WO2000055309A1 - Nouvelles lyases de pectate - Google Patents

Nouvelles lyases de pectate Download PDF

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Publication number
WO2000055309A1
WO2000055309A1 PCT/DK2000/000111 DK0000111W WO0055309A1 WO 2000055309 A1 WO2000055309 A1 WO 2000055309A1 DK 0000111 W DK0000111 W DK 0000111W WO 0055309 A1 WO0055309 A1 WO 0055309A1
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enzyme
pectate lyase
polypeptide
dna
seq
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PCT/DK2000/000111
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English (en)
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Mads Eskelund BJØRNVAD
Jens Tønne ANDERSEN
Kirk Schnorr
Martin Schülein
Lars Kongsbak
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Novozymes A/S
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Priority to AU32730/00A priority Critical patent/AU3273000A/en
Publication of WO2000055309A1 publication Critical patent/WO2000055309A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y402/00—Carbon-oxygen lyases (4.2)
    • C12Y402/02—Carbon-oxygen lyases (4.2) acting on polysaccharides (4.2.2)
    • C12Y402/02002—Pectate lyase (4.2.2.2)
    • 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
    • A23K20/10—Organic substances
    • A23K20/189—Enzymes
    • C—CHEMISTRY; METALLURGY
    • C11—ANIMAL OR VEGETABLE OILS, FATS, FATTY SUBSTANCES OR WAXES; FATTY ACIDS THEREFROM; DETERGENTS; CANDLES
    • C11D—DETERGENT COMPOSITIONS; USE OF SINGLE SUBSTANCES AS DETERGENTS; SOAP OR SOAP-MAKING; RESIN SOAPS; RECOVERY OF GLYCEROL
    • C11D3/00—Other compounding ingredients of detergent compositions covered in group C11D1/00
    • C11D3/16—Organic compounds
    • C11D3/38—Products with no well-defined composition, e.g. natural products
    • C11D3/386—Preparations containing enzymes, e.g. protease or amylase
    • C11D3/38636—Preparations containing enzymes, e.g. protease or amylase containing enzymes other than protease, amylase, lipase, cellulase, oxidase or reductase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12G—WINE; PREPARATION THEREOF; ALCOHOLIC BEVERAGES; PREPARATION OF ALCOHOLIC BEVERAGES NOT PROVIDED FOR IN SUBCLASSES C12C OR C12H
    • C12G1/00—Preparation of wine or sparkling wine
    • C12G1/02—Preparation of must from grapes; Must treatment and fermentation
    • 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
    • C12N9/88—Lyases (4.)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide

Definitions

  • the present invention relates to microbial pectate lyases, more specifically to a novel subclass of pectate lyases (EC 4.2.2.2), especially to a novel family of polysaccharide lyases exhibiting pectate lyase activity, ie enzymes which are capable of eliminative cleavage of pectate to give oligosaccharides with 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends; to a method of producing such enzymes; and to methods for using such enzymes in the textile, detergent and cellulose fiber processing industries.
  • Pectin polymers are important constituents of plant cell walls.
  • Pectin is a hetero-polysaccharide with a backbone composed of alternating homogalacturonan (smooth regions) and rhamnogalacturonan (hairy regions) .
  • the smooth regions are linear polymers of 1,4-linked alpha-D-galacturonic acid.
  • the galacturonic acid residues can be methyl-esterified on the carboxyl group to a varying degree, usually in a non-random fashion with blocks of polygalacturonic acid being completely methyl-esterified.
  • Pectinases can be classified according to their preferential substrate, highly methyl-esterified pectin or low methyl-esterified pectin and polygalacturonic acid (pectate) , and their reaction mechanism, beta-elimination or hydrolysis. Pectinases can be mainly endo-acting, cutting the polymer at random sites within the chain to give a mixture of oligomers, or they may be exo-acting, attacking from one end of the polymer and producing monomers or dimers .
  • pectinase activities acting on the smooth regions of pectin are included in the classification of enzymes provided by the Enzyme Nomenclature (1992) such as pectate lyase (EC 4.2.2.2), pectin lyase (EC 4.2.2.10), polygalacturonase (EC 3.2.1.15), exo- polygalacturonase (EC 3.2.1.67), exo-polygalacturonate lyase (EC 4.2.2.9) and exo-poly-alpha-galacturonosidase (EC 3.2.1.82).
  • pectate lyase EC 4.2.2.2
  • pectin lyase EC 4.2.2.10
  • polygalacturonase EC 3.2.1.15
  • exo- polygalacturonase EC 3.2.1.67
  • exo-polygalacturonate lyase EC 4.2.2.9
  • Pectate lyases have been cloned from different bacterial genera such as Erwinia, Pseudomonas , Klebsiella and Xanthomonas . Also from Bacillus subtilis (Nasser et al . (1993) FEBS 335:319- 326) and Bacillus sp. YA-14 (Kim et al . (1994) Biosci. Biotech. Biochem. 58:947-949) cloning of a pectate lyase has been described. Purification of pectate lyases with maximum activity in the pH range of 8-10 produced by Bacillus pumilus (Dave and Vaughn (1971) J. Bacteriol.
  • pectate lyases All the pectate lyases described require divalent cations for maximum activity, calcium ions being the most stimulatory.
  • Polysaccharide lyases are classified into families according to their three-dimensional structure or folding; conventionally the Clustal method is used the for family determination. Based on amino acid sequence alignment and the Clustal W method, a polypeptide or protein can be classified into a specific polysaccharide lyase family, ie either a known family or a novel and hitherto unknown family (The Sanger Centre: Protein Families Database of alignments and HMMs; www. sanger.ac.uk) . At present known pectate lyases belong to polysaccharide lyase family 1, family 2 and family 9 (ExPASy - molecular biology WWW server of the Swiss Institute of Bioinformatics (SIB) ) .
  • WO 98/45393 discloses detergent compositions containing protopectinase with remarkable detergency against muddy soilings.
  • pectinase producing microorganisms exhibit a broad range of pectin degrading or modifying enzymes.
  • the microorganisms also produce cellulases and/or hemicellulases .
  • Complex multi-component enzyme preparations from such microorganisms may be difficult to optimise for use in various applications, a.o. since they even may contain enzymes with detrimental effect.
  • the inventors have now found and identified a novel enzyme having substantial pectate lyase activity which enzyme has excellent performance in various industrial processes. Further, the inventors have succeeded in identifying a DNA sequence encoding the enzyme. It was found that the novel pectate lyase enzyme is a member of a hitherto unknown class of pectate lyases, ie the present enzyme belongs to a hitherto unknown family of polysaccharide lyases. Based on the present disclosure, especially the materials, methods and sequence listings provided herein, it is contemplated that the skilled person can find and identify other members of this novel polysaccharide lyase family, preferably pectate lyases of microbial origin, especially bacterial or fungal pectate lyases.
  • this invention relates to a pectate lyase enzyme belonging to a polysaccharide family other that family 1,2 and 9, which enzyme is selected from one of a) polypeptide encoded by the DNA sequence of positions 88-1033 of SEQ ID NO:l; b) a polypeptide produced by culturing a cell comprising the sequence of SEQ ID NO : 1 under conditions wherein the DNA sequence is expressed; c) a pectate lyase enzyme comprising an amino acid sequence of at least 35% identity to positions 30-344 of SEQ ID NO: 2 when identity is determined by GAP provided in the GCG program package using a GAP creation penalty of 3.0 and GAP extension penalty of 0.1; or d) a polypeptide encoded by the pectate lyase encoding part of the DNA sequence obtainable from the plasmid in Escherichia coli DSM 12712.
  • the present invention relates to isolated pectate lyase enzyme, in which the enzyme is (i) free from homologous impurities, and (ii) produced by culturing a cell comprising the DNA sequence of positions 88-1033 of SEQ ID NO:l, wherein the enzyme is produced and isolated.
  • the invention relates to an isolated polynucleotide molecule encoding a polypeptide having pectate WO 00/55309 PCT/DKOO/00111 .
  • lyase activity selected from the group consisting of (a) polynucleotide molecules comprising a nucleotide sequence as shown in SEQ ID NO:l from nucleotide 88 to nucleotide 1033; (b) species homologs of (a) ; (c) polynucleotide molecules encoding a polypeptide being at least 35% identical to the amino acid sequence of SEQ ID NO:2 from amino acid residue 30 to amino acid residue 344; (d) molecules complementary to (a), (b) , or (c) ; (e) degenerate nucleotide sequences of (a) or (b) ; and (f) polynucleotide molecules encoding a polypeptide having pectate lyase activity which polynucleotide molecule hybridises to a denatured double-stranded DNA probe under medium stringency conditions, wherein the probe is selected from the group consisting of DNA probes comprising the sequence shown in positions 88-1033
  • the present invention provides an expression vector comprising the following operably linked elements: a transcription promoter; a DNA segment selected from the group consisting of a) polynucleotide molecules encoding a polypeptide having pectate lyase activity comprising a nucleotide sequence as shown in SEQ ID NO:l from nucleotide 88 to nucleotide 1033, b) polynucleotide molecules encoding a polypeptide having pectate lyase activity that is at least 35% identical to the amino acid sequence of SEQ ID NO: 2 from amino acid residue 30 to amino acid residue 344, and (c) degenerate nucleotide sequences of (a) or (b) ; and a transcription terminator.
  • a transcription promoter a DNA segment selected from the group consisting of a) polynucleotide molecules encoding a polypeptide having pectate lyase activity comprising a nucleotide sequence as shown in SEQ ID NO
  • an enzyme composition or preparation comprising a purified pectate lyase according to the invention optionally in combination with other polypeptides having enzymatic activity.
  • novel pectate lyase enzymes of the present invention are useful for the treatment of cellulosic material, especially cellulose-containing fiber, yarn, woven or non-woven fabric, treatment of mechanical paper-making pulps or recycled waste paper, and for retting of fibres.
  • the treatment can be carried out during the processing of cellulosic material into a material ready for garment manufacture or fabric manufacture, e.g. in the desizing or scouring step; or during industrial or household laundering of such fabric or garment.
  • the present invention relates to a detergent composition comprising an enzyme having substantial pectate lyase activity; and to use of the enzyme of the invention for the treatment of cellulose-containing fibers, yarn, woven or non-woven fabric.
  • the pectate lyases of the invention are very effective for use in an enzymatic scouring process in the preparation of cellulosic material e.g. for proper response in subsequent dyeing operations. Further, it is contemplated that detergent compositions comprising the novel pectate lyases are capable of removing or bleaching certain soils or stains present on laundry, especially soils and spots resulting from galactan or arabinogalactan containing food, plants, and the like. It is also contemplated that treatment with detergent compositions comprising the novel enzyme can prevent binding of certain soils to the cellulosic material.
  • the enzymes of the invention are also useful as ingredients in hard surface cleaning compositions having the effect of removing or assisting in removing certain soils or stains from hard surfaces in need of cleaning.
  • the plasmid pSJ1678 comprising the polynucleotide molecule (the DNA sequence) encoding a pectate lyase of the present invention has been transformed into a strain of the Escherichia coli which was deposited by the inventors according to the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure at the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg lb, D-38124 Braunschweig, Federal Republic of Germany, on 4 March 1999 under the deposition number DSM 12712.
  • ortholog (or "species homolog” ) denotes a polypeptide or protein obtained from one species that has homology to an analogous polypeptide or protein from a different species .
  • paralog denotes a polypeptide or protein obtained from a given species that has homology to a distinct polypeptide or protein from that same species.
  • expression vector denotes a DNA molecule, linear or circular, that comprises a segment encoding a polypeptide of interest operably linked to additional segments that provide for its transcription. Such additional segments may include promoter and terminator sequences, and may optionally include one or more origins of replication, one or more selectable markers, an enhancer, a polyadenylation signal, and the like.
  • Expression vectors are generally derived from plasmid or viral DNA, or may contain elements of both.
  • the expression vector of the invention may be any expression vector that is conveniently subjected to recombinant DNA procedures, and the choice of vector will often depend on the host cell into which the vector it is to be introduced.
  • the vector may be an autonomously replicating vector, i.e. a vector which exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g. a plasmid.
  • the vector may be one which, when introduced into a host cell, is integrated into the host cell genome and replicated together with the chromosome (s) into which it has been integrated.
  • recombinant expressed or “recombinantly expressed” used herein in connection with expression of a polypeptide or protein is defined according to the standard definition in the art. Recombinantly expression of a protein is generally performed by using an expression vector as described immediately above .
  • isolated when applied to a polynucleotide molecule, denotes that the polynucleotide has been removed from its natural genetic milieu and is thus free of other extraneous or unwanted coding sequences, and is in a form suitable for use within genetically engineered protein production systems.
  • isolated molecules are those that are separated from their natural environment and include cDNA and genomic clones.
  • Isolated DNA molecules of the present invention are free of other genes with which they are ordinarily associated, but may include naturally occurring 5 1 and 3' untranslated regions such as promoters and terminators. The identification of associated regions will be evident to one of ordinary skill in the art (see for example, Dynan and Tijan, Nature 3_l£:774-78, 1985).
  • the term "an isolated polynucleotide” may alternatively be termed "a cloned polynucleotide”.
  • the term "isolated” indicates that the protein is found in a condition other than its native environment.
  • the isolated protein is substantially free of other proteins, particularly other homologous proteins (i.e. "homologous impurities” (see below) ) .
  • homologous impurities i.e. "homologous impurities” (see below)
  • isolated protein/polypeptide may alternatively be termed “purified protein/polypeptide” .
  • homologous impurities means any impurity (e.g. another polypeptide than the polypeptide of the invention) which originate from the homologous cell where the polypeptide of the invention is originally obtained from.
  • the term "obtained from” as used herein in connection with a specific microbial source means that the polynucleotide and/or polypeptide produced by the specific source, or by a cell in which a gene from the source have been inserted.
  • endogeneous to means that a polypeptide is 8 produced by the specific source due to the presence in the source of a native gene, ie a gene which has not been recombinantly inserted into a cell of the source but is naturally occurring.
  • operably linked when referring to DNA segments, denotes that the segments are arranged so that they function in concert for their intended purposes, e.g.
  • polynucleotide denotes a single- or double- stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5' to the 3' end.
  • Polynucleotides include RNA and DNA, and may be isolated from natural sources, synthesized in vi tro, or prepared from a combination of natural and synthetic molecules.
  • complements of polynucleotide molecules denotes polynucleotide molecules having a complementary base sequence and reverse orientation as compared to a reference sequence. For example, the sequence 5 1 ATGCACGGG 3' is complementary to 5 1 CCCGTGCAT 3 ' .
  • degenerate nucleotide sequence denotes a sequence of nucleotides that includes one or more degenerate codons (as compared to a reference polynucleotide molecule that encodes a polypeptide) .
  • Degenerate codons contain different triplets of nucleotides, but encode the same amino acid residue (i.e., GAU and GAC triplets each encode Asp) .
  • promoter denotes a portion of a gene containing DNA sequences that provide for the binding of RNA polymerase and initiation of transcription. Promoter sequences are commonly, but not always, found in the 5' non-coding regions of genes.
  • secretory signal sequence denotes a DNA sequence that encodes a polypeptide (a "secretory peptide") that, as a component of a larger polypeptide, directs the larger polypeptide through a secretory pathway of a cell in which it is synthesized.
  • secretory peptide a polypeptide that, as a component of a larger polypeptide, directs the larger polypeptide through a secretory pathway of a cell in which it is synthesized.
  • the larger peptide is commonly cleaved to remove the secretory peptide during transit through the secretory pathway.
  • enzyme core is to be understood as being the part of a single- or multi-domain structure polypeptide exhibiting enzymatic activity which part is a single domain part containing the catalytically active domain. Accordingly, the enzyme core does not contain other domains than the catalytic domain.
  • pectin denotes pectate, polygalacturonic acid, and pectin which may be esterified to a higher or lower degree .
  • pectinase denotes a pectinase enzyme defined according to the art where pectinases are a group of enzymes that cleave glycosidic linkages of pectic substances mainly poly (1, 4-alpha-D-galacturonide and its derivatives (see reference Sakai et al . , Pectin, pectinase and protopectinase : production, properties and applications, pp 213-294 in: Advances in Applied Microbiology vol:39,1993) .
  • a pectinase of the invention is a pectinase enzyme which catalyzes the random cleavage of alpha-1,4- glycosidic linkages in pectic acid also called polygalacturonic acid by transelimination such as the enzyme class polygalacturonate lyase (EC 4.2.2.2) (PGL) also known as poly (1, 4-alpha-D-galacturonide) lyase also known as pectate lyase.
  • PGL enzyme class polygalacturonate lyase
  • poly (1, 4-alpha-D-galacturonide) lyase also known as pectate lyase.
  • the disclosed sequence information herein relating to a polynucleotide sequence encoding a pectate lyase of the invention can be used as a tool to identify other homologous pectate lyases, preferably pectate lyases belonging to the same novel family of polysaccharide lyases as the pectate lyase represented by the amino acid sequence of the appended SEQ ID NO:2.
  • polymerase chain reaction PCR
  • an isolated polynucleotide of the invention will hybridize to similar sized regions of SEQ ID No. 1 or a sequence complementary thereto, under at least medium stringency conditions.
  • polynucleotides of the invention will hybridize to a denatured double-stranded DNA probe comprising either the full sequence (encoding for the mature part of the polypeptide) shown in positions 88-1033 of SEQ ID NO:l, or any probe comprising a subsequence of SEQ ID N0:1, or any probe comprising a subsequence of SEQ ID NO:l having a length of at least about 100 base pairs under at least medium stringency conditions, but preferably at high stringency conditions as described in detail below.
  • Suitable experimental conditions for determining hybridization at medium, or high stringency between a nucleotide probe and a homologous DNA or RNA sequence involves pre-soaking of the filter containing the DNA fragments or RNA to hybridize in 5 x SSC (Sodium chloride/Sodium citrate, Sambrook et al . 1989) for 10 min, and prehybridization of the filter in a solution of 5 x SSC, 5 x Denhardt ' s solution (Sambrook et al . 1989), 0.5 % SDS and 100 ⁇ g/ml of denatured sonicated salmon sperm DNA (Sambrook et al .
  • 5 x SSC Sodium chloride/Sodium citrate, Sambrook et al . 1989
  • the isolated polynucleotides of the present invention include DNA and RNA. Methods for isolating DNA and RNA are well known in the art. DNA and RNA encoding genes of interest can be cloned in Gene Banks or DNA libraries by means of methods known in the art . Polynucleotides encoding polypeptides having pectate lyase activity of the invention are then identified and isolated by, for example, hybridization or PCR.
  • the present invention further provides counterpart polypeptides and polynucleotides from different bacterial strains (orthologs or paralogs) .
  • polypeptides and polynucleotides from different bacterial strains (orthologs or paralogs) .
  • pectate lyase polypeptides from gram-positive alkalophilic strains, including species of Bacillus .
  • Species homologues of a polypeptides pectate lyase activity of the invention can be cloned using information and compositions provided by the present invention in combination with conventional cloning techniques.
  • DNA can be cloned using chromosomal DNA obtained from a cell type that expresses the protein. Suitable sources of DNA can be identified by probing Northern blots with probes designed from the sequences disclosed herein. A library is then prepared from chromosomal DNA of a positive cell line.
  • a DNA encoding an polypeptide having pectate lyase activity of the invention can then be isolated by a variety of methods, such as by probing with a complete or partial DNA or with one or more sets of degenerate probes based on the disclosed sequences .
  • a DNA can also be cloned using the polymerase chain reaction, or PCR (Mullis, U.S. Patent 4,683,202), using primers designed from the sequences disclosed herein.
  • the DNA library can be used to transform or transfect host cells, and expression of the DNA of interest can be detected with an antibody (mono-clonal or polyclonal) raised against the pectate lyase cloned from a Bacillus species which is expressed and purified as described in Materials and Methods and the Examples, or by an activity test relating to a polypeptide having pectate lyase activity. Similar techniques can also be applied to the isolation of genomic clones.
  • the polypeptide encoding part of the DNA sequence cloned into plasmid pSJ1678 present in Escherichia coli DSM 12712 and/or an analogue DNA sequence of the invention may be cloned from a Bacillus strain producing the pectate lyase enzyme, or another or related organism as described herein.
  • the analogous sequence may be constructed on the basis of the DNA sequence obtainable from the plasmid present in Escherichia coli DSM 12712, e.g be a sub-sequence thereof, and/or by introduction of nucleotide substitutions which do not give rise to another amino acid sequence of the pectat lyase encoded by the DNA sequence, but which corresponds to the codon usage of the host organism intended for production of the enzyme, or by introduction of nucleotide substitutions which may give rise to a different amino acid sequence (i.e. a variant of the pectate lyase of the invention) .
  • Cloning of is performed by standard procedures known in the art such as by, preparing a genomic library from a Bacillus strain,-plating such a library on suitable substrate plates; identifying a clone comprising a polynucleotide sequence of the invention by standard hybridization techniques using a probe based on SEQ ID No 1; or by identifying a clone from e.g. a Bacillus strain by an Inverse PCR strategy using primers based on sequence information from SEQ ID No 1.
  • M.J. MCPherson et al ("PCR A practical approach" Information Press Ltd, Oxford England) for further details relating to Inverse PCR.
  • SEQ ID No 1 and 2 Based on the sequence information disclosed herein (SEQ ID No 1 and 2) is it routine work for a person skilled in the art to isolate homologous polynucleotide sequences encoding homologous pectinases of the invention by a similar strategy using genomic libraries from related microbial organisms, in particular from genomic libraries from other strains of the genus Bacillus such as Bacillus subtilis .
  • the DNA encoding the pectate lyase of the invention may, in accordance with well-known procedures, conveniently be cloned from a suitable source, such as any of the below mentioned organisms, by use of synthetic oligonucleotide probes prepared on the basis of the DNA sequence obtainable from the plasmid present in Escherichia coli DSM 12712.
  • the polynucleotide molecule of the invention may be isolated from Escherichia coli , DSM 12712, in which the plasmid obtained by cloning such as described above is deposited. Also, the present invention relates to an isolated substantially pure biological culture of the strain Escherichia coli , DSM 12712.
  • POLYPEPTIDES The sequence of amino acids no. 30-344 of SEQ ID No 2 is a mature pectate lyase sequence; positions 1-29 is a propeptide.
  • the present invention also provides pectate lyase polypeptides that are substantially homologous to the mature polypeptide of SEQ ID NO: 2 and its species homologs (paralogs or orthologs.
  • substantially homologous is used herein to denote polypeptides having at least 35%, preferably at least 40%, preferably at least 45%, preferably at least 50%, preferably at least 60%, more preferably at least 70%, more preferably at least 85%, and even more preferably at least 90%, sequence identity to the sequence shown in SEQ ID NO:2 or its orthologs or paralogs.
  • polypeptides will more preferably be at least 95% identical, and most preferably 98% or more identical to the sequence shown in SEQ ID NO: 2 or its orthologs or paralogs.
  • Percent sequence identity is determined by conventional methods, by means of computer programs known in the art such as GAP provided in the GCG program package (Program Manual for the Wisconsin Package, Version 8, August 1994, Genetics Computer Group, 575 Science Drive, Madison, Wisconsin, USA 53711) as disclosed in Needleman, S.B. and Wunsch, CD., (1970), Journal of Molecular Biology, 48, 443-453, which is hereby incorporated by reference in its entirety.
  • GAP is used with the following settings for polypeptide sequence comparison: GAP creation penalty of 3.0 and GAP extension penalty of 0.1.
  • Sequence identity of polynucleotide molecules is determined by similar methods using GAP with the following settings for DNA sequence comparison: GAP creation penalty of 5.0 and GAP extension penalty of 0.3.
  • Substantially homologous proteins and polypeptides are characterized as having one or more amino acid substitutions, deletions or additions. These changes are preferably of a minor nature, that is conservative amino acid substitutions (see Table 2) and other substitutions that do not significantly affect the folding or activity of the protein or polypeptide; small deletions, typically of one to about 30 amino acids; and small amino- or carboxyl-terminal extensions, such as an amino- terminal methionine residue, a small linker peptide of up to about 20-25 residues, or a small extension that facilitates purification (an affinity tag) , such as a poly-histidine tract, protein A (Nilsson et al . , EMBQ J.
  • non-standard amino acids such as 4-hydroxyproline, 6 -N-methyl lysine, 2- aminoisobutyric acid, isovaline and a-methyl serine
  • a limited number of non-conservative amino acids, amino acids that are not encoded by the genetic code, and unnatural amino acids may be substituted for amino acid residues.
  • "Unnatural amino acids” have been modified after protein synthesis, and/or have a chemical structure in their side chain (s) different from that of the standard amino acids.
  • Unnatural amino acids can be chemically synthesized, or preferably, are commercially available, and include pipecolic acid, thiazolidine carboxylic acid, dehydroproline, 3- and 4- methylproline, and 3 , 3-dimethylproline .
  • Essential amino acids in the pectate lyase polypeptides of the present invention can be identified according to procedures known in the art, such as site-directed mutagenesis or alanine- scanning mutagenesis (Cunningham and Wells, Sc.i en p 244 : 1081- 1085, 1989). In the latter technique, single alanine mutations are introduced at every residue in the molecule, and the resultant mutant molecules are tested for biological activity (i.e pectate lyase activity) to identify amino acid residues that are critical to the activity of the molecule. See also, Hilton et al . , J. Biol . Ch m . 221: 4699-4708 , 1996.
  • the active site of the enzyme or other biological interaction can also be determined by physical analysis of structure, as determined by such techniques as nuclear magnetic resonance, crystallography, electron diffraction or photoaffinity labeling, in conjunction with mutation of putative contact site amino acids. See, for example, de Vos et al . , Science 253. : 306-312, 1992; Smith et al . , .T. Mnl ⁇ Biol . 224.: 899-904 , 1992; Wlodaver et al . , FEBS Let . 2 2. : 59-64 , 1992.
  • the identities of essential amino acids can also be inferred from analysis of homologies with polypeptides which are related to a polypeptide according to the invention.
  • these authors disclose methods for simultaneously randomizing two or more positions in a polypeptide, or recombination/shuffling of different mutations (W095/17413, W095/22625) , followed by selecting for functional a polypeptide, and then sequencing the mutagenized polypeptides to determine the spectrum of allowable substitutions at each position.
  • Other methods that can be used include phage display (e.g., Lowman et al . , Biochem. 3.0.: 10832- 10837, 1991; Ladner et al . , U.S. Patent No. 5,223,409; Huse, WIPO Publication WO 92/06204) and region-directed mutagenesis (Derbyshire et al . , Gene 4.6:145, 1986; Ner et al . , DNA 2:127, 1988) .
  • Mutagenesis/shuffling methods as disclosed above can be combined with high-throughput , automated screening methods to detect activity of cloned, mutagenized polypeptides in host cells.
  • Mutagenized DNA molecules that encode active polypeptides can be recovered from the host cells and rapidly sequenced using modern equipment. These methods allow the rapid determination of the importance of individual amino acid residues or entire regions in a polypeptide of interest, and can be applied to polypeptides of unknown structure.
  • the present invention relates to pectate lyases having an amino acid sequence which is derived from the amino acid sequence SEQ ID No: 2 by deletion, replacement or addition of one or more amino acid residues (hereinafter referred to as mutation) provided that the pectate lyase activity is not deactivated.
  • mutation an amino acid sequence which is derived from the amino acid sequence SEQ ID No: 2 by deletion, replacement or addition of one or more amino acid residues (hereinafter referred to as mutation) provided that the pectate lyase activity is not deactivated.
  • the degree of mutation is not particularly limited. Preferably, 30% or higher homology exists between such mutation variants of the native or parent pectate lyase enzyme, calculated on the sequence SEQ ID No : 2.
  • the homology is at least 35%, preferably at least 40%, preferably at least 45%, preferably at least 50%, more preferably at least 55%, more preferably at least 60%, even more preferably at least 70%, even more preferably at least 75%, even more preferably at least 80%, even more preferably at least 85%, even more preferably at least 90%, even more preferably at least 95%, especially at least 98%.
  • amino acid residue Alanine (Ala) in position 30 may be substituted by WO 00/55309 PCT/DKOO/00111 -
  • Glutamic acid (Glu) ie A30E, and/or Glutamic acid in position 32 may be substituted by Alanine, ie E32A. These substitutions corresponds to the following changes in the coding gene, cf. SEQ ID NO:l: C89A and A95C, respectively.
  • the pectate lyase of the invention may, in addition to the enzyme core comprising the catalytically domain, also comprise a cellulose binding domain (CBD) , the cellulose binding domain and enzyme core (the catalytically active domain) of the enzyme being operably linked.
  • the cellulose binding domain (CBD) may exist as an integral part of the encoded enzyme, or a CBD from another origin may be introduced into the pectin degrading enzyme thus creating an enzyme hybrid.
  • the term "cellulose-binding domain” is intended to be understood as defined by Peter Tomme et al . "Cellulose-Binding Domains: Classification and Properties" in "Enzymatic Degradation of Insoluble Carbohydrates", John N. Saddler and Michael H.
  • CBDs are found in various enzymes such as cellulases, xylanases, mannanases, arabinofuranosidases, acetyl esterases and chitinases. CBDs have also been found in algae, e.g. the red alga Porphyra purpurea as a non-hydrolytic polysaccharide-binding protein, see Tomme et al . , op. ci t .
  • CBDs are from cellulases and xylanases, CBDs are found at the N and C termini of proteins or are internal .
  • Enzyme hybrids are known in the art, see e.g. WO 90/00609 and WO 95/16782, and may be prepared by transforming into a host cell a DNA construct comprising at least a fragment of DNA encoding the cellulose-binding domain ligated, with or without a linker, to a DNA sequence encoding the pectin degrading enzyme and growing the host cell to express the fused gene.
  • Enzyme hybrids may be described by the following formula: CBD - MR - X wherein CBD is the N-terminal or the C-terminal region of an amino acid sequence corresponding to at least the cellulose- binding domain; MR is the middle region (the linker) , and may be a bond, or a short linking group preferably of from about 2 to about 100 carbon atoms, more preferably of from 2 to 40 carbon WO 00/55309 PCT/DKOO/00111 -
  • the enzymes of the present invention have their maximum catalytic activity at a pH of at least 8, more preferably higher than 8.5, more preferably higher than 9, more preferably higher than 9.5, more preferably higher than 10, even more preferably higher than 10.5, especially higher than 11; and 10 preferably the maximum activity of the enzyme is obtained at a temperature of at least 50°C, more preferably of at least 55°C, especially of at least 60°C.
  • polypeptides of the present invention can be produced in genetically engineered host cells according to conventional techniques.
  • Suitable host cells are those cell types that can be transformed or transfected with exogenous DNA
  • Bacillus 20 and grown in culture include bacteria, fungal cells, and cultured higher eukaryotic cells.
  • Bacterial cells particularly cultured cells of gram-positive organisms, are preferred.
  • Gram- positive cells from the genus of Bacillus are especially preferred, such as Bacillus subtilis, Bacillus lentus, Bacillus
  • a DNA sequence encoding a pectate lyase of the present invention is operably linked to other genetic elements required for its expression, generally including a transcription promoter and terminator within an expression vector.
  • the vector will also commonly contain one or more selectable markers and one or more origins of replication, although those skilled in the art will recognize that within certain systems selectable markers may be provided on separate vectors, and replication of the exogenous DNA may be provided by integration into the host cell genome.
  • a secretory signal sequence also known as a leader sequence, prepro sequence or pre sequence
  • the secretory signal sequence may be that of the polypeptide, or may be derived from another secreted protein or synthesized de novo.
  • suitable secretory signal sequences are known in the art and reference is made to (Bacillus subtilis and Other Gram-Positive Bacteria, Sonensheim et al .
  • secretory signal sequences especially for secretion in a Bacillus host cell.
  • the secretory signal sequence is joined to the DNA sequence in the correct reading frame.
  • Secretory signal sequences are commonly positioned 5' to the DNA sequence encoding the polypeptide of interest, although certain signal sequences may be positioned elsewhere in the DNA sequence of interest (see, e.g., Welch et al . , U.S. Patent No. 5,037,743; Holland et al . , U.S. Patent No. 5,143,830).
  • Transformed or transfected host cells are cultured according to conventional procedures in a culture medium containing nutrients and other components required for the growth of the chosen host cells.
  • suitable media including defined media and complex media, are known in the art and generally include a carbon source, a nitrogen source, essential amino acids, vitamins and minerals. Media may also contain such components as growth factors or serum, as required.
  • the growth medium will generally select for cells containing the exogenously added DNA by, for example, drug selection or deficiency in an essential nutrient which is complemented by the selectable marker carried on the expression vector or co- transfected into the host cell .
  • the polypeptides of the present invention may also be produced by fermenting a wildtype strain belonging to the genus Bacillus and mutants and variants derived therefrom.
  • a mutant may be obtained by using conventional mutagenesis by subjecting the strain in question to treatment with a mutagen (eg NTG (n-methyl-N-nitro-N-nitrosoguanidine) ) or to ultraviolet radiation, eg as described in Manual of methods for General Bacteriology; ASM 1981, Chapter 13.
  • a mutagen eg NTG (n-methyl-N-nitro-N-nitrosoguanidine)
  • ultraviolet radiation eg as described in Manual of methods for General Bacteriology; ASM 1981, Chapter 13.
  • This mutagenesis is performed to stimulate mutation of the strains.
  • a screening for mutants giving higher pectinase yields aer possible using conventional plate assays or liquid assays.
  • the fermentation may be carried out by cultivation of the strain under aerobic conditions in a nutrient medium containing carbon and nitrogen sources together with other essential nutrients, the medium being composed in accordance with the principles of the known art.
  • the medium may be a complex rich medium or a minimal medium.
  • the nitrogen source may be of inorganic and/or organic nature. Suitable inorganic nitrogen sources are nitrates and ammonium salts. Among the organic nitrogen sources quite a number are used regularly in fermentations. Examples are soybean meal, casein, corn, corn steep liquor, yeast extract, urea and albumin.
  • Suitable carbon sources are carbohydrates or carbohydrate containing materials.
  • the nutrient medium contains pectate, polygalacturonic acid and/or pectin esterified to a higher or lower degree as carbon source and/or inducer of pectinase production.
  • the medium contains a pectin rich material such as soybean meal, apple pulp or citrus peel.
  • the cultivation is preferably conducted at alkaline pH values such as at least pH 8 or at least pH 9, which can be obtained by addition of suitable buffers such as sodium carbonate or mixtures of sodium carbonate and sodium bicarbonate after sterilisation of the growth medium. It is contemplated that fermentation of a wildtype strain or mutant in a suitable medium can result in a yield of at least 0.5 g of pectinase protein per litre of culture broth or even at least 1 g/1 or 2 g/1.
  • PROTEIN ISOLATION When the expressed recombinant polypeptide is secreted the polypeptide may be purified from the growth media. Preferably the expression host cells are removed from the media before purification of the polypeptide ( e . g. by centrifugation) .
  • the host cell When the expressed recombinant polypeptide is not secreted from the host cell, the host cell are preferably disrupted and the polypeptide released into an aqueous "extract" which is the first stage of such purification techniques.
  • the expression host cells are removed from the media before the cell disruption ( e. g. by centrifugation) .
  • the cell disruption may be performed by conventional techniques such as by lysozyme digestion or by forcing the cells through high pressure. See (Robert K. Scobes, Protein Purification, Second edition, Springer-Verlag) for further description of such cell disruption techniques.
  • the expressed recombinant polypeptides or chimeric polypeptides
  • it can be purified using fractionation and/or conventional purification methods and media.
  • Ammonium sulfate precipitation and acid or chaotrope extraction may be used for fractionation of samples.
  • Exemplary purification steps may include hydroxyapatite, size exclusion, FPLC and reverse-phase high performance liquid chromatography.
  • Suitable anion exchange media include derivatized dextrans, agarose, cellulose, polyacrylamide, specialty silicas, and the like. PEI, DEAE, QAE and Q derivatives are preferred, with DEAE Fast-Flow Sepharose (Pharmacia, Piscataway, NJ) being particularly preferred.
  • Exemplary chromatographic media include those media derivatized with phenyl , butyl, or octyl groups, such as Phenyl-Sepharose FF (Pharmacia) , Toyopearl butyl 650 (Toso Haas, Montgomeryville, PA) , Octyl-Sepharose (Pharmacia) and the like; or polyacrylic resins, such as Amberchrom CG 71 (Toso Haas) and the like.
  • Suitable solid supports include glass beads, silica-based resins, cellulosic resins, agarose beads, cross-linked agarose beads, polystyrene beads, cross-linked polyacrylamide resins and the like that are insoluble under the conditions in which they are to be used. These supports may be modified with reactive groups that allow attachment of proteins by amino groups, carboxyl groups, sulfhydryl groups, hydroxyl groups and/or carbohydrate moieties.
  • Examples of coupling chemistries include cyanogen bromide activation, N- hydroxysuccinimide activation, epoxide activation, sulfhydryl activation, hydrazide activation, and carboxyl and amino derivatives for carbodiimide coupling chemistries. These and other solid media are well known and widely used in the art, and are available from commercial suppliers.
  • Selection of a particular method is a matter of routine design and is determined in part by the properties of the chosen support. See, for example, Affinity Chromatography: Principles & ⁇ Methods, Pharmacia LKB Biotechnology, Uppsala, Sweden, 1988.
  • Polypeptides of the invention or fragments thereof may also be prepared through chemical synthesis.
  • Polypeptides of the invention may be monomers or multimers; glycosylated or non- glycosylated; pegylated or non-pegylated; and may or may not include an initial methionine amino acid residue.
  • the present invention also relates to a transgenic plant, plant part or plant cell which has been transformed with a DNA sequence encoding the pectin degrading enzyme of the invention so as to express and produce this enzyme in recoverable quantities.
  • the enzyme may be recovered from the plant or plant part.
  • the plant or plant part containing the recombinant enzyme may be used as such.
  • the transgenic plant can be dicotyledonous or monocotyledonous, for short a dicot or a monocot . Examples of monocot plants are grasses, such as meadow grass (blue grass, Poa) , forage grass such as festuca, lolium, temperate grass, such as Agrostis, and cereals, e.g. wheat, oats, rye, barley, rice, sorghum and maize (corn) .
  • dicot plants examples include sugar beet, solanaceous plants such as tobacco and potato, legumes, such as lupins, pea, bean and soybean, and cruciferous (family Brassicaceae) , such as cauliflower, oil seed rape and the closely related model organism Arabidopsis thaliana .
  • plant parts are stem, callus, leaves, root, fruits, seeds, and tubers.
  • plant tissues such as chloroplast, apoplast, mitochondria, vacuole, peroxisomes and cytoplasm are considered to be a plant part.
  • any plant cell, whatever the tissue origin, is considered to be a plant part.
  • transgenic plant or plant cell expressing the enzyme of the invention may be constructed in accordance with methods known in the art.
  • the plant or plant cell is constructed by incorporating one or more expression constructs encoding the enzyme of the invention into the plant host genome and propagating the resulting modified plant or plant cell into a transgenic plant or plant cell.
  • the expression construct is a DNA construct which comprises a gene encoding the enzyme of the invention in operable association with appropriate regulatory sequences required for expression of the gene in the plant or plant part of choice.
  • the expression construct may comprise a selectable marker useful for identifying host cells into which the expression construct has been integrated and DNA sequences necessary for introduction of the construct into the plant in question (the latter depends on the DNA introduction method to be used) .
  • regulatory sequences such as promoter and terminator sequences and optionally signal or transit sequences is determined, eg on the basis of when, where and how the enzyme is desired to be expressed.
  • the expression of the gene encoding the enzyme of the invention may be constitutive or inducible, or may be developmental, stage or tissue specific, and the gene product may be targeted to a specific tissue or plant part such as seeds or leaves.
  • Regulatory sequences are eg described by Tague et al, Plant, Phys . , 86, 506, 1988.
  • the 35S-CaMV promoter may be used (Franck et al . , 1980. Cell 21: 285-294).
  • Organ-specific promoters may eg be a promoter from storage sink tissues such as seeds, potato tubers, and fruits (Edwards & Coruzzi, 1990. Annu. Rev. Genet. 24: 275-303), or from metabolic sink tissues such as meristems (Ito et al . , 1994. Plant Mol . Biol . 24: 863-878), a seed specific promoter such as the glutelin, prolamin, globulin or albumin promoter from rice (Wu et al . , Plant and Cell Physiology Vol. 39, No. 8 pp .
  • the promoter may be a leaf specific promoter such as the rbcs promoter from rice or tomato (Kyozuka et al . , Plant Physiology Vol. 102, No. 3 pp. 991-1000 (1993), the chlorella virus adenine methyltransferase gene promoter (Mitra, A. and Higgins, DW, Plant Molecular Biology Vol. 26, No. 1 pp. 85-93 (1994), or the aldP gene promoter from rice (Kagaya et al . , Molecular and General Genetics Vol. 248, No. 6 pp. 668-674 (1995) , or a wound inducible promoter such as the potato pin2 promoter (Xu et al, Plant Molecular Biology Vol. 22, No. 4 pp. 573-588 (1993) .
  • a leaf specific promoter such as the rbcs promoter from rice or tomato (Kyozuka et al . , Plant Physiology Vol. 102, No
  • a promoter enhancer element may be used to achieve higher expression of the enzyme in the plant.
  • the promoter enhancer element may be an intron which is placed between the promoter and the nucleotide sequence encoding the enzyme.
  • Xu et al . op ci t disclose the use of the first intron of the rice actin 1 gene to enhance expression.
  • the selectable marker gene and any other parts of the expression construct may be chosen from those available in the art.
  • the DNA construct is incorporated into the plant genome according to conventional techniques known in the art, including Agrobacterium-mediated transformation, virus-mediated transformation, micro injection, particle bombardment, biolistic transformation, and electroporation (Gasser et al, Science, 244, 1293; Potrykus, Bio/Techn. 8, 535, 1990; Shimamoto et al, Nature, 338, 274, 1989) .
  • Agrobacterium tumefaciens mediated gene transfer is the method of choice for generating transgenic dicots (for review Hooykas & Schilperoort , 1992. Plant Mol . Biol . 19: 15-38), however it can also be used for transforming monocots, although other transformation methods are generally preferred for these plants.
  • the method of choice for generating transgenic monocots is particle bombardment (microscopic gold or tungsten particles coated with the transforming DNA) of embryonic calli or developing embryos (Christou, 1992. Plant J. 2: 275-281; Shimamoto, 1994. Curr. Opin. Biotechnol. 5: 158-162; Vasil et al . , 1992. Bio/Technology 10: 667-674) .
  • An alternative method for trans ormation of monocots is based on protoplast transformation as described by Omirulleh S, et al . , Plant Molecular biology Vol. 21, No. 3 pp. 415-428 (1993) . Following transformation, the transformants having incorporated the expression construct are selected and regenerated into whole plants according to methods well-known in the art .
  • the term "enzyme preparation” is intended to mean either be a conventional enzymatic fermentation product, possibly isolated and purified, from a single species of a microorganism, such preparation usually comprising a number of different enzymatic activities; or a mixture of monocomponent enzymes, preferably enzymes derived from bacterial or fungal species by using conventional recombinant techniques, which enzymes have been fermented and possibly isolated and purified separately and which may originate from different species, preferably fungal or bacterial species; or the fermentation product of a microorganism which acts as a host cell for expression of a recombinant pectate lyase, but which microorganism simultaneously produces other enzymes, e.g. pectin lyases, proteases, or cellulases, being naturally occurring fermentation products of the microorganism, i.e. the enzyme complex conventionally produced by the corresponding naturally occurring microorganism.
  • the pectate lyase preparation of the invention may further comprise one or more enzymes selected from the group consisting of proteases, cellulases (endo- ⁇ -1, 4-glucanases) , ⁇ -glucanases (endo- ⁇ -1, 3 (4) -glucanases) , lipases, cutinases, peroxidases, laccases, amylases, glucoamylases, pectinases, reductases, oxidases, phenoloxidases, ligninases, pullulanases, arabinanases, hemicellulases, mannanases, xyloglucanases, xylanases, pectin acetyl esterases, rhamnogalacturonan acetyl esterases, polygalacturonases, rhamnogalacturonases, galactanases, pectin lyases, pectin methylesterases
  • one or more or all enzymes in the preparation is produced by using recombinant techniques, i.e. the enzyme (s) is/are mono-component enzyme (s) which is/are mixed with the other enzyme (s) to form an enzyme preparation with the desired enzyme blend.
  • Polyclonal antibodies (which are monospecific for a given enzyme protein) to be used in determining immunological cross- reactivity may be prepared by use of a purified pectate lyase enzyme. More specifically, antiserum against the pectate lyase of the invention may be raised by immunizing rabbits (or other rodents) according to the procedure described by N. Axelsen et al . in: A Manual of Quantitative Immunoelectrophoresis, Blackwell Scientific Publications, 1973, Chapter 23, or A. Johnstone and R. Thorpe, Immunochemistry in Practice, Blackwell Scientific Publications, 1982 (more specifically p. 27-31) .
  • Purified immunoglobulins may be obtained from the antisera, for example by salt precipitation ((NH 4 ) 2 S0 4 ) , followed by dialysis and ion exchange chromatography, e . g. on DEAE-Sephadex.
  • Immunochemical characterization of proteins may be done either by Outcherlony double-diffusion analysis (O. Ouchterlony in: Handbook of Experimental Immunology (D.M. Weir, Ed.), Blackwell Scientific Publications, 1967, pp. 655-706) , by crossed immunoelectrophoresis (N. Axelsen et al . , ___upra, Chapters 3 and 4), or by rocket immunoelectrophoresis (N. Axelsen et al . , Chapter 2) .
  • the present invention relates to a detergent composition comprising the pectate lyase enzyme or enzyme preparation of the invention, to a process for machine treatment of fabrics comprising treating fabric during a washing cycle of a machine washing process with a washing solution comprising the pectate lyase enzyme or enzyme preparation of the invention, and to cleaning compositions, including laundry, hard surface cleaner, personal cleansing and oral/dental compositions, comprising a pectate lyase enzyme or enzyme preparation of the invention providing superior cleaning performance, i.e. superior stain removal.
  • the pectate lyase of the present invention is capable of effectively degrading or hydrolysing any soiling or spots containing pectins and, accordingly, of cleaning laundry comprising such soilings or spots.
  • the cleaning compositions of the invention must contain at least one additional detergent component.
  • additional detergent component The precise nature of these additional components, and levels of incorporation thereof will depend on the physical form of the composition, and the nature of the cleaning operation for which it is to be used.
  • the cleaning compositions of the present invention preferably further comprise a detergent ingredient selected from a selected surfactant, another enzyme, a builder and/or a bleach system.
  • the cleaning compositions according to the invention can be liquid, paste, gels, bars, tablets, spray, foam, powder or granular.
  • Granular compositions can also be in "compact” form and the liquid compositions can also be in a "concentrated” form.
  • compositions of the invention may for example, be formulated as hand and machine dishwashing compositions, hand and machine laundry detergent compositions including laundry additive compositions and compositions suitable for use in the soaking and/or pretreatment of stained fabrics, rinse added fabric softener compositions, and compositions for use in general household hard surface cleaning operations.
  • Compositions containing such carbohydrases can also be formulated as sanitization products, contact lens cleansers and health and beauty care products such as oral/dental care and personal cleaning compositions.
  • compositions of the invention When formulated as compositions for use in manual dishwashing methods the compositions of the invention preferably contain a surfactant and preferably other detergent compounds selected from organic polymeric compounds, suds enhancing agents, group II metal ions, solvents, hydrotropes and additional enzymes.
  • a surfactant preferably other detergent compounds selected from organic polymeric compounds, suds enhancing agents, group II metal ions, solvents, hydrotropes and additional enzymes.
  • compositions suitable for use in a laundry machine washing method preferably contain both a surfactant and a builder compound and additionally one or more detergent components preferably selected from organic polymeric compounds, bleaching agents, additional enzymes, suds suppressors, dispersants, lime- soap dispersants, soil suspension and anti-redeposition agents and corrosion inhibitors.
  • Laundry compositions can also contain softening agents, as additional detergent components.
  • Such compositions containing carbohydrase can provide fabric cleaning, stain removal, whiteness maintenance, softening, colour appearance, dye transfer inhibition and sanitization when formulated as laundry detergent compositions.
  • compositions of the invention can also be used as detergent additive products in solid or liquid form.
  • Such additive products are intended to supplement or boost the performance of conventional detergent compositions and can be added at any stage of the cleaning process.
  • the density of the laundry detergent compositions herein ranges from 400 to 1200 g/litre, preferably 500 to 950 g/litre of composition measured at 20°C.
  • the "compact" form of the compositions herein is best reflected by density and, in terms of composition, by the amount of inorganic filler salt; inorganic filler salts are conventional ingredients of detergent compositions in powder form; in conventional detergent compositions, the filler salts are present in substantial amounts, typically 17-35% by weight of the total composition. In the compact compositions, the filler salt is present in amounts not exceeding 15% of the total composition, preferably not exceeding 10%, most preferably not exceeding 5% by weight of the composition.
  • the inorganic filler salts, such as meant in the present compositions are selected from the alkali and alkaline-earth-metal salts of sulphates and chlorides. A preferred filler salt is sodium sulphate.
  • Liquid detergent compositions according to the present invention can also be in a "concentrated form", in such case, the liquid detergent compositions according the present invention will contain a lower amount of water, compared to conventional liquid detergents.
  • the water content of the concentrated liquid detergent is preferably less than 40%, more preferably less than 30%, most preferably less than 20% by weight of the detergent composition.
  • Suitable specific detergent compounds for use herein are selected from the group consisting of the specific compounds as described in WO 97/01629 which is hereby incorporated by reference in its entirety.
  • Mannanase may be incorporated into the cleaning compositions in accordance with the invention preferably at a level of from 0.0001% to 2%, more preferably from 0.0005% to 0.5%, most preferred from 0.001% to 0.1% pure enzyme by weight of the composition.
  • the cellulases usable in the present invention include both bacterial or fungal cellulases. Preferably, they will have a pH optimum of between 5 and 12 and a specific activity above 50 CEVU/mg (Cellulose Viscosity Unit) .
  • Suitable cellulases are disclosed in U.S. Patent 4,435,307, J61078384 and WO96/02653 which discloses fungal cellulase produced from Hu icola insolens, Trichoderma, Thielavia and Sporotrichum, respectively.
  • EP 739 982 describes cellulases isolated from novel Bacillus species. Suitable cellulases are also disclosed in GB-A-2075028; GB-A-2095275; DE-OS-22 47 832 and W095/26398.
  • cellulases examples include cellulases produced by a strain of Humicola insolens (Humicola grisea var. thermoidea) , particularly the strain Humicola insolens, DSM 1800.
  • Other suitable cellulases are cellulases originated from Humicola insolens having a molecular weight of about 50kD, an isoelectric point of 5.5 and containing 415 amino acids; and a ⁇ 43kD endo- beta-l,4-glucanase derived from Humicola insolens, DSM 1800; a preferred cellulase has the amino acid sequence disclosed in PCT Patent Application No. WO 91/17243.
  • suitable cellulases are the EGIII cellulases from Tricoderma longibrachia urn described in WO94/21801. Especially suitable cellulases are the cellulases having color care benefits. Examples of such cellulases are the cellulases described in W096/29397, EP-A-0495257 , WO 91/17243, W091/17244 and WO91/21801. Other suitable cellulases for fabric care and/or cleaning properties are described in WO96/34092, W096/17994 and W095/24471.
  • Said cellulases are normally incorporated in the detergent composition at levels from 0.0001% to 2% of pure enzyme by weight of the detergent composition.
  • Preferred cellulases for the purpose of the present invention are alkaline cellulases, i.e. enzyme having at least 25%, more preferably at least 40% of their maximum activity at a pH ranging from 7 to 12. More preferred cellulases are enzymes having their maximum activity at a pH ranging from 7 to 12.
  • a preferred alkaline cellulase is the cellulase sold under the tradename Carezyme ® by Novo Nordisk A/S.
  • Amylases can be included for removal of carbohydrate-based stains.
  • WO94/02597 Novo Nordisk A/S published February 03, 1994, describes cleaning compositions which incorporate mutant amylases. See also WO95/10603, Novo Nordisk A/S, published April 20, 1995.
  • Other amylases known for use in cleaning compositions include both ⁇ - and ⁇ -amylases.
  • ⁇ - Amylases are known in the art and include those disclosed in US Pat. no. 5,003,257; EP 252,666; WO/91/00353 ; FR 2,676,456; EP 285,123; EP 525,610; EP 368,341; and British Patent specification no. 1,296,839 (Novo).
  • amylases are stability-enhanced amylases described in W094/18314, published August 18, 1994 and WO96/05295, Genencor, published February 22, 1996 and amylase variants having additional modification in the immediate parent available from Novo Nordisk A/S, disclosed in WO 95/10603, published April 95. Also suitable are amylases described in EP 277 216, W095/26397 and W096/23873 (all by Novo Nordisk) .
  • ⁇ -amylases characterised by having a specific activity at least 25% higher than the specific activity of Termamyl® at a temperature range of 25°C to 55°C and at a pH value in the range of 8 to 10, measured by the
  • Phadebas® ⁇ -amylase activity assay Suitable are variants of the above enzymes, described in W096/23873 (Novo Nordisk) .
  • Other amylolytic enzymes with improved properties with respect to the activity level and the combination of thermostability and a higher activity level are described in W095/35382.
  • amylases for the purpose of the present invention are the amylases sold under the tradename Termamyl, Duramyl and
  • Preferred amylases for specific applications are alkaline amylases, ie enzymes having an enzymatic activity of at least 10%, preferably at least 25%, more preferably at least 40% of their maximum activity at a pH ranging from 7 to 12. More preferred amylases are enzymes having their maximum activity at a pH ranging from 7 to 12.
  • amylolytic enzymes are incorporated in the detergent compositions of the present invention a level of from 0.0001% to 2%, preferably from 0.00018% to 0.06%, more preferably from 0.00024% to 0.048% pure enzyme by weight of the composition.
  • xyloglucanase encompasses the family of enzymes described by Vincken and Voragen at Wageningen University [Vincken et al (1994) Plant Physiol . , 104, 99-107] and are able to degrade xyloglucans as described in Hayashi et al (1989) Plant. Physiol. Plant Mol . Biol . , 40, 139-168. Vincken et al demonstrated the removal of xyloglucan coating from cellulase of the isolated apple cell wall by a xyloglucanase purified from Trichoderma viride (endo-IV-glucanase) . This enzyme enhances the enzymatic degradation of cell wall-embedded cellulose and work in synergy with pectic enzymes. Rapidase LIQ+ from Gist-Brocades contains an xyloglucanase activity.
  • This xyloglucanase is incorporated into the cleaning compositions in accordance with the invention preferably at a level of from 0.0001% to 2%, more preferably from ⁇ .0005% to 0.5%, most preferred from 0.001% toO .1 % pure enzyme by weight of the composition.
  • Preferred xyloglucanases for specific applications are alkaline xyloglucanases, ie enzymes having an enzymatic activity of at least 10%, preferably at least 25%, more preferably at least 40% of their maximum activity at a pH ranging from 7 to 12. More preferred xyloglucanases are enzymes having their maximum activity at a pH ranging from 7 to 12.
  • the above-mentioned enzymes may be of any suitable origin, such as vegetable, animal, bacterial, fungal and yeast origin. Origin can further be mesophilic or extremophilic
  • the variants may be designed such that the compatibility of the enzyme to commonly encountered ingredients of such compositions is increased.
  • the variant may be designed such that the optimal pH, bleach or chelant stability, catalytic activity and the like, of the enzyme variant is tailored to suit the particular cleaning application.
  • the isoelectric point of such enzymes may be modified by the substitution of some charged amino acids, e.g. an increase in isoelectric point may help to improve compatibility with anionic surfactants.
  • the stability of the enzymes may be further enhanced by the creation of e.g. additional salt bridges and enforcing metal binding sites to increase chelant stability.
  • the pectate lyase of the present invention can be used in combination with other carbohydrate degrading enzymes (for instance arabinanase, xyloglucanase, pectinase) for biopreparation of fibers or for cleaning of fibers in combination with detergents.
  • Cotton fibers consist of a primary cell wall layer containing pectin and a secondary layer containing mainly cellulose. Under cotton preparation or cotton refining part of the primary cell wall will be removed.
  • the present invention relates to either help during cotton refining by removal of the primary cell wall. Or during cleaning of the cotton to remove residual pectic substances and prevent graying of the textile.
  • cellulosic material is intended to mean fibers, sewn and unsewn fabrics, including knits, wovens, denims, yarns, and toweling, made from cotton, cotton blends or natural or manmade cellulosics (e.g. originating from xylan-containing cellulose fibers such as from wood pulp) or blends thereof.
  • blends are blends of cotton or rayon/viscose with one or more companion material such as wool, synthetic fibers (e.g.
  • polyamide fibers acrylic fibers, polyester fibers, polyvinyl alcohol fibers, polyvinyl chloride fibers, polyvinylidene chloride fibers, polyurethane fibers, polyurea fibers, aramid fibers) , and cellulose-containing fibers (e.g. rayon/viscose, ramie, hemp, flax/linen, jute, cellulose acetate fibers, lyocell) .
  • cellulose-containing fibers e.g. rayon/viscose, ramie, hemp, flax/linen, jute, cellulose acetate fibers, lyocell
  • the preparation of the present invention is useful in the cellulosic fiber processing industry for the pretreatment or retting of fibers from hemp, flax or linen.
  • the processing of cellulosic material for the textile industry, as for example cotton fiber, into a material ready for garment manufacture involves several steps : spinning of the fiber into a yarn; construction of woven or knit fabric from the yarn and subsequent preparation, dyeing and finishing operations.
  • Woven goods are constructed by weaving a filling yarn between a series of warp yarns; the yarns could be two different types.
  • Knitted goods are constructed by forming a network of interlocking loops from one continuous length of yarn.
  • the cellulosic fibers can also be used for non-woven fabric.
  • the preparation process prepares the textile for the proper response in dyeing operations.
  • the sub-steps involved in preparation are a. Desizing (for woven goods) using polymeric size like e.g.
  • starch, CMC or PVA is added before weaving in order to increase the warp speed; This material must be removed before further processing.
  • Scouring the aim of which is to remove non-cellulosic material from the cotton fiber, especially the cuticle (mainly consisting of waxes) and primary cell wall (mainly consisting of pectin, protein and xyloglucan) .
  • a proper wax removal is necessary for obtaining a high wettability, being a measure for obtaining a good dyeing.
  • Removal of the primary cell wall - especially the pectins - improves wax removal and ensures a more even dyeing. Further this improves the whiteness in the bleaching process.
  • the main chemical used in scouring is sodium hydroxide in high concentrations, up to 70 g/kg cotton and at high temperatures, 80-95°C; and c.
  • Bleaching normally the scouring is followed by a bleach using hydrogen peroxide as the oxidizing agent in order to obtain either a fully bleached (white) fabric or to ensure a clean shade of the dye.
  • a one step combined scour/bleach process is also used by the industry. Although preparation processes are most commonly employed in the fabric state; scouring, bleaching and dyeing operations can also be done at the fiber or yarn stage.
  • the processing regime can be either batch or continuous with the fabric being contacted by the liquid processing stream in open width or rope form.
  • Continuous operations generally use a saturator whereby an approximate equal weight of chemical bath per weight of fabric is applied to the fabric, followed by a heated dwell chamber where the chemical reaction takes place.
  • a washing section then prepares the fabric for the next processing step.
  • Batch processing generally takes place in one processing bath whereby the fabric is contacted with approximately 8 -15 times its weight in chemical bath. After a reaction period, the chemicals are drained, fabric rinsed and the next chemical is applied.
  • Discontinuous pad-batch processing involves a saturator whereby an approximate equal weight of chemical bath per weight of fabric is applied to the fabric, followed by a dwell period which in the case of cold pad-batch might be one or more days.
  • Woven goods are the prevalent form of textile fabric construction.
  • the weaving process demands a "sizing" of the warp yarn to protect it from abrasion.
  • Starch polyvinyl alcohol (PVA)
  • carboxymethyl cellulose carboxymethyl cellulose
  • waxes and acrylic binders are examples of typical sizing chemicals used because of availability and cost.
  • the size must be removed after the weaving process as the first step in preparing the woven goods.
  • the sized fabric in either rope or open width form is brought in contact with the processing liquid containing the desizing agents.
  • the desizing agent employed depends upon the type of size to be removed. For PVA sizes, hot water or oxidative processes are often used.
  • the most common sizing agent for cotton fabric is based upon starch.
  • woven cotton fabrics are desized by a combination of hot water, the enzyme ⁇ -amylase to hydrolyze the starch and a wetting agent or surfactant.
  • the cellulosic material is allowed to stand with the desizing chemicals for a "holding period" sufficiently long to accomplish the desizing.
  • the holding period is dependent upon the type of processing regime and the temperature and can vary from 15 minutes to 2 hours, or in some cases, several days.
  • the desizing chemicals are applied in a saturator bath which generally ranges from about 15°C to about 55°C.
  • the fabric is then held in equipment such as a "J-box" which provides sufficient heat, usually between about 55°C and about 100°C, to enhance the activity of the desizing agents.
  • the chemicals, including the removed sizing agents are washed away from the fabric after the termination of the holding period.
  • the scouring process removes much of the non-cellulosic compounds naturally found in cotton. In addition to the natural non-cellulosic impurities, scouring can remove dirt, soils and residual manufacturing introduced materials such as spinning, coning or slashing lubricants.
  • the scouring process employs sodium hydroxide or related causticizing agents such as sodium carbonate, potassium hydroxide or mixtures thereof. Generally an alkali stable surfactant is added to the process to enhance solubilization of hydrophobic compounds and/or prevent their redeposition back on the fabric.
  • the treatment is generally at a high temperature, 80°C - 100°C, employing strongly alkaline solutions, pH 13-14, of the scouring agent.
  • the softness of the cellulosic fabric is a function of residual natural cotton waxes.
  • the non-specific nature of the high temperature strongly alkaline scouring process cannot discriminate between the desirable natural cotton lubricants and the manufacturing introduced lubricants.
  • the conventional scouring process can cause environmental problems due to the highly alkaline effluent from these processes.
  • the scouring stage prepares the fabric for the optimal response in bleaching. An inadequately scoured fabric will need a higher level of bleach chemical in the subsequent bleaching stages.
  • the bleaching step decolorizes the natural cotton pigments and removes any residual natural woody cotton trash components not completely removed during ginning, carding or scouring.
  • the main process in use today is an alkaline hydrogen peroxide bleach. In many cases, especially when a very high whiteness is not needed, bleaching can be combined with scouring.
  • the scouring step can be carried out using the pectate lyase or pectate lyase preparation of the present invention a temperature of about 50°C - 80°C and a pH of about 7-11, thus substituting or supplementing the highly causticizing agents.
  • An optimized enzymatic process ensures a high pectin removal and full wettability.
  • the enzyme or enzyme preparation according to the invention is preferably used as an agent for degradation or modification of plant cell walls or any pectin-containing material originating from plant cells walls due to the high plant cell wall degrading activity of the pectate lyase of the invention.
  • the pectate lyase of the present invention may be used alone or together with other enzymes like glucanases, pectinases and/or hemicellulases to improve the extraction of oil from oil-rich plant material, like soy-bean oil from soy-beans, olive-oil from olives or rapeseed-oil from rape-seed or sunflower oil from sunflower.
  • the pectate lyase of the present invention may be used for separation of components of plant cell materials.
  • the separation of sugar or starch rich plant material into components of considerable commercial interest like sucrose from sugar beet or starch from potato
  • components of low interest like pulp or hull fractions
  • the separation of protein-rich or oil-rich crops into valuable protein and oil and invaluable hull fractions The separation process may be performed by use of methods known in the art.
  • the pectate lyase of the invention may also be used in the preparation of fruit or vegetable juice in order to increase yield, and in the enzymatic hydrolysis of various plant cell wall-derived materials or waste materials, e.g. from wine or juice production, or agricultural residues such as vegetable hulls, bean hulls, sugar beet pulp, olive pulp, potato pulp, and the like.
  • the plant material may be degraded in order to improve different kinds of processing, facilitate purification or extrac- tion of other component than the galactans like purification of pectins from citrus, improve the feed value, decrease the water binding capacity, improve the degradability in waste water plants, improve the conversion of plant material to ensilage, etc.
  • an enzyme preparation of the invention it is possible to regulate the consistency and appearence of processed fruit or vegetables.
  • the consistency and appearence has been shown to be a product of the actual combination of enzymes used for processing, i.e. the specificity of the enzymes with which the pectate lyase of the invention is combined. Examples include the production of clear juice e.g. from apples, pears or berries; cloud stable juice e.g.
  • the pectate lyase of the invention may be used in modifying the viscosity of plant cell wall derived material.
  • the pectate lyase may be used to reduce the viscosity of feed which contain pectin and to promote processing of viscous pectin containing material .
  • the viscosity reduction may be obtained by treating the pectin containing plant material with an enyme preparation of the invention under suitable conditions for full or partial degradation of the pectin containing material
  • the pectate lyase can be used e.g. in combination with other enzymes for the removal of pectic substances from plant fibres. This removal is essential e.g. in the production of textile fibres or other cellulosic materials.
  • plant fibre material is treated with a suitable amount of the pectate lyase of the invention under suitable conditions for obtaining full or partial degradation of pectic substances associated with the plant fibre material .
  • Pectate lyases of the present invention may be used for modification of animal feed and may exert their effect either in vitro (by modifying components of the feed) or in vivo, the pectate lyase is particularly suited for addition to animal feed compositions containing high amounts of arabinogalactans or galactans, e.g. feed containing plant material from soy bean, rape seed, lupin etc.
  • the pectate lyase significantly improves the in vivo break-down of plant cell wall material, whereby a better utilization of the plant nutrients by the animal is achieved. Thereby, the growth rate and/or feed conversion ratio (i.e. the weight of ingested feed relative to weight gain) of the animal is improved.
  • the indigestible galactan is degraded by pectate lyase, e.g. in combination with ⁇ -galactosidase, to galactose or galactooligomers which are digestible by the animal and thus contribute to the available energy of the feed.
  • pectate lyase e.g. in combination with ⁇ -galactosidase
  • galactose or galactooligomers which are digestible by the animal and thus contribute to the available energy of the feed.
  • the pectate lyase may improve the digestibility and uptake of non-carbohydrate feed constituents such as protein, fat and minerals.
  • the enzyme or enzyme preparation of the invention may be used for de-pectinization and viscosity reduction in vegetable or fruit juice, especially in apple or pear juice. This may be accomplished by treating the fruit or vegetable juice with an enzyme preparation of the invention in an amount effective for degrading pectin-containing material contained in the fruit or vegetable juice.
  • the enzyme or enzyme preparation may be used in the treatment of mash from fruits and vegetables in order to improve the extractability or degradability of the mash.
  • the enzyme preparation may be used in the treatment of mash from apples and pears for juice production, and in the mash treatment of grapes for wine production.
  • the lyase assay (at 235 nm)
  • Pectate lyase activity can be measured by applying a test solution to 4 mm holes punched out in agar plates (such as, for example, LB agar), containing 0.7% w/v sodium polygalacturonate (Sigma P 1879) . The plates are then incubated for 6 h at a particular temperature (such as, e.g., 75°C) . The plates are then soaked in either (i) 1M CaCl2 for 0.5h or (ii) 1% mixed alkyl trimethylammonium Br (MTAB, Sigma M-7635) for 1 h. Both of these procedures cause the precipitation of polygalacturonate within the agar.
  • agar plates such as, for example, LB agar
  • MTAB mixed alkyl trimethylammonium Br
  • Pectate lyase activity can be detected by the appearance of clear zones within a background of precipitated polygalacturonate. Sensitivity of the assay is calibrated using dilutions of a standard preparation of pectate lyase.
  • the substrate and enzyme is incubated for 20 min at 37°C followed by measurement at 235 nm of the formation of double bounds. Finally, the rate of the degradation is calculated based on the molar extinction coefficient in terms of Trans Units. Procedure : Mixing of 0.5 ml enzyme dilution with 0.5 ml 2*substrate solution.
  • Substrate Polygalacturonic acid from Sigma P-1879 lot 77H3784
  • Buffer 2x 0.1M Glycin pH 10 + 0.8 mmol CaCl 2 Stop reagent: 0.02 M H 3 P0 4
  • E. coli DSM 12712 comprises the plasmid containing the pectate lyase encoding DNA sequence of the invention presented in SEQ ID NO:l.
  • This strain is the B. subtilis DN1885 with disrupted apr and npr genes (Diderichsen, B., Wedsted, U. , Hedegaard, L., Jensen, B. R., Sj ⁇ holm, C. (1990) Cloning of aldB, which encodes alpha-acetolactate decarboxylase, an exoenzyme from Bacillus brevis. J. Bacteriol., 172, 4315-4321) disrupted in the transcriptional unit of the known Bacillus subtilis cellulase gene, resulting in cellulase negative cells. The disruption was performed essentially as described in ( Eds. A.L. Sonenshein, J.A. Hoch and Richard Losick (1993) Bacillus subtilis and other Gram-Positive Bacteria, American Society for microbiology, p.618).
  • Competent cells were prepared and transformed as described by Yasbin, R.E., Wilson, G.A. and Young, F.E. (1975) Transformation and transfection in lysogenic strains of Bacillus subtilis : evidence for selective induction of prophage in competent cells. J. Bacteriol, 121:296-304.
  • Escherichia coli SJ2 Escherichia coli SJ2 (Diderichsen, B. et al . , (1990)).
  • Plasmids pSJ1678 The gene bank vector was pSJ1678 which is further disclosed in W094/19454 which is hereby incorporated by reference in its entirety.
  • This plasmid is a pUBllO derivative essentially containing elements making the plasmid propagatable in Bacillus subtilis, kanamycin resistance gene and having a strong promoter and signal peptide cloned from the amyL gene of B . licheniformis ATCC14580.
  • the signal peptide contains a SacII site making it convenient to clone the DNA encoding the mature part of a protein in-fusion with the signal peptide. This results in the expression of a Pre-protein which is directed towards the exterior of the cell.
  • the plasmid was constructed by means of conventional genetic engineering techniques which are briefly described in the following.
  • the pUBllO plasmid (McKenzie, T. et al . , 1986, Plasmid 15:93-103) was digested with the unique restriction enzyme Neil.
  • a PCR fragment amplified from the amyL promoter encoded on the plasmid pDN1981 (P.L. J ⁇ rgensen et al.,1990, Gene, 96, p37-41.) was digested with Neil and inserted in the Neil digested pUBllO to give the plasmid pSJ2624.
  • the two PCR primers used have the following sequences:
  • the primer #LWN5494 inserts a NotI site in the plasmid.
  • the plasmid pSJ2624 was then digested with Sad and Notl and a new PCR fragment amplified on amyL promoter encoded on the pDN1981 was digested with Sacl and Notl and this DNA fragment was inserted in the Sacl -Notl digested pSJ2624 to give the plasmid pSJ2670.
  • This cloning replaces the first amyL promoter cloning with the same promoter but in the opposite direction.
  • the two primers used for PCR amplification have the following sequences: #LWN5938 5 " -GTCGGCGGCCGCTGATCACGTACCAAGCTTGTCGACCTGCAGAATG
  • the plasmid pSJ2670 was digested with the restriction enzymes Pstl and Bell and a PCR fragment amplified from a cloned DNA sequence encoding the alkaline amylase SP722 (disclosed in the International Patent Application published as W095/26397 which is hereby incorporated by reference in its entirety) was digested with Pstl and Bell and inserted to give the plasmid pMOL944.
  • the two primers used for PCR amplification have the following sequence:
  • the primer #LWN7901 inserts a SacII site in the plasmid.
  • LB agar (as described in Ausubel, F. M. et al . (eds.) "Current protocols in Molecular Biology”. John Wiley and Sons, 1995).
  • LBPG is LB agar supplemented with 0.5% Glucose and 0.05 M potassium phosphate, pH 7.0
  • BPX media is described in EP 0 506 780 (WO 91/09129) .
  • the fragments were cloned into the BamHI site of the cloning vector pSJ1678 and transformed by electroporation, using a Gene PulserTM electroporator from BIO- RAD as described by the supplier, into Escherichia coli SJ2 (Diderichsen, B. et al . , (1990)), thereby creating a gene library of Bacillus sp.
  • a Bacillus sp. library was screened by fluorescence polarisation using fluorescently labelled pectin.
  • the labeling strategy comprised labeling of the carboxylic acid groups of pectin/polygalacturonic acids by coupling a hydrazine or amine activated probe (e.g. fluorescein-5-thiosemicarbazide) to the carboxylic acids using l-ethyl-3- (dimethylaminopropyl) carbodiimide hydrochloride (FLUKA, Switzerland) as a mediator.
  • a hydrazine or amine activated probe e.g. fluorescein-5-thiosemicarbazide
  • the polygalacturonic acid with a degree of esterification of 3% (1 g) was dissolved in 25 ml of demineralized water and subsequently 20 mg of fluorescein-5-thiosemicarbazide (Molecular Probes, OR, USA) was applied while stirring.
  • the pH was adjusted to 5.9 with 1 M NaOH and (1 g) l-ethyl-3- (dimethylaminopropyl) carbodiimide hydro-chloride was added gradually over 1 h while stirring.
  • the solution was then incubated overnight in darkness. 10% acetic acid (v/v) was added to the solution followed by addition of methanol to a final concentration of 75% (v/v) methanol . This solution was placed in darkness for 1 h.
  • the precipitated pectin was subsequently collected by filtration on 2 layers of Miracloth (Calbiochem, Germany) and washed with acetic acid:ethanol (1:19 v/v), ethanol (96%) and finally with acetone.
  • the labeled pectin was dried in darkness. The degree of labeling were between 0.3 and 0.7 %.
  • the assay mix consisted of 34 ⁇ g/ml apple pectin DE 3% trace labelled fluorescein (as described above) , 2 mM CaCl 2 and 100 mM glycin buffer at pH 10.
  • the microtitter plates were incubated at ambient temperature for 2 hours prior to being read by a fluorescence polarisation reader (Polarstar, BMG, Germany) .
  • the fluorescence polarisation value of substrate was significantly lower in two wells indicating the presence of pectinase activity. From the masterplates, two clones were purified which encoded a pectinase gene.
  • Standard dideoxy sequencing methods were employed on plasmid template using an ABI 373 automated sequencer.
  • a combination of restriction subcloning and primer walking was employed to determine the sequence of the gene .
  • the DNA sequence is SEQ ID N0.:1 and the derived amino acid sequence is SEQ ID No.:2.
  • pectate lyase (vide supra, represented by amino acid sequence SEQ ID NO:2j encoding DNA sequence of the invention was PCR amplified using the PCR primer set consisting of these two oligo nucleotides:
  • Chromosomal DNA isolated from Bacillus sp. as described above was used as template in a PCR reaction using Amplitaq DNA Polymerase (Perkin Elmer) according to manufacturers instructions.
  • the PCR reaction was set up in PCR buffer (10 mM Tris-HCl, pH 8.3, 50 mM KCl, 1.5 mM MgCl 2 , 0.01 % (w/v) gelatin) containing 200 ⁇ M of each dNTP, 2.5 units of AmpliTaq polymerase (Perkin-Elmer, Cetus, USA) and 100 pmol of each primer
  • the PCR reactions was performed using a DNA thermal cycler (Landgraf, Germany) . One incubation at 94°C for 1 min followed by thirty cycles of PCR performed using a cycle profile of denaturation at 94°C for 30 sec, annealing at 60°C for 1 min, and extension at 72°C for 2 min. Five- ⁇ l aliquots of the amplification product was analysed by electrophoresis in 0.7 % agarose gels (NuSieve, FMC) . The appearance of a DNA fragment size 1.0 kb indicated proper amplification of the gene segment.
  • the isolated PCR DNA fragment was then ligated to the SacII -Notl digested and purified pM0L944. The ligation was performed overnight at 16°C using 0.5 ⁇ g of each DNA fragment, 1 U of T4 DNA ligase and T4 ligase buffer (Boehringer Mannheim, Germany) .
  • the ligation mixture was used to transform competent B. subtilis PL2306.
  • the transformed cells were plated onto LBPG- 10 ⁇ g/ml of Kanamycin plates. After 18 hours incubation at 37°C several clones were restreaked on fresh agar plates and also grown in liquid TY cultures with 10 ⁇ g/ ml kanamycin and incubated overnight at 37°C. Next day 1 ml of cells were used to isolate plasmid from the cells using the Qiaprep Spin Plasmid Miniprep Kit #27106 according to the manufacturers recommendations for B . subtilis plasmid preparations. This plasmid DNA was used as template for DNA sequencing.
  • the DNA corresponding to the mature part of the pectate lyase was characterised by DNA sequencing by primerwalking, using the Taq deoxy-terminal cycle sequencing kit (Perkin-Elmer, USA) , fluorescent labelled terminators and appropriate oligonucleotides as primers.
  • MB939 was grown in 15 x 200 ml BPX media with 10 ⁇ g/ml of Kanamycin in 500 ml two baffled shakeflasks for 5 days at 37°C at 300 rpm, whereby 2500 ml of culture broth was obtained.
  • the pH was adjusted to 6.1, using acetic acid and 25 ml of cationic agent (C521 10%) and 60 ml of anionic agent (A130 0.1%) was added during agitation for flocculation.
  • the flocculated material was separated by centrifugation using a Sorval RC 3B centrifuge at 10000 rpm for 30 min at 6°C.
  • the resulting supernatant contained 820 Trans units per ml in a total volume of 2400 ml. 5
  • the supernatant was clarified using Whatman glass filters GF/D and C and finally concentrated on a filtron UF membrane with a cut off of 10 kDa.
  • the total volume of 500 ml was adjusted to pH 8.0.
  • the pure enzyme constitutes a single band in SDS-PAGE of 36 kDa and has an isoelectric point of about 5.6.
  • the protein concentration was determined using a molar 20 extinction coefficient of 80510 (based on the amino acid composition deducted from the sequence) .
  • the activity could be inhibited by EDTA. However, as long as the EDTA concentration did not exceed the Ca concentration more than 75% of relative activity could be obtained (cf . Table 25 lb) . The enzyme was not further activated by increasing the calcium concentration (cf. Table la).
  • the pH dependency of activity showed more than 50% relative activity between pH 8.5 and 11.0 at 37°C (cf. Table 2).
  • the temperature optima at pH 10 was 60°C (cf . Table 3) .
  • 30 Differential Scanning Calorimetry DSC of the pure enzyme revealed a melting temperature of 58.8°C at pH 8 in 0.1 M Tris buffer.
  • Table la The relative activity at different levels of Ca (at pH 35 10, 50 mM glycine buffer; substrate 1% polygalacturonic acid)
  • Table lb The relative activity at different levels of EDTA + 0.38 mmmol CaCl 2 (at pH 10, 50 mM glycine buffer; substrate 1% polygalacturonic acid)

Abstract

L'invention concerne une nouvelle lyase de pectate appartenant à une nouvelle famille des lyases de polysaccharides et très efficace dans les procédés industriels sous conditions neutres ou alcalines comme par exemple le blanchissage et la transformation des textiles. La lyase de pectate peut être dérivée d'espèces de bacilles.
PCT/DK2000/000111 1999-03-16 2000-03-15 Nouvelles lyases de pectate WO2000055309A1 (fr)

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WO2004053039A2 (fr) 2002-12-11 2004-06-24 Novozymes A/S Composition detergente
WO2004092479A2 (fr) * 2003-04-16 2004-10-28 Novozymes A/S Traitement enzymatique de pates a papier
US7601529B2 (en) 2002-05-14 2009-10-13 Novozymes A/S Pectate lyase variants
WO2011080267A2 (fr) 2009-12-29 2011-07-07 Novozymes A/S Polypeptides amplifiant la detergence
WO2011104339A1 (fr) 2010-02-25 2011-09-01 Novozymes A/S Variants d'un lysozyme et polynucléotides pour les coder
WO2012028483A1 (fr) 2010-08-30 2012-03-08 Novozymes A/S Lavage à trempage concentré
WO2012028482A1 (fr) 2010-08-30 2012-03-08 Novozymes A/S Lavage à deux trempages
WO2012035103A1 (fr) 2010-09-16 2012-03-22 Novozymes A/S Lysozymes
CN104233893A (zh) * 2014-09-03 2014-12-24 稼禾生物股份有限公司 一种清洁化高效纸浆清洗工艺
EP2787070A3 (fr) * 2011-07-21 2015-03-11 AB Enzymes GmbH Procédé pour lyser des parois cellulaires de levure
CN108004821A (zh) * 2017-11-28 2018-05-08 嘉兴温华环保科技有限公司 一种废纸造纸工艺
CN109385416A (zh) * 2018-10-09 2019-02-26 中国农业科学院饲料研究所 果胶酸裂解酶pl1w及其基因和应用
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WO2002092741A2 (fr) * 2001-05-14 2002-11-21 Novozymes A/S Compositions detergentes comprenant des lyases de pectates de bacillus subtilis
WO2002092741A3 (fr) * 2001-05-14 2003-05-01 Novozymes As Compositions detergentes comprenant des lyases de pectates de bacillus subtilis
US7611882B2 (en) 2001-05-14 2009-11-03 Novozymes A/S Detergent compositions comprising Bacillus subtilis pectate lyases
US9005950B2 (en) 2002-05-14 2015-04-14 Novozymes A/S Pectate lyase variants
US8563290B2 (en) 2002-05-14 2013-10-22 Novozymes A/S Pectate lyase variants
US7601529B2 (en) 2002-05-14 2009-10-13 Novozymes A/S Pectate lyase variants
US8288144B2 (en) 2002-05-14 2012-10-16 Novozymes A/S Pectate lyase variants
WO2004053039A2 (fr) 2002-12-11 2004-06-24 Novozymes A/S Composition detergente
EP2311941A1 (fr) 2002-12-11 2011-04-20 Novozymes A/S Detergent comprenant une endoglucanase
WO2004092479A2 (fr) * 2003-04-16 2004-10-28 Novozymes A/S Traitement enzymatique de pates a papier
WO2004092479A3 (fr) * 2003-04-16 2004-11-25 Novozymes As Traitement enzymatique de pates a papier
WO2011080267A2 (fr) 2009-12-29 2011-07-07 Novozymes A/S Polypeptides amplifiant la detergence
WO2011104339A1 (fr) 2010-02-25 2011-09-01 Novozymes A/S Variants d'un lysozyme et polynucléotides pour les coder
WO2012028483A1 (fr) 2010-08-30 2012-03-08 Novozymes A/S Lavage à trempage concentré
WO2012028482A1 (fr) 2010-08-30 2012-03-08 Novozymes A/S Lavage à deux trempages
WO2012035103A1 (fr) 2010-09-16 2012-03-22 Novozymes A/S Lysozymes
EP2787070A3 (fr) * 2011-07-21 2015-03-11 AB Enzymes GmbH Procédé pour lyser des parois cellulaires de levure
CN104233893A (zh) * 2014-09-03 2014-12-24 稼禾生物股份有限公司 一种清洁化高效纸浆清洗工艺
CN104233893B (zh) * 2014-09-03 2016-07-06 稼禾生物股份有限公司 一种清洁化高效纸浆清洗工艺
US10662417B2 (en) 2016-07-05 2020-05-26 Novozymes A/S Pectate lyase variants and polynucleotides encoding same
CN108004821A (zh) * 2017-11-28 2018-05-08 嘉兴温华环保科技有限公司 一种废纸造纸工艺
CN108004821B (zh) * 2017-11-28 2020-05-19 嘉兴温华环保科技有限公司 一种废纸造纸工艺
CN109385416A (zh) * 2018-10-09 2019-02-26 中国农业科学院饲料研究所 果胶酸裂解酶pl1w及其基因和应用
CN109385416B (zh) * 2018-10-09 2021-03-26 中国农业科学院北京畜牧兽医研究所 果胶酸裂解酶pl1w及其基因和应用

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