Patent Application
20080020088
The present invention concerns novel enzymes with xylanolytic activity as well as their corresponding genes. In particular, the present invention concerns xylanases isolated from psychrophilic microorganisms and/or belonging to glycoside hydrolase Family 8. The enzymes of the invention find many applications and are highly suitable for use in bread improving compositions.
Xylans are heteropolysaccharides that form the major component of hemicellulose in plant biomass. The backbone of these polysaccharides consists of a chain of β-1,4-linked xylopyranoside residues. This backbone chain may be substituted to varying degrees with various side chain groups, including acetyl, arabinosyl and/or glucuronosyl substituents. Furthermore, phenolic compounds such as ferulic or hydroxycinnamic acids may also be involved, through ester binding, in the cross linking of the xylan chains or/and in the cross-linking of xylan and lignin chains.
Endoxylanases (also referred to as endo-β-1,4-xylanases, pentosanases or hemicellulases) specifically hydrolyse the backbone of xylan. In some cases, however, their activity may be sterically hindered by side groups. Different types of xylanases have been described and their specificity towards their substrate may vary from one to another, some being more active on insoluble arabinoxylans for instance. In addition, the length of the oligomers produced also depends on the type of xylanase considered.
Glycoside hydrolases have been classified into 93 families (http://afmb.cnrs-mrs.fr/CAZY/) based on sequence homologies and thus reflects structural and mechanistic features. Because the fold of proteins is better conserved than the sequence, some of the families can be grouped in ‘clans’ (Henrissat B. 1991, Biochem. J. Vol. 280, p. 309). Endo-beta-1,4-xylanases are generally classified in Families 10 (formerly Family F) and 11 (formerly Family G) and are found to frequently have an inverse relationship between their pI and molecular weight. The Family 10 xylanases (EXs10) are generally larger and more complex than the Family 11 xylanases (EXs11). Moreover, these families display significant differences in their structures and catalytic properties. EXs10 present an (α/β)8 barrel fold, have about 40% α-helix structures and belong to clan GH-A (Dominguez et al. 1995, Nat. Struct. Biol. Vol. 2, p. 569) while EXs11 exhibit a β-jelly roll fold, have about 3-5% α-helix structures and belong to clan GH-C (Törrönen et al. 1994, EMBO J. Vol. 13 , p. 2493). EXs10 have a smaller substrate binding site and a lower substrate specificity. Furthermore, they frequently have endoglucanase activity and produce smaller oligosaccharides as compared to EXs11 (Biely et al. 1997, J. Biotechnol. Vol. 57, p. 151). Xylanases of both families as characterized to date retain the anomeric configuration of the glycosidic oxygen following hydrolysis in which two glutamates typically function as the catalytic residues (Jeffries, 1997, Curr. Opin. Biotechnol. Vol. 7, p. 337).
Xylanases are used in various industrial sectors including the food, feed and some technical industries.
In the food industry, xylanases are used in fruit, vegetable and plant processing, in wine making and brewing, in baking, milling, pastry and confectionery and in coffee processing. Their functions in these industries are very diverse. For example, in fruit and plant processing they improve the maceration process, juice clarification, the extraction yield and filtration efficiency, hence improving the process performance and product quality. Xylanases also reduce the wart viscosity in beer making, improve grape skin maceration in wine making and reduce haze in the final products. In baking, xylanases improve elasticity and strength of doughs, thereby allowing easier handling, larger loaf volume and improved bread texture. In coffee processing, xylanases reduce the viscosity of coffee extracts and improve the drying/lyophilization processes.
Xylanases are further used in feed for monogastric animals (swine and poultry) and ruminants. They decrease among others the content of non-starch polysaccharides, thereby reducing the intestinal viscosity and improving the utilization of proteins and starch present in the feed. Xylanases improve animal performance and increase the digestibility and nutritive value of poorly degradable feeds such as barley and wheat.
In the starch industry, the use of xylanases improves the gluten-starch separation process.
In the pulp and paper industry, xylanases are used to facilitate the pulping process and to reduce the use of mechanical pulping methods, hence reducing energy consumption. Xylanases also improve the fibrillation and drainage properties of pulp, hence improving the process efficiency and the paper strength. They also facilitate the de-inking processes and reduce the use of alkali in these processes.
Xylanases are further used in the enzymatic retting of textiles (flax, jute, ramie, hemp, . . . ) and therefore reduce or replace chemical retting methods. They are also used in bioremediation for the treatment of agricultural and food industry wastes. Some bioconversion processes such as the production of fermentable products, renewable fuel (bioethanol) or fine chemicals for instance are also performed with the aid of xylanases.
Further applications for xylanases may still arrive in the future.
The use of xylanases (also referred to as endoxylanases, endo-β-1, 4-xylanases, pentosanases or hemicellulases) in baking has been well known for a number of years. These dough-conditioning enzymes can improve the dough machinability and stability as well as the oven-spring and the crumb structure. Other effects of the enzymes are a larger loaf volume and a softer crumb.
The mechanism of action of xylanases in bread preparation is still not clearly elucidated. Wheat flour contains about 3 to 4% pentosans. These pentosans can absorb large amounts of water (up to 30%) and this water absorption contributes to the properties of the dough as well as to the quality of the final product. Partial hydrolysis of pentosans by pentosanases into water soluble short chain oligosaccharides increases the water binding capacity. In addition, the pentosans strongly interact with the gluten fraction of the flour to form a network. Pentosanases may help to relax this strong and rigid network, thereby allowing better dough expansion by the carbon dioxide formed by the yeast.
Many types of hemicellulase preparations have been used for the applications mentioned above, and are commercially available. They are produced by microbial fermentation using various microorganisms as enzyme sources. Some of these enzymes are also produced by genetically modified microorganisms. All documented commercial uses of xylanases relate to xylanases belonging to either glycoside hydrolase Family 10 or Family 11, as defined previously.
Examples of commercial xylanases are the xylanases from Bacillus sp., Trichoderma sp., Humicola sp. and Aspergillus sp.
A number of reviews describing the actual state of art in the field of xylanases have been recently published (see for example Shallom D & Shoham Y. 2003, Curr. Opin. Microbiol. Vol. 6, p. 219- Subramaniyan S & Prema P. 2002, Crit Rev Biotechnol. Vol 22, p. 33-Beg Q K, Kapoor M, Mahajan L & Hoondal G S. 2001, Appl Microbiol Biotechnol. Vol. 56, p. 326).
Xylanases belonging to families other than glycoside hydrolase Families 10 and 11 have been recently described (see e.g. http://afmb.cnrs-mrs.fr/CAZY/ with the EC code for xylanase 3.1.2.8. for an overview). Among these, one example is the xylanase from Pseudoalteromonas haloplanktis TAH3a belonging to glycoside hydrolase Family 8 which has been characterized and for which the corresponding gene has been cloned (Collins T. et al. 2002, J. Biol. Chem. Vol. 277, p. 35133; Collins T. et al. 2003, J. Mol. Biol. Vol 328, P. 419; Van Petegem F. et al. 2003, J. Biol. Chem. Vol 278, p. 7531). This enzyme is a typical psychrophilic enzyme and presents a high catalytic activity at low temperatures. It is not homologous to family 10 or 11 xylanases, but has 20 to 30% identity with glycoside hydrolase Family 8 members (formerly Family D), a family that comprises mainly endoglucanases, but also lichenases and chitosanases. Furthermore, a FingerPRINTScan against PRINTS using the InterPro Scan search program (Zdobnov and Apweiler, 2001, Bioinformatics Vol. 17, p. 847) indicated that the isolated sequence contained the glycosyl hydrolase Family 8 fingerprint. In addition, the isolated sequence contains Family 8 residues that are strictly conserved in the 53 Family 8 enzymes analyzed thus far.
In contrast to most EXs10 and EXs11, this Family 8 xylanase (EXs8) has both a high pI and a high molecular weight. Structural and catalytic properties are different from those of both EXs10 and EXs11. The EXs8 xylanase presents a distorted (α/α)6 barrel fold with 13 α-helices and 13 β-strands and belongs to clan GH-M (Van Petegem et al. 2003, J. Biol. Chem. Vol. 278 (9), p7531-9) . This enzyme has no endoglucanase, chitosanase or licheninase activity and appears to be functionally similar to EXs11, being more active on long chain xylo-oligosaccharides.
In contrast to other characterized EXs10 and EXs11 that retain the anomeric configuration, Family 8 glycoside hydrolases (Fierobe et al., 1993. Eur. J. Biochem. Vol. 217, p557; http://afmb.cnrs-mrs.fr/CAZY/) tend to hydrolyse the substrate with inversion of the anomeric configuration of the glycosidic oxygen. This has been shown for the psychrophilic xylanase from Pseudoalteromonas haloplanktis (Collins, T. et al. 2002. J. Biol. Chem. Vol. 277, p. 35133). In addition, the catalytic residues involved in hydrolysis are believed to be a glutamate and an aspartate.
A variety of methods exist for evaluating the xylanase activity in an enzyme preparation. Examples of such methods for xylanase activity determination include: the measurement of the release of reducing sugars from xylan (Miller G. L. 1959, Anal. Chem. Vol. 31, p. 426), or the measurement of the release of coloured compounds from modified substrates (for examples AzoWAX or Xylazyme AX from Megazyme). However, no direct correlation has been shown between the xylanolytic activity found in various enzyme preparations and the effect in a particular application. For example in baking, dose-related results can be observed to a certain extent for a single enzyme, but the same dosage of two xylanases of different origins does not give the same result in the dough or in the bread. Several reasons could explain this: differences in substrate specificity, differences in temperature and pH optimum, differences in catalytic efficiency, . . .
It is of great interest to develop novel enzyme preparations, such as, but not restricted to ingredients for bread improver compositions or agents with new or improved properties. One of these properties could be that the xylanase content is as low as possible (in terms of weight of enzymes needed to obtain a particular result).
The present invention aims to provide novel enzymes and enzyme preparations with xylanolytic activity.
The present invention further aims to provide amino acid and nucleotide sequences encoding such enzymes and their variants.
Another aim of the invention is to provide enzymes and enzyme preparations for use in agrofood, feed and many other technical processes.
Yet another aim of the present invention is to provide enzymes and enzyme preparations with xylanolytic activity of which the amount needed to observe a specific effect in a particular application is far lower than for any conventional commercial enzymes.
Still another aim of the present invention is to provide enzymes and enzyme preparations with xylanolytic activity, which are remarkably more stable than enzymes known in the art, and which preferably are more effective at the same time (reflected by a significantly lower amount needed to obtain a given effect).
The present invention is directed to novel xylanolytic enzymes that preferably belong to glycoside hydrolase Family 8 and preferably are psychrophilic enzymes, most preferably psychrophilic enzymes that hydrolyse with inversion of the anomeric configuration, with the proviso that said xylanolytic enzyme is not encoded by SEQ ID NO: 1.
Advantageously, the enzymes of the present invention increase the loaf volume of a baked product by at least 10% when applied in a concentration of 1500 to 6000 xylanase units/100 kg flour and/or increase the width of cut on the surface of a baked product when applied in a concentration of 1500 to 6000 xylanase units/100 kg flour. The enzymes of the present invention may be advantageously used in frozen doughs and/or in applications that involve low temperature proofing.
Preferably, the enzymes comprise an amino acid sequence, or consist of an amino acid sequence, corresponding to any of SEQ ID NOs: 4, 6, 8, 10, 12, 14, 16 or 35. These sequences contain 426 amino acids (aa), of which the first 21 constitute a signal peptide. A preferred sequence is SEQ ID NO: 4, representing the xylanase isolated from TAH 2a.
Preferably, said enzymes—identified by one of the above SEQ ID NOs—belong to glycoside hydrolase Family 8 and are preferably psychrophilic enzymes.
Another aspect of the invention concerns the mature polypeptides of any of the above, corresponding to aa 22-426 of any of the above sequences. Prefered amino acid sequences according to the invention are SEQ ID NOs: 21, 23, 25, 27, 29, 31, 33 and 37 and SEQ ID NOs: 20, 22, 24, 26, 28, 30, 32 and 36, the corresponding nucleotide sequences encoding such mature polypeptides.
The enzymes of the invention may also have an amino acid sequence that differs in less than 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 aa from any of the above (mature protein or propeptide) , or have an amino acid sequence that has more than 50%, 70%, more preferably more than 80%, 85%, 90%, most preferably more than 95%, 97%, 98% or even more than 99% sequence identity with any of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 35, 21, 23, 25, 27, 29, 31, 33 or 37.
The enzymes of the invention preferably are isolated from any of the following bacterial strains: TAH 2a, TAH 4a, TAH 7a, Sp.10.1, Sp.10.2, Sp.11.2, Sp.23.2 or SP.23.2bis. These strains concern another aspect of the invention.
Another aspect of the invention concerns nucleotide sequences that encode any of the above xylanolytic enzymes.
A preferred such nucleotide sequence is one that comprises SEQ ID NO: 19 and codes for a TAH 2a, TAH 4a, TAH 7a, Sp.10.1, Sp.10.2 or Sp.11.2 xylanase as identified by any of SEQ ID NOs: 4, 6, 8, 10, 12, 14, 21, 23, 25, 27, 29 or 31.
Other preferred nucleotide sequences are those coding for one of the above-identified preproteins or mature polypeptides. Examples of such nucleotide sequences include SEQ ID NOs: 3, 5, 7, 9, 11, 13, 15, 34, 20, 22, 24, 26, 28, 30, 32 and 36.
A further aspect of the present invention concerns recombinant nucleotide sequences that comprise one or more of the above nucleotide sequences, operably linked to one or more adjacent regulatory sequence(s). Another aspect of the invention concerns vectors harboring the latter and host cells transformed therewith.
A preferred embodiment of the invention is directed to a plasmid incorporated in Escherichia coli having a deposit number selected from the group consisting of LMBP 4860, LMBP 4861, LMBP 4862, LMBP 4863, LMBP 4864, LMBP 4865 and LMBP 4866. LMBP 4862 is preferred.
The enzymes of the invention may be extra-cellularly expressed or may be intracellularly expressed. It is possible to use directly cells or cell cultures that express the enzymes according to the invention and/or to use the supernatant only of cell cultures in which the enzymes are secreted. Alternatively, cell extracts and/or cell-free extracts may be used as source of the enzymes of the invention. Finally, the enzymes may be used after being purified or partly purified (after at least one purification step), id est in more or less pure form.
The xylanases of the invention are highly suitable for use in applications that involve the degradation of plant cell wall components. They are for instance advantageously used in processes for decomposing plants and fruits, preferably fruit, legume juice, beer, paper, starch, gluten or vegetable oil preparation processes. Other applications include their use in fruit, vegetable and plant processing, wine making or brewing, coffee processing, the processing of paper or textile, in bioconversion processes, in processes for decomposing wastes, preferably for decomposing agricultural wastes or wastes from paper mills, in starch-gluten separation processes, in feed preparations, in baking, milling, pastry and confectionery processes.
The enzymes of the invention are particularly suitable for use in food applications.
For some applications it is advantageous to fix the above described cells, components of the above cell extracts and/or one or more purified enzymes with xylanolytic activity according to the invention to a solid support.
The enzymes of the invention may be used in a bread improver or bread improving composition. Apart from one or more xylanolytic enzymes according to the invention, said improver or improving composition may further contain at least one other bread-improving agent selected from the list consisting of other enzymes, emulsifiers, oxidants, milk powder, fats, sugars, amino acids, salts and proteins (gluten, cellulose binding sites) or a mixture thereof. Said other enzyme preferably is selected from the list consisting of alpha-amylases, beta-amylases, maltogenic amylases, other xylanases, proteases, glucose oxidase, oxido-reductases, glucanases, cellulases, transglutaminases, isomerases, lipases, phospholipases, pectinases or a mixture thereof. Said alpha-amylase preferably is an alpha-amylase obtained from Aspergillus oryzae.
Preferably the above-described bread improving composition is added during the mixing of the dough.
The enzymes of the invention may be combined with any other enzyme or ingredient and may be used in the form of for instance a dry powder or a granulate, in particular a non-dusting granulate. Alternatively, they may be used in the form of a liquid, preferably with one or more stabilizer(s) such as polyols, sugars, organic acids or sugar alcohols.
A last aspect of the invention concerns compositions comprising at least one, preferably at least two or three of the enzymes of the invention, possibly combined with a Pseudoalteromonas haloplanktis TAH 3a xylanase, encoded for instance by SEQ ID NO:1.
a and b represent, respectively, the nucleotide (a) and the amino acid (b) sequences of the Pseudoalteromonas haloplanktis TAH 3a xylanase.
a and b represent, respectively, the nucleotide (a) and the amino acid (b) sequences of the strain TAH 2a xylanase.
a and b represent, respectively, the nucleotide (a) and the amino acid (b) sequences of the strain TAH 4a xylanase.
a and b represent, respectively, the nucleotide (a) and the amino acid (b) sequences of the strain TAH 7a xylanase.
a and b represent, respectively, the nucleotide (a) and the amino acid (b) sequences of the strain Sp.10.1 xylanase.
a and b represent, respectively, the nucleotide (a) and the amino acid (b) sequences of the strain Sp.10.2 xylanase.
a and b represent, respectively, the nucleotide (a) and the amino acid (b) sequences of the strain Sp 11.2 xylanase.
a and b represent, respectively, the nucleotide (a) and the amino acid (b) sequences of the strain Sp.23.2 xylanase.
a and b represent, respectively, the nucleotide (a) and the amino acid (b) sequences of the strain Sp.23.2bis xylanase
The invention will be described in further details in the following examples and embodiments by reference to the enclosed drawings. Particular embodiments and examples are not in any way intended to limit the scope of the invention as claimed.
A. Isolation of the Enzyme Producing Microorganisms according to the Invention
A first aspect of the invention is related to the isolation of uncharacterized microorganisms able to produce xylanases with new properties.
Advantageously, these microorganisms are psychrophilic microorganisms isolated from environmental samples collected in the Antarctic and Arctic environments. Methods are described in the literature that relate to the isolation of psychrophilic microorganisms from such samples (Collins T. et al., 2002, J. Biol. Chem. Vol. 277, p. 35133). Typically these methods consist of spread-plating appropriate dilutions of the samples onto solid media of various compositions. Incubations are generally performed at low temperatures (about 4 to about 20° C.), to allow the growth of the psychrophilic microorganisms.
According to a preferred embodiment of the present invention, the solid medium contains a substrate for xylanase such as a hemicellulose-containing material or xylan.
According to a more preferred embodiment of the invention, the solid medium contains a derivatized substrate for the xylanase such as for example RBB-xylan (Remazol Brilliant Blue xylan, Sigma). This substrate allows a better, generally more sensitive, screening of the positive xylanase-producing microorganisms.
It is obvious that techniques other than those described here, exist for the screening of xylanase-positive microorganisms. One such technique involves systematic liquid culturing of microorganisms using e.g. media that contain an inducer for the xylanase such as, but not restricted to, xylan, wheat bran, etc., followed by enzymatic analysis of the culture supernatant and/or of a cell extract.
According to another embodiment of the present invention, the isolated xylanase-positive microorganisms may or may not be identified at the genus or the species level. Techniques such as fatty acid analysis or 16S rDNA sequence analysis are examples of well known identification techniques.
The present invention is more in particular related to isolated strains TAH 2a, TAH 4a, TAH 7a, Sp10.1, Sp10.2, Sp11.2, Sp23.2 and Sp23.2bis.
TAH2a, TAH4a and TAH7a are bacterial strains, more specifically bacterial strains from the genus Pseudoal teromonas.
B. Isolation of Xylanase Encoding Genes
The present invention relates to the isolation of xylanase encoding genes from the above mentioned strains.
It is well know to persons skilled in the art that several techniques may be used to isolate a particular gene from microorganisms. Examples of such techniques include the construction of a gene library from the genomic DNA of the strain in a suitable vector, followed by screening of this library by direct expression of the gene of interest, or by hybridization with a presumed closely related gene or with oligonucleotides designed from reverse transcription of the partial or complete amino acid sequence of the said enzyme.
Other techniques include the amplification of the gene by molecular techniques, for instance PCR techniques, using degenerate or non-degenerate oligonucleotide primers that are designed from a presumed closely related gene.
According to a preferred embodiment of the present invention, the starting sequence used to design such oligonucleotide primers is the sequence of the xylanase gene isolated from Pseudoalteromonas haloplanktis TAH 3a (EMBL Accession number AJ427921, sequence enclosed by reference thereto, see also
An aspect of the invention is related to isolated (and purified) nucleotide sequences SEQ ID NOs: 3, 5, 7, 9, 11, 13, 15, 34, 20, 22, 24, 26, 28, 30, 32, 36 or variants thereof that encode an enzyme according to the invention.
“Variant”, in the present context, is defined as an isolated nucleotide sequence wherein one, or several, nucleotides have been replaced by other nucleotide(s) or wherein one, or several, nucleotides have been added and/or deleted while the encoding enzyme still presents xylanolytic activity.
According to a preferred embodiment of the present invention, the nucleotide sequence of the variant presents more than 50%, 60%, 70%, 80%, 85%, 90%, 95%, preferably more than 97%, 98% or even more than 99% sequence identity to the isolated sequences. According to a more preferred embodiment of the present invention, the nucleotide sequence of the variant presents less than 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 modified nucleotide(s) compared to SEQ ID NOs: 3, 5, 7, 9, 11, 13, 15, 34, 20, 22, 24, 26, 28, 30, 32 or 36.
C. Characterization of the Xylanases of the Invention
Another aspect of the present invention is related to enzymes with xylanolytic activity encoded by any of the nucleotide sequences described above.
According to a preferred embodiment of the present invention, the amino acid sequence of such an enzyme is selected from the group consisting of SEQ ID NOs: 4, 6, 8, 10, 12, 14, 16, 35, 21, 23, 25, 27, 29, 31, 33, 37 or a variant thereof.
In the present context, “variant” is defined as an isolated amino acid sequence wherein one, or several, amino acids have been substituted by one, or several, others, or as an isolated amino acid sequence wherein one, or several, amino acids have been added and/or deleted while preserving all or most of the xylanase activity. Variant enzymes preferably retain at least 80%, more preferably at least 90% and most preferably at least 95% or even 99% of the xylanolytic activity of any of the enzymes characterized by SEQ ID NO: 4, 6, 8, 10, 12, 14, 16, 35, 21, 23, 25, 27, 29, 31, 33 or 37.
According to a preferred embodiment of the present invention, the amino acid sequence of the variant presents more than 50%, 70%, more preferably more than 80%, 85%, 90%, most preferably more than 95%, 97%, 98% or even more than 99% sequence identity with any of SEQ ID NOs: 4, 6, 8, 10, 12, 14, 16, 35, 21, 23, 25, 27, 29, 31, 33 or 37. According to a more preferred embodiment of the present invention, the amino acid sequence of the variant presents less than 4, 3, 2 or 1 modified amino acid(s) compared to any of SEQ ID NOs: 4, 6, 8, 10, 12 14, 16, 35, 21, 23, 25, 27, 29, 31, 33 or 37.
It is well known that most secreted enzymes, such as the enzymes of the present invention, possess a small amino acid sequence at their N terminus that drives the enzyme out of the cell. It is therefore an objective of the present invention to also consider the mature portions of the enzymes as an integral part of the present invention (see e.g. SEQ ID NOs: 21, 23, 25, 27, 29, 31, 33 or 37). However, variants containing modifications in the signal sequence could advantageously be used, as these could eventually be better expressed and/or be better secreted in a recombinant host.
The mature protein starts at amino aid position No. 22 for the enzymes identified by any of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16 or 35.
Another means of characterizing proteins and/or enzymes is to study their identity or their similarity with already known proteins. A first approach could be to use the Blast program that compares a defined sequence to all available published sequences. This program can be used on-line at the following URL (http://www.ncbi.nlm.nih.gov/blast/). To refine and precise the percentage of identity/similarity between two or more proteins the programs Clustal (http://www.ebi.ac.uk/clustalw/) or Align (http://www2.igh.cnrs.fr/bin/align-guess.cgi) may advantageously be used.
A further means of characterizing new proteins and/or enzymes is to analyze their three-dimensional structures. In some cases, this three-dimensional structure is not known. However, by comparing with other available structures of related proteins, this three-dimensional structure could be deduced by a person skilled in the art by using for instance specialized software. Furthermore, for very closely related proteins, e.g. proteins with more than 90% identity/similarity, the changes in properties caused by a particular modification in the amino acid sequence (e.g. amino acid substitution) could be predicted. Such changes could be e.g. substrate binding, protein stabilisation, . . .
Another aspect of the present invention concerns the characterization of the xylanases of the invention by their biochemical properties such as their molecular weight, their temperature optimum or pH optimum. Indeed the enzymes described in the present invention, by means of the examples below, have a relatively low temperature optimum activity. Furthermore, they retain a high catalytic efficiency at low temperature and are therefore considered as psychrophilic xylanases. One way of defining a psychrophilic enzyme is to consider that it is an enzyme that retains at least 40% of its maximal activity at 5° C. Other properties may also be used to define psychrophilic enzymes (see e.g. Georlette D. et al., 2004, FEMS Microbiol. Rev. Vol 28, p. 25 ; D'Amico S. 2002, Philos Trans R Soc Lond B Biol Sci. Vol. 357, p.917).
However, it can not be excluded that there exist enzymes with the sequence characteristics described above that have different biochemical properties.
D. Expression and/or Purification of the Enzymes
Another aspect of the present invention is related to a recombinant nucleotide sequence comprised of one or more adjacent regulatory sequence(s) operably linked to one or more of the nucleotide sequence(s) of the invention as described above.
Said adjacent regulatory sequences may originate from homologous and/or from heterologous microorganisms.
These adjacent regulatory sequences are specific sequences such as but not restricted to promoters, regulators, secretion signals and/or terminators.
Another aspect of the invention is related to a vector containing one or more nucleotide sequences of the invention, possibly operably linked to one or more adjacent regulatory sequence(s) which originate from homologous or/and from heterologous microorganisms.
In the present context, “vector” is defined as any biochemical construct which may be used for the introduction of a nucleotide sequence (by transduction, transfection, transformation, infection, conjugation, etc.) into a cell. Advantageously, the vector described in the invention is selected from the group consisting of plasmids, viruses, phagemids, chromosomes, transposons, liposomes, cationic vesicles, and/or a mixture thereof. Said vector may already contain one or more of the above-described adjacent regulatory sequence(s) (allowing its expression and its transcription into a corresponding peptide by said microorganism). Preferably, said vector is a plasmid incorporated in E. coli and having a deposit number selected from the group consisting of numbers LMBP 4860, LMBP 4861, LMBP 4862, LMBP 4863, LMBP 4864, LMBP 4865 and LMBP 4866.
The present invention is also related to a host cell, preferably a recombinant host cell, “transformed” with one or more of the nucleotide sequences and/or vectors according to the invention that have been described above.
In the present context, “host cell “transformed by one or more of the nucleotide sequences and/or vectors according to the invention” is defined as a cell having incorporated said nucleotide sequence(s) and/or said vector. The transformed host cell may be a cell in which said vector and/or said nucleotide sequence(s) are introduced by means of genetic transformation, preferably by means of homologous recombination, or by another well known method to generate/create a recombinant organism.
A “host cell” may be a cell that, prior to transformation, did not naturally (originally) contain said nucleotide sequence(s) and/or said vector. Alternatively, the “host cell” may also be the original cell containing already one of the nucleotide sequences of the present invention, and genetically modified (recombinant host cell) to overexpress, or express more efficiently, said enzyme (better pH or temperature profile, higher extracellular expression, . . . ).
Preferably, said host cell is capable of overexpressing (higher expression than the expression observed in the original or wild-type microorganism) said nucleotide sequence(s) and/or said vector, advantageously allowing a high production of an amino acid sequence encoded by said nucleotide sequence and/or said vector. The isolated and purified nucleotide sequence(s) described in the present invention may be integrated into the genome of the selected host cell and/or may be present on an episomal vector in said host cell.
Advantageously, the recombinant host cell of the invention is selected from the microbial world, preferably from bacteria or fungi, including yeast.
More preferably the recombinant host cell belongs to the genus Bacillus.
Preferably, said recombinant host cell is modified to obtain an expression of the xylanase enzyme at high levels. This may be obtained by the use of adjacent regulatory sequences capable of directing the overexpression of one or more of the nucleotide sequences of the invention in the recombinant host cell, or by increasing the number of nucleotide copies of the sequences according to the invention.
Above, some of the conditions (culture media, temperature and pH conditions, etc.) have been described that preferably are applied for culturing of the host cell selected for the expression of the xylanase of the invention. For this purpose, the original production species and/or a suitable host cell, transformed with a DNA construct designed to express the said enzyme, are present in or on a suitable growth medium and/or expression medium.
According to the present invention, said protein with xylanolytic activity may be obtained by first culturing the strain in/on a medium suitable for expressing the xylanase, followed by one or several purification steps, such as, but not limited to, centrifugation, cell disruption, microfiltration, ultrafiltration, precipitation, liquid chromatography, freeze-drying, etc. All these techniques are described in the scientific literature and are well known to persons skilled in the art.
Accordingly, the enzyme with xylanolytic activity which is produced according to the present invention, can be used directly for one of the purposes of the present invention and/or, alternatively, may undergo one or more purification and/or (further) culturing steps as described above. In a particular embodiment of the invention, the enzyme(s) of the invention may be used in pure form.
Preparation methods for the enzyme of the present invention include, among others, the preparation and/or purification from cultures of microorganisms, recombinant or not, in shake flasks or in fermentors, and the preparation or purification from immobilized cultures as well as the extraction and/or purification from living cells (plants, . . . )
E. Application of the Enzyme
The xylanase of the invention may be used in different types of applications.
The enzymes with xylanolytic activity described in the present invention, purified or not purified, are particularly suited as bread improving agents or formulas. Bread improving agents or compositions are products that are able to improve and/or increase texture, flavour, anti-staling effects, softness, crumb softness upon storage, freshness, dough machinability and/or volume of a dough and/or a final baked product. Preferably, said enzymes with xylanolytic activity improve the dough handling and/or increase the specific volume of the final baked product.
The term “baked product” includes any product prepared from a dough and obtained after baking of the dough, and includes in particular yeast raised baked products. Dough is obtained from any type of flour or meal (e.g. based on wheat, rye, barley, oat, or maize). Preferably, dough is prepared with wheat and/or with mixes including wheat.
It is one of the aspects of the present invention to show that the enzymes with xylanolytic activity described in the present invention could advantageously be used in a bread improver formula or bread improving composition.
These enzymes with xylanolytic activity advantageously are selected from glycoside hydrolase Family 8 enzymes.
These enzymes with xylanolytic activity advantageously are psychrophilic enzymes.
It is shown in sequel that said enzymes increase the loaf volume of a baked product.
It is further shown that the amount of said enzymes, needed to obtain a particular result in baking, is much lower than the amount generally used/needed when working with commercially available enzymes. Such amount is further referred to as the amount sufficient to obtain the desired result and/or as the effective amount.
In a further aspect, the present invention relates to the additive effect of said enzymes with xylanolytic activity with other enzymes, in particular with an alpha-amylase, preferably an alpha-amylase from Aspergillus oryzae. Said enzymes with xylanolytic activity may be used in combination with other bread improving agents, such as, but not limited to enzymes, emulsifiers, oxidants, milk powder, fats, sugars, amino acids, salts, proteins (gluten, cellulose binding sites), such improving agents being well known to persons skilled in the art. Examples of such enzymes include, but are not restricted to, alpha-amylases, beta-amylases, maltogenic amylases, xylanases, proteases, glucose oxidases, oxido-reductases, glucanases, cellulases, transglutaminases, isomerases, lipases, phospholipases, pectinases, etc.
According to the present invention, the enzymes with xylanolytic activity, purified or not, show hydrolytic activities in the presence of cell wall components. Particularly, said enzymes degrade the wheat cell wall components. Said enzymes may thus be advantageously used in the separation of components of plant cell materials, such as cereal components. Particularly, said enzymes may be used to improve the separation of wheat into gluten and starch by the so-called batter process.
According to the present invention, the enzymes with xylanolytic activity, purified or not, may be used in food processing. They may be used in fruit, vegetable and plant processing. They may be used in wine making and brewing as well as in coffee processing.
Another application of said enzymes resides in feed, where they may be used to improve the growth rate or the feed conversion ratio of animals such as poultry, swine or ruminants.
Yet other applications are the use of the xylanases of the invention in the pulp and paper industry (bio-mechanical pulping, bio-modification of fibers, bio-de-inking, . . . ), in textile processing, in bioremediation, in bioconversion processes,.
The enzymes with xylanolytic activity according to the present invention may be used under several forms. Cells expressing the enzyme, such as yeast, fungi, Archeal bacteria or bacteria, may be used directly in the process. Said enzymes may further be used as a cell extract, a cell-free extract (i.e. portions of the host cell that have been submitted to one or more disruption, centrifugation, extraction and/or other purification steps) or as a purified protein. Any of the above-described forms may be used in combination with one or more enzyme(s) under any of the above-described forms. These whole cells, cell extracts, cell-free extracts and/or purified enzymes may be immobilized by any conventional means on a solid support to allow protection of the enzyme, continuous hydrolysis of the substrate and/or recycling of the enzyme preparation. Said cells, cell extracts (including crude and partially purified extracts), cell-free extracts and/or enzymes may be mixed with different ingredients, and be used e.g. in the form of a dry powder or a granulate, in particular a non-dusting granulate, in the form of a liquid, for example with stabilisers such as polyols, sugars, organic acids or sugar alcohols according to established methods.
The xylanase producing microorganisms were isolated from either wood samples collected in the vicinity of the abandoned French Antarctic station in Port Martin, Terre Adelie, Antarctica (66°40′S; 140°01′E) or from sea water samples collected in the vicinity of Ny-Alesund, Spitzberg, Svalbard, Norway. Screening for xylanase activity was carried out on marine agar (5 g/l tryptone (Difco), 1 g/l yeast extract (Difco), 33 g/l marine salts (Wiegandt), 18 g/l agar (Difco)) supplemented with 0.15% Remazol Brilliant Blue-xylan at 4° C. A clear halo appeared around the xylanase producing microorganisms, allowing the isolation of 7 strains. Those isolated from Antarctica were designated TAH 2a, TAH 4a, TAH 7a, and those isolated from Spitzberg were termed Sp.10.1, Sp.10.2, Sp.11.2, Sp.23.2 and Sp.23.2bis.
The cellular fatty acid composition of strains TAH 2a, TAH 4a and TAH 7a has been determined. These three strains belong most probably to the Pseudoalteromonas sp.
The isolated xylanase producing bacterial strains TAH 2a, TAH 4a, TAH 7a, Sp.10.1, Sp.10.2, Sp.11.2, Sp.23.2 and Sp.23.2bis were cultivated in modified marine broth (5g/liter tryptone (Difco), lg/liter yeast extract (Difco), 20g/liter marine salts (Wiegandt)) supplemented with 15g/liter birchwood xylan (Sigma) (in the case of TAH2a, TAH7a, Sp.10.1, Sp10.2, Sp.11.2, Sp.23.2 and Sp.23.2bis) or 15 g/liter wheat hemicellulose (Beldem) (in the case of TAH 4a) for 72 hours at 4° C.
Preparation of the Enzymes
After centrifugation of the above cultures (see culture conditions above) for 1 h at 18,000× g and 4° C., the supernatant was concentrated by precipitation with 80% ammonium sulphate and resuspended in 20 mM MOPS (3-(N-Morpholino)propanesulfonic acid) at pH 8.0. This suspension was used in baking trials with TAH 4a, Sp.10.1, Sp.10.2, Sp.11.2 and Sp.23.2bis xylanases. In the case of TAH 2a and TAH 7a, however, the resuspended samples were first dialysed overnight against 20 mM MOPS containing 300 mM NaCl and centrifuged at 18,000× g for 1 hour. The soluble (supernatant) and insoluble fractions hence obtained were used in the baking trials for these samples (see example 3).
Characterization of the Enzymes
The activity of the xylanases obtained from strains TAH 2a, TAH 7a (soluble and insoluble fractions as described above) and obtained from strain TAH 4a was determined at various temperatures. The results of this experiment are presented in
Baking trials were performed to demonstrate the positive effect of the xylanases obtained in example 2 in baking. The positive effect was evaluated by the increase in bread volume as compared to a commercially available xylanase and as compared to a reference not containing any of these enzymes.
The xylanases of the invention were tested in Belgian hard rolls that are produced on a large scale every day in Belgium. The procedure described is well known to the craft baker and it is obvious to one skilled in the art that the same results may be obtained by using other protocols or equipment from other suppliers.
The ingredients used are listed in table 1 below:
The ingredients were mixed for 2 min at low and 8 min at high speed in a Diosna SP24 mixer. The final dough temperature as well as the resting and proofing temperature was 25° C. After resting for 15 min at 25° C., the dough was reworked manually and rested for another 10 min. Thereafter, 2 kg dough pieces were made up and proofed for 10 min. The 2-kg dough pieces were divided and made up using the Eberhardt Optimat. 66 g round dough pieces were obtained. After another 5 min resting time, the dough pieces were cut by pressing and submitted to a final proofing stage for 70 min. The dough pieces were baked at 230° C. in a MIWE Condo™ oven with steam (Michael Wenz-Arnstein-Germany). The volume of 6 rolls was measured using the commonly used rapeseed displacement method.
The results of the baking trials are presented in table 2 below:
(*)One unit of Belase B210 xylanase is defined as the amount of enzyme needed to release 1 μmole of reducing sugar (expressed as xylose) from birchwood xylan at 30° C. and pH 4.5 (Nelson-Somogyi method). One unit of the other xylanases is defined as the amount of enzyme needed to release 1 μmole of reducing sugar (expressed as xylose) from birchwood xylan at 25° C. and pH 6.5 (dinitrosalicylic acid method, Miller, G. 1959, Anal. Chem. Vol. 31, p. 426).
(**)With soluble is meant the (soluble) enzyme fraction present in the supernatant (see above).
The above results show that all the xylanases tested had a positive effect on the volume of bread.
Bacterial Strains and Culture Conditions
The strains TAH 2a, TAH 4a, TAH 7a, Sp10.1, Sp10.2, Sp11.2, Sp23.2 and Sp23.2bis described in example 1 were cultivated for 16 h in the modified Marine broth described above (see example 2).
Preparation of Genomic DNA
Genomic DNA was extracted and purified from 16 hour cultures, cultivated at 37° C. in the medium described above, with the Wizard® Genomic DNA Purification kit (Promega).
Cloning of the Xylanase Genes
The xylanase genes were PCR-amplified using VENT polymerase (Biolabs) with the sense primer:
containing an NdeI site (underlined) and the antisense primer:
containing an Xho I site (underlined) and the stop codon (in italics). The concentration of the genomic DNA template used was optimized for each source isolate. After 3 min initial denaturation at 95° C., 25 cycles of amplification were performed using a Progene apparatus (Techne Cambridge, UK). Each cycle included denaturation at 95° C. for 1 min, hybridization at 54° C. for 30 sec, and elongation at 72° C. for 1.5 min.
The fragment obtained from each isolate was cloned into a PCRScript Amp SK (+) vector (Stratagene), using the procedure recommended by the supplier, and used to transform XL10-Gold® Kan ultracompetent cells (Stratagene). Blue-white selection allowed selection of white colonies carrying the PCR-fragment. The sequence of the inserted fragment was determined with an ALF DNA sequencer (Pharmacia Biotech) using purified plasmid preparation (Nucleospin plasmid, Macherey-Nagel).
Sequences of the Xylanases Genes
The sequences of the TAH 2a, TAH 4a, TAH 7a, Sp.10.1, Sp.10.2, Sp.11.2, Sp.23.2 and Sp.23.2bis xylanase genes are shown in
These sequences are highly similar to each other and are also homologous to the published sequence of the xylanase gene from Pseudoalteromonas haloplanktis TAH 3a (EMBL Accession number AJ427921). All enzymes described in the present invention belong to glycoside hydrolase Family 8.
The result of a Clustalw multiple sequence alignment using the default parameters (http://www.ebi.ac.uk/clustalw/) are presented in FIGS. 10 (nucleotide sequences) and 11 (amino acid sequences).
All new sequences differ by at least 20 nucleotides or by at least 4 amino acids from the known published sequence (see below).
In all of the above-identified amino acid sequences, the mature protein (enzyme) starts at amino acid position No. 22.
The closest related amino acid sequences identified by a Blast search using the default parameters (http://www.ncbi.nlm.nih.gov/blast/) are:
The amino acid differences between the published Pseudoalteromonas haloplanktis TAH3a xylanase sequence and the xylanase sequences of the present invention have been identified and are listed in Table 3 below. Their respective positions in the structure, as based on the published structure (Van Petegem F. et al., 2003, J. Biol. Chem. Vol. 278, p. 7531) are also shown.
Overexpression of the Isolated Xylanases
The xylanase gene fragments were excised from PCRScript Amp SK(+) (see example 4 above) with Nde I and Xho I and ligated into the pET 22b(+) expression vector (Novagen). The resulting recombinant plasmids were transformed to E. coli BL21 (DE3) cells (Stratagene).
Plasmids pXYP4 to pXYP10 were transformed to Escherichia coli JM109 (LMBP 4860 to LMBP 4866).
The plasmid containing the xylanase gene from strain TAH 4a was labeled pXYP4 (see LMBP 4860).
The plasmid containing the xylanase gene from strain TAH 7a was labeled pXYP5 (see LMBP 4861).
The plasmid containing the xylanase gene from strain TAH 2a was labeled pXYP6 (see LMBP 4862).
The plasmid containing the xylanase gene from strain Sp.10.1 was labeled pXYP7 (see LMBP 4863).
The plasmid containing the xylanase gene from strain Sp.10.2 was labeled pXYP8 (see LMBP 4864).
The plasmid containing the xylanase gene from strain Sp.11.2 was labeled pXYP9 (see LMBP 4865).
The plasmid containing the xylanase gene from strain Sp.23.2bis was labeled pXYP10 (see LMBP 4866).
Purification of the Xylanases
The xylanases from the TAH 2a, TAH 4a, TAH 7a, Sp10.1, Sp10.2, Sp11.2, Sp23.2 and Sp23.2bis strains were purified as described (Collins et al, 2002, see above) from liquid cultures of recombinant E. coli BL21 (DE3) strains. Five ml of an overnight preculture (18° C.) of the E. coli recombinant strain, expressing one of the cloned genes of example 2, was centrifuged at 10,000× g for 1 min and the pellet was resuspended in 300 ml of Terrific broth (12g/l Bacto tryptone (Difco), 24 g/l yeast extract (Difco), 4 ml/l glycerol, 12.54 g/l K2HPO4, 2.31 g/l KH2PO4) containing 200 μg/ml ampicillin in a 3-liter shake flask. The culture was incubated at 18° C. and 250 rpm until an absorbance at 550 nm of between 3 and 4 was reached, whereupon the expression of the enzyme was induced with 1 mM isopropyl-l-thio-β-galactopyranoside.
Following a further 20 hours incubation at 18° C., the cells were harvested by centrifugation at 18,000× g for 30 min at 4° C., resuspended in buffer A (50 mM BICINE, pH 8.5), disrupted in a prechilled cell disrupter (Constant Systems Ltd.) at 28 Kpounds/square inch, centrifuged at 40.000× g, and dialyzed against buffer A. The dialysate was loaded on a Q-Sepharose Fast flow (Amersham Biosciences) column (50×2.5 cm) equilibrated in the same buffer, and the void was collected. In the case of the xylanases from TAH 2a (SEQ ID NO: 4), TAH 4a (SEQ ID NO: 6), TAH 7a (SEQ ID NO: 8), Sp.11.2 (SEQ ID NO: 14), Sp.23.2 (SEQ ID NO: 16) and Sp.23.2bis (SEQ ID NO: 35), this solution was immediately loaded on a S-Sepharose Fast flow (Amersham Biosciences) column (50×2.5 cm), also equilibrated in the above mentioned buffer, while in the case of the xylanase from Sp10.1 (SEQ ID NO: 10) and Sp10.2 (SEQ ID NO: 12) the pH of this solution was first adjusted to pH 7.6 before loading on a S-Sepharose Fast flow (Amersham Biosciences) column (50×2.5 cm) equilibrated in 50 mM BICINE, pH7.6. Bound protein was eluted with a linear NaCl gradient (0-100 mM in 350 ml) and active fractions were pooled and concentrated by ultrafiltration (Millipore PBGC 10,000 NMWL). This solution was used in the baking trials with xylanases from the strains Sp.10.1 and Sp.10.2, while the xylanases from TAH 2a, TAH 4a, TAH 7a, Sp.11.2, SP.23.2 and Sp.23.2bis strains were firstly further purified on a Sephacryl S-100 (Amersham Biosciences) column (90×2.5 cm) equilibrated in 20 mM MOPS, 100 mM NaCl, pH 7.5 at 1 ml/min.
The purity of the enzymes was demonstrated by electrophoresis on a SDS-polyacrylamide gel. The results thereof are presented in
Baking trials were performed to demonstrate similar positive effect of the recombinant xylanases of the present invention in baking. The positive effect was evaluated by the increase in bread volume as compared to a commercially available xylanase and as compared to a reference not containing any of these enzymes.
The purified or partially purified xylanases from example 5 were evaluated in mini baking tests consisting of preparing dough with 100 g of flour.
The procedure described is well known to one skilled in the art and it is obvious that the same results may be obtained by using other protocols or equipment from other suppliers.
The ingredients used are listed in table 4 below:
The ingredients were mixed for 4.5 min in a National mixer. 150 g dough pieces were weighed and rested for 20 min at 25° C. in plastic boxes. The doughs were reworked and rested for a further 20 min. The final proofing time was 50 min at 36° C. The dough pieces were then baked at 225° C. for 20 min. The volume of the bread was measured using the commonly used rapeseed displacement method.
The results of the baking trials with the recombinant enzymes are presented in table 5 below:
(*)One unit of Belase B210 xylanase is defined as the amount of enzyme needed to release 1 μmole of reducing sugar (expressed as xylose) from birchwood xylan at 30° C. and pH 4.5 (Nelson-Somogyi method). One unit of the other xylanases is defined as the amount of enzyme needed to release 1 μmole of reducing sugar (expressed as xylose) from birchwood xylan at 25° C. and pH 6.5 (dinitrosalicylic acid method, Miller, G. 1959, Anal. Chem. Vol. 31, p. 426).
(1) mean value of three independent trials
(2) mean value of two independent trials
The above results show that the xylanases produced by a recombinant host cell have a similar positive effect on the volume of bread as compared to the wild type enzymes.
Baking trials were performed to demonstrate similar positive effect of the recombinant xylanases of the present invention in baking and to determine the effect of the amounts of xylanase added. The positive effect was evaluated by the increase in bread volume.
The results of the baking trials, with the recombinant enzymes are presented in table 6 below. The protocol as described in Example 3 was followed:
(*)One unit of the other xylanases is defined as the amount of enzyme needed to release 1 μmole of reducing sugar (expressed as xylose) from birchwood xylan at 25° C. and pH 6.5 (dinitrosalicylic acid method, Miller, G. 1959, Anal. Chem. Vol. 31, p. 426).
The results are graphically represented in
The relative amounts of the xylanases described in the above examples, needed to obtain a defined effect on the volume in the Belgian hard rolls assay, have been compared to a commercial commonly used bacterial xylanase (Bel'ase B210—Beldem—Belgium).
The protein concentration of the purified xylanases was determined by absorbance measurement at 280nm using extinction coefficients of 92,860 (in the case of TAH 2a), 94,140 (in the case of TAH 4a and Sp.11.2), 89,730 (in the case of TAH 7a and Sp.23.2), 95,420 (in the case of Sp.10.1) and 94,140 (in the case of Sp.10.2) M−cm−1, and/or with the Bradford protein assay kit (Pierce) as described by the manufacturers.
Several baking trials were performed, according to the method described in example 6, with various amounts of the purified enzymes as described in example 5.
The applicant has made on 4 march 2004 a deposit (under the expert solution) of the micro-organisms Escherichia coli JM109 (pXYP4), Escherichia coli JM109 (pXYP5), Escherichia coli JM109 (pXYP6), Escherichia coli JM109 (pXYP7), Escherichia coli JM109 (pXYP8), Escherichia coli JM109 (pXYP9), Escherichia coli JMlO9 (pXYP10) according to the invention, at the BCCM/LMBP culture collection (Laboratorium voor Moleculaire Biologie, Universiteit Ghent, ‘Fiers-Schell-Van Montagu’ building, Technologiepark 927, B-9052 Gent-Zwijnaarde, Belgium). These deposits received accession numbers LMBP 4860, LMBP 4861, LMBP 4862, LMBP 4863, LMBP 4864, LMBP 4865 and LMBP 4866 respectively.
| Number | Date | Country | Kind |
|---|---|---|---|
| 04447062.3 | Mar 2004 | EP | regional |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/BE05/00035 | 3/11/2005 | WO | 7/19/2007 |
