WO2007148224A2 - Polypeptide - Google Patents

Polypeptide Download PDF

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Publication number
WO2007148224A2
WO2007148224A2 PCT/IB2007/002056 IB2007002056W WO2007148224A2 WO 2007148224 A2 WO2007148224 A2 WO 2007148224A2 IB 2007002056 W IB2007002056 W IB 2007002056W WO 2007148224 A2 WO2007148224 A2 WO 2007148224A2
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WO
WIPO (PCT)
Prior art keywords
polypeptide
variant
sequence
variant polypeptide
seq
Prior art date
Application number
PCT/IB2007/002056
Other languages
French (fr)
Other versions
WO2007148224A8 (en
WO2007148224A3 (en
Inventor
Patrick Maria Franciscus Derkx
Anja Kellet-Smith Hemmingsen
Rie Mejldal
Bo Spange SØRENSEN
Karsten Matthias Kragh
Original Assignee
Danisco A/S
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority to ES07789503.5T priority Critical patent/ES2644745T3/en
Priority to MX2012006758A priority patent/MX345513B/en
Application filed by Danisco A/S filed Critical Danisco A/S
Priority to EP07789503.5A priority patent/EP2035447B1/en
Priority to AU2007262442A priority patent/AU2007262442B2/en
Priority to RU2009101321/10A priority patent/RU2539776C2/en
Priority to CN200780030527.7A priority patent/CN101528769B/en
Priority to DK07789503.5T priority patent/DK2035447T3/en
Priority to CA2656313A priority patent/CA2656313C/en
Priority to MX2008016444A priority patent/MX2008016444A/en
Priority to NZ573564A priority patent/NZ573564A/en
Priority to JP2009515989A priority patent/JP5448812B2/en
Priority to BRPI0713286-7A priority patent/BRPI0713286A2/en
Priority to KR1020147033965A priority patent/KR20150004920A/en
Publication of WO2007148224A2 publication Critical patent/WO2007148224A2/en
Publication of WO2007148224A3 publication Critical patent/WO2007148224A3/en
Priority to ZA2008/10738A priority patent/ZA200810738B/en
Priority to US12/339,718 priority patent/US8178336B2/en
Publication of WO2007148224A8 publication Critical patent/WO2007148224A8/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C12N9/2405—Glucanases
    • C12N9/2408—Glucanases acting on alpha -1,4-glucosidic bonds
    • C12N9/2411—Amylases
    • C12N9/2414—Alpha-amylase (3.2.1.1.)
    • C12N9/2417—Alpha-amylase (3.2.1.1.) from microbiological source
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C12N9/2405—Glucanases
    • C12N9/2408—Glucanases acting on alpha -1,4-glucosidic bonds
    • C12N9/2411—Amylases
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A—HUMAN NECESSITIES
    • A21—BAKING; EDIBLE DOUGHS
    • A21D—TREATMENT, e.g. PRESERVATION, OF FLOUR OR DOUGH, e.g. BY ADDITION OF MATERIALS; BAKING; BAKERY PRODUCTS; PRESERVATION THEREOF
    • A21D13/00—Finished or partly finished bakery products
    • A—HUMAN NECESSITIES
    • A21—BAKING; EDIBLE DOUGHS
    • A21D—TREATMENT, e.g. PRESERVATION, OF FLOUR OR DOUGH, e.g. BY ADDITION OF MATERIALS; BAKING; BAKERY PRODUCTS; PRESERVATION THEREOF
    • A21D2/00—Treatment of flour or dough by adding materials thereto before or during baking
    • A21D2/08—Treatment of flour or dough by adding materials thereto before or during baking by adding organic substances
    • A21D2/24—Organic nitrogen compounds
    • A21D2/26—Proteins
    • A—HUMAN NECESSITIES
    • A21—BAKING; EDIBLE DOUGHS
    • A21D—TREATMENT, e.g. PRESERVATION, OF FLOUR OR DOUGH, e.g. BY ADDITION OF MATERIALS; BAKING; BAKERY PRODUCTS; PRESERVATION THEREOF
    • A21D8/00—Methods for preparing or baking dough
    • A21D8/02—Methods for preparing dough; Treating dough prior to baking
    • A21D8/04—Methods for preparing dough; Treating dough prior to baking treating dough with microorganisms or enzymes
    • A21D8/042—Methods for preparing dough; Treating dough prior to baking treating dough with microorganisms or enzymes with enzymes
    • A—HUMAN NECESSITIES
    • A21—BAKING; EDIBLE DOUGHS
    • A21D—TREATMENT, e.g. PRESERVATION, OF FLOUR OR DOUGH, e.g. BY ADDITION OF MATERIALS; BAKING; BAKERY PRODUCTS; PRESERVATION THEREOF
    • A21D8/00—Methods for preparing or baking dough
    • A21D8/06—Baking processes
    • A—HUMAN NECESSITIES
    • A23—FOODS OR FOODSTUFFS; TREATMENT THEREOF, NOT COVERED BY OTHER CLASSES
    • A23K—FODDER
    • A23K20/00—Accessory food factors for animal feeding-stuffs
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C12N9/2405—Glucanases
    • C12N9/2408—Glucanases acting on alpha -1,4-glucosidic bonds
    • C12N9/2411—Amylases
    • C12N9/2414—Alpha-amylase (3.2.1.1.)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
    • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
    • C12Y302/0106—Glucan 1,4-alpha-maltotetraohydrolase (3.2.1.60)

Definitions

  • This invention relates to polypeptides, specifically amylase polypeptides and nucleic acids encoding these, and their uses as non-maltogenic exoamylases in producing food products.
  • the amylases of the present invention have been engineered to have more beneficial qualities.
  • the amylases of the current invention show an altered exospecifity and/or altered thermostability.
  • the polypeptides are derived from polypeptides having non-maltogenic exoamylase activity, in particular, glucan 1,4-alpha- maltotetrahydrolase (EC 3.2.1.60) activity.
  • BACKGROUND Improved amylases can ameliorate problems inherent in certain processes, such as baking. Crystallisation of amylopectin takes place in starch granules days after baking, which leads to increased firmness of bread and causes bread staling. When bread stales, bread loses crumb softness and crumb moisture. As a result, crumbs become less elastic, and bread develops a leathery crust.
  • Enzymatic hydrolysis (by amylases, for example) of amylopectin side chains can reduce crystallization and increase anti-staling. Crystallization depends upon the length of amylopectin side chains: the longer the side chains, the greater the crystallization. Most starch granules are composed of a mixture of two polymers: amylopectin and amylose, of which about 75% is amylopectin.
  • Amylopectin is a very large, branched molecule consisting of chains of ⁇ -D-glucopyranosyl units joined by (1-4) linkages, where the chains are attached by ⁇ -D-(l-6) linkages to form branches. Amylose is a linear chain of (1-4) linked ⁇ -D-glucopyranosyl units having few ⁇ -D-(l-6) branches.
  • Baking of farinaceous bread products such as white bread, bread made from bolted rye flour and wheat flour and rolls is accomplished by baking the bread dough at oven temperatures in the range of from 180 to 250°C for about 15 to 60 minutes.
  • a steep temperature gradient 200 ⁇ 120 0 C
  • the temperature in the crumb is only about 100 0 C at the end of the baking process.
  • temperatures of about 85 0 C enzyme inactivation can take place and the enzyme will have no anti-staling properties. Only thermostable amylases, thus, are able to modify starch efficiently during baking.
  • Endoamylase activity can negatively affect the quality of the final bread product by producing a sticky or gummy crumb due to the accumulation of branched dextrins.
  • Exo- amylase activity is preferred, because it accomplishes the desired modification of starch that leads to retardation of staling, with fewer of the negative effects associated with endoamylase activity. Reduction of endoamylase activity can lead to greater exospecifity, which can reduce branched dextrins and produce a higher quality bread.
  • PS4 variant polypeptide as set out in the claims.
  • PS4 variant polypeptide including in and as food additives, food products, bakery products, improver compositions, feed products including animal feeds, etc as set out in the claims.
  • nucleic acids which encode and which relate to PS4 variant polypeptides, as set out in the claims. Methods for producing such PS4 variant polypeptides, as well as other aspects of the invention, are also set out in the claims.
  • Figure 1 shows an example of a curve from a Texture Analyser.
  • Figure 2 shows the results of an experiment to determine the temperature stability of the PS4 variant polypeptides described here.
  • X-axis temperature
  • Y-axis half-life (minutes).
  • Figure 3 shows the results of a baking trial in which firmness of bread treated with various concentrations of PS4 variant polypeptide and untreated bread are tested.
  • the X- axis shows the number of days, while the Y-axis shows firmness expressed as hPa (see Example 13).
  • Figure 4 shows the results of a baking trial in which resilience of bread treated with various concentrations of PS4 variant polypeptide and untreated bread are tested.
  • the X- axis shows the number of days, while the Y-axis shows resilience expressed as Resilience Units (see Example 14).
  • Triangle 60,000 Betamyl units/kg of pSac- pMS382.
  • Cross Control (no enzyme).
  • Figure 5 shows the results of a baking trial in which cohesiveness of bread treated 100 with various concentrations of PS4 variant polypeptide and untreated bread are tested.
  • the X-axis shows the number of days, while the Y-axis shows cohesiveness expressed as Cohesiveness Units (see Example 15).
  • Diamond 20,000 Betamyl/kg of pSac-pMS382.
  • Square 40,000 Betamyl/kg of pSac-pMS382.
  • Triangle 60,000 Betamyl/kg of pSac- pMS382.
  • Cross Control (no enzyme).
  • PS4 variant polypeptide with substitution at 307 is tested.
  • the X-axis shows the number of days, while the Y-axis shows firmness expressed as hPa (see Example 13).
  • Figure 7 shows the results of a baking trial in which resilience of bread treated with PS4 variant polypeptide with substitution at 307 is tested.
  • the X-axis shows the number of days, while the Y-axis shows resilience expressed as resilience units (see Example 14).
  • Figure 8 shows the results of a baking trial in which cohesiveness of bread treated with PS4 variant polypeptide with substitution at 307 is tested.
  • the X-axis shows the number of days, while the Y-axis shows cohesiveness expressed as cohesiveness units (see 120 Example 15).
  • Figure 9 Foldability test day 8 after baking of tortillas with 400 ppm Novamyl (TM) 1500 and 50 BMK/kg pSac-pMS382 (SEQ ID NO: 21).
  • SEQ ID NO: 1 shows a PS4 reference sequence, derived from Pseudomonas
  • SEQ ID NO: 2 shows a pSac- D34 sequence; Pseudomonas saccharophila maltotetrahydrolase amino acid sequence with 11 substitutions and deletion of the starch binding domain.
  • SEQ ID NO: 3 shows a pSac-D20 sequence; Pseudomonas saccharophila maltotetrahydrolase amino acid sequence with 13 substitutions and deletion of the starch binding domain.
  • SEQ ID NO: 4 shows a pSac-D20 sequence; Pseudomonas saccharophila maltotetrahydrolase amino acid sequence with 13 substitutions and deletion of the starch binding domain.
  • SEQ ID NO: 5 shows a Pseudomonas saccharophila Glucan 1,4-alpha-maltotetrahydrolase precursor (EC 3.2.1.60) (G4-amylase) (Maltotetraose-forming amylase) (Exo- maltotetraohydrolase) (Maltotetraose-forming exo-amylase).
  • SEQ ID NO:7 shows a PS4 reference sequence, derived from Pseudomonas stutzeri maltotetrahydrolase amino acid sequence.
  • SEQ ID NO: 8 shows a PStu-D34 sequence; Pseudomonas stutzeri maltotetrahydrolase amino acid sequence with 9 substitutions.
  • 150 ID NO: 9 shows a PStu-D20 sequence; Pseudomonas stutzeri maltotetrahydrolase amino acid sequence with 11 substitutions.
  • SEQ ID NO: 10 shows a PStu-D14 sequence; Pseudomonas stutzeri maltotetrahydrolase amino acid sequence with 12 substitutions.
  • SEQ ID NO: 11 shows a Pseudomonas stutzeri ⁇ Pseudomonas per fectomarin ⁇ ).
  • Glucan 1,4-alpha-maltotetrahydrolase precursor EC 3.2.1.60
  • G4-amylase (Maltotetraose-
  • SEQ ID NO: 13 shows a pSac-pMD229 amino acid sequence having mutations 160 33Y, 34N, 121F, 134R, 141P, 146G, 157L, 161A 5 178F, 179T, 223E, 229P, 272Q, 303E, 307L, 309P and 334P.
  • SEQ ID NO: 14 shows a pSac-pMD229 nucleic acid sequence.
  • SEQ ID NO: 15 shows a pSac-pMD248 amino acid sequence having mutations 33 Y, 34N, 121F, 134R, 141P, 145D, 146G, 157L, 178F, 179T, 223E, 229P, 272Q, 303E, 307L and 334P.
  • SEQ ID NO: 16 shows a pSac-pMD248 nucleic acid sequence.
  • SEQ ID NO: 165 17 shows a pSac-pMD253 amino acid sequence having mutations 33Y, 34N, 121D, 134R, 141P, 146G, 157L, 178F, 179T, 223E 5 229P, 272Q, 303E, 307L, 309P and 334P.
  • SEQ ID NO: 18 shows a pSac-pMD253 nucleic acid sequence.
  • SEQ ID NO: 19 shows a pSac- pMD271 amino acid sequence having mutations 3S, 33Y, 34N, 7OD, 121D, 134R, 141P, 146G, 157L, 178F, 179T, 223E 5 229P 5 272Q 5 303E 5 307L, 309P and 334P.
  • SEQ ID NO: 170 20 shows a pSac-pMD271 nucleic acid sequence.
  • SEQ ID NO: 21 shows a pSac-pMS382 amino acid sequence having mutations 33Y 5 34N 5 7OD, 121F, 134R, 141P 5 146G 5 157L 5 161A, 178F, 179T 5 223E 5 229P 5 307K 5 309P and 334P.
  • SEQ ID NO: 22 shows a pSac-pMS382 nucleotide sequence sequence.
  • SEQ ID NO: 23 shows a pSac— pMS382R amino acid sequence having mutations 33Y 5 175 34N 5 7OD, 121F 5 134R 5 141P 5 146G 5 157L, 161A, 178F, 179T 5 223E 5 229P 5 307R 5 309P and 334P.
  • SEQ ID NO: 24 shows a pSac-pMS382R nucleotide sequence sequence.
  • SEQ DD NO: 25 shows a pSac-pMS382H amino acid sequence having mutations 33Y 5 34N 5 70D 5 121F 5 134R 5 141P, 146G, 157L, 161A 5 178F 5 179T 5 223E 5 229P 5 309P and 334P.
  • SEQ ID NO: 26 shows a pSac-pMS382H nucleotide sequence sequence.
  • SEQ ED NO: 27 shows a SSM471 BlO amino acid sequence having mutations
  • SEQ ED NO: 28 shows a SSM471 BlO nucleic acid sequence.
  • SEQ ED NO: 29 shows a SSM471 C04 amino acid sequence having mutations 33Y 5 34N 5 121F 5 134R, 141P 5 146G 5 157L 5 161A, 178F 5 179T, 223E, 229P 5 272Q 5 303E 5 307K 5 309P
  • SEQ ED NO: 30 shows a SSM471 C04 nucleic acid sequence.
  • SEQ ED NO: 31 shows a PMS 370 amino acid sequence having mutations 33Y 5 34N, 121F 5 134R 5 141P 5 146G 5 157L 5 161A 5 178F 5 179T 5 223E 5 229P 5 272Q 5 303E 5 309P and 334P.
  • SEQ ID NO: 32 shows a PMS 370 nucleic acid sequence.
  • dosages of PS4 variant polypeptides are given in parts per million (micrograms per gram) of flour.
  • “1 D34” indicates 1 part per million of pSac-D34 based on weight per weight.
  • enzyme quantities or amounts are determined based on activity assays as equivalents of pure enzyme protein measured with bovine serum albumin (BSA)
  • substitution includes a number and a letter, e.g., 141P, then this refers to [position according to the numbering system/substituted amino acid]. Accordingly, for example, the substitution of an amino acid to proline in position 141 is designated as 141 P;
  • substitution includes a letter, a number and a letter, e.g., A141P, then this refers to [original amino acid/position according to the numbering system/substituted amino acid]. Accordingly, for example, the substitution of alanine with proline in position 141 is designated as Al 4 IP.
  • this 210 will be designated by contiguous letters, which may optionally be separated by slash marks "/", e.g., G303ED or G3O3E/D.
  • the relevant amino acid at a position can be substituted by any amino acid, this is designated by [position according to the numbering system/X], e.g., 121X.
  • Multiple mutations may be designated by being separated by slash marks "/”, e.g. 215 A141P/G223A or commas ",", e.g., A141P, G223A representing mutations in position 141 and 223 substituting alanine with proline and glycine with alanine respectively.
  • nucleic acids are written left to right in 5' to 3' orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.
  • Antibodies A Laboratory Manual : Portable Protocol NO. I by Edward Harlow, David Lane, Ed Harlow (1999, Cold Spring Harbor Laboratory Press, ISBN 0-87969-544-7); Antibodies : A Laboratory Manual by Ed Harlow (Editor), David Lane (Editor) (1988, Cold Spring Harbor Laboratory Press, ISBN 0-87969-314-2), 1855, Lars-Inge Larsson
  • polypeptide having a substitution at one or more positions which effect an altered property which may be any combination of altered exospecificity or altered thermostability, or an altered handling property, relative to the parent enzyme.
  • Such variant polypeptides are referred to in this document for convenience as "PS4 variant 260 polypeptides”.
  • the PS4 variant polypeptides preferably exhibit enzyme activity. More preferably, the PS4 variant polypeptides comprise amylase activity, preferably exoamylase activity. In highly preferred embodiments, the PS4 variant polypeptides exhibit non-maltogenic exoamylase activity. 265
  • compositions including food additives, food products, bakery products, improver compositions, feed products including animal feeds, etc comprising such altered PS4 variant polypeptides, preferably those which have non- maltogenic exoamylase activity, as well as methods of making and using such polypeptides and the compositions.
  • the PS4 variant polypeptides may comprise one or more improved handling properties, preferably improved baking properties.
  • the PS4 variant polypeptides are such that the food products so treated have one or more of (preferably all of) a lower firmness, a higher resilience, a higher cohesiveness, a lower crumbliness or a higher foldability.
  • compositions such as in the preparation of 280 detergents, as sweeteners, syrups, etc.
  • the compositions include the polypeptide together with at least one other component, hi particular, we provide for food or feed additives comprising the polypeptides.
  • Such polypeptides and nucleic acids vary from their parent sequences by including a number of mutations.
  • the sequence of the PS4 variant polypeptide or 285 nucleic acid is different from that of its parent at a number of positions or residues.
  • the mutations comprise amino acid substitutions, that is, a change of one amino acid residue for another.
  • the PS4 variant polypeptides comprise a number of changes in the nature of the amino acid residue at one or more positions of the parent sequence.
  • variants should be taken to mean a molecule being derivable from a parent molecule.
  • Variants include polypeptides as well as nucleic acids.
  • Variants include deletions, insertions and substitutions at the amino acid level and transversions, transitions and inversions at the nucleic acid level among other things, at one or more locations.
  • Variants also include truncations.
  • Variants include homologous and
  • Variants include sequences that are complementary to sequences that are capable of hybridising to the nucleotide sequences presented herein.
  • POSITION 307 BASIC RESIDUE MUTANTS
  • PS4 variant polypeptides with sequence alterations comprising 300 amino acid substitutions in a amylase sequence, preferably an exoamylase activity, more preferably a non-maltogenic exoamylase sequence.
  • a PS4 variant polypeptide derivable from a parent polypeptide having non-maltogenic exoamylase activity comprising an amino acid mutation at position 307 with reference to the position numbering of a Pseudomonas 305 saccharophilia exoamylase sequence shown as SEQ ID NO: 1.
  • the position 307 substitution is preferably a substitution to a basic or positively charged amino acid, preferably lysine (K) or arginine (R).
  • PS4 variant polypeptide in which the amino acid substitution at position 307 is a substitution to lysine (307K), preferably H307K.
  • PS4 variant polypeptide according to Claim 1 or 2 in which the amino acid substitution at position 307 is a substitution to arginine (307R), preferably H307R.
  • the PS4 variant polypeptide may further comprise a mutation at position 70 to aspartic acid (D), preferably 7OD.
  • the substitution is G70D. 315 Accordingly, in some embodiments, we provide for a PS4 variant polypeptide comprising substitutions G70D, H307K or G70D, H307R relative to a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ID NO: 1.
  • residues at positions 272 and 303 may be "wild type", or they may be mutated, hi preferred embodiments, the residue at position 272 is a wild type residue, i.e., histidine
  • the residue at position 303 is also a wild type residue, i.e., glycine (G).
  • G glycine
  • PS4 variant polypeptides Such variant polypeptides, and others as described hi this document, are referred to in this document as "PS4 variant polypeptides". Nucleic acids encoding such variant polypeptides are also disclosed and will be referred to for convenience as “PS4 variant nucleic acids”. PS4 variant polypeptides and nucleic acids will be described in further 330 detail below.
  • the "parent” sequences i.e., the sequences on which the PS4 variant polypeptides and nucleic acids are based, preferably are polypeptides having non-maltogenic exoamylase activity.
  • the terms "parent enzymes” and “parent polypeptides” should be interpreted accordingly, and taken to mean the enzymes and polypeptides on which the 335 PS4 variant polypeptides are based. They are described in further detail below.
  • the mutations and amino acid changes may be made on any suitable polypeptide backbone or background, wild type or mutated, as described in further detail below.
  • the parent sequences are non-maltogenic exoamylase enzymes, preferably bacterial non-maltogenic exoamylase enzymes.
  • the parent sequence comprises a glucan 1 ,4-alpha- maltotetrahydrolase (EC 3.2.1.60).
  • the parent sequence is derivable from Pseudomonas species, for example Pseudomonas saccharophilia or Pseudomonas stutzeri.
  • the parent polypeptide comprises, or is homologous to, a wild type non-maltogenic exoamylase sequence, e.g., from Pseudomonas spp.
  • the parent polypeptide may comprise a Pseudomonas saccharophilia non- maltogenic exoamylase having a sequence shown as SEQ ID NO: 1.
  • the parent polypeptide comprises a non-maltogenic exoamylase from Pseudomonas stutzeri having a sequence shown as SEQ ID NO: 11, or a Pseudomonas stutzeri non-maltogenic exoamylase having SWISS-PROT accession number P13507.
  • the parent polypeptide may be a variant of any of the wild type sequences, that is to say, the parent polypeptide may itself be engineered, or comprise a PS4 variant polypeptide.
  • the mutations and changes are made on a PS4 sequence which is already mutated, preferably pMD 229 (SEQ ID NO: 13 or 14).
  • PS4 variant polypeptides may be derivable by mutating already mutated sequences, it is possible to construct such variant polypeptides by starting from a wild type sequence (or indeed any suitable sequence), identifying the differences between the starting sequence and the desired variant, and introducing the required mutations into the starting sequence in order
  • Proteins and nucleic acids related to, preferably having sequence or functional homology with Pseudomonas saccharophilia non-maltogenic exoamylase sequence shown as SEQ DD NO: 1 or a Pseudomonas stutzeri non-maltogenic exoamylase having a sequence shown as SEQ ID NO: 11 are referred to in this document as members of the 365 "PS4 family".
  • PS4 family non-maltogenic exoamylase enzymes suitable for use in generating the PS4 variant polypeptides and nucleic acids are disclosed in further detail below.
  • the PS4 variant polypeptides described in this document preferably retain the features of the parent polypeptides, and additionally preferably have additional beneficial 370 properties, for example, enhanced activity or thermostability, or pH resistance, or any combination (preferably all). This is described in further detail below.
  • the PS4 substitution mutants described here may be used for any suitable purpose. They may preferably be used for purposes for which the parent enzyme is suitable. In particular, they may be used in any application for which exo-maltotetraohydrolase is 375 used. In highly preferred embodiments, they have the added advantage of higher thermostability, or higher exoamylase activity or higher pH stability, or any combination.
  • suitable uses for the PS4 variant polypeptides and nucleic acids include food production, in particular baking, as well as production of foodstuffs; further examples are set out in detail below.
  • the PS4 variant polypeptides may comprise one or more further mutations in addition to those positions set out above. There may be one, two, three, four, five, six, seven or more mutations preferably substitutions in addition to those already set out. Other mutations, such as deletions, insertions and substitutions at the amino acid level and transversions, transitions and inversions at the nucleic acid level, at one or more other
  • PS4 variants need not have all the substitutions at the positions listed. Indeed, they may have one, two, three, four, or five substitutions missing, i.e., the wild type amino acid residue is present at such positions.
  • the PS4 variant polypeptide may comprise one or more further mutations at other sites or positions in its sequence.
  • the PS4 variant polypeptide may further comprise one or more 395 mutations selected from the group consisting of positions: 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or 334.
  • the residues at these positions may preferably comrpise 33Y 5 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E, 229P, 307K, 309P or 334P.
  • the PS4 variant polypeptide may therefore comprise, in addition to 307K/R/H, 1, 400 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or all 15 mutations at positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or 334.
  • the position 307 residue in such embodiments may comprise histidine (H), particularly where such further mutations are present.
  • the PS4 variant polypeptide may therefore comprise, in addition to 307K/R/H, 1 405 further mutation at any of positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or 334, as shown in "Annex A: 1 Mutation", i.e., 33Y; 34N; 7OD; 121F; 134R; 141P; 146G; 157L; 161A; 178F; 179T; 223E; 229P; 309P; or 334P.
  • the PS4 variant polypeptide may comprise any of the following: 33Y, 307K/R/H; 34N, 307K/R/H; 7OD, 307K/R/H; 121F, 307K/R/H; 134R, 307K/R/H; 410 141P, 307K/R/H; 146G, 307K/R/H, 157L, 307K/R/H; 161 A, 307K/R/H; 178F, 307K/R/H; 179T, 307K/R/H; 223E, 307K/R/H; 229P, 307K/R7H; 309P, 307K/R/H; or 334P, 307K/R/H.
  • the PS4 variant polypeptide may alternatively comprise, in addition to 307K/R/H,
  • the PS4 variant polypeptide may comprise any of the following:
  • the PS4 variant polypeptide may alternatively comprise, in addition to 307K/R/H, 3 further mutations at any of positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or 334, as shown in "Annex A: 3 Mutations".
  • the PS4 variant polypeptide may alternatively comprise, in addition to 307K/R/H,
  • the PS4 variant polypeptide may alternatively comprise, in addition to 307K/R/H,
  • the PS4 variant polypeptide may alternatively comprise, in addition to 307K/R/H,
  • the PS4 variant polypeptide may alternatively comprise, in addition to 307K/R/H,
  • the PS4 variant polypeptide may comprise, a sequence with 9 mutations, viz each of the following residues 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 178F,
  • the PS4 variant polypeptide may comprise, a sequence with 10 mutations, viz each of the following residues 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E, 229P, 307K/R/H, 309P, 334P, but not including the sextets of residues shown in "Annex A: 6 Mutations".
  • the PS4 variant polypeptide may comprise, a sequence with 11 mutations, viz each of the following residues 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E, 229P, 307K/R/H, 309P, 334P, but not including the quintets of residues shown in "Annex A: 5 Mutations".
  • the PS4 variant polypeptide may comprise, a sequence with 12 mutations, viz each of the following residues 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E, 229P, 307K/R/H, 309P, 334P, but not including the quadruplets of residues shown in "Annex A: 4 Mutations".
  • the PS4 variant polypeptide may comprise, a sequence with 13 mutations, viz each of the following residues 33Y 5 34N, 7OD, 121F, 134R, 141P, 146G 5 157L, 161A 5 178F 5 179T, 223E 5 229P 5 307K/R/H, 309P 5 334P, but not including the triplets of residues shown in "Annex A: 3 Mutations".
  • the PS4 variant polypeptide may comprise, a sequence with 14 mutations, viz each 500 of the following residues 33Y 5 34N 5 70D 5 121F, 134R, 141P, 146G 5 157L, 161A, 178F 5 179T 5 223E, 229P 5 307K/R/H, 309P 5 334P 5 but not including the pairs of residues shown in "Annex A: 2 Mutations".
  • the PS4 variant polypeptide may comprise, a sequence with 15 mutations, viz each of the following residues 33Y, 34N, 7OD, 121F, 134R, 141P 5 146G 5 157L 5 161A 5 178F 5 505 179T, 223E 5 229P, 307K/R/H, 309P, 334P 5 but not including the single residues shown in "Annex A: 1 Mutations".
  • the PS4 variant polypeptide further comprises mutations at each of these positions.
  • PS4 variant polypeptide derivable from a parent polypeptide having non-maltogenic exoamylase activity in which the PS4 variant polypeptide comprises a mutation at each of the following positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 307, 309, 334, with reference to the position numbering of a Pseudomon ⁇ s s ⁇ cch ⁇ rophili ⁇ exoamylase sequence shown as SEQ ID NO:
  • the position 307 mutation comprises a basic or positively charged residue.
  • the position 307 mutation comprises 307K or 307R.
  • the position 307 residue is H.
  • a PS4 variant polypeptide derivable from a parent polypeptide 520 having non-maltogenic exoamylase activity in which the PS4 variant polypeptide comprises a mutation at position 307 to K or R 5 or in which the position 307 residue is H 5 together with mutations at each of position 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 307, 309, 334.
  • the position 33 residue may comprise Y, preferably 33 Y, more 525 preferably N33Y.
  • the position 34 residue may comprise N 5 preferably 34N 5 more preferably D34N.
  • the position 70 residue may comprise D, preferably 7OD, more preferably G70D.
  • the position 121 residue may comprise F, preferably 12 IF, more preferably Gl 2 IF.
  • the position 134 residue may comprise R, preferably 134R, more preferably G134R.
  • the position 141 residue may comprise Y, preferably 33 Y, more 525 preferably N33Y.
  • the position 34 residue may comprise N 5 preferably 34N 5 more preferably D34N.
  • the position 70 residue may comprise D, preferably 7OD, more preferably G70D.
  • the position 121 residue may comprise F, preferably 12 IF, more preferably Gl 2 IF.
  • the position 134 residue may comprise R, preferably 134R, more preferably G134R.
  • the position 141 residue may comprise R, preferably 134
  • the position 530 may comprise P, preferably 141P, more preferably A141P.
  • the position 146 residue may comprise G, preferably 146G, more preferably Y146G.
  • the position 157 residue may comprise L, preferably 157L, more preferably I157L.
  • the position 161 residue may comprise A, preferably 161 A, more preferably S 161 A.
  • the position 178 residue may comprise F, preferably 178F, more preferably
  • the position 179 residue may comprise T, preferably 179T, more preferably A179T.
  • the position 223 residue may comprise E, preferably 223E, more preferably G223E.
  • the position 229 residue may comprise P, preferably 229P, more preferably S229P.
  • the position 307 residue may comprise K, preferably 307K 5 more preferably H307K.
  • the position 309 residue may
  • the position 334 residue . may comprise P, preferably 334P, more preferably S334P.
  • the position 70 mutation is 7OD, preferably G70D.
  • a PS4 variant polypeptide derivable from a parent polypeptide having non-maltogenic exoamylase activity in which the PS4 variant 545 polypeptide comprises a mutation at position 307 to K or R, or in which the position 307 residue is H, and a mutation at position 70 to 7OD, together with mutations at each of position 33, 34, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 307, 309, 334.
  • the residue at position 272 is "wild type", i.e., unmutated.
  • the position 272 residue is therefore preferably histidine (H).
  • PS4 variant polypeptide derivable from a parent polypeptide having non- maltogenic exoamylase activity in which the PS4 variant polypeptide comprises a mutation at position 307 to K or R, or in which the position 307 residue is H, and a mutation at position 70 to 7OD, in which the position 272 residue is H, together with mutations at each of position 33, 34, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229,
  • the residue at position 303 is "wild type" or unmutated, and is preferably glycine (G) in other preferred embodiments.
  • the PS4 variant polypeptide comprises a mutation at position 307 to K or 560 R, or in which the position 307 residue is H, and a mutation at position 70 to 7OD, in which the position 303 residue is G, together with mutations at each of position 33, 34, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 307, 309, 334.
  • the PS4 variant polypeptide which comprise further mutations at positions 33, 34, 70, 121, 134, 141, 146,
  • the position 33 residue is preferably Y, the position 34 residue is preferably N, the position 70 residue is preferably D, the position 121 residue is preferably F, the position 134 residue is preferably R, the position 141 residue is preferably P, the position 146 residue is preferably G, the position 157 residue is preferably L, the position 161 residue is preferably A, the position 178 residue is
  • the position 179 residue is preferably T
  • the position 223 residue is preferably E
  • the position 229 residue is preferably P
  • the position 309 residue is preferably P
  • the position 334 residue is preferably P.
  • PS4 variant polypeptide which comprises the following residues 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 575 178F, 179T, 223E, 229P, 307K/R/H, 309P, 334P.
  • the PS4 variant polypeptide may comprise each of the following mutations N33Y, D34N, G70D, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, H307K/R, A309P and S334P.
  • PS4 variant polypeptide which comprises the following substitutions 33Y, 34N, 7OD, 121F, 134R, 141P 5 146G, 157L, 161A, 178F, 580 179T, 223E, 229P, 307K, 309P, 334P, preferably N33Y, D34N, G70D, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, H307K, A309P, S334P relative to a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ID NO: 1.
  • the PS4 variant polypeptide may comprise a sequence SEQ ED NO: 21.
  • PS4 variant polypeptide which comprises the following substitutions 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E, 229P, 307R, 309P, 334P, preferably N33 Y 5 D34N, G70D, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, H307R, A309P, S334P relative to a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ED NO: 1.
  • SEQ ED NO: 1 Pseudomonas saccharophilia exoamylase sequence
  • the PS4 variant polypeptide may comprise a sequence SEQ ID NO: 23.
  • PS4 variant polypeptide derivable from a parent polypeptide having non-maltogenic exoamylase activity in which the PS4 variant polypeptide comprises the following substitutions 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161 A, 178F, 179T, 223E, 229P, 309P, 334P, preferably N33 Y, D34N, 595 G70D, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, A309P, S334P relative to a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ID NO: 1.
  • the PS4 variant polypeptide may comprise a sequence SEQ ED NO: 25.
  • One or more other mutations as set out in the table below may further be present in the PS4 variant polypeptide described here.
  • PS4 nucleic acids having sequences which correspond to or encode the alterations in the P S4 variant polypeptide sequences, for use in producing such 605 polypeptides for the purposes described here.
  • nucleic acids capable of encoding any polypeptide sequence set out in this document we also describe PS4 nucleic acids having sequences which correspond to or encode the alterations in the P S4 variant polypeptide sequences, for use in producing such 605 polypeptides for the purposes described here.
  • the PS4 variant polypeptide comprises more than one substitution, for example
  • the corresponding PS4 nucleic acids may comprise pairwise combinations of the codons which encode respectively the two amino acid changes.
  • the PS4 variant nucleic acid sequences may be derivable from parent nucleic acids which encode any of the parent polypeptides described above.
  • parent nucleic 620 acids may comprise wild type sequences, e.g., SEQ ID NO: 6 or SEQ ID NO: 12.
  • the PS4 variant nucleic acids may therefore comprise nucleic acids encoding wild type non- maltogenic exoamylases, but which encode another amino acid at the relevant position instead of the wild type amino acid residue.
  • the PS4 variant nucleic acid sequences may also comprise wild type sequences with one or more mutations, e.g., which encode parent 625 polypeptides described above under "Combinations".
  • PS4 variant nucleic acid sequences which are not identical to the particular PS4 variant nucleic acid sequences, but are related to these, will also be useful for the methods and compositions described here, such as a variant, homologue, derivative or fragment of a PS4 variant nucleic acid sequence, or a complement or a sequence capable 630 of hybridising thereof.
  • PS4 variant nucleic acid should be taken to include each of these entities listed above.
  • Mutations in amino acid sequence and nucleic acid sequence may be made by any of a number of techniques, as known in the art. Variant sequences may easily be made using any of the known mutagenesis techniques, for example, site directed mutagenesis 635 using PCR with appropriate oligonucleotide primers, 5' add-on mutagenesis, mismatched primer mutagenesis, etc. Alternatively, or in addition, the PS4 variant nucleic acid sequences may be made de novo.
  • the mutations are introduced into parent sequences by means of PCR (polymerase chain reaction) using appropriate primers, as
  • 645 is altered by altering the sequence of a nucleic acid which encodes the non-maltogenic exoamylase.
  • the PS4 variant polypeptide does not need in fact to be actually derived from a wild type polypeptide or nucleic acid sequence by, for example, step by step mutation. Rather, once the sequence of the PS4 variant 650 polypeptide is established, the skilled person can easily make that sequence from the wild type with all the mutations, via means known in the art, for example, using appropriate oligonucleotide primers and PCR. In fact, the PS4 variant polypeptide can be made de novo with all its mutations, through, for example, peptide synthesis methodology.
  • the PS4 variant polypeptides and/or nucleic acids are derived 655 or derivable from a "precursor" sequence.
  • the term "precursor” as used herein means an enzyme that precedes the enzyme which is modified according to the methods and compositions described here.
  • a precursor therefore includes an enzyme used to produce a modified enzyme.
  • the precursor may be an enzyme that is modified by mutagenesis as described elsewhere in this document.
  • the precursor may be a wild type 660 enzyme, a variant wild type enzyme or an already mutated enzyme.
  • the PS4 variant polypeptides and nucleic acids may be produced by any means known in the art. Specifically, they may be expressed from expression systems, which may be in vitro or in vivo in nature. Specifically, we describe plasmids and expression vectors comprising PS4 nucleic acid sequences, preferably capable of expressing PS4 665 variant polypeptides. Cells and host cells which comprise and are preferably transformed with such PS4 nucleic acids, plasmids and vectors are also disclosed, and it should be made clear that these are also encompassed in this document.
  • PS4 variant polypeptides may for example be made using site directed mutagenesis using PCR with appropriate oligonucleotide primers, 5' add-on mutagenesis,
  • PS4 variant polypeptides with mutations at positions 307 for example, a nucleic acid sequence corresponding to a pSac— pMD229 sequence; Pseudomonas saccharophila maltotetrahydrolase nucleotide sequence with 17 substitutions and deletion of the starch binding domain (SEQ ID NO: 14) may be made and the relevant changes introduced.
  • SEQ ID NO: 14 Pseudomonas saccharophila maltotetrahydrolase nucleotide sequence with 17 substitutions and deletion of the starch binding domain
  • the PS4 variant polypeptide sequence is used as a food additive in an isolated form.
  • isolated means that the sequence is at least 680 substantially free from at least one other component with which the sequence is naturally associated in nature and as found in nature, hi one aspect, preferably the sequence is in a purified form.
  • purified means that the sequence is in a relatively pure state - e.g. at least about 90% pure, or at least about 95% pure or at least about 98% pure.
  • the nucleic acid sequence comprises the 685 sequences shown in SEQ ID NO: 22, 24 or 26.
  • the reference sequence is derived from the Pseudomonas saccharophilia sequence having SWISS-PROT accession number P22963, but without the signal sequence
  • AAAGASTSGS F may optionally be deleted or disregarded. Alternatively, it may be included in the PS4 variant polypeptide sequence.
  • the numbering system is also applicable to all relevant homologous sequences.
  • the position numbering may be applied to homologous sequences from other Pseudomonas species, or homologous sequences from other bacteria.
  • such homologues have 60% or greater homology, for example 70% or more, 80% or more, 90% or more or 95% or more homology, with the reference sequence SEQ ID NO: 1 above, or the sequences having SWISS-PROT accession numbers P22963 or Pl 3507, preferably with all these sequences. Sequence homology between proteins may be ascertained using well known alignment programs and hybridisation techniques described herein.
  • PS4 Family Such homologous sequences, as well as the functional equivalents described below, will be referred to in this document as the "PS4 Family". Furthermore, and as noted above, the numbering system used hi this document makes reference to a reference sequence SEQ ID NO: 1, which is derived from the Pseudomonas saccharophilia sequence having SWISS-PROT accession number P22963, but without the signal sequence MSHILRAAVLAAVLLPFPALA. This signal sequence is
  • N terminal of the reference sequence located N terminal of the reference sequence and consists of 21 amino acid residues. Accordingly, it will be trivial to identify the particular residues to be mutated or substituted in corresponding sequences comprising the signal sequence, or indeed, corresponding sequences comprising any other N- or C- terminal extensions or deletions, hi relation to N- terminal additions or deletions, all that is required is to offset the position
  • position 1 in SEQ ID NO: 1 corresponds to position 22 in a sequence with the signal sequence.
  • the PS4 variant polypeptides are derived from, or are variants of, another sequence, known as a "parent enzyme", a "parent polypeptide” or a "parent sequence”.
  • parent enzyme as used in this document means the enzyme that has a close, preferably the closest, chemical structure to the resultant variant, i.e., the PS4 variant polypeptide or nucleic acid.
  • the parent enzyme may be a precursor enzyme (i.e. the enzyme that is actually mutated) or it may be prepared de novo.
  • the parent enzyme may be a wild type enzyme, or it may be a wild type enzyme comprising one or more
  • precursor means an enzyme that precedes the enzyme which is modified to produce the enzyme.
  • the precursor may be an enzyme that is modified by mutagenesis.
  • the precursor may be a wild type enzyme, a variant wild type enzyme or an already mutated enzyme.
  • wild type is a term of the art understood by skilled persons and means a phenotype that is characteristic of most of the members of a species occurring naturally and contrasting with the phenotype of a mutant.
  • the wild type enzyme is a form of the enzyme naturally found hi most members of the relevant species.
  • the relevant wild type enzyme in relation to the variant polypeptides described
  • the parent enzyme or polypeptide can be any suitable starting polypeptide. It may preferably have some enzymatic activity. Preferably, this enzymatic activity is an amylase activity. More preferably, the parent polypeptide comprises exoamylase activity.
  • the parent enzyme is preferably a polypeptide which preferably exhibits non- maltogenic exoamylase activity.
  • the parent enzyme is a non-maltogenic 765 exoamylase itself.
  • the parent enzyme may be a Pseudomonas saccharophila non-maltogenic exoamylase, such as a polypeptide having SWISS-PROT accession number P22963, or a Pseudomonas stutzeri non-maltogenic exoamylase, such as a polypeptide having SWISS-PROT accession number P13507.
  • PS4 770 family members will generally be similar to, homologous to, or functionally equivalent to either of these two enzymes, and may be identified by standard methods, such as hybridisation screening of a suitable library using probes, or by genome sequence analysis.
  • a “functional equivalent" of a protein means something that shares one or more, preferably substantially all, of the functions of that protein.
  • functions are biological functions, preferably enzymatic functions, such as amylase activity, preferably non-maltogenic exoamylase activity.
  • Such functions may include any property of the 780 protein, including exo-specificity, thermostability, and improved handling such as firmness, resilience, cohesiveness, crumbliness and foldability (as described below).
  • the term "functional equivalent” preferably means a molecule having similar or identical function to a parent molecule.
  • the parent molecule may be a Pseudomonas saccharophila non-maltogenic exoamylase or a Pseudomonas 785 stutzeri non-maltogenic exoamylase or a polypeptide obtained from other sources.
  • the term "functional equivalent" in relation to a parent enzyme being a Pseudomonas saccharophila non-maltogenic exoamylase, such as a polypeptide having SWISS-PROT accession number P22963, or a Pseudomonas stutzeri non-maltogenic exoamylase, such as a polypeptide having SWISS-PROT accession number P13507 means 790 that the functional equivalent could be obtained from other sources.
  • the functionally equivalent enzyme may have a different amino acid sequence but will have non- maltogenic exoamylase activity. Examples of assays to determine functionality are described herein and are known to one skilled in the art.
  • the functional equivalent may also have sequence homology with any of the sequences set out as SEQ ED NOs: 1 to 14, preferably SEQ ED NO: 1 or SEQ ED NO: 7 or both. Sequence homology between such sequences is preferably at least 60%, preferably 65% or more, preferably 75% or more,
  • sequence homologies may be generated by any of a number of computer programs known in the art, for example BLAST or FASTA, etc.
  • a suitable computer program for carrying out such an alignment is the GCG Wisconsin Bestfit package (University of Wisconsin, U. S. A; Devereux et al, 1984, Nucleic Acids Research
  • Examples of other software than can perform sequence comparisons include, but are not limited to, the BLAST package (see Ausubel et al., 1999 ibid- Chapter 18), FASTA (Atschul et al, 1990, J. MoI. Biol., 403-410) and the GENEWORKS suite of comparison tools. Both BLAST and FASTA are available for offline and online searching (see Ausubel et al., 1999 ibid, pages 7-58 to 7-60). However it is preferred to use the GCG
  • functional equivalents which have sequence homology to Pseudomonas saccharophila and Pseudomonas stutzeri non-maltogenic exoamylases are suitable for use as parent enzymes.
  • Such sequences may differ from the Pseudomonas 820 saccharophila sequence at any one or more positions.
  • non-maltogenic exoamylases from other strains of Pseudomonas spp, such as ATCC 17686 may also be used as a parent polypeptide.
  • the PS4 variant polypeptide residues may be inserted into any of these parent sequences to generate the variant PS4 polypeptide sequences.
  • PS4 variant polypeptides to 825 additionally comprise one or more mutations, as set out above, corresponding mutations may be made in the nucleic acid sequences of the functional equivalents of Pseudomonas spp non-maltogenic exoamylase, as well as other members of the "PS4 family", in order that they may be used as starting points or parent polypeptides for the generation of PS4 variant polypeptides as described here.
  • PS4 variant polypeptides are the polypeptides disclosed in: US 60/485,413, 60/485,539 and 60/485,616; PCT/US2004/021723 and PCT/US2004/021739; US 10/886,905 and 10/866,903; US 60/608,919; US 60/612,407; US 60/485,539; PCT/B2004/002487; US 10/886,023; US 10/886,505, US 10/886,527 and US 10/886,504; US 10/947,612.
  • polypeptides are suitable for use in the applications described herein, in particular, as food additives, to treat starch as described, to prepare a food product, to make a bakery product, for the formulation of improver compositions, for the formulation of combinations, etc.
  • the parent enzymes may be modified at the amino acid level or the nucleic acid level to generate the PS4 variant sequences described here. Therefore, we provide for the generation of PS4 variant polypeptides by introducing one or more corresponding codon changes in the nucleotide sequence encoding a non-maltogenic exoamylase polypeptide.
  • the nucleic acid numbering should preferably be with reference to the position numbering of a. Pseudomonas saccharophilia exoamylase nucleotide sequence shown as SEQ ID NO: 6. Alternatively, or in addition, reference may be made to the sequence with GenBank accession number Xl 6732. In preferred embodiments, the nucleic acid numbering should be with reference to the nucleotide sequence shown as SEQ ID NO: 6.
  • sequence changes can be made in any PS4 family nucleic acid sequence.
  • sequence changes can be made to a Pseudomonas saccharophila or a Pseudomonas stutzeri non-maltogenic exoamylase nucleic acid sequence (e.g., X16732, SEQ ID NO: 6
  • the parent en2yme may comprise the "complete" enzyme, i.e., in its entire length as it occurs in nature (or as mutated), or it may comprise a truncated form thereof.
  • the PS4 variant derived from such may accordingly be so truncated, or be "full-length".
  • the truncation may be at the N-te ⁇ ninal end, or the C-te ⁇ ninal end, preferably the C-terminal 860 end.
  • the parent enzyme or PS4 variant may lack one or more portions, such as subsequences, signal sequences, domains or moieties, whether active or not etc.
  • the parent enzyme or the PS4 variant polypeptide may lack a signal sequence, as described above.
  • the parent enzyme or the PS4 variant may lack one or more catalytic or binding domains.
  • the parent enzyme or PS4 variant may lack one or more of the domains present in non-maltogenic exoamylases, such as the starch binding domain.
  • the PS4 polypeptides may have only sequence up to position 429, relative to the numbering of a Pseudomonas saccharophilia non-maltogenic exoamylase shown as SEQ ID NO: 1. It is to be noted that this is the case for the PS4 variants pSac-
  • the parent enzyme or PS4 variant may comprise a e "complete" enzyme, i.e., in its entire length as it occurs in nature (or as mutated), together with one or more additional amino acid sequences at the N terminus or C terminus.
  • the parent enzyme or PS4 variant polypeptide may comprise a single extra amino 875 acid residue at the C terminus or N terminus, e.g., M, A, G, etc.
  • the additional amino acid residue is present at the N terminus. Where one or more additional residues is included, the position numbering will be offset by the length of the addition.
  • the PS4 variant polypeptides generally comprise amylase activity.
  • amylase is used in its normal sense - e.g. an enzyme that is inter alia capable of catalysing the degradation of starch.
  • hydrolases which are capable of cleaving ⁇ -D-(l— >4) O-glycosidic linkages in starch.
  • Amylases are starch-degrading enzymes, classified as hydrolases, which cleave ⁇ - D-(I ->4) O-glycosidic linkages in starch.
  • hydrolases cleave ⁇ - D-(I ->4) O-glycosidic linkages in starch.
  • ⁇ -amylases E.C. 3.2.1.1, ⁇ -D-
  • Amylases, ⁇ -glucosidases (E.C. 3.2.1.20, ⁇ -D-glucoside glucohydrolase), glucoamylase (E.C. 3.2.1.3, ⁇ -D-(l-)4)-glucan glucohydrolase), and product-specific amylases can produce malto-oligosaccharides of a specific length from starch.
  • the PS4 variant polypeptides described in this document are derived from (or 895 variants of) polypeptides which preferably exhibit non-maltogenic exoamylase activity.
  • these parent enzymes are non-maltogenic exoamylases themselves.
  • the PS4 variant polypeptides themselves in highly preferred embodiments also exhibit non- maltogenic exoamylase activity.
  • non-maltogenic exoamylase enzyme 900 as used in this document should be taken to mean that the enzyme does not initially degrade starch to substantial amounts of maltose as analysed in accordance with the product determination procedure as described in this document.
  • the non-maltogenic exoamylase comprises an exo-maltotetraohydrolase.
  • Exo-maltotetraohydrolase (E.C.3.2.1.60) is more formally 905 known as glucan 1,4-alpha-maltotetrahydrolase. This enzyme hydrolyses 1,4-alpha-D- glucosidic linkages in amylaceous polysaccharides so as to remove successive maltotetraose residues from the non-reducing chain ends.
  • Non-maltogenic exoamylases are described in detail in US Patent number 6,667,065, hereby incorporated by reference.
  • the following system is used to characterize polypeptides having non-maltogenic exoamylase activity which are suitable for use according to the methods and compositions described here.
  • This system may for example be used to characterise the PS4 parent or variant polypeptides described here.
  • waxy maize amylopectin (obtainable as
  • WAXILYS 200 from Roquette, France is a starch with a very high amylopectin content (above 90%). 20 mg/ml of waxy maize starch is boiled for 3 min. in a buffer of 50 mM MES (2-(N-mo ⁇ holino)ethanesulfonic acid), 2 mM calcium chloride, pH 6.0 and subsequently incubated at 50 0 C and used within half an hour.
  • MES 2-(N-mo ⁇ holino)ethanesulfonic acid
  • One unit of the non-maltogenic exoamylase is defined as the amount of enzyme which releases hydrolysis products equivalent to 1 ⁇ mol of reducing sugar per min. when incubated at 50 degrees C in a test tube with 4 ml of 10 mg/ml waxy maize starch in 50 mM MES, 2 mM calcium chloride, pH 6.0 prepared as described above.
  • Reducing sugars are measured using maltose as standard and using the dinitrosalicylic acid method of 925 Bernfeld, Methods Enzymol, (1954), /, 149-158 or another method known in the art for quantifying reducing sugars.
  • the hydrolysis product pattern of the non-maltogenic exoamylase is determined by incubating 0.7 units of non-maltogenic exoamylase for 15 or 300 min. at 5O 0 C in a test tube with 4 ml of 10 mg/ml waxy maize starch in the buffer prepared as described above. 930 The reaction is stopped by immersing the test tube for 3 min. in a boiling water bath.
  • the hydrolysis products are analyzed and quantified by anion exchange HPLC using a Dionex PA 100 column with sodium acetate, sodium hydroxide and water as eluents, with pulsed amperometric detection and with known linear maltooligosaccharides of from glucose to maltoheptaose as standards.
  • the response factor used for maltooctaose 935 to maltodecaose is the response factor found for maltoheptaose.
  • the PS4 variant polypeptides have non-maltogenic exoamylase activity such that if an amount of 0.7 units of said non-maltogenic exoamylase were to incubated for 15 minutes at a temperature of 50°C at pH 6.0 in 4 ml of an aqueous solution of 10 mg preboiled waxy maize starch per ml buffered solution containing 50 mM 2-(N-)
  • hydrolysis product(s) that would consist of one or more linear malto-oligosaccharides of from two to ten D-glucopyranosyl units and optionally glucose; such that at least 60%, preferably at least 70%, more preferably at least 80% and most preferably at least 85% by weight of the said hydrolysis products would consist of linear maltooligosaccharides of
  • the feature of incubating an amount of 0.7 units of the non-maltogenic exoamylase for 15 minutes at a temperature of 5O 0 C at pH 6.0 in 4 ml of an aqueous solution of 10 mg preboiled waxy maize starch per 950 ml buffered solution containing 50 mM 2-(N-mo ⁇ holino)ethane sulfonic acid and 2 mM calcium chloride may be referred to as the "Waxy Maize Starch Incubation Test".
  • PS4 variant polypeptides which are non- maltogenic exoamylases are characterised as having the ability in the waxy maize starch incubation test to yield hydrolysis product(s) that would consist of one or more linear 955 malto-oligosaccharides of from two to ten D-glucopyranosyl units and optionally glucose; such that at least 60%, preferably at least 70%, more preferably at least 80% and most preferably at least 85% by weight of the said hydrolysis product(s) would consist of linear maltooligosaccharides of from three to ten D-glucopyranosyl units, preferably of linear maltooligosaccharides consisting of from four to eight D-glucopyranosyl units.
  • the hydrolysis products in the waxy maize starch incubation test may include one or more linear malto-oligosaccharides of from two to ten D-glucopyranosyl units and optionally glucose.
  • the hydrolysis products in the waxy maize starch incubation test may also include other hydrolytic products. Nevertheless, the % weight amounts of linear maltooligosaccharides of from three to ten D-glucopyranosyl units are based on the
  • the hydrolysis product that consists of one or more linear maltooligosaccharides of from two to ten D-glucopyranosyl units and optionally glucose.
  • the % weight amounts of linear maltooligosaccharides of from three to ten D- glucopyranosyl units are not based on the amount of hydrolysis products other than one or more linear malto-oligosaccharides of from two to ten D-glucopyranosyl units and
  • the hydrolysis products can be analysed by any suitable means.
  • the hydrolysis products may be analysed by anion exchange HPLC using a Dionex PA 100 column with pulsed amperometric detection and with, for example, known linear maltooligosaccharides of from glucose to maltoheptaose as standards.
  • a preferred PS4 variant polypeptide is one which has non-maltogenic exoamylase such that it has the ability in a waxy maize starch incubation test to yield hydrolysis product(s) that would consist of one or more linear maltooligosaccharides of from two to ten D-glucopyranosyl units and optionally glucose, said 985 hydrolysis products being capable of being analysed by anion exchange; such that at least 60%, preferably at least 70%, more preferably at least 80% and most preferably at least 85% by weight of the said hydrolysis product(s) would consist of linear maltooligosaccharides of from three to ten D-glucopyranosyl units, preferably of linear maltooligosaccharides consisting of from four to eight D-glucopyranosyl units.
  • the term "linear malto-oligosaccharide" is used in the normal sense as meaning 2-10 units of ⁇ -D-glucopyranose linked by an
  • the PS4 polypeptides described here have improved exoamylase activity, preferably non-maltogenic exoamylase activity, when compared to the parent polypeptide, preferably when tested under the same conditions.
  • the PS4 variant polypeptides have 10% or more, preferably 20% or more, preferably 50% or more, exoamylase activity compared to their parents, preferably when measured in a waxy maize starch test.
  • the hydrolysis products can be analysed by any suitable means.
  • the hydrolysis products may be analysed by anion exchange HPLC using a Dionex PA 100 1000 column with pulsed amperometric detection and with, for example, known linear maltooligosaccharides of from glucose to maltoheptaose as standards.
  • linear malto-oligosaccharide is used in the normal sense as meaning 2-20 units of ⁇ -D-glucopyranose linked by an ⁇ -(l->4) bond.
  • the PS4 variants described here preferably have improved properties when compared to their parent enzymes, such as any one or more of improved thermostability, improved pH stability, or improved exo-specificity.
  • the PS4 variants described here preferably also have improved handling properties, such that a food product treated with a the PS4 variant polypeptide has any one or all of lower firmness, higher resilience, higher
  • the PS4 variant polypeptide is thermostable; preferably, it has higher thermostability than its parent enzyme.
  • amylopectin In wheat and other cereals the external side chains in amylopectin are in the range of DP 12-19. Thus, enzymatic hydrolysis of the amylopectin side chains, for example, by 1020 PS4 variant polypeptides as described having non-maltogenic exoamylase activity, can markedly reduce their crystallisation tendencies.
  • Starch in wheat and other cereals used for baking purposes is present in the form of starch granules which generally are resistant to enzymatic attack by amylases.
  • starch modification is mainly limited to damaged starch and is progressing very slowly during
  • PS4 variant polypeptides as described here when added to the starch at any stage of its processing into a food product, e.g., before during or after baking into bread can retard or impede or slow down the retrogradation. Such use is described in further detail below.
  • thermoostable relates to the ability of the enzyme to retain activity after exposure to elevated temperatures.
  • the PS4 variant polypeptide is capable of degrading starch at temperatures of from about 55 0 C to about 8O 0 C or more.
  • the enzyme retains its activity after exposure to temperatures of up to about 95 0 C.
  • thermostability of an enzyme such as a non-maltogenic exoamylase is measured by its half life.
  • the PS4 variant polypeptides described here have half lives extended relative to the parent enzyme by preferably 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or more, preferably at elevated temperatures of from 55 0 C to about 95 0 C or more, preferably at about 8O 0 C.
  • the half life is the time (in minutes) during which half the enzyme activity is inactivated under defined heat conditions, hi preferred embodiments, the half life is assayed at 80 degrees C. Preferably, the sample is heated for 1-10 minutes at 8O 0 C or higher. The half life value is then calculated by measuring the residual amylase activity, by any of the methods described here. Preferably, a half life assay is conducted as
  • the PS4 variants described here are active during baking and hydrolyse starch during and after the gelatinization of the starch granules which starts at tempera- tures of about 55 0 C.
  • enzyme inactivation can take place. If this happens, the non-maltogenic exoamylase may be gradually inactivated so that there is substantially no activity after the baking process in the final bread. Therefore preferentially the non-maltogenic exoamylases suitable for use as described have an optimum temperature above 5O 0 C and below 98°C.
  • thermostability of the PS4 variants described here can be improved by using protein engineering to become more thermostable and thus better suited for the uses described here; we therefore encompass the use of PS4 variants modified to become more thermostable by protein engineering.
  • the PS4 variant polypeptide is pH stable; more preferably, it has a 1065 higher pH stability than its cognate parent polypeptide.
  • pH stable relates to the ability of the enzyme to retain activity over a wide range of pHs.
  • the PS4 variant polypeptide is capable of degrading starch at a pH of from about 5 to about 10.5.
  • the degree of pH stability may be assayed by measuring the half life of the enzyme in specific pH conditions.
  • 1070 the degree of pH stability may be assayed by measuring the activity or specific activity of the enzyme in specific pH conditions.
  • the specific pH conditions may be any pH from pH5 to pH10.5.
  • the PS4 variant polypeptide may have a longer half life, or a higher activity (depending on the assay) when compared to the parent polypeptide under identical 1075 conditions.
  • the PS4 variant polypeptides may have 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or longer half life when compared to their parent polypeptides under identical pH conditions. Alternatively, or in addition, they may have such higher activity when compared to the parent polypeptide under identical pH conditions.
  • Exo-specificity can usefully be measured by determining the ratio of total amylase activity to the total endoamylase activity. This ratio is referred to in this document as a "Exo-specificity index".
  • an enzyme is considered an exoamylase if it has a exo-specificity index of 20 or more, i.e., its total amylase activity 1090 (including exo-amylase activity) is 20 times or more greater than its endoamylase activity.
  • the exo-specificity index of exoamylases is 30 or more, 40 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, or 100 or more.
  • the exo-specificity index is 150 or more, 200 or more, 300 or more, 400 or more, 500 or more or 600 or more.
  • the total amylase activity and the endoamylase activity may be measured by any means known in the art.
  • the total amylase activity may be measured by assaying the total number of reducing ends released from a starch substrate.
  • Betamyl assay is described in further detail in the Examples, and for convenience, amylase activity as assayed in the Examples is described in terms of
  • Endoamylase activity may be assayed by use of a Phadebas Kit (Pharmacia and Upjohn). This makes use of a blue labelled crosslinked starch (labelled with an azo dye); only internal cuts in the starch molecule release label, while external cuts do not do so. Release of dye may be measured by spectrophotometry. Accordingly, the Phadebas Kit 1105 measures endoamylase activity, and for convenience, the results of such an assay (described in the Examples) are referred to in this document as "Phadebas units".
  • the exo-specificity index is expressed in terms of Betamyl Units / Phadebas Units, also referred to as "B/Phad".
  • Exo-specificity may also be assayed according to the methods described in the 1110 prior art, for example, in our International Patent Publication Number WO99/50399. This measures exo-specificity by way of a ratio between the endoamylase activity to the exoamylase activity.
  • the PS4 variants described here will have less than 0.5 endoamylase units (EAU) per unit of exoamylase activity.
  • the non-maltogenic exoamylases which are suitable for use according to the present invention 1115 have less than 0.05 EAU per unit of exoamylase activity and more preferably less than 0.01 EAU per unit of exoamylase activity.
  • the PS4 variants described here will preferably have exospecificity, for example measured by exo-specificity indices, as described above, consistent with their being exoamylases. Moreoever, they preferably have higher or increased exospecificity when 1120 compared to the parent enzymes or polypeptides from which they are derived.
  • the PS4 variant polypeptides may have 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or higher exo-specificity index when compared to their parent polypeptides, preferably under identical conditions. They may have 1.5x or higher, 2x or higher, 5 x or higher, 10 x or higher, 50 x or higher, 100 x or higher, when compared to
  • the PS4 variants described here preferably comprise one or more improved handling properties compared to a parent polypeptide or a wild type polypeptide.
  • the improved handling properties may in preferred embodiments comprise improved baking 1130 properties.
  • the PS4 variants are such that a food product treated with the PS4 variant polypeptide an improved handling or preferably baking property compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • the handling or baking property may be selected from the group consisting of: firmness, 1135 resilience, cohesiveness, crumbliness and foldability.
  • handling properties may be tested by any means known in the art. For example, firmness, resilience and cohesiveness may be determined by analysing bread slices by Texture Profile Analysis using for example a Texture Analyser, as described in the Examples.
  • the PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide lower firmness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • the firmness is in preferred embodiments inversely correlated with the softness of 1145 the food product; thus, a higher softness may reflect a lower firmness, and vice versa.
  • the PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide has a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 1150 80%, 90%, 100%, 200% or more lower firmness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • a food product treated with the PS4 variant polypeptide may have a l.lx, 1.5x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 1Ox or more lower firmness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • the PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide higher resilience compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • Resilience is preferably measured by the "Resilience Evaluation Protocol" set out 1160 in Example 14.
  • the PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide has a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or more higher resilience compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • a food product treated 1165 with the PS4 variant polypeptide may have a l.lx, 1.5x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 10x or more higher resilience compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • the PS4 variants described here are preferably such that a food product treated 1170 with the PS4 variant polypeptide higher cohesiveness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • Cohesiveness is preferably measured by the "Cohesiveness Evaluation Protocol" set out in Example 15.
  • the PS4 variants described here are preferably such that a food product 1175 treated with the PS4 variant polypeptide has a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or more higher cohesiveness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • a food product treated with the PS4 variant polypeptide may have a 1. Ix, 1.5x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 10x or more higher cohesiveness compared to a food product which has been treated 1180 with a parent polypeptide or a wild type polypeptide.
  • the PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide lower crumbliness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • 1185 Crumbliness is preferably measured by the "Crumbliness Evaluation Protocol" set out in Example 16.
  • the PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide has a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or more lower crumbliness compared to a food product which has 1190 been treated with a parent polypeptide or a wild type polypeptide.
  • a food product treated with the PS4 variant polypeptide may have a l.lx, 1.5x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 10x or more lower crumbliness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • the PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide higher foldability compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • Foldability is preferably measured by the "Foldability Evaluation Protocol" set out in Example 17.
  • the PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide has a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or more higher foldability compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
  • a food product treated with the PS4 variant polypeptide may have a l.lx, 1.5x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 10x
  • ThePS4 variant polypeptides, nucleic acids, host cells, expression vectors, etc, may be used in any application for which an amylase may be used. In particular, they may be used to substitute for any non-maltogenic exoamylase. They may be used to supplement amylase or non-maltogenic exoamylase activity, whether alone or in combination with other known amylases or non-maltogenic exoamylases.
  • PS4 variant sequences described here may be used in various applications in the food industry - such as in bakery and drink products, they may also be used in other applications such as a pharmaceutical composition, or even in the chemical industry.
  • the PS4 variant polypeptides and nucleic acids are useful for various industrial applications including baking (as disclosed in WO 99/50399) and flour standardisation
  • volume enhancement or improvement They may be used to produce maltotetraose from starch and other substrates.
  • a method for preparing a food product comprising: (a) obtaining a non-maltogenic exoamylase; (b) introducing a mutation at any one or more of the positions of the non-maltogenic exoamylase as set out in this 1225 document; (c) admixing the resulting polypeptide with a food ingredient.
  • the PS4 variant polypeptides may be used to enhance the volume of bakery products such as bread. While not wishing to be bound by any particular theory, we believe that this results from the reduction in viscosity of the dough during heating (such as baking) as a result of the exoamylase shortening amylose molecules. This enables the 1230 carbon dioxide generated by fermentation to increase the size of the bread with less hindrance.
  • food products comprising or treated with PS4 variant polypeptides are expanded in volume when compared to products which have not been so treated, or treated with parent polypeptides.
  • the food products have a larger volume of air per
  • the food products treated with PS4 variant polypeptides have a lower density, or weight (or mass) per volume ratio.
  • the PS4 variant polypeptides are used to enhance the volume of bread. Volume enhancement or expansion is beneficial because it reduces the gumminess or starchiness of foods. Light foods are preferred by consumers, and the
  • PS4 variant polypeptides enhances the volume by 10%, 20%, 30% 40%, 50% or more.
  • the PS4 variant polypeptides and nucleic acids described here may be used as — or in the preparation of - a food. In particular, they may be added to a food, i.e., as a food additive.
  • the term "food” is intended to include both prepared food, as well as an ingredient for a food, such as a flour. In a preferred aspect, the food is for human consumption.
  • the food may be in the from of a solution or as a solid - depending on the
  • the PS4 variant polypeptides and nucleic acids may be used as a food ingredient.
  • the term "food ingredient” includes a formulation, which is or can be added to functional foods or foodstuffs and includes formulations which can be used at low levels in a wide variety of products that require, for example, acidifying or emulsifying.
  • the food 1255 ingredient may be in the from of a solution or as a solid - depending on the use and/or the mode of application and/or the mode of administration.
  • the PS4 variant polypeptides and nucleic acids disclosed here may be - or may be added to - food supplements.
  • the PS4 variant polypeptides and nucleic acids disclosed here may be - or may be added to - functional foods.
  • the term "functional 1260 food” means food which is capable of providing not only a nutritional effect and/or a taste satisfaction, but is also capable of delivering a further beneficial effect to consumer. Although there is no legal definition of a functional food, most of the parties with an interest in this area agree that they are foods marketed as having specific health effects.
  • the PS4 variant polypeptides may also be used in the manufacture of a food 1265 product or a foodstuff.
  • Typical foodstuffs include dairy products, meat products, poultry products, fish products and dough products.
  • the dough product may be any processed dough product, including fried, deep fried, roasted, baked, steamed and boiled doughs, such as steamed bread and rice cakes.
  • the food product is a bakery product.
  • the foodstuff is a bakery product.
  • Typical bakery (baked) products include bread - such as loaves, rolls, buns, pizza bases etc. pastry, pretzels, tortillas, cakes, cookies, biscuits, krackers etc.
  • the food products preferably benefit from one or more of the improved handling or baking properties of the PS4 variant polypeptides described here.
  • the improved 1275 handling or baking property may be selected from the group consisting of: improved firmness, improved resilience, improved cohesiveness, improved crumbliness and improved foldability.
  • PS4 variant proteins that are capable of retarding the staling 1285 of starch media, such as starch gels.
  • the PS4 variant polypeptides are especially capable of retarding the detrimental retrogradation of starch.
  • starch granules are composed of a mixture of two polymers: an essentially linear amylose and a highly branched amylopectin.
  • Amylopectin is a very large, branched molecule consisting of chains of ⁇ -D-glucopyranosyl units joined by (1-4) linkages, 1290 wherein said chains are attached by ⁇ -D-(l-6) linkages to form branches.
  • Amylopectin is present in all natural starches, constituting about 75% of most common starches.
  • Amylose is essentially a linear chain of (1-4) linked ⁇ -D-glucopyranosyl units having few ⁇ -D-(l- 6) branches. Most starches contain about 25% amylose.
  • Gelatinization temperatures vary for different starches. Upon cooling of freshly baked bread the amylose fraction, within hours, retrogrades to develop a network. This process is beneficial in that it creates a desirable crumb structure with a low degree of firmness and improved slicing properties. More gradually crystallisation of amylopectin takes place 1300 within the gelatinised starch granules during the days after baking. In this process amylopectin is believed to reinforce the amylose network in which the starch granules are embedded. This reinforcement leads to increased firmness of the bread crumb. This reinforcement is one of the main causes of bread staling.
  • PS4 variant polypeptides as described here when added to the starch at any stage of its processing into a food product, e.g., before during or after 1315 baking into bread can retard or impede or slow down the retrogradation. Such use is described in further detail below.
  • the crumb firmness can be measured 1, 3 and 7 days after baking by means of an Instron 4301 Universal Food Texture Analyzer or 1325 similar equipment known in the art.
  • Another method used traditionally in the art and which is used to evaluate the effect on starch retrogradation of a PS4 variant polypeptide having non-maltogenic exoamylase activity is based on DSC (differential scanning calorimetry).
  • DSC differential scanning calorimetry
  • the melting enthalpy of retrograded amylopectin in bread crumb or crumb from a model system dough 1330 baked with or without enzymes (control) is measured.
  • the DSC equipment applied in the described examples is a Mettler-Toledo DSC 820 run with a temperature gradient of 10°C per min. from 20 to 95°C.
  • For preparation of the samples 10-20 mg of crumb are weighed and transferred into Mettler-Toledo aluminiurn pans which then are hermetically sealed.
  • the model system doughs used in the described examples contain standard wheat 1335 flour and optimal amounts of water or buffer with or without the non-maltogenic PS4 variant exoamylase. They are mixed in a 10 or 50 g Brabender Farinograph for 6 or 7 min., respectively. Samples of the doughs are placed in glass test tubes (15*0.8 cm) with a lid. These test tubes are subjected to a baking process in a water bath starting with 30 min. incubation at 33 0 C followed by heating from 33 to 95°C with a gradient of 1.1 0 C per min. 1340 and finally a 5 min. incubation at 95 0 C. Subsequently, the tubes are stored in a thermostat at 2O 0 C prior to DSC analysis.
  • the PS4 variants described here have a reduced melting enthalpy, compared to the control.
  • the PS4 variants have a 10% or more reduced melting enthalpy.
  • they have a 20% or more, 30%, 1345 40%, 50%, 60%, 70%, 80%, 90% or more reduced melting enthalpy when compared to the control.
  • the method comprises forming the starch product 1350 by adding a non-maltogenic exoamylase enzyme such as a PS4 variant polypeptide, to a starch medium. If the starch medium is a dough, then the dough is prepared by mixing together flour, water, the non-maltogenic exoamylase which is a PS4 variant polypeptide and optionally other possible ingredients and additives.
  • a non-maltogenic exoamylase enzyme such as a PS4 variant polypeptide
  • starch should be taken to mean starchier se or a component thereof, 1355 especially amylopectin.
  • starch medium means any suitable medium comprising starch.
  • starch product means any product that contains or is based on or is derived from starch.
  • starch product contains or is based on or is derived from starch obtained from wheat flour.
  • flag as used herein is a synonym for the finely-ground meal of wheat or other grain.
  • the term 1360 means flour obtained from wheat per se and not from another grain.
  • references to "wheat flour” as used herein preferably mean references to wheat flour per se as well as to wheat flour when present hi a medium, such as a dough.
  • a preferred flour is wheat flour or rye flour or mixtures of wheat and rye flour.
  • dough comprising flour derived from other types of cereals such as for example from rice, maize, barley, and durra are also contemplated.
  • the starch product is a bakery product. More preferably, the starch product is a bread product. Even more preferably, the starch product is a baked farinaceous bread product.
  • the term "baked farinaceous bread product" refers to any baked product based on a dough obtainable by
  • the process comprises mixing - in any suitable order - flour, water, and a leavening agent under dough forming conditions and further adding a PS4 variant polypeptide, optionally in the form of 1375 a premix.
  • the leavening agent may be a chemical leavening agent such as sodium bicarbonate or any strain of Saccharomyces cerevisiae (Baker's Yeast).
  • the PS4 variant non-maltogenic exoamylase can be added together with any dough ingredient including the water or dough ingredient mixture or with any additive or additive mixture.
  • the dough can be prepared by any conventional dough preparation method 1380 common in the baking industry or in any other industry making flour dough based products.
  • Baking of farinaceous bread products such as for example white bread, bread made from bolted rye flour and wheat flour, rolls and the like is typically accomplished by baking the bread dough at oven temperatures in the range of from 180 to 25O 0 C for about 1385 15 to 60 minutes.
  • a steep temperature gradient 200 -> 12O 0 C
  • the temperature in the crumb is only close to 100°C at the end of the baking process.
  • the non-maltogenic exoamylase PS4 variant polypeptide can be added as a liquid 1395 preparation or as a dry pulverulent composition either comprising the enzyme as the sole active component or in admixture with one or more additional dough ingredient or dough additive.
  • improver compositions which include bread improving compositions 1400 and dough improving compositions. These comprise a PS4 variant polypeptide, optionally together with a further ingredient, or a further enzyme, or both.
  • a dough may be prepared by admixing flour, water, a dough improving composition comprising PS4 variant polypeptide (as described above) and optionally other 1410 ingredients and additives.
  • the dough improving composition can be added together with any dough ingredient including the flour, water or optional other ingredients or additives.
  • the dough improving composition can be added before the flour or water or optional other ingredients and additives.
  • the dough improving composition can be added after the flour 1415 or water, or optional other ingredients and additives.
  • the dough can be prepared by any conventional dough preparation method common in the baking industry or in any other industry making flour dough based products.
  • the dough improving composition can be added as a liquid preparation or in the form of a dry powder composition either comprising the composition as the sole active 1420 component or in admixture with one or more other dough ingredients or additive.
  • the amount of the PS4 variant polypeptide non-maltogenic exoamylase that is added is normally in an amount which results in the presence in the finished dough of 50 to 100,000 units per kg of flour, preferably 100 to 50,000 units per kg of flour. Preferably, the amount is in the range of 200 to 20,000 units per kg of flour.
  • the PS4 1425 variant polypeptide non-maltogenic exoamylase is added in an amount which results in the presence in the finished dough of 0.02 - 50 ppm of enzyme based on flour (0.02 - 50 mg enzyme per kg of flour), preferably 0.2 - 10 ppm.
  • 1 unit of the non-maltogenic exoamylase is defined as the amount of enzyme which releases hydrolysis products equivalent to 1 ⁇ mol of reducing 1430 sugar per min. when incubated at 50 degrees C in a test tube with 4 ml of 10 mg/ml waxy maize starch in 50 mM MES, 2 mM calcium chloride, pH 6.0 as described hereinafter.
  • the dough as described here generally comprises wheat meal or wheat flour and/or other types of meal, flour or starch such as corn flour, corn starch, maize flour, rice flour, rye meal, rye flour, oat flour, oat meal, soy flour, sorghum meal, sorghum flour, potato 1435 meal, potato flour or potato starch.
  • the dough may be fresh, frozen, or part-baked.
  • the dough may be a leavened dough or a dough to be subjected to leavening.
  • the dough may be leavened in various ways, such as by adding chemical leavening agents, e.g., sodium bicarbonate or by adding a leaven (fermenting dough), but it is preferred to leaven the dough by adding a suitable yeast culture, such as a culture of Saccharomyces 1440 cerevisiae (baker's yeast), e.g. a commercially available strain of S. cerevisiae.
  • the dough may comprise fat such as granulated fat or shortening.
  • the dough may further comprise a further emulsifier such as mono- or diglycerides, sugar esters of fatty acids, polyglycerol esters of fatty acids, lactic acid esters of monoglycerides, acetic acid esters of monoglycerides, polyoxethylene stearates, or lysolecithin.
  • the pre-mix may contain other dough-improving and/or bread- improving additives, e.g. any of the additives, including enzymes, mentioned herein.
  • dough ingredients and/or dough additives may be incorporated into the dough.
  • further added components may include dough ingredients such as salt, grains, fats and oils, sugar or sweeteber, dietary fibres, protein sources such as milk powder, gluten soy or eggs and dough additives such as emulsifiers, other enzymes, hydrocolloids, flavouring agents, oxidising agents, minerals 1455 and vitamins
  • the emulsifiers are useful as dough strengtheners and crumb softeners.
  • dough strengtheners the emulsifiers can provide tolerance with regard to resting time and tolerance to shock during the proofing.
  • dough strengtheners will improve the tolerance of a given dough to variations in the fermentation time.
  • Most dough 1460 strengtheners also improve on the oven spring which means the increase in volume from the proofed to the baked goods.
  • dough strengtheners will emulsify any fats present in the recipe mixture.
  • Suitable emulsifiers include lecithin, polyoxyethylene stearat, mono- and diglycerides of edible fatty acids, acetic acid esters of mono- and diglycerides of edible 1465 fatty acids, lactic acid esters of mono- and diglycerides of edible fatty acids, citric acid esters of mono- and diglycerides of edible fatty acids, diacetyl tartaric acid esters of mono- and diglycerides of edible fatty acids, sucrose esters of edible fatty acids, sodium stearoyl- 2-lactylate, and calcium stearoyl-2-lactylate.
  • the further dough additive or ingredient can be added together with any dough 1470 ingredient including the flour, water or optional other ingredients or additives, or the dough improving composition.
  • the further dough additive or ingredient can be added before the flour, water, optional other ingredients and additives or the dough improving composition.
  • the further dough additive or ingredient can be added after the flour, water, optional other ingredients and additives or the dough improving composition.
  • the further dough additive or ingredient may conveniently be a liquid preparation.
  • the further dough additive or ingredient may be conveniently in the form of a dry composition.
  • the further dough additive or ingredient is at least 1% the weight of the flour component of dough. More preferably, the further dough additive or ingredient is at 1480 least 2%, preferably at least 3%, preferably at least 4%, preferably at least 5%, preferably at least 6%. If the additive is a fat, then typically the fat may be present in an amount of from 1 to 5%, typically 1 to 3%, more typically about 2%.
  • One or more further enzymes may be used in combination with the PS4 variant 1485 polypeptides. Such combinations may for example added to the food, dough preparation, foodstuff or starch composition.
  • the further enzymes may be selected from, for example, any combination of the following: (a) Novamyl, or a variant, homologue, or mutants thereof which have maltogenic alpha-amylase activity; (b) a xylanase such as GRIND AMYLTM POWERBake 1490 900 (Danisco A/S); (c) a bacterial ⁇ -amylase such as Max-Life U4 (Danisco A/S); and (d) a lipase such as GRIND AMYLTM POWERBake 4050 (Danisco A/S).
  • a PS4 variant polypeptide according to the invention is used in combination with at least one enzyme selected from the list consisting of oxidoreductases, hydrolases, lipases, esterases, glycosidases, amylases, pullulanases, xylanases, cellulases, 1495 hemicellulases, starch degrading enzymes, proteases and lipoxygenases.
  • the composition comprises at least one PS4 variant and a maltogenic amylase from Bacillus, as disclosed in WO91/04669.
  • a preferred embodiment comprises a PS4 variant and flour.
  • oxidoreductases 1500 hydrolases, such as lipases and esterases as well as glycosidases like ⁇ -amylase, pullulanase, and xylanase.
  • Oxidoreductases such as for example glucose oxidase and hexose oxidase, can be used for dough strengthening and control of volume of the baked products and xylanases and other hemicellulases may be added to improve dough handling properties, crumb firmness and bread volume.
  • Lipases are useful as dough strengtheners 1505 and crumb softeners and ⁇ -amylases and other amylolytic enzymes may be incorporated into the dough to control bread volume and further reduce crumb firmness.
  • Further enzymes may be selected from the group consisting of a cellulase, a hemicellulase, a starch degrading enzyme, a protease, a lipoxygenase.
  • oxidises sush as maltose oxidising 1510 enzyme a glucose oxidase (EC 1.1.3.4), carbohydrate oxidase, glycerol oxidase, pyranose oxidase, galactose oxidase (EC 1.1.3.10) and hexose oxidase (EC 1.1.3.5). These enzymes can be used for dough strengthening and control of volume of the baked products.
  • amylases are particularly useful as dough improving additives
  • ⁇ -amylase breaks downs starch into dextrins which are further
  • amylases include maltogenic alpha-amylase also called glucan 1 ,4- ⁇ -maltohydrolase (EC 3.2.1.133) from Bacillus stearothermophilus (such as NovamylTM (Novozymes)), ⁇ -amylase (EC 3.2.1.1) from Bacillus amyloliqufaciens (such as Max Life U4 (Danisco AJS)), B. flavothermus amylase (US 2005004861 IAl), Fungal amylase variants with insertions of alpha-amylase (EC 3.2.1.133) from Bacillus stearothermophilus (such as NovamylTM (Novozymes)), ⁇ -amylase (EC 3.2.1.1) from Bacillus amyloliqufaciens (such as Max Life U4 (Danisco AJS)), B. flavothermus amylase (US 2005004861 IAl), Fungal amylase variants with insertions of alpha-amylase (EC 3.
  • a PS4 variant polypeptide may be combined with amylases, in particular, maltogenic amylases.
  • Maltogenic alpha-amylase glucan 1,4-a-maltohydrolase, E.C. 3.2.1.133
  • E.C. 3.2.1.133 is able to
  • starch degrading enzymes which may be added to a dough composition include glucoamylases and pullulanases.
  • the further enzyme is at least a xylanase and/or at least an amylase.
  • xylanase refers to xylanases (EC 3.2.1.32) which hydrolyse
  • xylosidic linkages 1530 xylosidic linkages.
  • a lipase may also be added.
  • suitable xylanases include bakery xylanases (EC 3.2.1.8) from e.g. Bacillus sp., Aspergillus sp., Thermomyces sp. or Trichoderma sp. (such as GRIND AMYLTM POWERBake 900 (Danisco AZS)) and xylanases pertaining to Family 10 or 11 e.g. from Thermomyces lanoginosus (previously called Humicola insolens), Aspergillus aculeatus (WO 94/21785), Bacillus halodurans
  • amylase refers to amylases such as ⁇ -amylases (EC 3.2.1.1), ⁇ -amylases (EC 3.2.1.2) and ⁇ -amylases (EC 3.2.1.3).
  • the further enzyme can be added together with any dough ingredient including the 1540 flour, water or optional other ingredients or additives, or the dough improving composition.
  • the further enzyme can be added before the flour, water, and optionally other ingredients and additives or the dough improving composition.
  • the further enzyme can be added after the flour, water, and optionally other ingredients and additives or the dough improving composition.
  • the further enzyme may conveniently be a liquid 1545 preparation. However, the composition may be conveniently in the form of a dry composition.
  • Some enzymes of the dough improving composition are capable of interacting with each other under the dough conditions to an extent where the effect on improvement of the rheological and/or machineability properties of a flour dough and/or the quality of the 1550 product made from dough by the enzymes is not only additive, but the effect is synergistic.
  • the further enzyme may be a lipase (EC 3.1.1) capable of hydrolysing carboxylic ester bonds to release carboxylate.
  • lipases include but are not limited to triacylglycerol lipase (EC 3.1.1.3), galactolipase (EC 3.1.1.26), phospholipase Al (EC 3.1.1.32, phospholipase A2 (EC 3.1.1.4) and lipoprotein lipase A2 (EC 3.1.1.34). More specifically, suitable lipases include lipases from Mucor miehei, F. venenatwn, H.
  • the PS4 variants are suitable for the production of maltose and high maltose 1565 syrups. Such products are of considerable interest in the production of certain confectioneries because of the low hygroscoposity, low viscosity, good heat stability and mild, not too sweet taste of maltose.
  • the industrial process of producing maltose syrups comprises liquefying starch, then saccharification with a maltose producing enzyme, and optionally with an enzyme cleaving the 1.6- branching points in amylopectin, for instance 1570 an .alpha.- 1.6- amyloglucosidase.
  • the PS4 variants described here may be added to and thus become a component of a detergent composition.
  • the detergent composition may for example be formulated as a hand or machine laundry detergent composition including a laundry additive composition suitable for pre-treatment of stained fabrics and a rinse added fabric softener composition,
  • a detergent additive comprising the PS4 variant.
  • the detergent additive as well as the detergent composition may comprise one or more other enzymes such as a protease, a lipase, a cutinase, an amylase, a carbohydrase, a cellulase, a
  • pectinase 1580 pectinase, a mannanase, an arabinase, a galactanase, a xylanase, an oxidase, e.g., a laccase, and/or a peroxidase.
  • the properties of the chosen enzyme(s) should be compatible with the selected detergent, (i.e., pH-optimum, compatibility with other enzymatic and non-enzymatic ingredients, etc.), and the enzyme(s) should be present in effective amounts.
  • the PS4 variant may also be used in the production of lignocellulosic materials, such as pulp, paper and cardboard, from starch reinforced waste paper and cardboard, especially where repulping occurs at pH above 7 and where amylases can facilitate the disintegration of the waste material through degradation of the reinforcing starch.
  • the PS4 variants may especially be useful in a process for producing a papermaking pulp from
  • the process may be performed as described in WO 95/14807, comprising the following steps: a) disintegrating the paper to produce a pulp, b) treating , with a starch-degrading enzyme before, during or after step a), and c) separating ink part ⁇ cles from the pulp after steps a) and b).
  • the PS4 variant may also be very useful in modifying starch where enzymatically modified starch is used in papermaking together
  • a PS4 variant may also be very useful in textile desizing.
  • amylases are traditionally used as auxiliaries in the desizing process to facilitate the removal of starch-containing size which has served as
  • the PS4 variant may be used alone or in combination with a cellulase when desizing cellulose-containing fabric 1605 or textile.
  • the PS4 variant may also be an amylase of choice for production of sweeteners from starch
  • a "traditional" process for conversion of starch to fructose syrups normally consists of three consecutive enzymatic processes, viz., a liquefaction process followed by a saccharif ⁇ cation process and an isomerization process. During the liquefaction process,
  • 1610 starch is degraded to dextrins by an amylase at pH values between 5.5 and 6.2 and at temperatures of 95-160° C. for a period of approx. 2 hours.
  • 1 mM of calcium is added (40 ppm free calcium ions).
  • the dextrins are converted into dextrose by addition of a glucoamylase and a debranching enzyme, such as an isoamylase or a pullulanase .
  • the pH is reduced to a value below 4.5, maintaining the high temperature (above 95° C), and the liquefying .amylase activity is denatured.
  • the temperature is lowered to 60° C, and glucoamylase and debranching enzyme are added.
  • the saccharif ⁇ cation process proceeds for 24-72 hours.
  • the ⁇ -amylase variants discussed herein can be formulated in detergent compositions for use in cleaning dishes or other cleaning compositions, for example. These can be gels, powders or liquids.
  • the compositions can comprise the ⁇ -amylase variant alone, other amylolytic enzymes, other cleaning enzymes, and other components 1625 common to cleaning compositions.
  • a dishwashing detergent composition can comprise a surfactant.
  • the surfactant may be anionic, non-ionic, cationic, amphoteric or a mixture of these types.
  • the detergent can contain 0% to about 90% by weight of a non-ionic surfactant, such as low- to non-foaming ethoxylated propoxylated straight-chain alcohols.
  • ⁇ -amylase variants are usually used in a liquid composition containing propylene glycol.
  • the ⁇ -amylase variant can be solubilized in propylene glycol, for example, by circulating in a 25% volume/volume propylene glycol solution containing 10% calcium chloride.
  • the dishwashing detergent composition may contain detergent builder salts of 1635 inorganic and/or organic types.
  • the detergent builders may be subdivided into phosphorus-containing and non-phosphorus-containing types.
  • the detergent composition usually contains about 1% to about 90% of detergent builders.
  • Examples of phosphorus- containing inorganic alkaline detergent builders, when present, include the water-soluble salts, especially alkali metal pyrophosphates, orthophosphates, and polyphosphates.
  • An 1640 example of phosphorus-containing organic alkaline detergent builder, when present, includes the water-soluble salts of phosphonates.
  • non-phosphorus-containing inorganic builders when present, include water-soluble alkali metal carbonates, borates, and silicates, as well as the various types of water-insoluble crystalline or amorphous alumino silicates, of which zeolites are the best-known representatives.
  • Suitable organic builders include the alkali metal; ammonium and substituted ammonium; citrates; succinates; malonates; fatty acid sulphonates; carboxymethoxy succinates; ammonium polyacetates; carboxylates; polycarboxylates; aminopolycarboxylates; polyacetyl carboxylates; and polyhydroxsulphonates.
  • suitable organic builders include the higher molecular weight polymers and 1650 co-polymers known to have builder properties, for example appropriate polyacrylic acid, polymaleic and polyacrylic/polymaleic acid copolymers, and their salts.
  • the cleaning composition may contain bleaching agents of the chlorine/bromine- type or the oxygen-type.
  • inorganic chlorine/bromine-type bleaches are lithium, sodium or calcium hypochlorite, and hypobromite, as well as chlorinated 1655 trisodium phosphate.
  • organic chlorine/bromine-type bleaches are heterocyclic N-bromo- and N-chloro-imides such as trichloroisocyanuric, tribromoisocyanuric, dibromoisocyanuric, and dichloroisocyanuric acids, and salts thereof with water- solubilizing cations such as potassium and sodium. Hydantoin compounds are also suitable.
  • the cleaning composition may contain oxygen bleaches, for example in the form of an inorganic persalt, optionally with a bleach precursor or as a peroxy acid compound.
  • oxygen bleaches for example in the form of an inorganic persalt, optionally with a bleach precursor or as a peroxy acid compound.
  • suitable peroxy bleach compounds are alkali metal perborates, both tetrahydrates and monohydrates, alkali metal percarbonates, persilicates, and perphosphates.
  • Suitable activator materials include tetraacetylethylenediamine (TAED)
  • Enzymatic bleach activation systems may also be present, such as perborate or percarbonate, glycerol triacetate and perhydrolase, as disclosed in WO 2005/056783, for example.
  • the cleaning composition may be stabilized using conventional stabilizing agents for the enzyme(s), e.g., a polyol such as, e.g., propylene glycol, a sugar or a sugar alcohol, 1670 lactic acid, boric acid, or a boric acid derivative (e.g., an aromatic borate ester).
  • the cleaning composition may also contain other conventional detergent ingredients, e.g., deflocculant material, filler material, foam depressors, anti-corrosion agents, soil- suspending agents, sequestering agents, anti-soil redeposition agents, dehydrating agents, dyes, bactericides, fluorescent agents, thickeners, and perfumes.
  • the ⁇ -amylase variants may be used in conventional dishwashing detergents, e.g., in any of the detergents described in the following patent publications, with the consideration that the ⁇ -amylase variants disclosed herein are used instead of, or in addition to, any ⁇ -amylase disclosed in the listed patents and published applications: CA 2006687, GB 2200132, GB 2234980, GB 2228945, DE 3741617, DE 3727911, DE
  • one or more ⁇ -amylase variants may typically be a component of a detergent composition.
  • it may be included in the detergent composition in the form of a non-dusting granulate, a stabilized liquid, or a protected enzyme.
  • Non-dusting granulates may be produced, e.g., as disclosed in U.S. Patent Nos.
  • 1690 4, 106,991 and 4,661 ,452 may optionally be coated by methods known in the art.
  • waxy coating materials are poly(ethylene oxide) products; (polyethyleneglycol, PEG) with mean molar weights of 1,000 to 20,000; ethoxylated nonylphenols having from 16 to 50 ethylene oxide units; ethoxylated fatty alcohols in which the alcohol contains from 12 to 20 carbon atoms and in which there are 15 to 80
  • Liquid enzyme preparations may, for instance, be stabilized by adding a polyol such as propylene glycol, a sugar or sugar alcohol, lactic acid or boric acid according to established methods.
  • a polyol such as propylene glycol, a sugar or sugar alcohol, lactic acid or boric acid according to established methods.
  • 1700 enzyme stabilizers are well known in the art.
  • Protected enzymes may be prepared according to the method disclosed in US 5,879,920 (Genencor International, Inc.) or EP 238216, for example.
  • Polyols have long been recognized as stabilizers of proteins as well as for improving the solubility of proteins. See, e.g., Kaushik et al., "Why is trehalose an exceptional protein stabilizer? An analysis of the thermal stability of proteins in the
  • the detergent composition may be in any convenient form, e.g., as gels, powders, granules, pastes, or liquids.
  • a liquid detergent may be aqueous, typically containing up to 1710 about 70% of water, and 0% to about 30% of organic solvent, it may also be in the form of a compact gel type containing only about 30% water.
  • the detergent composition comprises one or more surfactants, each of which may be anionic, nonionic, cationic, or zwitterionic.
  • the detergent will usually contain 0% to about 50% of anionic surfactant, such as linear alkylbenzenesulfonate (LAS); ⁇ -
  • AOS olefinsulfonate
  • AS alkyl sulfate (fatty alcohol sulfate)
  • AEOS or AES alcohol ethoxysulfate
  • SAS secondary alkanesulfonates
  • ⁇ -sulfo fatty acid methyl esters alkyl- or alkenylsuccinic acid; or soap.
  • the composition may also contain 0% to about 40% of nonionic surfactant such as alcohol ethoxylate (AEO or AE), carboxylated alcohol ethoxylates, nonylphenol ethoxylate, alkylpolyglycoside, alkyldimethylamineoxide,
  • the detergent composition may additionally comprise one or more other enzymes, such as lipase, cutinase, protease, cellulase, peroxidase, and/or laccase in any combination.
  • enzymes such as lipase, cutinase, protease, cellulase, peroxidase, and/or laccase in any combination.
  • the detergent may contain about 1% to about 65% of a detergent builder or 1725 complexing agent such as zeolite, diphosphate, triphosphate, phosphonate, citrate, nitrilotriacetic acid (NTA), ethylenediaminetetraacetic acid (EDTA), diethylenetriaminepentaacetic acid (DTMPA), alkyl- or alkenylsuccinic acid, soluble silicates or layered silicates (e.g., SKS-6 from Hoechst).
  • the detergent may also be unbuilt, i.e., essentially free of detergent builder. Enzymes may be used in any 1730 composition compatible with the stability of the enzyme.
  • Enzymes can be protected against generally deleterious components by known forms of encapsulation, as by granulation or sequestration in hydro gels, for example. Enzymes and specifically ⁇ - amylases either with or without the starch binding domains are not limited to laundry and dishwashing applications, but may bind use in surface cleaners and ethanol production 1735 from starch or biomass.
  • the detergent may comprise one or more polymers. Examples include carboxymethylcellulose (CMC), poly(vinylpyrrolidone) (PVP), polyethyleneglycol (PEG), poly(vinyl alcohol) (PVA), polycarboxylates such as polyacrylates, maleic/acrylic acid copolymers and lauryl methacrylate/acrylic acid copolymers. 1740
  • the detergent may contain a bleaching system, which may comprise a H 2 O 2 source such as perborate or percarbonate optionally combined with a peracid-forming bleach activator, such as TAED or nonanoyloxybenzenesulfonate (NOBS).
  • the bleaching system may comprise peroxy acids of the amide, imide, or sulfone type, for example.
  • the bleaching system can also be an enzymatic bleaching system where a
  • the enzymes of the detergent composition may be stabilized using conventional stabilizing agents, e.g., a polyol such as propylene glycol or glycerol; a sugar or sugar alcohol; lactic acid; boric acid or a boric acid derivative, such as an aromatic borate ester; and the composition may be formulated as described in WO 92/19709 and WO 92/19708, 1750 for example.
  • a polyol such as propylene glycol or glycerol
  • a sugar or sugar alcohol lactic acid
  • boric acid or a boric acid derivative such as an aromatic borate ester
  • the detergent may also contain other conventional detergent ingredients such as fabric conditioners including clays, foam boosters, suds suppressors, anti-corrosion agents, soil-suspending agents, anti-soil redeposition agents, dyes, bactericides, optical brighteners, or perfume, for example.
  • fabric conditioners including clays, foam boosters, suds suppressors, anti-corrosion agents, soil-suspending agents, anti-soil redeposition agents, dyes, bactericides, optical brighteners, or perfume, for example.
  • the pH (measured in aqueous solution at use 1755 concentration) is usually neutral or alkaline, e.g., pH about 7.0 to about 11.0.
  • the ⁇ -amylase variant may be incorporated in concentrations conventionally employed in detergents. It is at present contemplated that, in the detergent composition, the ⁇ -amylase variant may be added in an amount corresponding to 0.00001-1.0 mg (calculated as pure enzyme protein) of ⁇ -amylase variant per liter of wash liquor. 1760 Particular forms of detergent compositions comprising the ⁇ -amylase variants can be formulated to include:
  • a detergent composition formulated as a granulate having a bulk density of at 1775 least 600 g/L comprising linear alkylbenzenesulfonate (calculated as acid) about 6% to about 11%; alcohol ethoxysulfate (e.g., Ci 2-18 alcohol, 1-2 EO) or alkyl sulfate (e.g., C 16- 18 ) about 1% to about 3%; alcohol ethoxylate (e.g., C 14-15 alcohol, 7 EO) about 5% to about 9%; sodium carbonate (e.g., Na 2 CO 3 ) about 15% to about 21%; soluble silicate, about 1% to about 4%; zeolite (e.g., NaAlSiO 4 ) about 24% to about 34%; sodium sulfate 1780 (e.g,. Na 2 SO 4 ) about 4% to about 10%; sodium citrate/citric acid (e.g., C 6 H 5 Na 3 O 7 /
  • C 6 H 8 O 7 0% to about 15%; carboxymethylcellulose (CMC) 0% to about 2%; polymers (e.g., maleic/acrylic acid copolymer, PVP, PEG) 1-6%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; minor ingredients (e.g., suds suppressors, perfume) 0-5%.
  • CMC carboxymethylcellulose
  • polymers e.g., maleic/acrylic acid copolymer, PVP, PEG
  • enzymes calculated as pure enzyme protein
  • minor ingredients e.g., suds suppressors, perfume
  • a detergent composition formulated as a granulate having a bulk density of at least 600 g/L comprising linear alkylbenzenesulfonate (calculated as acid) about 8% to about 12%; alcohol ethoxylate (e.g., C 12-15 alcohol, 7 EO) about 10% to about 25%; sodium carbonate (as Na 2 CO 3 ) about 14% to about 22%; soluble silicate, about 1% to about 5%; zeolite (e.g., NaAlSiO 4 ) about 25% to about 35%; sodium sulfate (e.g., Na 2 SO 4 )
  • CMC carboxymethylcellulose
  • PVP maleic/acrylic acid copolymer
  • PEG polymers
  • enzymes calculated as pure enzyme protein
  • minor ingredients e.g., suds suppressors, perfume
  • An aqueous liquid detergent composition comprising linear alkylbenzenesulfonate (calculated as acid) about 15% to about 21%; alcohol ethoxylate 1805 (e.g., C 12-15 alcohol, 7 EO or C 12-15 alcohol, 5 EO) about 12% to about 18%; soap as fatty acid (e.g., oleic acid) about 3% to about 13%; alkenylsuccinic acid (C 12-14 ) 0% to about 13%; aminoethanol about 8% to about 18%; citric acid about 2% to about 8%; phosphonate 0% to about 3%; polymers (e.g., PVP, PEG) 0% to about 3%; borate (e.g., B 4 O 7 ) 0% to about 2%; ethanol 0% to about 3%; propylene glycol about 8% to about 14%; 1810 enzymes (calculated as pure enzyme protein) 0.0001-0.1%; and minor ingredients (e.g., dispersants, suds,
  • An aqueous structured liquid detergent composition comprising linear alkylbenzenesulfonate (calculated as acid) about 15% to about 21%; alcohol ethoxylate (e.g., C 12-15 alcohol, 7 EO, or C 12-15 alcohol, 5 EO) 3-9%; soap as fatty acid (e.g., oleic
  • a detergent composition formulated as a granulate having a bulk density of at least 600 g/L comprising fatty alcohol sulfate about 5% to about 10%; ethoxylated fatty acid monoethanolamide about 3% to about 9%; soap as fatty acid 0-3%; sodium carbonate
  • 1825 (e.g., Na 2 CO 3 ) about 5% to about 10%; soluble silicate, about 1% to about 4%; zeolite (e.g., NaAlSiO 4 ) about 20% to about 40%; sodium sulfate (e.g., Na 2 SO 4 ) about 2% to about 8%; sodium perborate (e.g., NaBO 3 -H 2 O) about 12% to about 18%; TAED about 2% to about 7%; polymers (e.g., maleic/acrylic acid copolymer, PEG) about 1% to about 5%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; and minor ingredients
  • a detergent composition formulated as a granulate comprising linear alkylbenzenesulfonate (calculated as acid) about 8% to about 14%; ethoxylated fatty acid monoethanolamide about 5% to about 11%; soap as fatty acid 0% to about 3%; sodium carbonate (e.g., Na 2 CO 3 ) about 4% to about 10%; soluble silicate, about 1% to about 4%;
  • zeolite e.g., NaAlSiO 4
  • sodium sulfate e.g., Na 2 SO 4
  • sodium citrate e.g., C 6 H 5 Na 3 O 7
  • polymers e.g., PVP, maleic/acrylic acid copolymer, PEG
  • enzymes calculated as pure enzyme protein
  • minor ingredients e.g., suds suppressors, perfume
  • a detergent composition formulated as a granulate comprising linear alkylbenzenesulfonate (calculated as acid) about 6% to about 12%; nonionic surfactant about 1% to about 4%; soap as fatty acid about 2% to about 6%; sodium carbonate (e.g., Na 2 CO 3 ) about 14% to about 22%; zeolite (e.g., NaAlSiO 4 ) about 18% to about 32%; sodium sulfate (e.g., Na 2 SO 4 ) about 5% to about 20%; sodium citrate (e.g., CeHsNa 3 O 7 ) 1845 about 3% to about 8%; sodium perborate (e.g., NaBO 3 -H 2 O) about 4% to about 9%; bleach activator (e.g., NOBS or TAED) about 1% to about 5%; carboxymethylcellulose (CMC) 0% to about 2%; polymers (e.g., polycarboxylate or
  • An aqueous liquid detergent composition comprising linear alkylbenzenesulfonate (calculated as acid) about 15% to about 23%; alcohol ethoxysulfate (e.g., Cn -15 alcohol, 2-3 EO) about 8% to about 15%; alcohol ethoxylate (e.g., Ci 2-15 alcohol, 7 EO, or C 12-15 alcohol, 5 EO) about 3% to about 9%; soap as fatty acid (e.g., lauric acid) 0% to about 3%; aminoethanol about 1% to about 5%; sodium citrate about
  • linear alkylbenzenesulfonate calculated as acid
  • alcohol ethoxysulfate e.g., Cn -15 alcohol, 2-3 EO
  • alcohol ethoxylate e.g., Ci 2-15 alcohol, 7 EO, or C 12-15 alcohol, 5 EO
  • soap as fatty acid e.g., lauric acid
  • aminoethanol about 1% to about 5%
  • sodium citrate about
  • hydrotrope e.g., sodium toluensulfonate
  • borate e.g., B 4 O 7
  • carboxymethylcellulose 0% to about 1%
  • ethanol about 1% to about 3%
  • propylene glycol about 2% to about 5%
  • enzymes calculated as pure enzyme protein
  • minor ingredients e.g., polymers, dispersants, perfume, optical brighteners
  • An aqueous liquid detergent composition comprising linear alkylbenzenesulfonate (calculated as acid) about 20% to about 32%; alcohol ethoxylate (e.g., Ci 2-15 alcohol, 7 EO, or C 12-15 alcohol, 5 EO) 6-12%; aminoethanol about 2% to about 6%; citric acid about 8% to about 14%; borate (e.g., B 4 O 7 ) about 1% to about 3%; polymer (e.g., maleic/acrylic acid copolymer, anchoring polymer, such as lauryl
  • nonionic surfactant e.g., alcohol ethoxylate
  • sodium carbonate e.g., Na 2 CO 3
  • soluble silicates about 5% to about 15%
  • sodium sulfate e.g., Na 2 SO 4
  • zeolite NaAlSiO 4
  • sodium perborate e.g., NaBO 3 H 2 O
  • compositions as described in compositions I)- 12) supra, wherein all or part of the linear alkylbenzenesulfonate is replaced by (C 12 -C 18 ) alkyl sulfate.
  • a detergent composition formulated as a granulate having a bulk density of at 1880 least 600 g/L comprising (C 12 -C 18 ) alkyl sulfate about 9% to about 15%; alcohol ethoxylate about 3% to about 6%; polyhydroxy alkyl fatty acid amide about 1% to about 5%; zeolite (e.g., NaAlSiO 4 ) about 10% to about 20%; layered disilicate (e.g., SK56 from Hoechst) about 10% to about 20%; sodium carbonate (e.g., Na 2 COs) about 3% to about 12%; soluble silicate, 0% to about 6%; sodium citrate about 4% to about 8%; sodium 1885 percarbonate about 13% to about 22%; TAED about 3% to about 8%; polymers (e.g., polycarboxylates and PVP) 0% to about 5%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; and minor ingredients (e.
  • a detergent composition formulated as a granulate having a bulk density of at 1890 least 600 g/L comprising (C 12 -C 18 ) alkyl sulfate about 4% to about 8%; alcohol ethoxylate about 11% to about 15%; soap about 1% to about 4%; zeolite MAP or zeolite A about 35% to about 45%; sodium carbonate (as Na 2 COs) about 2% to about 8%; soluble silicate, 0% to about 4%; sodium percarbonate about 13% to about 22%; TAED 1-8%; carboxymethylcellulose (CMC) 0% to about 3%; polymers (e.g., polycarboxylates and 1895 PVP) 0% to about 3 %; enzymes (calculated as pure enzyme protein) 0.0001 -0.1 %; and minor ingredients (e.g., optical brightener, phosphonate, perfume) 0-3%.
  • CMC carboxymethylcellulose
  • polymers e.g., polycarboxy
  • a liquid nonionic surfactant such as, e.g. , linear alkoxylated primary alcohol, a builder system (e.g., phosphate), an enzyme(s), and alkali.
  • the detergent may also comprise anionic surfactant and/or a bleach system.
  • the 2,6- ⁇ -D-fructan hydrolase can be incorporated in detergent compositions and used for removal/cleaning of biofihn present on household 1910 and/or industrial textile/laundry.
  • the detergent composition may for example be formulated as a hand or machine laundry detergent composition, including a laundry additive composition suitable for pre- treatment of stained fabrics and a rinse added fabric softener composition, or be formulated as a detergent composition for use in general household hard surface cleaning 1915 operations, or be formulated for hand or machine dishwashing operations.
  • the detergent composition can comprise 2,6- ⁇ -D-fructan hydrolase, one or more ⁇ -amylase variants, and one or more other cleaning enzymes, such as a protease, a lipase, a cutinase, a carbohydrase, a cellulase, a pectinase, a mannanase, an arabinase, a galactanase, a xylanase, an oxidase, a laccase, and/or a peroxidase, and/or 1920 combinations thereof.
  • the properties of the chosen enzyme(s) should be compatible with the selected detergent, (e.g., pH-optimum, compatibility with other enzymatic and non-enzymatic ingredients, etc.), and the enzyme(s) should be present in effective amounts.
  • proteases include those of animal, vegetable or microbial origin.
  • the protease may be a serine protease or a metalloprotease, e.g., an alkaline microbial protease or a trypsin-like protease.
  • alkaline proteases are subtilisins, especially those derived from Bacillus sp., e.g., subtilisin Novo, subtilisin Carlsberg, subtilisin 309 (see, e.g., U.S. Patent No. 6,287,841), subtilisin 147, and subtilisin 168 (see, e.g., WO 89/06279).
  • subtilisins especially those derived from Bacillus sp., e.g., subtilisin Novo, subtilisin Carlsberg, subtilisin 309 (see, e.g., U.S. Patent No. 6,287,841), subtilisin 147, and subtilisin 168 (see, e.g., WO 89/06279).
  • trypsin-like proteases are trypsin (e.g., of porcine or bovine origin), and Fusarium proteases (see, e.g., WO 89/06270 and WO 94/25583).
  • useful proteases also include but are not limited to the variants described in WO 92/19729 and WO 98/20115.
  • Suitable commercially available protease enzymes include Alcalase®, Savinase®, Esperase®, and KannaseTM (Novozymes, formerly Novo Nordisk A/S); Maxatase®,
  • lipases include those of bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Examples of useful lipases include, but are not limited to, Upases from Humicola (synonym Thermomyces), e.g. H. lanuginosa 1940 (T. lanuginosa) (see, e.g., EP 258068 and EP 305216) and H. insolens (see, e.g., WO
  • a Pseudomonas lipase e.g., from P. alcaligenes or P. pseudoalcaligenes; see, e.g., EP 218 272
  • P. cepacia e.g., EP 331 376
  • P. stutzeri e.g., GB 1,372,034
  • P. fluorescens Pseudomonas sp. strain SD 705 ⁇ see, e.g., WO 95/06720 and WO 96/27002
  • P. wisconsinensis ⁇ see, e.g., WO 96/12012
  • Bacillus lipase e.g., from B.
  • Lipolase® and Lipolase® Ultra Novo Nordisk A/S
  • Polyesterases include, but are not limited to, those described in WO 01/34899 (Genencor International, Inc.) and WO 01/14629 (Genencor International, Inc.), and can be included in any combination with other enzymes discussed 1955 herein.
  • Amylases The compositions can be combined with other ⁇ -amylases, such as a non-variant ⁇ -amylase. These can include commercially available amylases, such as but not limited to Duramyl®, TermamylTM, Fungamyl® and BANTM (Novozymes, formerly Novo Nordisk A/S), Rapidase®, and Purastar® (Genencor International, Inc.).
  • Cellulases can be added to the compositions. Suitable cellulases include those of bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Suitable cellulases include cellulases from the genera Bacillus, Pseudomonas, Humicola, Fusarium, Thielavia, Acremonium, e.g., the fungal cellulases produced from Humicola insolens, Myceliophthora thermophila and Fusarium oxysporum disclosed in
  • Exemplary cellulases contemplated for use are those having color care benefit for the textile. Examples of such cellulases are cellulases described in EP 0495257; EP 531 372; WO 99/25846 (Genencor International, Inc.), WO 96/34108 (Genencor International, Inc.), WO 96/11262; WO 96/29397; and WO 98/08940, for example.
  • Other cellulases are cellulases described in EP 0495257; EP 531 372; WO 99/25846 (Genencor International, Inc.), WO 96/34108 (Genencor International, Inc.), WO 96/11262; WO 96/29397; and WO 98/08940, for example.
  • cellulase variants such as those described in WO 94/07998; WO 98/12307; WO 95/24471; PCT/DK98/00299; EP 531 315; U.S. Patent Nos. 5,457,046; 5,686,593; and 5,763,254.
  • Commercially available cellulases include Celluzyme® and Carezyme® (Novozymes, formerly Novo Nordisk A/S); ClazinaseTM and Puradax® HA (Genencor International, Inc.); and KAC-500(B)TM (Kao Corporation).
  • Peroxidases/Oxidases Suitable peroxidases/oxidases contemplated for use in the compositions include those of plant, bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Examples of useful peroxidases include peroxidases from Coprinus, e.g., from C. cinereus, and variants thereof as those described in WO 93/24618, WO 95/10602, and WO 98/15257.
  • the detergent enzyme(s) may be included in a detergent composition by adding separate additives containing one or more enzymes, or by adding a combined additive comprising all of these enzymes.
  • a detergent additive i.e., a separate additive or a combined additive, can be formulated as a granulate, liquid, slurry, etc. Suitable granulate detergent additive formulations include non-dusting granulates.
  • Non-dusting granulates may be produced, e.g., as disclosed in U.S. Patent Nos.
  • waxy coating materials are poly(ethylene oxide) products (e.g., polyethyleneglycol, PEG) with mean molar weights of 1,000 to 20,000; ethoxylated nonylphenols having from 16 to 50 ethylene oxide units; ethoxylated fatty alcohols in
  • Liquid enzyme preparations may, for instance, be stabilized by adding a polyol such as propylene glycol, a sugar or sugar
  • the detergent composition may be in any convenient form, e.g., a bar, tablet, gel, powder, granule, paste, or liquid.
  • a liquid detergent may be aqueous, typically containing up to about 70% water, and 0% to about 30% organic solvent.
  • Compact detergent gels 2000 containing 30% or less water are also contemplated.
  • the detergent composition comprises one or more surfactants, which may be non-ionic, including semi-polar, anionic, cationic, or zwitterionic, or any combination thereof.
  • the surfactants are typically present at a level of from 0.1% to 60% by weight.
  • the detergent When included therein the detergent typically will contain from about 1% to about 2005 40% of an anionic surfactant, such as linear alkylbenzenesulfonate, ⁇ -olefinsulfonate, alkyl sulfate (fatty alcohol sulfate), alcohol ethoxysulfate, secondary alkanesulfonate, ⁇ - sulfo fatty acid methyl ester, alkyl- or alkenylsuccinic acid, or soap.
  • an anionic surfactant such as linear alkylbenzenesulfonate, ⁇ -olefinsulfonate, alkyl sulfate (fatty alcohol sulfate), alcohol ethoxysulfate, secondary alkanesulfonate, ⁇ - sulfo fatty acid methyl ester, alkyl- or alkenylsuccinic acid, or soap.
  • the detergent When included therein, the detergent will usually contain from about 0.2% to about 40% of a non-ionic surfactant such as alcohol ethoxylate, nonylphenol ethoxylate, 2010 alkylpolyglycoside, alkyldimethylamineoxide, ethoxylated fatty acid monoethanolamide, fatty acid monoethanolamide, polyhydroxy alkyl fatty acid amide, or N-acyl-N-alkyl derivatives of glucosamine (“glucamides”).
  • a non-ionic surfactant such as alcohol ethoxylate, nonylphenol ethoxylate, 2010 alkylpolyglycoside, alkyldimethylamineoxide, ethoxylated fatty acid monoethanolamide, fatty acid monoethanolamide, polyhydroxy alkyl fatty acid amide, or N-acyl-N-alkyl derivatives of glucosamine (“glucamides”).
  • the detergent may contain 0% to about 65% of a detergent builder or complexing agent such as zeolite, diphosphate, triphosphate, phosphonate, carbonate, citrate, 2015 nitrilotriacetic acid, ethylenediaminetetraacetic acid (EDTA), diethylenetriaminepentaacetic acid, alkyl- or alkenylsuccinic acid, soluble silicates or layered silicates (e.g., SKS-6 from Hoechst).
  • a detergent builder or complexing agent such as zeolite, diphosphate, triphosphate, phosphonate, carbonate, citrate, 2015 nitrilotriacetic acid, ethylenediaminetetraacetic acid (EDTA), diethylenetriaminepentaacetic acid, alkyl- or alkenylsuccinic acid, soluble silicates or layered silicates (e.g., SKS-6 from Hoechst).
  • the detergent may comprise one or more polymers.
  • examples are carboxymethylcellulose (CMC), polyvinylpyrrolidone) (PVP), poly(ethylene glycol) 2020 (PEG), polyvinyl alcohol) (PVA), poly(vinylpyridine-N-oxide), poly(vinylimidazole), polycarboxylates, e.g., polyacrylates, maleic/acrylic acid copolymers), and lauryl methacrylate/acrylic acid copolymers.
  • the detergent may contain a bleaching system that may comprise a source of H 2 O 2 , such as perborate or percarbonate, which may be combined with a peracid-forming 2025 bleach activator (e.g., tetraacetylethylenediamine or nonanoyloxybenzenesulfonate).
  • a bleaching system may comprise a source of H 2 O 2 , such as perborate or percarbonate, which may be combined with a peracid-forming 2025 bleach activator (e.g., tetraacetylethylenediamine or nonanoyloxybenzenesulfonate).
  • the bleaching system may comprise peroxyacids (e.g., the amide-, imide-, or sulfone-type peroxyacids).
  • the bleaching system can also be an enzymatic bleaching system.
  • the enzyme(s) of the detergent composition may be stabilized using conventional 2030 stabilizing agents, e.g., polyol (e.g., propylene glycol or glyceroi ⁇ _a sugar or sugar alcohol, lactic acid, boric acid, a boric .acid derivative (e.g., an aromatic borate ester), or a phenyl boronic acid derivative (e.g., 4-formylphenyl boronic acid).
  • the composition may be formulated as described in WO 92/19709 and WO 92/19708.
  • the detergent may also contain other conventional detergent ingredients such as 2035 e.g., fabric conditioners including clays, foam boosters, suds suppressors, anti-corrosion agents, soil-suspending agents, anti-soil redeposition agents, dyes, bactericides, optical brighteners, hydrotropes, tarnish inhibitors, or perfumes.
  • fabric conditioners including clays, foam boosters, suds suppressors, anti-corrosion agents, soil-suspending agents, anti-soil redeposition agents, dyes, bactericides, optical brighteners, hydrotropes, tarnish inhibitors, or perfumes.
  • the enzyme variants may be added in an amount corresponding to about 0.01 to about 100 mg of enzyme protein per 2040 liter of wash liquor, particularly about 0.05 to about 5.0 mg of enzyme protein per liter of wash liquor, or even more particularly in 0.1 to about 1.0 mg of enzyme protein per liter of wash liquor.
  • compositions with the disclosed ⁇ -amylase variants can be 2045 utilized for starch liquefaction and/or saccharification.
  • Starch processing is useful for producing sweetener, producing alcohol for fuel or drinking (i.e., potable alcohol), producing a beverage, processing cane sugar, or producing desired organic compounds, e.g., citric acid, itaconic acid, lactic acid, gluconic acid, ketones, amino acids, antibiotics, enzymes, vitamins, and hormones.
  • Conversion of starch to fructose syrups normally 2050 consists of three consecutive enzymatic processes: a liquefaction process, a saccharification process, and an isomerization process.
  • a variant ⁇ -amylase degrades starch to dextrins by at pH between about 5.5 and about 6.2 and at temperatures of about 95 0 C to about 160 0 C for a period of approximately 2 hours. About 1 mM of calcium (40 ppm free calcium ions) typically is added to optimize enzyme 2055 stability under these conditions. Other ⁇ -amylase variants may require different conditions.
  • the dextrins can be converted into dextrose by addition of a glucoamylase (e.g., AMGTM) and optionally a debranching enzyme, such as an isoamylase or a pullulanase (e.g., Promozyme®).
  • a glucoamylase e.g., AMGTM
  • a debranching enzyme such as an isoamylase or a pullulanase (e.g., Promozyme®).
  • the pH is reduced to 2060 a value below about 4.5, maintaining the high temperature (above 95°C), and the liquefying ⁇ -amylase variant activity is denatured.
  • the temperature is lowered to 60 0 C, and a glucoamylase and a debranching enzyme can be added.
  • the saccharification process proceeds typically for about 24 to about 72 hours.
  • the pH is increased to a value in the range of 2065 about 6.0 to about 8.0, e.g., pH 7.5, and the calcium is removed by ion exchange.
  • the dextrose syrup is then converted into high fructose syrup using an immobilized glucose isomerase (such as Sweetzyme®), for example.
  • the ⁇ -amylase variant may provide at least one improved enzymatic property for conducting the process of liquefaction.
  • the variant ⁇ -amylase may have a 2070 higher activity, or it may have a reduced requirement for calcium. Addition of free calcium is required to ensure adequately high stability of the ⁇ -amylase; however, free calcium strongly inhibits the activity of the glucose isomerase. Accordingly, the calcium should be removed prior to the isomerization step, by means of an expensive unit operation, to an extent that reduces the level of free calcium to below 3-5 ppm. Cost 2075 savings can be obtained if such an operation could be avoided, and the liquefaction process could be performed without addition of free calcium ions.
  • ⁇ -amylase variants that do not require calcium ions or that have a reduced requirement for calcium are particularly advantageous.
  • a less calcium-dependent ⁇ -amylase variant which is stable and highly active at low concentrations of free calcium ( ⁇ 40 ppm) can be
  • Such an ⁇ -amylase variant should have a pH optimum in the range of about 4.5 to about 6.5, e.g., about pH 4.5 to about pH 5.5.
  • the ⁇ - amylase variants can be used alone to provide specific hydrolysis or can be combined with other amylases to provide a "cocktail" with a broad spectrum of activity.
  • the starch to be processed may be a highly refined starch quality, for instance, at 2085 least 90%, at least 95%, at least 97%, or at least 99.5% pure.
  • the starch can be a more crude starch containing material comprising milled whole grain, including non- starch fractions such as germ residues and fibers.
  • the raw material, such as whole grain is milled to open up the structure and allow further processing. Two milling processes are suitable: wet and dry milling. Also, corn grits, and milled corn grits may be applied. Dry 2090 milled grain will comprise significant amounts of non-starch carbohydrate compounds, in addition to starch.
  • ⁇ -amylase variants having a high activity towards ungelatinized starch are advantageously applied in a. process comprising liquefaction and/or saccharification jet cooked dry milled starch.
  • a variant ⁇ -amylase having a superior hydrolysis activity during the liquefaction process advantageously increases the efficiency of the saccharification step ⁇ see WO 98/22613) and the need for glucoamylase during the saccharification step.
  • the glucoamylase advantageously is present in an amount of no more than, or even less than, 0.5 glucoamylase activity unit (AGU)/g DS (i.e., glucoamylase activity units per gram of
  • the glucoamylase may be derived from a strain within Aspergillus sp.,
  • the process also comprises the use of a carbohydrate- binding domain of the type disclosed in WO 98/22613.
  • the process may comprise hydrolysis of a slurry of gelatinized or granular starch, in particular hydrolysis of granular starch into a soluble starch hydrolysate at a temperature below the initial gelatinization temperature of the granular starch.
  • the starch may be contacted with one or more enzyme selected from the group consisting of a fungal ⁇ - 2110 amylase (EC 3.2.1.1), a ⁇ -amylase (EC 3.2.1.2), and a glucoamylase (EC 3.2.1.3).
  • a fungal ⁇ - 2110 amylase EC 3.2.1.1
  • a ⁇ -amylase EC 3.2.1.2
  • a glucoamylase EC 3.2.1.3
  • another amylolytic enzyme or a debranching enzyme such as an isoamylase (EC 3.2.1.68), or a pullulanases (EC 3.2.1.41) may be added to the ⁇ -amylase variant.
  • the process is conducted at a temperature below the initial
  • the pH at which the process is conducted may in be in the range of about 3.0 to about 7.0, from about 3.5 to about 6.0, or from about 4.0 to about 5.0.
  • One aspect contemplates a process comprising fermentation with a yeast, for example, to produce ethanol at a temperature around 32 0 C, such as from 3O 0 C to 35 0 C.
  • the process comprises simultaneous saccharification and
  • the ethanol content reaches at least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 11%, at least about 12%, at least about 13%, at least about 14%, at least
  • the starch slurry to be used in any of the above aspects may have about 20% to about 55% dry solids granular starch, about 25% to about 40% dry solids granular starch, or about 30% to about 35% dry solids granular starch.
  • the enzyme variant converts the soluble starch into a soluble starch hydrolysate of the granular starch in the amount of at 2135 least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%.
  • the ⁇ -amylase variant is used in a process for liquefaction or saccharification of a gelatinized starch, including, but not limited to, gelatinization by 2140 jet cooking.
  • the process may comprise fermentation to produce a fermentation product, e.g., ethanol.
  • a process for producing ethanol from starch-containing material by fermentation comprises: (i) liquefying the starch-containing material with an ⁇ -amylase variant; (ii) saccharifying the liquefied mash obtained; and (iii) fermenting the material obtained in step (ii) in the presence of a fermenting organism.
  • the process 2145 further comprises recovery of the ethanol.
  • the saccharif ⁇ cation and fermentation processes may be carried out as a simultaneous saccharif ⁇ cation and fermentation (SSF) process.
  • SSF simultaneous saccharif ⁇ cation and fermentation
  • the ethanol content reaches at least about 7%, at least about 8%, at least about 9%, at least about 10% such as at least about 11%, at least about 12%, at least about 13%, at least about 14%, at least 15%, or at least 16% ethanol.
  • the starch to be processed in the above aspects may be obtained from tubers, roots, stems, legumes, cereals or whole grain. More specifically, the granular starch may be obtained from corns, cobs, wheat, barley, rye, milo, sago, cassava, tapioca, sorghum, rice, peas, bean, banana, or potatoes. Specially contemplated are both waxy and non-waxy types of corn and barley.
  • liquefaction or “liquefy” means a process by which starch is converted to less viscous and shorter chain dextrins. Generally, this process involves gelatmization of starch simultaneously with or followed by the addition of an ⁇ - amylase variant. Additional liquefaction-inducing enzymes optionally may be added.
  • primary liquefaction refers to a step of liquefaction when the
  • 2160 slurry' s temperature is raised to or near its gelatinization temperature. Subsequent to the raising of the temperature, the slurry is sent through a heat exchanger or jet to temperatures from about 90-150°C, e.g., 100-110 0 C. Subsequent to application to a heat exchange or jet temperature, the slurry is held for a period of 3-10 minutes at that temperature. This step of holding the slurry at 90-150 0 C is termed primary liquefaction.
  • secondary liquefaction refers the liquefaction step subsequent to primary liquefaction (heating to 90-150 0 C), when the slurry is allowed to cool to room temperature. This cooling step can be 30 minutes to 180 minutes, e.g. 90 minutes to 120 minutes.
  • minutes of secondary liquefaction refers to the time that has elapsed from the start of secondary liquefaction to the time that
  • ⁇ -amylases EC 3.2.1.2
  • ⁇ -amylases EC 3.2.1.2
  • ⁇ -amylases EC 3.2.1.2
  • ⁇ -amylases are characterized by having optimum temperatures in the range from 40 0 C to 65 0 C, and optimum pH in the range from about 4.5 to about 7.0.
  • Contemplated ⁇ -amylases include, but are not limited to, ⁇ -amylases from barley Spezyme® BBA 1500, Spezyme® DBA, 2180 OptimaltTM ME, OptimaltTM BBA (Genencor International, Inc.); and NovozymTM WBA (Novozymes AJS).
  • Glucoamylases are derived from a microorganism or a plant.
  • glucoamylases can be of fungal or bacterial origin.
  • Exemplary bacterial glucoamylases are 2185 Aspergillus glucoamylases, in particular A. niger Gl or G2 glucoamylase (Boel et al.
  • Contemplated bacterial glucoamylases include glucoamylases from the genus Clostridium, in particular C. thermoamylolyticum (EP 135138) and C. thermohydrosulfuricum (WO 86/01831). Suitable glucoamylases include
  • glucoamylases derived from Aspergillus oryzae, such as a glucoamylase having 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, or even 90% homology to the amino acid sequence shown in SEQ ID NO:2 in WO 00/04136.
  • glucoamylases such as AMG 200L; AMG 300 L; SANTM SUPER and AMGTME (Novozymes); OPTIDEX® 300 (Genencor International, Inc.); AMIGASETMand
  • Glucoamylases may be added in an amount of 0.02-2.0 AGU/g DS or 0.1-1.0 AGU/g DS, e.g., 0.2 AGU/g DS.
  • ⁇ - amylase variants can be included in the composition.
  • Two or more ⁇ - amylase variants can be used alone or in combination with other enzymes discussed 2210 herein.
  • a third enzyme may be another ⁇ -amylase, e.g., a yeast ⁇ -amylase, or another ⁇ -amylase variant. These can be Bacillus ⁇ -amylases or non-Bacillus ⁇ -amylases.
  • Another enzyme that can optionally be added is a debranching enzyme, such as an isoamylase (EC 3.2.1.68) or a pullulanases (EC 3.2.1.41).
  • Isoamylase hydrolyses ⁇ -l,6-D- glucosidic branch linkages in amylopectin and ⁇ -limit dextrins and can be distinguished 2215 from pullulanases by the inability of isoamylase to attack pullulan and by the limited action of isoamylase on ⁇ -limit dextrins.
  • Debranching enzymes may be added in effective amounts well known to the person skilled in the art.
  • composition of the products of the process depends on the combination of enzymes applied, as well as the type of granular starch processed.
  • the soluble fraction of the products of the process depends on the combination of enzymes applied, as well as the type of granular starch processed.
  • hydrolysate may be maltose with a purity of at least about 85%, at least about 90%, at least about 95.0%, at least about 95.5%, at least about 96.0%, at least about 96.5%, at least about 97.0%, at least about 97.5%, at least about 98.0%, at least about 98.5%, at least about 99.0% or at least about 99.5%.
  • the soluble starch hydrolysate is glucose, or the starch hydrolysate has a DE (glucose percent of total solubilLzed dry solids)
  • a process of manufacturing ice creams, cakes, candies, canned fruit uses a specialty syrup containing a mixture of glucose, maltose, DP3 and DPn.
  • wet milling Two milling processes are suitable: wet milling and dry milling.
  • dry milling the 2230 whole kernel is milled and used.
  • Wet milling gives a good separation of germ and meal (starch granules and protein) and is usually used when the starch hydrolysate is used in production of syrups.
  • Both dry and wet milling are well known in the art of starch processing and also are contemplated for use with the compositions and methods disclosed.
  • the process may be conducted in an ultrafiltration system where the retentate is 2235 held under recirculation in presence of enzymes, raw starch and water, where the permeate is the soluble starch hydrolysate.
  • Another method is the process conducted in a continuous membrane reactor with ultrafiltration membranes, where the retentate is held under recirculation in presence of enzymes, raw starch and water, and where the permeate is the soluble starch hydrolysate. Also contemplated is the process conducted in a continuous 2240 membrane reactor with microfiltration membranes and where the retentate is held under recirculation in presence of enzymes, raw starch and water, and where the permeate is the soluble starch hydrolysate.
  • the soluble starch hydrolysate of the process is subjected to conversion into high fructose starch-based syrup (HFSS), such as high fructose corn syrup 2245 (HFCS).
  • HFSS high fructose starch-based syrup
  • This conversion can be achieved using a glucose isomerase, particularly a glucose isomerase immobilized on a solid support.
  • Contemplated isomerases included the commercial products Sweetzyme®, IT (Novozymes AJS); G-zyme® IMGI, and G-zyme® G993, Ketomax®, G-zyme® G993, G-zyme® G993 liquid, and GenSweet® IGI.
  • the soluble starch hydrolysate of produced yields production of 2250 fuel or potable ethanol.
  • the fermentation may be carried out simultaneously or separately/sequential to the hydrolysis of the granular starch slurry.
  • the temperature can be between 30°C and 35 0 C, particularly between 31 °C and 34°C.
  • the process may be conducted in an ultrafiltration system where the retentate is held under recirculation in 2255 presence of enzymes, raw starch, yeast, yeast nutrients and water and where the permeate is an ethanol containing liquid.
  • Also contemplated is the process conducted in a continuous membrane reactor with ultrafiltration membranes and where the retentate is held under recirculation in presence of enzymes, raw starch, yeast, yeast nutrients and water and where the permeate is an ethanol containing liquid.
  • the soluble starch hydrolysate of the process may also be used for production of a fermentation product comprising fermenting the treated starch into a fermentation product, such as citric acid, monosodium glutamate, gluconic acid, sodium gluconate, calcium gluconate, potassium gluconate, glucono delta-lactone, or sodium erythorbate.
  • a fermentation product such as citric acid, monosodium glutamate, gluconic acid, sodium gluconate, calcium gluconate, potassium gluconate, glucono delta-lactone, or sodium erythorbate.
  • the amylolytic activity of the ⁇ -amylase variant may be determined using potato 2265 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 samples of the starch/enzyme solution with an iodine solution. Initially, a blackish-blue color is formed, but during the breakdown of the starch the blue color gets weaker and gradually turns into a reddish-brown, which is compared to a colored glass standard.
  • the PS4 variant polypeptide may in general be used to convert starch into sugars that can then be processed into ethanol or other value-added products such as high fructose corn sweetener.
  • PS4 variant polypeptides in the production of ethanol and specifically bioethanol, which in this document should be regarded as any 2275 ethanol produced by biomass fermentation.
  • the ethanol so produced may be used as a fuel or beverage or may be used in a fermentation process for producing organic compounds, such as citric acid, ascorbic acid, lysine, glutamic acid. These are described in further detail below.
  • Ethanol or ethyl alcohol
  • ethanol has many uses in the production of industrial chemicals, pharmaceuticals and as a transportation fuel.
  • Ethanol can be produced from almost any raw material containing sugar or carbohydrates. As such, ethanol can be made from a wide variety of biological material.
  • the 3 major types of biomass feedstocks used to produce ethanol include sugar crops, 2285 such as sugar cane; starch crops, including wheat and corn, and cellulosic materials, such as crop residues (straw, etc.), and forestry waste. Ethanol production from readily available sources of cellulose provides a stable, renewable fuel source.
  • the processing technology most frequently used is dry grain milling, hi this process, the grain is first milled to a grain meal consistency. The meal is then mixed with
  • Ethanol may also be made from cellulose containing sources, such as wood pulp.
  • Cellulose-based feedstocks are comprised of agricultural wastes, grasses and woods and 2300 other low-value biomass such as municipal waste (e.g., recycled paper, yard clippings, etc.).
  • Ethanol may be produced from the fermentation of any of these cellulosic feedstocks.
  • the cellulose must first be converted to sugars before there can be conversion to ethanol, by treatment with a suitable enzyme such as cellulase.
  • ethanol Once ethanol leaves the processing plant, it can theoretically be used as an 2305 automotive fuel by itself or it can be mixed with gasoline at a ratio of 85 to 15 to form what is called "neat ethanol fuel". However, most commonly, ethanol is blended with gasoline at concentrations of 7 to 10 % by volume. The ethanol may be used as an octane enhancer. Ethanol as a fuel source is more environmentally friendly than petroleum derived products. It is known that the use of ethanol will improve air quality and possibly 2310 reduce local ozone levels and smog. Moreover, utilization of ethanol in lieu of gasoline can be of strategic importance in buffering the impact of sudden shifts in non-renewable energy and petro-chemical supplies. BREWERY APPLICATIONS
  • Ethanol (or ethyl alcohol) is best known as being the basis of alcoholic beverages 2315 like spirits, beer and wine.
  • the PS4 variant polypeptides described here may be used for brewing, in particular, brewing beer. All beers are brewed using a process based on a simple formula.
  • the brewery process involves the use of malted grain, which depending on the region may traditionally be barley, wheat or sometimes rye.
  • Malt is made by allowing a 2320 grain to germinate, after which it is then dried in a kiln and sometimes roasted.
  • the germination process creates a number of enzymes, notably ⁇ -amylase and ⁇ -amylase, which will be used to convert the starch in the grain into sugar.
  • the malt will take on dark colour and strongly influence the colour and flavour of the beer.
  • the malt is crushed to break apart the grain kernels, increase their surface area, and separate the smaller pieces from the husks.
  • the resulting grist is mixed with heated water in a vat called a "mash tun” for a process known as “mashing".
  • mash tun heated water in a vat
  • natural enzymes within the malt break down much of the starch into sugars which play a vital part in the fermentation process.
  • Mashing usually takes 1 to 2 hours, and during this
  • the mash tun generally contains a slotted "false bottom” or other form of manifold which acts as a strainer allowing for the separation of
  • a mash rest from 120 0 F to 130 °F activates various proteinases, which break down proteins that might otherwise cause the beer to be hazy. But care is of the essence since the head on beer is also composed primarily of proteins, so too aggressive a protein rest can result in a beer that cannot hold a head. This rest is generally
  • a mash rest temperature of 149 to 160 0 F (65 to 71 0 C) is used to convert the starches in the malt to sugar, which is then usable by the yeast later in the brewing process. Doing the latter rest at the lower end of the range produces more low-order sugars which are more fermentable by the yeast. This in turn creates a beer lower in body and higher in alcohol. A rest closer to the higher 2350 end of the range creates more higher-order sugars which are less fermentable by the yeast, so a fuller-bodied beer with less alcohol is the result.
  • the resulting liquid is strained from the grains in a process known as lautering.
  • the mash temperature may be raised to 165 0 F to 170 °F (about 75 0 C) (known as a mashout) to deactivate enzymes.
  • Additional water may 2355 be sprinkled on the grains to extract additional sugars (a process known as sparging).
  • the liquid is known as wort.
  • the wort is moved into a large tank known as a "copper” or kettle where it is boiled with hops and sometimes other ingredients such as herbs or sugars.
  • the boiling process serves to terminate enzymatic processes, precipitate proteins, isomerize hop resins, concentrate and sterilize the wort. 2360 Hops add flavour, aroma and bitterness to the beer.
  • the hopped wort settles to clarify it in a vessel called a "whirl-pool” and the clarified wort is then cooled.
  • the wort is then moved into a "fermentation vessel" where yeast is added or “pitched” with it.
  • the yeast converts the sugars from the malt into alcohol, carbon dioxide and other components through a process called Glycolysis.
  • Glycolysis After a week to three weeks, 2365 the fresh (or “green”) beer is run off into conditioning tanks. After conditioning for a week to several months, the beer is often filtered to remove yeast and particulates. The "bright beer” is then ready for serving or packaging.
  • PS4 variant polypeptides described here may therefore be added at any stage of the brewing process to supplement or the amylase activity generated 2370 naturally.
  • the PS4 variant polypeptide is capable of degrading resistant starch.
  • 'degrading' relates to the partial or complete hydrolysis or 2375 degradation of resistant starch to glucose and/or oligosaccharides - such as maltose and/or dextrins.
  • the PS4 variant polypeptide may degrade residual resistant starch that has not been completely degraded by an animals amylase.
  • the PS4 variant polypeptide may be used to assist an animal's amylase (eg. pancreatic amylase) in 2380 improving the degradation of resistant starch.
  • Pancreatic ⁇ -amylase is excreted in the digestive system by animals.
  • Pancreatic ⁇ -amylase degrades starch in the feed.
  • a part of the starch, the resistant starch is not degraded fully by the pancreatic ⁇ -amylase and is therefore not absorbed in the small intestine (see definition of resistant starch).
  • the PS4 variant polypeptide in some embodiments is able to assist the pancreatic ⁇ -amylase in 2385 degrading starch in the digestive system and thereby increase the utilisation of starch by the animal.
  • the ability of an enzyme to degrade resistant starch may be analysed for example by a method developed and disclosed by Megazyme International Ireland Ltd. for the measurement of resistant starch, solubilised starch and total starch content of a sample 2390 (Resistant Starch Assay Procedure, AOAC Method 2002.02, AACC Method 32-40).
  • the PS4 variant polypeptides may be ingested by an animal for beneficial purposes, and may therefore be incorporated into animal feeds.
  • a PS4 variant polypeptide as a component for use in a feed comprising starch, or for use in a feed improvement composition, in which the 2395 PS4 variant polypeptide is capable of degrading resistant starch.
  • a feed comprising a starch and a PS4 variant polypeptide.
  • a method of degrading resistant starch in a feed comprising contacting said resistant starch with a PS4 variant polypeptide.
  • PS4 variant polypeptide in the preparation of a 2400 feed comprising a starch, to degrade resistant starch. Furthermore, we disclose the use of a PS4 variant polypeptide in the preparation of a feed to improve the calorific value of said feed. We disclose the use of an enzyme in the preparation of a feed to improve animal performance, hi a further embodiment, we describe a process for preparing a feed comprising admixing a starch and a PS4 variant polypeptide enzyme.
  • a component comprising PS4 variant polypeptides and which is capable of degrading resistant starch is advantageous because there is a marked increase in the degradation of starch and/or starch degradation products in an animal. Furthermore, such use is advantageous because there is a marked increase in the digestibility of starch and/or starch degradation products by an animal. Furthermore, such
  • Animal feeds for which the PS4 variant polypeptides are suitable for use may be 2415 formulated to meet the specific needs of particular animal groups and to provide the necessary carbohydrate, fat, protein and other nutrients in a form that can be metabolised by the animal.
  • the animal feed is a feed for swine or poultry.
  • swine' relates to non-ruminant omnivores such as pigs, 2420 hogs or boars.
  • swine feed includes about 50 percent carbohydrate, about 20 percent protein and about 5% fat.
  • An example of a high energy swine feed is based on corn which is often combined with feed supplements for example, protein, minerals, vitamins and amino acids such as lysine and tryptophan.
  • feed supplements for example, protein, minerals, vitamins and amino acids such as lysine and tryptophan.
  • swine feeds include animal protein products, marine products, milk products, grain products and plant protein 2425 products, all of which may further comprise natural flavourings, artificial flavourings, micro and macro minerals, animal fats, vegetable fats, vitamins, preservatives or medications such as antibiotics.
  • 'poultry' relates to fowl such as chickens, broilers, hens, roosters, capons, turkeys, ducks, game fowl, pullets or chicks.
  • Poultry feeds may be
  • poultry feeds may further comprise vitamins, minerals or medications such as coccidiostats (for example Monensin sodium, Lasalocid, Amprolium, Salinomycin, and Sulfaquinoxaline) and/or antibiotics (for example Penicillin, Bacitracin,
  • Animal feeds may be formulated to meet the animal's nutritional needs with 2450 respect to, for example, meat production, milk production, egg production, reproduction and response to stress.
  • the animal feeds are formulated to improve manure quality.
  • the animal feed contains a raw material such as a legume, for example pea or soy or a cereal, for example wheat, corn (maize), rye or barley.
  • a raw material such as a legume, for example pea or soy or a cereal, for example wheat, corn (maize), rye or barley.
  • the raw material may be potato.
  • the PS4 variant polypeptides may be used in feeds for animal consumption by the indirect or direct application of the PS4 variant polypeptides to the feed, whether alone or in combination with other ingredients, such as food ingredients.
  • Typical food ingredients may include any one or more of an additive such as an animal or vegetable fat, a natural or synthetic seasoning, antioxidant, viscosity modifier, essential oil, and/or flavour, dye and/or colorant, vitamin, mineral, natural and/or non- natural amino acid, nutrient, additional enzyme (including genetically manipulated enzymes), a binding agent such as guar gum or xanthum gum, buffer, emulsifier, lubricant,
  • an additive such as an animal or vegetable fat, a natural or synthetic seasoning, antioxidant, viscosity modifier, essential oil, and/or flavour, dye and/or colorant, vitamin, mineral, natural and/or non- natural amino acid, nutrient, additional enzyme (including genetically manipulated enzymes), a binding agent such as guar gum or xanthum gum, buffer, emulsifier, lubricant,
  • Examples of the application methods include, but are not limited to, coating the feed in a material comprising the PS4 variant polypeptide, direct application by mixing the PS4 variant polypeptide with the feed, spraying the PS4 variant polypeptide onto the feed surface or dipping the feed into a preparation of the PS4 variant polypeptide.
  • the PS4 variant polypeptide is preferably applied by mixing it with a feed or by spraying onto feed particles for animal consumption.
  • the PS4 variant polypeptide may be included in the emulsion of a feed, or the interior of solid products by injection or tumbling.
  • the PS4 variant polypeptide may be applied to intersperse, coat and/or impregnate 2475 a feed. Mixtures with other ingredients may also be used and may be applied separately, simultaneously or sequentially. Chelating agents, binding agents, emulsif ⁇ ers and other additives such as micro and macro minerals, amino acids, vitamins, animal fats, vegetable fats, preservatives, flavourings, colourings, may be similarly applied to the feed simultaneously (either in mixture or separately) or applied sequentially.
  • the optimum amount of the PS4 variant polypeptide to be used will depend on the feed to be treated and/or the method of contacting the feed with the PS4 variant polypeptide and/or the intended use for the same.
  • the amount of PS4 variant polypeptide should be in a sufficient amount to be effective to substantially degrade resistant starch 2485 following ingestion and during digestion of the feed.
  • the PS4 variant polypeptide would remain effective following ingestion of a feed for animal consumption and during digestion of the feed until a more complete digestion of the feed is obtained, i.e. an increased calorific value of the feed is released.
  • PS4 variant polypeptides with amylases, in particular, maltogenic amylases.
  • Maltogenic alpha-amylase glucan 1,4-a- maltohydrolase, E.C. 3.2.1.133
  • E.C. 3.2.1.133 glucan 1,4-a- maltohydrolase
  • a maltogenic alpha-amylase from Bacillus (EP 120 693) is commercially available under the trade name Novamyl (Novo Nordisk A/S, Denmark) and is widely used in the baking industry as an anti-staling agent due to its ability to reduce retrogradation of starch.
  • Novamyl is described in detail in International Patent Publication WO 91/04669.
  • the maltogenic alpha-amylase Novamyl shares several characteristics with cyclodextrin
  • CGTases 2500 glucanotransferases (CGTases), including sequence homology (Henrissat B, Bairoch A; Biochem. J., 316, 695-696 (1996)) and formation of transglycosylation products (Christophersen, C, et al., 1997, Starch, vol. 50, No. 1, 39-45).
  • combinations comprising PS4 variant polypeptides together with Novamyl or any of its variants.
  • Such combinations are 2505 useful for food production such as baking.
  • the Novamyl may in particular comprise Novamyl 1500 MG.
  • Variants, homologues, and mutants of Novamyl may be used for the combinations, 2515 provided they retain alpha amylase activity.
  • any of the Novamyl variants disclosed in US Patent Number 6,162,628, the entire disclosure of which is hereby incorporated by reference, may be used in combination with the PS4 variant polypeptides described here.
  • any of the polypeptides described in that document specifically variants of SEQ ID NO:1 of US 6,162,628 at any one or more positions 2520 corresponding to Q13, 116, D17, N26, N28, P29, A30, S32, Y33, G34, L35, K40, M45, P73, V74, D76 N77, D79, N86, R95, N99, 1100, H103, Ql 19, N120, N131, S141, T142, A148, N152, A163, H169, N171, G172, 1174, N176, N187, F188, A192, Q201, N203, H220, N234, G236, Q247, K249, D261, N266, L268, R272, N275, N276, V279, N280, V281, D285, N287, F297, Q299, N305, K316, N320, L321, N327, A341, N342, A348, 2525 Q
  • the invention makes use of a PS4 variant nucleic acid, and the amino acid sequences of such PS4 variant nucleic acids are encompassed by the methods and compositions described here.
  • amino acid sequence is synonymous with the term “polypeptide” and/or the term “protein”.
  • amino acid 2535 sequence is synonymous with the term “peptide”.
  • amino acid sequence is synonymous with the term “enzyme”.
  • amino acid sequence may be prepared/isolated from a suitable source, or it may be made synthetically or it may be prepared by use of recombinant DNA techniques.
  • the PS4 variant enzyme described here may be used in conjunction with other 2540 enzymes.
  • the combination comprises a PS4 variant polypeptide enzyme described here and another enzyme, which itself may be another PS4 variant polypeptide enzyme.
  • nucleotide sequence refers to an oligonucleotide sequence or polynucleotide sequence, and variant, homologies, fragments and derivatives thereof (such as portions thereof).
  • the nucleotide sequence may be of genomic or synthetic or recombinant origin, which may be double-stranded or 2550 single-stranded whether representing the sense or anti-sense strand.
  • nucleotide sequence as used in this document includes genomic DNA, cDNA, synthetic DNA, and RNA. Preferably it means DNA, more preferably cDNA sequence coding for a PS4 variant polypeptide.
  • the PS4 variant nucleotide sequence is prepared using recombinant 2555 DNA techniques (i.e. recombinant DNA).
  • the nucleotide sequence could be synthesised, in whole or in part, using chemical methods well known in the art (see Caruthers MH et al, (1980) Nuc Acids Res Symp Ser 215-23 and Horn T et al, (1980) Nuc Acids Res Symp Ser 225-232).
  • a nucleotide sequence encoding either an enzyme which has the specific properties as defined herein (e.g., a PS4 variant polypeptide) or an enzyme which is suitable for modification, such as a parent enzyme, may be identified and/or isolated and/or purified from any cell or organism producing said enzyme.
  • an enzyme which has the specific properties as defined herein e.g., a PS4 variant polypeptide
  • an enzyme which is suitable for modification such as a parent enzyme
  • PCR amplification techniques to prepare more of a sequence may be used once a suitable sequence has been identified and/or isolated and/or purified.
  • a genomic DNA and/or cDNA library may be constructed using chromosomal DNA or messenger RNA from the organism producing 2570 the enzyme. If the amino acid sequence of the enzyme or a part of the amino acid sequence of the enzyme is known, labelled oligonucleotide probes may be synthesised and used to identify enzyme-encoding clones from the genomic library prepared from the organism. Alternatively, a labelled oligonucleotide probe containing sequences homologous to another known enzyme gene could be used to identify enzyme-encoding 2575 clones. In the latter case, hybridisation and washing conditions of lower stringency are used.
  • enzyme-encoding clones could be identified by inserting fragments of genomic DNA into an expression vector, such as a plasmid, transforming enzyme- negative bacteria with the resulting genomic DNA library, and then plating the 2580 transformed bacteria onto agar plates containing a substrate for enzyme (i.e. maltose), thereby allowing clones expressing the enzyme to be identified.
  • an expression vector such as a plasmid, transforming enzyme- negative bacteria with the resulting genomic DNA library
  • the nucleotide sequence encoding the enzyme may be prepared synthetically by established standard methods, e.g. the phosphoroamidite method described by Beucage S.L. et al, (1981) Tetrahedron Letters 22, p 1859-1869, or the 2585 method described by Matthes et al, (1984) EMBO J. 3, p 801-805.
  • the phosphoroamidite method oligonucleotides are synthesised, e.g. in an automatic DNA synthesiser, purified, annealed, ligated and cloned in appropriate vectors.
  • the nucleotide sequence may be of mixed genomic and synthetic origin, mixed synthetic and cDNA origin, or mixed genomic and cDNA origin, prepared by ligating 2590 fragments of synthetic, genomic or cDNA origin (as appropriate) in accordance with standard techniques. Each ligated fragment corresponds to various parts of the entire nucleotide sequence.
  • the DNA sequence may also be prepared by polymerase chain reaction (PCR) using specific primers, for instance as described in US 4,683,202 or in Saiki R K et al, ⁇ Science (1988) 239, pp 487-491).
  • PS4 variant nucleic acid should be taken to include each of the nucleic 2600 acid entities described below, and the term “PS4 variant polypeptide” should likewise be taken to include each of the polypeptide or amino acid entities described below.
  • homologue means an entity having a certain homology with the subject amino acid sequences and the subject nucleotide sequences.
  • the term “homology” can be equated with "identity”. 2605
  • a homologous sequence is taken to include an amino acid sequence which may be at least 75, 80, 85 or 90% identical, preferably at least 95, 96, 97, 98 or 99% identical to the subject sequence.
  • the homologues will comprise the same active sites etc. as the subject amino acid sequence.
  • homology can also be considered in terms of similarity (i.e. amino acid residues having similar chemical
  • an homologous sequence is taken to include a nucleotide sequence which may be at least 75, 80, 85 or 90% identical, preferably at least 95, 96, 97, 98 or 99% identical to a nucleotide sequence encoding a PS4 variant polypeptide enzyme 2615 (such as a PS4 variant nucleic acid).
  • the homologues will comprise the same sequences that code for the active sites etc as the subject sequence.
  • homology can also be considered in terms of similarity (i.e. amino acid residues having similar chemical properties/functions), in the context of this document it is preferred to express homology in terms of sequence identity.
  • Homology comparisons can be conducted by eye, or more usually, with the aid of readily available sequence comparison programs. These commercially available computer programs can calculate % homology between two or more sequences.
  • % homology may be calculated over contiguous sequences, i.e. one sequence is aligned with the other sequence and each amino acid in one sequence is directly compared 2625 with the corresponding amino acid in the other sequence, one residue at a time. This is called an "ungapped" alignment. Typically, such ungapped alignments are performed only over a relatively short number of residues.
  • BLAST Altschul et al, 1990 J MoI Biol. 403-410
  • GENEWORKS GENEWORKS suite of comparison tools. Both BLAST and FASTA are available for offline and online searching (see
  • GCG Bestfit program A new tool, called BLAST 2 Sequences is also available for comparing protein and nucleotide sequence (see FEMS Microbiol Lett 1999 174(2): 247-50; FEMS Microbiol Lett 1999 177(1): 187-8 and tatiana@ncbi.nlm.nih.gov).
  • % homology can be measured in terms of identity
  • the alignment process itself is typically not based on an all-or-nothing pair comparison.
  • a scaled similarity score matrix is generally used that assigns scores to each pairwise comparison based on chemical similarity or evolutionary distance.
  • An example of such a matrix commonly used is the BLOSUM62 matrix - the default matrix for the
  • GCG Wisconsin programs generally use either the public default values or a custom symbol comparison table if supplied (see user manual for further details). For some applications, it is preferred to use the public default values for the GCG package, or in the case of other software, the default matrix, such as BLOSUM62.
  • percentage homologies may be calculated using the multiple alignment feature in DNASIS (Hitachi Software), based on an algorithm, analog CLUSTAL (Higgins DG & Sharp PM (1988), Gene 73(1), 237-244). Once the software has produced an optimal alignment, it is possible to calculate % homology, preferably % sequence identity. The software typically does this as part of the 2675 sequence comparison and generates a numerical result.
  • sequences may also have deletions, insertions or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent substance.
  • Deliberate amino acid substitutions may be made on the basis of similarity in amino acid properties (such as polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the
  • substitution and replacement are both used herein to mean the interchange of an existing amino acid residue, with an alternative residue
  • substitution and replacement are both used herein to mean the interchange of an existing amino acid residue, with an alternative residue
  • Non-homologous substitution may also occur i.e. from one class of residue to another or alternatively involving the inclusion
  • Z ornithine
  • B diaminobutyric acid ornithine
  • O norleucine ornithine
  • pyriylalanine thienylalanine
  • naphthylalanine phenylglycine
  • Variant amino acid sequences may include suitable spacer groups that may be inserted between any two amino acid residues of the sequence including alkyl groups such
  • peptoid form is used to refer to variant amino acid residues wherein the ⁇ -carbon substituent group is on the residue's nitrogen atom rather than the ⁇ -
  • nucleotide sequences described here, and suitable for use in the methods and compositions described here may include within them
  • nucleotide sequences described herein may be modified by any method available
  • nucleotide sequences that are complementary to the sequences presented herein, or any derivative, fragment or derivative thereof. If the sequence is complementary to a fragment thereof then that sequence can be used as a 2720 probe to identify similar coding sequences in other organisms etc.
  • Polynucleotides which are not 100% homologous to the PS4 variant sequences may be obtained in a number of ways.
  • Other variants of the sequences described herein may be obtained for example by probing DNA libraries made from a range of individuals, for example individuals from different populations.
  • other homologues may be 2725 obtained and such homologues and fragments thereof in general will be capable of selectively hybridising to the sequences shown in the sequence listing herein.
  • Such sequences may be obtained by probing cDNA libraries made from or genomic DNA libraries from other species, and probing such libraries with probes comprising all or part of any one of the sequences in the attached sequence listings under conditions of medium to high stringency. 2730 Similar considerations apply to obtaining species homologues and allelic variants of the polypeptide or nucleotide sequences described here.
  • Variants and strain/species homologues may also be obtained using degenerate PCR which will use primers designed to target sequences within the variants and homologues encoding conserved amino acid sequences.
  • conserved sequences can be predicted, for 2735 example, by aligning the amino acid sequences from several variants/homologues. Sequence alignments can be performed using computer software known in the art. For example the GCG Wisconsin PiIeUp program is widely used.
  • the primers used in degenerate PCR will contain one or more degenerate positions and will be used at stringency conditions lower than those used for cloning sequences with 2740 single sequence primers against known sequences.
  • polynucleotides may be obtained by site directed mutagenesis of characterised sequences. This may be useful where for example silent codon sequence changes are required to optimise codon preferences for a particular host cell in which the polynucleotide sequences are being expressed. Other sequence changes may be desired in 2745 order to introduce restriction enzyme recognition sites, or to alter the property or function of the polypeptides encoded by the polynucleotides.
  • the polynucleotides such as the PS4 variant nucleic acids described in this document may be used to produce a primer, e.g. a PCR primer, a primer for an alternative amplification reaction, a probe e.g. labelled with a revealing label by 2750 conventional means using radioactive or non-radioactive labels, or the polynucleotides may be cloned into vectors.
  • a primer e.g. a PCR primer, a primer for an alternative amplification reaction, a probe e.g. labelled with a revealing label by 2750 conventional means using radioactive or non-radioactive labels
  • Such primers, probes and other fragments will be at least 15, preferably at least 20, for example at least 25, 30 or 40 nucleotides in length, and are also encompassed by the term polynucleotides.
  • Polynucleotides such as DNA polynucleotides and probes may be produced
  • Longer polynucleotides will generally be produced using recombinant means, for example using a PCR (polymerase chain reaction) cloning techniques.
  • the primers may be designed to contain suitable restriction enzyme recognition sites so that the amplified DNA can be cloned into a suitable cloning vector.
  • the variant sequences etc. are at least as biologically active as the sequences presented herein.
  • biologically active refers to a sequence having a similar structural function (but not necessarily to the same degree), and/or similar regulatory function (but not necessarily to the same degree), and/or similar biochemical function (but not necessarily to the same degree) of the naturally occurring sequence.
  • hybridisation shall include “the process by which a strand of nucleic acid joins with a complementary strand through base pairing” as well as 2775 the process of amplification as carried out in polymerase chain reaction (PCR) technologies. Therefore, we disclose the use of nucleotide sequences that are capable of hybridising to the sequences that are complementary to the sequences presented herein, or any derivative, fragment or derivative thereof.
  • variant also encompasses sequences that are complementary to 2780 sequences that are capable of hybridising to the nucleotide sequences presented herein.
  • sequences 2785 that are complementary to sequences that are capable of hybridising under high stringent conditions (e.g. 65 0 C and 0.IxS
  • nucleotide sequences that can hybridise to the nucleotide sequences of PS4 variants include complementary sequences of those presented herein), 2790 as well as nucleotide sequences that are complementary to sequences that can hybridise to the nucleotide sequences of PS4 variants (including complementary sequences of those presented herein).
  • polynucleotide sequences that are capable of hybridising to the nucleotide sequences presented herein under conditions of intermediate to maximal stringency. 2795 In a preferred aspect, we disclose nucleotide sequences that can hybridise to the nucleotide sequence of a PS4 variant nucleic acid, or the complement thereof, under stringent conditions (e.g.
  • nucleotide sequences can hybridise to the nucleotide sequence of a PS4 variant, or the complement thereof, under high stringent conditions (e.g. 65 0 C and 0. IxSSC).
  • a PS4 variant sequence may be prepared from a parent sequence. Mutations may be introduced using synthetic 2805 oligonucleotides. These oligonucleotides contain nucleotide sequences flanking the desired mutation sites.
  • sequence for use in the methods and compositions described here is a recombinant sequence - i.e. a sequence that has been prepared using recombinant DNA techniques.
  • recombinant DNA techniques are within the capabilities of a 2815 person of ordinary skill in the art. Such techniques are explained in the literature, for example, J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Books 1-3, Cold Spring Harbor Laboratory Press.
  • sequence for use in the methods and compositions described here is a synthetic sequence - i.e. a sequence that has been prepared by in vitro chemical or 2820 enzymatic synthesis. It includes, but is not limited to, sequences made with optimal codon usage for host organisms - such as the methylotrophic yeasts Pichia and Hansenula.
  • the nucleotide sequence for use in the methods and compositions described here may be incorporated into a recombinant replicable vector.
  • the vector may be used to replicate and express the nucleotide sequence, in enzyme form, in and/or from a 2825 compatible host cell. Expression may be controlled using control sequences eg. regulatory sequences.
  • the enzyme produced by a host recombinant cell by expression of the nucleotide sequence may be secreted or may be contained intracellularly depending on the sequence and/or the vector used.
  • the coding sequences may be designed with signal sequences which direct secretion of the substance coding sequences through a particular 2830 prokaryotic or eukaryotic cell membrane.
  • the PS4 polynucleotides and nucleic acids may include DNA and RNA of both synthetic and natural origin which DNA or RNA may contain modified or unmodified deoxy- or dideoxy- nucleotides or ribonucleotides or analogs thereof.
  • the PS4 nucleic acid 2835 may exist as single- or double-stranded DNA or RNA, an RNA/DNA heteroduplex or an RNA/DNA copolymer, wherein the term "copolymer” refers to a single nucleic acid strand that comprises both ribonucleotides and deoxyribonucleotides.
  • the PS4 nucleic acid may even be codon optimised to further increase expression.
  • synthetic is defined as that which is produced by in 2840 vitro chemical or enzymatic synthesis. It includes but is not limited to PS4 nucleic acids made with optimal codon usage for host organisms such as the the methylotrophic yeasts Pichia and Hansenula.
  • Polynucleotides for example variant PS4 polynucleotides described here, can be incorporated into a recombinant replicable vector.
  • the vector may be used to replicate the 2845 nucleic acid in a compatible host cell.
  • the vector comprising the polynucleotide sequence may be transformed into a suitable host cell.
  • Suitable hosts may include bacterial, yeast, insect and fungal cells.
  • transformed cell includes cells that have been transformed by use of recombinant DNA techniques. The transformation typically occurs by insertion of one or
  • the inserted nucleotide sequence may be a heterologous nucleotide sequence (i.e. is a sequence that is not natural to the cell that is to be transformed, hi addition, or in the alternative, the inserted nucleotide sequence may be an homologous nucleotide sequence (i.e. is a sequence that is natural to the cell that is to be transformed) - so that the cell receives one or more extra
  • PS4 variant polypeptides and polynucleotides by introducing a polynucleotide into a replicable vector, introducing the vector into a compatible host cell, and growing the host cell under conditions which bring about replication of the vector.
  • the vector may be recovered from 2860 the host cell.
  • the PS4 nucleic acid may be operatively linked to transcriptional and translational regulatory elements active in a host cell of interest.
  • the PS4 nucleic acid may also encode a fusion protein comprising signal sequences such as, for example, those derived from the 2865 glucoamylase gene from Schwanniomyces occidentalis, ⁇ -factor mating type gene from
  • the PS4 nucleic acid may encode a fusion protein comprising a membrane binding domain.
  • the PS4 nucleic acid may be expressed at the desired levels in a host organism using an expression vector.
  • An expression vector comprising a PS4 nucleic acid can be any vector which is capable of expressing the gene encoding PS4 nucleic acid in the selected host organism, and the choice of vector will depend on the host cell into which it is to be introduced.
  • the vector can be an autonomously replicating vector, i.e. a vector that exists as an episomal entity, the replication of which is independent of chromosomal replication, such as, for example, a plasmid, a bacteriophage or an episomal element, a minichromosome or an artificial chromosome.
  • the vector may be one which, when introduced into a host cell, is integrated into the host cell genome and replicated together with the
  • the expression vector typically includes the components of a cloning vector, such as, for example, an element that permits autonomous replication of the vector in the selected host organism and one or more phenotypically detectable markers for selection
  • the expression vector normally comprises control nucleotide sequences encoding a promoter, operator, ribosome binding site, translation initiation signal and optionally, a repressor gene or one or more activator genes. Additionally, the expression vector may comprise a sequence coding for an amino acid sequence capable of targeting the PS4 variant polypeptide to a host cell organelle such as a peroxisome or to a particular
  • Such a targeting sequence includes but is not limited to the sequence SKL.
  • the term 'expression signal includes any of the above control sequences, repressor or activator sequences.
  • the nucleic acid sequence the PS4 variant polypeptide is operably linked to the control sequences in proper manner with respect to expression.
  • a polynucleotide in a vector is operably linked to a control sequence that is capable of providing for the expression of the coding sequence by the host cell, i.e. the vector is an expression vector.
  • operably linked means that the components described are in a relationship permitting them to function in their intended manner.
  • a regulatory sequence "operably linked" to a coding sequence is ligated in such a way that
  • control sequences may be modified, for example by the addition of further transcriptional regulatory elements to make the level of transcription directed by the control sequences more responsive to transcriptional modulators.
  • the control sequences 2905 may in particular comprise promoters.
  • the nucleic acid sequence encoding for the variant PS4 polypeptide is operably combined with a suitable promoter sequence.
  • the promoter can be any DNA sequence having transcription activity in the host organism of choice and can be derived 2910 from genes that are homologous or heterologous to the host organism.
  • Suitable promoters for directing the transcription of the modified nucleotide sequence, such as PS4 nucleic acids, in a bacterial host include the promoter of the lac operon of E. coli, the Streptomyces coelicolor agarase gene dagA promoters, the
  • a suitable promoter can be selected, for example, from a bacteriophage promoter including a T7 promoter and a phage lambda promoter.
  • examples of useful promoters are those 2925 derived from the genes encoding the, Aspergillus oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, Aspergillus niger neutral ⁇ -amylase, A. niger acid stable ⁇ - amylase, A. niger glucoamylase, Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease, Aspergillus oryzae triose phosphate isomerase or Aspergillus nidulans acetamidase.
  • Suitable promoters for the expression in a yeast species include but are not limited to the Gal 1 and Gal 10 promoters of Saccharomyces cerevisiae and the Pichia pastoris AOXl or A0X2 promoters.
  • suitable bacterial host organisms are gram positive bacterial species such as Bacillaceae including Bacillus clausii. Bacillus subtilis, Bacillus licheniformis, Bacillus lentus, Bacillus brevis, Bacillus stearothermophilus, Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus coagulans, Bacillus lautus, Bacillus megaterium and
  • a suitable yeast host organism can be selected from the biotechnologically relevant yeasts species such as but not limited to yeast species such as Pichia sp., Hansenula sp or Kluyveromyces, Yarrowinia species or a species of Saccharomyces including 2950 Saccharomyces cerevisiae or a species belonging to Schizosaccharomyce such as, for example, S. Pombe species.
  • yeast species such as Pichia sp., Hansenula sp or Kluyveromyces, Yarrowinia species or a species of Saccharomyces including 2950 Saccharomyces cerevisiae or a species belonging to Schizosaccharomyce such as, for example, S. Pombe species.
  • a strain of the methylotrophic yeast species Pichia pastoris is used as the host organism.
  • the host organism is a Hansenula species.
  • Suitable host organisms among filamentous fungi include species of Aspergillus, e.g. Aspergillus niger, Aspergillus oryzae, Aspergillus tubigensis, Aspergillus awamori or Aspergillus nidulans.
  • strains of a Fus ⁇ rium species e.g. Fus ⁇ rium oxysporum or of a Rhizomucor species such as Rhizomucor miehei can be used as the host organism.
  • Other suitable strains include Thermomyces and Mucor species.
  • Suitable fungal host organisms may also include Trichoderm ⁇ spp (especially
  • Host cells comprising polynucleotides may be used to express polypeptides, such 2965 as variant PS4 polypeptides, fragments, homologues, variants or derivatives thereof.
  • Host cells may be cultured under suitable conditions which allow expression of the proteins. Expression of the polypeptides may be constitutive such that they are continually produced, or inducible, requiring a stimulus to initiate expression, hi the case of inducible expression, protein production can be initiated when required by, for example, addition of 2970 an inducer substance to the culture medium, for example dexamethasone or EPTG.
  • Polypeptides can be extracted from host cells by a variety of techniques known in the art, including enzymatic, chemical and/or osmotic lysis and physical disruption. Polypeptides may also be produced recombinantly in an in vitro cell-free system, such as the TnTTM (Promega) rabbit reticulocyte system.
  • TnTTM Promega
  • Pseudomon ⁇ s s ⁇ ch ⁇ rophil ⁇ is grown overnight on LB media and chromosomal DNA is isolated by standard methods (Sambrook J, 1989). A 2190 bp fragment containing the PS4 open reading frame (Zhou et ⁇ l, 1989) is amplified from P. s ⁇ ch ⁇ rophil ⁇
  • 2980 chromosomal DNA by PCR using the primers Pl and P2 (see Table 3).
  • the resulting fragment is used as a template in a nested PCR with primers P3 and P4, amplifying the openreading frame of PS4 without its signal sequence and introducing a Ncol site at the 5' end of the gene and a BamHI site at the 3 'end. Together with the Ncol site a codon for a N-terminal Methionine is introduced, allowing for intracellular expression of PS4.
  • 2985 1605 bp fragment is cloned into pCRBLUNT TOPO (Invitrogen) and the integrity of the construct analysed by sequencing.
  • the E.coli Bacillus shuttle vector pZ ⁇ P66K (Penninga et al, 1996) is modified to allow for expression of the PS4 under control of the P32 promoter and the ctgase signal sequence.
  • the resulting plasmid, pGSmta is transformed into B. subtilis.
  • a second expression construct is made in which the starch binding domain of PS4 is removed.
  • a PCR with primers P3 and P6 (Table 3) on pCSmta a truncated version of the mta gene is generated.
  • the full length mta gene in pCSmta is exchanged with the truncated version which resulted in the plasmid pCSmta-SBD.
  • 2995 Mutations are introduced into the mta gene by 2 methods. Either by a 2 step PCR based method, or by a Quick Exchange method (QE). For convenience the mta gene is split up in 3 parts; a Pvul-Fspl fragment, a Fspl-Pstl fragment and a Pstl-Aspl fragment, further on referred to as fragment 1, 2 and 3 respectively.
  • QE Quick Exchange method
  • mutations are introduced using Pfu DNA 3000 polymerase (Stratagene).
  • a first PCR is carried out with a mutagenesis primer (Table 4) for the coding strand plus a primer downstream on the lower strand (either 2R or 3R Table 3).
  • the reaction product is used as a primer in a second PCR together with a primer upstream on the coding strand.
  • the product of the last reaction is cloned into pCRBLUNT topo (Invitrogen) and after sequencing the fragment is exchanged with the corresponding 3005 fragment in pCSmta.
  • mutations are introduced using two complementary primers in a PCR on a plasmid containing the mta gene, or part of the mta gene.
  • plasmids comprising of 3 SDM 3010 plasmids and 3 pCS ⁇ plasmids.
  • the SDM plasmids each bear 1 of the fragments of the mta gene as mentioned above, in which the desired mutation is introduced by QE. After verification by sequencing, the fragments are cloned into the corresponding recipient pCS ⁇ plasmid.
  • the pCS ⁇ plasmids are inactive derivatives from pCSmta. Activity is restored by cloning the corresponding fragment from the SDM plasmid, enabling easy 3015 screening.
  • the PS4 variants were generated using a QuikChange ® Multi Site Directed Mutagenesis Kit (Stratagene) according to the manufactures protocol with some modifications as described.
  • Step 3 Transformation of XLIO-Gold ® Ultracompetent Cells
  • the vector system used for pPD77 is based on pCRbluntTOPO ⁇ (invitrogen).
  • the zeocin resistance cassette has been removed by pmll, 393 bp fragment removed.
  • the expression 3095 cassette from the pCC vector (P32-ssCGTase-PS4-tt) has then been inserted into the vector.
  • the vector pCCMini is then cut with restriction enzymes, Nco 1 and Hind III, and the 3110 digestion is then run on a 1% agarose gel.
  • the fragment sized 3569 bp is cut out of the gel and purified using Qiagen gel purification kit.
  • Sequence pSac-pMD229 (SEQ ID NO: 14) comprising mutations at N33 Y, D34N, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, H272Q, G303E, H307L, A309P, S334P relative to wild type non-maltogenic exoamylase is made 3135 from a wild type sequence using site directed mutagenesis (as described above in Example 2) or Multi Site Directed Mutagenesis (as described above in Example 3), with the primers in the table below:
  • Sequence pSac-pMS382 (SEQ ID NO: 22) comprising 307K is made from pSac- pSac-pMD229 using Multi Site Directed Mutagenesis (as described above in Example 3), with the primers in the table below:
  • PS4 variant polypeptides with other residues at position 307 are generated using Multi Site Directed Mutagenesis (as described above in Example 3), with the primers in the table below:
  • Bacillus subtilis (strain DB104A; Smith et al. 1988; Gene 70, 351-361) is transformed with the mutated plasmids according to the following protocol.
  • SMMP mix equal volumes of 2 x SMM and 4 x YT.
  • DM3 regeneration medium mix at 60 C (waterbath; 500-ml bottle):
  • the shake flask substrate is prepared as follows:
  • the substrate is adjusted to pH 6.8 with 4N sulfuric acid or sodium hydroxide before autoclaving. 100 ml of substrate is placed in a 500 ml flask with one baffle and
  • dextrose syrup is prepared by mixing one volume of 50% w/v dextrose with one volume of water followed by autoclaving for 20 minutes.
  • the shake flasks are inoculated with the variants and incubated for 24 hours at 35°C/180rpm in an incubator. After incubation cells are separated from broth by
  • Betamyl unit is defined as activity degrading 0,0351 mmole per 1 min. of
  • the assay mix contains 50 ul 50 mM Na-citrate, 5 mM CaC12, pH 6,5 with 25 ul enzyme sample and 25 ul Betamyl substrate (Glc5-PNP and a-glucosidase) from Megazyme, Ireland (1 vial dissolved in 10 ml water).
  • the assay mix is incubated for 30 min. at 4OC and then stopped by adding 150 ul 4% Tris.
  • the endo-amylase assay is identical to the Phadebas assay run according to manufacturer (Pharmacia & Upjohn Diagnostics AB).
  • 11/2 is defined as the time (in minutes) during which half the enzyme activity is 3250 inactivated under defined heat conditions.
  • the sample is heated for 1-40 minutes at constant temperatures of 60°C to 90 0 C. The half life is calculated based on the residual Betamyl assay.
  • the doughs are made in the Farinograph at 30.0 0 C. 10.00 g reformed flour is 3265 weighed out and added in the Farinograph; after 1 min. mixing the reference/sample
  • FU should be 400 on the reference, if it is not, this should be adjusted with, for example, the quantity of liquid.
  • the reference/sample is removed with a spatula and placed in the hand (with a disposable glove on it), before it is filled into small glass tubes (of approx. 4.5 em's length) that are put in NMR tubes and corked up. 7 tubes per dough are made.
  • the tubes are stored at 20.0°C in a thermo cupboard.
  • the solid content of the 3280 crumb was measured by proton NMR using a Bruker NMS 120 Minispec NMR analyser at day 1, 3 and 7 as shown for crumb samples prepared with 0, 05, 1 abnd 2 ppm PSacD34 in Fig. 2.
  • the lower increase in solid content over time represents the reduction in amylopectin retrogradation.
  • the capsules are used for Differential Scanning Calorimetry on a Mettler Toledo DSC 820 instrument. As parameters are used a heating cycle of 20-95 0 C with 10 0 C per min. heating and Gas/flow: N 2 /80 ml per min. The results are analysed and the enthalpy for melting of retrograded amylopectin is calculated in J/g.
  • PS4 variants show a strong reduction of the amylopectin retrogradation after baking as measured by Differential Scanning Calorimetry in comparison to the control.
  • the PS4 variants show a clear dosage effect.
  • the sponge dough is prepared from 1400 g of flour "Gold Medal” from General Mills, USA, 800 g of water, 40 g of rape seed oil, 7,5 g GRINDSTEDTM SSL P55 Veg, 1O g emulsif ⁇ er DIMOD ANTM PH200 and 60 g of compressed yeast.
  • the sponge is 3300 mixed for 1 min. at low speed and subsequently 3 min. at speed 2 on a Hobart spiral mixer.
  • the sponge is subsequently fermented for 3 hours at 25°C, 85% RH.
  • the dough is rested for 5 min. at ambient temperature, and then 550 g dough pieces are scaled, moulded on Glimek sheeter with the settings 1:4, 2:4, 3:15, 4:12 and width 8 on both sides and transferred to a baking form. After 65 min. proofing at 43 °C at 3310 95% RH the doughs are baked for 26 min. at 200°C in an MIWE oven.
  • Danish Rolls are prepared from a dough based on 2000 g Danish reform flour (from Cerealia), 12O g compressed yeast, 32 g salt, and 32 g sucrose. Water is added to the dough according to prior water optimisation.
  • the dough is mixed on a Diosna mixer (2 min. at low speed and 5 min. at high speed).
  • the dough temperature after mixing is kept at 26°C. 1350 g dough is scaled and rested for 10 min. in a heating cabinet at 30°C.
  • the rolls are moulded on a Fortuna molder and proofed for 45 min. at 34°C and at 85% relative humidity. Subsequently the rolls are baked in a Bago 2 oven for 18 min. at 250°C with steam in the first 13 seconds.
  • the rolls are evaluated regarding crust appearance, crumb homogeneity, capping of the crust, ausbund and specific volume (measuring the volume with the rape seed displacement method).
  • PS4 variants increase the specific 3325 volume and improve the quality parameters of Danish rolls. Thus PS4 variants are able to control the volume of baked products.
  • Firmness, resilience and cohesiveness are determined by analysing bread slices by 3330 Texture Profile Analysis using a Texture Analyser From Stable Micro Systems, UK. Calculation of firmness and resilience is done according to preset standard supplied by Stable Micro System, UK. The probe used is aluminium 50 mm round.
  • Bread is sliced with the width of 12.5 mm. The slices are stamped out to a circular piece with a diameter of 45 mm and measured individually.
  • the mode of compression is a modification to the one used in Standard method AACC 74-09.
  • the sample is compressed twice in the test.
  • Figure 1 shows an example of a curve from the Texture Analyser.
  • 3350 Firmness is determined at 40% compression during the first compression. The figure is the force needed to compress the slice to 40% of the total thickness. The lower the value, the softer the bread. The firmness is expressed as a pressure, for example, in hPa.
  • This assay may be referred to as the "Firmness Evaluation Protocol”.
  • the ratio between Al and A2 is defined as the resilience of the sample, and is 3360 expressed as Resilience Units.
  • True elastic material will give a symmetric curve, as the force applied during the first part will be equal to the force in the second part.
  • A2 is normally smaller than A2 due to disturbance of the structure during compression. Hence, resilience is always lower than 1.
  • This assay may be referred to as the "Resilience Evaluation Protocol”.
  • the cohesiveness is defined as the ratio between the area under second compression to the area under first compression (A3/A1+A2), and is expressed as Cohesiveness Units. It is a measure of the decay of the sample during compression. The higher the ability of the sample to regain its shape after first compression the closer the 3370 value will be to 1. For bread and bread-like material cohesiveness is always lower than 1.
  • This assay may be referred to as the "Cohesiveness Evaluation Protocol”.
  • 3375 Tearing is done by pulling the crumb apart by the fingers. First the slice is torn from the middle of the top bread surface to the middle of the bottom bread surface. Thereafter, each half of the original slice is torn from the crust side to the inside of the slice.
  • the small crumb pieces, which are separated from the 4 squares, are removed by shaking each piece after a tear at least 3 times by moving the hand up and down. 3380 The weight of the separated small crumb pieces is determined as a measure of crumbliness. This assay may be referred to as the "Crumbliness Evaluation Protocol".
  • the toast bread is sliced using an automatic bread slicer with set slice thickness of 15 mm.
  • the slice is folded by hand from the top of the slice towards the bottom, so that 3385 the direction of the crease is from side to side.
  • the foldability is visually assessed using the following scoring system:
  • This assay may be referred to as the "Foldability Evaluation Protocol”.
  • Thermal stability of amylase pSac-pMS382 is measured as described above and 3390 compared to that of pSac-D34 / pMD3 (SEQ ID NO: 2) and pSac-pMD229 (SEQ ID NO: 13).
  • half-life defined as the time (in minutes) for 50% inactivation is determined based on residual activity using the Betamyl assay after incubation for 1-40 minutes at 75, 80 and 85°C (167, 176 and 185°F, 3395 respectively) in 50 mM sodium-citrate, 5 mM calcium chloride, pH 6.5.
  • pSac-pMS382 (SEQ ID NO: 21) comprising a substitution to a basic or positively charged residue at position 307, i.e., 20,000, 40,000 and 60,000 Betamyl units/kg of pSac-pMS382.
  • Figure 3 shows the results of a baking trial in which firmness of bread is tested.
  • pSac-pMS382 (SEQ BD NO: 21) comprising a substitution to a basic or positively charged residue at position 307, i.e., 20,000, 40,000 and 60,000 Betamyl units/kg of pSac-pMS382.
  • the resilience of the bread is tested according to the protocol set out in Example 14 3415 at various times after baking. As a control, resilience of bread baked without any enzyme is also measured.
  • Figure 4 shows the results of a baking trial in which resilience of bread is tested.
  • 3420 Bread is baked with varying amounts of pSac-pMS382 (SEQ ID NO: 21) comprising a substitution to a basic or positively charged residue at position 307, i.e., 20,000, 40,000 and 60,000 Betamyl units/kg of pSac-pMS382.
  • the cohesiveness of the bread is tested according to the protocol set out in Example 15 at various times after baking. As a control, cohesiveness of bread baked 3425 without any enzyme is also measured.
  • Figure 5 shows the results of a baking trial in which cohesiveness of bread is tested.
  • Example 22 Improved Handling Properties of Food Products Treated with PS4 Variant Polypeptides: Firmness
  • Bread is also baked with 60,000 Betamyl units/kg of pSac-D34 / pMD3 (SEQ ID 3435 NO: 2) and 60,000 Betamyl units/kg of pSac-pMD229 (SEQ ID NO: 13), each without a substitution at position 307 to a basic or positively charged amino acid. The firmness of the bread is tested.
  • Figure 6 shows the results of a baking trial in which firmness of bread treated with 3440 PS4 variant polypeptide with and without substitution at 307 is tested.
  • Example 23 Improved Handling Properties of Food Products Treated with PS4 Variant Polypeptides: Firmness, Resilience and Cohesiveness
  • Bread is also baked with 60,000 Betamyl units/kg of pSac-D34 / pMD3 (SEQ ID NO: 2) and 60,000 Betamyl units/kg of pSac-pMD229 (SEQ ID NO: 13), each without a substitution at position 307 to a basic or positively charged amino acid. The resilience of 3450 the bread is tested.
  • Figure 7 shows the results of a baking trial in which resilience of bread treated with PS4 variant polypeptide with and without substitution at 307 is tested.
  • Betamyl units/kg of pSac-pMD229 (SEQ ID NO: 13), each without a substitution at position 307 to a basic or positively charged amino acid. The cohesiveness of the bread is tested.
  • Figure 8 shows the results of a baking trial in which cohesiveness of bread treated with PS4 variant polypeptide with and without substitution at 307 is tested.
  • Sponge and dough toast bread treated with 4 ppm of pSac-pMS382 (SEQ ID NO: 3470 21, H307K substitution) is baked and foldability of the resulting breads is tested and scored as described above.
  • sponge and dough toast bread not treated with enzyme is baked and foldability tested and scored.
  • Tests are done on three slices on day 13 after baking.
  • Sponge and dough toast bread treated with 4 ppm of pSac-pMS382 (SEQ ID NO: 21, H307K substitution) is baked and foldability of the resulting breads is tested and scored as described above.
  • sponge and dough toast bread not treated with enzyme is baked and foldability tested and scored. Foldability of sponge and dough toast breads treated with other enzymes as shown below is also tested.
  • Enzyme pSac-D34 (also known as pMD3) comprises mutations N33Y, D34N,G121D, G134R, A141P, I157L, L178F, A179T, G223A, H307L, S334P relative to 3490 wild type non-maltogenic exoamylase and its sequence is shown as SEQ ID NO: 2.
  • Enzyme pSac-pMD229 comprises mutations N33Y, D34N, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, H272Q, G303E, H307L, A309P, S334P relative to wild type non-maltogenic exoamylase and its sequence is shown as SEQ ID NO: 13.
  • Sponge and dough toast bread treated with 6 ppm of pSac-pMS382 (SEQ ID NO: 21, 307K substitution) alone or in combination with other enzymes as shown below is baked and foldability of the resulting breads is tested and scored as described above.
  • Combination 3 6 ppm pSac-pMS382 + 50 ppm GRINDAMYLTM POWERBake 3510 900 + 150 ppm GRINDAMYLTM POWERBake 4050
  • GRINDAMYLTM POWERBake 900 is a xylanase commercially available from Danisco A/S.
  • GRINDAMYLTM Max-Life U4 is a bacterial ⁇ -amylase commercially available from Danisco A/S.
  • GRINDAMYLTM POWERBake 4050 is a lipase commercially available from Danisco A/S.
  • Tests are done on three slices on day 5 after baking.
  • Sponge and dough toast bread treated with 4 ppm of pSac-pMS382 (SEQ ID NO: 21, 307K substitution) is baked and crumbliness of the resulting breads is tested and scored as described above.
  • sponge and dough toast bread not treated with enzyme is baked and 3530 foldability tested and scored.
  • Tests are done on day 13 after baking.
  • crumbliness is reduced in sponge and dough toast bread after 13 days, treated with a PS4 variant polypeptide comprising a substitution at 3535 position 307 to a basic or positively charged amino acid.
  • Sponge and dough toast bread treated with 4 ppm of pSac-pMS382 (SEQ ID NO: 21, 307K substitution) is baked and crumbliness of the resulting breads is tested and 3540 scored as described above.
  • sponge and dough toast bread not treated with enzyme is baked and foldability tested and scored.
  • Tests are done on day 15 after baking.
  • polypeptides with substitutions at position 307 to lysine are made 3550 and their properties tested as described above.
  • sequences of the polypeptides comprise the sequence of SEQ ID NO: 2 together with the substitutions specified.
  • polypeptides with histidine at position 307 together with other mutations are made and their properties tested as described above.
  • sequences of the polypeptides comprise the sequence of SEQ ID NO: 2 together with the substitutions specified.
  • 3560 L307K are generated using Multi Site Directed Mutagenesis (as described above in Example 3), with the primers in the table below:
  • Primer used for site scan in osition 307 :
  • SSM471 BlO amino acid sequence of SSM471 BlO
  • SSM471 BlO nucleic acid sequence of SSM471 BlO
  • amino acid sequence of SSM471 C04 is set out as SEQ ID NO: 29, while the 3570 nucleic acid sequence of SSM471 C04 is set out as SEQ ID NO: 30.
  • PS4 variant polypeptides derived from a parent polypeptide and with mutations L307R or L307K are likewise generated using Multi Site Directed Mutagenesis (as described above hi Example 3), with the primers in the table below:
  • Primer used for site scan in osition 307 :
  • the additional mutation is generated by Multi Site Directed Mutagenesis (according to the method described in Example 3).
  • Tortillas are baked to a recipe as follows:

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Abstract

We describe a PS4 variant polypeptide derivable from a parent polypeptide having non-maltogenic exoamylase activity, in which the PS4 variant polypeptide comprises an amino acid substitution at position 307 to lysine (K) or arginine (R), with reference to the position numbering of a Pseudomonαs sαcchαrophiliα exoamylase sequence shown as SEQ ID NO: 1. Preferably, the PS4 variant polypeptide further comprises an amino acid substitution at position 70, preferably G70D. The amino acid at positions 272 and 303 of the sequence of the are preferably histidine (H) and glycine (G).

Description

POLYPEPTIDE
Reference is made to US provisional applications serial nos. 60/485,413, 60/485,539 and 60/485,616 filed July 7, 2003. Reference is also made to international applications PCT/US2004/021723 and PCT/US2004/021739 filed July 7, 2004 and designating the US (applicant: Genencor International, Inc). Reference is also made to US utility applications serial numbers 10/886,905 and 10/866,903 all of which were also filed July 7, 2004.
Reference is also made to US provisional application serial number 60/608,919 (filed as US utility application serial number 10/887,056 on July 7, 2004 but converted to a provisional application on September 15, 2004). Reference is also made to US provisional application serial number 60/612,407 which was filed September 22, 2004.
Reference is additionally made to US application serial no. 60/485,539 filed July 7, 2003. Reference is also made to international application PCT/IB2004/002487 filed July 7, 2004 and designating the US (applicant: Danisco AJS). Reference is also made to US utility application serial number 10/886,023 filed July 7, 2004.
Reference is also made to US utility applications serial numbers 10/886,505, 10/886,527 and 10/886,504, all of which were filed July 7, 2004. Reference is also made to US utility application serial number 10/947,612 filed September 22nd, 2004.
Reference is also made to International Patent Application serial number PCT/GB2005/002675 filed July 7, 2005 and designating the US (applicants: Danisco A/S and Genencor International, Inc, D Young & Co Attorney Reference: P020161WO). Reference is also made to US provisional application serial number 60/697,302 filed July 7th, 2005.
The foregoing applications, and each document cited or referenced in each of the present and foregoing applications, including during the prosecution of each of the foregoing applications ("application and article cited documents"), and any manufacturer's instructions or catalogues for any products cited or mentioned in each of the foregoing applications and articles and in any of the application and article cited documents, are hereby incorporated herein by reference. Furthermore, all documents cited in this text, and all documents cited or reference in documents cited in this text, and any manufacturer's instructions or catalogues for any products cited or mentioned in this text or in any document hereby incorporated into this text, are hereby incorporated herein by reference. Documents incorporated by reference into this text or any teachings therein may be used in the practice of this invention. Documents incorporated by reference into this text are not admitted to be prior art.
FIELD
This invention relates to polypeptides, specifically amylase polypeptides and nucleic acids encoding these, and their uses as non-maltogenic exoamylases in producing food products. The amylases of the present invention have been engineered to have more beneficial qualities. Specifically, the amylases of the current invention show an altered exospecifity and/or altered thermostability. In particular, the polypeptides are derived from polypeptides having non-maltogenic exoamylase activity, in particular, glucan 1,4-alpha- maltotetrahydrolase (EC 3.2.1.60) activity.
BACKGROUND Improved amylases can ameliorate problems inherent in certain processes, such as baking. Crystallisation of amylopectin takes place in starch granules days after baking, which leads to increased firmness of bread and causes bread staling. When bread stales, bread loses crumb softness and crumb moisture. As a result, crumbs become less elastic, and bread develops a leathery crust.
Enzymatic hydrolysis (by amylases, for example) of amylopectin side chains can reduce crystallization and increase anti-staling. Crystallization depends upon the length of amylopectin side chains: the longer the side chains, the greater the crystallization. Most starch granules are composed of a mixture of two polymers: amylopectin and amylose, of which about 75% is amylopectin. Amylopectin is a very large, branched molecule consisting of chains of α-D-glucopyranosyl units joined by (1-4) linkages, where the chains are attached by α-D-(l-6) linkages to form branches. Amylose is a linear chain of (1-4) linked α-D-glucopyranosyl units having few α-D-(l-6) branches.
Baking of farinaceous bread products such as white bread, bread made from bolted rye flour and wheat flour and rolls is accomplished by baking the bread dough at oven temperatures in the range of from 180 to 250°C for about 15 to 60 minutes. During the baking process a steep temperature gradient (200 → 1200C) prevails over the outer dough layers where the crust of the baked product is developed. However, due to steam, the temperature in the crumb is only about 1000C at the end of the baking process. Above temperatures of about 850C, enzyme inactivation can take place and the enzyme will have no anti-staling properties. Only thermostable amylases, thus, are able to modify starch efficiently during baking. Endoamylase activity can negatively affect the quality of the final bread product by producing a sticky or gummy crumb due to the accumulation of branched dextrins. Exo- amylase activity is preferred, because it accomplishes the desired modification of starch that leads to retardation of staling, with fewer of the negative effects associated with endoamylase activity. Reduction of endoamylase activity can lead to greater exospecifity, which can reduce branched dextrins and produce a higher quality bread.
SUMMARY
We provide, according to the invention, a PS4 variant polypeptide as set out in the claims. We further provide for the use of such a PS4 variant polypeptide, including in and as food additives, food products, bakery products, improver compositions, feed products including animal feeds, etc as set out in the claims. We provide for nucleic acids which encode and which relate to PS4 variant polypeptides, as set out in the claims. Methods for producing such PS4 variant polypeptides, as well as other aspects of the invention, are also set out in the claims.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 shows an example of a curve from a Texture Analyser.
Figure 2 shows the results of an experiment to determine the temperature stability of the PS4 variant polypeptides described here. X-axis: temperature, Y-axis: half-life (minutes). Diamonds: pSac-D34 / pMD3 (SEQ ID NO: 2), Squares: pSac-pMD229 (SEQ ID NO: 13), Triangles: pSac-pMS382 (SEQ ID NO: 21)
Figure 3 shows the results of a baking trial in which firmness of bread treated with various concentrations of PS4 variant polypeptide and untreated bread are tested. The X- axis shows the number of days, while the Y-axis shows firmness expressed as hPa (see Example 13). Diamond: 20,000 Betamyl units/kg of pSac-pMS382. Square: 40,000
Betamyl units/kg of pSac-pMS382. Triangle: 60,000 Betamyl units/kg of pSac-pMS382. Cross: Control (no enzyme).
Figure 4 shows the results of a baking trial in which resilience of bread treated with various concentrations of PS4 variant polypeptide and untreated bread are tested. The X- axis shows the number of days, while the Y-axis shows resilience expressed as Resilience Units (see Example 14). Diamond: 20,000 Betamyl units/kg of pSac-pMS382. Square: 40,000 Betamyl units/kg of pSac-pMS382. Triangle: 60,000 Betamyl units/kg of pSac- pMS382. Cross: Control (no enzyme). Figure 5 shows the results of a baking trial in which cohesiveness of bread treated 100 with various concentrations of PS4 variant polypeptide and untreated bread are tested. The X-axis shows the number of days, while the Y-axis shows cohesiveness expressed as Cohesiveness Units (see Example 15).. Diamond: 20,000 Betamyl/kg of pSac-pMS382. Square: 40,000 Betamyl/kg of pSac-pMS382. Triangle: 60,000 Betamyl/kg of pSac- pMS382. Cross: Control (no enzyme).
105 Figure 6 shows the results of a baking trial in which firmness of bread treated with
PS4 variant polypeptide with substitution at 307 is tested. The X-axis shows the number of days, while the Y-axis shows firmness expressed as hPa (see Example 13). Diamond: Control (no enzyme). Square: 60,000 Betamyl units / kg pSac-D34 / pMD3 (SEQ ID NO: 2). Triangle: 60,000 Betamyl units/kg of pSac-pMD229 (SEQ ID NO: 13). Cross: 60,000
110 Betamyl units/kg of pSac-pMS382.
Figure 7 shows the results of a baking trial in which resilience of bread treated with PS4 variant polypeptide with substitution at 307 is tested. The X-axis shows the number of days, while the Y-axis shows resilience expressed as resilience units (see Example 14). Diamond: Control (no enzyme). Square: 60,000 Betamyl units / kg pSac-D34 / pMD3 115 (SEQ ID NO: 2). Triangle: 60,000 Betamyl units/kg of pSac-pMD229 (SEQ ID NO: 13). Cross: 60,000 Betamyl units/kg of pSac-pMS382.
Figure 8 shows the results of a baking trial in which cohesiveness of bread treated with PS4 variant polypeptide with substitution at 307 is tested. The X-axis shows the number of days, while the Y-axis shows cohesiveness expressed as cohesiveness units (see 120 Example 15). Diamond: Control (no enzyme). Square: 60,000 Betamyl units / kg pSac-
D34 / pMD3 (SEQ ID NO: 2). Triangle: 60,000 Betamyl units/kg of pSac-pMD229 (SEQ ID NO: 13). Cross: 60,000 Betamyl units/kg of pSac-pMS382.
Figure 9. Foldability test day 8 after baking of tortillas with 400 ppm Novamyl (TM) 1500 and 50 BMK/kg pSac-pMS382 (SEQ ID NO: 21).
125 Figure 10. Foldability test day 8 after baking of tortillas with 400 ppm
NovamylTM 1500 and 50 BMK/kg pSac-pMS382 (SEQ ID NO: 21).
Figure 11.Firmness test of US toast prepared with SSM 471 BlO (SEQ ID NO: 27) and SSM 471 C04 (SEQ ID NO: 29).
Figure 12.Resilience test of US toast prepared with SSM 471 BlO(SEQ ID NO: 130 27) and SSM 471 C04 (SEQ ID NO: 29). Figure 13. Resilience test of US toast prepared with pMS 370 (SEQ ID NO: 31) and SSM 471 C04(SEQ ID NO: 29).
SEQUENCE LISTINGS
SEQ ID NO: 1 shows a PS4 reference sequence, derived from Pseudomonas
135 saccharophila maltotetrahydrolase amino acid sequence. SEQ ID NO: 2 shows a pSac- D34 sequence; Pseudomonas saccharophila maltotetrahydrolase amino acid sequence with 11 substitutions and deletion of the starch binding domain. SEQ ID NO: 3 shows a pSac-D20 sequence; Pseudomonas saccharophila maltotetrahydrolase amino acid sequence with 13 substitutions and deletion of the starch binding domain. SEQ ID NO: 4
140 shows a pSac— D14 sequence; Pseudomonas saccharophila maltotetrahydrolase amino acid sequence with 14 substitutions and deletion of the starch binding domain. SEQ ID NO: 5 shows a Pseudomonas saccharophila Glucan 1,4-alpha-maltotetrahydrolase precursor (EC 3.2.1.60) (G4-amylase) (Maltotetraose-forming amylase) (Exo- maltotetraohydrolase) (Maltotetraose-forming exo-amylase). SWISS-PROT accession
145 number P22963. SEQ ID NO: 6 shows a P. saccharophila mta gene encoding maltotetraohydrolase (EC number = 3.2.1.60). GenBank accession number X16732. SEQ ID NO:7 shows a PS4 reference sequence, derived from Pseudomonas stutzeri maltotetrahydrolase amino acid sequence. SEQ ID NO: 8 shows a PStu-D34 sequence; Pseudomonas stutzeri maltotetrahydrolase amino acid sequence with 9 substitutions. SEQ
150 ID NO: 9 shows a PStu-D20 sequence; Pseudomonas stutzeri maltotetrahydrolase amino acid sequence with 11 substitutions. SEQ ID NO: 10 shows a PStu-D14 sequence; Pseudomonas stutzeri maltotetrahydrolase amino acid sequence with 12 substitutions. SEQ ID NO: 11 shows a Pseudomonas stutzeri {Pseudomonas per fectomarinά). Glucan 1,4-alpha-maltotetrahydrolase precursor (EC 3.2.1.60) (G4-amylase) (Maltotetraose-
155 forming amylase) (Exo-maltotetraohydrolase)(Maltotetraose-forming exo-amylase). SWISS-PROT accession number P13507. SEQ ID NO: 12 shows a P.stutzeri maltotetraose-forming amylase (amyP) gene, complete cds. GenBank accession number M24516.
SEQ ID NO: 13 shows a pSac-pMD229 amino acid sequence having mutations 160 33Y, 34N, 121F, 134R, 141P, 146G, 157L, 161A5 178F, 179T, 223E, 229P, 272Q, 303E, 307L, 309P and 334P. SEQ ID NO: 14 shows a pSac-pMD229 nucleic acid sequence. SEQ ID NO: 15 shows a pSac-pMD248 amino acid sequence having mutations 33 Y, 34N, 121F, 134R, 141P, 145D, 146G, 157L, 178F, 179T, 223E, 229P, 272Q, 303E, 307L and 334P. SEQ ID NO: 16 shows a pSac-pMD248 nucleic acid sequence. SEQ ID NO: 165 17 shows a pSac-pMD253 amino acid sequence having mutations 33Y, 34N, 121D, 134R, 141P, 146G, 157L, 178F, 179T, 223E5 229P, 272Q, 303E, 307L, 309P and 334P. SEQ ID NO: 18 shows a pSac-pMD253 nucleic acid sequence. SEQ ID NO: 19 shows a pSac- pMD271 amino acid sequence having mutations 3S, 33Y, 34N, 7OD, 121D, 134R, 141P, 146G, 157L, 178F, 179T, 223E5 229P5 272Q5 303E5 307L, 309P and 334P. SEQ ID NO: 170 20 shows a pSac-pMD271 nucleic acid sequence.
SEQ ID NO: 21 shows a pSac-pMS382 amino acid sequence having mutations 33Y5 34N5 7OD, 121F, 134R, 141P5 146G5 157L5 161A, 178F, 179T5 223E5 229P5 307K5 309P and 334P. SEQ ID NO: 22 shows a pSac-pMS382 nucleotide sequence sequence. SEQ ID NO: 23 shows a pSac— pMS382R amino acid sequence having mutations 33Y5 175 34N5 7OD, 121F5 134R5 141P5 146G5 157L, 161A, 178F, 179T5 223E5 229P5 307R5 309P and 334P. SEQ ID NO: 24 shows a pSac-pMS382R nucleotide sequence sequence. SEQ DD NO: 25 shows a pSac-pMS382H amino acid sequence having mutations 33Y5 34N5 70D5 121F5 134R5 141P, 146G, 157L, 161A5 178F5 179T5 223E5 229P5 309P and 334P. SEQ ID NO: 26 shows a pSac-pMS382H nucleotide sequence sequence.
180 SEQ ED NO: 27 shows a SSM471 BlO amino acid sequence having mutations
33Y5 34N5 121F5 134R5 141P, 146G5 157L, 161A5 178F5 179T5 223E5 229P5 272Q5 303E5 307R5 309P and 334P. SEQ ED NO: 28 shows a SSM471 BlO nucleic acid sequence. SEQ ED NO: 29 shows a SSM471 C04 amino acid sequence having mutations 33Y5 34N5 121F5 134R, 141P5 146G5 157L5 161A, 178F5 179T, 223E, 229P5 272Q5 303E5 307K5 309P
185 and 334P. SEQ ED NO: 30 shows a SSM471 C04 nucleic acid sequence. SEQ ED NO: 31 shows a PMS 370 amino acid sequence having mutations 33Y5 34N, 121F5 134R5 141P5 146G5 157L5 161A5 178F5 179T5 223E5 229P5 272Q5 303E5 309P and 334P. SEQ ID NO: 32 shows a PMS 370 nucleic acid sequence.
DETAILED DESCRIPTION
190 In the following description and examples, unless the context dictates otherwise, dosages of PS4 variant polypeptides are given in parts per million (micrograms per gram) of flour. For example, "1 D34" indicates 1 part per million of pSac-D34 based on weight per weight. Preferably, enzyme quantities or amounts are determined based on activity assays as equivalents of pure enzyme protein measured with bovine serum albumin (BSA)
195 as a standard, using the assay described in Bradford (1976, A rapid and sensitive method for the quantification of microgram quantities of protein utilizing the principle of protein- dye binding. Anal. Biochem. 72:248-254). In describing the different PS4 variant polypeptide variants produced or which are contemplated to be encompassed by this document, the following nomenclature will be 200 adopted for ease of reference:
(i) where the substitution includes a number and a letter, e.g., 141P, then this refers to [position according to the numbering system/substituted amino acid]. Accordingly, for example, the substitution of an amino acid to proline in position 141 is designated as 141 P;
205 (ii) where the substitution includes a letter, a number and a letter, e.g., A141P, then this refers to [original amino acid/position according to the numbering system/substituted amino acid]. Accordingly, for example, the substitution of alanine with proline in position 141 is designated as Al 4 IP.
Where two or more possible substituents are possible at a particular position, this 210 will be designated by contiguous letters, which may optionally be separated by slash marks "/", e.g., G303ED or G3O3E/D. Where the relevant amino acid at a position can be substituted by any amino acid, this is designated by [position according to the numbering system/X], e.g., 121X.
Multiple mutations may be designated by being separated by slash marks "/", e.g. 215 A141P/G223A or commas ",", e.g., A141P, G223A representing mutations in position 141 and 223 substituting alanine with proline and glycine with alanine respectively.
Unless defined otherwise herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Singleton, et al, DICTIONARY OF MICROBIOLOGY AND MOLECULAR
220 BIOLOGY, 2D ED., John Wiley and Sons, New York (1994), and Hale & Marham, THE
HARPER COLLINS DICTIONARY OF BIOLOGY, Harper Perennial, NY (1991) provide one of skill with a general dictionary of many of the terms used in this invention. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are
225 described. Numeric ranges are inclusive of the numbers defining the range. Unless otherwise indicated, nucleic acids are written left to right in 5' to 3' orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of chemistry, molecular biology, microbiology, recombinant 230 DNA and immunology, which are within the capabilities of a person of ordinary skill in the art. Such techniques are explained in the literature. See, for example, J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Books 1-3, Cold Spring Harbor Laboratory Press; Ausubel, F. M. et al. (1995 and periodic supplements; Current Protocols in Molecular Biology, ch. 9, 13, and 16, John
235 Wiley & Sons, New York, N.Y.); B. Roe, J. Crabtree, and A. Kahn, 1996, DNA Isolation and Sequencing: Essential Techniques, John Wiley & Sons; J. M. Polak and James O'D. McGee, 1990, In Situ Hybridization: Principles and Practice; Oxford University Press; M. J. Gait (Editor), 1984, Oligonucleotide Synthesis: A Practical Approach, IrI Press; D. M. J. Lilley and J. E. Dahlberg, 1992, Methods of Enzymology: DNA Structure Part A: Synthesis
240 and Physical Analysis of DNA Methods in Enzymology, Academic Press; Using
Antibodies : A Laboratory Manual : Portable Protocol NO. I by Edward Harlow, David Lane, Ed Harlow (1999, Cold Spring Harbor Laboratory Press, ISBN 0-87969-544-7); Antibodies : A Laboratory Manual by Ed Harlow (Editor), David Lane (Editor) (1988, Cold Spring Harbor Laboratory Press, ISBN 0-87969-314-2), 1855, Lars-Inge Larsson
245 "Immunocytochemistry: Theory and Practice", CRC Press inc., Baca Raton, Florida, 1988, ISBN 0-8493-6078-1, John D. Pound (ed); "Immunochemical Protocols, vol 80", in the series: "Methods in Molecular Biology", Humana Press, Totowa, New Jersey, 1998, ISBN 0-89603-493-3, Handbook of Drug Screening, edited by Ramakrishna Seethala, Prabhavathi B. Fernandes (2001, New York, NY, Marcel Dekker, ISBN 0-8247-0562-9);
250 and Lab Ref: A Handbook of Recipes, Reagents, and Other Reference Tools for Use at the Bench, Edited Jane Roskams and Linda Rodgers, 2002, Cold Spring Harbor Laboratory, ISBN 0-87969-630-3. Each of these general texts is herein incorporated by reference.
All patents and publications, including all sequences disclosed within such patents and publications, referred to herein are expressly incorporated by reference.
255 PS4 VARIANT POLYPEPTIDES
We provide a polypeptide having a substitution at one or more positions which effect an altered property, which may be any combination of altered exospecificity or altered thermostability, or an altered handling property, relative to the parent enzyme. Such variant polypeptides are referred to in this document for convenience as "PS4 variant 260 polypeptides".
The PS4 variant polypeptides preferably exhibit enzyme activity. More preferably, the PS4 variant polypeptides comprise amylase activity, preferably exoamylase activity. In highly preferred embodiments, the PS4 variant polypeptides exhibit non-maltogenic exoamylase activity. 265 We further provide for compositions, including food additives, food products, bakery products, improver compositions, feed products including animal feeds, etc comprising such altered PS4 variant polypeptides, preferably those which have non- maltogenic exoamylase activity, as well as methods of making and using such polypeptides and the compositions.
270 As noted above, the PS4 variant polypeptides may comprise one or more improved handling properties, preferably improved baking properties. Thus, the PS4 variant polypeptides are such that the food products so treated have one or more of (preferably all of) a lower firmness, a higher resilience, a higher cohesiveness, a lower crumbliness or a higher foldability. Such improved handling or baking properties exhibited by the PS4
275 variant polypeptides are described in further detail below.
We provide for the treatment of food products, particularly doughs and bakery products with such polypeptides, and such that the food products exhibit the desired qualities set out above.
We provide for other uses of such compositions such as in the preparation of 280 detergents, as sweeteners, syrups, etc. The compositions include the polypeptide together with at least one other component, hi particular, we provide for food or feed additives comprising the polypeptides.
Such polypeptides and nucleic acids vary from their parent sequences by including a number of mutations. In other words, the sequence of the PS4 variant polypeptide or 285 nucleic acid is different from that of its parent at a number of positions or residues. In preferred embodiments, the mutations comprise amino acid substitutions, that is, a change of one amino acid residue for another. Thus, the PS4 variant polypeptides comprise a number of changes in the nature of the amino acid residue at one or more positions of the parent sequence.
290 As used herein, the term "variant" should be taken to mean a molecule being derivable from a parent molecule. Variants include polypeptides as well as nucleic acids. Variants include deletions, insertions and substitutions at the amino acid level and transversions, transitions and inversions at the nucleic acid level among other things, at one or more locations. Variants also include truncations. Variants include homologous and
295 functional derivatives of parent molecules. Variants include sequences that are complementary to sequences that are capable of hybridising to the nucleotide sequences presented herein. POSITION 307 BASIC RESIDUE MUTANTS
We provide for PS4 variant polypeptides with sequence alterations comprising 300 amino acid substitutions in a amylase sequence, preferably an exoamylase activity, more preferably a non-maltogenic exoamylase sequence.
Specifically, we provide for a PS4 variant polypeptide derivable from a parent polypeptide having non-maltogenic exoamylase activity comprising an amino acid mutation at position 307 with reference to the position numbering of a Pseudomonas 305 saccharophilia exoamylase sequence shown as SEQ ID NO: 1. The position 307 substitution is preferably a substitution to a basic or positively charged amino acid, preferably lysine (K) or arginine (R).
In one embodiment, we provide a PS4 variant polypeptide in which the amino acid substitution at position 307 is a substitution to lysine (307K), preferably H307K. In 310 another embodiment, we provide a PS4 variant polypeptide according to Claim 1 or 2, in which the amino acid substitution at position 307 is a substitution to arginine (307R), preferably H307R.
The PS4 variant polypeptide may further comprise a mutation at position 70 to aspartic acid (D), preferably 7OD. In preferred embodiments, the substitution is G70D. 315 Accordingly, in some embodiments, we provide for a PS4 variant polypeptide comprising substitutions G70D, H307K or G70D, H307R relative to a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ID NO: 1.
The residues at positions 272 and 303 may be "wild type", or they may be mutated, hi preferred embodiments, the residue at position 272 is a wild type residue, i.e., histidine
320 (H) Preferably, the residue at position 303 is also a wild type residue, i.e., glycine (G). We therefore provide for a PS4 variant polypeptide comprising substitutions G70D and H307K with the residue at position 272 being H and the residue at position 303 being G, or G70D and H307R with the residue at position 272 being H and the residue at position 303 being G relative to a Pseudomonas saccharophilia exoamylase sequence shown as
325 SEQ ID NO: 1.
Such variant polypeptides, and others as described hi this document, are referred to in this document as "PS4 variant polypeptides". Nucleic acids encoding such variant polypeptides are also disclosed and will be referred to for convenience as "PS4 variant nucleic acids". PS4 variant polypeptides and nucleic acids will be described in further 330 detail below. The "parent" sequences, i.e., the sequences on which the PS4 variant polypeptides and nucleic acids are based, preferably are polypeptides having non-maltogenic exoamylase activity. The terms "parent enzymes" and "parent polypeptides" should be interpreted accordingly, and taken to mean the enzymes and polypeptides on which the 335 PS4 variant polypeptides are based. They are described in further detail below.
The mutations and amino acid changes may be made on any suitable polypeptide backbone or background, wild type or mutated, as described in further detail below.
In particularly preferred embodiments, the parent sequences are non-maltogenic exoamylase enzymes, preferably bacterial non-maltogenic exoamylase enzymes. In highly 340 preferred embodiments, the parent sequence comprises a glucan 1 ,4-alpha- maltotetrahydrolase (EC 3.2.1.60). Preferably, the parent sequence is derivable from Pseudomonas species, for example Pseudomonas saccharophilia or Pseudomonas stutzeri.
In some embodiments, the parent polypeptide comprises, or is homologous to, a wild type non-maltogenic exoamylase sequence, e.g., from Pseudomonas spp.
345 Thus, the parent polypeptide may comprise a Pseudomonas saccharophilia non- maltogenic exoamylase having a sequence shown as SEQ ID NO: 1. La other preferred embodiments, the parent polypeptide comprises a non-maltogenic exoamylase from Pseudomonas stutzeri having a sequence shown as SEQ ID NO: 11, or a Pseudomonas stutzeri non-maltogenic exoamylase having SWISS-PROT accession number P13507.
350 On the other hand, the parent polypeptide may be a variant of any of the wild type sequences, that is to say, the parent polypeptide may itself be engineered, or comprise a PS4 variant polypeptide.
In preferred embodiments, the mutations and changes are made on a PS4 sequence which is already mutated, preferably pMD 229 (SEQ ID NO: 13 or 14).
355 However, it will be clear to the skilled reader that although the PS4 variant polypeptides may be derivable by mutating already mutated sequences, it is possible to construct such variant polypeptides by starting from a wild type sequence (or indeed any suitable sequence), identifying the differences between the starting sequence and the desired variant, and introducing the required mutations into the starting sequence in order
360 to achieve the desired variant.
Proteins and nucleic acids related to, preferably having sequence or functional homology with Pseudomonas saccharophilia non-maltogenic exoamylase sequence shown as SEQ DD NO: 1 or a Pseudomonas stutzeri non-maltogenic exoamylase having a sequence shown as SEQ ID NO: 11 are referred to in this document as members of the 365 "PS4 family". Examples of "PS4 family" non-maltogenic exoamylase enzymes suitable for use in generating the PS4 variant polypeptides and nucleic acids are disclosed in further detail below.
The PS4 variant polypeptides described in this document preferably retain the features of the parent polypeptides, and additionally preferably have additional beneficial 370 properties, for example, enhanced activity or thermostability, or pH resistance, or any combination (preferably all). This is described in further detail below.
The PS4 substitution mutants described here may be used for any suitable purpose. They may preferably be used for purposes for which the parent enzyme is suitable. In particular, they may be used in any application for which exo-maltotetraohydrolase is 375 used. In highly preferred embodiments, they have the added advantage of higher thermostability, or higher exoamylase activity or higher pH stability, or any combination. Examples of suitable uses for the PS4 variant polypeptides and nucleic acids include food production, in particular baking, as well as production of foodstuffs; further examples are set out in detail below.
380 The PS4 variant polypeptides may comprise one or more further mutations in addition to those positions set out above. There may be one, two, three, four, five, six, seven or more mutations preferably substitutions in addition to those already set out. Other mutations, such as deletions, insertions and substitutions at the amino acid level and transversions, transitions and inversions at the nucleic acid level, at one or more other
385 locations, may also be included, as described below. In addition, the PS4 variants need not have all the substitutions at the positions listed. Indeed, they may have one, two, three, four, or five substitutions missing, i.e., the wild type amino acid residue is present at such positions.
FURTHER MUTATIONS
390 Positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 and/or
334
In preferred embodiments, the PS4 variant polypeptide may comprise one or more further mutations at other sites or positions in its sequence.
For example, the PS4 variant polypeptide may further comprise one or more 395 mutations selected from the group consisting of positions: 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or 334. The residues at these positions may preferably comrpise 33Y5 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E, 229P, 307K, 309P or 334P.
The PS4 variant polypeptide may therefore comprise, in addition to 307K/R/H, 1, 400 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or all 15 mutations at positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or 334. The position 307 residue in such embodiments may comprise histidine (H), particularly where such further mutations are present.
The PS4 variant polypeptide may therefore comprise, in addition to 307K/R/H, 1 405 further mutation at any of positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or 334, as shown in "Annex A: 1 Mutation", i.e., 33Y; 34N; 7OD; 121F; 134R; 141P; 146G; 157L; 161A; 178F; 179T; 223E; 229P; 309P; or 334P.
In other words, the PS4 variant polypeptide may comprise any of the following: 33Y, 307K/R/H; 34N, 307K/R/H; 7OD, 307K/R/H; 121F, 307K/R/H; 134R, 307K/R/H; 410 141P, 307K/R/H; 146G, 307K/R/H, 157L, 307K/R/H; 161 A, 307K/R/H; 178F, 307K/R/H; 179T, 307K/R/H; 223E, 307K/R/H; 229P, 307K/R7H; 309P, 307K/R/H; or 334P, 307K/R/H.
The PS4 variant polypeptide may alternatively comprise, in addition to 307K/R/H,
2 further mutations at any of positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 415 223, 229, 309 or 334, as shown in "Annex A: 2 Mutations", i.e., 33Y,34N; 33Y,70D;
33Y,121F; 33YJ34R; 33Y,141P; 33Y,146G; 33Y,157L; 33YJ61A; 33Y,178F;
33Y,179T; 33Y,223E; 33Y,229P; 33Y,309P; 33Y,334P; 34N,70D; 34N,121F; 34N,134R;
34N,141P; 34N,146G; 34N,157L; 34N,161A; 34N,178F; 34N,179T; 34N,223E;
34N,229P; 34N,309P; 34N,334P; 70D,121F; 70D,134R; 70D,141P; 70D,146G; 420 70D,157L; 70D,161A; 70D,178F; 70D,179T; 70D,223E; 70D,229P; 70D,309P;
70D,334P; 121F,134R; 121F,141P; 121F,146G; 121F,157L; 121F,161A; 121F,178F;
121F,179T; 121F,223E; 121F,229P; 121F,309P; 121F,334P; 134R,141P; 134R,146G;
134R,157L; 134R,161A; 134RJ78F; 134R,179T; 134R,223E; 134R,229P; 134R,309P;
134R,334P; 141P,146G; 141P,157L; 141P,161A; 141P,178F; 141P,179T; 141P,223E; 425 141P,229P; 141P,309P; 141P,334P; 146G,157L; 146G,161A; 146G,178F; 146G,179T;
146G,223E; 146G,229P; 146G,309P; 146G,334P; 157L,161A; 157L,178F; 157L,179T;
157L,223E; 157L,229P; 157L,309P; 157L,334P; 161A,178F; 161A,179T; 161A,223E;
161A,229P; 161A,309P; 161A,334P; 178F,179T; 178F,223E; 178F,229P; 178F,309P; 178F,334P; 179T,223E; 179T,229P; 179T,309P; 179T,334P; 223E,229P; 223E,309P; 430 223E,334P; 229P,309P; 229P,334P; or,309P,334P.
In other words, the PS4 variant polypeptide may comprise any of the following:
33Y,34N,307K/R/H; 33Y,70D,307K/R/H; 33Y,121F,307K/R/H; 33Y,134R,307K/R/H;
33Y5141P,307K/R/H; 33Y,146G,307K/R/H; 33Y,157L,307K/R/H; 33Y,161A,307K/R/H;
33Y,178F,307K/R/H; 33Y,179T,307K/R/H; 33Y,223E,307K/R/H; 33Y,229P,307K/R/H; 435 33Y,309P,307K/R/H; 33Y,334P,307K/R/H; 34Ns70D,307K/R/H; 34N,121F,307K/R/H;
34N,134R,307K/R/H; 34N,141P,307K/R/H; 34N,146G,307K/R/H; 34N,157L,307K/R/H;
34N,161A,307K/R/H; 34N,178F,307K/R/H; 34N,179T,307K/R/H; 34N,223E,307K/R/H;
34N,229P,307K/R/H; 34N,309P,307K/R/H; 34N,334P,307K/R/H; 70D,121F,307K/R/H;
70D,134R,307K/R/H; 70D,141P,307K/R/H; 70D,146G,307K/R/H; 70D,157L,307K/R/H; 440 70D,161A,307K/R/H; 70D,178F,307K/R/H; 70D,179T,307K/R/H; 70D,223E,307K/R/H;
70D,229P,307K/R/H; 70D,309P,307K/R/H; 70D,334P,307K/R/H; 121F,134R,307K/R/H;
121F,141P,307K/R/H; 121F,146G,307K/R/H; 121F,157L,307K/RyH;
121F,161A,307K/R/H; 121F,178F,307K/R/H; 121F,179T,307K/R/H;
121F,223E,307K/R/H; 121F,229P,307K/R/H; 121F,309P,307K/R/H; 445 121F,334P,307K/R/H; 134R,141P,307K/R/H; 134R,146G,307K/R/H;
134R,157L,307K/R/H; 134R,161A,307K/R/H; 134R,178F,307K/R/H;
134R,179T,-307K/R/H; 134R,223E,307K/R/H; 134R,229P^307K/R/H;
134R,309P,307K/R/H; 134R,334P,307K/R/H; 141P,146G,307K/R/H;
141P,157L,307K/RyH; 141P,161A,307K/R/H; 141P,178F,307K/R/H; 450 141P,179T,307K/R/H; 141P,223E,307K/R/H; 141P,229P,307K/R/H;
141P,309P,307K/R/H; 141P,334P,307K/R/H; 146G,157L,307K/R7H;
146G,161A,307K/R/H; 146G,178F,307KJR/H; 146G,179T,307K/R/H;
146G,223E,307K/R/H; 146G,229P,307K/R/H; 146G,309P,307K/R/H;
146G,334P,307K/R/H; 157L,161A,307K/R/H; 157L,178F,307K/R/H; 455 157L,179T,307K/R7H; 157L,223E,307K7R/H; 157L,229P,307K/PJH;
157L,309P,307K/R/H; 157L,334P,307K/R/H; 161A,178F,307K/R/H;
161A5179T,307K/R/H; 161A,223E,307K/R/H; 161A,229P,307K/R/H;
161A,309P,307K/R/H; 161A,334P,307K/RyH; 178F,179T,307K/R/H;
178F,223E,307K/R/H; 178F,229P,307K/R/H; 178F,309P,307K/R/H; 460 178F,334P,307K/R/H; 179T,223E,307K/R/H; 179T,229P,307K/R/H;
179T,309P,307K/R/H; 179T,334P,307K7R/H; 223E,229P,307K/R/H;
223E,309P,307K/R/H; 223E,334P,307K/R/H; 229P,309P,307K/R/H;
229P,334P,307K/R7H; 309P,334P,307K/R/H. The PS4 variant polypeptide may alternatively comprise, in addition to 307K/R/H, 3 further mutations at any of positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or 334, as shown in "Annex A: 3 Mutations".
The PS4 variant polypeptide may alternatively comprise, in addition to 307K/R/H,
4 further mutations at any of positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or 334, as shown in "Annex A: 4 Mutations".
The PS4 variant polypeptide may alternatively comprise, in addition to 307K/R/H,
5 further mutations at any of positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or 334, as shown in "Annex A: 5 Mutations".
The PS4 variant polypeptide may alternatively comprise, in addition to 307K/R/H,
6 further mutations at any of positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or 334, as shown in "Annex A: 6 Mutations".
The PS4 variant polypeptide may alternatively comprise, in addition to 307K/R/H,
7 further mutations at any of positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or 334, as shown in "Annex A: 7 Mutations".
The PS4 variant polypeptide may comprise, a sequence with 9 mutations, viz each of the following residues 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 178F,
179T, 223E, 229P, 307K/R/H, 309P, 334P, but not including the septets of residues shown in "Annex A: 7 Mutations".
The PS4 variant polypeptide may comprise, a sequence with 10 mutations, viz each of the following residues 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E, 229P, 307K/R/H, 309P, 334P, but not including the sextets of residues shown in "Annex A: 6 Mutations".
The PS4 variant polypeptide may comprise, a sequence with 11 mutations, viz each of the following residues 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E, 229P, 307K/R/H, 309P, 334P, but not including the quintets of residues shown in "Annex A: 5 Mutations".
The PS4 variant polypeptide may comprise, a sequence with 12 mutations, viz each of the following residues 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E, 229P, 307K/R/H, 309P, 334P, but not including the quadruplets of residues shown in "Annex A: 4 Mutations". 495 The PS4 variant polypeptide may comprise, a sequence with 13 mutations, viz each of the following residues 33Y5 34N, 7OD, 121F, 134R, 141P, 146G5 157L, 161A5 178F5 179T, 223E5 229P5 307K/R/H, 309P5 334P, but not including the triplets of residues shown in "Annex A: 3 Mutations".
The PS4 variant polypeptide may comprise, a sequence with 14 mutations, viz each 500 of the following residues 33Y5 34N5 70D5 121F, 134R, 141P, 146G5 157L, 161A, 178F5 179T5 223E, 229P5 307K/R/H, 309P5 334P5 but not including the pairs of residues shown in "Annex A: 2 Mutations".
The PS4 variant polypeptide may comprise, a sequence with 15 mutations, viz each of the following residues 33Y, 34N, 7OD, 121F, 134R, 141P5 146G5 157L5 161A5 178F5 505 179T, 223E5 229P, 307K/R/H, 309P, 334P5 but not including the single residues shown in "Annex A: 1 Mutations".
Preferred PS4 Variant Polypeptide Sequences
Preferably, however, the PS4 variant polypeptide further comprises mutations at each of these positions.
510 We specifically provide for a PS4 variant polypeptide derivable from a parent polypeptide having non-maltogenic exoamylase activity, in which the PS4 variant polypeptide comprises a mutation at each of the following positions 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 307, 309, 334, with reference to the position numbering of a Pseudomonαs sαcchαrophiliα exoamylase sequence shown as SEQ ID NO:
515 1.
In preferred embodiments, the position 307 mutation comprises a basic or positively charged residue. In some embodiments, the position 307 mutation comprises 307K or 307R. In another preferred embodiment, the position 307 residue is H. We therefore provide for a PS4 variant polypeptide derivable from a parent polypeptide 520 having non-maltogenic exoamylase activity, in which the PS4 variant polypeptide comprises a mutation at position 307 to K or R5 or in which the position 307 residue is H5 together with mutations at each of position 33, 34, 70, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 307, 309, 334.
Preferably, the position 33 residue may comprise Y, preferably 33 Y, more 525 preferably N33Y. Preferably, the position 34 residue may comprise N5 preferably 34N5 more preferably D34N. Preferably, the position 70 residue may comprise D, preferably 7OD, more preferably G70D. Preferably, the position 121 residue may comprise F, preferably 12 IF, more preferably Gl 2 IF. Preferably, the position 134 residue may comprise R, preferably 134R, more preferably G134R. Preferably, the position 141 residue
530 may comprise P, preferably 141P, more preferably A141P. Preferably, the position 146 residue may comprise G, preferably 146G, more preferably Y146G. Preferably, the position 157 residue may comprise L, preferably 157L, more preferably I157L. Preferably, the position 161 residue may comprise A, preferably 161 A, more preferably S 161 A. Preferably, the position 178 residue may comprise F, preferably 178F, more preferably
535 L178F. Preferably, the position 179 residue may comprise T, preferably 179T, more preferably A179T. Preferably, the position 223 residue may comprise E, preferably 223E, more preferably G223E. Preferably, the position 229 residue may comprise P, preferably 229P, more preferably S229P. Preferably, the position 307 residue may comprise K, preferably 307K5 more preferably H307K. Preferably, the position 309 residue may
540 comprise P, preferably 309P, more preferably A309P. Preferably, the position 334 residue . may comprise P, preferably 334P, more preferably S334P.
As noted above, in preferred embodiments the position 70 mutation is 7OD, preferably G70D. We therefore provide for a PS4 variant polypeptide derivable from a parent polypeptide having non-maltogenic exoamylase activity, in which the PS4 variant 545 polypeptide comprises a mutation at position 307 to K or R, or in which the position 307 residue is H, and a mutation at position 70 to 7OD, together with mutations at each of position 33, 34, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 307, 309, 334.
In preferred embodiments, the residue at position 272 is "wild type", i.e., unmutated. The position 272 residue is therefore preferably histidine (H). We therefore
550 provide for a PS4 variant polypeptide derivable from a parent polypeptide having non- maltogenic exoamylase activity, in which the PS4 variant polypeptide comprises a mutation at position 307 to K or R, or in which the position 307 residue is H, and a mutation at position 70 to 7OD, in which the position 272 residue is H, together with mutations at each of position 33, 34, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229,
555 307, 309, 334.
Similarly, the residue at position 303 is "wild type" or unmutated, and is preferably glycine (G) in other preferred embodiments. We therefore provide for a PS4 variant polypeptide derivable from a parent polypeptide having non-maltogenic exoamylase activity, in which the PS4 variant polypeptide comprises a mutation at position 307 to K or 560 R, or in which the position 307 residue is H, and a mutation at position 70 to 7OD, in which the position 303 residue is G, together with mutations at each of position 33, 34, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 307, 309, 334. In preferred embodiments, in each of the above embodiments of the PS4 variant polypeptide which comprise further mutations at positions 33, 34, 70, 121, 134, 141, 146,
565 157, 161, 178, 179, 223, 229, 309, 334, the position 33 residue is preferably Y, the position 34 residue is preferably N, the position 70 residue is preferably D, the position 121 residue is preferably F, the position 134 residue is preferably R, the position 141 residue is preferably P, the position 146 residue is preferably G, the position 157 residue is preferably L, the position 161 residue is preferably A, the position 178 residue is
570 preferably F, the position 179 residue is preferably T, the position 223 residue is preferably E, the position 229 residue is preferably P, the position 309 residue is preferably P, and the position 334 residue is preferably P.
In highly preferred embodiments, we provide a PS4 variant polypeptide which comprises the following residues 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 575 178F, 179T, 223E, 229P, 307K/R/H, 309P, 334P. The PS4 variant polypeptide may comprise each of the following mutations N33Y, D34N, G70D, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, H307K/R, A309P and S334P.
We specifically provide for a PS4 variant polypeptide which comprises the following substitutions 33Y, 34N, 7OD, 121F, 134R, 141P5 146G, 157L, 161A, 178F, 580 179T, 223E, 229P, 307K, 309P, 334P, preferably N33Y, D34N, G70D, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, H307K, A309P, S334P relative to a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ID NO: 1. In such an embodiment, the PS4 variant polypeptide may comprise a sequence SEQ ED NO: 21.
585 We further provide for a PS4 variant polypeptide which comprises the following substitutions 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E, 229P, 307R, 309P, 334P, preferably N33 Y5 D34N, G70D, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, H307R, A309P, S334P relative to a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ED NO: 1. In such an
590 embodiment, the PS4 variant polypeptide may comprise a sequence SEQ ID NO: 23.
We further provide for a PS4 variant polypeptide derivable from a parent polypeptide having non-maltogenic exoamylase activity, in which the PS4 variant polypeptide comprises the following substitutions 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161 A, 178F, 179T, 223E, 229P, 309P, 334P, preferably N33 Y, D34N, 595 G70D, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, A309P, S334P relative to a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ID NO: 1. In such an embodiment, the PS4 variant polypeptide may comprise a sequence SEQ ED NO: 25.
FURTHER SUBSTITUTIONS
One or more other mutations as set out in the table below may further be present in the PS4 variant polypeptide described here.
Figure imgf000021_0001
Figure imgf000022_0001
PS4 VARIANT NUCLEIC ACIDS
We also describe PS4 nucleic acids having sequences which correspond to or encode the alterations in the P S4 variant polypeptide sequences, for use in producing such 605 polypeptides for the purposes described here. Thus, we provide nucleic acids capable of encoding any polypeptide sequence set out in this document.
The skilled person will be aware of the relationship between nucleic acid sequence and polypeptide sequence, in particular, the genetic code and the degeneracy of this code, and will be able to construct such PS4 nucleic acids without difficulty. For example, he
610 will be aware that for each amino acid substitution in the PS4 variant polypeptide sequence, there may be one or more codons which encode the substitute amino acid. Accordingly, it will be evident that, depending on the degeneracy of the genetic code with respect to that particular amino acid residue, one or more PS4 nucleic acid sequences may be generated corresponding to that PS4 variant polypeptide sequence. Furthermore, where
615 the PS4 variant polypeptide comprises more than one substitution, for example
H307K/G70D, the corresponding PS4 nucleic acids may comprise pairwise combinations of the codons which encode respectively the two amino acid changes.
The PS4 variant nucleic acid sequences may be derivable from parent nucleic acids which encode any of the parent polypeptides described above. In particular, parent nucleic 620 acids may comprise wild type sequences, e.g., SEQ ID NO: 6 or SEQ ID NO: 12. The PS4 variant nucleic acids may therefore comprise nucleic acids encoding wild type non- maltogenic exoamylases, but which encode another amino acid at the relevant position instead of the wild type amino acid residue. The PS4 variant nucleic acid sequences may also comprise wild type sequences with one or more mutations, e.g., which encode parent 625 polypeptides described above under "Combinations".
It will be understood that nucleic acid sequences which are not identical to the particular PS4 variant nucleic acid sequences, but are related to these, will also be useful for the methods and compositions described here, such as a variant, homologue, derivative or fragment of a PS4 variant nucleic acid sequence, or a complement or a sequence capable 630 of hybridising thereof. Unless the context dictates otherwise, the term "PS4 variant nucleic acid" should be taken to include each of these entities listed above.
Mutations in amino acid sequence and nucleic acid sequence may be made by any of a number of techniques, as known in the art. Variant sequences may easily be made using any of the known mutagenesis techniques, for example, site directed mutagenesis 635 using PCR with appropriate oligonucleotide primers, 5' add-on mutagenesis, mismatched primer mutagenesis, etc. Alternatively, or in addition, the PS4 variant nucleic acid sequences may be made de novo.
In particularly preferred embodiments, the mutations are introduced into parent sequences by means of PCR (polymerase chain reaction) using appropriate primers, as
640 illustrated in the Examples. It is therefore possible to alter the sequence of a polypeptide by introducing any desired amino acid substitutions into a parent polypeptide, preferably having non-maltogenic exoamylase activity, such as into a Pseudomonas saccharophilia or a Pseudomonas stutzeri exoamylase sequence at amino acid or nucleic acid level, as described. We describe a method in which the sequence of a non-maltogenic exoamylase
645 is altered by altering the sequence of a nucleic acid which encodes the non-maltogenic exoamylase.
However, it will of course be appreciated that the PS4 variant polypeptide does not need in fact to be actually derived from a wild type polypeptide or nucleic acid sequence by, for example, step by step mutation. Rather, once the sequence of the PS4 variant 650 polypeptide is established, the skilled person can easily make that sequence from the wild type with all the mutations, via means known in the art, for example, using appropriate oligonucleotide primers and PCR. In fact, the PS4 variant polypeptide can be made de novo with all its mutations, through, for example, peptide synthesis methodology.
In general, however, the PS4 variant polypeptides and/or nucleic acids are derived 655 or derivable from a "precursor" sequence. The term "precursor" as used herein means an enzyme that precedes the enzyme which is modified according to the methods and compositions described here. A precursor therefore includes an enzyme used to produce a modified enzyme. Thus, the precursor may be an enzyme that is modified by mutagenesis as described elsewhere in this document. Likewise, the precursor may be a wild type 660 enzyme, a variant wild type enzyme or an already mutated enzyme.
The PS4 variant polypeptides and nucleic acids may be produced by any means known in the art. Specifically, they may be expressed from expression systems, which may be in vitro or in vivo in nature. Specifically, we describe plasmids and expression vectors comprising PS4 nucleic acid sequences, preferably capable of expressing PS4 665 variant polypeptides. Cells and host cells which comprise and are preferably transformed with such PS4 nucleic acids, plasmids and vectors are also disclosed, and it should be made clear that these are also encompassed in this document.
The PS4 variant polypeptides may for example be made using site directed mutagenesis using PCR with appropriate oligonucleotide primers, 5' add-on mutagenesis,
670 mismatched primer mutagenesis, etc as described Example 4A. hi order to produce PS4 variant polypeptides with mutations at positions 307, for example, a nucleic acid sequence corresponding to a pSac— pMD229 sequence; Pseudomonas saccharophila maltotetrahydrolase nucleotide sequence with 17 substitutions and deletion of the starch binding domain (SEQ ID NO: 14) may be made and the relevant changes introduced. The
675 skilled reader will be aware, however, that any suitable starting sequence can be used, and indeed that it is possible to start from a wild type exoamylase sequence to get to the desired variant polypeptide either in a single step, or via other intermediate sequences.
In preferred embodiments, the PS4 variant polypeptide sequence is used as a food additive in an isolated form. The term "isolated" means that the sequence is at least 680 substantially free from at least one other component with which the sequence is naturally associated in nature and as found in nature, hi one aspect, preferably the sequence is in a purified form. The term "purified" means that the sequence is in a relatively pure state - e.g. at least about 90% pure, or at least about 95% pure or at least about 98% pure.
hi highly preferred embodiments, the nucleic acid sequence comprises the 685 sequences shown in SEQ ID NO: 22, 24 or 26.
POSITION NUMBERING
All positions referred to in the present document by numbering refer to the numbering of a. Pseudomonas saccharophilia exoamylase reference sequence shown below (SEQ ID NO: !): 1 DQAGKSPAGV RYHGGDEIIL QGFHWNWRE APNDWYNILR QQASTIAADG FSAIWMPVPW
61 RDFSSWTDGG KSGGGEGYFW HDFNKNGRYG SDAQLRQAAG ALGGAGVKVL YDWPNHMNR
121 GYPDKEINLP AGQGFWRNDC ADPGNYPNDC DDGDRFIGGE SDLNTGHPQI YGMFRDELAN
181 LRSGYGAGGF RFDFVRGYAP ERVDSWMSDS ADSSFCVGEL WKGPSEYPSW DWRNTASWQQ
241 IIKDWSDRAK CPVFDFALKE RMQNGSVADW KHGLNGNPDP RWREVAVTFV DNHDTGYSPG 301 QNGGQHHWAL QDGLIRQAYA YILTSPGTPV VYWSHMYDWG YGDFIRQLIQ VRRTAGVRAD 361 SAISFHSGYS GLVATVSGSQ QTLWALNSD LANPGQVASG SFSEAVNASN GQVRVWRSGS 421 GDGGGNDGGE GGLVNVNFRC DNGVTQMGDS VYAVGNVSQL GNWSPASAVR LTDTSSYPTW 481 KGSIALPDGQ NVEWKCLIRN EADATLVRQW QSGGNNQVQA AAGASTSGSF
The reference sequence is derived from the Pseudomonas saccharophilia sequence having SWISS-PROT accession number P22963, but without the signal sequence
MSHILRAAVLAAVLLPFPALA.
The C-terminal starch binding domain EGGLVNVNFR CDNGVTQMGD SVYAVGNVSQ
LGNWSPASAV RLTDTSSYPT WKGSIALPDG QNVEWKCLIR NEADATLVRQ WQSGGNNQVQ
AAAGASTSGS F may optionally be deleted or disregarded. Alternatively, it may be included in the PS4 variant polypeptide sequence.
In the context of the present description a specific numbering of amino acid residue positions in PS4 exoamylase enzymes is employed, hi this respect, by alignment of the amino acid sequences of various known exoamylases it is possible to unambiguously allot a exoamylase amino acid position number to any amino acid residue position in any exoamylase enzyme, the amino acid sequence of which is known. Using this numbering system originating from for example the amino acid sequence of the exoamylase obtained from Pseudomonas saccharophilia, aligned with amino acid sequences of a number of other known exoamylase, it is possible to indicate the position of an amino acid residue in a exoamylase unambiguously.
Therefore, the numbering system, even though it may use a specific sequence as a base reference point, is also applicable to all relevant homologous sequences. For example, the position numbering may be applied to homologous sequences from other Pseudomonas species, or homologous sequences from other bacteria. Preferably, such homologues have 60% or greater homology, for example 70% or more, 80% or more, 90% or more or 95% or more homology, with the reference sequence SEQ ID NO: 1 above, or the sequences having SWISS-PROT accession numbers P22963 or Pl 3507, preferably with all these sequences. Sequence homology between proteins may be ascertained using well known alignment programs and hybridisation techniques described herein. Such homologous sequences, as well as the functional equivalents described below, will be referred to in this document as the "PS4 Family". Furthermore, and as noted above, the numbering system used hi this document makes reference to a reference sequence SEQ ID NO: 1, which is derived from the Pseudomonas saccharophilia sequence having SWISS-PROT accession number P22963, but without the signal sequence MSHILRAAVLAAVLLPFPALA. This signal sequence is
730 located N terminal of the reference sequence and consists of 21 amino acid residues. Accordingly, it will be trivial to identify the particular residues to be mutated or substituted in corresponding sequences comprising the signal sequence, or indeed, corresponding sequences comprising any other N- or C- terminal extensions or deletions, hi relation to N- terminal additions or deletions, all that is required is to offset the position
735 numbering by the number of residues inserted or deleted. For example, position 1 in SEQ ID NO: 1 corresponds to position 22 in a sequence with the signal sequence.
PARENT ENZYME / POLYPEPTIDE
The PS4 variant polypeptides are derived from, or are variants of, another sequence, known as a "parent enzyme", a "parent polypeptide" or a "parent sequence".
740 The term "parent enzyme" as used in this document means the enzyme that has a close, preferably the closest, chemical structure to the resultant variant, i.e., the PS4 variant polypeptide or nucleic acid. The parent enzyme may be a precursor enzyme (i.e. the enzyme that is actually mutated) or it may be prepared de novo. The parent enzyme may be a wild type enzyme, or it may be a wild type enzyme comprising one or more
745 mutations.
The term "precursor" as used herein means an enzyme that precedes the enzyme which is modified to produce the enzyme. Thus, the precursor may be an enzyme that is modified by mutagenesis. Likewise, the precursor may be a wild type enzyme, a variant wild type enzyme or an already mutated enzyme.
750 The term "wild type" is a term of the art understood by skilled persons and means a phenotype that is characteristic of most of the members of a species occurring naturally and contrasting with the phenotype of a mutant. Thus, in the present context, the wild type enzyme is a form of the enzyme naturally found hi most members of the relevant species. Generally, the relevant wild type enzyme in relation to the variant polypeptides described
755 here is the most closely related corresponding wild type enzyme in terms of sequence homology. However, where a particular wild type sequence has been used as the basis for producing a variant PS4 polypeptide as described here, this will be the corresponding wild type sequence regardless of the existence of another wild type sequence that is more closely related in terms of amino acid sequence homology. 760 The parent enzyme or polypeptide can be any suitable starting polypeptide. It may preferably have some enzymatic activity. Preferably, this enzymatic activity is an amylase activity. More preferably, the parent polypeptide comprises exoamylase activity.
The parent enzyme is preferably a polypeptide which preferably exhibits non- maltogenic exoamylase activity. Preferably, the parent enzyme is a non-maltogenic 765 exoamylase itself. For example, the parent enzyme may be a Pseudomonas saccharophila non-maltogenic exoamylase, such as a polypeptide having SWISS-PROT accession number P22963, or a Pseudomonas stutzeri non-maltogenic exoamylase, such as a polypeptide having SWISS-PROT accession number P13507.
Other members of the PS4 family may be used as parent enzymes; such "PS4 770 family members" will generally be similar to, homologous to, or functionally equivalent to either of these two enzymes, and may be identified by standard methods, such as hybridisation screening of a suitable library using probes, or by genome sequence analysis.
In particular, functional equivalents of either of these two enzymes, as well as other members of the "PS4 family" may also be used as starting points or parent 775 polypeptides for the generation of PS4 variant polypeptides as described here.
A "functional equivalent" of a protein means something that shares one or more, preferably substantially all, of the functions of that protein. Preferably, such functions are biological functions, preferably enzymatic functions, such as amylase activity, preferably non-maltogenic exoamylase activity. Such functions may include any property of the 780 protein, including exo-specificity, thermostability, and improved handling such as firmness, resilience, cohesiveness, crumbliness and foldability (as described below).
In relation to a parent enzyme, the term "functional equivalent" preferably means a molecule having similar or identical function to a parent molecule. The parent molecule may be a Pseudomonas saccharophila non-maltogenic exoamylase or a Pseudomonas 785 stutzeri non-maltogenic exoamylase or a polypeptide obtained from other sources.
The term "functional equivalent" in relation to a parent enzyme being a Pseudomonas saccharophila non-maltogenic exoamylase, such as a polypeptide having SWISS-PROT accession number P22963, or a Pseudomonas stutzeri non-maltogenic exoamylase, such as a polypeptide having SWISS-PROT accession number P13507 means 790 that the functional equivalent could be obtained from other sources. The functionally equivalent enzyme may have a different amino acid sequence but will have non- maltogenic exoamylase activity. Examples of assays to determine functionality are described herein and are known to one skilled in the art.
In highly preferred embodiments, the functional equivalent will have sequence
795 homology to either of the Pseudomonas saccharophila and Pseudomonas stutzeri non- maltogenic exoamylases mentioned above, preferably both. The functional equivalent may also have sequence homology with any of the sequences set out as SEQ ED NOs: 1 to 14, preferably SEQ ED NO: 1 or SEQ ED NO: 7 or both. Sequence homology between such sequences is preferably at least 60%, preferably 65% or more, preferably 75% or more,
800 preferably 80% or more, preferably 85% or more, preferably 90% or more, preferably 95% or more. Such sequence homologies may be generated by any of a number of computer programs known in the art, for example BLAST or FASTA, etc. A suitable computer program for carrying out such an alignment is the GCG Wisconsin Bestfit package (University of Wisconsin, U. S. A; Devereux et al, 1984, Nucleic Acids Research
805 12:387). Examples of other software than can perform sequence comparisons include, but are not limited to, the BLAST package (see Ausubel et al., 1999 ibid- Chapter 18), FASTA (Atschul et al, 1990, J. MoI. Biol., 403-410) and the GENEWORKS suite of comparison tools. Both BLAST and FASTA are available for offline and online searching (see Ausubel et al., 1999 ibid, pages 7-58 to 7-60). However it is preferred to use the GCG
810 Bestfit program.
In other embodiments, the functional equivalents will be capable of specifically hybridising to any of the sequences set out above. Methods of determining whether one sequence is capable of hybridising to another are known in the art, and are for example described in Sambrook, et al (supra) and Ausubel, F. M. et al. (supra). In highly preferred 815 embodiments, the functional equivalents will be capable of hybridising under stringent conditions, e.g. 65°C and 0.IxSSC {lxSSC = 0.15 M NaCl, 0.015 MNa3 Citrate pH 7.0}.
For example, functional equivalents which have sequence homology to Pseudomonas saccharophila and Pseudomonas stutzeri non-maltogenic exoamylases are suitable for use as parent enzymes. Such sequences may differ from the Pseudomonas 820 saccharophila sequence at any one or more positions. Furthermore, non-maltogenic exoamylases from other strains of Pseudomonas spp, such as ATCC 17686, may also be used as a parent polypeptide. The PS4 variant polypeptide residues may be inserted into any of these parent sequences to generate the variant PS4 polypeptide sequences.
It will be understood that where it is desired for PS4 variant polypeptides to 825 additionally comprise one or more mutations, as set out above, corresponding mutations may be made in the nucleic acid sequences of the functional equivalents of Pseudomonas spp non-maltogenic exoamylase, as well as other members of the "PS4 family", in order that they may be used as starting points or parent polypeptides for the generation of PS4 variant polypeptides as described here.
830 Specifically included within the term "PS4 variant polypeptides" are the polypeptides disclosed in: US 60/485,413, 60/485,539 and 60/485,616; PCT/US2004/021723 and PCT/US2004/021739; US 10/886,905 and 10/866,903; US 60/608,919; US 60/612,407; US 60/485,539; PCT/B2004/002487; US 10/886,023; US 10/886,505, US 10/886,527 and US 10/886,504; US 10/947,612. These documents
835 however are not admitted to be prior art.
Such polypeptides are suitable for use in the applications described herein, in particular, as food additives, to treat starch as described, to prepare a food product, to make a bakery product, for the formulation of improver compositions, for the formulation of combinations, etc.
840 Modification of Parent Sequences
The parent enzymes may be modified at the amino acid level or the nucleic acid level to generate the PS4 variant sequences described here. Therefore, we provide for the generation of PS4 variant polypeptides by introducing one or more corresponding codon changes in the nucleotide sequence encoding a non-maltogenic exoamylase polypeptide.
845 The nucleic acid numbering should preferably be with reference to the position numbering of a. Pseudomonas saccharophilia exoamylase nucleotide sequence shown as SEQ ID NO: 6. Alternatively, or in addition, reference may be made to the sequence with GenBank accession number Xl 6732. In preferred embodiments, the nucleic acid numbering should be with reference to the nucleotide sequence shown as SEQ ID NO: 6.
850 However, as with amino acid residue numbering, the residue numbering of this sequence is to be used only for reference purposes only. In particular, it will be appreciated that the above codon changes can be made in any PS4 family nucleic acid sequence. For example, sequence changes can be made to a Pseudomonas saccharophila or a Pseudomonas stutzeri non-maltogenic exoamylase nucleic acid sequence (e.g., X16732, SEQ ID NO: 6
855 or M24516, SEQ ID NO: 12).
The parent en2yme may comprise the "complete" enzyme, i.e., in its entire length as it occurs in nature (or as mutated), or it may comprise a truncated form thereof. The PS4 variant derived from such may accordingly be so truncated, or be "full-length". The truncation may be at the N-teπninal end, or the C-teπninal end, preferably the C-terminal 860 end. The parent enzyme or PS4 variant may lack one or more portions, such as subsequences, signal sequences, domains or moieties, whether active or not etc. For example, the parent enzyme or the PS4 variant polypeptide may lack a signal sequence, as described above. Alternatively, or in addition, the parent enzyme or the PS4 variant may lack one or more catalytic or binding domains.
865 In highly preferred embodiments, the parent enzyme or PS4 variant may lack one or more of the domains present in non-maltogenic exoamylases, such as the starch binding domain. For example, the PS4 polypeptides may have only sequence up to position 429, relative to the numbering of a Pseudomonas saccharophilia non-maltogenic exoamylase shown as SEQ ID NO: 1. It is to be noted that this is the case for the PS4 variants pSac-
870 pMS382, pSac-pMS382R and pSac-pMS382H.
In other embodiments, the parent enzyme or PS4 variant may comprise a e "complete" enzyme, i.e., in its entire length as it occurs in nature (or as mutated), together with one or more additional amino acid sequences at the N terminus or C terminus. For example, the parent enzyme or PS4 variant polypeptide may comprise a single extra amino 875 acid residue at the C terminus or N terminus, e.g., M, A, G, etc. Preferably, the additional amino acid residue is present at the N terminus. Where one or more additional residues is included, the position numbering will be offset by the length of the addition.
AMYLASE
The PS4 variant polypeptides generally comprise amylase activity.
880 The term "amylase" is used in its normal sense - e.g. an enzyme that is inter alia capable of catalysing the degradation of starch. In particular they are hydrolases which are capable of cleaving α-D-(l— >4) O-glycosidic linkages in starch.
Amylases are starch-degrading enzymes, classified as hydrolases, which cleave α- D-(I ->4) O-glycosidic linkages in starch. Generally, α-amylases (E.C. 3.2.1.1, α-D-
885 (l-»4)-glucan glucanohydrolase) are defined as endo-acting enzymes cleaving α-D-(l-»4) O-glycosidic linkages within the starch molecule in a random fashion. In contrast, the exo- acting amylolytic enzymes, such as β-amylases (E.C. 3.2.1.2, α-D-(l->4)-glucan maltohydrolase), and some product-specific amylases like maltogenic alpha-amylase (E.C. 3.2.1.133) cleave the starch molecule from the non-reducing end of the substrate, β-
890 Amylases, α-glucosidases (E.C. 3.2.1.20, α-D-glucoside glucohydrolase), glucoamylase (E.C. 3.2.1.3, α-D-(l-)4)-glucan glucohydrolase), and product-specific amylases can produce malto-oligosaccharides of a specific length from starch.
NON-MALTOGENIC EXO AMYLASE
The PS4 variant polypeptides described in this document are derived from (or 895 variants of) polypeptides which preferably exhibit non-maltogenic exoamylase activity. Preferably, these parent enzymes are non-maltogenic exoamylases themselves. The PS4 variant polypeptides themselves in highly preferred embodiments also exhibit non- maltogenic exoamylase activity.
In highly preferred embodiments, the term "non-maltogenic exoamylase enzyme" 900 as used in this document should be taken to mean that the enzyme does not initially degrade starch to substantial amounts of maltose as analysed in accordance with the product determination procedure as described in this document.
In highly preferred embodiments, the non-maltogenic exoamylase comprises an exo-maltotetraohydrolase. Exo-maltotetraohydrolase (E.C.3.2.1.60) is more formally 905 known as glucan 1,4-alpha-maltotetrahydrolase. This enzyme hydrolyses 1,4-alpha-D- glucosidic linkages in amylaceous polysaccharides so as to remove successive maltotetraose residues from the non-reducing chain ends.
Non-maltogenic exoamylases are described in detail in US Patent number 6,667,065, hereby incorporated by reference.
910 ASSAYS FOR NON-MALTOGENIC EXOAMYLASE ACTIVITY
The following system is used to characterize polypeptides having non-maltogenic exoamylase activity which are suitable for use according to the methods and compositions described here. This system may for example be used to characterise the PS4 parent or variant polypeptides described here.
915 By way of initial background information, waxy maize amylopectin (obtainable as
WAXILYS 200 from Roquette, France) is a starch with a very high amylopectin content (above 90%). 20 mg/ml of waxy maize starch is boiled for 3 min. in a buffer of 50 mM MES (2-(N-moφholino)ethanesulfonic acid), 2 mM calcium chloride, pH 6.0 and subsequently incubated at 500C and used within half an hour.
920 One unit of the non-maltogenic exoamylase is defined as the amount of enzyme which releases hydrolysis products equivalent to 1 μmol of reducing sugar per min. when incubated at 50 degrees C in a test tube with 4 ml of 10 mg/ml waxy maize starch in 50 mM MES, 2 mM calcium chloride, pH 6.0 prepared as described above. Reducing sugars are measured using maltose as standard and using the dinitrosalicylic acid method of 925 Bernfeld, Methods Enzymol, (1954), /, 149-158 or another method known in the art for quantifying reducing sugars.
The hydrolysis product pattern of the non-maltogenic exoamylase is determined by incubating 0.7 units of non-maltogenic exoamylase for 15 or 300 min. at 5O0C in a test tube with 4 ml of 10 mg/ml waxy maize starch in the buffer prepared as described above. 930 The reaction is stopped by immersing the test tube for 3 min. in a boiling water bath.
The hydrolysis products are analyzed and quantified by anion exchange HPLC using a Dionex PA 100 column with sodium acetate, sodium hydroxide and water as eluents, with pulsed amperometric detection and with known linear maltooligosaccharides of from glucose to maltoheptaose as standards. The response factor used for maltooctaose 935 to maltodecaose is the response factor found for maltoheptaose.
Preferably, the PS4 variant polypeptides have non-maltogenic exoamylase activity such that if an amount of 0.7 units of said non-maltogenic exoamylase were to incubated for 15 minutes at a temperature of 50°C at pH 6.0 in 4 ml of an aqueous solution of 10 mg preboiled waxy maize starch per ml buffered solution containing 50 mM 2-(N-
940 morpholino)ethane sulfonic acid and 2 mM calcium chloride then the enzyme would yield hydrolysis product(s) that would consist of one or more linear malto-oligosaccharides of from two to ten D-glucopyranosyl units and optionally glucose; such that at least 60%, preferably at least 70%, more preferably at least 80% and most preferably at least 85% by weight of the said hydrolysis products would consist of linear maltooligosaccharides of
945 from three to ten D-glucopyranosyl units, preferably of linear maltooligosaccharides consisting of from four to eight D-glucopyranosyl units.
For ease of reference, and for the present purposes, the feature of incubating an amount of 0.7 units of the non-maltogenic exoamylase for 15 minutes at a temperature of 5O0C at pH 6.0 in 4 ml of an aqueous solution of 10 mg preboiled waxy maize starch per 950 ml buffered solution containing 50 mM 2-(N-moφholino)ethane sulfonic acid and 2 mM calcium chloride, may be referred to as the "Waxy Maize Starch Incubation Test".
Thus, alternatively expressed, preferred PS4 variant polypeptides which are non- maltogenic exoamylases are characterised as having the ability in the waxy maize starch incubation test to yield hydrolysis product(s) that would consist of one or more linear 955 malto-oligosaccharides of from two to ten D-glucopyranosyl units and optionally glucose; such that at least 60%, preferably at least 70%, more preferably at least 80% and most preferably at least 85% by weight of the said hydrolysis product(s) would consist of linear maltooligosaccharides of from three to ten D-glucopyranosyl units, preferably of linear maltooligosaccharides consisting of from four to eight D-glucopyranosyl units.
960 The hydrolysis products in the waxy maize starch incubation test may include one or more linear malto-oligosaccharides of from two to ten D-glucopyranosyl units and optionally glucose. The hydrolysis products in the waxy maize starch incubation test may also include other hydrolytic products. Nevertheless, the % weight amounts of linear maltooligosaccharides of from three to ten D-glucopyranosyl units are based on the
965 amount of the hydrolysis product that consists of one or more linear maltooligosaccharides of from two to ten D-glucopyranosyl units and optionally glucose. In other words, the % weight amounts of linear maltooligosaccharides of from three to ten D- glucopyranosyl units are not based on the amount of hydrolysis products other than one or more linear malto-oligosaccharides of from two to ten D-glucopyranosyl units and
970 glucose.
The hydrolysis products can be analysed by any suitable means. For example, the hydrolysis products may be analysed by anion exchange HPLC using a Dionex PA 100 column with pulsed amperometric detection and with, for example, known linear maltooligosaccharides of from glucose to maltoheptaose as standards.
975 For ease of reference, and for the present purposes, the feature of analysing the hydrolysis product(s) using anion exchange HPLC using a Dionex PA 100 column with pulsed amperometric detection and with known linear maltooligosaccharides of from glucose to maltoheptaose used as standards, can be referred to as "analysing by anion exchange". Of course, and as just indicated, other analytical techniques would suffice, as
980 well as other specific anion exchange techniques.
Thus, alternatively expressed, a preferred PS4 variant polypeptide is one which has non-maltogenic exoamylase such that it has the ability in a waxy maize starch incubation test to yield hydrolysis product(s) that would consist of one or more linear maltooligosaccharides of from two to ten D-glucopyranosyl units and optionally glucose, said 985 hydrolysis products being capable of being analysed by anion exchange; such that at least 60%, preferably at least 70%, more preferably at least 80% and most preferably at least 85% by weight of the said hydrolysis product(s) would consist of linear maltooligosaccharides of from three to ten D-glucopyranosyl units, preferably of linear maltooligosaccharides consisting of from four to eight D-glucopyranosyl units. 990 As used herein, the term "linear malto-oligosaccharide" is used in the normal sense as meaning 2-10 units of α-D-glucopyranose linked by an α-(l->4) bond.
In highly preferred embodiments, the PS4 polypeptides described here have improved exoamylase activity, preferably non-maltogenic exoamylase activity, when compared to the parent polypeptide, preferably when tested under the same conditions. In 995 particular, in highly preferred embodiments, the PS4 variant polypeptides have 10% or more, preferably 20% or more, preferably 50% or more, exoamylase activity compared to their parents, preferably when measured in a waxy maize starch test.
The hydrolysis products can be analysed by any suitable means. For example, the hydrolysis products may be analysed by anion exchange HPLC using a Dionex PA 100 1000 column with pulsed amperometric detection and with, for example, known linear maltooligosaccharides of from glucose to maltoheptaose as standards.
As used herein, the term "linear malto-oligosaccharide" is used in the normal sense as meaning 2-20 units of α-D-glucopyranose linked by an α-(l->4) bond.
IMPROVED HANDLING PROPERTIES
1005 The PS4 variants described here preferably have improved properties when compared to their parent enzymes, such as any one or more of improved thermostability, improved pH stability, or improved exo-specificity. The PS4 variants described here preferably also have improved handling properties, such that a food product treated with a the PS4 variant polypeptide has any one or all of lower firmness, higher resilience, higher
1010 cohesiveness, lower crumbliness, or higher foldability compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
Withoutwishing to be bound by any particular theory, we believe that the mutations at the particular positions have individual and cumulative effects on the properties of a polypeptide comprising such mutations.
1015 THERMOSTABILITY AND PH STABILITY
Preferably, the PS4 variant polypeptide is thermostable; preferably, it has higher thermostability than its parent enzyme.
In wheat and other cereals the external side chains in amylopectin are in the range of DP 12-19. Thus, enzymatic hydrolysis of the amylopectin side chains, for example, by 1020 PS4 variant polypeptides as described having non-maltogenic exoamylase activity, can markedly reduce their crystallisation tendencies.
Starch in wheat and other cereals used for baking purposes is present in the form of starch granules which generally are resistant to enzymatic attack by amylases. Thus starch modification is mainly limited to damaged starch and is progressing very slowly during
1025 dough processing and initial baking until gelatinisation starts at about 6OC. As a consequence hereof only amylases with a high degree of thermostability are able to modify starch efficiently during baking. And generally the efficiency of amylases is increased with increasing thermostability. That is because the more thermostable the enzyme is the longer time it can be active during baking and thus the more antistaling
1030 effect it will provide.
Accordingly, the use of PS4 variant polypeptides as described here when added to the starch at any stage of its processing into a food product, e.g., before during or after baking into bread can retard or impede or slow down the retrogradation. Such use is described in further detail below.
1035 As used herein the term "thermostable" relates to the ability of the enzyme to retain activity after exposure to elevated temperatures. Preferably, the PS4 variant polypeptide is capable of degrading starch at temperatures of from about 550C to about 8O0C or more. Suitably, the enzyme retains its activity after exposure to temperatures of up to about 950C.
1040 The thermostability of an enzyme such as a non-maltogenic exoamylase is measured by its half life. Thus, the PS4 variant polypeptides described here have half lives extended relative to the parent enzyme by preferably 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or more, preferably at elevated temperatures of from 550C to about 950C or more, preferably at about 8O0C.
1045 As used here, the half life (tl/2) is the time (in minutes) during which half the enzyme activity is inactivated under defined heat conditions, hi preferred embodiments, the half life is assayed at 80 degrees C. Preferably, the sample is heated for 1-10 minutes at 8O0C or higher. The half life value is then calculated by measuring the residual amylase activity, by any of the methods described here. Preferably, a half life assay is conducted as
1050 described in more detail in the Examples.
Preferably, the PS4 variants described here are active during baking and hydrolyse starch during and after the gelatinization of the starch granules which starts at tempera- tures of about 550C. The more thermostable the non-maltogenic exoamylase is the longer time it can be active and thus the more antistaling effect it will provide. However, during 1055 baking above temperatures of about 85°C, enzyme inactivation can take place. If this happens, the non-maltogenic exoamylase may be gradually inactivated so that there is substantially no activity after the baking process in the final bread. Therefore preferentially the non-maltogenic exoamylases suitable for use as described have an optimum temperature above 5O0C and below 98°C.
1060 The thermostability of the PS4 variants described here can be improved by using protein engineering to become more thermostable and thus better suited for the uses described here; we therefore encompass the use of PS4 variants modified to become more thermostable by protein engineering.
Preferably, the PS4 variant polypeptide is pH stable; more preferably, it has a 1065 higher pH stability than its cognate parent polypeptide. As used herein the term "pH stable" relates to the ability of the enzyme to retain activity over a wide range of pHs. Preferably, the PS4 variant polypeptide is capable of degrading starch at a pH of from about 5 to about 10.5. In one embodiment, the degree of pH stability may be assayed by measuring the half life of the enzyme in specific pH conditions. In another embodiment, 1070 the degree of pH stability may be assayed by measuring the activity or specific activity of the enzyme in specific pH conditions. The specific pH conditions may be any pH from pH5 to pH10.5.
Thus, the PS4 variant polypeptide may have a longer half life, or a higher activity (depending on the assay) when compared to the parent polypeptide under identical 1075 conditions. The PS4 variant polypeptides may have 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or longer half life when compared to their parent polypeptides under identical pH conditions. Alternatively, or in addition, they may have such higher activity when compared to the parent polypeptide under identical pH conditions.
1080 EXO-SPECEFICITY
It is known that some non-maltogenic exoamylases can have some degree of endoamylase activity. In some cases, this type of activity may need to be reduced or eliminated since endoamylase activity can possibly negatively effect the quality of the final bread product by producing a sticky or gummy crumb due to the accumulation of 1085 branched dextrins . Exo-specificity can usefully be measured by determining the ratio of total amylase activity to the total endoamylase activity. This ratio is referred to in this document as a "Exo-specificity index". In preferred embodiments, an enzyme is considered an exoamylase if it has a exo-specificity index of 20 or more, i.e., its total amylase activity 1090 (including exo-amylase activity) is 20 times or more greater than its endoamylase activity. In highly preferred embodiments, the exo-specificity index of exoamylases is 30 or more, 40 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, or 100 or more. In highly preferred embodiments, the exo-specificity index is 150 or more, 200 or more, 300 or more, 400 or more, 500 or more or 600 or more.
1095 The total amylase activity and the endoamylase activity may be measured by any means known in the art. For example, the total amylase activity may be measured by assaying the total number of reducing ends released from a starch substrate. Alternatively , the use of a Betamyl assay is described in further detail in the Examples, and for convenience, amylase activity as assayed in the Examples is described in terms of
1100 "Betamyl Units" in the Tables.
Endoamylase activity may be assayed by use of a Phadebas Kit (Pharmacia and Upjohn). This makes use of a blue labelled crosslinked starch (labelled with an azo dye); only internal cuts in the starch molecule release label, while external cuts do not do so. Release of dye may be measured by spectrophotometry. Accordingly, the Phadebas Kit 1105 measures endoamylase activity, and for convenience, the results of such an assay (described in the Examples) are referred to in this document as "Phadebas units".
In a highly preferred embodiment, therefore, the exo-specificity index is expressed in terms of Betamyl Units / Phadebas Units, also referred to as "B/Phad".
Exo-specificity may also be assayed according to the methods described in the 1110 prior art, for example, in our International Patent Publication Number WO99/50399. This measures exo-specificity by way of a ratio between the endoamylase activity to the exoamylase activity. Thus, in a preferred aspect, the PS4 variants described here will have less than 0.5 endoamylase units (EAU) per unit of exoamylase activity. Preferably the non-maltogenic exoamylases which are suitable for use according to the present invention 1115 have less than 0.05 EAU per unit of exoamylase activity and more preferably less than 0.01 EAU per unit of exoamylase activity.
The PS4 variants described here will preferably have exospecificity, for example measured by exo-specificity indices, as described above, consistent with their being exoamylases. Moreoever, they preferably have higher or increased exospecificity when 1120 compared to the parent enzymes or polypeptides from which they are derived. Thus, for example, the PS4 variant polypeptides may have 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or higher exo-specificity index when compared to their parent polypeptides, preferably under identical conditions. They may have 1.5x or higher, 2x or higher, 5 x or higher, 10 x or higher, 50 x or higher, 100 x or higher, when compared to
1125 their parent polypeptides, preferably under identical conditions.
IMPROVED HANDLING PROPERTIES
The PS4 variants described here preferably comprise one or more improved handling properties compared to a parent polypeptide or a wild type polypeptide. The improved handling properties may in preferred embodiments comprise improved baking 1130 properties.
Thus, the PS4 variants are such that a food product treated with the PS4 variant polypeptide an improved handling or preferably baking property compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide. The handling or baking property may be selected from the group consisting of: firmness, 1135 resilience, cohesiveness, crumbliness and foldability.
These handling properties may may be tested by any means known in the art. For example, firmness, resilience and cohesiveness may be determined by analysing bread slices by Texture Profile Analysis using for example a Texture Analyser, as described in the Examples.
1140 Firmness
The PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide lower firmness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
The firmness is in preferred embodiments inversely correlated with the softness of 1145 the food product; thus, a higher softness may reflect a lower firmness, and vice versa.
Firmness is preferably measured by the "Firmness Evaluation Protocol" set out in Example 13.
Thus, the PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide has a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 1150 80%, 90%, 100%, 200% or more lower firmness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide. A food product treated with the PS4 variant polypeptide may have a l.lx, 1.5x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 1Ox or more lower firmness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
1155 Resilience
The PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide higher resilience compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
Resilience is preferably measured by the "Resilience Evaluation Protocol" set out 1160 in Example 14.
Thus, the PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide has a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or more higher resilience compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide. A food product treated 1165 with the PS4 variant polypeptide may have a l.lx, 1.5x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 10x or more higher resilience compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
Cohesiveness
The PS4 variants described here are preferably such that a food product treated 1170 with the PS4 variant polypeptide higher cohesiveness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
Cohesiveness is preferably measured by the "Cohesiveness Evaluation Protocol" set out in Example 15.
Thus, the PS4 variants described here are preferably such that a food product 1175 treated with the PS4 variant polypeptide has a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or more higher cohesiveness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide. A food product treated with the PS4 variant polypeptide may have a 1. Ix, 1.5x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 10x or more higher cohesiveness compared to a food product which has been treated 1180 with a parent polypeptide or a wild type polypeptide. Crumbliness
The PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide lower crumbliness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
1185 Crumbliness is preferably measured by the "Crumbliness Evaluation Protocol" set out in Example 16.
Thus, the PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide has a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or more lower crumbliness compared to a food product which has 1190 been treated with a parent polypeptide or a wild type polypeptide. A food product treated with the PS4 variant polypeptide may have a l.lx, 1.5x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 10x or more lower crumbliness compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
Foldability
1195 The PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide higher foldability compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
Foldability is preferably measured by the "Foldability Evaluation Protocol" set out in Example 17.
1200 Thus, the PS4 variants described here are preferably such that a food product treated with the PS4 variant polypeptide has a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200% or more higher foldability compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide. A food product treated with the PS4 variant polypeptide may have a l.lx, 1.5x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 10x
1205 or more higher foldability compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
We specifically describe the use of the PS4 variant polypeptides described here in combination with a xylanase for improviing fodability.
USES OF PS4 VARIANT POLYPEPTIDES AND NUCLEIC ACIDS
1210 ThePS4 variant polypeptides, nucleic acids, host cells, expression vectors, etc, may be used in any application for which an amylase may be used. In particular, they may be used to substitute for any non-maltogenic exoamylase. They may be used to supplement amylase or non-maltogenic exoamylase activity, whether alone or in combination with other known amylases or non-maltogenic exoamylases.
1215 The PS4 variant sequences described here may be used in various applications in the food industry - such as in bakery and drink products, they may also be used in other applications such as a pharmaceutical composition, or even in the chemical industry. In particular, the PS4 variant polypeptides and nucleic acids are useful for various industrial applications including baking (as disclosed in WO 99/50399) and flour standardisation
1220 (volume enhancement or improvement). They may be used to produce maltotetraose from starch and other substrates.
We therefore describe a method for preparing a food product, the method comprising: (a) obtaining a non-maltogenic exoamylase; (b) introducing a mutation at any one or more of the positions of the non-maltogenic exoamylase as set out in this 1225 document; (c) admixing the resulting polypeptide with a food ingredient.
The PS4 variant polypeptides may be used to enhance the volume of bakery products such as bread. While not wishing to be bound by any particular theory, we believe that this results from the reduction in viscosity of the dough during heating (such as baking) as a result of the exoamylase shortening amylose molecules. This enables the 1230 carbon dioxide generated by fermentation to increase the size of the bread with less hindrance.
Thus, food products comprising or treated with PS4 variant polypeptides are expanded in volume when compared to products which have not been so treated, or treated with parent polypeptides. In other words, the food products have a larger volume of air per
1235 volume of food product. Alternatively, or in addition, the food products treated with PS4 variant polypeptides have a lower density, or weight (or mass) per volume ratio. In particularly preferred embodiments, the PS4 variant polypeptides are used to enhance the volume of bread. Volume enhancement or expansion is beneficial because it reduces the gumminess or starchiness of foods. Light foods are preferred by consumers, and the
1240 customer experience is enhanced. In preferred embodiments, the use of PS4 variant polypeptides enhances the volume by 10%, 20%, 30% 40%, 50% or more.
The use of PS4 variant polypeptides to increase the volume of foods is described in detail in the Examples. FOOD USES
1245 The PS4 variant polypeptides and nucleic acids described here may be used as — or in the preparation of - a food. In particular, they may be added to a food, i.e., as a food additive. The term "food" is intended to include both prepared food, as well as an ingredient for a food, such as a flour. In a preferred aspect, the food is for human consumption. The food may be in the from of a solution or as a solid - depending on the
1250 use and/or the mode of application and/or the mode of administration.
The PS4 variant polypeptides and nucleic acids may be used as a food ingredient. As used herein the term "food ingredient" includes a formulation, which is or can be added to functional foods or foodstuffs and includes formulations which can be used at low levels in a wide variety of products that require, for example, acidifying or emulsifying. The food 1255 ingredient may be in the from of a solution or as a solid - depending on the use and/or the mode of application and/or the mode of administration.
The PS4 variant polypeptides and nucleic acids disclosed here may be - or may be added to - food supplements. The PS4 variant polypeptides and nucleic acids disclosed here may be - or may be added to - functional foods. As used herein, the term "functional 1260 food" means food which is capable of providing not only a nutritional effect and/or a taste satisfaction, but is also capable of delivering a further beneficial effect to consumer. Although there is no legal definition of a functional food, most of the parties with an interest in this area agree that they are foods marketed as having specific health effects.
The PS4 variant polypeptides may also be used in the manufacture of a food 1265 product or a foodstuff. Typical foodstuffs include dairy products, meat products, poultry products, fish products and dough products. The dough product may be any processed dough product, including fried, deep fried, roasted, baked, steamed and boiled doughs, such as steamed bread and rice cakes. In highly preferred embodiments, the food product is a bakery product.
1270 Preferably, the foodstuff is a bakery product. Typical bakery (baked) products include bread - such as loaves, rolls, buns, pizza bases etc. pastry, pretzels, tortillas, cakes, cookies, biscuits, krackers etc.
The food products preferably benefit from one or more of the improved handling or baking properties of the PS4 variant polypeptides described here. The improved 1275 handling or baking property may be selected from the group consisting of: improved firmness, improved resilience, improved cohesiveness, improved crumbliness and improved foldability.
We therefore describe a method of modifying a food additive comprising a non- maltogenic exoamylase, the method comprising introducing a mutation at any one or more 1280 of the positions of the non-maltogenic exoamylase as set out in this document. The same method can be used to modify a food ingredient, or a food supplement, a food product, or a foodstuff.
RETROGRADATION / STALING
We describe the use of PS4 variant proteins that are capable of retarding the staling 1285 of starch media, such as starch gels. The PS4 variant polypeptides are especially capable of retarding the detrimental retrogradation of starch.
Most starch granules are composed of a mixture of two polymers: an essentially linear amylose and a highly branched amylopectin. Amylopectin is a very large, branched molecule consisting of chains of α-D-glucopyranosyl units joined by (1-4) linkages, 1290 wherein said chains are attached by α-D-(l-6) linkages to form branches. Amylopectin is present in all natural starches, constituting about 75% of most common starches. Amylose is essentially a linear chain of (1-4) linked α -D-glucopyranosyl units having few α-D-(l- 6) branches. Most starches contain about 25% amylose.
Starch granules heated in the presence of water undergo an order-disorder phase 1295 transition called gelatinization, where liquid is taken up by the swelling granules.
Gelatinization temperatures vary for different starches. Upon cooling of freshly baked bread the amylose fraction, within hours, retrogrades to develop a network. This process is beneficial in that it creates a desirable crumb structure with a low degree of firmness and improved slicing properties. More gradually crystallisation of amylopectin takes place 1300 within the gelatinised starch granules during the days after baking. In this process amylopectin is believed to reinforce the amylose network in which the starch granules are embedded. This reinforcement leads to increased firmness of the bread crumb. This reinforcement is one of the main causes of bread staling.
It is known that the quality of baked products gradually deteriorates during storage 1305 As a consequence of starch recystallisation (also called retrogradation), the water-holding capacity of the crumb is changed with important implications on the organoleptic and dietary properties. The crumb loses softness and elasticity and becomes firm and crumbly. The increase in crumb firmness is often used as a measure of the staling process of bread. The rate of detrimental retrogradation of amylopectin depends on the length of the 1310 side chains of amylopectin. Thus, enzymatic hydrolysis of the amylopectin side chains, for example, by PS4 variant polypeptides having non-maltogenic exoamylase activity, can markedly reduce their crystallisation tendencies.
Accordingly, the use of PS4 variant polypeptides as described here when added to the starch at any stage of its processing into a food product, e.g., before during or after 1315 baking into bread can retard or impede or slow down the retrogradation. Such use is described in further detail below.
We therefore describe a method of improving the ability of a non-maltogenic exoamylase to prevent staling, preferably detrimental retrogradation, of a dough product, the method comprising introducing a mutation at any one or more of the positions of the 1320 non-maltogenic exoamylase as set out in this document.
ASSAYS FOR MEASUREMENT OF RETROGRADATION (INC. STALING)
For evaluation of the antistaling effect of the PS4 variant polypeptides having non- maltogenic exoamylase activity described here, the crumb firmness can be measured 1, 3 and 7 days after baking by means of an Instron 4301 Universal Food Texture Analyzer or 1325 similar equipment known in the art.
Another method used traditionally in the art and which is used to evaluate the effect on starch retrogradation of a PS4 variant polypeptide having non-maltogenic exoamylase activity is based on DSC (differential scanning calorimetry). Here, the melting enthalpy of retrograded amylopectin in bread crumb or crumb from a model system dough 1330 baked with or without enzymes (control) is measured. The DSC equipment applied in the described examples is a Mettler-Toledo DSC 820 run with a temperature gradient of 10°C per min. from 20 to 95°C. For preparation of the samples 10-20 mg of crumb are weighed and transferred into Mettler-Toledo aluminiurn pans which then are hermetically sealed.
The model system doughs used in the described examples contain standard wheat 1335 flour and optimal amounts of water or buffer with or without the non-maltogenic PS4 variant exoamylase. They are mixed in a 10 or 50 g Brabender Farinograph for 6 or 7 min., respectively. Samples of the doughs are placed in glass test tubes (15*0.8 cm) with a lid. These test tubes are subjected to a baking process in a water bath starting with 30 min. incubation at 330C followed by heating from 33 to 95°C with a gradient of 1.10C per min. 1340 and finally a 5 min. incubation at 950C. Subsequently, the tubes are stored in a thermostat at 2O0C prior to DSC analysis. In preferred embodiments, the PS4 variants described here have a reduced melting enthalpy, compared to the control. In highly preferred embodiments, the PS4 variants have a 10% or more reduced melting enthalpy. Preferably, they have a 20% or more, 30%, 1345 40%, 50%, 60%, 70%, 80%, 90% or more reduced melting enthalpy when compared to the control.
PREPARATION OF STARCH PRODUCTS
We provide the use of PS4 variant polypeptides in the preparation of food products, in particular, starch products. The method comprises forming the starch product 1350 by adding a non-maltogenic exoamylase enzyme such as a PS4 variant polypeptide, to a starch medium. If the starch medium is a dough, then the dough is prepared by mixing together flour, water, the non-maltogenic exoamylase which is a PS4 variant polypeptide and optionally other possible ingredients and additives.
The term "starch" should be taken to mean starchier se or a component thereof, 1355 especially amylopectin. The term "starch medium" means any suitable medium comprising starch. The term "starch product" means any product that contains or is based on or is derived from starch. Preferably, the starch product contains or is based on or is derived from starch obtained from wheat flour. The term "flour" as used herein is a synonym for the finely-ground meal of wheat or other grain. Preferably, however, the term 1360 means flour obtained from wheat per se and not from another grain. Thus, and unless otherwise expressed, references to "wheat flour" as used herein preferably mean references to wheat flour per se as well as to wheat flour when present hi a medium, such as a dough.
A preferred flour is wheat flour or rye flour or mixtures of wheat and rye flour.
1365 However, dough comprising flour derived from other types of cereals such as for example from rice, maize, barley, and durra are also contemplated. Preferably, the starch product is a bakery product. More preferably, the starch product is a bread product. Even more preferably, the starch product is a baked farinaceous bread product. The term "baked farinaceous bread product " refers to any baked product based on a dough obtainable by
1370 mixing flour, water, and a leavening agent under dough forming conditions. Further components can of course be added to the dough mixture.
Thus, if the starch product is a baked farinaceous bread product, then the process comprises mixing - in any suitable order - flour, water, and a leavening agent under dough forming conditions and further adding a PS4 variant polypeptide, optionally in the form of 1375 a premix. The leavening agent may be a chemical leavening agent such as sodium bicarbonate or any strain of Saccharomyces cerevisiae (Baker's Yeast).
The PS4 variant non-maltogenic exoamylase can be added together with any dough ingredient including the water or dough ingredient mixture or with any additive or additive mixture. The dough can be prepared by any conventional dough preparation method 1380 common in the baking industry or in any other industry making flour dough based products.
Baking of farinaceous bread products such as for example white bread, bread made from bolted rye flour and wheat flour, rolls and the like is typically accomplished by baking the bread dough at oven temperatures in the range of from 180 to 25O0C for about 1385 15 to 60 minutes. During the baking process a steep temperature gradient (200 -> 12O0C) is prevailing in the outer dough layers where the characteristic crust of the baked product is developed. However, owing to heat consumption due to steam generation, the temperature in the crumb is only close to 100°C at the end of the baking process.
We therefore describe a process for making a bread product comprising: (a) 1390 providing a starch medium; (b) adding to the starch medium a PS4 variant polypeptide as described in this document; and (c) applying heat to the starch medium during or after step (b) to produce a bread product. We also describe a process for making a bread product comprising adding to a starch medium a PS4 variant polypeptide as described.
The non-maltogenic exoamylase PS4 variant polypeptide can be added as a liquid 1395 preparation or as a dry pulverulent composition either comprising the enzyme as the sole active component or in admixture with one or more additional dough ingredient or dough additive.
IMPROVING COMPOSITION
We describe improver compositions, which include bread improving compositions 1400 and dough improving compositions. These comprise a PS4 variant polypeptide, optionally together with a further ingredient, or a further enzyme, or both.
We also provide for the use of such a bread and dough improving compositions in baking. In a further aspect, we provide a baked product or dough obtained from the bread improving composition or dough improving composition. In another aspect, we describe a 1405 baked product or dough obtained from the use of a bread improving composition or a dough improving composition. DOUGH PREPARATION
A dough may be prepared by admixing flour, water, a dough improving composition comprising PS4 variant polypeptide (as described above) and optionally other 1410 ingredients and additives.
The dough improving composition can be added together with any dough ingredient including the flour, water or optional other ingredients or additives. The dough improving composition can be added before the flour or water or optional other ingredients and additives. The dough improving composition can be added after the flour 1415 or water, or optional other ingredients and additives. The dough can be prepared by any conventional dough preparation method common in the baking industry or in any other industry making flour dough based products.
The dough improving composition can be added as a liquid preparation or in the form of a dry powder composition either comprising the composition as the sole active 1420 component or in admixture with one or more other dough ingredients or additive.
The amount of the PS4 variant polypeptide non-maltogenic exoamylase that is added is normally in an amount which results in the presence in the finished dough of 50 to 100,000 units per kg of flour, preferably 100 to 50,000 units per kg of flour. Preferably, the amount is in the range of 200 to 20,000 units per kg of flour. Alternatively, the PS4 1425 variant polypeptide non-maltogenic exoamylase is added in an amount which results in the presence in the finished dough of 0.02 - 50 ppm of enzyme based on flour (0.02 - 50 mg enzyme per kg of flour), preferably 0.2 - 10 ppm.
In the present context, 1 unit of the non-maltogenic exoamylase is defined as the amount of enzyme which releases hydrolysis products equivalent to 1 μmol of reducing 1430 sugar per min. when incubated at 50 degrees C in a test tube with 4 ml of 10 mg/ml waxy maize starch in 50 mM MES, 2 mM calcium chloride, pH 6.0 as described hereinafter.
The dough as described here generally comprises wheat meal or wheat flour and/or other types of meal, flour or starch such as corn flour, corn starch, maize flour, rice flour, rye meal, rye flour, oat flour, oat meal, soy flour, sorghum meal, sorghum flour, potato 1435 meal, potato flour or potato starch. The dough may be fresh, frozen, or part-baked.
The dough may be a leavened dough or a dough to be subjected to leavening. The dough may be leavened in various ways, such as by adding chemical leavening agents, e.g., sodium bicarbonate or by adding a leaven (fermenting dough), but it is preferred to leaven the dough by adding a suitable yeast culture, such as a culture of Saccharomyces 1440 cerevisiae (baker's yeast), e.g. a commercially available strain of S. cerevisiae.
The dough may comprise fat such as granulated fat or shortening. The dough may further comprise a further emulsifier such as mono- or diglycerides, sugar esters of fatty acids, polyglycerol esters of fatty acids, lactic acid esters of monoglycerides, acetic acid esters of monoglycerides, polyoxethylene stearates, or lysolecithin.
1445 We also describe a pre-mix comprising flour together with the combination as described herein. The pre-mix may contain other dough-improving and/or bread- improving additives, e.g. any of the additives, including enzymes, mentioned herein.
FURTHER DOUGH ADDITIVES OR INGREDIENTS
In order to improve further the properties of the baked product and impart
1450 distinctive qualities to the baked product further dough ingredients and/or dough additives may be incorporated into the dough. Typically, such further added components may include dough ingredients such as salt, grains, fats and oils, sugar or sweeteber, dietary fibres, protein sources such as milk powder, gluten soy or eggs and dough additives such as emulsifiers, other enzymes, hydrocolloids, flavouring agents, oxidising agents, minerals 1455 and vitamins
The emulsifiers are useful as dough strengtheners and crumb softeners. As dough strengtheners, the emulsifiers can provide tolerance with regard to resting time and tolerance to shock during the proofing. Furthermore, dough strengtheners will improve the tolerance of a given dough to variations in the fermentation time. Most dough 1460 strengtheners also improve on the oven spring which means the increase in volume from the proofed to the baked goods. Lastly, dough strengtheners will emulsify any fats present in the recipe mixture.
Suitable emulsifiers include lecithin, polyoxyethylene stearat, mono- and diglycerides of edible fatty acids, acetic acid esters of mono- and diglycerides of edible 1465 fatty acids, lactic acid esters of mono- and diglycerides of edible fatty acids, citric acid esters of mono- and diglycerides of edible fatty acids, diacetyl tartaric acid esters of mono- and diglycerides of edible fatty acids, sucrose esters of edible fatty acids, sodium stearoyl- 2-lactylate, and calcium stearoyl-2-lactylate.
The further dough additive or ingredient can be added together with any dough 1470 ingredient including the flour, water or optional other ingredients or additives, or the dough improving composition. The further dough additive or ingredient can be added before the flour, water, optional other ingredients and additives or the dough improving composition. The further dough additive or ingredient can be added after the flour, water, optional other ingredients and additives or the dough improving composition.
1475 The further dough additive or ingredient may conveniently be a liquid preparation.
However, the further dough additive or ingredient may be conveniently in the form of a dry composition.
Preferably the further dough additive or ingredient is at least 1% the weight of the flour component of dough. More preferably, the further dough additive or ingredient is at 1480 least 2%, preferably at least 3%, preferably at least 4%, preferably at least 5%, preferably at least 6%. If the additive is a fat, then typically the fat may be present in an amount of from 1 to 5%, typically 1 to 3%, more typically about 2%.
FURTHER ENZYME
One or more further enzymes may be used in combination with the PS4 variant 1485 polypeptides. Such combinations may for example added to the food, dough preparation, foodstuff or starch composition.
The further enzymes may be selected from, for example, any combination of the following: (a) Novamyl, or a variant, homologue, or mutants thereof which have maltogenic alpha-amylase activity; (b) a xylanase such as GRIND AMYL™ POWERBake 1490 900 (Danisco A/S); (c) a bacterial α-amylase such as Max-Life U4 (Danisco A/S); and (d) a lipase such as GRIND AMYL™ POWERBake 4050 (Danisco A/S).
In one embodiment a PS4 variant polypeptide according to the invention is used in combination with at least one enzyme selected from the list consisting of oxidoreductases, hydrolases, lipases, esterases, glycosidases, amylases, pullulanases, xylanases, cellulases, 1495 hemicellulases, starch degrading enzymes, proteases and lipoxygenases. In a preferred embodiment, the composition comprises at least one PS4 variant and a maltogenic amylase from Bacillus, as disclosed in WO91/04669. A preferred embodiment comprises a PS4 variant and flour.
Further enzymes that may be added to the dough include oxidoreductases, 1500 hydrolases, such as lipases and esterases as well as glycosidases like α-amylase, pullulanase, and xylanase. Oxidoreductases, such as for example glucose oxidase and hexose oxidase, can be used for dough strengthening and control of volume of the baked products and xylanases and other hemicellulases may be added to improve dough handling properties, crumb firmness and bread volume. Lipases are useful as dough strengtheners 1505 and crumb softeners and α-amylases and other amylolytic enzymes may be incorporated into the dough to control bread volume and further reduce crumb firmness.
Further enzymes that may be used may be selected from the group consisting of a cellulase, a hemicellulase, a starch degrading enzyme, a protease, a lipoxygenase.
Examples of useful oxidoreductases include oxidises sush as maltose oxidising 1510 enzyme, a glucose oxidase (EC 1.1.3.4), carbohydrate oxidase, glycerol oxidase, pyranose oxidase, galactose oxidase (EC 1.1.3.10) and hexose oxidase (EC 1.1.3.5). These enzymes can be used for dough strengthening and control of volume of the baked products.
Among starch degrading enzymes, amylases are particularly useful as dough improving additives, α-amylase breaks downs starch into dextrins which are further
1515 broken down by β-amylase to maltose. Examples of suitable amylases include maltogenic alpha-amylase also called glucan 1 ,4-α-maltohydrolase (EC 3.2.1.133) from Bacillus stearothermophilus (such as Novamyl™ (Novozymes)), α-amylase (EC 3.2.1.1) from Bacillus amyloliqufaciens (such as Max Life U4 (Danisco AJS)), B. flavothermus amylase (US 2005004861 IAl), Fungal amylase variants with insertions of alpha-amylase (EC
1520 3.2.1.133) from Bacillus stearothermophilus (WO2005019443), hybrids of amylase as described in US20060147581A1, and variants, homologues and derivatives thereof which have maltogenic alpha-amylase activity. In a preferred embodiment, a PS4 variant polypeptide may be combined with amylases, in particular, maltogenic amylases. Maltogenic alpha-amylase (glucan 1,4-a-maltohydrolase, E.C. 3.2.1.133) is able to
1525 hydrolyze amylose and amylopectin to maltose in the alpha-configuration. Other useful starch degrading enzymes which may be added to a dough composition include glucoamylases and pullulanases.
Preferably, the further enzyme is at least a xylanase and/or at least an amylase. The term "xylanase" as used herein refers to xylanases (EC 3.2.1.32) which hydrolyse
1530 xylosidic linkages. A lipase may also be added. Examples of suitable xylanases include bakery xylanases (EC 3.2.1.8) from e.g. Bacillus sp., Aspergillus sp., Thermomyces sp. or Trichoderma sp. (such as GRIND AMYL™ POWERBake 900 (Danisco AZS)) and xylanases pertaining to Family 10 or 11 e.g. from Thermomyces lanoginosus (previously called Humicola insolens), Aspergillus aculeatus (WO 94/21785), Bacillus halodurans
1535 (WO 2005/059084), Bacillus sp (EP 0 720 649 Bl), B. agadeherens (US 5,770,424), and variants, homologues and derivatives thereof. The term "amylase" as used herein refers to amylases such as α-amylases (EC 3.2.1.1), β-amylases (EC 3.2.1.2) and γ-amylases (EC 3.2.1.3).
The further enzyme can be added together with any dough ingredient including the 1540 flour, water or optional other ingredients or additives, or the dough improving composition. The further enzyme can be added before the flour, water, and optionally other ingredients and additives or the dough improving composition. The further enzyme can be added after the flour, water, and optionally other ingredients and additives or the dough improving composition. The further enzyme may conveniently be a liquid 1545 preparation. However, the composition may be conveniently in the form of a dry composition.
Some enzymes of the dough improving composition are capable of interacting with each other under the dough conditions to an extent where the effect on improvement of the rheological and/or machineability properties of a flour dough and/or the quality of the 1550 product made from dough by the enzymes is not only additive, but the effect is synergistic.
In relation to improvement of the product made from dough (finished product), it may be found that the combination results in a substantial synergistic effect in respect to crumb structore. Also, with respect to the specific volume of baked product a synergistic effect may be found.
1555 The further enzyme may be a lipase (EC 3.1.1) capable of hydrolysing carboxylic ester bonds to release carboxylate. Examples of lipases include but are not limited to triacylglycerol lipase (EC 3.1.1.3), galactolipase (EC 3.1.1.26), phospholipase Al (EC 3.1.1.32, phospholipase A2 (EC 3.1.1.4) and lipoprotein lipase A2 (EC 3.1.1.34). More specifically, suitable lipases include lipases from Mucor miehei, F. venenatwn, H.
1560 lanuginosa, , Rhizomucor miehei Candida antarctica, F. oxysporum, glycolipase from Fusarium heterosporum (such as GRIND AMYL™ POWERBake 4050 (Danisco A/S)) and variants, homologues and derivatives thereof.
OTHER USES
The PS4 variants are suitable for the production of maltose and high maltose 1565 syrups. Such products are of considerable interest in the production of certain confectioneries because of the low hygroscoposity, low viscosity, good heat stability and mild, not too sweet taste of maltose. The industrial process of producing maltose syrups comprises liquefying starch, then saccharification with a maltose producing enzyme, and optionally with an enzyme cleaving the 1.6- branching points in amylopectin, for instance 1570 an .alpha.- 1.6- amyloglucosidase.
The PS4 variants described here may be added to and thus become a component of a detergent composition. The detergent composition may for example be formulated as a hand or machine laundry detergent composition including a laundry additive composition suitable for pre-treatment of stained fabrics and a rinse added fabric softener composition,
1575 or be formulated as a detergent composition for use in general household hard surface cleaning operations, or be formulated for hand or machine dishwashing operations. In a specific aspect, we describe a detergent additive comprising the PS4 variant. The detergent additive as well as the detergent composition may comprise one or more other enzymes such as a protease, a lipase, a cutinase, an amylase, a carbohydrase, a cellulase, a
1580 pectinase, a mannanase, an arabinase, a galactanase, a xylanase, an oxidase, e.g., a laccase, and/or a peroxidase. In general the properties of the chosen enzyme(s) should be compatible with the selected detergent, (i.e., pH-optimum, compatibility with other enzymatic and non-enzymatic ingredients, etc.), and the enzyme(s) should be present in effective amounts.
1585 The PS4 variant may also be used in the production of lignocellulosic materials, such as pulp, paper and cardboard, from starch reinforced waste paper and cardboard, especially where repulping occurs at pH above 7 and where amylases can facilitate the disintegration of the waste material through degradation of the reinforcing starch. The PS4 variants may especially be useful in a process for producing a papermaking pulp from
1590 starch-coated printed paper. The process may be performed as described in WO 95/14807, comprising the following steps: a) disintegrating the paper to produce a pulp, b) treating , with a starch-degrading enzyme before, during or after step a), and c) separating ink partϊcles from the pulp after steps a) and b). The PS4 variant may also be very useful in modifying starch where enzymatically modified starch is used in papermaking together
1595 with alkaline fillers such as calcium carbonate, kaolin and clays. With the PS4 variants described here it becomes possible to modify the starch in the presence of the filler thus allowing for a simpler integrated process. A PS4 variant may also be very useful in textile desizing. In the textile processing industry, amylases are traditionally used as auxiliaries in the desizing process to facilitate the removal of starch-containing size which has served as
1600 a protective coating on weft yarns during weaving. Complete removal of the size coating after weaving is import-ant to ensure optimum results in the subsequent processes, in which the fabric is scoured, bleached and dyed. Enzymatic starch break-down is preferred because it does not involve any harmful effect on the fiber material. The PS4 variant may be used alone or in combination with a cellulase when desizing cellulose-containing fabric 1605 or textile.
The PS4 variant may also be an amylase of choice for production of sweeteners from starch A "traditional" process for conversion of starch to fructose syrups normally consists of three consecutive enzymatic processes, viz., a liquefaction process followed by a saccharifϊcation process and an isomerization process. During the liquefaction process,
1610 starch is degraded to dextrins by an amylase at pH values between 5.5 and 6.2 and at temperatures of 95-160° C. for a period of approx. 2 hours. In order to ensure an optimal enzyme stability under these conditions, 1 mM of calcium is added (40 ppm free calcium ions). After the liquefaction process the dextrins are converted into dextrose by addition of a glucoamylase and a debranching enzyme, such as an isoamylase or a pullulanase .
1615 Before this step the pH is reduced to a value below 4.5, maintaining the high temperature (above 95° C), and the liquefying .amylase activity is denatured. The temperature is lowered to 60° C, and glucoamylase and debranching enzyme are added. The saccharifϊcation process proceeds for 24-72 hours.
1620 LAUNDRY DETERGENT COMPOSITIONS AND USE
The α-amylase variants discussed herein can be formulated in detergent compositions for use in cleaning dishes or other cleaning compositions, for example. These can be gels, powders or liquids. The compositions can comprise the α-amylase variant alone, other amylolytic enzymes, other cleaning enzymes, and other components 1625 common to cleaning compositions.
Thus, a dishwashing detergent composition can comprise a surfactant. The surfactant may be anionic, non-ionic, cationic, amphoteric or a mixture of these types. The detergent can contain 0% to about 90% by weight of a non-ionic surfactant, such as low- to non-foaming ethoxylated propoxylated straight-chain alcohols.
1630 In the detergent applications, α-amylase variants are usually used in a liquid composition containing propylene glycol. The α-amylase variant can be solubilized in propylene glycol, for example, by circulating in a 25% volume/volume propylene glycol solution containing 10% calcium chloride.
The dishwashing detergent composition may contain detergent builder salts of 1635 inorganic and/or organic types. The detergent builders may be subdivided into phosphorus-containing and non-phosphorus-containing types. The detergent composition usually contains about 1% to about 90% of detergent builders. Examples of phosphorus- containing inorganic alkaline detergent builders, when present, include the water-soluble salts, especially alkali metal pyrophosphates, orthophosphates, and polyphosphates. An 1640 example of phosphorus-containing organic alkaline detergent builder, when present, includes the water-soluble salts of phosphonates. Examples of non-phosphorus-containing inorganic builders, when present, include water-soluble alkali metal carbonates, borates, and silicates, as well as the various types of water-insoluble crystalline or amorphous alumino silicates, of which zeolites are the best-known representatives.
1645 Examples of suitable organic builders include the alkali metal; ammonium and substituted ammonium; citrates; succinates; malonates; fatty acid sulphonates; carboxymethoxy succinates; ammonium polyacetates; carboxylates; polycarboxylates; aminopolycarboxylates; polyacetyl carboxylates; and polyhydroxsulphonates.
Other suitable organic builders include the higher molecular weight polymers and 1650 co-polymers known to have builder properties, for example appropriate polyacrylic acid, polymaleic and polyacrylic/polymaleic acid copolymers, and their salts.
The cleaning composition may contain bleaching agents of the chlorine/bromine- type or the oxygen-type. Examples of inorganic chlorine/bromine-type bleaches are lithium, sodium or calcium hypochlorite, and hypobromite, as well as chlorinated 1655 trisodium phosphate. Examples of organic chlorine/bromine-type bleaches are heterocyclic N-bromo- and N-chloro-imides such as trichloroisocyanuric, tribromoisocyanuric, dibromoisocyanuric, and dichloroisocyanuric acids, and salts thereof with water- solubilizing cations such as potassium and sodium. Hydantoin compounds are also suitable.
1660 The cleaning composition may contain oxygen bleaches, for example in the form of an inorganic persalt, optionally with a bleach precursor or as a peroxy acid compound. Typical examples of suitable peroxy bleach compounds are alkali metal perborates, both tetrahydrates and monohydrates, alkali metal percarbonates, persilicates, and perphosphates. Suitable activator materials include tetraacetylethylenediamine (TAED)
1665 and glycerol triacetate. Enzymatic bleach activation systems may also be present, such as perborate or percarbonate, glycerol triacetate and perhydrolase, as disclosed in WO 2005/056783, for example.
The cleaning composition may be stabilized using conventional stabilizing agents for the enzyme(s), e.g., a polyol such as, e.g., propylene glycol, a sugar or a sugar alcohol, 1670 lactic acid, boric acid, or a boric acid derivative (e.g., an aromatic borate ester). The cleaning composition may also contain other conventional detergent ingredients, e.g., deflocculant material, filler material, foam depressors, anti-corrosion agents, soil- suspending agents, sequestering agents, anti-soil redeposition agents, dehydrating agents, dyes, bactericides, fluorescent agents, thickeners, and perfumes.
1675 Finally, the α-amylase variants may be used in conventional dishwashing detergents, e.g., in any of the detergents described in the following patent publications, with the consideration that the α-amylase variants disclosed herein are used instead of, or in addition to, any α-amylase disclosed in the listed patents and published applications: CA 2006687, GB 2200132, GB 2234980, GB 2228945, DE 3741617, DE 3727911, DE
1680 4212166, DE 4137470, DE 3833047, DE 4205071, WO 93/25651, WO 93/18129, WO
93/04153, WO 92/06157, WO 92/08777, WO 93/21299, WO 93/17089, WO 93/03129, EP 481547, EP 530870, EP 533239, EP 554943, EP 429124, EP 346137, EP 561452, EP 318204, EP 318279, EP 271155, EP 271156, EP 346136, EP 518719, EP 518720, EP 518721, EP 516553, EP 561446, EP 516554, EP 516555, EP 530635, EP 414197, and
1685 U.S. Patent Nos. 5,112,518; 5,141,664; and 5,240,632.
According to the embodiment, one or more α-amylase variants may typically be a component of a detergent composition. As such, it may be included in the detergent composition in the form of a non-dusting granulate, a stabilized liquid, or a protected enzyme. Non-dusting granulates may be produced, e.g., as disclosed in U.S. Patent Nos.
1690 4, 106,991 and 4,661 ,452 and may optionally be coated by methods known in the art. Examples of waxy coating materials are poly(ethylene oxide) products; (polyethyleneglycol, PEG) with mean molar weights of 1,000 to 20,000; ethoxylated nonylphenols having from 16 to 50 ethylene oxide units; ethoxylated fatty alcohols in which the alcohol contains from 12 to 20 carbon atoms and in which there are 15 to 80
1695 ethylene oxide units; fatty alcohols; fatty acids; and mono- and di- and triglycerides of fatty acids. Examples of film-foπning coating materials suitable for application by fluid bed techniques are given in, for example, GB Patent No. 1483591. Liquid enzyme preparations may, for instance, be stabilized by adding a polyol such as propylene glycol, a sugar or sugar alcohol, lactic acid or boric acid according to established methods. Other
1700 enzyme stabilizers are well known in the art. Protected enzymes may be prepared according to the method disclosed in US 5,879,920 (Genencor International, Inc.) or EP 238216, for example. Polyols have long been recognized as stabilizers of proteins as well as for improving the solubility of proteins. See, e.g., Kaushik et al., "Why is trehalose an exceptional protein stabilizer? An analysis of the thermal stability of proteins in the
1705 presence of the compatible osmolyte trehalose" J Biol. Chem. 278: 26458-65 (2003) and references cited therein; and M. Conti et al., "Capillary isoelectric focusing: the problem of protein solubility," J Chromatography 757: 237-245 (1997).
The detergent composition may be in any convenient form, e.g., as gels, powders, granules, pastes, or liquids. A liquid detergent may be aqueous, typically containing up to 1710 about 70% of water, and 0% to about 30% of organic solvent, it may also be in the form of a compact gel type containing only about 30% water.
The detergent composition comprises one or more surfactants, each of which may be anionic, nonionic, cationic, or zwitterionic. The detergent will usually contain 0% to about 50% of anionic surfactant, such as linear alkylbenzenesulfonate (LAS); α-
1715 olefinsulfonate (AOS); alkyl sulfate (fatty alcohol sulfate) (AS); alcohol ethoxysulfate (AEOS or AES); secondary alkanesulfonates (SAS); α-sulfo fatty acid methyl esters; alkyl- or alkenylsuccinic acid; or soap. The composition may also contain 0% to about 40% of nonionic surfactant such as alcohol ethoxylate (AEO or AE), carboxylated alcohol ethoxylates, nonylphenol ethoxylate, alkylpolyglycoside, alkyldimethylamineoxide,
1720 ethoxylated fatty acid monoethanolamide, fatty acid monoethanolamide, or polyhydroxy alkyl fatty acid amide, as described in WO 92/06154, for example.
The detergent composition may additionally comprise one or more other enzymes, such as lipase, cutinase, protease, cellulase, peroxidase, and/or laccase in any combination.
The detergent may contain about 1% to about 65% of a detergent builder or 1725 complexing agent such as zeolite, diphosphate, triphosphate, phosphonate, citrate, nitrilotriacetic acid (NTA), ethylenediaminetetraacetic acid (EDTA), diethylenetriaminepentaacetic acid (DTMPA), alkyl- or alkenylsuccinic acid, soluble silicates or layered silicates (e.g., SKS-6 from Hoechst). The detergent may also be unbuilt, i.e., essentially free of detergent builder. Enzymes may be used in any 1730 composition compatible with the stability of the enzyme. Enzymes can be protected against generally deleterious components by known forms of encapsulation, as by granulation or sequestration in hydro gels, for example. Enzymes and specifically α- amylases either with or without the starch binding domains are not limited to laundry and dishwashing applications, but may bind use in surface cleaners and ethanol production 1735 from starch or biomass.
The detergent may comprise one or more polymers. Examples include carboxymethylcellulose (CMC), poly(vinylpyrrolidone) (PVP), polyethyleneglycol (PEG), poly(vinyl alcohol) (PVA), polycarboxylates such as polyacrylates, maleic/acrylic acid copolymers and lauryl methacrylate/acrylic acid copolymers. 1740 The detergent may contain a bleaching system, which may comprise a H2O2 source such as perborate or percarbonate optionally combined with a peracid-forming bleach activator, such as TAED or nonanoyloxybenzenesulfonate (NOBS). Alternatively, the bleaching system may comprise peroxy acids of the amide, imide, or sulfone type, for example. The bleaching system can also be an enzymatic bleaching system where a
1745 perhydrolase activates peroxide, such as that described in WO 2005/056783.
The enzymes of the detergent composition may be stabilized using conventional stabilizing agents, e.g., a polyol such as propylene glycol or glycerol; a sugar or sugar alcohol; lactic acid; boric acid or a boric acid derivative, such as an aromatic borate ester; and the composition may be formulated as described in WO 92/19709 and WO 92/19708, 1750 for example.
The detergent may also contain other conventional detergent ingredients such as fabric conditioners including clays, foam boosters, suds suppressors, anti-corrosion agents, soil-suspending agents, anti-soil redeposition agents, dyes, bactericides, optical brighteners, or perfume, for example. The pH (measured in aqueous solution at use 1755 concentration) is usually neutral or alkaline, e.g., pH about 7.0 to about 11.0.
The α-amylase variant may be incorporated in concentrations conventionally employed in detergents. It is at present contemplated that, in the detergent composition, the α-amylase variant may be added in an amount corresponding to 0.00001-1.0 mg (calculated as pure enzyme protein) of α-amylase variant per liter of wash liquor. 1760 Particular forms of detergent compositions comprising the α-amylase variants can be formulated to include:
(I) A detergent composition formulated as a granulate having a bulk density of at least 600 g/L comprising linear alkylbenzenesulfonate (calculated as acid) about 7% to about 12%; alcohol ethoxysulfate (e.g., C12-18 alcohol, 1-2 ethylene oxide (EO)) or alkyl
1765 sulfate (e.g., C16-18) about 1% to about 4%; alcohol ethoxylate (e.g., C14-15 alcohol, 7 EO) about 5% to about 9%; sodium carbonate (e.g., Na2CO3) about 14% to about 20%; soluble silicate, about 2 to about 6%; zeolite (e.g., NaAlSiO4) about 15% to about 22%; sodium sulfate (e.g., Na2SO4) 0% to about 6%; sodium citrate/citric acid (e.g., C6H5Na3O7ZC6H8O7) about 0% to about 15%; sodium perborate (e.g., NaBO3-H2O) about
1770 11% to about 18%; TAED about 2% to about 6%; carboxymethylcellulose (CMC) and 0% to about 2%; polymers (e.g., maleic/acrylic acid, copolymer, PVP, PEG) 0-3%; enzymes (calculated as pure enzyme) 0.0001-0.1% protein; and minor ingredients (e.g., suds suppressors, perfumes, optical brightener, photobleach) 0-5%. (2) A detergent composition formulated as a granulate having a bulk density of at 1775 least 600 g/L comprising linear alkylbenzenesulfonate (calculated as acid) about 6% to about 11%; alcohol ethoxysulfate (e.g., Ci2-18 alcohol, 1-2 EO) or alkyl sulfate (e.g., C16- 18) about 1% to about 3%; alcohol ethoxylate (e.g., C14-15 alcohol, 7 EO) about 5% to about 9%; sodium carbonate (e.g., Na2CO3) about 15% to about 21%; soluble silicate, about 1% to about 4%; zeolite (e.g., NaAlSiO4) about 24% to about 34%; sodium sulfate 1780 (e.g,. Na2SO4) about 4% to about 10%; sodium citrate/citric acid (e.g., C6H5Na3O7/
C6H8O7) 0% to about 15%; carboxymethylcellulose (CMC) 0% to about 2%; polymers (e.g., maleic/acrylic acid copolymer, PVP, PEG) 1-6%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; minor ingredients (e.g., suds suppressors, perfume) 0-5%.
(3) A detergent composition formulated as a granulate having a bulk density of at 1785 least 600 g/L comprising linear alkylbenzenesulfonate (calculated as acid) about 5% to about 9%; alcohol ethoxylate (e.g., C12-15 alcohol, 7 EO) about 7% to about 14%; Soap as fatty acid (e.g., C16-22 fatty acid) about 1 to about 3%; sodium carbonate (as Na2CO3) about 10% to about 17%; soluble silicate, about 3% to about 9%; zeolite (as NaAlSiO4) about 23% to about 33%; sodium sulfate (e.g., Na2SO4) 0% to about 4%; sodium perborate 1790 (e.g., NaBO3-H2O) about 8% to about 16%; TAED about 2% to about 8%; phosphonate (e.g., EDTMPA) 0% to about 1%; carboxymethylcellulose (CMC) 0% to about 2%; polymers (e.g., maleic/acrylic acid copolymer, PVP, PEG) 0-3%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; minor ingredients (e.g., suds suppressors, perfume, optical brightener) 0-5%.
1795 (4) A detergent composition formulated as a granulate having a bulk density of at least 600 g/L comprising linear alkylbenzenesulfonate (calculated as acid) about 8% to about 12%; alcohol ethoxylate (e.g., C12-15 alcohol, 7 EO) about 10% to about 25%; sodium carbonate (as Na2CO3) about 14% to about 22%; soluble silicate, about 1% to about 5%; zeolite (e.g., NaAlSiO4) about 25% to about 35%; sodium sulfate (e.g., Na2SO4)
1800 0% to about 10%; carboxymethylcellulose (CMC) 0% to about 2%; polymers (e.g., maleic/acrylic acid copolymer, PVP, PEG) 1-3%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; and minor ingredients (e.g., suds suppressors, perfume) 0-5%.
(5) An aqueous liquid detergent composition comprising linear alkylbenzenesulfonate (calculated as acid) about 15% to about 21%; alcohol ethoxylate 1805 (e.g., C12-15 alcohol, 7 EO or C12-15 alcohol, 5 EO) about 12% to about 18%; soap as fatty acid (e.g., oleic acid) about 3% to about 13%; alkenylsuccinic acid (C12-14) 0% to about 13%; aminoethanol about 8% to about 18%; citric acid about 2% to about 8%; phosphonate 0% to about 3%; polymers (e.g., PVP, PEG) 0% to about 3%; borate (e.g., B4O7) 0% to about 2%; ethanol 0% to about 3%; propylene glycol about 8% to about 14%; 1810 enzymes (calculated as pure enzyme protein) 0.0001-0.1%; and minor ingredients (e.g., dispersants, suds suppressors, perfume, optical brightener) 0-5%.
(6) An aqueous structured liquid detergent composition comprising linear alkylbenzenesulfonate (calculated as acid) about 15% to about 21%; alcohol ethoxylate (e.g., C12-15 alcohol, 7 EO, or C12-15 alcohol, 5 EO) 3-9%; soap as fatty acid (e.g., oleic
1815 acid) about 3% to about 10%; zeolite (as NaAlSiO4) about 14% to about 22%; potassium citrate about 9% to about 18%; borate (e.g., B4O7) 0% to about 2%; carboxymethylcellulose (CMC) 0% to about 2%; polymers (e.g., PEG, PVP) 0% to about 3%; anchoring polymers (e.g., lauryl methacrylate/acrylic acid copolymer); molar ratio 25:1, MW 3800) 0% to about 3%;glycerol 0% to about 5%; enzymes (calculated as pure
1820 enzyme protein) 0.0001-0.1%; and minor ingredients (e.g., dispersants, suds suppressors, perfume, optical brighteners) 0-5%.
(7) A detergent composition formulated as a granulate having a bulk density of at least 600 g/L comprising fatty alcohol sulfate about 5% to about 10%; ethoxylated fatty acid monoethanolamide about 3% to about 9%; soap as fatty acid 0-3%; sodium carbonate
1825 (e.g., Na2CO3) about 5% to about 10%; soluble silicate, about 1% to about 4%; zeolite (e.g., NaAlSiO4) about 20% to about 40%; sodium sulfate (e.g., Na2SO4) about 2% to about 8%; sodium perborate (e.g., NaBO3-H2O) about 12% to about 18%; TAED about 2% to about 7%; polymers (e.g., maleic/acrylic acid copolymer, PEG) about 1% to about 5%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; and minor ingredients
1830 (e.g., optical brightener, suds suppressors, perfume) 0-5%.
(8) A detergent composition formulated as a granulate comprising linear alkylbenzenesulfonate (calculated as acid) about 8% to about 14%; ethoxylated fatty acid monoethanolamide about 5% to about 11%; soap as fatty acid 0% to about 3%; sodium carbonate (e.g., Na2CO3) about 4% to about 10%; soluble silicate, about 1% to about 4%;
1835 zeolite (e.g., NaAlSiO4) about 30% to about 50%; sodium sulfate (e.g., Na2SO4) about 3% to about 11%; sodium citrate (e.g., C6H5Na3O7) about 5% to about 12%; polymers (e.g., PVP, maleic/acrylic acid copolymer, PEG) about 1% to about 5%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; and minor ingredients (e.g., suds suppressors, perfume) 0-5%.
1840 (9) A detergent composition formulated as a granulate comprising linear alkylbenzenesulfonate (calculated as acid) about 6% to about 12%; nonionic surfactant about 1% to about 4%; soap as fatty acid about 2% to about 6%; sodium carbonate (e.g., Na2CO3) about 14% to about 22%; zeolite (e.g., NaAlSiO4) about 18% to about 32%; sodium sulfate (e.g., Na2SO4) about 5% to about 20%; sodium citrate (e.g., CeHsNa3O7) 1845 about 3% to about 8%; sodium perborate (e.g., NaBO3-H2O) about 4% to about 9%; bleach activator (e.g., NOBS or TAED) about 1% to about 5%; carboxymethylcellulose (CMC) 0% to about 2%; polymers (e.g., polycarboxylate or PEG) about 1% to about 5%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; and minor ingredients (e.g., optical brightener, perfume) 0-5%.
1850 (10) An aqueous liquid detergent composition comprising linear alkylbenzenesulfonate (calculated as acid) about 15% to about 23%; alcohol ethoxysulfate (e.g., Cn-15 alcohol, 2-3 EO) about 8% to about 15%; alcohol ethoxylate (e.g., Ci2-15 alcohol, 7 EO, or C12-15 alcohol, 5 EO) about 3% to about 9%; soap as fatty acid (e.g., lauric acid) 0% to about 3%; aminoethanol about 1% to about 5%; sodium citrate about
1855 5% to about 10%; hydrotrope (e.g., sodium toluensulfonate) about 2% to about 6%; borate (e.g., B4O7) 0% to about 2%; carboxymethylcellulose 0% to about 1%; ethanol about 1% to about 3%; propylene glycol about 2% to about 5%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; and minor ingredients (e.g., polymers, dispersants, perfume, optical brighteners) 0-5%.
1860 (11) An aqueous liquid detergent composition comprising linear alkylbenzenesulfonate (calculated as acid) about 20% to about 32%; alcohol ethoxylate (e.g., Ci2-15 alcohol, 7 EO, or C12-15 alcohol, 5 EO) 6-12%; aminoethanol about 2% to about 6%; citric acid about 8% to about 14%; borate (e.g., B4O7) about 1% to about 3%; polymer (e.g., maleic/acrylic acid copolymer, anchoring polymer, such as lauryl
1865 methacrylate/acrylic acid copolymer) 0% to about 3%; glycerol about 3% to about 8%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; and minor ingredients (e.g., hydrotropes, dispersants, perfume, optical brighteners) 0-5%.
(12) A detergent composition formulated as a granulate having a bulk density of at least 600 g/L comprising anionic surfactant (linear alkylbenzenesulfonate, alkyl sulfate, α-
1870 olefinsulfonate, α-sulfo fatty acid methyl esters, alkanesulfonates, soap) about 25% to about 40%; nonionic surfactant (e.g., alcohol ethoxylate) about 1% to about 10%; sodium carbonate (e.g., Na2CO3) about 8% to about 25%; soluble silicates, about 5% to about 15%; sodium sulfate (e.g., Na2SO4) 0% to about 5%; zeolite (NaAlSiO4) about 15% to about 28%; sodium perborate (e.g., NaBO3 H2O) 0% to about 20%; bleach activator
1875 (TAED or NOBS) about 0% to about 5%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; minor ingredients (e.g., perfume, optical brighteners) 0-3%. (13) Detergent compositions as described in compositions I)- 12) supra, wherein all or part of the linear alkylbenzenesulfonate is replaced by (C12-C18) alkyl sulfate.
(14) A detergent composition formulated as a granulate having a bulk density of at 1880 least 600 g/L comprising (C12-C18) alkyl sulfate about 9% to about 15%; alcohol ethoxylate about 3% to about 6%; polyhydroxy alkyl fatty acid amide about 1% to about 5%; zeolite (e.g., NaAlSiO4) about 10% to about 20%; layered disilicate (e.g., SK56 from Hoechst) about 10% to about 20%; sodium carbonate (e.g., Na2COs) about 3% to about 12%; soluble silicate, 0% to about 6%; sodium citrate about 4% to about 8%; sodium 1885 percarbonate about 13% to about 22%; TAED about 3% to about 8%; polymers (e.g., polycarboxylates and PVP) 0% to about 5%; enzymes (calculated as pure enzyme protein) 0.0001-0.1%; and minor ingredients (e.g., optical brightener, photobleach, perfume, suds suppressors) 0-5%.
(15) A detergent composition formulated as a granulate having a bulk density of at 1890 least 600 g/L comprising (C12-C18) alkyl sulfate about 4% to about 8%; alcohol ethoxylate about 11% to about 15%; soap about 1% to about 4%; zeolite MAP or zeolite A about 35% to about 45%; sodium carbonate (as Na2COs) about 2% to about 8%; soluble silicate, 0% to about 4%; sodium percarbonate about 13% to about 22%; TAED 1-8%; carboxymethylcellulose (CMC) 0% to about 3%; polymers (e.g., polycarboxylates and 1895 PVP) 0% to about 3 %; enzymes (calculated as pure enzyme protein) 0.0001 -0.1 %; and minor ingredients (e.g., optical brightener, phosphonate, perfume) 0-3%.
(16) Detergent formulations as described in I)- 15) supra, which contain a stabilized or encapsulated peracid, either as an additional component or as a substitute for already specified bleach systems.
1900 (17) Detergent compositions as described supra in 1), 3), 7), 9), and 12), wherein perborate is replaced by percarbonate.
(18) Detergent compositions as described supra in 1), 3), 7), 9), 12), 14), and 15), which additionally contains a manganese catalyst.
(19) Detergent composition formulated as a non-aqueous detergent liquid
1905 comprising a liquid nonionic surfactant such as, e.g. , linear alkoxylated primary alcohol, a builder system (e.g., phosphate), an enzyme(s), and alkali. The detergent may also comprise anionic surfactant and/or a bleach system. In another embodiment, the 2,6-β-D-fructan hydrolase can be incorporated in detergent compositions and used for removal/cleaning of biofihn present on household 1910 and/or industrial textile/laundry.
The detergent composition may for example be formulated as a hand or machine laundry detergent composition, including a laundry additive composition suitable for pre- treatment of stained fabrics and a rinse added fabric softener composition, or be formulated as a detergent composition for use in general household hard surface cleaning 1915 operations, or be formulated for hand or machine dishwashing operations.
In a specific aspect, the detergent composition can comprise 2,6-β-D-fructan hydrolase, one or more α-amylase variants, and one or more other cleaning enzymes, such as a protease, a lipase, a cutinase, a carbohydrase, a cellulase, a pectinase, a mannanase, an arabinase, a galactanase, a xylanase, an oxidase, a laccase, and/or a peroxidase, and/or 1920 combinations thereof. In general the properties of the chosen enzyme(s) should be compatible with the selected detergent, (e.g., pH-optimum, compatibility with other enzymatic and non-enzymatic ingredients, etc.), and the enzyme(s) should be present in effective amounts.
Proteases: suitable proteases include those of animal, vegetable or microbial origin.
1925 Chemically modified or protein engineered mutants are also suitable. The protease may be a serine protease or a metalloprotease, e.g., an alkaline microbial protease or a trypsin-like protease. Examples of alkaline proteases are subtilisins, especially those derived from Bacillus sp., e.g., subtilisin Novo, subtilisin Carlsberg, subtilisin 309 (see, e.g., U.S. Patent No. 6,287,841), subtilisin 147, and subtilisin 168 (see, e.g., WO 89/06279). Examples of
1930 trypsin-like proteases are trypsin (e.g., of porcine or bovine origin), and Fusarium proteases (see, e.g., WO 89/06270 and WO 94/25583). Examples of useful proteases also include but are not limited to the variants described in WO 92/19729 and WO 98/20115. Suitable commercially available protease enzymes include Alcalase®, Savinase®, Esperase®, and Kannase™ (Novozymes, formerly Novo Nordisk A/S); Maxatase®,
1935 Maxacal™, Maxapem™, Properase™, Purafect®, Purafect OxP™, FN2™, and FN3 ™ (Genencor International, Inc.).
Lipases: suitable lipases include those of bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Examples of useful lipases include, but are not limited to, Upases from Humicola (synonym Thermomyces), e.g. H. lanuginosa 1940 (T. lanuginosa) (see, e.g., EP 258068 and EP 305216) and H. insolens (see, e.g., WO
96/13580); a Pseudomonas lipase (e.g., from P. alcaligenes or P. pseudoalcaligenes; see, e.g., EP 218 272), P. cepacia {see, e.g., EP 331 376), P. stutzeri {see, e.g., GB 1,372,034), P. fluorescens, Pseudomonas sp. strain SD 705 {see, e.g., WO 95/06720 and WO 96/27002), P. wisconsinensis {see, e.g., WO 96/12012); a Bacillus lipase (e.g., from B.
1945 subtilis; see, e.g., Dartois et al. Biochemica Biophysica Acta, 1131: 253-360 (1993)), B. stearothermophilus {see, e.g., JP 64/744992), oτ B. pumilus {see, e.g., WO 91/16422). Additional lipase variants contemplated for use in the formulations include those described, for example, in: WO 92/05249, WO 94/01541, WO 95/35381, WO 96/00292, WO 95/30744, WO 94/25578, WO 95/14783, WO 95/22615, WO 97/04079, WO
1950 97/07202, EP 407225, and EP 260105. Some commercially available lipase enzymes include Lipolase® and Lipolase® Ultra (Novozymes, formerly Novo Nordisk A/S).
Polyesterases: Suitable polyesterases include, but are not limited to, those described in WO 01/34899 (Genencor International, Inc.) and WO 01/14629 (Genencor International, Inc.), and can be included in any combination with other enzymes discussed 1955 herein.
Amylases: The compositions can be combined with other α-amylases, such as a non-variant α-amylase. These can include commercially available amylases, such as but not limited to Duramyl®, Termamyl™, Fungamyl® and BAN™ (Novozymes, formerly Novo Nordisk A/S), Rapidase®, and Purastar® (Genencor International, Inc.).
1960 Cellulases: Cellulases can be added to the compositions. Suitable cellulases include those of bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Suitable cellulases include cellulases from the genera Bacillus, Pseudomonas, Humicola, Fusarium, Thielavia, Acremonium, e.g., the fungal cellulases produced from Humicola insolens, Myceliophthora thermophila and Fusarium oxysporum disclosed in
1965 U.S. Patent Nos. 4,435,307; 5,648,263; 5,691,178; 5,776,757; and WO 89/09259, for example. Exemplary cellulases contemplated for use are those having color care benefit for the textile. Examples of such cellulases are cellulases described in EP 0495257; EP 531 372; WO 99/25846 (Genencor International, Inc.), WO 96/34108 (Genencor International, Inc.), WO 96/11262; WO 96/29397; and WO 98/08940, for example. Other
1970 examples are cellulase variants, such as those described in WO 94/07998; WO 98/12307; WO 95/24471; PCT/DK98/00299; EP 531 315; U.S. Patent Nos. 5,457,046; 5,686,593; and 5,763,254. Commercially available cellulases include Celluzyme® and Carezyme® (Novozymes, formerly Novo Nordisk A/S); Clazinase™ and Puradax® HA (Genencor International, Inc.); and KAC-500(B)™ (Kao Corporation). 1975 Peroxidases/Oxidases: Suitable peroxidases/oxidases contemplated for use in the compositions include those of plant, bacterial or fungal origin. Chemically modified or protein engineered mutants are included. Examples of useful peroxidases include peroxidases from Coprinus, e.g., from C. cinereus, and variants thereof as those described in WO 93/24618, WO 95/10602, and WO 98/15257.
1980 The detergent enzyme(s) may be included in a detergent composition by adding separate additives containing one or more enzymes, or by adding a combined additive comprising all of these enzymes. A detergent additive, i.e., a separate additive or a combined additive, can be formulated as a granulate, liquid, slurry, etc. Suitable granulate detergent additive formulations include non-dusting granulates.
1985 Non-dusting granulates may be produced, e.g., as disclosed in U.S. Patent Nos.
4,106,991 and 4,661,452 and optionally may be coated by methods known in the art. Examples of waxy coating materials are poly(ethylene oxide) products (e.g., polyethyleneglycol, PEG) with mean molar weights of 1,000 to 20,000; ethoxylated nonylphenols having from 16 to 50 ethylene oxide units; ethoxylated fatty alcohols in
1990 which the alcohol contains from 12 to 20 carbon atoms and in which there are 15 to 80 ethylene oxide units; fatty alcohols; fatty acids; and mono- and di- and triglycerides of fatty acids. Examples of film-forming coating materials suitable for application by fluid bed techniques are given in GB 1483591, for example. Liquid enzyme preparations may, for instance, be stabilized by adding a polyol such as propylene glycol, a sugar or sugar
1995 alcohol, lactic acid or boric acid according to established methods. Protected enzymes may be prepared according to the method disclosed in EP 238 216.
The detergent composition may be in any convenient form, e.g., a bar, tablet, gel, powder, granule, paste, or liquid. A liquid detergent may be aqueous, typically containing up to about 70% water, and 0% to about 30% organic solvent. Compact detergent gels 2000 containing 30% or less water are also contemplated. The detergent composition comprises one or more surfactants, which may be non-ionic, including semi-polar, anionic, cationic, or zwitterionic, or any combination thereof. The surfactants are typically present at a level of from 0.1% to 60% by weight.
When included therein the detergent typically will contain from about 1% to about 2005 40% of an anionic surfactant, such as linear alkylbenzenesulfonate, α-olefinsulfonate, alkyl sulfate (fatty alcohol sulfate), alcohol ethoxysulfate, secondary alkanesulfonate, α- sulfo fatty acid methyl ester, alkyl- or alkenylsuccinic acid, or soap. When included therein, the detergent will usually contain from about 0.2% to about 40% of a non-ionic surfactant such as alcohol ethoxylate, nonylphenol ethoxylate, 2010 alkylpolyglycoside, alkyldimethylamineoxide, ethoxylated fatty acid monoethanolamide, fatty acid monoethanolamide, polyhydroxy alkyl fatty acid amide, or N-acyl-N-alkyl derivatives of glucosamine ("glucamides").
The detergent may contain 0% to about 65% of a detergent builder or complexing agent such as zeolite, diphosphate, triphosphate, phosphonate, carbonate, citrate, 2015 nitrilotriacetic acid, ethylenediaminetetraacetic acid (EDTA), diethylenetriaminepentaacetic acid, alkyl- or alkenylsuccinic acid, soluble silicates or layered silicates (e.g., SKS-6 from Hoechst).
The detergent may comprise one or more polymers. Examples are carboxymethylcellulose (CMC), polyvinylpyrrolidone) (PVP), poly(ethylene glycol) 2020 (PEG), polyvinyl alcohol) (PVA), poly(vinylpyridine-N-oxide), poly(vinylimidazole), polycarboxylates, e.g., polyacrylates, maleic/acrylic acid copolymers), and lauryl methacrylate/acrylic acid copolymers.
The detergent may contain a bleaching system that may comprise a source of H2O2, such as perborate or percarbonate, which may be combined with a peracid-forming 2025 bleach activator (e.g., tetraacetylethylenediamine or nonanoyloxybenzenesulfonate).
Alternatively, the bleaching system may comprise peroxyacids (e.g., the amide-, imide-, or sulfone-type peroxyacids). The bleaching system can also be an enzymatic bleaching system.
The enzyme(s) of the detergent composition may be stabilized using conventional 2030 stabilizing agents, e.g., polyol (e.g., propylene glycol or glyceroiχ_a sugar or sugar alcohol, lactic acid, boric acid, a boric .acid derivative (e.g., an aromatic borate ester), or a phenyl boronic acid derivative (e.g., 4-formylphenyl boronic acid). The composition may be formulated as described in WO 92/19709 and WO 92/19708.
The detergent may also contain other conventional detergent ingredients such as 2035 e.g., fabric conditioners including clays, foam boosters, suds suppressors, anti-corrosion agents, soil-suspending agents, anti-soil redeposition agents, dyes, bactericides, optical brighteners, hydrotropes, tarnish inhibitors, or perfumes.
It is contemplated that in the detergent compositions, the enzyme variants may be added in an amount corresponding to about 0.01 to about 100 mg of enzyme protein per 2040 liter of wash liquor, particularly about 0.05 to about 5.0 mg of enzyme protein per liter of wash liquor, or even more particularly in 0.1 to about 1.0 mg of enzyme protein per liter of wash liquor.
STARCH PROCESSING COMPOSITIONS AND USE
In another aspect, compositions with the disclosed α-amylase variants can be 2045 utilized for starch liquefaction and/or saccharification. Starch processing is useful for producing sweetener, producing alcohol for fuel or drinking (i.e., potable alcohol), producing a beverage, processing cane sugar, or producing desired organic compounds, e.g., citric acid, itaconic acid, lactic acid, gluconic acid, ketones, amino acids, antibiotics, enzymes, vitamins, and hormones. Conversion of starch to fructose syrups normally 2050 consists of three consecutive enzymatic processes: a liquefaction process, a saccharification process, and an isomerization process. During the liquefaction process, a variant α-amylase degrades starch to dextrins by at pH between about 5.5 and about 6.2 and at temperatures of about 950C to about 1600C for a period of approximately 2 hours. About 1 mM of calcium (40 ppm free calcium ions) typically is added to optimize enzyme 2055 stability under these conditions. Other α-amylase variants may require different conditions.
After the liquefaction process, the dextrins can be converted into dextrose by addition of a glucoamylase (e.g., AMG™) and optionally a debranching enzyme, such as an isoamylase or a pullulanase (e.g., Promozyme®). Before this step, the pH is reduced to 2060 a value below about 4.5, maintaining the high temperature (above 95°C), and the liquefying α-amylase variant activity is denatured. The temperature is lowered to 600C, and a glucoamylase and a debranching enzyme can be added. The saccharification process proceeds typically for about 24 to about 72 hours.
After the saccharification process, the pH is increased to a value in the range of 2065 about 6.0 to about 8.0, e.g., pH 7.5, and the calcium is removed by ion exchange. The dextrose syrup is then converted into high fructose syrup using an immobilized glucose isomerase (such as Sweetzyme®), for example.
The α-amylase variant may provide at least one improved enzymatic property for conducting the process of liquefaction. For example, the variant α-amylase may have a 2070 higher activity, or it may have a reduced requirement for calcium. Addition of free calcium is required to ensure adequately high stability of the α-amylase; however, free calcium strongly inhibits the activity of the glucose isomerase. Accordingly, the calcium should be removed prior to the isomerization step, by means of an expensive unit operation, to an extent that reduces the level of free calcium to below 3-5 ppm. Cost 2075 savings can be obtained if such an operation could be avoided, and the liquefaction process could be performed without addition of free calcium ions. Thus, α-amylase variants that do not require calcium ions or that have a reduced requirement for calcium are particularly advantageous. For example, a less calcium-dependent α-amylase variant, which is stable and highly active at low concentrations of free calcium (<40 ppm) can be
2080 utilized in the composition and procedures. Such an α-amylase variant should have a pH optimum in the range of about 4.5 to about 6.5, e.g., about pH 4.5 to about pH 5.5. The α- amylase variants can be used alone to provide specific hydrolysis or can be combined with other amylases to provide a "cocktail" with a broad spectrum of activity.
The starch to be processed may be a highly refined starch quality, for instance, at 2085 least 90%, at least 95%, at least 97%, or at least 99.5% pure. Alternatively, the starch can be a more crude starch containing material comprising milled whole grain, including non- starch fractions such as germ residues and fibers. The raw material, such as whole grain, is milled to open up the structure and allow further processing. Two milling processes are suitable: wet and dry milling. Also, corn grits, and milled corn grits may be applied. Dry 2090 milled grain will comprise significant amounts of non-starch carbohydrate compounds, in addition to starch. When such a heterogeneous material is processed by jet cooking, often only a partial gelatinization of the starch is achieved. Accordingly, α-amylase variants having a high activity towards ungelatinized starch are advantageously applied in a. process comprising liquefaction and/or saccharification jet cooked dry milled starch.
2095 A variant α-amylase having a superior hydrolysis activity during the liquefaction process advantageously increases the efficiency of the saccharification step {see WO 98/22613) and the need for glucoamylase during the saccharification step. The glucoamylase advantageously is present in an amount of no more than, or even less than, 0.5 glucoamylase activity unit (AGU)/g DS (i.e., glucoamylase activity units per gram of
2100 dry solids). The glucoamylase may be derived from a strain within Aspergillus sp.,
Tαlαromyces sp., Pαchykytosporα sp., or Trαmetes sp., with exemplary examples being Aspergillus niger, Tαlαromyces emersonii, Trαmetes cingulαtα, or Pαchykytosporα pαpyrαceα. In one embodiment, the process also comprises the use of a carbohydrate- binding domain of the type disclosed in WO 98/22613.
2105 In yet another aspect, the process may comprise hydrolysis of a slurry of gelatinized or granular starch, in particular hydrolysis of granular starch into a soluble starch hydrolysate at a temperature below the initial gelatinization temperature of the granular starch. In addition to being contacted with an α-amylase variant, the starch may be contacted with one or more enzyme selected from the group consisting of a fungal α- 2110 amylase (EC 3.2.1.1), a β-amylase (EC 3.2.1.2), and a glucoamylase (EC 3.2.1.3). In an embodiment further another amylolytic enzyme or a debranching enzyme, such as an isoamylase (EC 3.2.1.68), or a pullulanases (EC 3.2.1.41) may be added to the α-amylase variant.
In one embodiment, the process is conducted at a temperature below the initial
2115 gelatinization temperature. Such processes are often conducted at least at 30°C, at least
31°C, at least 32°C, at least 330C, at least 340C, at least 35°C, at least 36°C, at least 37°C, at least 38°C, at least 39°C, at least 400C, at least 41°C, at least 42°C, at least 43°C, at least 44°C, at least 45°C, at least 46°C, at least 47°C, at least 48°C, at least 49°C, at least 5O0C, at least 510C, at least 52°C, at least 53°C, at least 54°C, at least 55°C, at least 560C,
2120 at least 57°C, at least 58°C, at least 59°C, or at least 6O0C. The pH at which the process is conducted may in be in the range of about 3.0 to about 7.0, from about 3.5 to about 6.0, or from about 4.0 to about 5.0. One aspect contemplates a process comprising fermentation with a yeast, for example, to produce ethanol at a temperature around 320C, such as from 3O0C to 350C. In another aspect, the process comprises simultaneous saccharification and
2125 fermentation with a yeast to produce ethanol or with another suitable fermentation organism to produce a desired organic compound, for example, at a temperature from 300C to 35°C, e.g., at around 32°C. In the above fermentation processes, the ethanol content reaches at least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 11%, at least about 12%, at least about 13%, at least about 14%, at least
2130 about 15%, or at least about 16% ethanol.
The starch slurry to be used in any of the above aspects may have about 20% to about 55% dry solids granular starch, about 25% to about 40% dry solids granular starch, or about 30% to about 35% dry solids granular starch. The enzyme variant converts the soluble starch into a soluble starch hydrolysate of the granular starch in the amount of at 2135 least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%.
In another embodiment, the α-amylase variant is used in a process for liquefaction or saccharification of a gelatinized starch, including, but not limited to, gelatinization by 2140 jet cooking. The process may comprise fermentation to produce a fermentation product, e.g., ethanol. Such a process for producing ethanol from starch-containing material by fermentation comprises: (i) liquefying the starch-containing material with an α-amylase variant; (ii) saccharifying the liquefied mash obtained; and (iii) fermenting the material obtained in step (ii) in the presence of a fermenting organism. Optionally the process 2145 further comprises recovery of the ethanol. The saccharifϊcation and fermentation processes may be carried out as a simultaneous saccharifϊcation and fermentation (SSF) process. During the fermentation, the ethanol content reaches at least about 7%, at least about 8%, at least about 9%, at least about 10% such as at least about 11%, at least about 12%, at least about 13%, at least about 14%, at least 15%, or at least 16% ethanol.
2150 The starch to be processed in the above aspects may be obtained from tubers, roots, stems, legumes, cereals or whole grain. More specifically, the granular starch may be obtained from corns, cobs, wheat, barley, rye, milo, sago, cassava, tapioca, sorghum, rice, peas, bean, banana, or potatoes. Specially contemplated are both waxy and non-waxy types of corn and barley.
2155 As used herein, the term "liquefaction" or "liquefy" means a process by which starch is converted to less viscous and shorter chain dextrins. Generally, this process involves gelatmization of starch simultaneously with or followed by the addition of an α- amylase variant. Additional liquefaction-inducing enzymes optionally may be added. As used herein, the term "primary liquefaction" refers to a step of liquefaction when the
2160 slurry' s temperature is raised to or near its gelatinization temperature. Subsequent to the raising of the temperature, the slurry is sent through a heat exchanger or jet to temperatures from about 90-150°C, e.g., 100-1100C. Subsequent to application to a heat exchange or jet temperature, the slurry is held for a period of 3-10 minutes at that temperature. This step of holding the slurry at 90-1500C is termed primary liquefaction.
2165 As used herein, the term "secondary liquefaction" refers the liquefaction step subsequent to primary liquefaction (heating to 90-1500C), when the slurry is allowed to cool to room temperature. This cooling step can be 30 minutes to 180 minutes, e.g. 90 minutes to 120 minutes. As used herein, the term "minutes of secondary liquefaction" refers to the time that has elapsed from the start of secondary liquefaction to the time that
2170 the Dextrose Equivalent (DE) is measured.
Another aspect contemplates the additional use of a β-amylase in the composition comprising the α-amylase variant, β-amylases (EC 3.2.1.2) are exo-acting maltogenic amylases, which catalyze the hydrolysis of 1 ,4-α-glucosidic linkages into amylose, amylopectin, and related glucose polymers, thereby releasing maltose, β-amylases have 2175 been isolated from various plants and microorganisms (Fogarty et al., PROGRESS IN INDUSTRIAL MICROBIOLOGY, Vol. 15, pp. 112-115, 1979). These β-amylases are characterized by having optimum temperatures in the range from 400C to 650C, and optimum pH in the range from about 4.5 to about 7.0. Contemplated β-amylases include, but are not limited to, β-amylases from barley Spezyme® BBA 1500, Spezyme® DBA, 2180 Optimalt™ ME, Optimalt™ BBA (Genencor International, Inc.); and Novozym™ WBA (Novozymes AJS).
Another enzyme contemplated for use in the composition is a glucoamylase (EC 3.2.1.3). Glucoamylases are derived from a microorganism or a plant. For example, glucoamylases can be of fungal or bacterial origin. Exemplary bacterial glucoamylases are 2185 Aspergillus glucoamylases, in particular A. niger Gl or G2 glucoamylase (Boel et al.
(1984), EMBO J. 3(5): 1097-1102), or variants thereof, such as disclosed in WO 92/00381 and WO 00/04136; A. awamori glucoamylase (WO 84/02921); A. oryzae glucoamylase (Agric. Biol. Chem. (1991), 55(4): 941-949), or variants or fragments thereof.
Other contemplated Aspergillus glucoamylase variants include variants to enhance
2190 the thermal stability: G137A and G139A (Chen et al. (1996), Prot. Eng. 9: 499-505); D257E and D293E/Q (Chen et al. (1995), Prot. Eng. 8: 575-582); Nl 82 (Chen et al. (1994), Biochem. J. 301: 275-281); disulphide bonds, A246C (Fierobe et al. (1996), Biochemistry, 35: 8698-8704); and introduction of Pro residues in positions A435 and S436 (Li et al. (1997) Protein Eng. 10: 1199-1204). Other contemplated glucoamylases
2195 include Talaromyces glucoamylases, in particular derived from T. emersonii (WO
99/28448), T. leycettanus (U.S. Patent No. RE 32,153), T. duponti, or T. thermophilus (U.S. Patent No. 4,587,215). Contemplated bacterial glucoamylases include glucoamylases from the genus Clostridium, in particular C. thermoamylolyticum (EP 135138) and C. thermohydrosulfuricum (WO 86/01831). Suitable glucoamylases include
2200 the glucoamylases derived from Aspergillus oryzae, such as a glucoamylase having 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, or even 90% homology to the amino acid sequence shown in SEQ ID NO:2 in WO 00/04136. Also suitable are commercial glucoamylases, such as AMG 200L; AMG 300 L; SAN™ SUPER and AMG™E (Novozymes); OPTIDEX® 300 (Genencor International, Inc.); AMIGASE™and
2205 AMIGASE™ PLUS (from DSM); G-ZYME® G900 (Enzyme Bio-Systems); and G-
ZYME® G990 ZR (A. nigeτ glucoamylase and low protease content). Glucoamylases may be added in an amount of 0.02-2.0 AGU/g DS or 0.1-1.0 AGU/g DS, e.g., 0.2 AGU/g DS.
Additional enzyme variants can be included in the composition. Two or more α- amylase variants can be used alone or in combination with other enzymes discussed 2210 herein. For example, a third enzyme may be another α-amylase, e.g., a yeast α-amylase, or another α-amylase variant. These can be Bacillus α-amylases or non-Bacillus α-amylases. Another enzyme that can optionally be added is a debranching enzyme, such as an isoamylase (EC 3.2.1.68) or a pullulanases (EC 3.2.1.41). Isoamylase hydrolyses α-l,6-D- glucosidic branch linkages in amylopectin and β-limit dextrins and can be distinguished 2215 from pullulanases by the inability of isoamylase to attack pullulan and by the limited action of isoamylase on α-limit dextrins. Debranching enzymes may be added in effective amounts well known to the person skilled in the art.
The exact composition of the products of the process depends on the combination of enzymes applied, as well as the type of granular starch processed. The soluble
2220 hydrolysate may be maltose with a purity of at least about 85%, at least about 90%, at least about 95.0%, at least about 95.5%, at least about 96.0%, at least about 96.5%, at least about 97.0%, at least about 97.5%, at least about 98.0%, at least about 98.5%, at least about 99.0% or at least about 99.5%. Alternatively, the soluble starch hydrolysate is glucose, or the starch hydrolysate has a DE (glucose percent of total solubilLzed dry solids)
2225 of at least 94.5%, at least 95.0%, at least 95.5%, at least 96.0%, at least 96.5%, at least 97.0%, at least 97.5%, at least 98.0%, at least 98.5%, at least 99.0% or at least 99.5%. In one embodiment, a process of manufacturing ice creams, cakes, candies, canned fruit uses a specialty syrup containing a mixture of glucose, maltose, DP3 and DPn.
Two milling processes are suitable: wet milling and dry milling. In dry milling, the 2230 whole kernel is milled and used. Wet milling gives a good separation of germ and meal (starch granules and protein) and is usually used when the starch hydrolysate is used in production of syrups. Both dry and wet milling are well known in the art of starch processing and also are contemplated for use with the compositions and methods disclosed. The process may be conducted in an ultrafiltration system where the retentate is 2235 held under recirculation in presence of enzymes, raw starch and water, where the permeate is the soluble starch hydrolysate. Another method is the process conducted in a continuous membrane reactor with ultrafiltration membranes, where the retentate is held under recirculation in presence of enzymes, raw starch and water, and where the permeate is the soluble starch hydrolysate. Also contemplated is the process conducted in a continuous 2240 membrane reactor with microfiltration membranes and where the retentate is held under recirculation in presence of enzymes, raw starch and water, and where the permeate is the soluble starch hydrolysate.
In one regard, the soluble starch hydrolysate of the process is subjected to conversion into high fructose starch-based syrup (HFSS), such as high fructose corn syrup 2245 (HFCS). This conversion can be achieved using a glucose isomerase, particularly a glucose isomerase immobilized on a solid support. Contemplated isomerases included the commercial products Sweetzyme®, IT (Novozymes AJS); G-zyme® IMGI, and G-zyme® G993, Ketomax®, G-zyme® G993, G-zyme® G993 liquid, and GenSweet® IGI.
In another aspect, the soluble starch hydrolysate of produced yields production of 2250 fuel or potable ethanol. In the process of the third aspect the fermentation may be carried out simultaneously or separately/sequential to the hydrolysis of the granular starch slurry. When the fermentation is performed simultaneously with the hydrolysis, the temperature can be between 30°C and 350C, particularly between 31 °C and 34°C. The process may be conducted in an ultrafiltration system where the retentate is held under recirculation in 2255 presence of enzymes, raw starch, yeast, yeast nutrients and water and where the permeate is an ethanol containing liquid. Also contemplated is the process conducted in a continuous membrane reactor with ultrafiltration membranes and where the retentate is held under recirculation in presence of enzymes, raw starch, yeast, yeast nutrients and water and where the permeate is an ethanol containing liquid.
2260 The soluble starch hydrolysate of the process may also be used for production of a fermentation product comprising fermenting the treated starch into a fermentation product, such as citric acid, monosodium glutamate, gluconic acid, sodium gluconate, calcium gluconate, potassium gluconate, glucono delta-lactone, or sodium erythorbate.
The amylolytic activity of the α-amylase variant may be determined using potato 2265 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 samples of the starch/enzyme solution with an iodine solution. Initially, a blackish-blue color is formed, but during the breakdown of the starch the blue color gets weaker and gradually turns into a reddish-brown, which is compared to a colored glass standard.
2270 ETHANOL PRODUCTION
The PS4 variant polypeptide may in general be used to convert starch into sugars that can then be processed into ethanol or other value-added products such as high fructose corn sweetener. Thus, we disclose the use of PS4 variant polypeptides in the production of ethanol and specifically bioethanol, which in this document should be regarded as any 2275 ethanol produced by biomass fermentation.
The ethanol so produced may be used as a fuel or beverage or may be used in a fermentation process for producing organic compounds, such as citric acid, ascorbic acid, lysine, glutamic acid. These are described in further detail below. Ethanol (or ethyl alcohol) is best known as being the basis of alcoholic beverages 2280 like spirits, beer and wine, hi addition, ethanol has many uses in the production of industrial chemicals, pharmaceuticals and as a transportation fuel.
Ethanol can be produced from almost any raw material containing sugar or carbohydrates. As such, ethanol can be made from a wide variety of biological material. The 3 major types of biomass feedstocks used to produce ethanol include sugar crops, 2285 such as sugar cane; starch crops, including wheat and corn, and cellulosic materials, such as crop residues (straw, etc.), and forestry waste. Ethanol production from readily available sources of cellulose provides a stable, renewable fuel source.
The processing technology most frequently used is dry grain milling, hi this process, the grain is first milled to a grain meal consistency. The meal is then mixed with
2290 water and amylase and passed through cookers where the starch in the grain is liquefied. Under the addition of gluco-amylase the liquefied starch is converted into fermentable sugars. Yeast is then added to the mash to ferment the sugars to ethanol. After fermentation, the mash goes through a distillation and dehydration process where the alcohol is removed from the solids and the water. In practice about two thirds of each
2295 tonne of grain is converted to fuel ethanol. The remaining by-products - thin stillage and wet distillers grain - are a high protein livestock feed which is particularly well suited for animals such as cattle or sheep.
Ethanol may also be made from cellulose containing sources, such as wood pulp. Cellulose-based feedstocks are comprised of agricultural wastes, grasses and woods and 2300 other low-value biomass such as municipal waste (e.g., recycled paper, yard clippings, etc.). Ethanol may be produced from the fermentation of any of these cellulosic feedstocks. However, the cellulose must first be converted to sugars before there can be conversion to ethanol, by treatment with a suitable enzyme such as cellulase.
Once ethanol leaves the processing plant, it can theoretically be used as an 2305 automotive fuel by itself or it can be mixed with gasoline at a ratio of 85 to 15 to form what is called "neat ethanol fuel". However, most commonly, ethanol is blended with gasoline at concentrations of 7 to 10 % by volume. The ethanol may be used as an octane enhancer. Ethanol as a fuel source is more environmentally friendly than petroleum derived products. It is known that the use of ethanol will improve air quality and possibly 2310 reduce local ozone levels and smog. Moreover, utilization of ethanol in lieu of gasoline can be of strategic importance in buffering the impact of sudden shifts in non-renewable energy and petro-chemical supplies. BREWERY APPLICATIONS
Ethanol (or ethyl alcohol) is best known as being the basis of alcoholic beverages 2315 like spirits, beer and wine. Thus, the PS4 variant polypeptides described here may be used for brewing, in particular, brewing beer. All beers are brewed using a process based on a simple formula.
The brewery process involves the use of malted grain, which depending on the region may traditionally be barley, wheat or sometimes rye. Malt is made by allowing a 2320 grain to germinate, after which it is then dried in a kiln and sometimes roasted. The germination process creates a number of enzymes, notably α-amylase and β-amylase, which will be used to convert the starch in the grain into sugar. Depending on the amount of roasting, the malt will take on dark colour and strongly influence the colour and flavour of the beer.
2325 The malt is crushed to break apart the grain kernels, increase their surface area, and separate the smaller pieces from the husks. The resulting grist is mixed with heated water in a vat called a "mash tun" for a process known as "mashing". During this process, natural enzymes within the malt break down much of the starch into sugars which play a vital part in the fermentation process. Mashing usually takes 1 to 2 hours, and during this
2330 time various temperature rests (waiting periods) activate different enzymes depending upon the type of malt being used, its modification level, and the desires of the brewmaster. The activity of these enzymes convert the starches of the grains to dextrines and then to fermentable sugars such as maltose. The mash tun generally contains a slotted "false bottom" or other form of manifold which acts as a strainer allowing for the separation of
2335 the liquid from the grain.
A mash rest from 120 0F to 130 °F (49 0C to 55 0C) activates various proteinases, which break down proteins that might otherwise cause the beer to be hazy. But care is of the essence since the head on beer is also composed primarily of proteins, so too aggressive a protein rest can result in a beer that cannot hold a head. This rest is generally
2340 used only with undermodified (i.e. undermalted) malts which are decreasingly popular in Germany and the Czech Republic, or non-malted grains such as corn and rice, which are widely used in North American beers. A mash rest at 60°C or 14O0F activates beta- glucanase, which breaks down gummy beta-glucans in the mash, making the sugars flow out more freely later in the process. In the modern mashing process commercial fungal
2345 based beta-glucanase may be added as a supplement. Finally, a mash rest temperature of 149 to 160 0F (65 to 71 0C) is used to convert the starches in the malt to sugar, which is then usable by the yeast later in the brewing process. Doing the latter rest at the lower end of the range produces more low-order sugars which are more fermentable by the yeast. This in turn creates a beer lower in body and higher in alcohol. A rest closer to the higher 2350 end of the range creates more higher-order sugars which are less fermentable by the yeast, so a fuller-bodied beer with less alcohol is the result.
After the mashing, the resulting liquid is strained from the grains in a process known as lautering. Prior to lautering, the mash temperature may be raised to 165 0F to 170 °F (about 75 0C) (known as a mashout) to deactivate enzymes. Additional water may 2355 be sprinkled on the grains to extract additional sugars (a process known as sparging).
At this point the liquid is known as wort. The wort is moved into a large tank known as a "copper" or kettle where it is boiled with hops and sometimes other ingredients such as herbs or sugars. The boiling process serves to terminate enzymatic processes, precipitate proteins, isomerize hop resins, concentrate and sterilize the wort. 2360 Hops add flavour, aroma and bitterness to the beer. At the end of the boil, the hopped wort settles to clarify it in a vessel called a "whirl-pool" and the clarified wort is then cooled.
The wort is then moved into a "fermentation vessel" where yeast is added or "pitched" with it. The yeast converts the sugars from the malt into alcohol, carbon dioxide and other components through a process called Glycolysis. After a week to three weeks, 2365 the fresh (or "green") beer is run off into conditioning tanks. After conditioning for a week to several months, the beer is often filtered to remove yeast and particulates. The "bright beer" is then ready for serving or packaging.
One or more of the PS4 variant polypeptides described here may therefore be added at any stage of the brewing process to supplement or the amylase activity generated 2370 naturally.
FEED APPLICATIONS
In one embodiment, the PS4 variant polypeptide is capable of degrading resistant starch.
As used herein the term 'degrading' relates to the partial or complete hydrolysis or 2375 degradation of resistant starch to glucose and/or oligosaccharides - such as maltose and/or dextrins.
The PS4 variant polypeptide may degrade residual resistant starch that has not been completely degraded by an animals amylase. By way of example, the PS4 variant polypeptide may be used to assist an animal's amylase (eg. pancreatic amylase) in 2380 improving the degradation of resistant starch. Pancreatic α-amylase is excreted in the digestive system by animals. Pancreatic α-amylase degrades starch in the feed. However, a part of the starch, the resistant starch, is not degraded fully by the pancreatic α-amylase and is therefore not absorbed in the small intestine (see definition of resistant starch). The PS4 variant polypeptide in some embodiments is able to assist the pancreatic α-amylase in 2385 degrading starch in the digestive system and thereby increase the utilisation of starch by the animal.
The ability of an enzyme to degrade resistant starch may be analysed for example by a method developed and disclosed by Megazyme International Ireland Ltd. for the measurement of resistant starch, solubilised starch and total starch content of a sample 2390 (Resistant Starch Assay Procedure, AOAC Method 2002.02, AACC Method 32-40).
Accordingly, the PS4 variant polypeptides may be ingested by an animal for beneficial purposes, and may therefore be incorporated into animal feeds.
We therefore disclose the use of a PS4 variant polypeptide as a component for use in a feed comprising starch, or for use in a feed improvement composition, in which the 2395 PS4 variant polypeptide is capable of degrading resistant starch. We also disclose a feed comprising a starch and a PS4 variant polypeptide. We further disclose a method of degrading resistant starch in a feed comprising contacting said resistant starch with a PS4 variant polypeptide.
We further describe the use of a PS4 variant polypeptide in the preparation of a 2400 feed comprising a starch, to degrade resistant starch. Furthermore, we disclose the use of a PS4 variant polypeptide in the preparation of a feed to improve the calorific value of said feed. We disclose the use of an enzyme in the preparation of a feed to improve animal performance, hi a further embodiment, we describe a process for preparing a feed comprising admixing a starch and a PS4 variant polypeptide enzyme.
2405 By way of example, use of a component comprising PS4 variant polypeptides and which is capable of degrading resistant starch is advantageous because there is a marked increase in the degradation of starch and/or starch degradation products in an animal. Furthermore, such use is advantageous because there is a marked increase in the digestibility of starch and/or starch degradation products by an animal. Furthermore, such
2410 use is advantageous because it provides a means of enhancing the efficiency of deriving energy from a feed by an animal. Furthermore, such use is advantageous because it provides a means to enhance the bioavailability of resistant starch. ANIMAL FEEDS
Animal feeds for which the PS4 variant polypeptides are suitable for use may be 2415 formulated to meet the specific needs of particular animal groups and to provide the necessary carbohydrate, fat, protein and other nutrients in a form that can be metabolised by the animal.
Preferably, the animal feed is a feed for swine or poultry.
As used herein the term 'swine' relates to non-ruminant omnivores such as pigs, 2420 hogs or boars. Typically, swine feed includes about 50 percent carbohydrate, about 20 percent protein and about 5% fat. An example of a high energy swine feed is based on corn which is often combined with feed supplements for example, protein, minerals, vitamins and amino acids such as lysine and tryptophan. Examples of swine feeds include animal protein products, marine products, milk products, grain products and plant protein 2425 products, all of which may further comprise natural flavourings, artificial flavourings, micro and macro minerals, animal fats, vegetable fats, vitamins, preservatives or medications such as antibiotics.
It is to be understood that where reference is made in the present specification, including the accompanying claims, to 'swine feed' such reference is meant to include 2430 "transition" or "starter" feeds (used to wean young swine) and "finishing" or "grower" feeds (used following the transition stage for growth of swine to an age and/or size suitable for market).
As used herein the term 'poultry' relates to fowl such as chickens, broilers, hens, roosters, capons, turkeys, ducks, game fowl, pullets or chicks. Poultry feeds may be
2435 referred to as "complete" feeds because they contain all the protein, energy, vitamins, minerals, and other nutrients necessary for proper growth, egg production, and health of the birds. However, poultry feeds may further comprise vitamins, minerals or medications such as coccidiostats (for example Monensin sodium, Lasalocid, Amprolium, Salinomycin, and Sulfaquinoxaline) and/or antibiotics (for example Penicillin, Bacitracin,
2440 Chlortetracycline, and Oxytetracycline).
Young chickens or broilers, turkeys and ducks kept for meat production are fed differently from pullets saved for egg production. Broilers, ducks and turkeys have larger bodies and gain weight more rapidly than do the egg-producing types of chickens. Therefore, these birds are fed diets with higher protein and energy levels. 2445 It is to be understood that where reference is made in the present specification, including the accompanying claims, to 'poultry feed' such reference is meant to include "starter" feeds (post-hatching), "finisher", "grower" or "developer" feeds (from 6-8 weeks of age until slaughter size reached) and "layer" feeds (fed during egg production).
Animal feeds may be formulated to meet the animal's nutritional needs with 2450 respect to, for example, meat production, milk production, egg production, reproduction and response to stress. In addition, the animal feeds are formulated to improve manure quality.
In a preferred aspect the animal feed contains a raw material such as a legume, for example pea or soy or a cereal, for example wheat, corn (maize), rye or barley. Suitably, 2455 the raw material may be potato.
FEED STUFFS
The PS4 variant polypeptides may be used in feeds for animal consumption by the indirect or direct application of the PS4 variant polypeptides to the feed, whether alone or in combination with other ingredients, such as food ingredients.
2460 Typical food ingredients may include any one or more of an additive such as an animal or vegetable fat, a natural or synthetic seasoning, antioxidant, viscosity modifier, essential oil, and/or flavour, dye and/or colorant, vitamin, mineral, natural and/or non- natural amino acid, nutrient, additional enzyme (including genetically manipulated enzymes), a binding agent such as guar gum or xanthum gum, buffer, emulsifier, lubricant,
2465 adjuvant, suspending agent, preservative, coating agent or solubilising agent and the like.
Examples of the application methods include, but are not limited to, coating the feed in a material comprising the PS4 variant polypeptide, direct application by mixing the PS4 variant polypeptide with the feed, spraying the PS4 variant polypeptide onto the feed surface or dipping the feed into a preparation of the PS4 variant polypeptide.
2470 The PS4 variant polypeptide is preferably applied by mixing it with a feed or by spraying onto feed particles for animal consumption. Alternatively, the PS4 variant polypeptide may be included in the emulsion of a feed, or the interior of solid products by injection or tumbling.
The PS4 variant polypeptide may be applied to intersperse, coat and/or impregnate 2475 a feed. Mixtures with other ingredients may also be used and may be applied separately, simultaneously or sequentially. Chelating agents, binding agents, emulsifϊers and other additives such as micro and macro minerals, amino acids, vitamins, animal fats, vegetable fats, preservatives, flavourings, colourings, may be similarly applied to the feed simultaneously (either in mixture or separately) or applied sequentially.
2480 Amount ofPS4 Variant Polypeptide
The optimum amount of the PS4 variant polypeptide to be used will depend on the feed to be treated and/or the method of contacting the feed with the PS4 variant polypeptide and/or the intended use for the same. The amount of PS4 variant polypeptide should be in a sufficient amount to be effective to substantially degrade resistant starch 2485 following ingestion and during digestion of the feed.
Advantageously, the PS4 variant polypeptide would remain effective following ingestion of a feed for animal consumption and during digestion of the feed until a more complete digestion of the feed is obtained, i.e. an increased calorific value of the feed is released.
2490 AMYLASE COMBINATIONS
We disclose in particular combinations of PS4 variant polypeptides with amylases, in particular, maltogenic amylases. Maltogenic alpha-amylase (glucan 1,4-a- maltohydrolase, E.C. 3.2.1.133) is able to hydrolyze amylose and amylopectin to maltose in the alpha-configuration.
2495 A maltogenic alpha-amylase from Bacillus (EP 120 693) is commercially available under the trade name Novamyl (Novo Nordisk A/S, Denmark) and is widely used in the baking industry as an anti-staling agent due to its ability to reduce retrogradation of starch. Novamyl is described in detail in International Patent Publication WO 91/04669. The maltogenic alpha-amylase Novamyl shares several characteristics with cyclodextrin
2500 glucanotransferases (CGTases), including sequence homology (Henrissat B, Bairoch A; Biochem. J., 316, 695-696 (1996)) and formation of transglycosylation products (Christophersen, C, et al., 1997, Starch, vol. 50, No. 1, 39-45).
In highly preferred embodiments, we disclose combinations comprising PS4 variant polypeptides together with Novamyl or any of its variants. Such combinations are 2505 useful for food production such as baking. The Novamyl may in particular comprise Novamyl 1500 MG.
Other documents describing Novamyl and its uses include Christophersen, C, Pedersen, S., and Christensen, T., (1993) Method for production of maltose an a limit dextrin, the limit dextrin, and use of the limit dextrin. Denmark, and WO 95/10627. It is 2510 further described in U.S. Pat. No. 4,598,048 and U.S. Pat. No. 4,604,355. Each of these documents is hereby incorporated by reference, and any of the Novamyl polypeptides described therein may be used in combinations with any of the PS4 variant polypeptides described here.
Variants, homologues, and mutants of Novamyl may be used for the combinations, 2515 provided they retain alpha amylase activity. For example, any of the Novamyl variants disclosed in US Patent Number 6,162,628, the entire disclosure of which is hereby incorporated by reference, may be used in combination with the PS4 variant polypeptides described here. In particular, any of the polypeptides described in that document, specifically variants of SEQ ID NO:1 of US 6,162,628 at any one or more positions 2520 corresponding to Q13, 116, D17, N26, N28, P29, A30, S32, Y33, G34, L35, K40, M45, P73, V74, D76 N77, D79, N86, R95, N99, 1100, H103, Ql 19, N120, N131, S141, T142, A148, N152, A163, H169, N171, G172, 1174, N176, N187, F188, A192, Q201, N203, H220, N234, G236, Q247, K249, D261, N266, L268, R272, N275, N276, V279, N280, V281, D285, N287, F297, Q299, N305, K316, N320, L321, N327, A341, N342, A348, 2525 Q365, N371, N375, M378, G397, A381, F389, N401, A403, K425, N436, S442, N454, N468, N474, S479, A483, A486, V487, S493, T494, S495, A496, S497, A498, Q500, N507, 1510, N513, K520, Q526, A555, A564, S573, N575, Q581, S583, F586, K589, N595, G618, N621, Q624, A629, F636, K645, N664 and/or T681 may be used.
AMINO ACID SEQUENCES
2530 The invention makes use of a PS4 variant nucleic acid, and the amino acid sequences of such PS4 variant nucleic acids are encompassed by the methods and compositions described here.
As used herein, the term "amino acid sequence" is synonymous with the term "polypeptide" and/or the term "protein". In some instances, the term "amino acid 2535 sequence" is synonymous with the term "peptide". In some instances, the term "amino acid sequence" is synonymous with the term "enzyme".
The amino acid sequence may be prepared/isolated from a suitable source, or it may be made synthetically or it may be prepared by use of recombinant DNA techniques.
The PS4 variant enzyme described here may be used in conjunction with other 2540 enzymes. Thus we further disclose a combination of enzymes wherein the combination comprises a PS4 variant polypeptide enzyme described here and another enzyme, which itself may be another PS4 variant polypeptide enzyme.
PS4VARIANTNUCLEOTIDE SEQUENCE
As noted above, we disclose nucleotide sequences encoding the PS4 variant 2545 enzymes having the specific properties described.
The term "nucleotide sequence" or "nucleic acid sequence" as used herein refers to an oligonucleotide sequence or polynucleotide sequence, and variant, homologies, fragments and derivatives thereof (such as portions thereof). The nucleotide sequence may be of genomic or synthetic or recombinant origin, which may be double-stranded or 2550 single-stranded whether representing the sense or anti-sense strand.
The term "nucleotide sequence" as used in this document includes genomic DNA, cDNA, synthetic DNA, and RNA. Preferably it means DNA, more preferably cDNA sequence coding for a PS4 variant polypeptide.
Typically, the PS4 variant nucleotide sequence is prepared using recombinant 2555 DNA techniques (i.e. recombinant DNA). However, in an alternative embodiment, the nucleotide sequence could be synthesised, in whole or in part, using chemical methods well known in the art (see Caruthers MH et al, (1980) Nuc Acids Res Symp Ser 215-23 and Horn T et al, (1980) Nuc Acids Res Symp Ser 225-232).
PREPARATION OF NUCLEIC ACID SEQUENCES
2560 A nucleotide sequence encoding either an enzyme which has the specific properties as defined herein (e.g., a PS4 variant polypeptide) or an enzyme which is suitable for modification, such as a parent enzyme, may be identified and/or isolated and/or purified from any cell or organism producing said enzyme. Various methods are well known within the art for the identification and/or isolation and/or purification of nucleotide
2565 sequences. By way of example, PCR amplification techniques to prepare more of a sequence may be used once a suitable sequence has been identified and/or isolated and/or purified.
By way of further example, a genomic DNA and/or cDNA library may be constructed using chromosomal DNA or messenger RNA from the organism producing 2570 the enzyme. If the amino acid sequence of the enzyme or a part of the amino acid sequence of the enzyme is known, labelled oligonucleotide probes may be synthesised and used to identify enzyme-encoding clones from the genomic library prepared from the organism. Alternatively, a labelled oligonucleotide probe containing sequences homologous to another known enzyme gene could be used to identify enzyme-encoding 2575 clones. In the latter case, hybridisation and washing conditions of lower stringency are used.
Alternatively, enzyme-encoding clones could be identified by inserting fragments of genomic DNA into an expression vector, such as a plasmid, transforming enzyme- negative bacteria with the resulting genomic DNA library, and then plating the 2580 transformed bacteria onto agar plates containing a substrate for enzyme (i.e. maltose), thereby allowing clones expressing the enzyme to be identified.
In a yet further alternative, the nucleotide sequence encoding the enzyme may be prepared synthetically by established standard methods, e.g. the phosphoroamidite method described by Beucage S.L. et al, (1981) Tetrahedron Letters 22, p 1859-1869, or the 2585 method described by Matthes et al, (1984) EMBO J. 3, p 801-805. In the phosphoroamidite method, oligonucleotides are synthesised, e.g. in an automatic DNA synthesiser, purified, annealed, ligated and cloned in appropriate vectors.
The nucleotide sequence may be of mixed genomic and synthetic origin, mixed synthetic and cDNA origin, or mixed genomic and cDNA origin, prepared by ligating 2590 fragments of synthetic, genomic or cDNA origin (as appropriate) in accordance with standard techniques. Each ligated fragment corresponds to various parts of the entire nucleotide sequence. The DNA sequence may also be prepared by polymerase chain reaction (PCR) using specific primers, for instance as described in US 4,683,202 or in Saiki R K et al, {Science (1988) 239, pp 487-491).
2595 VARIANTS/HOMOLOGUES/DERIVATIVES
We further describe the use of variants, homologues and derivatives of any amino / acid sequence of an enzyme or of any nucleotide sequence encoding such an enzyme, such as a PS4 variant polypeptide or a PS4 variant nucleic acid. Unless the context dictates otherwise, the term "PS4 variant nucleic acid" should be taken to include each of the nucleic 2600 acid entities described below, and the term "PS4 variant polypeptide" should likewise be taken to include each of the polypeptide or amino acid entities described below.
Here, the term "homologue" means an entity having a certain homology with the subject amino acid sequences and the subject nucleotide sequences. Here, the term "homology" can be equated with "identity". 2605 In the present context, a homologous sequence is taken to include an amino acid sequence which may be at least 75, 80, 85 or 90% identical, preferably at least 95, 96, 97, 98 or 99% identical to the subject sequence. Typically, the homologues will comprise the same active sites etc. as the subject amino acid sequence. Although homology can also be considered in terms of similarity (i.e. amino acid residues having similar chemical
2610 properties/functions), in the context of this document it is preferred to express homology in terms of sequence identity.
In the present context, an homologous sequence is taken to include a nucleotide sequence which may be at least 75, 80, 85 or 90% identical, preferably at least 95, 96, 97, 98 or 99% identical to a nucleotide sequence encoding a PS4 variant polypeptide enzyme 2615 (such as a PS4 variant nucleic acid). Typically, the homologues will comprise the same sequences that code for the active sites etc as the subject sequence. Although homology can also be considered in terms of similarity (i.e. amino acid residues having similar chemical properties/functions), in the context of this document it is preferred to express homology in terms of sequence identity.
2620 Homology comparisons can be conducted by eye, or more usually, with the aid of readily available sequence comparison programs. These commercially available computer programs can calculate % homology between two or more sequences.
% homology may be calculated over contiguous sequences, i.e. one sequence is aligned with the other sequence and each amino acid in one sequence is directly compared 2625 with the corresponding amino acid in the other sequence, one residue at a time. This is called an "ungapped" alignment. Typically, such ungapped alignments are performed only over a relatively short number of residues.
Although this is a very simple and consistent method, it fails to take into consideration that, for example, in an otherwise identical pair of sequences, one insertion
2630 or deletion will cause the following amino acid residues to be put out of alignment, thus potentially resulting in a large reduction in % homology when a global alignment is performed. Consequently, most sequence comparison methods are designed to produce optimal alignments that take into consideration possible insertions and deletions without penalising unduly the overall homology score. This is achieved by inserting "gaps" in the
2635 sequence alignment to try to maximise local homology.
However, these more complex methods assign "gap penalties" to each gap that occurs in the alignment so that, for the same number of identical amino acids, a sequence alignment with as few gaps as possible - reflecting higher relatedness between the two compared sequences - will achieve a higher score than one with many gaps. "Affine gap 2640 costs" are typically used that charge a relatively high cost for the existence of a gap and a smaller penalty for each subsequent residue in the gap. This is the most commonly used gap scoring system. High gap penalties will of course produce optimised alignments with fewer gaps. Most alignment programs allow the gap penalties to be modified. However, it is preferred to use the default values when using such software for sequence comparisons. 2645 For example when using the GCG Wisconsin Bestfit package the default gap penalty for amino acid sequences is -12 for a gap and -4 for each extension.
Calculation of maximum % homology therefore firstly requires the production of an optimal alignment, taking into consideration gap penalties. A suitable computer program for carrying out such an alignment is the GCG Wisconsin Bestfit package
2650 (Devereux et al 1984 Nuc. Acids Research 12 p387). Examples of other software than can perform sequence comparisons include, but are not limited to, the BLAST package (see Ausubel et al, 1999 Short Protocols in Molecular Biology, 4th Ed - Chapter 18), FASTA (Altschul et al, 1990 J MoI Biol. 403-410) and the GENEWORKS suite of comparison tools. Both BLAST and FASTA are available for offline and online searching (see
2655 Ausubel et al, 1999, Short Protocols in Molecular Biology, pages 7-58 to 7-60).
However, for some applications, it is preferred to use the GCG Bestfit program. A new tool, called BLAST 2 Sequences is also available for comparing protein and nucleotide sequence (see FEMS Microbiol Lett 1999 174(2): 247-50; FEMS Microbiol Lett 1999 177(1): 187-8 and tatiana@ncbi.nlm.nih.gov).
2660 Although the final % homology can be measured in terms of identity, the alignment process itself is typically not based on an all-or-nothing pair comparison. Instead, a scaled similarity score matrix is generally used that assigns scores to each pairwise comparison based on chemical similarity or evolutionary distance. An example of such a matrix commonly used is the BLOSUM62 matrix - the default matrix for the
2665 BLAST suite of programs. GCG Wisconsin programs generally use either the public default values or a custom symbol comparison table if supplied (see user manual for further details). For some applications, it is preferred to use the public default values for the GCG package, or in the case of other software, the default matrix, such as BLOSUM62.
2670 Alternatively, percentage homologies may be calculated using the multiple alignment feature in DNASIS (Hitachi Software), based on an algorithm, analog CLUSTAL (Higgins DG & Sharp PM (1988), Gene 73(1), 237-244). Once the software has produced an optimal alignment, it is possible to calculate % homology, preferably % sequence identity. The software typically does this as part of the 2675 sequence comparison and generates a numerical result.
The sequences may also have deletions, insertions or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent substance. Deliberate amino acid substitutions may be made on the basis of similarity in amino acid properties (such as polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the
2680 amphipathic nature of the residues) and it is therefore useful to group amino acids together in functional groups. Amino acids can be grouped together based on the properties of their side chain alone. However it is more useful to include mutation data as well. The sets of amino acids thus derived are likely to be conserved for structural reasons. These sets can be described in the form of a Venn diagram (Livingstone CD. and Barton GJ. (1993)
2685 "Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation" Comput.Appl Biosci. 9: 745-756)(Taylor W.R. (1986) "The classification of amino acid conservation" J. Theor.Biol. 119; 205-218). Conservative substitutions may be made, for example according to the table below which describes a generally accepted Venn diagram grouping of amino acids.
Figure imgf000085_0001
2690 We further disclose sequences comprising homologous substitution (substitution and replacement are both used herein to mean the interchange of an existing amino acid residue, with an alternative residue) that may occur i.e. like-for-like substitution such as basic for basic, acidic for acidic, polar for polar etc. Non-homologous substitution may also occur i.e. from one class of residue to another or alternatively involving the inclusion
2695 of unnatural amino acids such as ornithine (hereinafter referred to as Z), diaminobutyric acid ornithine (hereinafter referred to as B), norleucine ornithine (hereinafter referred to as O), pyriylalanine, thienylalanine, naphthylalanine and phenylglycine.
Variant amino acid sequences may include suitable spacer groups that may be inserted between any two amino acid residues of the sequence including alkyl groups such
2700 as methyl, ethyl or propyl groups in addition to amino acid spacers such as glycine or β- alanine residues. A further form of variation, involves the presence of one or more amino acid residues in peptoid form, will be well understood by those skilled in the art. For the avoidance of doubt, "the peptoid form" is used to refer to variant amino acid residues wherein the α-carbon substituent group is on the residue's nitrogen atom rather than the α-
2705 carbon. Processes for preparing peptides in the peptoid form are known in the art, for example Simon RJ et al., PNAS (1992) 89(20), 9367-9371 and Horwell DC, Trends Biotechnol. (1995) 13(4), 132-134.
The nucleotide sequences described here, and suitable for use in the methods and compositions described here (such as PS4 variant nucleic acids) may include within them
2710 synthetic or modified nucleotides. A number of different types of modification to oligonucleotides are known in the art. These include methylphosphonate and phosphorothioate backbones and/or the addition of acridine or polylysine chains at the 3' and/or 5' ends of the molecule. For the purposes of this document, it is to be understood that the nucleotide sequences described herein may be modified by any method available
2715 in the art. Such modifications may be carried out in order to enhance the in vivo activity or life span of nucleotide sequences.
We further describe the use of nucleotide sequences that are complementary to the sequences presented herein, or any derivative, fragment or derivative thereof. If the sequence is complementary to a fragment thereof then that sequence can be used as a 2720 probe to identify similar coding sequences in other organisms etc.
Polynucleotides which are not 100% homologous to the PS4 variant sequences may be obtained in a number of ways. Other variants of the sequences described herein may be obtained for example by probing DNA libraries made from a range of individuals, for example individuals from different populations. In addition, other homologues may be 2725 obtained and such homologues and fragments thereof in general will be capable of selectively hybridising to the sequences shown in the sequence listing herein. Such sequences may be obtained by probing cDNA libraries made from or genomic DNA libraries from other species, and probing such libraries with probes comprising all or part of any one of the sequences in the attached sequence listings under conditions of medium to high stringency. 2730 Similar considerations apply to obtaining species homologues and allelic variants of the polypeptide or nucleotide sequences described here.
Variants and strain/species homologues may also be obtained using degenerate PCR which will use primers designed to target sequences within the variants and homologues encoding conserved amino acid sequences. Conserved sequences can be predicted, for 2735 example, by aligning the amino acid sequences from several variants/homologues. Sequence alignments can be performed using computer software known in the art. For example the GCG Wisconsin PiIeUp program is widely used.
The primers used in degenerate PCR will contain one or more degenerate positions and will be used at stringency conditions lower than those used for cloning sequences with 2740 single sequence primers against known sequences.
Alternatively, such polynucleotides may be obtained by site directed mutagenesis of characterised sequences. This may be useful where for example silent codon sequence changes are required to optimise codon preferences for a particular host cell in which the polynucleotide sequences are being expressed. Other sequence changes may be desired in 2745 order to introduce restriction enzyme recognition sites, or to alter the property or function of the polypeptides encoded by the polynucleotides.
The polynucleotides (nucleotide sequences) such as the PS4 variant nucleic acids described in this document may be used to produce a primer, e.g. a PCR primer, a primer for an alternative amplification reaction, a probe e.g. labelled with a revealing label by 2750 conventional means using radioactive or non-radioactive labels, or the polynucleotides may be cloned into vectors. Such primers, probes and other fragments will be at least 15, preferably at least 20, for example at least 25, 30 or 40 nucleotides in length, and are also encompassed by the term polynucleotides.
Polynucleotides such as DNA polynucleotides and probes may be produced
2755 recombinantly, synthetically, or by any means available to those of skill in the art. They may also be cloned by standard techniques, hi general, primers will be produced by synthetic means, involving a stepwise manufacture of the desired nucleic acid sequence one nucleotide at a time. Techniques for accomplishing this using automated techniques are readily available in the art.
2760 Longer polynucleotides will generally be produced using recombinant means, for example using a PCR (polymerase chain reaction) cloning techniques. The primers may be designed to contain suitable restriction enzyme recognition sites so that the amplified DNA can be cloned into a suitable cloning vector. Preferably, the variant sequences etc. are at least as biologically active as the sequences presented herein.
2765 As used herein "biologically active" refers to a sequence having a similar structural function (but not necessarily to the same degree), and/or similar regulatory function (but not necessarily to the same degree), and/or similar biochemical function (but not necessarily to the same degree) of the naturally occurring sequence.
HYBRIDISATION
2770 We further describe sequences that are complementary to the nucleic acid sequences of PS4 variants or sequences that are capable of hybridising either to the PS4 variant sequences or to sequences that are complementary thereto.
The term "hybridisation" as used herein shall include "the process by which a strand of nucleic acid joins with a complementary strand through base pairing" as well as 2775 the process of amplification as carried out in polymerase chain reaction (PCR) technologies. Therefore, we disclose the use of nucleotide sequences that are capable of hybridising to the sequences that are complementary to the sequences presented herein, or any derivative, fragment or derivative thereof.
The term "variant" also encompasses sequences that are complementary to 2780 sequences that are capable of hybridising to the nucleotide sequences presented herein.
Preferably, the term "variant" encompasses sequences that are complementary to sequences that are capable of hybridising under stringent conditions (e.g. 50°C and 0.2xSSC { IxSSC = 0.15 MNaCl, 0.015 M Na3citrate pH 7.0}) to the nucleotide sequences presented herein. More preferably, the term "variant" encompasses sequences 2785 that are complementary to sequences that are capable of hybridising under high stringent conditions (e.g. 650C and 0.IxSSC {lxSSC = 0.15 M NaCl, 0.015 M Na3citrate pH 7.0}) to the nucleotide sequences presented herein.
We further disclose nucleotide sequences that can hybridise to the nucleotide sequences of PS4 variants (including complementary sequences of those presented herein), 2790 as well as nucleotide sequences that are complementary to sequences that can hybridise to the nucleotide sequences of PS4 variants (including complementary sequences of those presented herein). We further describe polynucleotide sequences that are capable of hybridising to the nucleotide sequences presented herein under conditions of intermediate to maximal stringency. 2795 In a preferred aspect, we disclose nucleotide sequences that can hybridise to the nucleotide sequence of a PS4 variant nucleic acid, or the complement thereof, under stringent conditions (e.g. 5O0C and 0.2xSSC). More preferably, the nucleotide sequences can hybridise to the nucleotide sequence of a PS4 variant, or the complement thereof, under high stringent conditions (e.g. 650C and 0. IxSSC).
2800 SITE-DBRECTED MUTAGENESIS
Once an enzyme-encoding nucleotide sequence has been isolated, or a putative enzyme-encoding nucleotide sequence has been identified, it may be desirable to mutate the sequence in order to prepare an enzyme. Accordingly, a PS4 variant sequence may be prepared from a parent sequence. Mutations may be introduced using synthetic 2805 oligonucleotides. These oligonucleotides contain nucleotide sequences flanking the desired mutation sites.
A suitable method is disclosed in Morinaga et al, {Biotechnology (1984) 2, p646- 649). Another method of introducing mutations into enzyme-encoding nucleotide sequences is described in Nelson and Long {Analytical Biochemistry (1989), 180, p 147- 2810 151). A further method is described hi Sarkar and Sommer {Biotechniques (1990), 8, p404-407 - "The megaprimer method of site directed mutagenesis").
In one aspect the sequence for use in the methods and compositions described here is a recombinant sequence - i.e. a sequence that has been prepared using recombinant DNA techniques. These recombinant DNA techniques are within the capabilities of a 2815 person of ordinary skill in the art. Such techniques are explained in the literature, for example, J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Books 1-3, Cold Spring Harbor Laboratory Press.
In one aspect the sequence for use in the methods and compositions described here is a synthetic sequence - i.e. a sequence that has been prepared by in vitro chemical or 2820 enzymatic synthesis. It includes, but is not limited to, sequences made with optimal codon usage for host organisms - such as the methylotrophic yeasts Pichia and Hansenula.
The nucleotide sequence for use in the methods and compositions described here may be incorporated into a recombinant replicable vector. The vector may be used to replicate and express the nucleotide sequence, in enzyme form, in and/or from a 2825 compatible host cell. Expression may be controlled using control sequences eg. regulatory sequences. The enzyme produced by a host recombinant cell by expression of the nucleotide sequence may be secreted or may be contained intracellularly depending on the sequence and/or the vector used. The coding sequences may be designed with signal sequences which direct secretion of the substance coding sequences through a particular 2830 prokaryotic or eukaryotic cell membrane.
EXPRESSION OF PS4 NUCLEIC ACIDS AND POLYPEPTIDES
The PS4 polynucleotides and nucleic acids may include DNA and RNA of both synthetic and natural origin which DNA or RNA may contain modified or unmodified deoxy- or dideoxy- nucleotides or ribonucleotides or analogs thereof. The PS4 nucleic acid 2835 may exist as single- or double-stranded DNA or RNA, an RNA/DNA heteroduplex or an RNA/DNA copolymer, wherein the term "copolymer" refers to a single nucleic acid strand that comprises both ribonucleotides and deoxyribonucleotides. The PS4 nucleic acid may even be codon optimised to further increase expression.
The term "synthetic", as used herein, is defined as that which is produced by in 2840 vitro chemical or enzymatic synthesis. It includes but is not limited to PS4 nucleic acids made with optimal codon usage for host organisms such as the the methylotrophic yeasts Pichia and Hansenula.
Polynucleotides, for example variant PS4 polynucleotides described here, can be incorporated into a recombinant replicable vector. The vector may be used to replicate the 2845 nucleic acid in a compatible host cell. The vector comprising the polynucleotide sequence may be transformed into a suitable host cell. Suitable hosts may include bacterial, yeast, insect and fungal cells.
The term "transformed cell" includes cells that have been transformed by use of recombinant DNA techniques. The transformation typically occurs by insertion of one or
2850 more nucleotide sequences into a cell that is to be transformed. The inserted nucleotide sequence may be a heterologous nucleotide sequence (i.e. is a sequence that is not natural to the cell that is to be transformed, hi addition, or in the alternative, the inserted nucleotide sequence may be an homologous nucleotide sequence (i.e. is a sequence that is natural to the cell that is to be transformed) - so that the cell receives one or more extra
2855 copies of a nucleotide sequence already present in it.
Thus in a further embodiment, we provide a method of making PS4 variant polypeptides and polynucleotides by introducing a polynucleotide into a replicable vector, introducing the vector into a compatible host cell, and growing the host cell under conditions which bring about replication of the vector. The vector may be recovered from 2860 the host cell. EXPRESSION CONSTRUCTS
The PS4 nucleic acid may be operatively linked to transcriptional and translational regulatory elements active in a host cell of interest. The PS4 nucleic acid may also encode a fusion protein comprising signal sequences such as, for example, those derived from the 2865 glucoamylase gene from Schwanniomyces occidentalis, α-factor mating type gene from
Saccharomyces cerevisiae and the TAKA-amylase from Aspergillus oryzae. Alternatively, the PS4 nucleic acid may encode a fusion protein comprising a membrane binding domain.
Expression Vector
2870 The PS4 nucleic acid may be expressed at the desired levels in a host organism using an expression vector.
An expression vector comprising a PS4 nucleic acid can be any vector which is capable of expressing the gene encoding PS4 nucleic acid in the selected host organism, and the choice of vector will depend on the host cell into which it is to be introduced.
2875 Thus, the vector can be an autonomously replicating vector, i.e. a vector that exists as an episomal entity, the replication of which is independent of chromosomal replication, such as, for example, a plasmid, a bacteriophage or an episomal element, a minichromosome or an artificial chromosome. Alternatively, the vector may be one which, when introduced into a host cell, is integrated into the host cell genome and replicated together with the
2880 chromosome.
Components of the Expression Vector
The expression vector typically includes the components of a cloning vector, such as, for example, an element that permits autonomous replication of the vector in the selected host organism and one or more phenotypically detectable markers for selection
2885 purposes. The expression vector normally comprises control nucleotide sequences encoding a promoter, operator, ribosome binding site, translation initiation signal and optionally, a repressor gene or one or more activator genes. Additionally, the expression vector may comprise a sequence coding for an amino acid sequence capable of targeting the PS4 variant polypeptide to a host cell organelle such as a peroxisome or to a particular
2890 host cell compartment. Such a targeting sequence includes but is not limited to the sequence SKL. In the present context, the term 'expression signal" includes any of the above control sequences, repressor or activator sequences. For expression under the direction of control sequences, the nucleic acid sequence the PS4 variant polypeptide is operably linked to the control sequences in proper manner with respect to expression.
2895 Preferably, a polynucleotide in a vector is operably linked to a control sequence that is capable of providing for the expression of the coding sequence by the host cell, i.e. the vector is an expression vector. The term "operably linked" means that the components described are in a relationship permitting them to function in their intended manner. A regulatory sequence "operably linked" to a coding sequence is ligated in such a way that
2900 expression of the coding sequence is achieved under condition compatible with the control sequences.
The control sequences may be modified, for example by the addition of further transcriptional regulatory elements to make the level of transcription directed by the control sequences more responsive to transcriptional modulators. The control sequences 2905 may in particular comprise promoters.
Promoter hi the vector, the nucleic acid sequence encoding for the variant PS4 polypeptide is operably combined with a suitable promoter sequence. The promoter can be any DNA sequence having transcription activity in the host organism of choice and can be derived 2910 from genes that are homologous or heterologous to the host organism.
Bacterial Promoters
Examples of suitable promoters for directing the transcription of the modified nucleotide sequence, such as PS4 nucleic acids, in a bacterial host include the promoter of the lac operon of E. coli, the Streptomyces coelicolor agarase gene dagA promoters, the
2915 promoters of the Bacillus licheniformis α-amylase gene (amyL), the promoters of the Bacillus stearothermophilus maltogenic amylase gene (amyM), the promoters of the Bacillus amyloliquefaciens α-amylase gene (amyQ), the promoters of the Bacillus subtilis xylA andxylB genes, the promoter of the Bacillus subtilis aprΕ gene and a promoter derived from a Lactococcus sp.-derived promoter including the P170 promoter. When the
2920 gene encoding the PS4 variant polypeptide is expressed in a bacterial species such as E. coli, a suitable promoter can be selected, for example, from a bacteriophage promoter including a T7 promoter and a phage lambda promoter. Fungal Promoters
For transcription in a fungal species, examples of useful promoters are those 2925 derived from the genes encoding the, Aspergillus oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, Aspergillus niger neutral α-amylase, A. niger acid stable α- amylase, A. niger glucoamylase, Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease, Aspergillus oryzae triose phosphate isomerase or Aspergillus nidulans acetamidase.
2930 Yeast Promoters
Examples of suitable promoters for the expression in a yeast species include but are not limited to the Gal 1 and Gal 10 promoters of Saccharomyces cerevisiae and the Pichia pastoris AOXl or A0X2 promoters.
HOST ORGANISMS
2935 (T) Bacterial Host Organisms
Examples of suitable bacterial host organisms are gram positive bacterial species such as Bacillaceae including Bacillus clausii. Bacillus subtilis, Bacillus licheniformis, Bacillus lentus, Bacillus brevis, Bacillus stearothermophilus, Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus coagulans, Bacillus lautus, Bacillus megaterium and
2940 Bacillus thuringiensis, Streptomyces species such as Streptomyces murinus, lactic acid bacterial species including Lactococcus spp. such as Lactococcus lactis, Lactobacillus spp. including Lactobacillus reuteri, Leuconostoc spp., Pediococcus spp. and Streptococcus spp. Alternatively, strains of a gram-negative bacterial species belonging to Enterobacteriaceas including E. coli, or to Pseudomonαdαceαe can be selected as the host
2945 organism.
(II) Yeαst Host Organisms
A suitable yeast host organism can be selected from the biotechnologically relevant yeasts species such as but not limited to yeast species such as Pichia sp., Hansenula sp or Kluyveromyces, Yarrowinia species or a species of Saccharomyces including 2950 Saccharomyces cerevisiae or a species belonging to Schizosaccharomyce such as, for example, S. Pombe species.
Preferably a strain of the methylotrophic yeast species Pichia pastoris is used as the host organism. Preferably the host organism is a Hansenula species. (III) Fungal Host Organisms
2955 Suitable host organisms among filamentous fungi include species of Aspergillus, e.g. Aspergillus niger, Aspergillus oryzae, Aspergillus tubigensis, Aspergillus awamori or Aspergillus nidulans. Alternatively, strains of a Fusαrium species, e.g. Fusαrium oxysporum or of a Rhizomucor species such as Rhizomucor miehei can be used as the host organism. Other suitable strains include Thermomyces and Mucor species.
2960 Suitable fungal host organisms may also include Trichodermα spp (especially
Trichodermα reesei formerly Trichodermα longibrαchiαtum; also known as Hypocreα jecorinα).
PROTEIN EXPRESSION AND PURIFICATION
Host cells comprising polynucleotides may be used to express polypeptides, such 2965 as variant PS4 polypeptides, fragments, homologues, variants or derivatives thereof. Host cells may be cultured under suitable conditions which allow expression of the proteins. Expression of the polypeptides may be constitutive such that they are continually produced, or inducible, requiring a stimulus to initiate expression, hi the case of inducible expression, protein production can be initiated when required by, for example, addition of 2970 an inducer substance to the culture medium, for example dexamethasone or EPTG.
Polypeptides can be extracted from host cells by a variety of techniques known in the art, including enzymatic, chemical and/or osmotic lysis and physical disruption. Polypeptides may also be produced recombinantly in an in vitro cell-free system, such as the TnT™ (Promega) rabbit reticulocyte system.
2975 EXAMPLES
Example 1. Cloning of PS4
Pseudomonαs sαchαrophilα is grown overnight on LB media and chromosomal DNA is isolated by standard methods (Sambrook J, 1989). A 2190 bp fragment containing the PS4 open reading frame (Zhou et αl, 1989) is amplified from P. sαchαrophilα
2980 chromosomal DNA by PCR using the primers Pl and P2 (see Table 3). The resulting fragment is used as a template in a nested PCR with primers P3 and P4, amplifying the openreading frame of PS4 without its signal sequence and introducing a Ncol site at the 5' end of the gene and a BamHI site at the 3 'end. Together with the Ncol site a codon for a N-terminal Methionine is introduced, allowing for intracellular expression of PS4. The
2985 1605 bp fragment is cloned into pCRBLUNT TOPO (Invitrogen) and the integrity of the construct analysed by sequencing. The E.coli Bacillus shuttle vector pZλP66K (Penninga et al, 1996) is modified to allow for expression of the PS4 under control of the P32 promoter and the ctgase signal sequence. The resulting plasmid, pGSmta is transformed into B. subtilis.
2990 A second expression construct is made in which the starch binding domain of PS4 is removed. In a PCR with primers P3 and P6 (Table 3) on pCSmta, a truncated version of the mta gene is generated. The full length mta gene in pCSmta is exchanged with the truncated version which resulted in the plasmid pCSmta-SBD.
Example 2. Site Directed Mutagenesis of PS4
2995 Mutations are introduced into the mta gene by 2 methods. Either by a 2 step PCR based method, or by a Quick Exchange method (QE). For convenience the mta gene is split up in 3 parts; a Pvul-Fspl fragment, a Fspl-Pstl fragment and a Pstl-Aspl fragment, further on referred to as fragment 1, 2 and 3 respectively.
In the 2 step PCR based method, mutations are introduced using Pfu DNA 3000 polymerase (Stratagene). A first PCR is carried out with a mutagenesis primer (Table 4) for the coding strand plus a primer downstream on the lower strand (either 2R or 3R Table 3). The reaction product is used as a primer in a second PCR together with a primer upstream on the coding strand. The product of the last reaction is cloned into pCRBLUNT topo (Invitrogen) and after sequencing the fragment is exchanged with the corresponding 3005 fragment in pCSmta.
Using the Quick Exchange method (Stratagene), mutations are introduced using two complementary primers in a PCR on a plasmid containing the mta gene, or part of the mta gene.
For this purpose a convenient set of plasmids is constructed, comprising of 3 SDM 3010 plasmids and 3 pCSΔ plasmids. The SDM plasmids each bear 1 of the fragments of the mta gene as mentioned above, in which the desired mutation is introduced by QE. After verification by sequencing, the fragments are cloned into the corresponding recipient pCSΔ plasmid. The pCSΔ plasmids are inactive derivatives from pCSmta. Activity is restored by cloning the corresponding fragment from the SDM plasmid, enabling easy 3015 screening.
Table 3. Primers used in cloning the mta gene, and standard primers used in construction of site directed mutants with the 2 step PCR method.
Figure imgf000096_0001
Figure imgf000096_0002
Table 4: Primers used to introduce site directed mutations in mta
Figure imgf000096_0003
3020 Table 5. Features of the SDM and pCSΔ plasmids
Figure imgf000096_0004
Example 3. Multi SDM
The PS4 variants were generated using a QuikChange® Multi Site Directed Mutagenesis Kit (Stratagene) according to the manufactures protocol with some modifications as described.
3025 Step 1: Mutant Strand Synthesis Reaction (PCR)
Inoculate 3ml. LB (22g/l Lennox L Broth Base, Sigma) + antibiotics (0,05 μg/ml kanamycin, Sigma) in a 10ml Falcon tube - Incubate o/n 37°C, ca. 200 rpm.
Spin down the cells by centrifugation (5000 rpm/5 min) 3030 - Poor off the medium
- Prepare ds-DNA template using QIAGEN Plasmid Mini Purification Protocol
1. The mutant strand synthesis reaction for thermal cycling was prepared as follow:
3035 PCR Mix:
2,5 μl 1 OX QuickChange® Multi reaction buffer 0,75 μl QuickSolution
X μl Primers primer length 28-35 bp -> 10 pmol"
3040 7 pmol 5 pmol
Figure imgf000097_0001
X μl ds-DNA template (200 ng)
1 μl QuickChange® Multi enzyme blend (2,5 U/μl) (PfuTurbo® DNA 3045 polymerase)
X μl dH2O (to a final volume of 25 μl)
Mix all components by pipetting and briefly spin down the reaction mixtures.
3050 2. Cycle the reactions using the following parameters:
35 cycles of denaturation (96°C/lmin) primer annealing (62,8°C/lmin) elongation (65°C/15min) then hold at 4°C
3055 Preheat the lid of the PCR machine to 105°C and the plate to 95°C before the PCR tubes are placed in the machine (eppendorf thermal cycler).
Step 2: Dpn I Digestion
3060
1. Add 2 μl Dpn I restriction enzyme (10 U/μl) to each amplification reaction, mix by pipetting and spin down mixture.
2. Incubate at 37°C for ~3 hr.
3065
Step 3: Transformation of XLIO-Gold® Ultracompetent Cells
1. Thaw XLlO-GoId cells on ice. Aliquot 45 μl cells per mutagenesis reaction to prechilled Falcon tubes.
3070 2. Turn on the waterbath (420C) and place a tube with NZY+ broth in the bath to preheat.
3. Add 2 μl β-mercaptoethanol mix to each tube. Swirl and tap gently and incubate 10 min on ice, swirling every 2 min.
4. Add 1,5 μl Dpn /-treated DNA to each aliquot of cells, swirl to mix and incubate 3075 on ice for 30 min.
5. Heat-pulse the tubes in 42°C waterbath for 30 s and place on ice for 2 min. 6. Add 0.5 ml preheated NZY+ broth to each tube and incubate at 370C for lhr with shaking at 225-250 rpm.
7. Plate 200 μl of each transformation reaction on LB plates (33,6 g/1 Lennox L
3080 Agar, Sigma) containing 1% starch and 0,05 μg/ml kanamycin
8. Incubate the transformation plates at 37°C overnight.
Table 6. Primer table for pPD77dl4:
3085
3090
Figure imgf000098_0001
Figure imgf000099_0001
Vector system based on pPD77
The vector system used for pPD77 is based on pCRbluntTOPOϋ (invitrogen). The zeocin resistance cassette has been removed by pmll, 393 bp fragment removed. The expression 3095 cassette from the pCC vector (P32-ssCGTase-PS4-tt) has then been inserted into the vector.
Ligation of PS4 variant into pCCMini
3100 The plasmid which contain the relevant mutations (created by MSDM) is cut with restriction enzyme Nco 1 and Hind III (Biolabs):
3 μg plasmid DNA, X μl 10x buffer 2, 10 units Ncol, 20 units Hindlll,
Incubation 2h at 37°C 3105
Run digestion on a 1% agarose gel. Fragments sized 1293 bp (PS4 gene) is cut out of the gel and purified using Qiagen gel purification kit.
The vector pCCMini is then cut with restriction enzymes, Nco 1 and Hind III, and the 3110 digestion is then run on a 1% agarose gel. The fragment sized 3569 bp is cut out of the gel and purified using Qiagen gel purification kit.
Ligation: Use Rapid DNA ligation kit (Roche) Use the double amount of insert compared to vector 3115 e.g. 2 μl insert (PS4 gene)
1 μl vector
5 μl T4 DNA ligation buffer 2xconc 1 μl (IH2O 1 μl T4 DNA ligase 3120 Ligate 5 min/RT
Transform the ligation into One Shot TOPO competent cells according to manufactures protocol (Invitrogen). Use 5 μl ligation per transformation.
3125 Plate 50 μl transformationsmix onto LB plates (33,6 g/1 Lennox L Agar, Sigma) containing 1% starch and 0,05 μg/ml kanamycin. Vectors containing insert (PS4 variants) can be recognised by halo formation on the starch plates. Example 3A. Production of PS4 Variant Polypeptide with Substitution at Position
3130 307
pSac-pMD229
Sequence pSac-pMD229 (SEQ ID NO: 14) comprising mutations at N33 Y, D34N, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, H272Q, G303E, H307L, A309P, S334P relative to wild type non-maltogenic exoamylase is made 3135 from a wild type sequence using site directed mutagenesis (as described above in Example 2) or Multi Site Directed Mutagenesis (as described above in Example 3), with the primers in the table below:
Figure imgf000100_0001
Figure imgf000101_0001
pSac-pMS382
Sequence pSac-pMS382 (SEQ ID NO: 22) comprising 307K is made from pSac- pSac-pMD229 using Multi Site Directed Mutagenesis (as described above in Example 3), with the primers in the table below:
Primers for pMD229 -> pMS382:
Figure imgf000101_0002
PS4 variant polypeptides with other residues at position 307 are generated using Multi Site Directed Mutagenesis (as described above in Example 3), with the primers in the table below:
Figure imgf000101_0003
Figure imgf000102_0001
3145
Example 4. Transformation into Bacillus subtilis (Protoplast Transformation)
Bacillus subtilis (strain DB104A; Smith et al. 1988; Gene 70, 351-361) is transformed with the mutated plasmids according to the following protocol.
3150 A. Media for protoplasting and transformation
2 x SMM per litre: 342 g sucrose (1 M); 4.72 g sodium maleate (0.04 M); 8:12 g MgCl2,6H20 (0.04 M); pH 6.5 with concentrated NaOH. Distribute in 50-ml portions and autoclave for 10
3155 min.
4 x YT (1/2 NaCl) 2 g Yeast extract + 3.2 g Tryptone + 0.5 g NaCl per 100 ml.
SMMP mix equal volumes of 2 x SMM and 4 x YT.
PEG 10 g polyethyleneglycol 6000 (BDH) or 8000 (Sigma) in 25
3160 ml 1 x SMM (autoclave for 10 min.).
B. Media for plating/regeneration
agar 4% Difco minimal agar. Autoclave for 15 min.
3165 sodium succinate 270 g/1 (1 M), pH 7.3 with HCl. Autoclave for 15 min. phosphate buffer 3.5 g K2HPO4 + 1.5 g KH2PO4 per 100ml. Autoclave for 15 min.
3170
MgCl2 20.3 g MgCl2, 6H2O per 100 ml (1 M). casamino acids 5% (w/v) solution. Autoclave for 15 min. yeast extract 1O g per 100 ml, autoclave for 15 min. glucose 20% (w/v) solution. Autoclave for 10 min.
3175
DM3 regeneration medium: mix at 60 C (waterbath; 500-ml bottle):
250 ml sodium succinate
50 ml casamino acids 3180 25 ml yeast extract
50 ml phosphate buffer
15 ml glucose
10 ml MgCl2
100 ml molten agar 3185
Add appropriate antibiotics: chloramphenicol and tetracycline, 5 ug/ml; erythromycin, 1 ug/ ml. Selection on kanamycin is problematic in DM3 medium: concentrations of 250 ug/ml may be required.
3190 C. Preparation of protoplasts
1. Use detergent-free plastic or glassware throughout.
2. Inoculate 10 ml of 2 x YT medium in a 100-ml flask from a single colony. Grow an overnight culture at 25-30 C in a shaker (200 rev/min).
3195 3. Dilute the overnight culture 20 fold into 100 ml of fresh 2 x YT medium
(250-ml flask) and grow until OD60O = 0.4-0.5 (approx. 2h) at 37C in a shaker (200-250 rev/min).
4. Harvest the cells by centrifugation (900Og, 20 min, 4 C).
5. Remove the supernatant with pipette and resuspend the cells in 5 ml of 3200 SMMP + 5 mg lysozyme, sterile filtered.
6. Incubate at 37 C in a waterbath shaker (100 rev/min).
After 30 min and thereafter at 15 min intervals, examine 25 ul samples by microscopy. Continue incubation until 99% of the cells are protoplasted (globular appearance). Harvest the protoplasts by centrifugation (4000g, 20 min, RT) and pipet off 3205 the supernatant. Resuspend the pellet gently in 1 -2 ml of SMMP.
The protoplasts are now ready for use. (Portions (e.g. 0.15 ml) can be frozen at -80 C for future use (glycerol addition is not required). Although this may result in some reduction of transformability, 106 transformants per ug of DNA can be obtained with frozen protoplasts).
3210 D. Transformation
1. Transfer 450 ul of PEG to a microtube. 2. Mix 1-10 ul of DNA (0.2 ug) with 150 ul of protoplasts and add the mixture to the microtube with PEG. Mix immediately, but gently.
3. Leave for 2 min at RT, and then add 1.5 ml of SMMP and mix.
3215 4. Harvest protoplasts by microfuging (10 min, 13.000 rev/min (10-12.000 g)) and pour off the supernatant. Remove the remaining droplets with a tissue.
Add 300 ul of SMMP (do not vortex) and incubate for 60-90 min at 37 C in a waterbath shaker (100 rev/min) to allow for expression of antibiotic resistance markers. (The protoplasts become sufficiently resuspended through the shaking action of the
3220 waterbath.). Make appropriate dilutions in 1 x SSM and plate 0.1 ml on DM3 plates
Example 5. Fermentation of PS4 Variants in Shake Flasks
The shake flask substrate is prepared as follows:
Figure imgf000104_0001
The substrate is adjusted to pH 6.8 with 4N sulfuric acid or sodium hydroxide before autoclaving. 100 ml of substrate is placed in a 500 ml flask with one baffle and
3225 autoclaved for 30 minutes. Subsequently, 6 ml of sterile dextrose syrup is added.The dextrose syrup is prepared by mixing one volume of 50% w/v dextrose with one volume of water followed by autoclaving for 20 minutes.
The shake flasks are inoculated with the variants and incubated for 24 hours at 35°C/180rpm in an incubator. After incubation cells are separated from broth by
3230 centrifugation (10.000 x g in 10 minutes) and finally, the supernatant is made cell free by microfiltration at 0,2μm. The cell free supernatant is used for assays and application tests.
Example 6. Amylase Assays
Betamyl assay
One Betamyl unit is defined as activity degrading 0,0351 mmole per 1 min. of
3235 PNP-coupled maltopentaose so that 0,0351 mmole PNP per 1 min. can be released by excess a-glucosidase in the assay mix. The assay mix contains 50 ul 50 mM Na-citrate, 5 mM CaC12, pH 6,5 with 25 ul enzyme sample and 25 ul Betamyl substrate (Glc5-PNP and a-glucosidase) from Megazyme, Ireland (1 vial dissolved in 10 ml water). The assay mix is incubated for 30 min. at 4OC and then stopped by adding 150 ul 4% Tris. Absorbance at 3240 420 nm is measured using an ELISA-reader and the Betamyl activity is calculate based on Activity = A420 * d in Betamyl units/ml of enzyme sample assayed.
Endo-amylase assay
The endo-amylase assay is identical to the Phadebas assay run according to manufacturer (Pharmacia & Upjohn Diagnostics AB).
3245 Exo-speciflcity
The ratio of exo-amylase activity to Phadebas activity was used to evaluate exo- specificity.
Example 7. Half-life Determination
11/2 is defined as the time (in minutes) during which half the enzyme activity is 3250 inactivated under defined heat conditions. In order to determine the half life of the enzyme, the sample is heated for 1-40 minutes at constant temperatures of 60°C to 900C. The half life is calculated based on the residual Betamyl assay.
Procedure: In an Eppendorf vial, 1000 μl buffer is preheated for at least 10 minutes at 6O0C or higher. The heat treatment of the sample is started addition of 100 μl of 3255 the sample to the preheated buffer under continuous mixing (800 rpm) of the Eppendorf vial in an heat incubator (Termomixer comfort from Eppendorf). After 0, 2, 4, 6, 8 and 9 minutes of incubation, the treatment is stopped by transferring 45 μl of the sample to 1000 μl of the buffer equilibrated at 200C and incubating for one minute at 1500 rpm and at 200C. The residual activity is measured with the Betamyl assay.
3260 Calculation: Calculation of 11/2 is based on the slope of log 10 (the base- 10 logarithm) of the residual Betamyl activity versus the incubation time. 11/2 is calculated as Slope/0.301=tl/2.
Example 8. Model System Baking Tests
The doughs are made in the Farinograph at 30.00C. 10.00 g reformed flour is 3265 weighed out and added in the Farinograph; after 1 min. mixing the reference/sample
(reference = buffer or water, sample = enzyme+ buffer or water) is added with a sterile pipette through the holes of the kneading vat. After 30 sec. the flour is scraped off the edges - also through the holes of the kneading vat. The sample is kneaded for 7 min.
A test with buffer or water is performed on the Farinograph before the final 3270 reference is run. FU should be 400 on the reference, if it is not, this should be adjusted with, for example, the quantity of liquid. The reference/sample is removed with a spatula and placed in the hand (with a disposable glove on it), before it is filled into small glass tubes (of approx. 4.5 em's length) that are put in NMR tubes and corked up. 7 tubes per dough are made.
3275 When all the samples have been prepared, the tubes are placed in a
(programmable) water bath at 330C (without corks) for 25 min. and hereafter the water bath is set to stay for 5 min. at 33°C, then to heated to 98°C over 56 min. (Ll0C per minute) and finally to stay for 5 min. at 96°C.
The tubes are stored at 20.0°C in a thermo cupboard. The solid content of the 3280 crumb was measured by proton NMR using a Bruker NMS 120 Minispec NMR analyser at day 1, 3 and 7 as shown for crumb samples prepared with 0, 05, 1 abnd 2 ppm PSacD34 in Fig. 2. The lower increase in solid content over time represents the reduction in amylopectin retrogradation. After 7 days of storage at 20.0°C in a thermo cupboard 10-20 mg samples of crumb weighed out and placed in 40 μl aluminium standard DSC capsules 3285 and kept at 200C.
The capsules are used for Differential Scanning Calorimetry on a Mettler Toledo DSC 820 instrument. As parameters are used a heating cycle of 20-950C with 100C per min. heating and Gas/flow: N2/80 ml per min. The results are analysed and the enthalpy for melting of retrograded amylopectin is calculated in J/g.
3290 Example 9. Antistaling Effects
Model bread crumbs are prepared and measured according to Example 8. PS4 variants show a strong reduction of the amylopectin retrogradation after baking as measured by Differential Scanning Calorimetry in comparison to the control. The PS4 variants show a clear dosage effect.
3295 Example 10. Recipe for Baking Trials
Baking trials were carried out with a standard white bread sponge and dough recipe for US toast. The sponge dough is prepared from 1400 g of flour "Gold Medal" from General Mills, USA, 800 g of water, 40 g of rape seed oil, 7,5 g GRINDSTED™ SSL P55 Veg, 1O g emulsifϊer DIMOD AN™ PH200 and 60 g of compressed yeast. The sponge is 3300 mixed for 1 min. at low speed and subsequently 3 min. at speed 2 on a Hobart spiral mixer. The sponge is subsequently fermented for 3 hours at 25°C, 85% RH.
Thereafter, 600 g of "Gold Medal" flour, 18 g of compressed yeast, 5 g of calcium propionate, 16O g of sucrose, 5 g of calcium propionate, 432 g of water and ascorbic acid (60 ppm final concentration) and ADA (azodicarbonamide; 40 ppm final concentration) 3305 are added to the sponge. The resulting dough is mixed for 1 min. at low speed and then 2 min. on high speed on a Diosna mixer. Then 30 g of salt is added to the dough.
The dough is rested for 5 min. at ambient temperature, and then 550 g dough pieces are scaled, moulded on Glimek sheeter with the settings 1:4, 2:4, 3:15, 4:12 and width 8 on both sides and transferred to a baking form. After 65 min. proofing at 43 °C at 3310 95% RH the doughs are baked for 26 min. at 200°C in an MIWE oven.
Example 11. Control of Volume of Danish Rolls
Danish Rolls are prepared from a dough based on 2000 g Danish reform flour (from Cerealia), 12O g compressed yeast, 32 g salt, and 32 g sucrose. Water is added to the dough according to prior water optimisation.
3315 The dough is mixed on a Diosna mixer (2 min. at low speed and 5 min. at high speed). The dough temperature after mixing is kept at 26°C. 1350 g dough is scaled and rested for 10 min. in a heating cabinet at 30°C. The rolls are moulded on a Fortuna molder and proofed for 45 min. at 34°C and at 85% relative humidity. Subsequently the rolls are baked in a Bago 2 oven for 18 min. at 250°C with steam in the first 13 seconds. After
3320 baking the rolls are cooled for 25 min. before weighing and measuring of volume.
The rolls are evaluated regarding crust appearance, crumb homogeneity, capping of the crust, ausbund and specific volume (measuring the volume with the rape seed displacement method).
Based on these criteria it is found that the PS4 variants increase the specific 3325 volume and improve the quality parameters of Danish rolls. Thus PS4 variants are able to control the volume of baked products. Example 12. Protocol for Evaluation of Firmness, Resilience and Cohesiveness
Texture Profile Analysis of Bread
Firmness, resilience and cohesiveness are determined by analysing bread slices by 3330 Texture Profile Analysis using a Texture Analyser From Stable Micro Systems, UK. Calculation of firmness and resilience is done according to preset standard supplied by Stable Micro System, UK. The probe used is aluminium 50 mm round.
Bread is sliced with the width of 12.5 mm. The slices are stamped out to a circular piece with a diameter of 45 mm and measured individually.
3335 The following settings are used:
Pre Test Speed: 2 mm/s
Test Speed: 2 mm/s
Post Test Speed: 10 mm/s
Rupture Test Distance: 1%
3340 Distance: 40%
Force: 0.098 N
Time: 5.00 sec
Count: 5
Load Cell: 5 kg
3345 Trigger Type: Auto - 0.01 N
The mode of compression is a modification to the one used in Standard method AACC 74-09. The sample is compressed twice in the test. Figure 1 shows an example of a curve from the Texture Analyser.
Example 13. Protocol for Evaluation of Firmness
3350 Firmness is determined at 40% compression during the first compression. The figure is the force needed to compress the slice to 40% of the total thickness. The lower the value, the softer the bread. The firmness is expressed as a pressure, for example, in hPa.
This assay may be referred to as the "Firmness Evaluation Protocol".
3355 Example 14. Protocol for Evaluation of Resilience
Area under the curve is a measure of work applied during the test. The area under the curve in the compression part (Al) and the withdrawal part (A2) during the first compression are shown in Figure 1.
The ratio between Al and A2 is defined as the resilience of the sample, and is 3360 expressed as Resilience Units. True elastic material will give a symmetric curve, as the force applied during the first part will be equal to the force in the second part. For bread and bread-like material, A2 is normally smaller than A2 due to disturbance of the structure during compression. Hence, resilience is always lower than 1.
This assay may be referred to as the "Resilience Evaluation Protocol".
3365 Example 15. Protocol for Evaluation of Cohesiveness
The cohesiveness is defined as the ratio between the area under second compression to the area under first compression (A3/A1+A2), and is expressed as Cohesiveness Units. It is a measure of the decay of the sample during compression. The higher the ability of the sample to regain its shape after first compression the closer the 3370 value will be to 1. For bread and bread-like material cohesiveness is always lower than 1.
This assay may be referred to as the "Cohesiveness Evaluation Protocol".
Example 16. Protocol for Evaluation of Crumbliness (Resistance to Crumbling)
Two slices of bread are placed on a piece of paper. Each slice is divided into 4 squares by vertical and subsequent horizontal tears of the slice.
3375 Tearing is done by pulling the crumb apart by the fingers. First the slice is torn from the middle of the top bread surface to the middle of the bottom bread surface. Thereafter, each half of the original slice is torn from the crust side to the inside of the slice. The small crumb pieces, which are separated from the 4 squares, are removed by shaking each piece after a tear at least 3 times by moving the hand up and down. 3380 The weight of the separated small crumb pieces is determined as a measure of crumbliness. This assay may be referred to as the "Crumbliness Evaluation Protocol".
Example 17. Protocol for Evaluation of Foldability
The toast bread is sliced using an automatic bread slicer with set slice thickness of 15 mm. The slice is folded by hand from the top of the slice towards the bottom, so that 3385 the direction of the crease is from side to side.
The foldability is visually assessed using the following scoring system:
Figure imgf000110_0001
This assay may be referred to as the "Foldability Evaluation Protocol".
Example 18. Improved Thermostability of PS4 Variant Polypeptides
Thermal stability of amylase pSac-pMS382 is measured as described above and 3390 compared to that of pSac-D34 / pMD3 (SEQ ID NO: 2) and pSac-pMD229 (SEQ ID NO: 13).
Because heat inactivation follows a 1st order reaction, half-life defined as the time (in minutes) for 50% inactivation is determined based on residual activity using the Betamyl assay after incubation for 1-40 minutes at 75, 80 and 85°C (167, 176 and 185°F, 3395 respectively) in 50 mM sodium-citrate, 5 mM calcium chloride, pH 6.5.
The results are shown in Figure 2. This figure shows that the thermostability (half life) of PS4 variant polypeptides comprising a substitution at position 307 to a basic or positively charged amino acid is improved compared to polypeptides without such a mutation. 3400 Example 19. Improved Handling Properties of Food Products Treated with PS4 Variant Polypeptides: Firmness
Bread is baked with varying amounts of pSac-pMS382 (SEQ ID NO: 21) comprising a substitution to a basic or positively charged residue at position 307, i.e., 20,000, 40,000 and 60,000 Betamyl units/kg of pSac-pMS382.
3405 The firmness of the bread is tested according to the protocol set out in Example 13 at various times after baking. As a control, firmness of bread baked without any enzyme is also measured.
Figure 3 shows the results of a baking trial in which firmness of bread is tested.
Example 20. Improved Handling Properties of Food Products Treated with PS4 3410 Variant Polypeptides: Resilience
Bread is baked with varying amounts of pSac-pMS382 (SEQ BD NO: 21) comprising a substitution to a basic or positively charged residue at position 307, i.e., 20,000, 40,000 and 60,000 Betamyl units/kg of pSac-pMS382.
The resilience of the bread is tested according to the protocol set out in Example 14 3415 at various times after baking. As a control, resilience of bread baked without any enzyme is also measured.
Figure 4 shows the results of a baking trial in which resilience of bread is tested.
Example 21. Improved Handling Properties of Food Products Treated with PS4 Variant Polypeptides: Cohesiveness
3420 Bread is baked with varying amounts of pSac-pMS382 (SEQ ID NO: 21) comprising a substitution to a basic or positively charged residue at position 307, i.e., 20,000, 40,000 and 60,000 Betamyl units/kg of pSac-pMS382.
The cohesiveness of the bread is tested according to the protocol set out in Example 15 at various times after baking. As a control, cohesiveness of bread baked 3425 without any enzyme is also measured.
Figure 5 shows the results of a baking trial in which cohesiveness of bread is tested. Example 22. Improved Handling Properties of Food Products Treated with PS4 Variant Polypeptides: Firmness
3430 Bread is baked with 60,000 Betamyl units/kg of pSac-pMS382 (SEQ ID NO: 21) comprising a substitution to a basic or positively charged residue at position 307 and the firmness of the bread is tested according to the protocol set out in Example 13 at various times after baking.
Bread is also baked with 60,000 Betamyl units/kg of pSac-D34 / pMD3 (SEQ ID 3435 NO: 2) and 60,000 Betamyl units/kg of pSac-pMD229 (SEQ ID NO: 13), each without a substitution at position 307 to a basic or positively charged amino acid. The firmness of the bread is tested.
As a control, firmness of bread baked without any enzyme is also measured.
Figure 6 shows the results of a baking trial in which firmness of bread treated with 3440 PS4 variant polypeptide with and without substitution at 307 is tested.
Example 23. Improved Handling Properties of Food Products Treated with PS4 Variant Polypeptides: Firmness, Resilience and Cohesiveness
Bread is baked with 60,000 Betamyl units/kg of pSac-pMS382 (SEQ ID NO: 21) comprising a substitution to a basic or positively charged residue at position 307 and the 3445 resilience of the bread is tested according to the protocol set out in Example 14 at various times after baking.
Bread is also baked with 60,000 Betamyl units/kg of pSac-D34 / pMD3 (SEQ ID NO: 2) and 60,000 Betamyl units/kg of pSac-pMD229 (SEQ ID NO: 13), each without a substitution at position 307 to a basic or positively charged amino acid. The resilience of 3450 the bread is tested.
As a control, resilience of bread baked without any enzyme is also measured.
Figure 7 shows the results of a baking trial in which resilience of bread treated with PS4 variant polypeptide with and without substitution at 307 is tested.
Example 24. Improved Handling Properties of Food Products Treated with PS4 3455 Variant Polypeptides: Cohesiveness
Bread is baked with 60,000 Betamyl units/kg of pSac-pMS382 (SEQ ID NO: 21) comprising a substitution to a basic or positively charged residue at position 307 and the cohesiveness of the bread is tested according to the protocol set out in Example 15 at various times after baking.
3460 Bread is also baked with 60,000 Betamyl units/kg of pSac-D34 / pMD3 (SEQ ID
NO: 2) and 60,000 Betamyl units/kg of pSac-pMD229 (SEQ ID NO: 13), each without a substitution at position 307 to a basic or positively charged amino acid. The cohesiveness of the bread is tested.
As a control, cohesiveness of bread baked without any enzyme is also measured.
3465 Figure 8 shows the results of a baking trial in which cohesiveness of bread treated with PS4 variant polypeptide with and without substitution at 307 is tested.
Example 25. Improved Handling Properties of Food Products Treated with PS4 Variant Polypeptides: Foldability
Sponge and dough toast bread treated with 4 ppm of pSac-pMS382 (SEQ ID NO: 3470 21, H307K substitution) is baked and foldability of the resulting breads is tested and scored as described above.
As a control, sponge and dough toast bread not treated with enzyme is baked and foldability tested and scored.
Tests are done on three slices on day 13 after baking.
Figure imgf000113_0001
3475
As shown in the table above and Figures, foldability is improved in sponge and dough toast bread treated with a PS4 variant polypeptide comprising a substitution at position 307 to a basic or positively charged amino acid compared to untreated toast bread. 3480 Example 26. Improved Handling Properties of Food Products Treated with PS4 Variant Polypeptides: Foldability
Sponge and dough toast bread treated with 4 ppm of pSac-pMS382 (SEQ ID NO: 21, H307K substitution) is baked and foldability of the resulting breads is tested and scored as described above.
3485 As controls, sponge and dough toast bread not treated with enzyme is baked and foldability tested and scored. Foldability of sponge and dough toast breads treated with other enzymes as shown below is also tested.
Enzyme pSac-D34 (also known as pMD3) comprises mutations N33Y, D34N,G121D, G134R, A141P, I157L, L178F, A179T, G223A, H307L, S334P relative to 3490 wild type non-maltogenic exoamylase and its sequence is shown as SEQ ID NO: 2.
Enzyme pSac-pMD229 comprises mutations N33Y, D34N, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, H272Q, G303E, H307L, A309P, S334P relative to wild type non-maltogenic exoamylase and its sequence is shown as SEQ ID NO: 13.
3495 Tests are done on three slices on day 8 after baking.
Figure imgf000114_0001
As shown in the table above, foldability is improved in sponge and dough toast bread treated with a PS4 variant polypeptide comprising a substitution at position 307 to a basic or positively charged amino acid compared to enzymes without this substitution. 3500 Example 27. Improved Handling Properties of Food Products Treated with Combinations of PS4 Variant Polypeptides and Other Enzymes: Foldability
Sponge and dough toast bread treated with 6 ppm of pSac-pMS382 (SEQ ID NO: 21, 307K substitution) alone or in combination with other enzymes as shown below is baked and foldability of the resulting breads is tested and scored as described above.
3505 Combination 1 : 6 ppm pSac-pMS382 + 50 ppm GRINDAMYL™ POWERBake
900 + 15 ppm GRINDAMYL™ Max-Life U4.
Combination 2: 6 ppm pSac-pMS382 + 50 ppm GRINDAMYL™ POWERBake
900
Combination 3: 6 ppm pSac-pMS382 + 50 ppm GRINDAMYL™ POWERBake 3510 900 + 150 ppm GRINDAMYL™ POWERBake 4050
GRINDAMYL™ POWERBake 900 is a xylanase commercially available from Danisco A/S. GRINDAMYL™ Max-Life U4 is a bacterial α-amylase commercially available from Danisco A/S. GRINDAMYL™ POWERBake 4050 is a lipase commercially available from Danisco A/S.
3515 As controls, sponge and dough toast bread not treated with enzyme is baked and foldability tested and scored.
Tests are done on three slices on day 5 after baking.
Figure imgf000115_0001
3520 As shown in the table above, foldability is improved in sponge and dough toast bread treated with a PS4 variant polypeptide comprising a substitution at position 307 to a basic or positively charged amino acid alone or in combination with other enzymes such as bacterial α-amylase, lipase and xylanase.
Example 28. Improved Handling Properties of Food Products Treated with PS4 3525 Variant Polypeptides: Crumbliness Tests
Sponge and dough toast bread treated with 4 ppm of pSac-pMS382 (SEQ ID NO: 21, 307K substitution) is baked and crumbliness of the resulting breads is tested and scored as described above.
As a control, sponge and dough toast bread not treated with enzyme is baked and 3530 foldability tested and scored.
Tests are done on day 13 after baking.
Figure imgf000116_0001
As shown in the table above, crumbliness is reduced in sponge and dough toast bread after 13 days, treated with a PS4 variant polypeptide comprising a substitution at 3535 position 307 to a basic or positively charged amino acid.
Example 29. Improved Handling Properties of Food Products Treated with PS4 Variant Polypeptides: Crumbliness Tests
Sponge and dough toast bread treated with 4 ppm of pSac-pMS382 (SEQ ID NO: 21, 307K substitution) is baked and crumbliness of the resulting breads is tested and 3540 scored as described above.
As a control, sponge and dough toast bread not treated with enzyme is baked and foldability tested and scored.
Tests are done on day 15 after baking.
Figure imgf000117_0001
3545 As shown in the table above, crumbliness is reduced in sponge and dough toast bread after 15 days, treated with a PS4 variant polypeptide comprising a substitution at position 307 to a basic or positively charged amino acid.
Example 30. PS4 Variant Polypeptides with Position 307K Substitutions
The following polypeptides with substitutions at position 307 to lysine are made 3550 and their properties tested as described above. The sequences of the polypeptides comprise the sequence of SEQ ID NO: 2 together with the substitutions specified.
Figure imgf000117_0002
Figure imgf000118_0001
Figure imgf000119_0001
Figure imgf000120_0001
Example 31. PS4 Variant Polypeptides with Position 307H
The following polypeptides with histidine at position 307 together with other mutations are made and their properties tested as described above. The sequences of the polypeptides comprise the sequence of SEQ ID NO: 2 together with the substitutions specified.
Figure imgf000121_0001
Example 32. Generation of PS4 Polypeptides with L307R and L307K Mutations
SSM 471 BlO and SSM 471 C04 with other residues at position 307 (L307R,
3560 L307K) are generated using Multi Site Directed Mutagenesis (as described above in Example 3), with the primers in the table below:
Primer used for site scan in osition 307:
Figure imgf000121_0002
96 clones from the Site Scan library are sequenced and the two variants SSM 471 3565 BlO and SSM 471 C04 containing amino acid R and K respectively in position 307 are identified. The amino acid sequence of SSM471 BlO is set out as SEQ ID NO: 27, while the nucleic acid sequence of SSM471 BlO is set out as SEQ ID NO: 28.
The amino acid sequence of SSM471 C04 is set out as SEQ ID NO: 29, while the 3570 nucleic acid sequence of SSM471 C04 is set out as SEQ ID NO: 30.
Other PS4 variant polypeptides derived from a parent polypeptide and with mutations L307R or L307K are likewise generated using Multi Site Directed Mutagenesis (as described above hi Example 3), with the primers in the table below:
Primer used for site scan in position 307
Primer used for site scan in osition 307:
Figure imgf000122_0001
3575
For polypeptides with an additional mutation in the region of 301 to 306 or 308 to 313, the additional mutation is generated by Multi Site Directed Mutagenesis (according to the method described in Example 3).
96 clones from the Site Scan libraries are sequenced and thereby variants 3580 containing amino acid R and K, respectively in position 307 are identified.
Example 33. Tortilla Trial
Tortillas are baked to a recipe as follows:
Figure imgf000122_0002
3585 Procedure
Dough temperature must be 3O0C. Put all dry ingredients into aK emper mixer and mix for 1 min slow. Add water - mix 12 min slow. Scaling: 1350 g. Moulding: Glimek: Press time 3,0 - rounding time: 3.0. Rest dough 10 min at 30°C. Pass the dough balls trough the CFO 40 tortilla machine:
3590 Settings:
Pressing: Hot press the dough balls:
Top plate: 205 °C; Bottom plate: 200 0C
Conveyers:
Top: 230 0C; Middle: 225 0C; Bottom: 160 °C
3595 Baking time: Approx 30 seconds
Cooling: 12 min. at: 20 °C, 80% RH
Packing: Vaccum With CO2
Settings: Vaccum: 40; CO2: 41; Temp: 82 0C
Example 34. Results of Foldability Test Day 8 After Baking
3600 A foldability test is conducted at day 8 after baking according to Example 17. Figure 9 shows the results of a foldability test day 8 after baking of tortillas with 400 ppm Novamyl (TM) 1500 and 50 BMK/kg pSac-pMS382 (SEQ ID NO: 21). Figure 10 shows the results of a foldability test day 8 after baking of tortillas with 400 ppm NovamylTM 1500 and 50 BMK/kg pSac-pMS382 (SEQ ID NO: 21).
3605 When 10 tortillas with 400 ppm of Novamyl™ 1500 are folded, all cracked during folding as shown in Figures 9 and 10.
When 10 tortillas with 50 BMK/kg pSac-pMS382 (SEQ ID NO: 21) are folded, none cracked during folding as shown in Figures 9 and 10.
3610 Example 35. Baking Trial with SSM 471 BlO (SEQ ID NO: 27, 307R) and SSM 471 C04 (SEQ ID NO: 29, 307K)
US toast prepared by a sponge and dough procedure as described hi Example 10 is used to test the variants SSM 471 BlO (SEQ ID NO: 27) with 307R and SSM 471 C04 3615 (SEQ ID NO: 29) with 307K at a 40 BMK/kg dosage.
The toast is evaluated for firmness and resilience as described in Examples 12 to 14.
Figure 11 shows the results of a firmness test of US toast prepared with SSM 471 BlO (SEQ ID NO: 27) and SSM 471 C04 (SEQ ID NO: 29). Figure 12 shows the results 3620 of a resilience test of US toast prepared with SSM 471 BlO(SEQ ID NO: 27) and SSM 471 C04 (SEQ ID NO: 29).
Both variants are seen to give a significant decrease in firmness (Figure 11) and a significant increase in resilience (Figure 12) indicating that 307R and 307K variants give significant antistaling effects.
3625 Example 36. Baking trial with PMS 370 (SEQ ID NO: 3I3 307H) and SSM 471 C04 (SEQ ID NO: 29, 307K)
PMS 370 is generated using Multi Site Directed Mutagenesis as described above in Example 3. The sequence of PMS 370 is set out as SEQ ID NO: 31.
US toast is prepared by a sponge and dough procedure as described hi Example 10. 3630 The toast is used to test the variants PMS 370 with 307H and SSM 471 C04 with 307K at 20, 40 and 60 BMK/kg dosage. The toast is evaluated for resilience as described in Examples 12 and 14.
Figure 13 shows the results of a resilience test of US toast prepared with pMS 370 (SEQ ED NO: 31) and SSM 471 C04(SEQ ID NO: 29).
3635 Both variants are shown to give a significant increase in resilience (Figure 13) with increasing dosage indicating that 307H and 307K variants give significantly improved resilience as a function of dosage. However, the effect of the 307K variant dosages is substantially stronger than the effect of the respective 307H variant dosages.
REFERENCES
3640 Penninga, D., van der Veen, B.A., Knegtel, R.M., van Hijum, S.A., Rozeboom,
H. J., KaIk, K.H., Dijkstra, B. W., Dijkhuizen, L. (1996). The raw starch binding domain of cyclodextrin glycosyltransferase from Bacillus circulans strain 251. J.Biol.Chem. 271, 32777-32784.
Sambrook J, F.E.M.T. (1989). Molecular Cloning: A Laboratory Manual, 2nd Edn. 3645 Cold Spring Harbor Laboratory, Cold Spring Harbor NY.
Zhou,J.H., Baba,T., Takano,T., Kobayashi,S., Arai,Y. (1989). Nucleotide sequence of the maltotetraohydrolase gene from Pseudomonas saccharophila. FEBS Lett. 255, 37- 41.
Each of the applications and patents mentioned in this document, and each 3650 document cited or referenced in each of the above applications and patents, including during the prosecution of each of the applications and patents ("application cited documents") and any manufacturer's instructions or catalogues for any products cited or mentioned in each of the applications and patents and in any of the application cited documents, are hereby incorporated herein by reference. Furthermore, all documents cited 3655 in this text, and all documents cited or referenced in documents cited in this text, and any manufacturer's instructions or catalogues for any products cited or mentioned in this text, are hereby incorporated herein by reference.
Various modifications and variations of the described methods and system of the invention will be apparent to those skilled in the art without departing from the scope and 3660 spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in molecular biology or related fields are intended to be within the scope of the claims.

Claims

9580 1. A PS4 variant polypeptide derivable from a parent polypeptide having amylase activity, in which the PS4 variant polypeptide comprises an amino acid substitution at position 307 to lysine (K) or arginine (R), with reference to the position numbering of a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ID NO: 1.
2. A PS4 variant polypeptide according to Claim 1, which is derivable from a parent 9585 polypeptide having exoamylase activity, preferably non-maltogenic exoamylase activity.
3. A PS4 variant polypeptide according to Claim 1, in which the amino acid substitution at position 307 is a substitution to lysine (307K), preferably H307K or a substitution to arginine (307R), preferably H307R.
4. A PS4 variant polypeptide according to Claim 1, 2 or 3, which further comprises 9590 an amino acid substitution at position 70.
5. A PS4 variant polypeptide according to any preceding claim, in which the amino acid substitution at position 70 is a substitution to aspartic acid (70D), preferably G70D.
6. A PS4 variant polypeptide according to any preceding claim, in which the amino acid at position 272 of the sequence of the PS4 variant polypeptide is histidine (H).
9595 7. A PS4 variant polypeptide according to any preceding claim, in which the amino acid at position 303 of the sequence of the PS4 variant polypeptide is glycine (G)..
8. A PS4 variant polypeptide according to any preceding claim, in which the PS4 variant polypeptide further comprises one or more mutations selected from the group consisting of positions: 33, 34, 121, 134, 141, 146, 157, 161, 178, 179, 223, 229, 309 or
9600 334
9. A PS4 variant polypeptide according to any preceding claim, in which the further mutation(s) hi the PS4 variant polypeptide are selected from the group consisting of: 33 Y, 34N, 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E, 229P, 309P, 334P, preferably N33 Y, D34N, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T,
9605 G223E, S229P, A309P and S334P.
10. A PS4 variant polypeptide according to any preceding claim, in which the PS4 variant polypeptide comprises the following substitutions 33Y, 34N, 7OD, 121F, 134R, 141P, 146G, 157L, 161 A, 178F, 179T, 223E, 229P, 307K, 309P, 334P, preferably N33 Y, D34N, G70D, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, 9610 S229P, H307K, A309P, S334P relative to a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ID NO: 1.
11. A PS4 variant polypeptide according to any preceding claim, in which the PS4 variant polypeptide comprises a sequence SEQ ID NO: 21 (pSac-pMS382).
12. A PS4 variant polypeptide according to any preceding claim, in which the PS4 9615 variant polypeptide comprises the following substitutions 33 Y, 34N, 7OD, 12 IF, 134R,
141P, 146G, 157L, 161 A, 178F, 179T5 223E, 229P, 307R, 309P, 334P, preferably N33 Y, D34N, G70D, G121F, G134R, A141P, Y146G, I157L, S161A, L178F, A179T, G223E, S229P, H307R, A309P, S334P relative to a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ID NO: 1.
9620 13. A PS4 variant polypeptide according to any preceding claim, in which the PS4 variant polypeptide comprises a sequence SEQ ID NO: 23 (pSac-pMS382R).
14. A PS4 variant polypeptide derivable from a parent polypeptide having non- maltogenic exoamylase activity, in which the PS4 variant polypeptide comprises the following substitutions 33Y5 34N, 7OD, 121F5 134R, 141P, 146G5 157L, 161A5 178F5
9625 179T5 223E5 229P5 309P5 334P, preferably N33Y, D34N, G70D, G121F, G134R, A141P, Y146G, 1157L5 S161A, L178F, A179T, G223E, S229P, A309P, S334P relative to a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ID NO: 1.
15. A PS4 variant polypeptide according to any preceding claim, in which the PS4 variant polypeptide comprises a sequence SEQ ID NO: 25 (pSac-pMS382H).
9630 16. A PS4 variant polypeptide according to any preceding claim, in which the parent polypeptide comprises a non-maltogenic exoamylase, preferably a glucan 1,4-alpha- maltotetrahydrolase (EC 3.2.1.60).
17. A PS4 variant polypeptide according to any preceding claim, in which the parent polypeptide is or is derivable from Pseudomonas species, preferably Pseudomonas
9635 saccharophilia or Pseudomonas stutzeri.
18. A PS4 variant polypeptide according to any preceding claim, in which the parent polypeptide is a non-maltogenic exoamylase from Pseudomonas saccharophilia exoamylase having a sequence shown as SEQ ED NO: 1 or SEQ ID NO: 5.
19. A PS4 variant polypeptide according to any preceding claim having an amino acid 9640 sequence which at least 75% identical to SEQ ID NO: 1 or SEQ ID NO: 5.
20. A PS4 variant polypeptide according to any of Claims 1 to 8, in which the parent polypeptide is a non-maltogenic exoamylase from Pseudomonas stutzeri having a sequence shown as SEQ ID NO: 7 or SEQ ID NO: 11.
21. A PS4 variant polypeptide according to according to any of Claims 1 to 8 or 11 9645 having an amino acid sequence which at least 75% identical to SEQ ID NO: 7 or SEQ ID
NO: 11.
22. A PS4 variant polypeptide according to any preceding claim, which comprises a sequence as set out in the description, claims or figures.
23. A PS4 variant polypeptide according to any preceding claim, which comprises a 9650 sequence selected from the group consisting of: SEQ ID NO: 21 (pSac-pMS382), SEQ ID
NO: 23 (pSac-pMS382R) and SEQ ID NO: 25 (pSac-pMS382H).
24. A PS4 variant polypeptide according to any preceding claim, in which the PS4 variant polypeptide has a higher thermostability compared to the parent polypeptide or a wild type polypeptide when tested under the same conditions.
9655 25. A PS4 variant polypeptide according to any preceding claim, in which the half life (tl/2), preferably at 60 degrees C, is increased by 15% or more, preferably 50% or more, most preferably 100% or more, relative to the parent polypeptide or the wild type polypeptide.
26. A PS4 variant polypeptide according to any preceding claim, in which a food 9660 product treated with a the PS4 variant polypeptide has any one or more, preferably all of the following properties: (a) lower firmness; (b) higher resilience; (c) higher cohesiveness; (d) lower crumbliness; and (e) higher foldability compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
27. A PS4 variant polypeptide according to Claim 26, in which the resilience, 9665 cohesiveness or foldability of the food product is independently increased by 15% or more, preferably 50% or more, most preferably 100% or more, relative to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
28. A PS4 variant polypeptide according to Claim 26 or 27, in which each of resilience cohesiveness and foldability of a food product treated with a the PS4 variant polypeptide 9670 is increased compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
29. A PS4 variant polypeptide according to Claim 26, in which the firmness or the crumbliness of the food product is independently decreased by 15% or more, preferably 50% or more, most preferably 100% or more, relative to a food product which has been
9675 treated with a parent polypeptide or a wild type polypeptide.
30. A PS4 variant polypeptide according to Claim 26 or 29, in which each of the firmness and crumblines of a food product treated with a the PS4 variant polypeptide is decreased compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
9680 31. A polypeptide comprising a fragment of at least 20 residues of a PS4 variant polypeptide according to any preceding claim, in which the polypeptide has non- maltogenic exoamylase activity.
32. A polypeptide derivable from a PS4 variant polypeptide according to any preceding claim by mutation at one or more residues of the PS4 variant polypeptide
9685 sequence, in which the polypeptide has a higher thermostability or a higher exo- specificity, or both, compared to the parent polypeptide of the PS4 variant polypeptide or a wild type polypeptide, or in which a food product treated with a the PS4 variant polypeptide has any one or more, preferably all of the following properties: (a) lower firmness; (b) higher resilience; (c) higher cohesiveness; (d) lower crumbliness; or (e)
9690 higher foldability as compared to a food product which has been treated with a parent polypeptide or a wild type polypeptide.
33 Use of a PS4 variant polypeptide as set out in any preceding claim as a food or feed additive.
34. A process for treating a starch comprising contacting the starch with a polypeptide 9695 as set out in any of Claims 1 to 32 and allowing the polypeptide to generate from the starch one or more linear products.
35. Use of a polypeptide as set out in any of Claims 1 to 32 in preparing a food or feed product.
36. A process of preparing a food or feed product comprising admixing a polypeptide 9700 as set out in any of Claims 1 to 32 with a food or feed ingredient.
37. Use according to Claim 35, or a process according to Claim 36, in which the food product comprises a dough or a dough product, preferably a processed dough product.
38. A use or process according to any of Claims 35 to 37, in which the food product is a bakery product.
9705 39. A process for making a bakery product comprising: (a) providing a starch medium; (b) adding to the starch medium a polypeptide as set out in any of Claims 1 to 32; and (c) applying heat to the starch medium during or after step (b) to produce a bakery product.
40. A food product, feed product, dough product or a bakery product obtained by a process according to any of Claims 35 to 39.
9710 41. An improver composition for a dough, in which the improver composition comprises a polypeptide as set out in any of Claims 1 to 32, and at least one further dough ingredient or dough additive.
42. A composition comprising a flour and a polypeptide as set out in any of Claims 1 to 32.
9715 43. Use of a PS4 variant polypeptide as set out in any of Claims 1 to 42, in a dough product to retard or reduce staling, preferably detrimental retrogradation, of the dough product.
44. Use of a PS4 variant polypeptide as set out in any of Claims 1 to 42, in a dough product to improve any one or more of firmness, resilience, cohesiveness, crumbliness or
9720 foldability of the dough product.
45. A combination of a PS4 variant polypeptide as set out in any preceding claim, together with any one or more of the following:
(a) maltogenic alpha-amylase also called glucan 1 ,4-α-maltohydrolase (EC 3.2.1.133) from Bacillus stearothermophilus, or a variant, homologue, or mutants
9725 thereof which have maltogenic alpha-amylase activity;
(b) a bakery xylanase (EC 3.2.1.8) from e.g. Bacillus sp., Aspergillus sp., Thermomyces sp. or Trichoderma sp.;
(c) α-amylase (EC 3.2.1.1) from Bacillus amyloliqufaciens or a variant, homologue, or mutants thereof which have alpha-amylase activity; and 9730 (d) a lipase such as glyco lipase from Fusarium heterosporum.
46. Use of a combination according to Claim 45 for an application according to any preceding claim.
47. A food or feed product produced by treatment with a combination according to Claim 31.
9735 48. A nucleic acid capable of encoding a polypeptide according to any of Claims 1 to 32.
49. A nucleic acid according to Claim 48 having a nucleic acid sequence which at least 75% identical to SEQ ID NO: 6 or SEQ ID NO: 12.
50. A nucleic acid comprising a fragment of at least 60 residues of a nucleic acid 9740 according to Claim 48 or 49 which is capable of encoding a polypeptide having non- maltogenic exoamylase activity.
51. A nucleic acid sequence derivable from a parent sequence, the parent sequence capable of encoding a non-maltogenic exoamylase, which nucleic acid sequence comprises a substitution at one or more residues such that the nucleic acid encodes a lysine
9745 (R) or arginine (K) residue at position 307, optionally together with one or more further mutation(s) such that the nucleic acid encodes one or more residues selected from the group consisting of: 33Y, 34N5 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E, 229P, 309P, 334P with reference to the position numbering of a Pseudomonαs sαcchαrophiliα exoamylase sequence shown as SEQ ID NO: 1.
9750 52. A PS4 nucleic acid sequence according to any of Claims 48 to 52, which is derived from a parent sequence encoding a non-maltogenic exoamylase by substitution of one or more nucleotide residues.
53. A nucleic acid sequence according to any of Claims 48 to 52, selected from the group consisting of: SEQ ID NO: 22 (pSac-pMS382), SEQ ID NO: 24 (pSac-pMS382R)
9755 and SEQ ID NO: 26 (pSac-pMS382H).
54. A plasmid comprising a PS4 nucleic acid according to any of Claims 48 to 53.
55. An expression vector comprising a PS4 nucleic acid according to any of Claims 48 to 54, or capable of expressing a polypeptide according to any of Claims 1 to 32.
56. A host cell comprising, preferably transformed with, a plasmid according to Claim 9760 54 or an expression vector according to Claim 55.
57. A cell capable of expressing a polypeptide according to any of Claims 1 to 32.
58. A host cell according to Claim 56, or a cell according to Claim 57, which is a bacterial, fungal or yeast cell.
59. A method of expressing a PS4 variant polypeptide, the method comprising 9765 obtaining a host cell or a cell according to Claim 56, 57 or 58 and expressing the polypeptide from the cell or host cell, and optionally purifying the polypeptide.
60. A method of altering the sequence of a polypeptide, preferably a non-maltogenic exoamylase, by introducing an amino acid substitution at position 70 to a basic or positively charged residue, optionally together with one or more further mutation(s)
9770 selected from the group consisting of: 33Y, 34N, 121F, 134R, 141P, 146G, 157L, 161 A, 178F, 179T, 223E, 229P, 272H, 303G, 309P, 334P (with reference to the position numbering of a Pseudomonas saccharophilia exoamylase sequence shown as SEQ ID NO: 1), into a parent polypeptide having non-maltogenic exoamylase activity.
61. A method according to Claim 60, in which the basic or positively charged residue 9775 comprises lysine (K), arginine (R) or histidine (H).
62. A method according to Claim 60 or 61, in which the sequence of the non- maltogenic exoamylase is altered by altering the sequence of a nucleic acid which encodes the non-maltogenic exoamylase.
63. A method of producing a PS4 polypeptide variant, the method comprising 9780 introducing an amino acid substitution into a parent polypeptide having non-maltogenic exoamylase activity, the amino acid substitution being selected from the group consisting of: 33Y, 34N, 70K/R7H, 121F, 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E5 229P, 272H, 303G, 309P, 334P with reference to the position numbering of a. Pseudomonas saccharophilia exoamylase sequence shown as SEQ ID NO: 1.
9785 64. A method according to Claim 62 or 63, in which the sequence of a nucleic acid encoding the parent polypeptide is altered to introduce the amino acid substitution.
65. A method of altering the sequence of a nucleic acid encoding a non-maltogenic exoamylase, the method comprising introducing into the sequence a codon which encodes an amino acid residue selected from the group consisting of: 33Y, 34N, 70K/R/H, 121F, 9790 134R, 141P, 146G, 157L, 161A, 178F, 179T, 223E5 229P, 272H, 303G, 309P, 334P, with reference to the position numbering of a Pseudomonαs sαcchαrophiliα exoamylase sequence shown as SEQ ID NO: 1.
66. A method of increasing the thermostability, or the exo-speciflcity, or both, of a polypeptide, the method comprising the steps as set out in any of Claims 58 to 65.
9795 67. A method according to any of Claims 58 to 66, in which the polypeptide is isolated or purified, or both.
68. A polypeptide obtainable by a method according to any of Claims 58 to 67.
69. A polypeptide obtained by a method according to any of Claims 58 to 68.
70. A PS4 variant polypeptide, use, process, food product, feed product, dough 9800 product, bakery product, improver composition, composition, nucleic acid, vector or host cell substantially as hereinbefore described with reference to and as shown in the accompanying drawings.
PCT/IB2007/002056 2006-06-19 2007-06-19 Polypeptide WO2007148224A2 (en)

Priority Applications (15)

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KR1020147033965A KR20150004920A (en) 2006-06-19 2007-06-19 Polypeptide
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RU2009101321/10A RU2539776C2 (en) 2006-06-19 2007-06-19 Polypeptide
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MX2012006758A MX345513B (en) 2006-06-19 2007-06-19 Polypeptide.
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WO2007148224A8 (en) 2009-05-14
ZA200810738B (en) 2018-11-28
AU2007262442B2 (en) 2012-11-01
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WO2007148224A3 (en) 2008-05-29
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US20090202675A1 (en) 2009-08-13
ES2644745T3 (en) 2017-11-30

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