WO2007124285A2

WO2007124285A2 - Polypeptides having glucoamylase activity and polynucleotides encoding same

Info

Publication number: WO2007124285A2
Application number: PCT/US2007/066618
Authority: WO
Inventors: Sara Landvik; Jiyin Liu; Carsten Horslev Hansen; Chee-Leong Soong; Jeppe Wegener Tams
Original assignee: Novozymes North America, Inc.; Novozymes A/S
Priority date: 2006-04-19
Filing date: 2007-04-13
Publication date: 2007-11-01
Also published as: EP2010653A4; WO2007124285A3; US20100120108A1; CA2645006A1; RU2008145591A; CN101443447A; US7871800B2; MX2008013100A; EP2010653A2

Abstract

The present invention relates to polypeptides having glucoamylase activity and isolated polynucleotides encoding said polypeptides preferably derived from a strain of Peniphora rufomarginata. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides. The invention also relates to the composition comprising a glucoamylase of the invention as well as the use such compositions for starch conversion processes, brewing, including processes for producing fermentation products or syrups.

Description

POLYPEPTIDES HAVING GLUCOAMYLASE ACTIVITY AND POLYNUCLEOTIDES ENCODING SAME

CROSS-REFERENCE TO A SEQUENCE LISTING This application contains a Sequence Listing in computer readable form. The computer readable form is incorporated herein by reference.

FIELD OF THE INVENTION

The present invention relates to polypeptides having giucoamyiase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides, and to the use of glucoamylases of the invention for starch conversion to producing fermentation products, such as ethano!, and syrups, such as glucose. Trie invention aiso relates to a composition comprising a giucoamyiase of the invention.

BACKGROUND OF THE INVENTION

GlucoamySase (1 ,4-alpha-D-glucan giυcohydrolase, EC 3.2.1.3) is an enzyme, which catalyzes the release of D-giucose from the non-reducing ends of starch or related oiigo- and polysaccharide molecules. Glucoarnylases are produced by several filamentous fungi and yeast, with those from Aspergillus being commercially most important.

Commercially, glucoamylases are used to convert starchy material, which is already partially hydrolyzed by an alpha-amylase, to glucose. The glucose may then be converted directly or indirectly into a fermentation product using a fermenting organism. Examples of commercial fermentation products include alcohols (e.g., ethano!, methanol, butanol, 1 ,3- propanediol); organic acids (e.g.. citric acid, acetic acid, itaconic acid, lactic acid, gluconic acid, gluconate, lactic acid, succinic acid. 2,5-diketo-D-gluconic acid); ketones (e.g., acetone); amino acids (e.g., glutamic acid); gases (e.g., H₂ and CO₂), and more complex compounds, including, for example, antibiotics (e.g., penicillin and tetracycline); enzymes; vitamins (e.g., riboflavin, B₁₂, beta-carotene); hormones, and other compounds which are difficult to produce synthetically. Fermentation processes are also commonly used in the consumable alcohol (e.g., beer and wine), dairy (e.g., in the production of yogurt and cheese), leather, and tobacco industries.

The end product may also be syrup. For instance, the end product may be giucose, but may also be converted, e.g., by glucose isomerase to fructose or a mixture composed almost equally of glucose and fructose. This mixture, or a mixture further enriched with fructose, is the most commonly used high fructose corn syrup (HFCS) commercialized throughout the world,

BoeS et al. (1984), EMBO J. 3 (5), p. 1097-1102 disclose Aspergillus n/ger G1 or G2 glυcoamylase. U.S. Patent No. 4.727.046 discloses a glucoamylase derived from Corticiutn rø/fei/ which is aSso referred to as AtheSia rolfsii.

WO 84/02921 discloses a glucoamyiase derived from Aspergillus awamoή.

WO 99/28248 discloses a glucoamyiase derived from Tafaromycøs mversoniL

WO 00/75296 discloses a glucoamyiase derived from Thβnnoascus crustaceus, WO 2008/069289 discloses glucoamylases derived from Tramet&s cingulata,

Pachykytospora papyracea, and Leucopaxillus giganteus.

It is an object of the present invention to provide polypeptides having glucαamyiase activity and polynucleotides encoding the polypeptides and which provide a high yield in fermentation product production processes, such as ethanα! production processes, including one-step ethanol fermentation processes from un-gelatinized raw {or uncooked) starch.

Summary of the invention

The present invention relates to polypeptides having glucoamyiase activity selected from the group consisting of: (a) a polypeptide having an amino acid sequence which has at least 60% identity with amino acids for mature polypeptide amino acids 1 to 558 of SEQ ID NO: 2;

(b) a polypeptide which is encoded by a nucleotide sequence (i) which hybridizes under at least low stringency conditions with nucleotides 61 to 2301 of SEQ ID NO: 1 , or (ii) which hybridizes under at least low stringency conditions with the cDNA sequence contained in nucleotides 61 to 1734 of SEQ ID NO: 3_; or (iii) a complementary strand of (i) or fii);

(c) a variant comprising a conservative substitution, deletion, and/or insertion of one or more amino acids of amino acids 1 to 558 of SEQ ID NO; 2.

The present invention also relates to polynucleotides encoding polypeptides having glucoamyiase activity, selected from the group consisting of; (a) a poiynucleotide encoding a poiypeptide having an amino acid sequence which has at least 60% identity with the mature polypeptide amino acids 1 to 558 of SEQ ID NO: 2;

(b) a polynucleotide having at least 60% identity with nucleotides 61 to 2301 of SEQ iD NO: 1 ; or (c) a polynucleotide having at Seast 60% identity with nucleotides 61 to 1734 of

SEQ ID NO: 3; (d) a polypeptide which is encoded by a nucleotide sequence (i) which hybridizes under at least low stringency conditions with nucleotides 61 to 2301 of SEQ ID NO: 1 , or (Ii) which hybridizes under at least low stringency conditions with the cDNA sequence contained in nucleotides 61 to 1734 of SEQ ID NO: 3, or (iii) a complementary strand of (i) or (if). In a preferred embodiment the polypeptide is derivabie from a strain of the genus

Peniphom, preferably a strain of the species Peniphora rvfomarginata or E. cots strain deposited at DSMZ on 3 Aprii 2006 under the terms of the Budapest Treaty on the international Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure at Deυtshe Sammmiung von Microorganismen und ZeiSkuituren GmbH (DSMZ). Maseheroder Weg 1 b, D-38124 Braunschweig DE. The clone was given the no. DSM 18150. Deposited strain DSM 18150 harbors plasmid pEN!251β comprising a sequence that, to the best belief of the inventors, is identical to SEQ ID NO: 1. A specific polypeptide of the invention is the mature polypeptide obtained when expressing plasmid pENI2516 in a suitable fungal host ceil. The present invention also relates to methods for producing such polypeptides having gSucoamySase activity comprising (a) cultivating a recombinant host ceil comprising a nucleic acid construct comprising a polynucleotide encoding the polypeptide under conditions conducive for production of the polypeptide; and (b) recovering the polypeptide.

The present invention also relates to processes of producing fermentation products or syrups.

Definitions

GIucoamylase activity; The term glucoamylase (1 ,4-alρha-D-giucan glucohydroiase, EC 3.2.1.3} is defined as an enzyme, which catalyzes the release of D- glucose from the non-reducing ends of starch or related oiigo- and polysaccharide molecules. For purposes of the present invention, giucoamyiase activity is determined according to the procedure described in the 'Materials & Methods -section below.

The polypeptides of the present invention have at least 20%, preferably at least 40%, more preferably at least 50%, more preferably at least 60%, more preferably at least 70% _: more preferably at least 80%, even more preferably at least 90%, most preferably at least

95%, and even most preferably at least 100% of the giucoamyiase activity of the polypeptide consisting of the amino acid sequence shown as amino acids 1 to 558 of SEQ ID NO: 2.

Polypeptide: The term "polypeptide^* as used herein refers to an isolated polypeptide which is at least 20% pure, preferably at least 40% pure, more preferably at least 60% pure, even more preferably at least 80% pure, most preferably at least 90% pure, and even most preferably at least 95% pure, as determined by SDS-PAGE. Substantially pure polypeptide: The term "substantially pure polypeptide" denotes herein a polypeptide preparation which contains at most 10%. preferably at most 8%, more preferably at most 6%, more preferably at most 5%, more preferably at most 4%₅ at most 3%, even more preferably at most 2%, most preferabiy at most 1%. and even most preferably at most 0.5% by weight of other polypeptide material with which ht is nativeiy associated. It is, therefore, preferred that the substantially pure polypeptide is at least 92% pure, preferably at least 94% pure, more preferably at least 95% pure, more preferably at least 96% pure, more preferably at least 96% pure, more preferably at least 97% pure, more preferably at least 98% pure, even more preferably at least 99%, most preferably at ieast 99.5% pure, and even most preferably 100% pure by weight of the total polypeptide material present in the preparation.

The poiypeptides of the present invention are preferabiy in a substantially pure form. in particular, it is preferred that the poiypeptides are in "essentially pure form", i.e., that the polypeptide preparation is essentially free of other polypeptide material with which it is natively associated. This can be accomplished, for example, by preparing the polypeptide by means of weSi-known recombinant methods or by classical purification methods.

Herein, the term "substantially pure polypeptide" is synonymous with the terms Isolated polypeptide" and "polypeptide in isolated form".

Identity: The relatedπess between two amino acid sequences or between two nucleotide sequences is described by the parameter "identity^*.

For purposes of the present invention, the degree of identity between two amino acid sequences is determined by the CSustal method (Higgins, 1989, CABIOS 5: 151-153) using the LASERGENE™ MEGALIGN™ software (DNASTAR, Inc., Madison, Wl) with an identity table and the following multiple alignment parameters; Gap penalty of 10 and gap length penalty of 10. Pairwise alignment parameters are Kiuple=1 , gap penalty=3, windows=5, and diagonais=5.

For purposes of the present invention, the degree of identity between two nucleotide sequences is determined by the WiSbur-LJpman method (Wilbur and ϋprnan, 1983, Proceedings of the National Academy of Science USA 80: 726-730) using the LASERGEWE™ IVEGALiGM™ software (DNASTAR, inc., Madison, Wl) with an identity table and the following multiple alignment parameters: Gap penalty of 10 and gap length penalty of 10. Pairwise alignment parameters are Ktuple=3, gap penalty=3, and windows=20.

Polypeptide Fragment: The term "polypeptide fragment" is defined herein as a polypeptide having one or more amino acids deleted from the amino and/or carfaoxyl terminus of SEQ ID NO: 2, or homologous sequences thereof, wherein the fragment has glucoamylase activity. Subsequence: The term "subsequence" is defined herein as a nucleotide sequence having one or more nucleotides deleted from the 5' and/or 3' end of SEQ ID NO: 1 or 3, or homologous sequences thereof, wherein the subsequence encodes a polypeptide fragment having glucoamylase activity. Allelic variant: The term "allelic variant" denotes herein any of two or more alternative forms of a gene occupying the same chromosomal locus. AISeiic variation arises naturally through mutation, and may resuit in polymorphism within populations. Gene mutations can be silent (no change in the encoded polypeptide) or may encode polypeptides having altered amino acid sequences. An allelic variant of a polypeptide is a polypeptide encoded by an allelic variant of a gene.

Substantial pure polynucleotide: The term ^"substantially pure polynucleotide" as used herein refers to a polynucleotide preparation free of other extraneous or unwanted nucleotides anά in a form suitable for use within genetically engineered protein production systems. Thus, a substantially pure polynucleotide contains at most 10%, preferably at most 8%, more preferably at most 6%, more preferably at most 5%, more preferably at most 4%, more preferably at most 3%, even more preferably at most 2%, most preferably at most 1%. and even most preferably at most 0.5% by weight of other polynucleotide materia! with which it is natively associated. A substantially pure polynucleotide may, however, include naturaily occurring 5' and 3' untranslated regions, such as promoters anύ terminators. It is preferred that the substantially pure polynucleotide is at least 90% pure, preferably at least 92% pure, more preferably at least 94% pure, more preferably at least 95% pure, more preferably at least 96% pure, more preferably at least 97% pure, even more preferably at least 98% pure, most preferably at ieast θθ%« and even most preferably at least 99,5% pure by weight. The polynucleotides of the present invention are preferably in a substantialiy pure form. In particular, it is preferred that the polynucleotides disclosed herein are in "essentially pure form^"', i.e.. that the polynucleotide preparation is essentially free of other polynucleotide materia! with which it is natively associated. Herein, the term "substantially pure polynucleotide" is synonymous with the terms "isolated polynucleotide" and "polynucleotide in isolated form." The polynucleotides may be of genomic, cDNA, RNA, semi-synthetic, synthetic origin, or any combinations thereof. cD!\JA: The term "cDNA" is defined herein as a DNA molecule which can be prepared by reverse transcription from a mature, spliced, mRNA molecule obtained from a eukaryotic cell. cDNA lacks intron sequences that are usually present in the corresponding genomic DNA, The initial, primary RNA transcript is a precursor to mRNA which is processed through a series of steps before appearing as mature spliced mRNA. These steps include the removal of intron sequences by a process called splicing. cDNA derived from mRNA Sacks, therefore, any intron sequences.

Nucleic acid construct: The term "nucleic acid construct" as used herein refers to a nucleic acid molecule, either single- or double-stranded, which is isolated from a naturaiiy occurring gene or which is modified to contain segments of nucleic acids in a manner that would not otherwise exist in nature. The term nucleic acid construct is synonymous with the term "expression cassette" when the nucleic acid construct contains the control sequences required for expression of a coding sequence of the present invention.

Control sequence: The term "control sequences" is defined herein to include ail components, which are necessary or advantageous for the expression of a polynucleotide encoding a polypeptide of the present invention. Each control sequence may be native or foreign to the nucleotide sequence encoding the polypeptide. Such control sequences include, but are not limited to, a leader, polyadenylation sequence, pro-peptide sequence, promoter, signal peptide sequence, and transcription terminator. At a minimum, the controi sequences include a promoter, and transcriptional and translationai stop signals. The control sequences may be provided with linkers for the purpose of introducing specific restriction sites faciiitating ligation of the control sequences with the coding region of the nucleotide sequence encoding a polypeptide.

Operably linked: The term "operably linked" denotes herein a configuration in which a control sequence is placed at an appropriate position relative to the coding sequence of the polynucleotide sequence such that the control sequence directs the expression of the coding sequence of a polypeptide.

Coding sequence: When used herein the term "coding sequence" means a nucleotide sequence, which directly specifies the amino acid sequence of its protein product. The boundaries of the coding sequence are generaliy determined by an open reading frame, which usually begins with the ATG start codon or alternative start codons such as GTG anά TTG. The coding sequence may a DNA, cDNA, or recombinant nucleotide sequence.

Expression: The term "expression" inciudes any step invoived in the production of the polypeptide including, but not iimited to, transcription, pαst-transcriptϊonai modification, translation, post-translatioπal modification, and secretion.

Expression vector; The term "expression vector" is defined herein as a iinear or circular DNA molecule that comprises a polynucleotide encoding a polypeptide of the invention, and which is operabiy linked to additional nucleotides that provide for its expression. Host celt: The term "host cell", as used herein, includes any cei! type which is susceptible to transformation, transfection, transduction, and the ϋke with a nucleic acid construct comprising a poiynucleotide of the present invention.

Modification; The term "modification^* means herein any chemicai modification of the polypeptide consisting of the amino acids 1 to 558 of SEQ !D NO; 2. as weil as genetic manipuiation of the DNA encoding the poSypeptides. The modifιcation(s) can be substitution^), deletion(s) and/or insertions(s) of the amino acici{s) as wel! as repiacement(s) of amino acid side chain(s).

Artificial variant; When used herein, the term "artϊftcia! variant" means a polypeptide having giucoamylase activity produced by an organism expressing a modified nυcieotide sequence of SEQ !D NOS: 1 (genomic DNA) or 3 (cDNA). The modified nucieotide sequence is obtained through human intervention by modification of the nucieotide sequence discSosed in SEQ ID NO: 1 or 3.

Detailed Description of the Invention

Polypeptides Having Glucoamylase Activity

In a first aspect, the present invention relates to polypeptides having an amino acid sequence which has a degree of identity to amino acids 1 to 558 of SEQ ID NO: 2 (i.e. , mature polypeptide), In an embodiment the polypeptide is a variant comprising a conservative substitution, deletion, and/or insertion of one or more amino acids of amino acids 1 to 558 of SEQ iD NO:

2.

In an embodiment the amino acid sequence has giucoamylase activity anύ is at ieast

60%, preferably at ieast 70% _: preferabiy at ieast 80%, more preferabiy at ieast 85%, even more preferably at least 90%, most preferably at least 95%, more preferred at ieast 96%, even more preferred at least 97%, even more preferred at least 98%, even more preferabiy at ieast 99% identicai to the mature part of SEQ !D NO: 2 {hereinafter "homologous polypeptides").

In a preferred aspect, the homologous polypeptides have an amino acid sequence which differs by ten amino acids, preferably by five amino acids, more preferably by four amino acids, even more preferably by three amino acids, most preferably by two amino acids, and even most preferabiy by one amino acid from amino acids 1 to 558 of SEQ ID

NO; 2,

A polypeptide of the present invention preferabiy comprises the mature amino acid sequences of SEQ iD NO: 2, or alSeiic variants thereof; or fragments thereof that have giucoamylase activity, e.g., the catalytic domain. Catalytic Domain

In an aspect, the invention relates to polypeptides that comprise the catalytic region/domain of the amino acid sequences of SEQ ID NO: 2, The cataiytic region/domain of the the invention exhibiting glucoarnyiase activity, preferably derived from a strain of Peniophora.. especiaiiy a strain of preferably Peniophora rufomarginata, is iocated from amino acids 1 to 448 in SEQ ID NO: 2. In one embodiment the region may be considered to include the Sinker region from amino acids 449 to 483 of SEQ !D NO: 2, or part thereof. The putative binding domain is encoded by poiyπucleotides 1845 to 2301 in SEQ ID NO: 1 or or polynucleotides 1450-1734 of SEQ ID NO: 3.

In a preferred embodiment the invention reiates to a catalytic region which has at least 60% identity, preferabiy at Seast 85% identity, more preferabiy at least 70% identity, more preferably at least 75% identity, more preferabiy at ieast 80% identity, more preferabiy at ieast 85% identity, even more preferably at ieast 90% identity, most preferabiy at ieast 95% identity, more preferred at ieast 96% identity, even more preferred at least 97% identity, even more preferred at ieast 98% identity, even more preferabiy at ieast 99% identity, especially 100% identity to amino acids 1 to 448 in SEQ ID NO: 2, and which have glucoamylase activity (hereinafter "homologous polypeptides"}, in a preferred aspect, the homologous catalytic regions have amino acid sequences which differs by fen amino acids, preferably by five amino acids, more preferabiy by four amino acids, even more preferabiy by three amino acids, most preferably by two amino acids, and even most preferabiy by one amino acid from amino acids 1 to 448 of SEQ SD NO: 2.

Binding Domain In another aspect, the invention relates to polypeptides having carbohydrate-binding affinity, preferabiy starch- binding affinity.

The binding domain in Peniophora rufomarginata glucoamyiase is iocated from amino acid 464 to 558 of SEQ !D NO: 2 and is encoded by poiynucleotides 1845-2301 in

SEQ ID NO: 1 or 1450-1734 of SEQ ID NO: 3. Consequentiy, in this aspect the invention relates to a poiypeptide having carbohydrate-binding affinity, seiected from the group consisting of:

(a) i) a poiypeptide comprising an amino acid sequence which has at ieast 60% identity with amino acids 464 to 558 of SEQ ID NO: 2;

(b) a polypeptide which Ss encoded by a nucleotide sequence which hybridizes under low stringency conditions with a polynucieotide probe which has the compiementary strand of nucleotides 1845 to 2301 of SEQ ID NO; 1 or nucleotides 1450 to 1734 of SEQ ID NO: 3, respectively;

(C) a fragment of (a) or (b) that has carbohydrate binding affinity.

In a preferred embodiment the carbohydrate binding affinity is starch- bind ing affinity. In a preferred embodiment the invention relates to a poiypepticie having carbohydrate binding affinity which has at ieast 80% identity, preferabiy at ieast 70% identity, more preferably at least 75% identity, more preferabiy at Seast 80% identity, more preferably at least 85% identity, even more preferably at Seast 90% identity, most preferably at ieast 95% identity, more preferred at least 96% identity, even more preferred at ieast 97% identity, even more preferred at ieast 98% identity, even more preferabiy at ieast 99% identity, especially 100% identity to amino acids 464 to 558 in SEQ ID NO: 2.

In a preferred aspect, homologous binding domains have amino acid sequences which differ by ten amino acids, preferabiy by five amino acids, more preferabiy by four amino acids, even more preferably by three amino acids, most preferably by two amino acids, and even most preferably by one amino acid from amino acids 464 to 558 of SEQ ID NO: 2,

The invention also relates to a polypeptide having carbohydrate- binding affinity, where the polypeptide is an artificial variant which comprises an amino acid sequence that has at least one substitution, deletion and/or insertion of an amino acid as compared to amino acids 464 to 558 of SEQ ID NO: 2.

The invention also relates to a polypeptide having carbohydrate-binding affinity, where the polypeptide is an artificial variant which comprises an amino acid sequence that has at ieast one substitution, deletion and/or insertion of an amino acid as compared to the amino acid sequence encoded by the carbohydrate-binding domain encoding part of the polynucleotide sequences shown in position 1845-2301 in SEQ ID NO: 1 , or 1450 to 1734 in SEQ ID NO: 3.

Hybrids

The giucoa myiases or catalytic regions of the invention may be linked, via a linker sequence or directly, to one or more foreign binding domains (also referred to as binding moduies (CBM)), A "foreign" binding domain is a binding-domain that is not derived from the wild-type giucoamyiase of the invention. The binding-domain is preferably a carbohydrate- binding domain (i.e., having affinity for binding to a carbohydrate), especially a starch- binding domain or a celluiose-binding domain. Preferred binding domains are of fungal or bacterial origin. Examples of specifically contemplated starch-binding domains are disclosed in WO 2005/003311 which is hereby incorporated by reference. In a preferred embodiment the linker in a glucoamylase of the invention is replaced with a more stable linker, i.e., a linker that is more difficult to cut than the parent linker. This is done to avoid that the binding-domain is cleaved off. Specifically contempiated stable linkers include the Aspergillus kawachii linker: TTTTTTAAAT STSKATTSSSSSSAAATTSSS (SEQ ID NO; 4)

Thus, in a preferred embodiment the invention relates to a hybrid giucoamyiase having the amino acid sequence shown in SEQ ID NO: 2, wherein the native Sinker iocated from amino acids 449 to 463 of SEQ SD NO: 2« or part thereof, is replaced with the Aspergillus kawachii linker shown in SEQ !D NO: 4, Thus, the invention also relates to hybrids consisting of a giucoamyiase of the invention or cataSytic domain of the invention having giucoamyiase activity fused to a stable linker (e.g., Aspergillus kawachii linker) and one or more carbohydrate-binding domains, e.g., a carbohydrate-binding module (CBM) disclosed in WO 2005/003311 on page 5. Sine 30 to page 8, iine 12, hereby incorporated by reference.

Hybridization

In another aspect, the present invention relates to poSypeptides having giucoamyiase activity which are encoded by polynucleotides (i) which hybridizes under at least Sow stringency conditions, preferabiy medium stringency conditions, more preferably medium- high stringency conditions, even more preferably high stringency conditions, and most preferably very high stringency conditions with a nucleotide sequence with nucSeotides 61 to 2301 of SEQ ID NO: 1 (Peniophora genomic DNA) or nucleotides 61 to 1734 of SEQ ID NO: 3 {Peniophora cDNA), or (ii) a subsequence of (i), or (iii) a compSementary strand of (i) or (ii) (J, Sambrook, E. F, Fritsch, and T. Maniatis, 1989, Molecular Cloning, A Laboratory Manual, 2d edition, CoSd Spring Harbor, New York). A subsequence of SEQ ID NOS: 1 or 3 contains at least 100 contiguous nucleotides or preferably at least 200 continguous nucieotides, Moreover, the subsequence may encode a polypeptide fragment which has glucoamySase activity.

The nucieotide sequence of SEQ SD NOS: 1 or 3, or a subsequence thereof, as weil as the amino acid sequence of SEQ !D NO: 2, or a fragment thereof, may be used to design a nucleic acid probe to identify and clone DNA encoding poiypepfides having glucoamySase activity from strains of different genera or species according to methods weii 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 biotting procedures, in order to identify and isoSate the corresponding gene therein. Such probes can be considerabSy shorter than the entire sequence, but should be at ieast 14, preferabiy at ieast 25, more preferably at least 35, and most preferably at ieast 70 nucleotides in length. It is however, preferred that the nucleic acid probe is at ieast 100 nucleotides in length. For example, the nucieic acid probe may be at ieast 200 nucleotides, preferabϊy at least 300 nucleotides, more preferably at ieast 400 nucleotides, or most preferably at least 500 nucieotides in length. Even longer probes may be used, e.g., nucleic acid probes which are at least 600 nucleotides, at least preferabiy at least 700 nucieotides, more preferably at least 800 nucieotides, or most preferably at least 900 nucleotides in length. Both DNA and RNA probes can be used. The probes are typically labeled for detecting the corresponding gene (for example, with ^3?P, ⁵H. ³⁵S, biotin, or avidin). Such probes are encompassed by the present invention.

A genomic DNA or cDNA library prepared from such other organisms may, therefore, be screened for DNA which hybridizes with the probes described above anύ which encodes a polypeptide having glucoamylase activity. Genomic or other DNA from such other organisms may be separated by agarose or poiyacrylamide 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 material. Sn order to identify a clone or DNA which is homologous with SEQ !D NOS: 1 or 3, or a subsequence thereof, the carrier material is used in a Southern blot.

For purposes of the present invention, hybridization indicates that the nucleotide sequences hybridize to labeled nucleic acid probes corresponding to the nucleotide sequence shown in SEQ ID NOS: 1 or 3, its complementary strands, or subsequences thereof, under low to very high stringency conditions. Molecules to which the nucleic acid probe hybridizes under these conditions can be detected using X-ray film.

In a preferred embodiment, the nucleic acid probe is nucleotides 81 to 2301 of SEQ ID NO: 1 or nucieotides 61 to 1734 of SEQ ID NO: 3. in another preferred aspect, the nucieic acid probe is a polynucleotide sequence which encodes the catalytic region between amino acids 1-448 of SEQ ID NO: 2.

In another aspect the invention relates to nucleic acid probes that encode the binding domain in amino acids 464 to 558 of SEQ ID NO: 2. In another preferred aspect, the nucleic acid probe Ss the mature polypeptide coding region of SEQ !D NOS: 1 or 3, respectively.

In another preferred aspect, the nucleic acid probe is the part of the sequences in plasmid pENI2516 coding for the mature polypeptides of the invention. Piasmid pEN!2516 which are contained in Escherichia cols DSM 18150 encode polypeptides having glucoamylase activity. For long probes of at least 100 nucleotides in length, low to very high stringency conditions are defined as prehybridization and hybhdization at 42^C in 5X SSPE, 0.3% SDS, 200 micro g/mi sheared and denatured salmon sperm DNA, and eitner 25% formamide for low stringencies, 35% formamide for medium and medium-high stringencies, or 50% formamide for high and very high stringencies, following standard Southern blotting procedures for 12 to 24 hours optimaily.

For long probes of at least 100 nucleotides in length, the carrier materia! is finaSiy washed three times each for 15 minutes using 2X SSC₁ 0.2% SOS preferably at least at

50^aC (low stringency), more preferably at least at 55X (medium stringency), more preferably at least at 6Q⁰C (medium-high stringency), even more preferably at least at 65"¹C

(high stringency), and most preferably at least at ?0"C (very high stringency).

For short probes which are about 15 nucleotides to about 70 nucleotides in length, stringency conditions are defined as prehybridization. hybridization, and washing post- hybridization at about 5"C to about 1O⁰C below the calculated T_!!S using the calculation according to Bolton and McCarthy {1962, Proceedings of the Nationa! Academy of Sciences USA 48:1390} in 0.9 M NaCi, 0.09 !Vl TrIs-HCI pH 7.6. 6 mU EDTA, 0.5% NP-40, 1X Deπhardt's solution, 1 mM sodium pyrophosphate, 1 mM sodium monobasic phosphate, 0.1 mM ATP, &nά 0.2 mg of yeast RNA per ml following standard Southern blotting procedures.

For short probes which are about 15 nucleotides to about 70 nucleotides 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 10¹⁵C below the calculated T_m.

Under salt-containing hybridization conditions, the effective T_m is what controls the degree of identity required between the probe anά the filter bound DMA for successful hybridization. The effective T_n, may be determined using the formula below to determine the degree of identity required for two DNAs to hybridize under various stringency conditions.

Effective T,,, = 81.5 + 16.β(log M[Ha^*]) + 0.41(%G+C) - 0.72(% formamide)

(See _.www,Msy,n^

Variants In a further aspect, the present invention relates to artificial variants comprising a conservative substitution, deletion, and/or insertion of one or more amino acids in SEQ ID NO: 2, or the mature polypeptide thereof. Preferably, amino acid changes are of a minor nature, that is conservative amino acid substitutions or insertions that do not significantly affect the folding and/or activity of the protein; small deletions, typically of one to about 30 amino acids; small amino- or carboxyl-termina! extensions, such as an amino-terminal methionine residue; a small linker peptide of up to about 20-25 residues; or a small extension that facilitates purification by changing net charge or another function, such as a poly-histidine tract, an antigenic epitope or a binding domain.

Exampies 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 (giutaminβ and asparagine), hydrophobic amino acids (leucine, isoieucine and vaSiπe), aromatic amino acids (phenylalanine, tryptophan and tyrosine), and smail amino acids {glycine, alanine, serine, threonine and methionine), Amino acid substitutions which do not generally aiter specific activity are known Sn 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 Aia/Ser, Val/ile, Asp/Giu, Thr/Ser, Aia/Gly, Ala/Thr_s Ser/Asn, Aia/Vai, Ser/Gly, Tyr/Phe, Ala/Pro, Lys/Arg, Asp/Asn_: Leu/He, Leυ/Val, Aia/Glυ, and Asp/Giy.

In addition to the 20 standard amino acids, non-standard amino acids (such as 4- hydroxyproline, δ~/V-rnethy! lysine, 2-aminoisobutyric acid, isovaiine, and alpha-methyl serine) may be substituted for amino acid residues of a wild-type polypeptide. A iimited number of non-conservative amino acids, amino acids that are not encoded by the genetic code, and υnnaturai amino acids may be substituted for amino acid residues. "Unnatural amino acids" have been modified after protein synthesis, and/or have a chemical structure in their side chain(s) different from that of the standard amino acids. Unnatural amino acids can be chemically synthesized, and preferably, are commercially available, and include pipecoiic acid, thiazolidine carboxyiic acid, dehydroproiine, 3- and 4-rnethylproline, and 3,3- dimethylproline.

Aitematively, the amino acid changes are of such a nature that the physico-chemical properties of the polypeptides are altered. For example, amino acid changes may improve the thermal stability of the polypeptide, alter the substrate specificity, change the pH optimum, and the like.

Essential amino acids in the parent polypeptide can be identified according to procedures known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (Cunningham and Weils, 1989, Science 244: 1081-1085). In the latter technique, single alanine mutations are introduced at every residue Sn the molecule, anύ the resultant mutant molecules are tested for biological activity (i.e., glucoamylase activity) to identify amino acid residues that are critical to the activity of the molecule. See also, Hilton et at. , 1998, J. Biol. Cftem. 271 : 4699-4708. The active site of the enzymes or other biological interaction can also be determined by physical analysis of structure, as determined by such techniques as nuclear magnetic resonance, crystallography, electron diffraction, or photoaffinity labeling, in conjunction with mutation of putative contact site amino acids. See, for example, de Vos ef a/. , 1992, Science 255; 306-312; Smith et at, 1992, J. Moi. Bioi. 224: 899-904; Wiodaver et a!., 1992, FEBS Lett, 309;59-64. The identifies of essential amino acids can also be inferred from analysis of identities with polypeptides which are related to a polypeptide according to the invention. Single or multiple amino acid substitutions can be made and tested using known methods of mutagenesis, recombination, and/or shuffling, followed by a relevant screening procedure, such as those disclosed by Reidhaar-Olson and Sauer, 1988, Science 241 ; 53- 57; Bowie and Sauer, 1989, Proc. Natl, Acaά, ScL USA 86; 2152-2156; WO 95/17413; or WO 95/22625. Other methods that can be used include error-prone PCR, phage display (e.g., lowman et at. , 1991 , Bioεbem, 30; 10832-10837; U.S. Patent No. 5,223,409; WO 92/06204), and region-directed mutagenesis (Derbyshire et ai , 1986, Gene 46:145; Ner et ai... I BBB.. DNA 7:127).

Mutagenesis/shuffliπg methods can be combined with high-throughput, automated screening methods to detect activity of cloned, mutagenized polypeptides expressed by host ceiis. Mutagenized DNA molecules that encode active polypeptides can be recovered from the host ceils and rapidly sequenced using standard methods Sn the art. These methods allow the rapid determination of the importance of individual amino acid residues in a polypeptide of interest, and can be applied to polypeptides of unknown structure.

The total number of amino acid substitutions, deletions and/or insertions of amino acids in position 1 to 558 of SEQ ID NO: 2, is 10, preferably 9, more preferably S, more preferably 7, more preferably at most 6, more preferably at most S, more preferably 4, even more preferably 3, most preferably 2, and even most preferabiy 1.

Sources of Polypeptides Having Glucoamylase Activity A polypeptide of the present invention may be obtained from microorganisms of any genus. For purposes of the present invention, the term "obtained from" as used herein in connection with a given source shall mean that the polypeptide encoded by a nucleotide sequence is produced by the source or by a strain in which the nucleotide sequence from the source has been inserted. In a preferred aspect, the polypeptide obtained from a given source is secreted extraceilularly.

In a preferred embodiment, the glucoamylase of the invention derived from the class Basidiomycetes. In a more preferred embodiment a glucoamylase of the invention is derived from a strain of the genus Peniophora, more preferably from a strain of the species Peniophora refomarginata, or deposited as Escherichia coii clone DSM 18150. It will be understood that for the aforementioned species, the invention encompasses both the perfect and imperfect states, and other taxonomic equivalents, e.g., anamorphs, regardless of the species name by which they are known. Those skilled in the art wil! readily recognize the identity of appropriate equivalents.

The Peniaphara refomarginata strain was collected in Denmark in 1997.

Furthermore, such polypeptides may be identified and obtained from other sources including microorganisms isolated from nature (e.g., sou, composts, water, etc.) using the above-mentioned probes. Techniques for isolating microorganisms from natural habitats are well known in the art. The polynucleotide may then be obtained by similarly screening a genomic or cDNA library of another microorganism. Once a poiynucieotide sequence encoding a poiypeptide has been detected with the probe(s), the poiynucieotide can be isolated or cioned by utilizing techniques which are weii known to those of ordinary skiil in the art (see, e.g., Sambrook et al , 1989, supra).

Poiypeptides of the present invention also include fused poiypeptides or cleavable fusion polypeptides in which another polypeptide is fused at the N-terminus or the C- terminus of the poiypeptide or fragment thereof. A fused polypeptide is produced by fusing a nucleotide sequence (or a portion thereof) encoding another poiypeptide to a nucieotide sequence (or a portion thereof) of the present invention. Techniques for producing fusion polypeptides are known in the art, and include iigating the coding sequences encoding the polypeptides so that they are in frame and that expression of the fused poiypeptide is under control of the same promoter(s) and terminator.

Polynucleotides

The present invention also relates to isoiated polynucleotides having a nucleotide sequence which encode a poiypeptide of the present invention. In a preferred aspect, the nucieotide sequence is set forth in any of SEQ ID NO: 1 (genomic DNA) or 3 (cDNA), respectively. In another more preferred aspect, the nucleotide sequence is the sequence contained in piasmid pENI2516 that is contained in Escherichia coli DSIVi 18150 In another preferred aspect, the nucleotide sequence is the mature polypeptide coding region of any of SEQ !D NOS: 1 or 3, respectively. The present invention also encompasses nucieotide sequences which encode a polypeptide having the amino acid sequence of SEQ ID NO: 2, or the mature poiypeptide thereof, which differs from SEQ SD NOS: 1 or 3, respectively, by virtue of the degeneracy of the genetic code. The present invention also relates to subsequences of any of SEQ ID NOS: 1 or 3, respectively, which encode fragments of SEQ ID NO: 2 that h&ve glucoamylase activity.

The present invention also reiates to mutant polynucleotides comprising at ieast one mutation in the mature poiypeptide coding sequence of any of SEQ ID NOS: 1 or 3, respectively, in which the mutant nucleotide sequence encodes a polypeptide which consists of amino acids 1 to 558 of SEQ ID NO: 2,

The techniques used to isolate or clone a polynucleotide encoding a polypeptide are known in the art and include isolation from genomic DNA, preparation from cDNA. or a combination thereof. The cloning of the polynucleotides 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 iibraries to detect cloned DNA fragments with shared structural features. See, e.g., lnnis e( a/,, 1990, PCR: A Guide to Methods and Application, Academic Press, New York, Other nucleic acid amplification procedures such as Sigase chain reaction (LCR). ligated activated transcription (LAT) and nucleotide sequence-based amplification (NASBA) may be used The polynucleotides may be cloned from any organism, especially a strain of the genus Peniophora or other or related organisms and thus, for example, may be an aSleiic or species variant of the polypeptide encoding region of the nucleotide sequences. The present invention also reiates to polynucieotides having nucleotide sequences which have a degree of identity to the mature polypeptide coding sequence of SEQ ID NO: 1 (i.e.. nucleotides 61 to 2301), or SEQ ID NO: 3 (i.e., nucleotides 61 to 1734), respectively, of at least 60%, preferably at least 65%, more preferably at least 70%, more preferably at least 75%, more preferably at least 80%, more preferably at least 85%, more preferably at least 90%. even more preferably at least 95%. even more prefer ably 98%, even more 97%, even more 98%, and most preferably at ieast 99% identity, which encode an active polypeptide.

Modification of a nucleotide sequence encoding a polypeptide of the present invention may be necessary for the synthesis of polypeptides substantially similar to the polypeptide. The term "substantially similar¹ to the polypeptide refers to non-naturaily occurring forms of the polypeptide. These polypeptides may differ in some engineered way from the polypeptide isolated from its native source, e.g., artificial variants that differ in specific activity, thermostabiSity, pH optimum, or the like. The variant sequence may be constructed on the basis of the nucleotide sequence presented as the mature polypeptide encoding region of any of SEQ ID NOS. 1 or 3, respectively, e.g.. subsequences thereof, and/or by introduction of nucleotide substitutions, which do not give rise to another amino acid sequence of the polypeptide encoded by the nucleotide sequence, but which correspond to the codon usage of the host organism intended for production of the enzyme, or by introduction of nucleotide substitutions which may give rise to a different amino acid sequence. For a general description of nucleotide substitution, see, e.g.. Ford et al., 1991 , Protein Expression anύ Purification 2: 95- 107. It will be apparent to those skilled in the art that such substitutions can be made outside the regions critical to the function of the molecule and still resuit in an active polypeptide. Amino acid residues essential to the activity of the polypeptide encoded by an isolated polynucleotide of the invention, and therefore preferabiy not subject to substitution, may be identified according to procedures known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis {see, e.g., Cunningham and Wells, 1989₅ Science 244: 1081-1085). In the latter technique, mutations are introduced at every positively charged residue in the molecule, and the resultant mutant molecules are tested for glucoamylase activity to identify amino acid residues that are critical to the activity of the molecuie. Sites of substrate-enzyme interaction can aiso be determined by analysis of the three-dimensional structure as determined by such techniques as nuclear magnetic resonance analysis, crystallography or photoaffinity labelling {see, e.g. , de Vos ef a/,, 1992, Science 255: 306-312; Smith et at, 1992_« Journal of Molecular Biology 224: 899-904; Wlodaver et a/., 1992, FEBS Letters 309: 59-64). The present invention also relates to isolated polynucleotides encoding a polypeptide of the present invention, (i) which hybridize under low stringency conditions, more preferabiy medium stringency conditions, more preferabiy medium-high stringency conditions, even more preferably high stringency conditions, and most preferably very high stringency conditions with nucleotides 61 to 2301 of SEQ ID NO: 1 or nucleotides 61 to 1734 of SEQ ID NO: 3, respectively, or (si) a compiementary strand of (S); or allelic variants and subsequences thereof (Sambrook et a/. , 19S9, supra), as defined herein.

The present invention also relates to isolated polynucleotides obtained by {a) hybridizing a population of DNA under low, medium, medium-high, high, or very high stringency conditions with (i) nucleotides 61 to 2301 of SEQ ID NO: 1 or nucleotides 61 to 1734 of SEQ ID NO: 3, respectively, or {ii} a complementary strand of {i}; and (b) isolating the hybridizing polynucleotide, which encodes a polypeptide having glucoamylase activity.

Nucleic Acid Constructs

The present invention also relates to nucleic acid constructs comprising an isolated polynucleotide of the present invention operably linked to one or more control sequences which direct the expression of the coding sequence in a suitable host cell under conditions compatible with the control sequences.

An isolated polynucieotide encoding a polypeptide of the present invention may be manipulated in a variety of ways to provide for expression of the polypeptide. Manipulation of the polynucleotide^'s sequence prior to its insertion into a vector may be desirable or necessary depending on the expression vector. The techniques for modifying polynucleotide sequences utilizing recombinant DNA methods are weil known in the art.

The control sequence may be an appropriate promoter sequence, a nucleotide sequence which is recognized by a host celi for expression of a polynucieotide encoding a polypeptide of the present invention. The promoter sequence contains transcriptional control sequences which mediate the expression of the poiypeptide. The promoter may be any nucleotide sequence which shows transcriptional activity in the host cell of choice inciuding mutant, truncated, and hybrid promoters, and may be obtained from genes encoding extraceϋular or intraceiiuiar polypeptides either homoiogous or heterologous to the host cell. Examples of suitabie promoters for directing the transcription of the nucleic acid constructs of the present invention in a filamentous funga! host eel! are promoters obtained from the genes for Aspergillus oryzae TAKA amylase, Rhizomucor rnlehei aspartic proteinase. Aspergillus nigβr neutral alpha-arnylase. Aspergillus niger acid stable alpha- amySase, Aspergillus niger or Aspergillus awamoή glucoamylase (glaA), Rhizomucor miehei lipase, Aspergillus oryiae alkaline protease, Aspergillus oryzae triose phosphate isomerase. Aspergillus nidulans aeetarnidase, Fusarium venenatum glucoamylase (WO 00/56900), Fusarium venenatum Daria (WO 00/56900). Fusarium venenatum Quinn (WO 00/56900), Fusarium oxysporum trypsin-like protease (WO 96/00787), Trichoderma reesei beta- glucosidase. Trichoderma reesei celSobiohydrølase !. Trichoderma reesei endogluεanase !. Trichodenva reesei endoglucanase Ii, Trlchoύerma reesei endogiucanase III, Trichoderma reesei endogiucanase IV, Trichoderma reesei endoglucanase V, Trichoderma reeses xylanase I. Trichoderma reesei xyianase II, Trichoderma reesei beta-xyiosidase, as we!! as the NA2-tpi promoter (a hybrid of the promoters from the genes for Aspergillus niger neutral alpha-amyiasβ and Aspergillus oryiae triose phosphate isomerase); and mutant, truncated, and hybrid promoters thereof.

In a yeast host, usefui promoters are obtained from the genes for Saccharomyces cerβvisiae enoiase (ENO-1), Saccharomyces cerevisiae gaSactokinase (GAL1). Saccharomyces cerevislae aicohol dehydrogenase/glyceraSdehyde-3-phosphate dehydrogenase (ADH 1.ADH2/G AP), Saccharomyces cerevisia® triose phosphate isomerase (TPI), Saccharomyces cerevisiae mβtallothionine (CUP1), anύ Saccharomyces cerevisiae Z- phosphogiyεerate kinase. Other useful promoters for yeast host cells are described by Romanos ef al., 1992, Yeast 8: 423-488.

The control sequence may a!so be a suitabie transcription terminator sequence, a sequence recognized by a host ceil to terminate transcription. The terminator sequence Ss operably linked to the 3" terminus of the nucieotfde sequence encoding the polypeptide. 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 giucoamyiase, Aspergillus nidulans anthranilate synthase, Aspergillus niger alpha-glucosidase, and Fusarium oxysporum trypsin-Sike protease. Preferred terminators for yeast host cells are obtained from the genes for

Saccharomyces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C (CYC1)_S and Saccharomycβs cerevisiae giyceraldehydβ-3-phosphaie dehydrogenase. Other useful terminators for yeast host ceils are described by Romanos et a?,, 1992, supra.

The control sequence may also be a suitable leader sequence, a nontranslated region of an rnRNA which is important for translation by the host cell. The leader sequence is operably linked to the 5^s terminus of the nucleotide sequence encoding the polypeptide. Any leader sequence that Ss functional in the host cell of choice may be used in the present invention.

Preferred leaders for filamentous fungal host ceils are obtained from the genes for Aspergillus oryzae TAKA amylase anύ Aspergillus nidulans triose phosphate isomerase,

Suitabie leaders for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase (ENG-1), Saccharomyces cerevisiae 3-phosphogiycerate kinase, Saccharomyces cerevisiae alpha-factor, and Saccharomyces cerevisiae alcohol dehydrogenase/giyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP). The control sequence may also be a polyadenylation sequence, a sequence operably linked to the 3' terminus of the nucieotide 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 ceils are obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger giucoamyiase, Aspergillus nidulans anthranilate synthase, Fusarium oxysporum trypsin-like protease, and Aspergillus niger aipha-giucosidase.

Useful polyadenylation sequences for yeast host celis are described by Guo and Sherman. 1995. Molecular Cellular Biology 15; 5Θ83-5990,

The controi sequence may aiso 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 polypeptide into the cell's secretory pathway. The 5' end of the coding sequence of the nucieotide 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 polypeptide. Alternatively, the 5' end of the coding sequence may contain a signal peptide coding region which is foreign to the coding sequence. The foreign signal peptide coding region may be required where the coding sequence does not naturally contain a signal peptide coding region. Aiternativeiy, the foreign signa! peptide coding region may simpiy replace the natural signal peptide coding region in order to enhance secretion of the polypeptide. However, any signa! peptide coding region which directs the expressed polypeptide into the secretory pathway of a host cell of choice may be used in the present invention.

Effective signal peptide coding regions for filamentous fungal host ceiis are the signal peptide coding regions obtained from the genes for Aspergillus oryzaβ TAKA amylase. Aspergillus niger neutrai amylase, Aspergillus n/ger glueoamylase, Rhizomucor rntehei aspartic proteinase, Humicota insolens cellulase, and Humicola lanuginosa iipase.

Useful signal peptides for yeast host cells are obtained from the genes for Saccharotnyces c&revisiae alpha-factor and Saccharomyces cerewssae invertase. Other useful signal peptide coding regions are described by Romanos et a/., 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 polypeptide. The resultant polypeptide is known as a proenzyme or propoiypeptidβ (or a zymogen in some cases). A propolypeptide is generally inactive and can be converted to a mature active polypeptide by catalytic or autocataiytiε cieavage of the propeptide from the propolypeptide. The propeptide coding region may be obtained from the genes for Bacillus subtilis alkaline protease (aprE), Bacillus subtilis neutral protease (nprT), Saccharomyces cwevisiae alpha- factor, Rhizomucor miehβi aspartic proteinase, and Myceliophthora thermophila laccase (WO 95/33836).

Where both signa! 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 signa! peptide region is positioned next to the amino terminus of the propeptide region.

It may also be desirable to add regulatory sequences which allow the regulation of the expression of the polypeptide relative to the growth of the host cell. Examples of regulatory systems are those which cause the expression of the gene to be turned on or off in response to a chemical or physical stimulus, including the presence of a regulatory compound. In yeast, the ADH2 system or GAL1 system may be used. In filamentous fungi, the TAKA alpha-amylase promoter, Aspergillus niger glucoamylase promoter, and Aspergillus oryzae glucoamySase promoter may be used as regulatory sequences. Other examples of regulatory sequences are those which aϋow 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.

5 Expression Vectors

The present invention also relates to recombinant expression vectors comprising a polynucleotide of the present invention, a promoter, and transcriptional and translationa! stop signals. The various nucleic acids and control sequences described above may be joined together to produce a recombinant expression vector which may include one or more

I O convenient restriction sites to aliow for insertion or substitution of the nucieotide sequence encoding the polypeptide at such sites. Alternatively, a 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

15 is operabiy linked with the appropriate control sequences for expression.

The recombinant expression vector may be any vector {e.g. , a plasmid or virus) which can be conveniently subjected to recombinant DNA procedures and can bring about expression of the nucleotide sequence. The choice of the vector will typically depend on the compatibility of the vector with the host cell into which the vector Ss to be introduced. The 0 vectors may be linear or closed circular plasmids.

The vector may be an autonomously replicating vector, i.e., a vector which 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 self-replication. 5 Alternatively, the vector may be one which, when introduced into the host cell, is integrated into the genome and replicated together with the chromosomβ(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. 0 The vectors of the present invention preferably contain one or more selectable markers which 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 suitable markers for yeast host cells are ADE2, H1S3, LEU2, LYS2, 5 MET3, TRPI , and URA3. Selectable markers for use in a filamentous fungal host ceil include, but are not limited to, amdS (acetamidase), argB (ornithine carbamoyltransferase), bar (phosphinothricin acetyl! ransferase), hph {hygromyciπ phosphotransferase), niaD (nitrate reductase), pyrG (orαtidine-δ'-phosphaie decarboxylase), sC (sulfate adenyltraπsferase), and trpC (anthraniiate synthase), as we!! as equivaients 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 Streptotnyces hygroscopicus.

The vectors of the present invention preferably contain an elements) that permits 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 reSy on the polynucleotide's sequence encoding the polypeptide or any other eiement of the vector for integration into the genome by homologous or non-homologous recombination. Alternativeiy, the vector may contain additiona! nucleotide sequences for directing integration by homoiogous recombination into the genome of the host cell at a precise location(s) in the chromosome(s). To increase the SikeSihood of integration at a precise iocation, the integrationa! eiements shouid preferably contain a sufficient number of nucleic acids, such as 100 to 10,000 base pairs, preferabiy 400 to 10,000 base pairs, and most preferably 800 to 10,000 base pairs, which have a high degree of identity with the corresponding target sequence to enhance the probability of homoSogous recombination. The integrational elements may be any sequence that is homologous with the target sequence in the genome of the host ceil. Furthermore, the integrational elements may be non-encoding or encoding nucieotide sequences. On the other hand, the vector may be integrated into the genome of the host ceil by non-homoiogous recombination.

For autonomous replication, the vector may further comprise an origin of replication enabling the vector to repiicate autonomousSy in the host eel! in question. The origin of replication may be any plasmid repiicator mediating autonomous replication which functions in a ceil. The term "origin of replication" or "plasmid replicator" is defined herein as a nucieotide sequence that enabies a plasmid or vector to repϋcate in vivo.

Exampies of origins of replication for use in a yeast host ceil are the 2 micron origin of replication, ARS 1 , ARS4_r the combination of ARS1 and CEN3, and the combination of ARS4 and CEN6.

Exampies of origins of replication useful in a fiiamentous fungal cell are AMA 1 and ANSI (Gems et a/., 1991 , Gene 98:61-67; Cullen et al. , 1987, Nucleic Acids Research 15: 9163-9175; WO 00/24883). isoiation of the AMA1 gene and construction of plasmids or vectors comprising the gene can be accompiished according to the methods disciosed in WO 00/24883. More than one copy of a polynucleotide 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 polynucleotide 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 poiynucleotide where cells containing amplified copies of the selectabie marker gene, and thereby additiona! copies of the polynucleotide, can be seiected for by cultivating the cells in the presence of the appropriate selectabie 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 Bt at. , 1989, supra).

Host Ceils

The present invention also relates to recombinant host ceils, comprising a polynucleotide of the present invention, which are advantageously used in the recombinant production of the polypeptides, A vector comprising a polynucleotide of the present invention is introduced into a host cell so that the vector is maintained as a chromosomal integrant or as a self-replicating extra-chromosomal vector as described earlier. The term

"host cell" encompasses any progeny of a parent cell that is not identical to the parent cell due to mutations that occur during replication. The choice of a host cell will to a large extent depend upon the gene encoding the polypeptide and its source.

The host cell may be a eukaryote, such as a mammalian, insect, plant, or fungal cell. In a preferred aspect, the host cell is a fungal cell. "Fungi" as used herein includes the phyla Ascoiwycoia, Basidiomycota, Chytridiomycota, and Zygomycete (as defined by Hawksworth et a/., 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 aspect, the fungal host ceil is a yeast eel!. "Yeast" as used herein includes ascosporogenous yeast (Endomycetaies), basidiosporogenous yeast, and yeast belonging to the Fungi Imperfects (Bla&iomycetes) Since the classification of yeast may change in the future, for the purposes of this invention, yeast shall be defined as described in Biology and Activities of Yeast (Skinner, F.A. , Passmore, SM., and Davenport, R. R,, eds, Soc. App. Bacferiot. Symposium Series No. 9, 1980).

In an even more preferred aspect, the yeast host cell is a Candida, Hansenula, Kluyveromyces, Pichia, Saccharomyces, Schizosaccharomyces, or Yarrowia cell. In a most preferred aspect the yeast host cell is a Saccharomyces carlsbergen$is_t

Saccharomyces cerevisiae, Saccharomyc&s diastaiicus, Saccharomyces douglasii,

Saccharomyces kluyveri, Saccharomyces norbensis or Saccharomyces oviformis eel!, in another most preferred aspect, the yeast host ceil is a Kluyveromyces iactis cell, in another most preferred aspect, the yeast host ceii is a Yatrowia Iψolytica ceil.

In another more preferred aspect, the fungal host cell is a filamentous fungal cell. "Filamentous fungi " include all filamentous forms of the subdivision Eumycoia and Oomycota {as defined by Hawksworth et at, 1995, supra). The filamentous fungi are generally characterized by a myceiial waS! composed of chitin, ceiSulose, glucan, chitosan, mannan, and other complex polysaccharides. Vegetative growth is by hyphal elongation and carbon catabolism is obligately aerobic. In contrast, vegetative growth by yeasts such as Saccharomyces cerevisiae is by budding of a unicellular thaSSus and carbon catabolSsm may be fermentative.

In an even more preferred aspect, the fiiamentous fungal host ceii is an Acremonium, Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis, Coprinus. Coriolus, Cryptococcus. Filobasidium, Fusarium, Humicofa, Magnaporthe, Mucor, tøycetiophthora, Neocaliimastix, Neurospora. Paeαiomyces, Peniciilium. Phanerochaete, Phtebia, Piromyces, Pleurotus, Schizophyltum, Talaromyces, Thermoascus, Thieiavia, TolypocSadtum, Trametes, or Triαhoderma ceil. In a most preferred aspect, the fiiamentous fungal host cell is an Aspergillus awamori, Aspergillus fumigatus_> Aspergillus foetidus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger, Aspergillus kawachil or Aspergillus oryzae cell in another most preferred aspect, the filamentous fungai host eel! is a Fusarium baαtridioides, Fusarium cerealis, Fusanum crookwellense, Fusanum culmorum, Fusarium graivmearum, Fusarium graminum, Fusarium heterosporum, Fusanum negundi. Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum, Fusarium sporotrichioides. Fusarium sulphureum, Fusanum torulosum. Fusarium irichothedoides, or Fusarium venenatum ceii. in another most preferred aspect, the fiiamentous fungal host ceil is a Bjerkandera adusta, Cwiporiopsis aneirina. Cwiporiopsis aneirina. Ceriporiopsis camgiea, Ceriporiopsis gllvescens, Ceriporiopsis pannocinta, Ceriporiopsis rivuiosa, Ceriporiopsis subrufa, or Ceriporiopsis subvermispora, Coprinus cinereus, Conolus hirsutus. Humicola insotens, Humicola lanuginosa, Mucor miehei, Myceliαphthora thermophtla, Neurospora crassa, Peniciilium purpurogenum, Phanerochaete chrysosporium, Phiebia radiata, Pleurotus eryngii, Thieiavia terrestris, Trameies viiiosa, Trametes versicolor, Tnchoderma haαianum, Trichoύerma konmgii, Trichoderma longibrachiatum, Tnchoderma reesei, or Trichoderma viride strain ceii. Fungal cells may be transformed by a process involving protoplast formation, transformation of the protoplasts, and regeneration of the cell wai! in a manner known per se. Suitabie procedures for transformation of Aspergillus and Tricliodetma host cells are described in EP 238 023 and Yeiton et a/, , 1984, Proceedings of the National Academy of Sciences USA 81 ; 1470-1474. Suitable methods for transforming Fusarkirn species are described by Malardier et a/., 1989, Gene 78: 147-158, and WO 96/00787. Yeast may be transformed using the procedures described by Becker and Guarente, In Abelson, J.N. and Simon, MJ,, editors, Guide to Yeast Genetics and Molecular Biology, Methods in Enzymology, VoSume 194, pp 182-187, Academic Press, inc., New York; lto et a/., 1983. Journal of Bacteriology 153: 163; and Hinnen et al., 1978, Proceedings of the National Academy of Sciences USA 75: 1920.

Methods of Production

The present inv entio also relates to methods for producing a polypeptide of the present invention, comprising (a) cultivating a cell, which in its wild-type form is capable of producing the polypeptide, under conditions conducive for production of the poiypeptide; and (b) recovering the polypeptide. Preferably, the cell is a strain of the genus Peniophora, more preferably a strain of the species Peniophora rufomarginata.

The present invention aiso relates to methods for producing a polypeptide of the present invention, comprising (a) cuitivating a host ceil under conditions conducive for production of the poiypeptide; and (b) recovering the poiypeptide.

The present invention aiso relates to methods for producing a polypeptide of the present invention, comprising (a) cultivating a host cell under conditions conducive for production of the poiypeptide, wherein the host cei! comprises a nucleotide sequence having the mature poiypeptide coding region of SEQ ID NOS: 1 or 3, respectively, wherein the nucleotide sequence encodes a polypeptide which consists of amino acids 1 to 558 of SEQ SD NO: 2, and (b) recovering the poiypeptide.

In the production methods of the present invention, the cells are cultivated in a nutrient medium suitable for production of the polypeptide using methods well known in the art. For example, the eel! may be cultivated by shake flask cultivation, and smail-scaie or large-scaie fermentation (including continuous, batch, fed-batch, or solid state fermentations) in laboratory or industrial fermentors performed in a suitabie 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 pubiished compositions (e.g., in catalogues of the American Type Cufture Collection). If the polypeptide is secreted into the nutrient medium, the polypeptide can be recovered directly from the medium, if the polypeptide is not secreted, it can be recovered from cei! lysates.

The polypeptides may be detected using methods known in the art that are specific for the polypeptides. These detection methods may include use of specific antibodies. formation of an enzyme product, or disappearance of an enzyme substrate. For example, an enzyme assay may be used to determine the activity of the polypeptide as described herein.

The resulting polypeptide may be recovered using methods known in the art. For example, the polypeptide may be recovered from the nutrient medium by conventional procedures including, but not limited to, centrifugation, filtration, extraction, spray-drying, 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 exciusion), electrophoretic procedures (e.g. , preparative isoelectric focusing), differential solubility (e.g., ammonium sulfate precipitation), SDS-PAGE, or extraction (see, e.g., Protein Purification, J.-C. Janson and Lars Ryden, editors, VCH Publishers, New York, 1989).

Plants

The present invention also relates to a transgenic plant, plant part, or plant cell which has been transformed with a nucleotide sequence encoding a polypeptide having glucoamylase activity of the present invention so as to express and produce the polypeptide in recoverable quantities. The polypeptide may be recovered from the plant or plant part. Alternatively, the plant or plant part containing the recombinant polypeptide may be used as such for improving the quality of a food or feed, e.g,, improving nutritional value, palaiabiiity, and rheological properties, or to destroy an antinutritive factor.

The transgenic plant can be dicotyledonous (a dicot) or monocotyiedonous (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, anά cereals, e.g., wheat, oats, rye, barley, rice, sorghum, and maize (com).

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 as well as the individual tissues comprising these parts, e.g., epidermis, mesophyll, parenchyma, vascular tissues, meristems. Specific plant eel! compartments, such as chSoroplasts, apopiasts, mitochondria, vacuoles, peroxisomes and cytoplasm are aiso considered to be a plant part. Furthermore, any plant cell, whatever the tissue origin, is considered to be a plant part. Likewise, plant parts such as specific tissues and ceils isolated to facilitate the utilisation of the invention are also considered plant parts, e.g.. embryos, endosperms, aleurone and seeds coats.

Aiso included within the scope of the present invention are the progeny of such plants, piant parts, and plant cells.

The transgenic plant or plant cell expressing a polypeptide of the present invention may be constructed in accordance with methods known in the art. in short, the plant or piant cell is constructed by incorporating one or more expression constructs encoding a polypeptide of the present invention into the plant host genome and propagating the resulting modified plant or plant cell into a transgenic plant or plant ceil.

The expression construct is conveniently a nucleic acid construct which comprises a polynucleotide encoding a polypeptide of the present invention operably linked with appropriate regulatory sequences required for expression of the nucSβotide sequence in the plant or plant part of choice. Furthermore, the expression construct may comprise a selectable marker useful for identifying host ceils 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 polypeptide is desired to be expressed. For instance, the expression of the gene encoding a poiypeptide of the present 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 piant part such as seeds or leaves. Regulatory sequences are, for example, described by Tague et a/. , 1988, Plant Physiology 88: 506.

For constitutive expression, the 35S-CaWiV, the maize ubiquitin 1 , and the rice actin 1 promoter may be used (Franck et a/., 1980, Cell 21 : 285-294, Christensen et a!., 1992, Plant Mo. Biol 18: 675-689; Zhang et at, 1991 , Plant Cell 3: 1 155-1165). Organ-specific promoters may be, for example, a promoter from storage sink tissues such as seeds, potato tubers, and fruits (Edwards & Coruzzi, 1990, Ann, Rev, Genet 24; 275-303), or from metabolic sink tissues such as meristems (Ito et 3/., 1994, Plant MoL Biol. 24: 863-878), a seed specific promoter such as the giuteiin, proiamin, globulin, or albumin promoter from rice (Wu et al... 1998, Plant anύ Cell Physiology 39: 885-889), a Vicia faba promoter from the legυmin B4 and the unknown seed protein gene from Vicia faba (Conrad et a/.. 1998, Journal of Plant Physiology 152; 708-711). a promoter from a seed oil body protein (Chen et a/., 1998, Plant and Cell Physiology 39: 935-941 ), the storage protein napA promoter from Brassica napus, or any other seed specific promoter known in the art, e.g., as described in WO 91/14772. Furthermore, the promoter may be a leaf specific promoter such as the rbcs promoter from rice or tomato (Kyozuka et a/,, 1993, Plant Physiology 102; 991-1000, the chSoreSia virus adenine methyitransferase gene promoter (ϊViitra and Higgins, 1994, Plant Molecular Biology 26: 85-93), or the aldP gene promoter from rice (Kagaya ei a/,, 1995, Molecular and Genera! Genetics 248: 888-674), or a wound inducible promoter such as the potato pin2 promoter (Xu et at., 1993, Plant Molecular Biology 22; 573-588). Likewise, the promoter may inducible by abiotic treatments such as temperature, drought, or alterations in salinity or induced by exogenously applied substances that activate the promoter, e.g. , ethanol, oestrogens, plant hormones such as ethylene, abscisic acid, and gibbereic acid, and heavy metals.

A promoter enhancer element may also be used to achieve higher expression of a polypeptide of the present 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 a polypeptide of the present invention. For instance, Xu et a!., 1993, supra, disclose the use of the first intron of the rice actin 1 gene to enhance expression.

The seiectable marker gene and any other parts of the expression construct may be chosen from those available in the art.

The nucleic acid construct is incorporated into the plant genome according to conventional techniques known in the art, including Agrobacterium-meύlBieά transformation, virus-mediated transformation, microinjection, particle bombardment, biolistic transformation, and electroporation (Gasser et a/.. 1990, Science 244: 1293; Potrykus, 1990, Bio/Technology 8: 535; Shimamoto et al. , 1989, Nature 338: 274).

Presently, Agrobacierium tumefaciens-meάM&ύ gene transfer is the method of choice for generating transgenic dicofs (for a review, see Hooykas and Schilperoort, 1992, Piant Molecular Biology 19; 15-38) and can aSso be used for transforming monocots, although other transformation methods are often used for these plants. Presently, the method of choice for generating transgenic monocots is particle bombardment (microscopic gold or tungsten particles coated with the transforming DNA) of embryonic calli or developing embryos (Christou, 1992, Plant Journal 2: 275-281 ; Shimamoto, 1994, Current Opinion Biotechnology 5: 158-182; Vasii et al... 1992, Bio/Technology 10: 667-674). An alternative method for transformation of monocots is based on protopiast transformation as described by Omirulleh ef al. , 1993, Plant Molecular Biology 21 : 415-428. Following transformation, the transformants having incorporated the expression construct are selected and regenerated into whole plants according to methods well-known in the art. Often the transformation procedure is designed for the selective elimination of selection genes either during regeneration or in the following generations by using, for example, co-transformation with two separate T-DNA constructs or site specific excision of the seSection gene by a specific recombinase.

The present invention aiso relates to methods for producing a polypeptide of the present invention comprising (a) cultivating a transgenic piant or a plant cell comprising a polynucleotide encoding a polypeptide having giucoamylase activity of the present invention under conditions conducive for production of the polypeptide; and (b) recovering the polypeptide.

Compositions

The present invention also relates to compositions comprising a polypeptide of the present invention. Preferably, the compositions are enriched in such a polypeptide. The term "enriched" indicates that the giucoamyiase activity of the composition has been increased, e.g , by an enrichment factor of 1.1 ,

The composition may compnse a polypeptide of the present invention as the major enzymatic component, e.g., a mono-component composition. Alternatively, the composition may comprise multiple enzymatic activities, such as an aminopeptidase, amySase, carbohydrase, carboxypeptidase, catalase, cellulase, chitinase, cutinase, cyclodextrin glycosyitransferase, deoxynbonuclease. esterase, aipha-gaiactosidase. beta-galactosidasβ. giucoamylase, alpha-glucosSdase, beta-giucosidase, haloperoxidase, invertase, laccase, lipase, mannosidase, oxidase, pectinoiytic enzyme, peptidoglutaminase, peroxidase, phytase, poiyphenoloxidase, proteolytic enzyme, ribonuclease, transglutaminase, or xylanase. The additional enzyme(s) may be produced, for exampSe, by a microorganism belonging to the genus Aspergillus, preferably Aspergillus aculeatus, Aspergillus awamori, Aspergillus fumigatus. Aspergillus foetidus, Aspergillus japonicus, Aspergillus niduians, Aspergillus niger, or Aspergillus oryzae: Fusarlum, preferably Fusarium bactridiotdes, Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum. Fusarium graminum, Fusarium heterosporuiw, Fusarium negundi. Fusarium oxysporυm, Fusarium reticulatum, Fusarium roseum. Fusarium sambucinum, Fusarium sarcochroum, Fusarium sulphureum, Fusarium toruloseum, Fusarium tήchαtheαoictes, or Fusβrlum venenatum; Humicola, preferably Humicola insolens or Humicola lanuginosa; or Trichodenva, preferably Tήchoderma barzianum. Tήchoderma koningls, Trichoderma longibrachsatum, Trichoderma reesei. or Trichoderma viride. The polypeptide compositions may be prepared in accordance with methods known in the art and may be in the form of a liquid or a dry composition. For instance, the polypeptide composition may be in the form of a granυiate or a microgranulate. The polypeptide to be included in the composition may be stabilized in accordance with methods known in the art.

Combination of ojucoamylase and acid alpha-aroyiase

According to this aspect of the invention a glucoamyiase of the invention may be combined with an alpha-amylase, preferabiy acid aSpha-amylase in a ratio of between 0,3 and 5,0 AFAU/AGU. More preferabiy the ratio between acid aipha-amylase activity and glucoamyiase activity is at ieast 0.35, at least 0.40, at least 0.50, at least 0.60, at least 0.7, at least 0.8, at least 0.9, at ieast 1.0, at ieast 1.1 at ieast 1.2. at least 1.3, at least 1 ,4, at least 1.5, at least 1.6, at ieast 1.7_« at ieast 1.8, at ieast 1.85_« or even at least 1.9 AFAU/AGU, However, the ratio between acid aipha-amylase activity and giucoarnyiase activity should preferably be less than 4.5, less than 4.0, Sess than 3.5, less than 3.0, less than 2,5, or even less than 2.25 AFAU/AGU. In AUU/AGI the activities of acid aipha-amylase and glucoamyiase are preferabiy present in a ratio of between 0.4 and 6.5 AUU/AGi. More preferably the ratio between acid alpha-amylase activity &nά glucoamyiase activity is at ieast 0.45, at least 0.50, at ieast 0.60, at least 0.7, at least 0,8, at ieast 0.9, at ieast 1.0, at ieast 11 , at least 1.2, at least 1.3, at ieast 1 ,4, at ieast 1.5, at ieast 1.6, at least 1.7, at ieast 1.8, at least 1.9, at least 2.0, at ieast 2.1 , at least 2.2, at least 2.3, at ieast 2.4, or even at ieast 2.5 AUU/AGI. However, the ratio between acid alpha-amylase activity and glucoamyiase activity is preferably iess than 6.0, iess than 5,5, less than 4.5, less than 4.0, less than 3.5, or even less than 3.0 AUU/AGI. Above composition is suitable for use in a starch conversion process mentioned below for producing syrup and fermentation products, such as ethanol

Exampies are given beiow of preferred uses of the poiypeptide compositions of the invention. The dosage of the poiypeptide composition of the invention and other conditions under which the composition is used may be determined on the basis of methods known in the art.

Uses

The present invention is aiso directed to processes/methods for using the polypeptides having glucoamyiase activity of the invention. Uses according to the invention include starch conversion of starch to e.g., syrup and fermentation products, including ethanol and beverages. Examples of processes where a glucoamylase of the invention may be used include the ones describee! in; WO 2004/081 193, WO 2004/080923, WO 2003/66816, WO 2003/66826, and WO 92/20777 which are hereby a!! incorporated by reference.

Production of fermentation products

Processes for producing fermentation products from gelatinized starch-containing material

In this aspect the present invention relates to a process for producing a fermentation product. especialSy ethanol, from starch-containing material, which process includes a liquefaction step and sequentially or simultaneously performed sacchaήfication and fermentation steps.

The invention relates to a process for producing a fermentation product from starch- containing material comprising the steps of:

(a) liquefying starch-containing material;

(b) saccharifying the ϋquefied materia! obtained in step (a) using a glucoamyiase of the invention;

(c) fermenting the saccharified materia! using a fermenting organism.

The fermentation product, such as especially ethanol, may optionaily be recovered after fermentation, e.g., by distillation. Suitable starch-containing starting materials are listed in the section "Starch-containing materiais'-section below. Contemplated enzymes are listed in the Εnzymes'-section below. The liquefaction is preferably carried out in the presence of an aSpha-amylase. The fermentation is preferably carried out in the presence of yeast, preferably a strain of Saccharomyces. Suitable fermenting organisms are listed in the "Fermenting Organisms" -section below. In preferred embodiments step (b) and (c) are carried out sequentially or simultaneously (i.e., as SSF process). In a particuiar embodiment, the process of the invention further comprises, prior to the step (a), the steps of: x) reducing the particle size of the starch-containing materia!, preferably by milling; y) forming a slurry comprising the starch-containing materia! and water.

The aqueous slurry may contain from 10-40 wt-%_« preferably 25-35 wt-% starch- containing material. The slurry is heated to above the gelatin ization temperature and alpha- amylase, preferably bacterial and/or acid fungal alpha-amyiase, may be added to initiate liquefaction (thinning). The slurry may in an embodiment be jet-cooked to further gelatinize the slurry before being subjected to an alpha-amylase in step (a) of the invention.

More specificaiSy liquefaction may be carried out as a three- step hot siurry process. The slurry is heated to between 60-95^*C_« preferably 80-85⁰C, and aipha-amylase is added to initiate liquefaction (thinning). Then the slurry may be jet-cooked at a temperature between 95-14G^aC. preferably 105-125X, for 1-15 minutes, preferably for 3-10 minute, especially around 5 minutes. The slurry is cooled to 6G-95"C and more alpha -amylase is added to finalize hydrolysis (secondary liquefaction). The liquefaction process is usually carried out at pH 4.5-6.5, in particuiar at a pH between 5 and 6. Milled and liquefied whole grains are known as mash.

The saccharification in step (b) may be carried out using conditions weli know in the art. For instance, a fuil saccharification process may last up to from about 24 to about 72 hours, however, it is common only to do a pre-saccharification of typicaSly 40-90 minutes at a temperature between 3G-65°C, typically about 6O°C₁ followed by compiete saccharification during fermentation in a simultaneous saccharification and fermentation process (SSF process). Saccharification is iypicaSiy carried out at temperatures from 30-85°C, iypicaiSy around 80°C₁ and at a pH between 4 and 5, normally at about pH 4,5.

The most widely used process in fermentation product, especially ethanoi, production is the simultaneous saccharification and fermentation (SSF) process, in which there is no holding stage for the saccharification, meaning that fermenting organism, such as yeast, and enzyrne(s) may be added together, SSF may typically be carried out at a temperature between 25^BC and 40°C₁ such as between 29^*C and 35^*C, such as between 30°C and 34"C, such as around 32X. According to the invention the temperature may be adjusted up or down during fermentation. In accordance with the present invention the fermentation step (c) includes, without limitation, fermentation processes used to produce aicohols (e.g., ethanoi, methanol, butanol); organic acids (e.g., citric acid, acetic acid, itaconic acid, lactic acid, gluconic acid); ketones (e.g., acetone); amino acids (e.g., giutamic acid); gases (e.g. , H₂ and CO₂); antibiotics (e.g., penicillin and tetracycline); enzymes; vitamins (e.g., riboflavin, B12, beta- carotene); and hormones. Preferred fermentation processes include alcohol fermentation processes, as are weSI known in the art. Preferred fermentation processes are anaerobic fermentation processes, as are weil known in the art.

Processes for producing fermentation products from un-gelatiπized starch-containing In this aspect the invention relates to processes for producing a fermentation product from starch-containing material without geiatinizafion of the starch-containing material, in one embodiment oniy a glucoamylase of the invention is used during saccharification and fermentation. According to the invention the desired fermentation product, such as ethanoi, can be produced without liquefying the aqueous slurry containing the starch-containing material. In one embodiment a process of the invention includes saccharifying (milled) starch-containing materia!, e.g., granular starch, below the gelatinization temperature in the presence of a glucoamylase of the invention to produce sugars that can be fermented into the desired fermentation product by a suitable fermenting organism.

Example 4 below discloses production of ethano! from un-gelatinized (uncooked) milled com using giucoamyiases of the invention derived from Peniphora rufomargmata for one-step fermentation alone and in combination with &n alpha-amylase.

Accordingly, in this aspect the invention relates to a process for producing a fermentation product from starch-containing materia! comprising:

(a) saccharifying starch-containing material with a glucoamylase having the sequence shown as amino acids 1 to 558 in SEQ SD NO; 2, or a glucoamylase having at least 60% identity thereto, at a temperature below the initial gelatinization temperature of said starch-containing material,

(b) fermenting using a fermenting organism.

Steps (a) &nά (b) of the process of the invention may be carried out sequentially or simultaneously, in an embodiment a slurry comprising water and starch-containing material is prepared before step (a).

The fermentation process may be carried out for a period of 1 to 250 hours, preferably is from 25 to 190 hours, more preferably from 30 to 180 hours, more preferably from 40 to 170 hours, even more preferably from 50 to 160 hours, yet more preferably from 60 to 150 hours, even yet more preferably from 70 to 140 hours, and most preferably from SO to 130 hours.

The term initial gelatinization temperature" means the lowest temperature at which gelafinization of the starch commences. Starch heated in water begins to gelatinize between 50°C and 75^aC: the exact temperature of gelatinization depends on the specific starch, and can readiiy be determined by the skilled artisan. Thus, the initial gelatinization temperature may vary according to the plant species, to the particular variety of the plant species as well as with the growth conditions. In the context of this invention the initial gelatinization temperature of a given starch-containing material is the temperature at which birefringence is lost in 5% of the starch granules using the method described by Gorinstein. S. and Lii. C, Starch/Starke, Vol. 44 (12) pp. 481-466 (1992).

Before step (a) a slurry of starch-containing material such as granular starch, having 10-55 wt-% dry solids, preferably 25-40 wt,-% dry solids, more preferably 30-35% dry solids of starch-containing materia! may be prepared. The slurry may include water and/or process waters, such as stiiSage (backset), scrubber water, evaporator condensate or distillate, side stripper water from distillation, or other fermentation product plant process water. Because the process of the invention is carried out below the geiatinization temperature and thus no significant viscosity increase takes place, high levels of stilSage may be used if desired. In an embodiment the aqueous slurry contains from about 1 to about 70 voi.-% stillage, preferably 15-60% vo!.-% stillage. especially from about 30 to 50 vo!.-% stillage.

The starch-containing materia! may be prepared by reducing the particle size. preferably by dry or wet milling, to 0,05 to 3.0 mm, preferably 0.1-0.5 mm. After being subjected to a process of the invention at least 85%, at least 88%, at ieast 87%. at Seast 88%, at least 89%, at least 90%. at least 91 %, at ieast 92%, at ieast 93%, at ieast 94%, at least 95%, at least 96%. at least 97%, at least 98%. or preferabiy at least 99% of the dry soiids of the starch-containing material is converted into a soiubie starch hydrolysate. The process of the invention is conducted at a temperature below the initial gelatinization temperature. Preferabiy the temperature at which step (a) is carried out is between 30-75*C, preferably between 45-6O⁰C.

In a preferred embodiment step (a) and step (b) are carried out as a sequentia! or simuitaneous saccharification &nά fermentation process, in such preferred embodiment the process is typicaiSy earned at a temperature between 25"C and 4Q"C, such as between 29⁰C and 35⁰C₁ such as between 30^cC and 34°C, such as around 32°C. According to the invention the temperature may be adjusted up or down during fermentation.

In an embodiment simuitaneous saccharification and fermentation is carried out so that the sugar level, such as gSucose levei, is kept at a low ievel such as below 6 wt.-%. preferably below about 3 wt.-%. preferabiy beiow about 2 wt-%, more preferred beiow about 1 wt-%., even more preferred below about 0.5%, or even more preferred 0.25% wt.-%, such as beiow about 0.1 wt.~%. Such Sow ievels of sugar can be accompiished by simpiy employing adjusted quantities of enzyme and fermenting organism. A skilied person in the art can easiiy determine which quantities of enzyme and fermenting organism to use. The employed quantities of enzyme and fermenting organism may also be selected to maintain low concentrations of maitose in the fermentation broth. For instance, the maltose Sevei may be kept beiow about 0.5 wt.-% or below about 0.2 wt.~%.

The process of the invention may be earned out at a pH in the range between 3 and 7. preferably from pH 3.5 to 6. or more preferabiy from pH 4 to 5.

Starch-containing materiais

Any suitable starch-containing starting material, inciuding granuiar starch, may be used according to the present invention. The starting material is generaiiy seiected based on the desired fermentation product, Exampies of starch-containing starting materiais, suitabie for use in a process of present invention, inciude tubers, roots, stems, whole grains, corns, cobs, wheat, barley, rye, milo, sago, cassava, tapioca, sorghum, rice peas, beans, or sweet potatoes, or mixtures thereof, or cereals, sugar-containing raw materials, such as molasses, fruit materials, sugar cane or sugar beet, potatoes, artel cellulose-containing materials, such as wood or plant residues, or mixtures thereof. ContempSated are both waxy and non-waxy types of com and barley, The term "granular starch" means raw uncooked starch, i.e.. starch in its natural form found in cereal, tubers or grains. Starch is formed within plant ceiis as tiny granules insoiuble in water. When put in coSd water, the starch granuies may absorb a small amount of the liquid and sweli. At temperatures up to 50⁰C to 75°C the swelling may be reversible. However, with higher temperatures an irreversible sweing called "gelatinization" begins, Granular starch to be processed may be a highly refined starch quality, preferably at least 90%, at least 95%, at least 97% or at least 99.5% pure or it may be a more crude starch containing material comprising milled whole grain including non-starch fractions such as germ residues and fibers. The raw materia!, such as whole grain, is milled in order to open up the structure and allowing for further processing. Two milling processes are preferred according to the invention: wet and dry rnϋiing, In dry rniiiing whole kernels are milled and used. Wet milling gives a good separation of germ and meal (starch granules and protein) and is often applied at locations where the starch hydrolysate is used in production of syrups. Both dry and wet milling is well known in the art of starch processing and is equally contemplated for the process of the invention. The starch-containing material is reduced in particle size, preferably by dry or wet milling, in order to expose more surface area. In an embodiment the particle size is between 0.05 to 3.0 mm, preferably 0.1-0.5 mm, or so that at ieast 30%, preferably at least 50%, more preferably at least 70%, even more preferably at ieast 90% of the starch-containing materia! fit through a sieve with a 0.05 to 3.0 mm screen, preferably 0.1-0,5 mm screen.

Fermentation Products

The term "fermentation product" means a product produced by a process inciuding a fermentation step using a fermenting organism. Fermentation products contemplated according to the invention inciude alcohols (e.g. , etbanol, methanol butanol); organic acids (e.g., citric acid, acetic acid, itaconic acid, lactic acid, gluconic acid); ketones {e.g., acetone); amino acids (e g., giutamic acid); gases {e.g,, H₃ and CO₂); antibiotics (e.g. , penicillin and tetracycline); enzymes; vitamins (e.g., riboflavin, B-,₂, beta-carotene); and hormones, in a preferred embodiment the fermentation product is ethanol, e.g., fuel ethanol; drinking ethanol, i.e., potable neutral spirits; or industrial ethanol or products used in the consumable alcohoi industry (e.g., beer and wine), dairy industry {e.g., fermented dairy products), leather industry and tobacco industry. Preferred beer types comprise ales, stouts, porters, lagers, bitters, malt liquors, happoushu, h igh-alcoho! beer, low-aicohol beer. iow-caSorie beer or Sight beer. Preferred fermentation processes used include alcohol fermentation processes, as are well known in the art. Preferred fermentation processes are anaerobic fermentation processes, as are we!S known in the art.

Ferrneπtinq Organisms

"Fermenting organism" refers to any organism, including bacterial and fungal organisms, suitabie for use in a fermentation process anύ capable of producing desired a fermentation product, Especiaily suitable fermenting organisms are able to ferment, i.e.. convert, sugars, such as giucose or maltose, directly or indirectly into the desired fermentation product. Examples of fermenting organisms include fungal organisms, such as yeast. Preferred yeast includes strains of Saccharoivyces spp,, in particular, Saccharomyces cβrevisiae. Commercially available yeast include, e.g.. Red Star™/Lesaffre Etfrano! Red (available from Red Star/Lesaffre, USA) FALI (available from Fleischmann's Yeast, a division of Bums Phiip Food inc., USA), SUPERSTART (avaiiabie from Ailtech), GERT STRAND (available from Gert Strand AB, Sweden) and FERMIOL {avaiiabie from DSM Specialties).

ENZYMES GJucoamyjase

The glucoamyiase is preferably a giucoamylase of the invention. However, as mentioned above a giucoamyiase of the invention may also be combined with other glucoamylases.

The glucoamyiase may added in an amount of 0.001 to 10 AGU/g DS, preferabiy from 0.01 to 5 AGU/g DS, such as around 0,1 , 0.3, 0.5, 1 or 2 AGU/g DS, especiaily 0.1 to 0.5 AGU/g DS or 0.02-20 AGU/g DS, preferably 0.1-10 AGU/g DS.

Alpha-Amylase

The alpha-amyiase may according to the invention be of any origin. Preferred are alpha-amySases of funga! or bacteria! origin.

In a preferred embodiment the aSpha-amylase is an acid aSpha-amylase, e.g., fungal acid aipha-amylase or bacteria! acid aipha-amylase. The term "acid alpha-amyiase" means an aipha-arnyiase (E.G. 3,2.1 ,1) which added in an effective amount has activity optimum at a pH in the range of 3 to 7, preferabiy from 3.5 to 6, or more preferably from 4-5. According to the invention a bacterial aipha-amylase may preferably be derived from the genus Bacillus.

In a preferred embodiment the Bacillus aipha-amyiase is derived from a strain of β. lichens formis, B. atnyloliqiiefaciens, B. subtiiss or S, stearothennoβhslus, but may also be derived from other Bacillus sp. Specific exampies of contemplated aipha-a myiases include the Bacillus lichβniformis alpha-arnylase (BLA) shown in SEQ ID NO: 4 in WO 99/19467, the Bacillus amyloliquefaci&ns alpha-arnylase (BAN) shown in SEQ ID NO: 5 in WO 99/19467, and the Bacillus stβaroihermophilus aSpha-amylase (BSG) shown in SEQ ID NO; 3 in WO 99/19467. Sn an embodiment of the invention the aSpha-amylase is an enzyme having a degree of identity of at least 60%, preferably at ieast 70%, more preferred at ieast 80%, even more preferred at least 90% , such as at least 95%, at least 96% , at least 97%, at ieast 98% or at least 99% identity to any of the sequences shown as SEQ ID NOS: 1, 2, 3, 4, or 5, respectively, in WO 99/19467. The Bacillus aSpha-amylase may also be a variant and/or hybrid, especiaSly one described in any of WO 96/23873, WO 96/23874, WO 97/41213, WO 99/19467, WO 00/60059, and WO 02/10355 (all documents hereby incorporated by reference). Specificaiiy contempiated aSpha-amylase variants are disciosed in US patent nos. 6,093,562, 6,297,038 or US patent no. 6,187,576 (hereby incorporated by reference) and inciude Bacillus stearottiermophilus aipha-arnylase (BSG aSpha-amylase) variants having a deletion of one or two amino acid in position 179 to 182, preferabiy a doυbie deietion disclosed in WO 1996/023873 - see e.g., page 20, Sines 1-10 (hereby incorporated by reference), preferabiy corresponding to delta{181-182) compared to the wild-type BSG aipha-amylase amino acid sequence set forth in SEQ iD NO: 3 discSosed in WO 99/19467 or deSetion of amino acids 179 and 180 using SEQ iD NO: 3 in WO 99/19467 for numbering (which reference is hereby incorporated by reference). Even more preferred are Bacillus alpha-amyiases, especiaiSy Bacillus stearothermoβhilus aipha-amylase, which have a double deletion corresponding to delta(181-182) anά further comprise a N193F substitution (aiso denoted II 81^* + G 182^* + N193F) compared to the wild-type BSG alpha-amyiase amino acid sequence set forth in SEQ SD NO: 3 disciosed in WO 99/19467.

The alpha-amyiase may aiso be a maifogenic aipha-amyiase. A "maltogenic alpha- amyiase" (giυcan 1 ,4-aipha-ma!tohydrolase, E.G. 3.2,1.133) is abie to hydralyze amyiose and amyiopectin to maitose in the aipha-configu ration. A maltogenic aipha-amylase from Bacillus støarothenvophilus strain NCIB 11837 is commerciaSiy avaiiable from Novozymes A/S, Denmark. The maltogenic aipha-amylase is described in US patent nos. 4,598,048, 4,604,355 anά 6,162,628, which are hereby incorporated by reference. Bacterial Hybrid Aipha-Amylases

A hybrid alpha-amyiase specifically contemplated comprises 445 C-ierminal amino acid residues of the Bacillus licheniformls alpha-amySase (shown as SEQ ID NO; 4 in WO 99/19487) and the 37 N-termina! amino acid residues of the alpha-amyiase derived from

Bacillus amylolsquefaciens {shown as SEQ ID NO. 3 in WO 99/194878), with one or more, especially all. of the following substitution:

G48A+T4θ!+G107A+H156Y+A181T+N1θ0F+i201 F+A20ΘV+Q264S {using the Bacillus licheniformis numbering). ASso preferred are variants having one or more of the folSowing mutations (or corresponding mutations in other Bacillus alpha-amyiase backbones): H154Y, A181T. N190F, A209V and Q264S and/or deietion of two residues between positions 176 and 179, preferabϊy deietion of E178 and G179 (using the SEQ iD NO; 5 numbering of WO 99/19467),

The bacteria! alpha-amylase may be added in amounts as are well-known in the art. When measured in KNU units (described below in the "Matenais & Methods'-section) the alpha-amyiase activity is preferably present in an amount of 0.5-5,000 NU/g of DS. in an amount of 1-500 NU/g of DS, or more preferably in an amount of 5-1 ,000 NU/g of DS, such as 10-100 NUZg DS.

Fungal Alpha-Amylases

Funga! acid alpha-amyiases include acid aipha-amyiasβs derived from a strain of the genus Aspergillus, such as Aspergillus oryzae, Aspergillus niger, or Aspergillus kawachii alpha-amySases.

A preferred acid fungal aipha-amylase is a Fungamyi-iike alpha-arnySase which is preferably derived from a strain of Aspergillus oryzae in the present disclosure, the term

"Fungamyl-like aSpha-amySase" indicates an alpha-amyiase which exhibits a high identity, i.e. more than 70%, more than 75%, more than 80%, more than 85% more than 90%, more than

95%, more than 96%, more than 97%, more than 98%, more than 99% or even 100% identity to the mature part of the amino acid sequence shown in SEQ !D NO: 10 in WO 96/23874.

Another preferred acid alpha-amyiase is derived from a strain Aspergillus niger. In a preferred embodiment the acid fungal aipha-amylase is the one from A. niger disclosed as

¹⁴AMYA-ASPNG- in the Swiss-prαt/TeEMBL database under the primary accession no.

P56271 and described in more detail in WO 89/01969 (Exampie 3), The acid Aspergillus niger acid aSpha-amyiase is also shown as SEQ ID NO. 1 in WO 2004/080923 (Novozymes) which is hereby incorporated by reference. Aiso variants of said acid fungal amylase having at least 70% identity, such as at ieast 80% or even at ieast 90% identity, such as at least 95%, at least 96%, at least 97%, at least 98%. or at least 99% identity to SEQ SD NO: 1 in WO 2004/080923 are contemplated. A suitable commercialiy available acid funga! alpha- amySase derived from Aspergillus niger is SP288 (available from Novozymes A/S, Denmark). In a preferred embodiment the alpha-amylase is derived from Aspergillus kawachis and disclosed by Kaneko et ai. J. Ferment. Bioeng 81 :292-298(1996) "Molecuiar-cloniπg and determination of the nucleotide-sequence of a gene encoding an acid-stabie alpha- amyiase from Aspergillus kawachil": and further as EMBL#AB008370.

The funga! acid alpha-amylase may also be a wiid-type enzyme comprising a carbohydrate-binding module (CBM) and an alpha-amylase catalytic domain (i.e , a none- hybrid), or a variant thereof. In an embodiment the wtSd-type acid alpha-amyiase is derived from a strain of Aspergillus kawacfiii.

Fungal Hybrid Alpha-Amylases In a preferred embodiment the fungai acid alpha-amySase is a hybrid alpha-amyiase.

Preferred examples of funga! hybrid alpha-amyiases include the ones disciosed Sn WO 2005/00331 1 or U.S. Patent Publication no. 2005/0054071 (Novozymes) or US patent application no. 80/638,614 (Novozymes) which is hereby incorporated by reference. A hybrid aipha-amylase may compnse an aipha-amylase catalytic domain (CD) and a carbohydrate- binding domain/module (CBM) and optional a linker.

Specific exampies of contemplated hybrid alpha-amySases include those disclosed in U.S. patent application no. 60/638,614 inciuding Fungamyl variant with cataiytic domain JA118 and Athelia rolfsii SBD (SEQ ID NO: 100 in U.S. application no. 60/638,614). Rhizoivucor pusiilus alpha-amyiase with Athelia rolfsii AIvIG Sinker and SBD (SEQ !D NO: 101 in U S. application no 60/638,614) and Meripiius giganteus alpha-amyiase with Athelta rolfsii glucoamylase linker &nά SBD (SEQ !D NO: 102 in U.S. application no, 60/638,614).

Other specific exampies of contemplated hybrid aipha-amyiases include those disclosed in U.S. Patent Publication no. 2005/0064071 , including those disclosed in Table 3 on page 15, such as Aspergillus niger aipha-amylase with Aspergillus kawachii iinker and starch binding domain.

Commercial Alpha-Amylase Products

Preferred commercial compositions comprising aipha-amylase include MYCOLASE from DSIVI {Gist Brocades). BAN™, TERMAMYL™ SC, FUNGAMYL™, LSQUOZYIVIE™ X and SAN™ SUPER, SAN™ EXTRA L (Novozymes A/S) and CLARASE™ L~4Q,000. DEX-

LO™, SPEZYME™ FRED. SPEZYME™ AA, SPEZYME™ Ethyl, and SPEZYME™ DELTA AA (Genencor int.), and the acid fungal aipha-amylase sold under the trade name SP288 (available from Novozymes A/S, Denmark).

An acid aipha-amylases may according to the invention be added in an amount of 0.1 to 10 AFAUZg DS, preferabiy 0.10 to 5 AFAU/g DS₁ especially 0.3 to 2 AFAU/g DS.

Production of syrup

The present invention also provides a process of using a giυcoamyiase of the invention for producing syrup, such as glucose and the like, from starch-containing material. Suitable starting materiais are exemplified in the "Starch-containing materiais"-section

I O above. Generaiiy, the process comprises the steps of partiaily hydroiyzing starch-containing material (liquefaction) in the presence of alpha-amyiase and then further saccharifying the release of gSucose from the πoπ-retiucing ends of the starch or reSateti oiigo- and polysaccharide molecules in the presence of glucoamylase of the invention.

Liquefaction and saccharification may be carried our as described above for

15 fermentation product production.

The glucoamylase of the invention may also be used in immobilized form. This is suitable and often used for producing speciaiity syrups, such as maltose syrups, and further for the raffinate stream of oligosaccharides in connection with the production of fructose syrups, e.g., high fructose syrup (HFS). 0 Consequently, this aspect of the invention relates to a process of producing syrup from starch-containing material, comprising

(a) liquefying starch-containing material in the presence of an alpha-amyiase,

(b) saccharifying the materiai obtained in step (a) using a glucoamylase of the invention, 5 A syrup may be recovered from the saccharified material obtained in step (b).

Details on suitable conditions can be found above.

Brewing

A giucoamyiase of the invention can aiso be used in a brewing process. The 0 glucoamylases of the invention is added in effective amounts which can be easily determined by the skilled person in the art.

The invention described and claimed herein is not to be limited in scope by the specific embodiments herein disclosed, since these embodiments are intended as 5 iilustrations of several aspects of the invention. Any equivalent embodiments are intended to be within the scope of this invention. Indeed, various modifications of the invention in

4«⁾ addition to those shown and de-scribed herein will become apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims. In the case of conflict, the present disclosure including definitions wiil control. Various references are cited herein, the disclosures of which are incorporated by reference in their entireties. The present invention is further described by the following exampies which should not be construed as limiting the scope of the invention.

Materials & Methods Glucoamylases: βlycoamyja_.se_..AN: Giueoamylase derived from Aspergillus niger disciosecJ in (8oei et al. (1984), EMBO J, 3 (5) p. 1097-1102} and availabie from Novozymes A/S, Denmark,

Alpha-Amylase: Alpha-Amylase A: Hybrid aipna-amyiase consisting of Rhizomucor pusilius alpna-amyiase (SEQ ID NO; 6 herein) with Aspergillus niger giucoamyiase linker (SEQ !D NO: 8 herein) and SBD (SEQ SD NO; 10 herein) disclosed as V039 in TabSe 5 in co-pending international Application no. PCT/US05/46725 (WO 2006/069290).

Yeast. RED STAR™ available from Red Star/Lesaffre, USA

Other materiais pENI2516 is described in WO 2004/069872.

Aspergillus niger MBini 18 is disclosed in WO 2004/090155 (see e.g., ExampSe 11)

Deposit of Biological Material

The following bioiogical materia! has been deposited under the terms of the

Budapest Treaty at Deutshe Sammmiung von Microorganismen υnd Zellkυituren GmbH (DSIvIZ)₁ Masehβroder Weg 1b, D-38124 Braunschweig DE, and given the following accession number:

Deposit Accession Number Date of Deposit

Escherichia coll NN49873 DSM 18150 3 April 2006

The strain has been deposited under conditions that assure that access to the culture will be avaiiable during the pendency of this patent appiication to one determined by the

Commissioner of Patents and Trademarks to be entitled thereto under 37 C. F. R. §1.14 and

35 U.S.C. §122. The deposit represents a substantially pure culture of the deposited strain. The deposit is available as required by foreign patent laws in countries wherein counterparts of the subject application, or its progeny are filed. However, it should be understood that the availabiSity of a deposit does not constitute a Sicense to practice the subject invention in derogation of patent rights granted by governmental action.

Media and _. reagents;

ChemicaSs used as buffers and substrates were commerciaS products of at ieast reagent grade,

PDA; 39 g/L Potato Dextrose Agar, 20 g/L agar, 50 rnl/L giycerol

Methods

Unless otherwise stated, DNA manipulations and transformations were performed using standard methods of moiecular bioiogy as described in Sambrook et a!, (1989)

Molecular cloning: A iaboratory manual CoSd Spring Harbor lab., Cold Spring Harbor, NY; Ausubel, F. M. et al, (eds ) "Current protocols in Molecular Biology", John Wiley and Sons,

1995; Harwood, C. R., and Cutting, S. M. (eds.) "Moiecular Biological Methods for Bacillus",

John Wiiey and Sons, 1990.

Giucoamyiase activity Giucoamyiase activity may be measured in AG! units or in Giucoamyiase Units

(AGU).

GJucoamyJase activity (AGI)

Giucoamyiase (equivalent to amyloglucosidase) converts starch into glucose. The amount of gSucose is determined here by the giucose oxidase method for the activity determination. The method described in the section 76-11 Starch — Giucoamyiase Method with Subsequent Measurement of Glucose with Glucose Oxidase in "Approved methods of the American Association of Cereal Chemists", Vo!,1~2 AACC, from American Association of Cerea! Chemists, (2000); IS8N: 1-891 127-12-8. One giucoamyiase unit (AGI) is the quantity of enzyme which will form 1 micro mole of glucose per minute under the standard conditions of the method. Standard conditions/reaction conditions;

Substrate: Soluble starch, concentration approx. 16 g dry matter/L.

Buffer: Acetate, approx, 0,04 IVS, ρH=4.3 pH: 4.3

Incubation temperature: 60^f-C

Reaction time: 15 minutes

Termination of the reaction: NaOH to a concentration of approximately 0.2 g/L (pH-9) Enzyme concentration: 0.15-0.55 AAU/mL

The starch should be Lintner starch, which is a thin-boiling starch used in the laboratory as colorimetric indicator. Lintner starch is obtained by diiυte hydrochloric acid treatment of native starch so that it retains the ability to color blue with iodine.

Giucoamyiase activity (AGU)

The Nαvo Giucoamyiase Unit (AGU) is defined as the amount of enzyme, which hydroiyzes 1 micromoie maltose per minute under the standard conditions 37'C, pH 4,3, substrate: maitose 23.2 mM, buffer: acetate 0,1 M, reaction time 5 minutes.

An autoanaiyzer system may be used. Mutarotase is added to the gSucose dehydrogenase reagent so that any alpha-D-giucose present is turned into beta-D-giucose.

GSucose dehydrogenase reacts specificaiSy with beta-D-glucose in the reaction mentioned above, forming NADH which is determined using a photometer at 340 nm as a measure of the originai giucose concentration.

A folder (ES-SM-0131.02/01) describing this analytical method in more detail is available on request from Nαvozymes /VS, Denmark, which folder is hereby included by reference,

Alpha-amylase activity (KNU)

The alpha-amyiase activity may be determined using potato starch as substrate. This method is based on the break-down of modified potato starch by the enzyme, and the reaction is followed by mixing sampies of the starch/enzyme solution with an iodine solution, Initially, a ølackish-biue color is formed, but during the break-down of the starch the blue coior gets weaker and gradually turns into a reddish-brown, which is compared to a colored glass standard.

One Kilo Novo alpha amyiase Unit (KNU) is defined as the amount of enzyme which, under standard conditions {i.e., at 37⁰C +/- 0.05; 0.0003 IvI Ca²⁺; and pH 5.6} dexlrinizes 5260 mg starch dry substance Merck Amylum solubile,

A foider EB-S M-0009.02/01 describing this anaiyticai method in more detail is available upon request to Novozymes A/S, Denmark, which folder is hereby inciuded by reference.

Acid alpha-amylase activity

Wnen used according to the present invention the activity of any acid alpha-amyiase may be measured in AFAU (Acid Fungal Alpha-amyiase Units), Alternatively activity of acid alpha-amylase may be measured in AAU (Acid Aipha-amylase Units).

Acid Alpha-amylase Units (AAU }

The acid alpha-amyiase activity can be measured in AAU (Acid Alpha-amyiase Units), which is an absolute method. One Acid Amylase Unit (AAU) is the quantity of enzyme converting 1 g of starch (100% of dry matter) per hour under standardized conditions into a product having a transmission at 620 nm after reaction with an iodine soiution of known strength equal to the one of a color reference. Standard conditions/reaction conditions;

Substrate: Soluble starch. Concentration approx. 20 g DS/L. Buffer: Citrate, approx. 0.13 M, pH=4,2

Iodine solution; 40.176 g potassium iodide + 0.088 g iodine/L

City water 15°-20°dH (German degree hardness) pH; 4,2 incubation temperature: 30^riC

Reaction time: 11 minutes

Wavelength: 620 nm

Enzyme concentration; 0, 13-0.19 AAU/rnl

Enzyme working range; 0.13-0.19 AAU/mL

The starch should be Lintner starch, whicn is a thin-boiling starch used in the laboratory as colorirnetric indicator. Lintner starch is obtained by dilute hydrochloric acid treatment of native starch so that it retains the ability to color blue with iodine. Further details can be found in EP 0140410 B2, which disclosure is hereby included by reference.

Acid aJpha-amylase activity (AFAU)

Acid alpha-amylase activity may be measured in AFAU (Acid Fungal Alpha-amylase Units), which are determined relative to an enzyme standard. 1 AFAU is defined as the amount of enzyme which degrades 5.260 mg starch dry matter per hour under the below mentioned standard conditions.

Acid alpha-amylase, an endo-aipha-amylase (1.Φ-aipha-D-glucan-glucanohydroiase, E.G. 3.2.1.1) hydrolyzes alpha-1.4~glucosidic bonds in the inner regions of the starch molecule to form dextrins anύ oligosaccharides with different chain lengths. The intensity of color formed with iodine is directiy proportional to the concentration of starch. Amylase activity is determined using reverse colorimetry as a reduction in the concentration of starch under the specified analytical conditions.

ALPHA - AMYLASE

STARCH + IODIN E -^ ^{■■»» ■■■ ■■} → DEXTRIN S + OLIGOSACCHARIDES λ ^::: 590 nm blue/violet t = 23 sec. decoloration

Standard conditions/reaction conditions:

Substrate: Soluble starch, approx, 0,17 g/L

Buffer; Citrate, approx. 0.03 M

Iodine (I2): 0.03 g/L CaC!2; 1.85 mM pH: 2.50 ± 0.05

Incubation temperature; 4O°C

Reaction lime; 23 seconds

Wavelength; 59Qnm

Enzyme concentration: 0.025 AFAU/mL

Enzyme working range: 0.01-0.04 AFAU/mL

A folder EB-SM-Q259.Q2/Q1 describing this analytical method in more detai! is available upon request to Novozymes AYS. Denmark, which folder is hereby included by reference.

EXAMPLES Example 1

DNA Extraction and PCR amplification of Peniophora rufomarginata Giucoamylase Gene

Aerial hyphae of Peniophora rufoiwarginata growing on a PDA (Potatoe Dextrose Agar) plate were scraped off the piate and used for genomic DNA extraction using FastDNA SPIN Kit for Sou (Qbiogene, USA) according to the manufacturer's instructions. PCR reaction was done on genome DNA with the degenerated primers EuAMF land EuAMR4; EuAMFI 5'- ACGTACGGATCCAYTWCTAYWCBTGGACHCGYGA -3' (SEQ ID NO: 11)

EuAMR4 5' GTACGTAAGCTTRTCYTCRGGGTAVCGDCC -3¹ (SEQ SD NO: 12} Where D = A or G or T: R = A or G; S = C or G; V = A or C or G; Y = C or T; W= A or T: B= G or C or T; H= A or T or C

The amplification reaction (13 microL) was composed of 1 microL genome DNA solution, 1 microM primer EuAfVIFI (25 pmol/microL), 1 microM primer EuAMR4 (25 pmol/microL), 11 microL Extensor Hi-Fidelity PCR Master Mix (ABgene, UK). The reaction was incubated in a DNA Engine Dyad PTC-0220 (MJ Research, USA) programmed as follows; 1 cycle at 94°C for 5 minutes; 20 cycles each at 94°C for 45 seconds, 65°C for 45 seconds, with an annealing temperature decline of 1°C per cycle, and 72°C for 1 minute; followed by 20 cycles at 94°C for 45 seconds, 48°C for 45 seconds and 72°C for 1 minute; 1 cycle at 72°C for 7 minutes; and a hold at 4°C. The PCR product was purified using ExoSAP-lT (USB. USA) according to the manufacturer's instructions and sequenced using the primers as used in the amplification reaction. The sequence was subsequently compared to the Aspergillus niger glucoamylase gene, showing that the PCR product encoded a part of a glucoamylase.

Example 2 Cloning of glucoamylase gene from Peniophora rufomarginata

From the partial sequence of the Peniophora rufomarginata glucoamylase more gene sequence was obtained with PCR based gene walking using the Vectorette Kit from SiGMA- Genosys. The gene walking was basicaiSy done as described in the manufacturer's protocol, 0,15 micro g genomic DNA of Peniophora rufomarginata was digested with EcoRI, BamHi, Hindi!!, and CSaS independentSy. The digested DNA was ligated with the corresponding Vectorette units supplied by the manufacture using a DNA Engine Dyad PTC-0220 (MJ Research. USA) programmed as foSSows: 1 cycle at 16⁰C for 60 minutes; 4 cycles each at 37⁰C for 20 minutes, 16⁰C for 60 minutes, 37⁰C for 10 minutes; folSowed by 1 cycie at 16⁰C for 60 minutes and a hold at 4⁰C. The ligation reactions were subsequent diluted 5 times with sterile water.

PCR reactions with the linker-lsgated genome DNA of the Peniophora rufomarginata as tempSate was performed with a DNA Engine Dyad PTC-0220 (MJ Research, USA) programmed as follows: 1 cycle at 94°C for 5 minutes; 40 cycles each at 94⁰C for 15 seconds, 72⁰C for 1 minute, 72⁰C for 1 minute, 1 cycie at 72⁰C for 7 minutes; and a hoid at 4⁰C using the suppϋed Vectorette primer and the specific Peniophora rufotnargiαata AMG primers 5031 1F1 and 5031 1 R2_S respectively, as shown beiow. 50311 F1 : 5 - CGATTCACACCTGGGACATCAAGG -3' (SEQ SD NO: 13} 5031 1R2: 5'- AAGACACAGTACCAGACGGGTTGG -3' (SEQ ID NO: 14)

The amplification reactions (12.5 microL) were composed of 0,5 microL of linker- ligated genome DNAs_s 400 nM Vectorette primer, 400 nM Peniophora rufomarginata specific primer, 11 microL Extensor Hi-Fidelity PCR Master Mix (ABgene, UK). After the PCR reaction the PCR products were purified using ExoSAP-ΪT (USB_; USA) according to the manufacturer's instructions and sequenced and subsequently compared to the Aspergillus n/ger giueøamylase gene. A 1.5 kb amplified band was obtained by the PCR reaction from BamH! digested genome DNA amplified with the primer 5031 1R2. Sequencing of the PCR product using this primer showed that it encoded the remaining 350 basepairs of the glucoamylase gene in the 5' direction (N-termina! of the encoded protein).

A 1.1 ampiified band was obtained by the PCR reaction from CIaI digested genome DNA amplified with the primer 50311 Ft , Sequencing of the PCR product using this primer showed that it encoded further 550 basepairs of the glucoamyiase gene in the 3' direction, however not reaching the end of the gene. Therefore, an additional sequencing primer 50311 F2, were designed based on the newly obtained additional sequence of the glucoamylase gene. A new DNA-Vectorette ligation and following amplification set up as described above was set up. A 2 kb PCR product obtained from the Hindi 11 digested genome ligation was sequenced with the 50311F2 primer, and was shown to encode the remaining part of the glucoamylase gene in the 3' direction (C-terminai of the encoded protein). 5Q311F2 5' GGTGGC AGCACCGTCGCTGTAACC (SEQ SD NO: 15)

Example 3

The gSucoarnySase gene from Peniophora rufomarginata was cloned by PCR using gDNA as template. Reddy PCR Master IVSix (ABgene, UK) and the primers 5031 1F3 and

50311R3 as shown beiow:

50311F3: 5' CAGCACGGATCCAAGATGCGTCTCCCACAACTTG 3' (SEQ ID NO: 16}

50311R3:

5" GCATCAAGGCGGCCGCCTAGCGCCAGGAATCGTTGGC 3' (SEQ ID NO: 17)

Primer 50311F3 and 5031 1 R3 introduced a BamH\ and NoH restrictions site in the amplified DNA fragment and it was subsequently Sigated into the BamHl and Noil restrictions site of the Aspergillus expression vector pENI2518. The ligation mixture was transformed into E. coli TOP10 (Invitrogen, USA) to create the expression piasmid pENI2S16AMGNNS031 1E1. The amplified piasmid was recovered using a GSAprep Spin

Miniprep kit (QiAGEN, USA) according to the manufacturer's instructions.

The glucoamylase of pENI25i6AMGNN503i 1 E1 was sequenced. Unfortunately, a PCR error occurred in the coding region of the gSucoarnySase gene. The PCR error was removed by a second cloning step as described beiow.

Two PCR reactions were performed, PCR reaction 1 contained 10 ng/microL

PENI2516AMGNN50311E1 as tempiate_s 0.2 mM dNTP, 1X buffer, 1 ,5 mM MgCl,, 1 unit

DyNAzyme EXT (New England Biolabs, UK) , and 1 pmol/microL of each of the primers NN50311fw1 and NN50311 bw2 (see beiow). The total volume was 50 microL

NN5G311fw1 ;

5' GCGGATCCACCATGCGTCTCCCACAACTTGGAGTC (SEQ ID NO: 18}

NN50311bw2:

5' AGCTTGATTACGGGCCAGAGCGTGTTCGTGAC (SEQ ID NO: 19) PCR reaction 2 contained 10 ng/microL pEN!2516AMGNN50311 E1 as template, 0.2 mU dNTP, 1X buffer, 1.5 mM MgCl₂, 1 unit DyNAzyme EXT (New England Biolabs, UK) and 1 pmoi/rnicroL of each of the primers NN5G311fw2 and NN5Q311bwi (see below). The total volume was 50 microL

NN50311fw2;

5' CGAACACGCTCTGGCCCGTAATCAAGCTTG (SEQ ID NO: 20) NN5Q311&W1 ;

5' GGGCGGCCGCTAGCGCCAGGAATCGTTGGCAGTA (SEQ ID NO: 21) Both PCR reaction 1 and PCR reaction 2 were performed with a DNA Engine Dyad PTC-

0220 (MJ Research, USA) programmed as follows: 1 cycie at 94⁰C for 3 minutes; 15 cycles each at 94°C for 20 seconds, 54⁰C for 20 seconds and 72⁰C for 1 minute, 1 cycie at 72⁰C for 5 minutes.

A 0.7 kbp DNA band and a 1.5 kbp DNA band was purified from PCR reaction 1 and PCR reaction 2, respectably, using GFX PCR DNA Gel Band Purification Kit (Amβrsharn

Biosciences, UK).

A third PCR reaction was done containing 1 micro gram of the purified 0.7 kbp DNA band and 1 micro gram of the purified 1.5 kbp DNA band as tempiate, 0,2 mM dNTP, 1X buffer, 1.5 rnSVi SVIgCI?, 1 unit DyNAzyme EXT (New England Bioiabs, UK) and 1 prnol/microL of each of the primers NN50311fw1 (SEQ ID NO: 20) and NN50311 bw1 (SEQ ID NQ: 21).

The total volume was 50 rnicroL. The PCR reaction was performed with a DNA Engine Dyad

PTC-0220 (MJ Research, USA) programmed as follows: 1 cycle at 94⁰C for 3 minutes; 9 cycles each at 94⁰C for 20 seconds, 54⁰C for 20 seconds and 72⁰C for 2 minute, 1 cycie at

72⁰C for 5 minutes. The DNA was purified from the PCR reaction using GFX PCR DNA Ge!

Band Purification Kit (Amersham Biosciences, UK) &nά subsequently digested with BamHl and Not\ and ligated into the BamHI and Not\ restrictions site of the Aspergillus expression vector pENI2516, The ligation mixture was transformed into £ coli TOP10 (invitrogen, USA) to create the expression plasmid pEN!2516AMGNN50311. The amplified plasmid was recovered using JETQUICK Plasmid Miniprep Spin Kit 50 (Genomed, Germany) according to the manufacturer's instructions.

The giucoamyiase gene of pEN!2516AMGNN50311 was sequenced and verified to be identical to the genome sequence. pEN!2516AMGNN50311 was transformed into Aspergillus niger MBin118 and the giucoamyiase expressed using standard method weli known in the art.

Example 4

Yeast was propagated prior to fermentation. Corn (yeiiow dent No. 2) was ground to pass through #45 mesh screen. 200ml tap water and 1 g urea were mixed with 300 g corn mash. PenicϊSlen was added to 3 mg/liter. in 50 g of the mash slurry, 6.4 microL Glucoamylase AN and 0.024 g dry yeast (from RED STAR™) were added and the pH was adjusted to 5.0. The yeast slurry was incubated at 32^CC with constant stirring at 300rpm for 7 hours in a partially open flask.

One-Step fermentation using Peniophora rufomarginaia qlucoamyiase

Ai! one step ground corn to ethanol treatments were evaluated via mini-scale fermentations. Briefly, 410 g of ground yelSow dent corn (with particle size around 0.5 mm) was added to 590 g tap water. This mixture was supplemented with 3.0 ml 1 g/L penicillin and 1 g of urea. The pH of this slurry was adjusted to 4.5 with 5 N NaOH. DS level was determined to be around 35 wt. % (The actual DS was measured with an SR-2QQ moisture analyzer from Denver Instrument Co.). Approximately 5 g of this slurry was added to 20 ml vials. Each vial was dosed with the appropriate amount of enzyme followed by addition of 200 micro liters yeast propagate per 5 g slurry. Actual enzyme dosages were based on the exact weight of corn slurry in each vial. VIaSs were closed and incubated at 32¹C immediately. 9 replicate fermentations of each treatment were run. Three replicates were selected for 24 hours, 48 hours and 70 hours time point analysis. Vials were vortexed at 24, 48 and 70 hours and analyzed by HPLC. The HPLC preparation consisted of stopping the reaction by addition of 50 microliters of 40% H₂SG^, centrifuging, and filtering through a 0.45 micrometer filter. Samples were stored at 4*C prior to analysis. Agilent™ 1 100 HPLC system coupled with Rl detector was used to determine ethanol and sugars. The HPLC system consists of a degasser, quat-pump, cooled autosampler and heated column compartment. The separation column was aminex HPX- 87H ion exclusion column (300mm x 7,8mm) from BioRad™, which links to 30mm x 4.6mm micro-guard cation-H cartridge guard column. 10 rnicroL sample was injected at the flow rate of 0.6 ml/min. The mobile phase was SmM H₂SO₄. The column was kept at 65°C and Rl defector at 5O'^;C. The tofai run time was 25 min per sample.

The results are shown in the table below. Increase of P rufomarginata glucoamylase results in increase of ethanol yield. High ethanol yield is achieved when P. rufomarginaia glucoamylase is used together with aipha-amylase Alpha-Amyiase A in one step corn to ethanol process.

Claims

1. A poiypeptide having gSucoamySase activity, selected from the group consisting of: (a) a polypeptide having an amino acid sequence which has at least 60% identity with amino acids for mature poiypeptide amino acids 1 to 558 of SEQ SD NO: 2;

(fa) a polypeptide which is encoded by a nucleotide sequence (s) which hybridizes under at least low stringency conditions with nucleotides 81 to 2301 of SEQ SD NO: 1, or (ii) which hybridizes under at least Sow stringency conditions with the cDNA sequence contained in nucleotides 81 to 1734 of SEQ ID NO: 3, or (US) a complementary strand of {i} or (ii); (C) a variant comprising a conservative substitution, deletion, and/or insertion of one or more amino acids of amino acids 1 to 558 of SEQ ID NO: 2.

2. A polypeptide having carbohydrate-binding affinity, selected from the group consisting of; (a) i) a polypeptide comprising an amino acid sequence which has at ieast 60% identity with amino acids 464 to 558 of SEQ ID NO: 2:

(b) a polypeptide which is encoded by a nucleotide sequence which hybridizes under low stringency conditions with a polynucleotide probe selected from the group of

(i) the complementary strand of nucleotides 1845-2301 of SEQ ID NO: 1 ; (ii) the complementary strand of nucSeotides 1450-1734 of SEQ ID NO: 3;

(C) a fragment of (a) or (b) that has carbohydrate binding affinity.

3. A polynucleotide having a nucleotide sequence which encodes for the polypeptide of claims 1-2.

4. A nucleic acid construct comprising the polynucleotide of claim 3 operabiy linked to one or more control sequences that direct the production of the polypeptide Sn an expression host.

5. A recombinant expression vector comprising the nucleic acid construct of claim 4.

6. A recombinant host eel! comprising the nucleic acid construct of claim 4 or recombinant expression vector of claim 5

7, A method for producing a polypeptide of any of claims 1-8, comprising

{a} cultivating a cell, which in its wild-type form is capable of producing the polypeptide, under conditions conducive for production of the polypeptide; and (b) recovering the poiy peptide.

8, A method for producing a poiypeptide of any of claims 1-2 comprising (a) cultivating a host ceiS comprising a nucleic acid construct comprising a nucieotide sequence encoding the polypeptide under conditions conducive for production of the poiypeptide; and (b) recovering the polypeptide.

9, A poiynucleotide encoding a poiypeptidβ having giucoamylase activity, seiected from the group consisting of:

(a) a poSynucleotide encoding a poiypeptide having an amino acid sequence which has at least 60% identity with the mature poiypeptide amino acids 1 to 558 of SEQ ID

NO: 2;

(b) a polynucleotide having at least 60% identity with nucieotides 61-2301 of SEQ iD NO: 1 ; or

(C) a polynucleotide having at least 60% identity with nucieotides 61-1734 of SEQ ID NO: 3;

(d) a polypeptide which is encoded by a nucieotide sequence (i) which hybridizes under at least Sow stringency conditions with nucieotides 61 to 2301 of SEQ SD NO: 1 , or (ii) which hybridizes under at teas! medium stringency conditions with the cDNA sequence contained in nucieotides 61 to 1734 of SEQ ID NO: 3, or (iii) a complementary strand of (i) or (ii).

10, A process for producing a fermentation product from starch-containing material comprising the steps of:

(a) iiquefying starch-containing materia!; (b) saccharifying the liquefied materia! using a giucoamylase of claim 1 ; (c) fermenting the saccharified material using a fermenting organism.

1 1 , A process for producing a fermentation product from starch-containing materia! comprising: (a) saccharifying starch-containing material with a glucoamylase of claim 1 , at a temperature below the initial gelatinization temperature of said starch-containing material,

(b) fermenting using a fermenting organism.

12. The process of any of claim 1. wherein the starch-containing materia! is granular starch,

13. The process of any of ciaims 28-39, wherein the glucoamylase is present in an amount of 0.001 to 10 AGU/g DS, preferably from 0,01 to 5 AGU/g DS₁ especially 0.1 to 0,5

AGU/g DS.

14. The process of any of ciaims 11-13, wherein an alpha-amylase is present,

15, The process of any of claims 11-14. wherein the temperature during saccharificatioπ in step (a) is from 3OX to 75^βC. preferably between 45 and 8O⁰G.

16. The process of any of claims 11-15, wherein step (a) and (b) is carried out sequentially or simultaneously {i.e., one-step fermentation)

17. A process of producing syrup from starch-containing materia!, comprising

(a) ϋquefying starch-containing material, preferabiy in the presence of an a!pha-amylase,

(b) saccharifying the material obtained in step (a) using a glucoamyiase of ciaim.

18. The process of ciaim 17, further comprising refining, conversion and/or recovery of the syrup.

19, Use of a g!ucoamy!ase of any of claims 1-2 for production of syrup and/or a fermentation product,

20. Use of ciaim 19, wherein the starting material is gelatinized and/or un-gelatinized starch-containing material.

21. Use of a giucoamylase of any of claims 1-2 for brewing.

22, A composition comprising a glucoamyiase of any of claims 1-2.

23. The composition of claim 22, further comprising an alpha-amyiase.

24. The composition of claim 23, wherein the aipha-amylase is an acidic aipna-amyiase, preferably a funga! acidic alpha-amylase.

25. The composition of claim 23 or 24, wherein the alpha-amylase is of fungal origin.

26. The composition of any of claims 23-25, wherein the aipha-arnylase is derived from the genus Aspergillus, preferably a strain of A niger, A. oryzae, Aspergillus awarnori, or A. kawachii, of the genus Rhizomucor, preferably a strain the Rhizomucor pusiilus, or the genus Menpilus, preferably a strain of Meripilus giganteus.

27. The composition of any of ciaims 23-25, wherein the alpha-amyiase is a hybrid, preferably Rhizomucor pυsillus aipha-amyiase with Athelia rolfsii AIViG Sinker and SBD;

Rhizomucor pusiilus alpha-amySase with Aspergillus niger glucoamylase linker and SBO; or Aspergillus niger alpha-amylase with Aspergillus kawachii Sinker and starch binding domain (SBD).

28 The composition of any of claims 23-27, further comprising another glucoamylase.

29. The composition of ciaim 28, wherein the giucoamyiase is derived from the genus Aspergillus, preferably a strain of Aspergillus niger, Aspergillus oryzae, Aspergillus awamori, or the genus Athelia, preferably a strain of Athelia rolfsii, the genus Talaromyces, preferably a strain the Talaromyces emersonii, or a strain of the genus Trametes, preferably a strain of Trametes cingulata: or a strain of the genus Rhizopus, such as a strain of Rhizopus nivius: or a strain of the genus Humicola, preferabiy a strain of Humicola grisea var thermoiϋea.