3lactamase conveys ampicillin resistance on E. coli only when the protein is secreted to the periplasm, whereas cytoplasmic expression of plactamase does not confer ampidllin resistance. Without a signal sequence, the plactamase enzyme will not be transported to the periplasm and therefore the clone will not grow on media containing ampitilin The signaltess βlactamase 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 inframe fusion with the target gene. This respited in a fusion gene product that is secreted to the periplasm of E coli and conveys resistance to the ampicilfin. If the transposon integrated even inframe into a gene encoding a nansecreted protein, the respective host will not become ampicillin resistance.
For the in vitro transposon tagging of the Alicyclobacillus sp. library, 4 or 8 microliter of SigA2 transposon containing approx. 2,6 ug DNA were mixed with 1 microliter of the DNA concentration of the plasmid pool DNA of the Alicyclobacilus sp. genomic library, 2 microliter of

Finnzymes MuA Transposase (0,22 microgram/microliter) and 5 microliter of 5x buffer from Finnzymes OY, Espoo, Finland) in a total volume of 50 microliter and incubated at 30 °C for 3,5 h and followed by heat inactivation at 75 °C for 10 min. The DNA was precipitated by addition of 5microliter 3M Naacetate pH5 and 110 microliter 96% ethanol and centrifugation for 30 min at 20000 rpm. The pellet was washed and dried and resuspended in 10 microliter TE buffer.
D. Transformation and selection
Electrocompetent E. coli DH10B cells were transferred by eletroporation in a Biorad Gene Pulse device (50uF, 25mAmpl 1.8 kV with 5 microliter of the transposon tagged plasmid pool, mixed with 1ml SOC medium, preincubated for 1h at 37C and plated on LB with 25 microliter/mililiter ampicillin, 50 microliter/mililiter kanamycin, 10 microliter/mililiter chloramphenicol and incubated for 23 days. Out of the resistant transformants 1056 colonies were selected and plasmids were prepared by applying the Qiaprep 96 Turbo Biorobot kit according to the instructions of the vender.
E. Plasmid preparation and sequencing
1056 transposon tagged plasmids were sequenced in with the A2up primer AGCGTTTGCGGCCGCGATCC (SEQ ID NO: 53) which read upstream into the into the transposon tagged gene, and, in a second reaction, with B primer TTATTCGGTCGAAAAGGATCC (SEQ ID NO: 54) which read downstream into the transposon tagged gene.
F. Sequence assembly and annotation
The obtained sequences were assembled into contigs by using the program PhredPhrap (Brent Ewing, LaDeana Hillier. Michael C. Wencdl, and Phil Green, Basecalling of automated sequencer traces using phred I. Accuracy assessment (1998) Genome Research 8:175185; Brent Ewing and Phil Green, Basecalling of automated sequencer traces using phred II. Error probabilities (1998) Genome Research 8:186194) The obtained contigs were subsequently compared to sequences available in standard public DNA and protein sequences databases by using the program BLASTX 2.0a19MPWashU I14Jul998] [Build Iinuxx86 18:51:44 30Jul998] (Gish, Warren (19941997). Unpublished; Gish, Warren and David J. States (1993). Identification of protein coding regions by database similarity search. Nat Genet 3:26672).
The obtained sequences were functional genes which encoded intact and functional polypeptides, because they were obtained as ampicillin resistant clones as explained supra.

Example 2. Determining function by homology
The function of the polypeptides SEQ ID NO: 26 to SEQ ID NO: 50 were annotated by sequences comparison with genes or polypeptides of known function. The polypeptides of the invention were compared to a list of closest related sequences from public and inhouse databases of contig's. The contigs, from which SEQ ID NO: 26 to SEQ ID NO: 50 were derived, were subsequently compared to sequences available in standard public DNA and protein sequences databases by using the program BLASTX 2.0a19MPWashU [14Jul1998]. A careful analysis of sequence alignments of SEQ ID NO: 26 to SEQ ID NO: 40 to their closest related sequences with known function from other databases made it possible to predict the function of these polypeptides on the basis of the degree of amino acid identity. Even when the overall amino acid identity was below 40%, which usually makes it difficult to make a good prediction, we were able to predict the function of SEQ ID NO: 26 to SEQ ID NO: 40 by carefully analysing and interpreting the amino acid residues in the catalytic sites or in important regions of the polypeptide sequences. If the amino acids of the catalytic site of a known sequences were also present in the polypeptide of the invention, combined with a sufficient overall amino acid identity, it was concluded that the polypeptide from Alicyclobacillus sp DSM 15716 had the same function as the known sequence.
Example 3 Preparing polypeptides of SEQ ID NO: 26 to SEQ ID NO: 50
To prepare the polypeptides of SEQ ID NO: 26 to SEQ ID NO: 50, the genes comprised in SEQ ID NO: 1 to SEQ ID NO: 25 encoding these polypeptides are expressed by fusing the DNA encoding the open reading frame to DNA a promoter, ribosome binding site and terminator suitable for genes expression in an appropriate host strain, for example Escherichia colt, Bacillus subtilis, Bacillus licheniformis or Bacillus clausii or a derivative of Alicyclobacillus sp. The promoter can either be an inducible promotor or a constitutive promoter. Any signal sequences of SEQ ID NO: 26 to SEQ ID NO: 50 can be exchanged with a suitable signal peptide of another bacterium. The expression construct can either be part of a plasmid or of a linear DNA. It can be integrated into the chromosome of the host strain by recombination or it can be present in the host cell on a plasmid. Then the transformed cells carrying the gene of interest are grown in a suitable medium in the desired volume. If an inducible promoter is used, the gene expression is started by adding the inducer. Otherwise a no inducer is needed and the cells will be grown until a suitable amount of protein from the gene of interest is produced. Then the culture is harvested and the proteins are recovered by standard methods.
Example 4. Determining serinecarboxyl protease activity
The culture fluid or a cell lysate of a host strain synthesising and secreting a serinecarboxy protease in a suitable buffer may be assayed for that activity. A suitable volume of such a

sample is spotted on agarose plates which contain the insoluble chromogenic substrate AZCLcollagen (Megazyme ™) or Azocoll (SigmaAldrich) and a suitable buffer at acidic pH, e.g. pH is 35. The plate is incubated for an appropriate time, e.g. one day at an appropriate temperature, e.g. 55°C. The activity is visible as blue halos around the spots. As an alternative to AZCLcolIagen or Azocoll, nonlabelled collagen is added to agar plates, on which enzyme activity can be detected as clearing zones. By addition of pepstatin, the protease activity of a serine carboxyl protease cannot be inhibited. As an alternative, the activity determination of a sample containing a serinecarboxyl protease can be measured as described in Tsuruoka N, Nakayama T, Ashida M, Hemmi H, Nakao M, Minakata H, Oyama H, Oda K, Nishino T; "Collagenolytic serinecarboxyl proteinase from Alicyclobacilius sendaiensis strain NTAP1: purification, characterization, gene cloning, and heterologous expression."Appl Environ Microbiol. Vol. 69(1); pp 162169; 2003 Jan.
Example 5. Determining multicopper oxidase activity
The culture fluid or a cell lysate of a host strain synthesising and secreting a multicopper oxidase in a suitable buffer may be assayed for that activity as described in Schneider et al., Enzyme and Microbial Technology 25, (1999) p. 502508).
For example a suitable volume, which can be 15 microliter, of such a sample is spotted on agarose plates which contain ABTS (2,2Azinobis 3Ethylbenzthiazolin6sulfonic acid) at a suitable concentration, e.g. 1mM, in a suitable puffer, e.g. 0,1 M sodium acetat buffer for pH 5,5. The plate is incubated for an appropriate time e.g. 16 hours, at an appropriate temperature, e.g. 55 °C. The activity is visible as a green zone around the sample. The assay works on supernatants and extracts.
Example 6. Determining serine protease activity
The culture fluid or a cell lysate of a host strain synthesising and secreting a serine protease in a suitable buffer may be assayed for that activity. A suitable volume of such a sample is spotted on agarose plates which contain the insoluble chromogenic substrate AZCLcasein (Megazyme ™) or AZCLcollagen (Megazyme ™) and a suitable buffer at suitable pH. The plate is incubated for an appropriate time, e.g. one day, at an appropriate temperature, e.g. 55°C. The activity is visible as blue halos around the spots. As an alternative to AZCLcasein and AZCLcollagen (Megazyme ™) nonlabelled casein or nonlabelled collagene can be used. On nonlabelled collagen or nonlabelled casein spotted on agarose plates, clearing zones form in the presence of a serine protease.

Example 7. Determining glutamic peptidase activity
The culture fluid or a cell lysate of a host strain synthesising and secreting a glutamic peptidase in a suitable buffer was assayed for that activity. A suitable volume of such a sample can be spotted on agarose plates, which contain the insoluble chromogenic substrate AZCLcollagen (Megazyme ™) and a suitable buffer at acidic pH, e.g. pH is 35. The plate can be incubated for an appropriate time, e.g. one day, at an appropriate temperature, e.g. 55°C. The activity is visible as blue halos around the spots. As an alternative to AZCLcollagen, nonlabelled collagen can be used. On nonlabelled collagen spotted on agarose plates, clearing zones form in the presence of a glutamic peptidase. Upon specifically testing the giutamic peptidase of ID NO: 27; the activity was determined as a spot test of 20 microliter culture fluid on 0.1% AZCLcollagen {Megazyme ™) spotted on LBPG agar plates at pH 3.4. The plates were incubated at 55 °C (over night) and the presence of the glutamic peptidase was visible as blue halos around the spots.
The glutamic peptidase comprised in SEQ ID NO: 27 showed significant sequence similarity to peptidases belonging to family A4 now reclassified as peptidase family G1 (PepG) (EC 3.4.23.19) by MEROPS see the section describing SEQ ID NO: 27, supra and Fujinaga M, Cherney MM, Oyama H, Oda K, James MN.; The molecular structure and catalytic mechanism of a novel carboxyl peptidase from Scytalidium lignicolum; Proc, Natl. Acad. Sci. U. S. A.; 101(10); pp. 33649; Epub 01Mar2004; 09Mar2004.
This family contains peptidase sequences, which have Q and E conserved in their active site. Both residues were conserved in the glutamic peptidase comprised in SEQ ID NO: 27. The glutamic peptidase comprised in SEQ ID NO: 27 is thus the first bacterial polypeptide of the G1 family previously counting only fungal peptidases.
SEQ ID NO: 27 was compared, inter alia, to a reference sequence of family G1 peptidases; Aspergillus niger aspergillopepsin II (SEQ ID NO: 55; Swissprot P24665; Takahashi,K; lnoue,H.; Sakai,K.; Kohama ,T, Kitahara,S.; Takishima,K.; Tanji,M.; Athauda.SBP.; Takahashi,T; Akanuma,H.; Mamiya,G.; Yamasaki, M); The primary structure of Aspergillus niger add proieinase A; J. Biol. Chem.; Vol 266; p. 19480; 1991). This polypeptide contained a signal peptide (aa1aa18), and two propeptides (aa 1958 and aa 99109), which are removed after secretion during maturation. During maturation a heavy and a light chain are formed, which are crosslinked by disulfide bridges between cysteine residues. (lnoue,H.; Kimura,T.; Makabe.O.; Takahashi.K.; The gene and deduced protein sequences of the zymogene of Aspergillus niger acid proteinase A;J. Biol. Chem.; vol. 266; p. 19484; 1991). The amino acids similar to the second propeptide (aa99109) and the amino acids corresponnding to the crosslinking cysteine residues of SEQ ID NO.55 are missing in SEQ ID 27 (see alignment). Only a fungal G1 peptidase has previously been described to lack cysteine residues (Maia,T .; Nagata,S.; Matsuda.G.; Maruta.S.; Oda,K.; Murao,S.; Tsuru.D.; Complete

amino acid sequence of Scytalidium lignicolum acid protease 6; J. Biochem.; vol. 95; p. 465; 1984).
Alignment of SEQ ID NO: 55 with SEQ ID NO: 27

* = amino adds forming the active site in Swissprot P24665
: = cysteine residues forming disulfide bonds in Swissprot P24665
n = propeptide removd from the Swissprot P24665 zymogene.
Example 8. Determining acid betaglucanase activity
The culture fluid or a cell lysate of a host strain synthesising and secreting an betaglucanase in a suitable buffer may be assayed for that activity. A suitable volume of such a sample is spotted on agarose plates which contain the insoluble chromogenic substrate AZCLbetag)ucan(Megaenzyme ™) and a suftable buffer at acidic pH, e.g. pH is 35. The plate is incubated for an appropriate time, e.g. one day, at an appropriate temperature, e.g. 55°C. The activity is visible as blue halos around the spots.

Example 9. Determining acid phosphatase activity
A suitable volume of the culture fluid or a cell lysate of a host strain synthesising and secreting the acid phosphatase in a suitable buffer at a suitable pH at an appropriate temperature, e.g. 55°C is incubated with paranitrophenolphosphate (pNPP) for measuring the enzyme activity. The products of the enzymatic reaction are pnitrophenol and inorganic phosphate or Pi. NaOH is added to end the phosphatase assay after a suitable reaction time and forms pnitraphenolate. The absorbation of pnitrophenolate is measured optically at 405 nm. As an alternative, a suitable volume of the culture fluid or a cell lysate of a host strain synthesising and secreting the acid phosphatase in a suitable buffer at a suitable pH at an appropriate temperature, e.g. 55 DC is used for measuring the enzyme activity with the EnzChek™ Acid Phosphatase Assay Kit (E12020) (Molecular Probes Europe BV; PoortGebouw, Rijnsburgerweg 10; 2333 AA Leiden, The Netherlands).
Example 10. Determining polysaccharide deacetylase activity
A suitable volume of the culture fluid or a cell lysate of a host strain synthesising and secreting the polysaccharide deacteylase in a suitable buffer at an appropriate temperature, e.g. 55CC is used for measuring the activity. Bacterial murein, N,N'diacetylchitobiose (Sigma) or galactose pentaacetate (Sigma) or and cellulose acetate (Sigma) can be used as substrate(s) for this enzyme type. The acetate released from the substrate by the enzyme can be measured with an acetic acid assay kit (Biopharm) adapted for the physical requierments of the enzyme (Kosugi A, Murashima K, and Doi RH; Xylanase and Acetyl Xylan Esterase Activities of XynA, a Key Subunit of the Clostridium cellulovorans Cellulosome for Xylan Degradation; Appl. Environm. I Microbiol.; vol. 68; pp. 63996402; 2002)
Example 11. Determining endobetaNacetylglucosaminidase activity
A suitable volume of the culture fluid or a cell lysate of a host strain synthesising and secreting the endobetaNacetylglucosaminidase activity in a suitable buffer, e.g. pH 35, at an appropriate temperature, e.g. 55 °C can be used for measuring the activity in accordance with MH Rashid, M Mori and J Sekiguchi; Glucosaminidase of Bacillus subtilis: cloning, regulation, primary structure and biochemical characterization; Microbiology; vol. 141; pp. 23912404; 1995.
Example 12. Determining peptidyl prolyisomerase activity
A suitable volume of the culture fluid or a cell lysate of a host strain synthesising and secreting the polysaccharide deacteylase in a suitable buffer at an appropriate temperature, e.g. 55 °C is used for measuring the activity. The activity can be determined in accordance to Fischer, G., Bang, H. and Mech, C; Determination of enzymatic catalysis for the cistransisomerization of peptide binding in prolinecontaining peptides:, Biomed. Biochim. Acta; vol. 43; pp. 1101

1111;1984. This assay may be modified appropriately to suit the specific peptidyl prolyisomerase such as that comprised in SEQ ID NO: 36,
Example 13. Determining acid cellulose activity
The culture fluid or a cell iysate of a host strain synthesising and secreting an acid cellulose in a suitable buffer may be assayed for that activity. A suitable volume of such a sample is spotted on agarose plates which contain the insoluble chromogenic substrate AZCLHEcellulose (Megazyme ™) and a suitable buffer at acidic pH, e.g. pH is 35. The plate is incubated for an appropriate time, e.g. one day, at an appropriate temperature, e.g. 55°C. Presence of acid cellulose is visible as bkie hate around the spots.
Example 14. Determining xylan deacetytase activity
A suitable volume of the culture fluid or a cell lysate of a host strain synthesising and secreting the polysaccharide cleacteylase in a suitable buffer at an appropriate temperature, e.g. 55°C can be used for measuring xylan deacetylase activity. Xylan deacetylase activity is measured as acetate release from acetylated xylan, which is prepared from birchwood xylan by the method of Johnson et al. 1988 (Johnson, K. G., J. D. Fontana, and C. R. Mackenzie. 1988. Measurement of acetylxylan esterase in Streptomyces. Methods Enzymol. 160:551560). The acetate released from acetyi xylan is measured with an acetic acid assay kit (Biopharm) adapted for the physical requierments of the enzyme (Kosugi A, Murashima K, and Doi RH; Xylanase and Acetyi Xylan Esterase Activities of XynA, a Key Subunit of the Clostridium cellulovorans Ceflulosome for Xytan Degradation; Appl. Environm. I Microbiol.; vol. 68; pp. 63996402; 2002).
Example 15. Determining phytase activity
The culture fluid or a cell lysate of a host strain synthesising and secreting a phytase in a suitable buffer may be assayed for phytase activity. A suitable volume of such a sample is diluted in 0.1 M sodium acetate and 0.01% Tween20, pH 5.5 in a suitable buffer, which can be HCI at pH 3.0 to 3.5, sodium acetate at pH 4.0 to 5.5, morpholincethanesulfonic acid (MES) at pH 6.0 to 6.5, and TrisHCI at pH 7.0 to 9.0, are further diluted in 26fold into the substrate solution (5 mM sodium phytate [sigma] in 0.1 M sodium acetate, and 0.01% Tween20 [pH 5.5], and preincubated at 37°C) to start the reaction. After 30 min at 37°C, the reaction is stopped by adding an equal volume of 10% trichloroacetic acid. Free inorganic phosphate is measured by the addition of an equal volume cf molybdate reagent containing, in 100 ml, 7.3 g of FeSO4, 1.0 g of (NH4)6M07O24 4H2O, and 3.2 ml of H2SO4. Absorbance was measured at 750 nm (Vmax microtiter plate reader, Molecular Devices) (Lassen SF; Breinholt J; Ostergaard PR; Brugger R; Bischoff A; Wyss M; Foglsang CC; Expression, gene cloning, and characterization

of five novel phytases from four basidiomycete fungi; Peniophora lycii, Agrocybe pediades, a Ceriporia sp., and Trametes pubescens; Appl. Environ. Micr.; 67; pp. 47014707; 2001).
Example 16. Determining phospholipase activity
The culture fluid or a cell lysate of a host strain synthesising and secreting a phospholipase in a suitable buffer may be assayed for phospholipase activity. Lecithin is added to suitable volume of such a sample. The Lecithin is hydrolyzed under constant pH and temperature, and the phospholipase activity is determined as the rate of titrant (0.1 N NaOH) consumption during neutralization of the liberated fatty acid. The substrate is soy lecithin (LaPhosphotidylCholine), and the conditions are pH 8.00, 40.0°C, reaction time 2 min. The unit (LEU) is defined relative to a standard
Example 17: Expression of glutamic peptidase gene (SEQ ID NO: 2) in Bacillus subtilis.
The signal peptide from the protease SAVINASE™ (also known as subtilisin 309 from B. Licheniformis from Novozymes A/S) was fused by PCR in frame to the gene encoding the glutamic peptidase (SEQ ID NO: 2). The DNA coding for the resulting coding sequence was integrated by homologous recombination on the Bacillus subtilis host cell genome. The gene construct was expressed under the control of a triple promoter system (as described in WO 99/43835), consisting of the promoters from Bacillus licheniformis alphaamylase gene {amyL), Bacillus amyloliquefaciens alphaamylase gene (amyQ), and the Bacillus thuringiensis crylllA promoter including stabilizing sequence. The gene coding for Chloramphenicol acetyltransferase was used as maker. (Described e.g in Diderichsen et al., A useful cloning vector for Bacillus subtilis. Plasmid, 30, p. 312,1993).
Chloramphenicol resistant transformants were analyzed by DNA sequencing to veriify the correct DNA sequence of the construct One such clone was selected.
Fermentations of the glutamic peptidase (SEQ ID NO: 2) expression clone was performed on a rotary shaking table in 500 ml baffled Erlenmeyer flasks each containing 100 ml PS1 media supplemented with 6 mg/I chloramphenicol. The clone was fermented for 6 days at 37 °C and sample was taken at day 3r 4, 5 and 6 and analyzed for proteotytic activity. The activity was determined (se example 7) as a spot test of 20 microliter culture fluid on 0.1 % AZCLcollagen (Megazyme ™) LBPG agar piates at pH 3.4. The plates were incubated at 55 °C (over night) and the activity was visible as blue halos around the spots.
Example 18: Purification and characterization of the family A4 protease from Alicyclobacillus sp.
Purification

Culture broth was centrifuged (20000 x g, 20 min) and the supernatants were carefully decanted from the precipitates. The combined supematants were filtered through a Seitz EKS plate in order to remove the rest of the Bacillus host cells. The EKS filtrate was adjusted to pH 4.0 with citric add and heated to 70°C with good stirring on a water bath. When the solution reached 70°C (it took approx. 15 minutes to get from 25°C to 70°C), the solution was immediately placed on ice. This heat treatment resulted in some precipitation, which was removed by another Seitz EKS filter plate filtration. Ammonium sulfate was added to the second EKS titrate to 1.6M final concentration and the pool was applied to a Butyl Toyopearl S column equilibrated in 20mM CH3COOH/NaOH, 1.6M (NH4)2SO4) pH 4.5. After washing the Butyl column extensively with the equilibration buffer, the enzyme was eluted with a linear (NH4)2SO4 gradient (1.6 to 0M) in the same buffer. Fractions from the column were analysed for protease activity (using the pH 4.0 Assay buffer and 37*C assay temperature) and fractions with activity were pooled. The pooled fractions were transferred to 20mM CH3COOH/NaOH, pH 5.5 on a G25 sephadex column and applied to a SOURCE 30Q column equilibrated in the same buffer. After washing the SOURCE 30Q column extensively with the equilibration buffer, the protease was eluted with a linear NaCl gradient (0 to 0.5M) in the same buffer. Fractions from the column were analysed for protease activity (pH 4.0, 37°C) and fractions with activity were pooled. The pool, which was slightly coloured, was treated with 1% (w/v) Activated charcoal for 5 minutes and the charcoal was removed by a 0.45 μm filtration. The purity of the filtrate was analysed by SDSPAGE, where only one band was seen on the coomassie stained gel.
Assay:
A Protazyme OL (crosslinked and dyed collagen) assay was used. A Protazyme OL tablet (from Megazyme) was suspended in 2.0ml 0.01% Triton X100 by gentle stirring. 500 microliter of this suspension and 500 microliter assay buffer were mixed in an Eppendorf tube and placed on ice. 20 microliter protease sample (diluted in 0.01% Triton X100) was added. The assay was initiated by transferring the Eppendorf tube to an Eppendorf thermomixer, which was set to the assay temperature. The tube was incubated for 15 minutes on the Eppendorf thermomixer at its highest shaking rate (1400 rpm). The incubation was stopped by transferring the tube back to the ice bath. Then the tube was centrifuged in an Icecold centrifuge for a few minutes, 200 microliter supernatant was transferred to a microtiter plate and ODB50 was read at 650 nm. A buffer blind was included in the assay (instead of enzyme). OD650(enzyme) OD650(buffer blind) was a measure of protease activity."
Protease assay.
Substrate: Protazyme OL tablets (Megazyme TPROL).
Temperature: Controlled.

Assay buffers : 100mM succinic acid, 100mM HEPES, 100mM CHES, 100mM CABS,
1mM CaCI2, 150mM KCl, 0.01% Triton X100 adjusted to pHvalues 2.0, 3.0,4.0, 5.0,6.0, 7.0, 8.0, 9.0, 10.0,11.0 and 12.0 with HCI or NaOH.
Characterisation: pH activity . pH stability, and temperature activity:
The above protease assay was used for obtaining the pH activity profile, the pH stability profile as well as the temperature activity profile at pH 3.0. For the pH stability profile the protease was diluted 5x in the Assay buffers and incubated for 2 hours at 37*C. After incubation the protease samples were transferred to pH 3.0, before assay for residual activity, by dilution in the pH 3 Assay buffer.



Other characteristics:
The relative molecular weight of the A4 protease as determined by SDSPAGE was:
Mr = 26 kDa
Example 19: Expression of acid cellulose gene (SEQ ID NO: 1) in Bacillus subtilis.
The signal peptide from Termamyl™ (Novozymes) was fused by PCR in frame to the gene encoding the acid cellulose (SEQ ID NO: 1). The DNA coding for the resulting coding sequence was integrated by homologous recombination on the Bacillus subtilis host cell genome. The gene construct was expressed under the control of a triple promoter system (as described in WO 99/43835), consisting of the promoters from Bacillus licheniformis alphaamylase gene {amyL), Bacillus amyloliquefadens alphaamylase gene (amyQ), and the Bacillus thuringiensis crylllA promoter including stabilizing sequence. The gene coding for Chloramphenicol acetyltransferase was used as maker (Described e.g in Diderichsen et al., A useful cloning vector for Bacillus subtilis. Plasmid, 30, p. 312, 1993).
Chloramphenicol resistant transformants were analyzed by DNA sequencing to verify the correct DNA sequence of the construct One such clone was selected.

Fermentations of the acid cellulose (SEQ ID NO: 1) expression clone was performed on a rotary shaking table in 500 ml baffled Erlenmeyer flasks each containing 100 ml PS1 media supplemented with 6 mg/I chloramphenicol. The clone was fermented for 3 days at 37 °C and sample was taken at day 1,2 and 3 and analyzed for cellulose activity. The activity was determined as a spot test of 20 microliter culture fluid on 0.1% AZCLHEcellulose (Megazyme ™) LBPG agar plates at pH 3.4. The plates were incubated at 55 °C (over night) and the activity was visible as blue halos around the spots.








CLAIMS
1. An isolated mature functional polypeptide which is at least 90% identical to and exhibits the
2. same function of a corresponding secreted polypeptide obtainable from the bacterium Alicy-
3. clobacillus sp. deposited under accession number DSM 15716.
4. A bacteria! glutamic peptidase (EC 3.4.23.19).
5. The polypeptide of claim 1 selected from the group consisting of:

(a) a polypeptide comprising an amino acid sequence which has at least 90% identity with
(b) a sequence of a mature polypeptide comprised in the group of SEQ ID NO: 26 to SEQ
(c) ID NO: 50;
(d) a polypeptide which is encoded a nucleotide sequence which hybridize under high
(e) stringency conditions with a polynucleotide probe selected from the group consisting of
(f) (i) the complementary strand to a nucleotide sequence selected from the group of
regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide. (ii) the complementary strand to the cDNA sequence contained in a nucleotide sequences selected from the group of regions of SEQ ID NO: 1 to SEQ ID NO: 25 encoding a mature polypeptide.
(c) a fragment of a mature polypeptide comprised in SEQ ID NO: 26 to SEQ ID NO: 50
and
wherein the polypeptide has a function of the corresponding mature polypeptides comprised in SEQ ID NO: 26 to SEQ JD NO: 50.
4. The pofypeptide of claim 1, wherein the polypeptide is an enzyme having a function se
5. lected from the group consisting of acid endoglucanase, acid cellulase, aspartyl protease, multi
6. capper oxidase, serine-carboxyl protease, serine protease, HtrA-like serine protease, disulfide
7. isomerase, gamma-D-glutamyl-L-diamino acid endopeptidase, endo-beta-N-
8. acetylglucosaminidase, peptidyl-prolyi-isomerase, acid phosphatase, phytase, phospholipase
9. C, pdysaccharide deacetylase, xylan deacetylase and sulfrte oxidase.
10. The enzyme of claim 4 selected from the group consisting of:

(a) an enzyme having an amino acid sequence which has at least 90% identity with an
(b) amino acid sequence selected from mature enzymes comprised in SEQ ID NO: 26 to
(c) SEQ ID NO: 40;
(d) an enzyme which is encoded by a nucleotide sequence which hybridize under high
(e) stringency conditions with a polynucleotide probe selected from the group consisting of
(f) (i) the complementary strand to a nucleotide sequence selected from the group of
regions of SEQ ID NO: 1 to SEQ ID NO: 15 encoding the mature enzyme,
(ii) the complementary strand to the cDNA sequence contained in a nucleotide se-quences selected from regions of SEQ ID NO: 1 to SEQ ID NO; 15 encodig the mature polypeptide;
(c) a fragment of the mature enzyme comprised in SEQ ID NO: 26 to SEQ ID NO: 40s and
wherein the enzyme has a function of the corresponding mature polypeptides comprised in SEQ ID NO: 26 to SEQ ID NO: 40.
6. The polypeptide of claim 1 wherein the stringency conditions are very high.
7. The polypeptide of claim 1, wherein the polynucleotide encoding the polypeptide consists
8. of a nucleotide sequence selected from the group of regions of SEQ ID NO: 1 to SEQ ID NO:
9. 25 encoding a mature polypeptide or a sequence differing there from by virtue of the degener
10. acy of the genetic code.
11. The enzyme of claim 4, characterized by being an acid endoglucanase or an add cellulase
12. obtainable from the strain of Alicyclobacillus sp. deposited under DSM accession No. 15716.
13. The acid endoglucanase or acid cellulase of claim 8, comprising or consisting of the mature
14. acid endoglucanase or acid cellulase comprised in SEQ ID NO: 26.
15. The acid endoglucanase or acid cellulase of claim 9, comprising or consisting of the se-
16. quences from position 25 to 959 of SEQ ID NO: 26.
17. The glutamic peptidase of claim 2, characterised by being free of disulphide bridges in the
18. protease structure.

19. The glutamic peptidase of claim 2f obtainable from the strain of Alicyclobacillus sp. depos
20. ited under DSM accession No. 15716.
21. The glutamic peptidase of claim 12, comprising or consisting of the mature aspartyl prote
22. ase comprised in SEQ ID NO: 27.
23. The glutamic peptidase enzyme of claim 13, comprising or consisting of the sequences
24. from position 33 to 272 of SEQ ID NO: 27.
25. The enzyme of claim 4, characterized by being a multi copper oxidase obtainable from the
26. strain of Alicyclobacillus sp. deposited under DSM accession No. 15716.
27. The multi copper oxidase of claim 15, comprising or consisting of the mature multi copper
28. oxidase comprised in SEQ ID NO: 28 or SEQ ID NO: 35.
29. The multi copper oxidase of claim 16, comprising or consisting of the sequences from posi
30. tion 26 to 315 of SEQ ID NO: 28 or position 50 to 597 of SEQ ID NO: 35.
31. The enzyme of claim 4, characterized by being a serine-carboxyl protease obtainable from
32. the strain of Alicyclobacillus sp. deposited under DSM accession No. 15716.
33. The serine-carboxyl protease of claim 18, comprising or consisting of the mature serine-
34. carboxyl protease comprised in SEQ ID NO: 29 or SEQ ID NO: 30.
35. The serine-carboxyl protease of claim 19, comprising or consisting of the sequences from
36. position 190 to 626 of SEQ ID NO: 29 or position 25 to 533 of SEQ ID NO: 30.
37. The enzyme of claim 4r characterized by being a serine protease or a HtrA-like serine pro-
38. tease obtainable from the strain of Alicyclobacillus sp. deposited under DSM accession No.
39. 15716.
40. The serine protease or a HtrA-like serine protease of claim 21, comprising or consisting of
41. the mature serine protease or a HtrA-like serine protease comprised in SEQ ID NO: 31.
42. The serine protease or a HtrA-like serine protease of claim 22, comprising or consisting of
43. the sequences from position 42 to 411 of SEQ ID NO: 31.

44. The enzyme of claim 4, characterized by being a disulfide isomerase obtainable from the
45. strain of Alicyclobacillus sp. deposited under DSM accession No. 15716.
46. The disulfide isomerase of claim 24, comprising or consisting of the mature disulfide isom
47. erase comprised in SEQ ID NO: 32.
48. The disulfide isomerase of claim 25, comprising or consisting of the sequences from posi
49. tion 42 to 411 of SEQ ID NO: 32.
50. The enzyme of claim 4, characterized by being a gamma-D-glutamyl-L-diamino acid ob-
51. tainable from the strain of Alicyclobacillus sp. deposited under DSM accession No. 15716.
52. The gamma-D-glutamyl-L-diamino acid of claim 27, comprising or consisting of the mature
53. gamma-D-glutamyl-L-diamino acid comprised in SEQ ID NO: 33.
54. The gamma-D-giutamyl-L-diamino acid of claim 28, comprising or consisting of the se
55. quences from position 30 to 266 of SEQ ID NO: 33.
56. The enzyme of claim 4, characterized by being an endo-beta-N-acetylglucos-aminidase
57. obtainable from the strain of Alicyclobacillus sp. deposited under DSM accession No. 15716.
58. The endo-beta-N-acetylglucosaminidase of claim 30, comprising or consisting of the ma
59. ture endo-beta-N-acetylglucosaminidase comprised in SEQ ID NO: 34.
60. The endo-beta-N-acetylglucosaminidase of claim 31, comprising or consisting of the se
61. quences from position 27 to 768 of SEQ ID NO: 34.
62. The enzyme of claim 4, characterized by being a peptidyl-prolyl-isomerase obtainable from
63. the strain of Alicyclobacillus sp. deposited under DSM accession No. 15716.
64. The peptidyl-prolyl-isomerase of claim 33, comprising or consisting of the mature peptidyl-
65. prolyl-isomerase comprised in SEQ ID NO: 36.
66. The peptidyl-prolyl-isomerase of claim 34, comprising or consisting of the sequences from
67. position 30 to 246 of SEQ ID NO: 36.

68. The enzyme of claim 4, characterized by being an acid phosphatase or a phytase or a
69. phospholipase C obtainable from the strain of Alicyclobacillus sp. deposited under DSM ac
70. cession No. 15716.
71. The acid phosphatase or phytase or phospholipase C of claim 36, comprising or consisting
72. of the mature acid phosphatase or phytase or phospholipase C comprised in SEQ ID NO: 37.
73. The acid phosphatase or phytase or phospholipase C of claim 37, comprising or consisting
74. of the sequences from position 28 to 608 of SEQ ID NO: 37.
75. The enzyme of claim 4, characterized by being a polysaccharide deacetylase or a xylan
76. deacetylase obtainable from the strain of Alicyclobacillus sp. deposited under DSM accession
77. No. 15716.
78. The polysaccharide deacetylase or a xylan deacetylase of claim 39, comprising or consist
79. ing of the polysaccharide deacetylase or a xylan deacetylase comprised in SEQ ID NO: 38 or
80. SEQ ID NO: 39.
81. The polysaccharide deacetylase or a xylan deacetylase of claim 40, comprising or consist
82. ing of the sequences from position 26 to 251 of SEQ ID NO: 38 or from position 22 to 324 of
83. SEQ ID NO: 39.
84. An isolated enzyme selected from the group consisting of:

(a) an enzyme comprising an amino acid sequence which has at least 90% identity with
(b) the amino acid sequence of a mature enzyme selected from the group consisting of
(c) acid endoglucanase or acid cellulase, aspartyl protease, multi copper oxidase, serine-
(d) carboxyl protease, serine protease or HtrA-like serine protease, disulflde isomerase,
(e) gamma-D-glutamyl-L-diamino acid endopeptidase, endo-beta-N-
(f) acetylglucosaminidase, peptidyl-prolyl-isomerase, acid phosphatase or phytase or
(g) phospholipase C, polysaccharide deacetylase or xylan deacetylase and sulfite oxidase
(h) secreted from the strain of AHcyclobacillus sp. deposited under DSM accession No.
(i) 15716;
(j) a polypeptide which is encoded by a nucleotide sequence which hybridize under high
(k) stringency conditions with a polynucleotide probe selected from the group consisting of:
(l) (i) the complementary strand to a nucleotide sequence comprised in the strain of
Alicyclobacillus sp. deposited under DSM accession No. 15716 encoding a ma-
68
SUBSTITUTE SHEET (RULE 26)

ture enzyme selected from the group consisting of acid endoglucanase or acid cellulase, aspartyl protease, multi copper oxidase, serine-carboxyl protease, serine protease or HtrA-like serine protease, disulfide isomerase, gamma-D-glutamyl-L-diamino acid endopeptidase, endo-beta-N-acetylglucosaminidase, peptidyl-prolyl-isomerase, acid phosphatase or phytase or phospholipase C, polysaccharide deacetylase or xylan deacetylase and sulfite oxidase secreted from that strain;
(ii) the complementary strand to the cDNA sequence contained in a nucleotide sequences comprised in the strain of Alicyctobacillus sp. deposited under DSM accession No. 15716 encoding a mature enzyme selected from the group consisting of acid endoglucanase or acid cellulase, aspartyl protease, multi copper oxidase, serine-carboxyl protease, serine protease or HtrA-like serine protease, disulfide isomerase, gamma-D-glutamyl-L-diamino acid endopeptidase, endo-beta-N-acetylglucosaminidase, peptidyl-prolyl-isomerase, acid phosphatase or phytase or phospholipase C, polysaccharide deacetylase or xylan deacetylase and sulfite oxidase secreted from that strain;
(c) a fragment of a mature enzyme selected from the group consisting of acid endoglucanase or acid cellulase, aspartyl protease, multi copper oxidase, serine-carboxyl protease, serine protease or HtrA-like serine protease, disulfide isomerase, gamma-D-glutamyl-L-diamino acid endopeptidase, endo-beta-N-acetylglucosaminidase, peptidyl-prolyl-isomerase, acid phosphatase or phytase or phospholipase C, polysaccharide deacetylase or xylan deacetylase and sulfite oxidase secreted from the strain of Alicy-clobacillus sp. deposited under DSM accession No. 15716;
wherein the enzyme have a function selected from acid endoglucanase or acid cellulase, aspartyl protease, multi copper oxidase, serine-carboxyl protease, serine protease or HtrA-like serine protease, disulfide isomerase, gamma-D-glutamyl-L-diamino acid endopeptidase, endo-beta-N-acetylglucosaminidase, peptidyl-prolyl-isomerase, acid phosphatase or phytase or phospholipase C, polysaccharide deacetylase or xylan deacetylase and sulfite oxidase.
43. A bacterial strain deposited under accession number DSM 15716.
44. A composition comprising the polypeptide of claims 1-42.

45. The composition of claim 44, comprising at least two different polypeptides of daims1-42,
46. preferably at least 3, more preferable at least 5, more preferable at least 10, more preferable at
47. least 15, more preferable at least 20 different polypeptides of claims 1-42.
48. The composition of claim 44, comprising all polypeptides secreted when fermenting a sample of Alicyclobacillus sp. DSM 15716 or a mutant thereof wherein one or more genes has
49. been deleted or added.
50. The composition of claim 44 further comprising one or more additional enzymes.
51. The composition of claim 44, characterized by being a detergent composition which, in ad
52. dition to the polypeptide, comprises a surfactant
53. The composition of claim 44, characterized by being a feed composition which in addition
54. to the polypeptide comprises a cereal or grain product.
55. The composition of claim 44, characterized by being a food composition.
56. The composition of claim 44, further comprising a polysaccharide or a mixture of polysaccharides.
57. A method for preparing a composition of claim 44, comprising damping the polypeptide of claims 1-42 with an excipient.
58. A polynucleotide having a nucleotide sequence which encodes for the polypeptide defined in any of claims 1-42.
59. A composition comprising the polynucleotide of claim 53.
55. A nucleic acid construct comprising the nucleotide sequence defined in claim 53 operably
finked to one or more control sequences that direct the production of the polypeptide in a host
cell.
56. A recombinant expression vector comprising the nucleic acid construct of claim 55.
57. A recombinant host cell comprising the nucleic add construct of claim 55.

58. A method for producing the polypeptide of claims 1-42 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.
59. A method for producing a polypeptide of claims 1-42 comprising:
(a) cultivating a recombinant host cell as defined in claim 45 under conditions conducive
for production of the polypeptide; and
(b) recovering the polypeptide.
60. The method of claim 59 comprising (i) fusing genes from the genome of the Alicyclobacillus
sp. DSM 15716 with a gene encoding a signalless reporter, via a transposon tag, (ii) growing host cell clones comprising a fused gene of the Alicyclobacillus sp. DSM 15716 in a medium revealing the presence of the reporter, (iii) detecting clones secreting the reporter and (iv) isolating gene and polypeptide of the Alicyclobacillus sp. DSM 15716 comprised in that clone.
61. A storage medium suitable for use in an electronic device comprising information of the
62. amino acid sequence of the polypeptide of claims 1-42 or the nucleotide sequence of the
63. polynucleotide of claim 53.
64. A process comprising employing a polypeptide of claims 1-42 or a polynucleotide of claim
65. 53 in an industrial or household technical process.
Dated this 5 day of July 2006


Documents:

2452-CHENP-2006 AMENDED PAGES OF SPECIFICATION 30-09-2011.pdf

2452-CHENP-2006 AMENDED CLAIMS 30-09-2011.pdf

2452-CHENP-2006 CORRESPONDENCE OTHERS 12-09-2011.pdf

2452-CHENP-2006 EXAMINATION REPORT REPLY RECEIVED 30-09-2011.pdf

2452-CHENP-2006 FORM-3 30-09-2011.pdf

2452-CHENP-2006 OTHER PATENT DOCUMENT 30-09-2011.pdf

2452-CHENP-2006 POWER OF ATTORNEY 30-09-2011.pdf

2452-chenp-2006-abstract.pdf

2452-chenp-2006-claims.pdf

2452-chenp-2006-correspondnece-others.pdf

2452-chenp-2006-description(complete).pdf

2452-chenp-2006-form 1.pdf

2452-chenp-2006-form 26.pdf

2452-chenp-2006-form 3.pdf

2452-chenp-2006-form 5.pdf

2452-chenp-2006-pct.pdf

2452-chenp-2006-sequence-listing.pdf


Patent Number 252204
Indian Patent Application Number 2452/CHENP/2006
PG Journal Number 18/2012
Publication Date 04-May-2012
Grant Date 01-May-2012
Date of Filing 05-Jul-2006
Name of Patentee NOVOZYMES A/S
Applicant Address Krogshojvej 36, DK-2880 Bagsværd
Inventors:
# Inventor's Name Inventor's Address
1 WILTING, Reinhard Kielshøj 76, DK-3520 Farum
2 LASSEN, Soren, Flensted Gydebakken 3B, DK-3520 Farum
3 OSTERGAARD, Peter, Rahbek Kvaedevej 111, DK-2830 Virum
PCT International Classification Number C12N9/42
PCT International Application Number PCT/DK2005/000004
PCT International Filing date 2005-01-06
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 PA 2004 00010 2004-01-06 U.S.A.
2 PA 2004 00298 2004-02-25 U.S.A.
3 PA 2004 00165 2004-02-04 U.S.A.
4 10/784,592 2004-02-23 U.S.A.