# Patent

## Title
Xylanse variants having altered sensitivity to xylanse inhibitors

## Abstract

The present invention relates to a variant xylanase polypeptide, or fragment thereof having xylanase activity, comprising one or more amino acid modifications such that the polypeptide or fragment thereof has an altered sensitivity to a xylanase inhibitor as compared with the parent enzyme.

## Background
REFERENCE TO RELATED APPLICATIONS
This application is a continuation-in-part of PCT/IB01/00426, filed Mar. 8, 2001, designating the U.S., published Sep. 13, 2001 as WO 01/66711 and claiming priority from GB 0005585.5 filed Mar. 8, 2000 and GB 0015751.1 filed Jun. 27, 2000. All of the above-mentioned applications, as well as all documents cited herein and documents referenced or cited in documents cited herein, are hereby incorporated by reference.


FIELD OF THE INVENTION
The present invention relates to mutant xylanase enzymes having an altered sensitivity to xylanase inhibitors. The present invention also relates to the use of these mutant enzymes in processing plant materials.
BACKGROUND TO THE INVENTION
For many years, endo-β-1,4-xylanases (EC 3.2.1.8) (referred to herein as xylanases) have been used for the modification of complex carbohydrates derived from plant cell wall material. It is well known in the art that the functionality of different xylanases (derived from different micro organisms or plants) differs enormously.
Comprehensive studies characterising the functionality of xylanases have been done on well characterised and pure substrates (Kormelink et al., 1992). These studies show that different xylanases have different specific requirements with respect to substitution of the xylose backbone of the arabinoxylan (AX). Some xylanases require three un-substituted xylose residues to hydrolyse the xylose backbone; others require only one or two. The reasons for these differences in specificity is thought to be due to the three dimensional structure within the catalytic domains, which in turn is dependent on the primary structure of the xylanase, i.e. the amino acid sequence. However, the translation of these differences in the amino acid sequences into differences in the functionality of the xylanases, has up until now not been documented when the xylanase acts in a complex environment, such as plant material.
The xylanase substrates found in wheat (wheat flour), have traditionally been divided into two fractions: The water un-extractable AX (WU-AX) and the water extractable AX (WE-AX). The WU-AX:WE-AX ratio is approx. 70:30 in wheat flour. There have been numerous explanations as to why there are two different fractions of AX. The older literature (D'Appolonia and MacArthur (1976) and Montgomery and Smith (1955)) describes quite high differences in the substitution degree between WE-AX and WU-AX. The highest degree of substitution was found in WE-AX. This was used to explain why some of the AX was extractable. The high degree of substitution made the polymer soluble, compared to a lower substitution degree, which would cause hydrogen bonding between polymers and consequently precipitation.
The difference between the functionality of different xylanases has been thought to be due to differences in xylanase specificity and thereby their preference for the WU-AX or the WE-AX substrates.
In some applications (e.g. bakery) it is desirable to produce high molecular weight (HMW) soluble polymers from the WU-AX fraction. Such polymers have been correlated to a volume increase in bread making (Rouau, 1993; Rouau et al., 1994 and Courtin et al., 1999).
In other applications it is desirable to modify the HMW WU-AX, making the molecular weight lower, reducing their hydrocolloid effect and hence water-binding in the product (crackers, flour separation, etc.)
These different applications require different functionalities of the xylanases used to do the job. As mentioned above, the difference in functionality has been explained by the different substrate specificities of the xylanases.
SUMMARY OF THE INVENTION
By contrast to earlier studies, we have now shown that other factors are more important in determining xylanase functionality than the substrate specificity of the xylanases determined on pure well-characterised substrates. The data presented herein show that endogenous xylanase inhibitors dictate the functionality of the xylanases currently used in, for example, wheat flour systems. This means that a xylanase that normally modifies the WU-AX, giving increased dough liquid viscosity in a wheat flour system, has a different functionality if the endogenous xylanase inhibitor is absent in the wheat flour. Thus, our findings indicate that the design and application of uninhibited xylanases, for example, using site-directed mutagenesis could be a way to mimic the absence of xylanase inhibitors in various plant materials, giving new xylanases with completely new functionality. Such xylanases would be very effective in applications where a reduction in viscosity is required. The uninhibited xylanase would act rapidly on the AX, and be primarily influenced by its specific activity, rather than by endogenous inhibitors. From our studies, we consider that the inhibitory effects are likely to be far more important than the specific activity. Indeed our results show for the first time that there are 10 to 50 fold differences in inhibition levels between the family 11 xylanases.
Furthermore, we have gone on to design and test a series of xylanases modified by site-directed mutagenesis to demonstrate that xylanases can be produced that have reduced sensitivity to xylanase inhibitors present in plant materials. In particular, we have identified a number of residues in family 11 xylanases which influence the degree of inhibition of the xylanase.
Thus, it will be possible to produce variant xylanases having reduced sensitivity to xylanase inhibitors and hence altered functionality. This will, for example, allow a reduction in the amount of xylanase required in a number of applications such as animal feed, starch production, bakery, flour separation (wetmilling) and, paper and pulp production.
Accordingly, the present invention provides a variant xylanase polypeptide, or fragment thereof having xylanase activity, comprising one or more amino acid modifications such that the polypeptide or fragment thereof has an altered sensitivity to a xylanase inhibitor as compared with the parent enzyme.
Here, the “parent enzyme” is the xylanase enzyme from which the variant xylanase enzyme is derived or derivable. With respect to the term “derivable”, the variant need not necessarily be derived from the parent enzyme. Instead, the variant could be prepared, for example, by use of recombinant DNA techniques that utilise nucleotide sequence(s) encoding said variant xylanase sequence—i.e. here the nucleotide sequence(s) are similar to mutated nucleotide sequence(s) but they are not prepared by mutation of the parent nucleotide sequence(s). The variant may even be prepared by chemically modifying a parent enzyme.
For some embodiments the parent enzyme is the wild type enzyme. The term “wild type” is a term of art understood by skilled persons and includes a phenotype that is characteristic of most of the members of a species occurring naturally and contrasting with the phenotype of a mutant. Thus, in the present context, the wild type enzyme may be a form of the enzyme naturally found in most members of the relevant species. Generally, the relevant wild type enzyme in relation to the variant polypeptides of the invention is the most closely related corresponding wild type enzyme in terms of sequence homology. For example, for the particular mutant xylanases described in the examples, the corresponding wild type enzyme is the wild type B. subtilis xylanase A, more specifically the wild type B. subtilis xylanase A published by Paice et al., 1986 and shown as SEQ I.D. 1. However, where a particular wild type sequence has been used as the basis for producing a variant polypeptide of the invention, this will be the corresponding wild type sequence regardless of the existence of another wild type sequence that is more closely related in terms of amino acid sequence homology.
For some embodiments, preferably the variant polypeptide is derived from a family 11 xylanase.
One of our surprising findings is that in our studies so far a mutation in the xylanase active site has no measurable effect on inhibition against the xylanase inhibitor. This is in direct contrast to the mutation(s) that are made outside of the active site—which mutations are discussed in more detail below.
In a preferred aspect the amino acid modification is of one or more surface amino acid residues.
In a more preferred aspect the amino acid modification is of one or more solvent accessible residues. Here, the solvent is water.
In a more preferred aspect the amino acid modification is of one or more surface residues outside of the active site.
In a highly preferred aspect the amino acid modification is of one or more surface residues outside of the active site and which is/are at least 8% solvent accessible. Here, the solvent is water.
In a highly preferred aspect the amino acid modification is of one or more surface residues outside of the active site and which is/are at least 10% solvent accessible. Here, the solvent is water.
Solvent accessibility can be determined using Swiss-PdbViewer (version 3.5b1), which can be located via the internet at web pages maintained by. Glaxo Wellcome Experimental Research.
The surface amino acids of xylanase enzymes are determinable by a person skilled in the art.
By way of example, the B. subtilis amino acid sequence for xylanase A is shown as SEQ I.D. No. 1. With respect to this sequence, the surface amino acid residues are:

    
    
        Ala1-Trp6, Asn8, Thr10-Gly23, Asn25, Ser27, Asn29, Ser31-Asn32, Gly34, Thr43-Thr44, Ser46-Thr50, Asn52, Asn54, Gly56-Asn61, Asn63, Arg73-Leu76, Thr87-Arg89, Thr91-Lys95, Thr97, Lys99, Asp101-Gly102, Thr104, Thr109-Thr111, Tyr113-Asn114, Asp119-Thr124, Thr126, Gln133-Asn141, Thr143, Thr145, Thr147-Asn148, Asn151, Lys154-Gly157, Asn159-Leu160, Ser162-Trp164, Gln175, Ser177, Ser179, Asn181, Thr183, Trp185.
    
    


As indicated, the surface amino acids of other xylanase enzymes (such as Thermomyces lanuginosus xylanase A, whose coding nucleotide sequence is presented as SEQ ID No. 9) are determinable by a person skilled in the art.
Hence, for some aspects the present invention encompasses a variant xylanase polypeptide, or fragment thereof having xylanase activity, which variant xylanase polypeptide or fragment comprises one or more amino acid modifications at any one of amino acid residues:

    
    
        Ala1-Trp6, Asn8, Thr10-Gly23, Asn25, Ser27, Asn29, Ser31-Asn32, Gly34, Thr43-Thr44, Ser46-Thr50, Asn52, Asn54, Gly56-Asn61, Asn63, Arg73-Leu76, Thr87-Arg89, Thr91-Lys95, Thr97, Lys99, Asp101-Gly102, Thr104, Thr109-Thr111, Tyr113-Asn114, Asp119-Thr124, Thr126, Gln133-Asn141, Thr143, Thr145, Thr147-Asn148, Asn151, Lys154-Gly157, Asn159-Leu160, Ser162-Trp164, Gln175, Ser177, Ser179, Asn181, Thr183, Trp185

of the B. subtilis amino acid sequence shown as SEQ I.D. No. 1 or its/their equivalent positions in other homologous xylanase polypeptides.

    
    


Thus, in one embodiment, the present invention provides a variant xylanase polypeptide, or fragment thereof having xylanase activity, comprising one or more amino acid modifications at any one of amino acid residues numbers:

    
    
        11, 12, 13, 15, 17, 29, 31, 32, 34, 113, 114, 119, 120, 121, 122, 123, 124 and 175

of the B. subtilis amino acid sequence shown as SEQ I.D. No. 1 or their equivalent positions in other homologous xylanase polypeptides.

    
    


In one embodiment, the present invention provides a variant xylanase polypeptide or fragment thereof having xylanase activity, comprising one or more amino acid modifications at any one of amino acid residues numbers 11, 12 and 13 of the B. subtilis amino acid sequence shown as SEQ I.D. No. 1 or their equivalent positions in other homologous xylanase polypeptides.
Specific preferred examples of modifications made are presented in the Examples section herein.
For some embodiments, preferably the variant xylanase polypeptide, or fragment thereof having xylanase activity, comprises one or more amino acid modifications at any one of amino acid residues numbers: 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 61, 62, 63, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 173, 174, 175, 176, 177, 178 of the B. subtilis amino acid sequence shown as SEQ I.D. No. 1 or their equivalent positions in other homologous xylanase polypeptides.
For convenience, we sometimes refer to the amino acid residues numbers: 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 36, 37, 61, 62, 63, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 173, 174, 175, 176, 177, 178 as BAND 1.
FIG. 1 shows the 3-D structure of B. subtilis xylanase having the amino acid sequence shown as SEQ I.D. No. 1. BAND 1 is depicted in FIG. 1 as the upper layer of the molecule and extends approximately 13 Ångstroms from the top of the molecule when the molecule is orientated as shown in FIG. 1. BAND 1 ends with the residue Phe 125 on the left hand side when viewing FIG. 1 and with the residue Asn 61 on the right hand side when viewing FIG. 1.
In addition, or in the alternative, for some embodiments, preferably the variant xylanase polypeptide, or fragment thereof having xylanase activity, comprises one or more amino acid modifications at any one of the other amino acid residues.
Preferably said other modifications may occur at any one or more of amino acid residues numbers: 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58, 59, 60, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 108, 109, 110, 126, 127, 128, 129, 130, 131, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 179, 180, 181, 182, 183 of the B. subtilis amino acid sequence shown as SEQ I.D. No. 1 or their equivalent positions in other homologous xylanase polypeptides.
For convenience, we sometimes refer to the amino acid residues numbers: 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56, 57, 58, 59, 60, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 108, 109, 110, 126, 127, 128, 129, 130, 131, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 179, 180, 181, 182, 183 of the B. subtilis amino acid sequence shown as BAND 2.
Preferably said other modifications may occur at any one or more of the surface amino acid residues numbers: 3, 4, 5, 6, 19, 20, 21, 22, 23, 25, 27, 43, 44, 56, 57, 58, 59, 60, 73, 74, 75, 76, 87, 89, 91, 92, 93, 94, 109, 110, 126, 159, 160, 162, 163, 164, 179, 181, 183 of the B. subtilis amino acid sequence shown as SEQ I.D. No. 1 or their equivalent positions in other homologous xylanase polypeptides.
Preferably, the present invention encompasses a variant xylanase polypeptide, or fragment thereof having xylanase activity, which comprises one or more amino acid modifications in BAND 1 and optionally/or BAND 2 of the B. subtilis amino acid sequence or their equivalent positions (bands) in other homologous xylanase polypeptides. Hence, the modification is in at least BAND 1; but could be in just BAND 2 alone.
The variant xylanase polypeptide may comprise other modifications in other amino acid residues, such as modification at any one of amino acid residues: 1, 2, 46, 47, 48, 49, 50, 51, 52, 53, 54, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 184, 185 of the B. subtilis amino acid sequence shown as SEQ I.D. No. 1 or their equivalent positions in other homologous xylanase polypeptides.
The variant xylanase polypeptide may comprise other modifications in other surface amino acid residues, such as modification at any one of the surface amino acid residues: 1, 2, 46, 47, 48, 49, 50, 52, 54, 95, 97, 99, 101, 102, 104, 133, 134, 135, 136, 137, 138, 139, 140, 141, 143, 145, 147, 148, 151, 154, 155, 156, 157, 185 of the B. subtilis amino acid sequence shown as SEQ I.D. No. 1 or their equivalent positions in other homologous xylanase polypeptides.
Preferably, the inhibitor is an inhibitor found naturally in plant tissues. Preferably the sensitivity of the variant xylanase enzyme to the inhibitor is reduced as compared to the parent xylanase enzyme.
The present invention also provides a nucleic acid molecule (a nucleotide sequence) encoding a polypeptide of the invention. Also provided is a vector comprising a nucleic acid of the invention, optionally operably linked to a regulatory sequence capable of directing expression of said nucleic acid in a suitable host cell. A host cell comprising a nucleic acid or a vector of the invention is also provided.
In another aspect the present invention provides a method of making a polypeptide of the invention comprising transforming a host cell with a nucleic acid encoding said polypeptide, culturing the transformed cell and expressing said polypeptide.
Our results show that these variant polypeptides have improved properties that make them suitable for a variety of applications, such as bakery, animal feed, starch production, flour separation (wetmilling) and, paper and pulp production.
Accordingly, the present invention also provides the use of a variant polypeptide of the invention in a method of modifying plant materials.
Also provided is the use of a variant polypeptide of the invention in baking. The invention further provides the use of a variant polypeptide of the invention in processing cereals, starch production and animal feed and the use of a variant polypeptide of the invention in processing wood, for example in enhancing the bleaching of wood pulp.
In a further aspect, the present invention provides a method of altering the sensitivity of a xylanase polypeptide to an inhibitor which method comprises modifying one or more amino acid residues of said enzyme selected from amino acid numbers 11, 12, 13, 15, 17, 29, 31, 32, 34, 113, 114, 119, 120, 121, 122, 123, 124 and 175 based on the amino acid numbering of B. subtilis xylanase shown as SEQ ID No. 1, or the equivalent residues in other homologous xylanase polypeptides. Preferably the sensitivity is reduced.
Importantly, our results also show for the first time that xylanase inhibitors play an important role in determining the functionality of xylanase enzymes in a complex system, such as a plant material. By the term “functionality”, we mean the biochemical properties of the xylanase in a given system. These properties include substrate specificity, Km and Vmax kinetic parameters (where appropriate) and the nature of the reaction products obtained by the action of the xylanase in that system. Functionality may also consequently be described in terms of the effect on the physical and/or chemical properties of the plant materials on which the xylanase acts, for example the extent to which the viscosity of the material is altered.
In the same way that variant xylanases may be used in a variety of processing applications, xylanase inhibitors may be used in a variety of processing applications such as bakery, wood pulp processing and cereal processing.



BRIEF DESCRIPTION OF THE DRAWINGS
The following Detailed Description, given by way of example, and not intended to limit the invention to specific embodiments described, may be understood in conjunction with the accompanying Figures, in which:
FIG. 1 shows the 3-D structure of B. subtilis xylanase having the amino acid sequence shown as SEQ I.D. No. 1; and,
FIG. 2 shows amino acid sequence alignment data in respect of 51 Family 11 xylanases (SEQ ID NOs: 16 to 66, from top to bottom).



DETAILED DESCRIPTION OF THE INVENTION
Although in general any molecular techniques mentioned herein are well known in the art, reference may be made in particular to Sambrook et al., Molecular Cloning, A Laboratory Manual (1989) and Ausubel et al., Short Protocols in Molecular Biology (1999)4th Ed, John Wiley & Sons, Inc.
A. Variant Xylanase Polypeptides
Xylanase enzymes have been reported from nearly 100 different organisms, including plants, fungi and bacteria. The xylanase enzymes are classified into several of the more than 40 families of glycosyl hydrolase enzymes. The glycosyl hydrolase enzymes, which include xylanases, mannanases, amylases, β-glucanases, cellulases, and other carbohydrases, are classified based on such properties as the sequence of amino acids, the three dimensional structure and the geometry of the catalytic site (Gilkes, et al., 1991, Microbiol. Reviews 55: 303-315).
Of particular interest for baking applications are the enzymes classified in Family 11. All of these are xylanases and are known as the “Family 11 xylanases”. Some publications refer to these synonymously as the Family G xylanases, but the term “Family 11 xylanases” will be used herein to refer to both Family G and Family 11 xylanases.
Table A lists a number of known Family 11 xylanases. Most of them have a molecular mass of about 21,000 Da. Three of the Family 11 xylanases (Clostridium stercorarium XynA, Streptomyces lividans XynB, and Thermomonospora fusca XynA) have a higher molecular mass of 31,000 to 50,000 Da. However, these xylanases have a catalytic core sequence of about 21,000 Da similar to the other Family 11 xylanases. The amino acid sequences of the Family 11 xylanases (or, for the larger enzymes, the catalytic core) show a high degree of similarity, usually with more than 40% identical amino acids in a proper amino acid alignment. The Family 11 xylanases, which are of bacterial, yeast, or fungal origin, share the same general molecular structure.
FIG. 2 shows amino acid sequence alignment data in respect of 51 Family 11 xylanases.







TABLE A





Family 11 xylanases
















Aspergillus niger Xyn A
Aspergillus kawachii Xyn C


Aspergillus tubigensis Xyn A
Bacillus circulans Xyn A


Bacillus pumilus Xyn A
Bacillus subtilis Xyn A


Cellulomonas fimi Xyn D
Chainia spp. Xyn


Clostridium acetobutylicum Xyn B
Clostridium stercorarium Xyn A


Fibrobacter succinogenes Xyn C
Neocallimastix patriciarum Xyn A


Nocardiopsis dassonvillei Xyn II
Ruminococcus flavefaciens Xyn A


Schizophyllum commune Xyn
Streptomyces lividans Xyn B


Streptomyces lividans Xyn C
Streptomyces sp. No. 36a Xyn


Streptomyces thermoviolaceus Xyn II
Thermomonospora fusca Xyn A


Trichoderma harzianum Xyn
Trichoderma reesei Xyn I


Trichoderma reesei Xyn II
Trichoderma viride Xyn









Variant Xylanases of the Invention

A variant xylanase polypeptide of the invention is typically obtained by modifying a xylanase polypeptide by substituting, deleting or adding one or more amino acid residues within the amino acid sequence of the xylanase polypeptide. Preferably the modification comprises one or more amino acid substitutions. Modification of polypeptide sequences can be carried out using standard techniques such as site directed mutagenesis. The modification may also occur by chemical techniques—such as chemical modification of one or more amino acid residues.
The starting sequence may be a wild type sequence or a non-naturally occurring sequence, for example a derivative that has already been subjected to protein engineering. The xylanase sequence to be modified may be from any source, for example a bacterial, fungal or plant source. Preferably the xylanase sequence to be modified is that of a Family 11 xylanase, more preferably a Family 11 xylanase selected from Trichoderma reesei xylanase I, Trichoderma reesei xylanase II, Trichoderma harzianum xylanase, Trichoderma viride xylanase, Bacillus circulans xylanase A, Bacillus subtilis xylanase A, Aspergillus niger xylanase A, Aspergillus kawachii xylanase C, Aspergillus tubigensis xylanase A, Streptomyces lividans xylanase B, and Streptomyces lividans xylanase C.
In a particularly preferred embodiment, the xylanase sequence to be modified is the B subtilis xylanase sequence shown as SEQ ID No. 1 or a homologue thereof. Preferably said homologue has at least 40, 50, 60 or 80% homology over at least 50 or 100 amino acid residues as determined using the GCG Wisconsin Bestfit package (University of Wisconsin, U.S.A.; Devereux et al., 1984, Nucleic Acids Research 12:387).
Specific modifications that are preferred according to the present invention include one or more amino acid substitutions at positions 11, 12, 13, 15, 17, 29, 31, 32, 34, 113, 114, 119, 120, 121, 122, 123, 124 and 175 based on the amino acid numbering of B. subtilis xylanase shown as SEQ ID No. 1, or the equivalent residues in other homologous xylanase polypeptides.
Particularly preferred substitutions include one or more of D11ΠY, D11ΠN, D11ΠF, D11ΠK, D11ΠS, D11ΠW, G12ΠF, G13ΠF, I15ΠK, N17ΠK, N17ΠY, N17ΠD, N29ΠK, N29ΠY, N29ΠD, S31ΠK, S31ΠY, S31ΠD, N32ΠK, G34ΠD, G34ΠF, G34ΠT, Y113ΠA, Y113ΠD, Y113ΠK, N114ΠA, N114ΠD, N114ΠF, N114ΠK, D119ΠK, D119Y, D119ΠN, G120ΠK, G120ΠD, G120ΠF, G120ΠY, G120ΠN, D121ΠN, D121ΠK, D121ΠF, D121ΠA, R122ΠD, R122ΠF, R122ΠA, T123ΠK, T123ΠY, T123ΠD, T124ΠK, T124ΠY, T124ΠD, Q175ΠE, Q175ΠS and Q175ΠL (with reference to the amino acid sequence of B. subtilis xylanase) or their equivalents in other homologous xylanase polypeptides. Further references to specific residues of the B. subtilis xylanase shown as SEQ ID No. 1 will also include their equivalents in other homologous xylanase polypeptides.
A combination of mutations may be carried out, for example mutations at two or more of the above-mentioned residues. Examples of such combinations are presented in the Examples section herein.
In a further embodiment, the variant polypeptides of the invention may be purified and isolated naturally occurring mutant xylanases. Alternatively, mutant xylanases may be generated by subjecting organisms to mutagens and then screening for individuals comprising mutations in their xylanase genes. Naturally occurring mutants and mutants generated by random mutagenesis may be identified/screened using a variety of techniques such as PCR screening using suitable nucleic acid primers to amplify regions of xylanase genes and sequencing the resulting fragments.
Thus variant polypeptides of the invention include naturally occurring mutant xylanases (purified and isolated from the organisms in which they occur or obtained recombinantly), mutant xylanases obtained by random mutagenesis and mutant xylanases obtained by site-directed mutagenesis.
Variant polypeptides of the invention may also be subjected to further modifications that do not necessarily affect sensitivity to inhibitors, including any substitution of, variation of, modification of, replacement of, deletion of or addition of one (or more) amino acids from or to the sequence providing the resultant amino acid sequence retains xylanase activity, preferably having at least substantially the same xylanase activity as the unmodified sequence.
Conservative substitutions may be made, for example according to the Table below. Amino acids in the same block in the second column and preferably in the same line in the third column may be substituted for each other:

















ALIPHATIC
Non-polar
G A P





I L V




Polar - uncharged
C S T M





N Q




Polar - charged
D E





K R



AROMATIC

H F W Y










Polypeptides of the invention also include fragments of the full length sequences mentioned above having xylanase activity.
Polypeptides of the invention may further comprise heterologous amino acid sequences, typically at the N-terminus or C-terminus, preferably the N-terminus. Heterologous sequence may include sequences that affect intra or extracellular protein targeting (such as leader sequences).
Polypeptides of the invention are typically made by recombinant means, for example as described below. However they may also be made by synthetic means using techniques well known to skilled persons such as solid phase synthesis. Polypeptides of the invention may also be produced as fusion proteins, for example to aid in extraction and purification. It may also be convenient to include a proteolytic cleavage site between the fusion protein partner and the protein sequence of interest to allow removal of fusion protein sequences, such as a thrombin cleavage site. Preferably the fusion protein will not hinder the function of the protein sequence of interest.
The use of appropriate host cells is expected to provide for such post-translational modifications as may be needed to confer optimal biological activity on recombinant expression products of the invention.
Polypeptides of the invention may be in a substantially isolated form. It will be understood that the protein may be mixed with carriers or diluents which will not interfere with the intended purpose of the protein and still be regarded as substantially isolated. A polypeptide of the invention may also be in a substantially purified form, in which case it will generally comprise the protein in a preparation in which more than 90%, e.g. 95%, 98% or 99% of the protein in the preparation is a polypeptide of the invention.
Variant polypeptides of the invention have altered sensitivity to xylanase inhibitors compared to the parent xylanase sequence—which may be a corresponding wild type xylanase. Preferably, variant polypeptides have reduced sensitivity to xylanase inhibitors. The term “altered sensitivity to xylanase inhibitors” means that extent to which the endo-β-1,4-xylanase activity of a variant polypeptide of the invention is inhibited by the xylanase inhibitor is different to that of the parent xylanase enzyme—which may be the corresponding wild type xylanase. Preferably the extent to which the variant polypeptide is inhibited by the inhibitor is less than that of the parent xylanase enzyme—which may be the wild type protein. This may, for example, be due to a change in the three-dimensional structure of the variant polypeptide such that the inhibitor no longer binds with the same affinity as it does to the parent xylanase enzyme—which may be the wild type enzyme.
The sensitivity of the variant polypeptides of the invention to xylanase inhibitors can be assayed using, for example, the assay described in example 4 and below. A suitable inhibitor for use in the assay is the inhibitor purified from wheat flour in example 1. Other inhibitors are described below.
Xylanase Assay (Endo-β-1,4-Xylanase Activity)
Xylanase samples are diluted in citric acid (0.1 M)-di-sodium-hydrogen phosphate (0.2 M) buffer, pH 5.0, to obtain approx. OD=0.7 in the final assay. Three dilutions of the sample and an internal standard with a defined activity are thermostated for 5 minutes at 40° C. At time=5 minutes, 1 Xylazyme tab (crosslinked, dyed xylan substrate) is added to the enzyme solution. At time=15 minutes (or in some cases longer, depending on the xylanase activity present in the sample) the reaction is terminated, by adding 10 ml of 2% TRIS. The reaction mixture is centrifuged and the OD of the supernatant is measured at 590 nm. Taking into account the dilutions and the amount of xylanase, the activity (TXU, Total-Xylanase-Units) of the sample can be calculated relative to the standard.
Xylanase Inhibitors
As used herein, the term “xylanase inhibitor” refers to a compound, typically a protein, whose role is to control the depolymerisation of complex carbohydrates, such as arabinoxylan, found in plant cell walls. These xylanase inhibitors are capable of reducing the activity of naturally occurring xylanase enzymes as well as those of fungal or bacterial origin. Although the presence of xylanase inhibitors have been reported in cereal seeds (see for example McLauchlan et al 1999a; Rouau and Suget 1998) their impact on the efficacy of xylanase enzymes has not been extensively examined.
McLauchlan et al (1999a) disclose the isolation and characterisation of a protein from wheat that binds to and inhibits two family-11 xylanases. Likewise, WO 98/49278 demonstrates the effect of a wheat flour extract on the activity of a group of microbial xylanases all of which are classified as family 11 xylanases. Debyser et al. (1999) also disclose that endoxylanases from Aspergillus niger and Bacillus subtilis, which are both members of the family 11 xylanases were inhibited by a wheat xylanase inhibitor called TAXI. McLauchlan et al (1999b) teach that extracts from commercial flours such as wheat, barley, rye and maize are capable of inhibiting both family 10 and 11 xylanases.
The xylanase inhibitor may be any suitable xylanase inhibitor. By way of example, the xylanase inhibitor may be the inhibitor described in WO-A-98/49278 and/or the xylanase inhibitor described by Rouau, X. and Surget, A. (1998), McLauchlan, R., et al. (1999) and/or the xylanase inhibitor described in UK patent application number 9828599.2 (filed 23 Dec. 1998), UK patent application number 9907805.7 (filed 6 Apr. 1999) and UK patent application number 9908645.6 (filed 15 Apr. 1999).
Xylanase Inhibitor Assay
100 μl of an candidate inhibitor fraction, 250 μl xylanase solution (containing 12 TXU microbial xylanase/ml) and 650 μl buffer (0.1 M citric acid-0.2M di-sodium hydrogen phosphate buffer, pH 5.0) are mixed. The mixture is thermostated for 5 minutes at 40.0° C. At time=5 minutes one Xylazyme tab is added. At time=15 minutes the reaction is terminated by adding 10 ml 2% TRIS. The reaction mixture is centrifuged (3500 g, 10 minutes, room temperature) and the supernatant is measured at 590 nm. The inhibition is calculated as residual activity compared to the blank. The blank is prepared the same way, except that the 100 μl inhibitor is substituted with 100 μl buffer (0.1 M citric acid-0.2 M di-sodium hydrogen phosphate buffer, pH 5.0).
Specific Xylanase Inhibitor
As indicated, a xylanase inhibitor that may be used in accordance with the present invention is the xylanase inhibitor described in UK patent application number 9828599.2 (filed 23 Dec. 1998), UK patent application number 9907805.7 (filed 6 Apr. 1999) and UK patent application number 9908645.6 (filed 15 Apr. 1999).
This endogenous endo-β-1,4-xylanase inhibitor is obtainable from wheat flour. The inhibitor is a di-peptide, having a MW of about 40 kDa (as measured by SDS-PAGE or mass spectrometry) and a pI of about 8 to about 9.5.
Sequence analysis to date has revealed the that the inhibitor has at least one or more of the sequences presented as SEQ ID No. 2, SEQ ID No. 3, SEQ ID No 4, SEQ ID No. 5, SEQ ID No. 6, SEQ ID No. 7 and/or SEQ ID No. 8.
These inhibitors described in the prior art may also be used in assays to determine the sensitivity of a variant polypeptide of the invention to xylanase inhibitors. They may also be used as described below to modulate the functionality of a xylanase.
Polynucleotides
Polynucleotides of the invention comprise nucleic acid sequences encoding the variant polypeptide sequences of the invention. It will be understood by a skilled person that numerous different polynucleotides can encode the same polypeptide as a result of the degeneracy of the genetic code. In addition, it is to be understood that skilled persons may, using routine techniques, make nucleotide substitutions that do not affect the polypeptide sequence encoded by the polynucleotides of the invention to reflect the codon usage of any particular host organism in which the polypeptides of the invention are to be expressed.
Polynucleotides of the invention may comprise DNA or RNA. They may be single-stranded or double-stranded. They may also be polynucleotides which include within them synthetic or modified nucleotides. A number of different types of modification to oligonucleotides are known in the art. These include methylphosphonate and phosphorothioate backbones, addition of acridine or polylysine chains at the 3′ and/or 5′ ends of the molecule. For the purposes of the present invention, it is to be understood that the polynucleotides described herein may be modified by any method available in the art. Such modifications may be carried out in order to enhance the in vivo activity or life span of polynucleotides of the invention.
Nucleotide Vectors and Host Cells
Polynucleotides of the invention can be incorporated into a recombinant replicable vector. The vector may be used to replicate the nucleic acid in a compatible host cell. Thus in a further embodiment, the invention provides a method of making polynucleotides of the invention by introducing a polynucleotide of the invention into a replicable vector, introducing the vector into a compatible host cell, and growing the host cell under conditions which bring about replication of the vector. The vector may be recovered from the host cell. Suitable host cells include bacteria such as E. coli, yeast and fungi.
Preferably, a polynucleotide of the invention in a vector is operably linked to a regulatory sequence which is capable of providing for the expression of the coding sequence by the host cell, i.e. the vector is an expression vector. The term “operably linked” refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner. A regulatory sequence “operably linked” to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences. The term “regulatory sequences” includes promoters and enhancers and other expression regulation signals.
Enhanced expression of the polynucleotide encoding the polypeptide of the invention may also be achieved by the selection of heterologous regulatory regions, e.g. promoter, secretion leader and terminator regions, which serve to increase expression and, if desired, secretion levels of the protein of interest from the chosen expression host and/or to provide for the inducible control of the expression of the polypeptide of the invention.
Aside from the promoter native to the gene encoding the polypeptide of the invention, other promoters may be used to direct expression of the polypeptide of the invention. The promoter may be selected for its efficiency in directing the expression of the polypeptide of the invention in the desired expression host.
In another embodiment, a constitutive promoter may be selected to direct the expression of the desired polypeptide of the invention. Examples of strong constitutive and/or inducible promoters which are preferred for use in fungal expression hosts are those which are obtainable from the fungal genes for xylanase (xlnA), phytase, ATP-synthetase, subunit 9 (oliC), triose phosphate isomerase (tpi), alcohol dehydrogenase (AdhA), α-amylase (amy), amyloglucosidase (AG—from the glaA gene), acetamidase (amdS) and glyceraldehyde-3-phosphate dehydrogenase (gpd) promoters.
Examples of strong yeast promoters are those obtainable from the genes for alcohol dehydrogenase, lactase, 3-phosphoglycerate kinase and triosephosphate isomerase.
Examples of strong bacterial promoters are the α-amylase and SP02 promoters as well as promoters from extracellular protease genes.
Hybrid promoters may also be used to improve inducible regulation of the expression construct.
Often, it is desirable for the polypeptide of the invention to be secreted from the expression host into the culture medium from where the polypeptide of the invention may be more easily recovered. According to the present invention, the polypeptide of the invention's native secretion leader sequence may be used to effect the secretion of the expressed polypeptide of the invention. However, an increase in the expression of the polypeptide of the invention sometimes results in the production of the protein in levels beyond that which the expression host is capable of processing and secreting, creating a bottleneck such that the protein product accumulates within the cell. Accordingly, the present invention also provides heterologous leader sequences to provide for the most efficient secretion of the polypeptide of the invention from the chosen expression host.
According to the present invention, the secretion leader may be selected on the basis of the desired expression host. A heterologous secretion leader may be chosen which is homologous to the other regulatory regions of the expression construct. For example, the leader of the highly secreted amyloglucosidase (AG) protein may be used in combination with the amyloglucosidase (AG) promoter itself, as well as in combination with other promoters. Hybrid signal sequences may also be used with the context of the present invention.
Examples of preferred heterologous secretion leader sequences are those originating from the fungal amyloglucosidase (AG) gene (glaA—both 18 and 24 amino acid versions e.g. from Aspergillus), the α-factor gene (yeasts e.g. Saccharomyces and Kluyveromyces) or the α-amylase gene (Bacillus).
Such vectors may be transformed into a suitable host cell as described above to provide for expression of a polypeptide of the invention. Thus, in a further aspect the invention provides a process for preparing polypeptides according to the invention which comprises cultivating a host cell transformed or transfected with an expression vector as described above under conditions to provide for expression by the vector of a coding sequence encoding the polypeptides, and recovering the expressed polypeptides. Suitable host cells include, for example, fungal cells, such as Aspergillus and yeast cells, such as yeast cells of the genus Kluyveromyces or Saccharomyces. Other suitable host cells are discussed below.
The vectors may be for example, plasmid, virus or phage vectors provided with an origin of replication, optionally a promoter for the expression of the said polynucleotide and optionally a regulator of the promoter. The vectors may contain one or more selectable marker genes. The most suitable selection systems for industrial micro-organisms are those formed by the group of selection markers which do not require a mutation in the host organism. Examples of fungal selection markers are the genes for acetamidase (amdS), ATP synthetase, subunit 9 (oliC), orotidine-5′-phosphate-decarboxylase (pvrA), phleomycin and benomyl resistance (benA). Examples of non-fungal selection markers are the bacterial G418 resistance gene (this may also be used in yeast, but not in fungi), the ampicillin resistance gene (E. coli), the neomycin resistance gene (Bacillus) and the E. coli uidA gene, coding for β-glucuronidase (GUS). Vectors may be used in vitro, for example for the production of RNA or used to transfect or transform a host cell.
A further embodiment of the invention provides host cells transformed or transfected with a polynucleotide of the invention. Preferably said polynucleotide is carried in a vector for the replication and expression of said polynucleotides. The cells will be chosen to be compatible with the said vector and may for example be prokaryotic (for example bacterial), fungal, yeast or plant cells.
Bacteria from the genus Bacillus are very suitable as heterologous hosts because of their capability to secrete proteins into the culture medium. Other bacteria suitable as hosts are those from the genera Streptomyces and Pseudomonas. 
Depending on the nature of the polynucleotide encoding the polypeptide of the invention, and/or the desirability for further processing of the expressed protein, eukaryotic hosts such as yeasts or fungi may be preferred. In general, yeast cells are preferred over fungal cells because they are easier to manipulate. However, some proteins are either poorly secreted from the yeast cell, or in some cases are not processed properly (e.g. hyperglycosylation in yeast). In these instances, a fungal host organism should be selected.
A heterologous host may also be chosen wherein the polypeptide of the invention is produced in a form which is substantially free from other xylanases. This may be achieved by choosing a host which does not normally produce such enzymes.
Examples of preferred expression hosts within the scope of the present invention are fungi such as Aspergillus species and Trichoderma species; bacteria such as Bacillus species, Streptomyces species and Pseudomonas species; and yeasts such as Kluyveromyces species and Saccharomyces species.
Particularly preferred expression hosts may be selected from Aspergillus niger, Aspergillus niger var. tubigenis, Aspergillus niger var. awamori, Aspergillus aculeatis, Aspergillus nidulans, Aspergillus oryzae, Trichoderma reesei, Bacillus subtilis, Bacillus licheniformis, Bacillus amyloliquefaciens, Kluyveromyces lactis and Saccharomyces cerevisiae. 
According to the present invention, the production of the polypeptide of the invention can be effected by the culturing of microbial expression hosts, which have been transformed with one or more polynucleotides of the present invention, in a conventional nutrient fermentation medium.
The fermentation medium can comprise a known culture medium containing a carbon source (e.g. glucose, maltose, molasses, etc.), a nitrogen source (e.g. ammonium sulphate, ammonium nitrate, ammonium chloride, etc.), an organic nitrogen source (e.g. yeast extract, malt extract, peptone, etc.) and inorganic nutrient sources (e.g. phosphate, magnesium, potassium, zinc, iron, etc.). Optionally, an inducer may be added.
The selection of the appropriate medium may be based on the choice of expression hosts and/or based on the regulatory requirements of the expression construct. Such media are well-known to those skilled in the art. The medium may, if desired, contain additional components favouring the transformed expression hosts over other potentially contaminating microorganisms.
After fermentation, the cells can be removed from the fermentation broth by means of centrifugation or filtration. After removal of the cells, the variant polypeptide of the invention may then be recovered and, if desired, purified and isolated by conventional means.
Organisms
The term “organism” in relation to the present invention includes any organism that could comprise the nucleotide sequence coding for the variant xylanase protein according to the present invention and/or products obtained therefrom, wherein a transcriptional regulatory sequence can allow expression of the nucleotide sequence according to the present invention when present in the organism. Suitable organisms may include a prokaryote, fungus, yeast or a plant. For the xylanase aspect of the present invention, a preferable organism may be a bacterium, preferably of the genus Bacillus, more preferably Bacillus subtilis. 
The term “transgenic organism” in relation to the present invention includes any organism that comprises the nucleotide sequence coding for the protein according to the present invention and/or products obtained therefrom, wherein the transcriptional regulatory sequence can allow expression of the nucleotide sequence according to the present invention within the organism. Preferably the nucleotide sequence is incorporated in the genome of the organism.
The term “transgenic organism” does not cover native nucleotide coding sequences in their natural environment when they are under the control of their native promoter which is also in its natural environment.
Therefore, the transgenic organism of the present invention includes an organism comprising any one of, or combinations of, the nucleotide sequence coding for the amino acid sequence according to the present invention, constructs according to the present invention (including combinations thereof), vectors according to the present invention, plasmids according to the present invention, cells according to the present invention, tissues according to the present invention or the products thereof. The transformed cell or organism could prepare acceptable quantities of the desired compound which would be easily retrievable from, the cell or organism.
Transformation of Host Cells/Host Organisms
As indicated earlier, the host organism can be a prokaryotic or a eukaryotic organism. Examples of suitable prokaryotic hosts include E. coli and Bacillus subtilis. Teachings on the transformation of prokaryotic hosts is well documented in the art, for example see Sambrook et al (Molecular Cloning: A Laboratory Manual, 2nd edition, 1989, Cold Spring Harbor Laboratory Press) and Ausubel et al., Short Protocols in Molecular Biology (1999), 4th Ed., John Wiley & Sons, Inc.
If a prokaryotic host is used then the nucleotide sequence may need to be suitably modified before transformation—such as by removal of introns.
As mentioned above, a preferred host organism is of the genus Bacillus, such as Bacillus subtilis. 
In another embodiment the transgenic organism can be a yeast. In this regard, yeasts have also been widely used as a vehicle for heterologous gene expression. The species Saccharomyces cerevisiae has a long history of industrial use, including its use for heterologous gene expression. Expression of heterologous genes in Saccharomyces cerevisiae has been reviewed by Goodey et al (1987, Yeast Biotechnology, D R Berry et al, eds, pp 401-429, Allen and Unwin, London) and by King et al (1989, Molecular and Cell Biology of Yeasts, E F Walton and G T Yarronton, eds, pp 107-133, Blackie, Glasgow).
For several reasons Saccharomyces cerevisiae is well suited for heterologous gene expression. First, it is non-pathogenic to humans and it is incapable of producing certain endotoxins. Second, it has a long history of safe use following centuries of commercial exploitation for various purposes. This has led to wide public acceptability. Third, the extensive commercial use and research devoted to the organism has resulted in a wealth of knowledge about the genetics and physiology as well as large-scale fermentation characteristics of Saccharomyces cerevisiae. 
A review of the principles of heterologous gene expression in Saccharomyces cerevisiae and secretion of gene products is given by E Hinchcliffe E Kenny (1993, “Yeast as a vehicle for the expression of heterologous genes”, Yeasts, Vol 5, Anthony H Rose and J Stuart Harrison, eds, 2nd edition, Academic Press Ltd.).
Several types of yeast vectors are available, including integrative vectors, which require recombination with the host genome for their maintenance, and autonomously replicating plasmid vectors.
In order to prepare the transgenic Saccharomyces, expression constructs are prepared by inserting the nucleotide sequence of the present invention into a construct designed for expression in yeast. Several types of constructs used for heterologous expression have been developed. The constructs contain a promoter active in yeast fused to the nucleotide sequence of the present invention, usually a promoter of yeast origin, such as the GAL1 promoter, is used. Usually a signal sequence of yeast origin, such as the sequence encoding the SUC2 signal peptide, is used. A terminator active in yeast ends the expression system.
For the transformation of yeast several transformation protocols have been developed. For example, a transgenic Saccharomyces according to the present invention can be prepared by following the teachings of Hinnen et al (1978, Proceedings of the National Academy of Sciences of the USA 75, 1929); Beggs, J D (1978, Nature, London, 275, 104); and Ito, H et al (1983, J Bacteriology 153, 163-168).
The transformed yeast cells are selected using various selective markers. Among the markers used for transformation are a number of auxotrophic markers such as LEU2, HIS4 and TRP1, and dominant antibiotic resistance markers such as aminoglycoside antibiotic markers, e.g. G418.
Another host organism is a plant. The basic principle in the construction of genetically modified plants is to insert genetic information in the plant genome so as to obtain a stable maintenance of the inserted genetic material.
A transgenic plant of the invention may be produced from any plant such as the seed-bearing plants (angiosperms), and conifers. Angiosperms include dicotyledons and monocotyledons. Examples of dicotyledonous plants include tobacco, (Nicotiana plumbaginifolia and Nicotiana tabacum), arabidopsis (Arabidopsis thaliana), Brassica napus, Brassica nigra, Datura innoxia, Vicia narbonensis, Vicia faba, pea (Pisum sativum), cauliflower, carnation and lentil (Lens culinaris). Examples of monocotyledonous plants include cereals such as wheat, barley, oats and maize.
Techniques for producing transgenic plants are well known in the art. Typically, either whole plants, cells or protoplasts may be transformed with a suitable nucleic acid construct encoding a zinc finger molecule or target DNA (see above for examples of nucleic acid constructs). There are many methods for introducing transforming DNA constructs into cells, but not all are suitable for delivering DNA to plant cells. Suitable methods include Agrobacterium infection (see, among others, Turpen et al., 1993, J. Virol. Methods, 42: 227-239) or direct delivery of DNA such as, for example, by PEG-mediated transformation, by electroporation or by acceleration of DNA coated particles. Acceleration methods are generally preferred and include, for example, microprojectile bombardment. A typical protocol for producing transgenic plants (in particular monocotyledons), taken from U.S. Pat. No. 5,874,265, is described below.
An example of a method for delivering transforming DNA segments to plant cells is microprojectile bombardment. In this method, non-biological particles may be coated with nucleic acids and delivered into cells by a propelling force. Exemplary particles include those comprised of tungsten, gold, platinum, and the like.
A particular advantage of microprojectile bombardment, in addition to it being an effective means of reproducibly stably transforming both dicotyledons and monocotyledons, is that neither the isolation of protoplasts nor the susceptibility to Agrobacterium infection is required. An illustrative embodiment of a method for delivering DNA into plant cells by acceleration is a Biolistics Particle Delivery System, which can be used to propel particles coated with DNA through a screen, such as a stainless steel or Nytex screen, onto a filter surface covered with plant cells cultured in suspension. The screen disperses the tungsten-DNA particles so that they are not delivered to the recipient cells in large aggregates. It is believed that without a screen intervening between the projectile apparatus and the cells to be bombarded, the projectiles aggregate and may be too large for attaining a high frequency of transformation. This may be due to damage inflicted on the recipient cells by projectiles that are too large.
For the bombardment, cells in suspension are preferably concentrated on filters. Filters containing the cells to be bombarded are positioned at an appropriate distance below the macroprojectile stopping plate. If desired, one or more screens are also positioned between the gun and the cells to be bombarded. Through the use of techniques set forth herein one may obtain up to 1000 or more clusters of cells transiently expressing a marker gene (“foci”) on the bombarded filter. The number of cells in a focus which express the exogenous gene product 48 hours post-bombardment often range from 1 to 10 and average 2 to 3.
After effecting delivery of exogenous DNA to recipient cells by any of the methods discussed above, a preferred step is to identify the transformed cells for further culturing and plant regeneration. This step may include assaying cultures directly for a screenable trait or by exposing the bombarded cultures to a selective agent or agents.
An example of a screenable marker trait is the red pigment produced under the control of the R-locus in maize. This pigment may be detected by culturing cells on a solid support containing nutrient media capable of supporting growth at this stage, incubating the cells at, e.g., 18° C. and greater than 180 μE m−2 s−1, and selecting cells from colonies (visible aggregates of cells) that are pigmented. These cells may be cultured further, either in suspension or on solid media.
An exemplary embodiment of methods for identifying transformed cells involves exposing the bombarded cultures to a selective agent, such as a metabolic inhibitor, an antibiotic, herbicide or the like. Cells which have been transformed and have stably integrated a marker gene conferring resistance to the selective agent used, will grow and divide in culture. Sensitive cells will not be amenable to further culturing.
To use the bar-bialaphos selective system, bombarded cells on filters are resuspended in nonselective liquid medium, cultured (e.g. for one to two weeks) and transferred to filters overlaying solid medium containing from 1-3 mg/l bialaphos. While ranges of 1-3 mg/l will typically be preferred, it is proposed that ranges of 0.1-50 mg/l will find utility in the practice of the invention. The type of filter for use in bombardment is not believed to be particularly crucial, and can comprise any solid, porous, inert support.
Cells that survive the exposure to the selective agent may be cultured in media that supports regeneration of plants. Tissue is maintained on a basic media with hormones for about 2-4 weeks, then transferred to media with no hormones. After 2-4 weeks, shoot development will signal the time to transfer to another media.
Regeneration typically requires a progression of media whose composition has been modified to provide the appropriate nutrients and hormonal signals during sequential developmental stages from the transformed callus to the more mature plant. Developing plantlets are transferred to soil, and hardened, e.g., in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO2, and 250 μE m−2 s−1 of light. Plants are preferably matured either in a growth chamber or greenhouse. Regeneration will typically take about 3-12 weeks. During regeneration, cells are grown on solid media in tissue culture vessels. An illustrative embodiment of such a vessel is a petri dish. Regenerating plants are preferably grown at about 19° C. to 28° C. After the regenerating plants have reached the stage of shoot and root development, they may be transferred to a greenhouse for further growth and testing.
Genomic DNA may be isolated from callus cell lines and plants to determine the presence of the exogenous gene through the use of techniques well known to those skilled in the art such as PCR and/or Southern blotting.
Several techniques exist for inserting the genetic information, the two main principles being direct introduction of the genetic information and introduction of the genetic information by use of a vector system. A review of the general techniques may be found in articles by Potrykus (Annu Rev Plant Physiol Plant Mol Biol [1991] 42:205-225) and Christou (Agro-Food-Industry Hi-Tech March/April 1994 17-27).
Thus, in one aspect, the present invention relates to a vector system which carries a construct encoding a variant xylanase polypeptide according to the present invention and which is capable of introducing the construct into the genome of a plant.
The vector system may comprise one vector, but it can comprise at least two vectors. In the case of two vectors, the vector system is normally referred to as a binary vector system. Binary vector systems are described in further detail in Gynheung An et al. (1980), Binary Vectors, Plant Molecular Biology Manual A3, 1-19.
One extensively employed system for transformation of plant cells with a given promoter or nucleotide sequence or construct is based on the use of a Ti plasmid from Agrobacterium tumefaciens or a Ri plasmid from Agrobacterium rhizogenes (An et al. (1986), Plant Physiol. 81, 301-305 and Butcher D. N. et al. (1980), Tissue Culture Methods for Plant Pathologists, eds.: D. S. Ingrams and J. P. Helgeson, 203-208).
Several different Ti and Ri plasmids have been constructed which are suitable for the construction of the plant or plant cell constructs described above.
B. Uses
In a general sense, a variant xylanase of the invention may be used to alter, for example reduce, the viscosity derived from the presence of hemicellulose or arabinoxylan in a solution or system comprising plant cell wall material. Typically said plant cell wall materials will comprise one or more xylanase inhibitors.
Specifically, a variant xylanase of the invention may be used in processing plant materials for use as foodstuffs, such as animal feed, in starch production, in baking and in the processing of wood pulp to make paper.
Preparation of Foodstuffs
A variant xylanase of the invention may be used to process plant materials such as cereals that are used in foodstuffs including animal feed. As used herein, the term “cereal” means any kind of grain used for food and/or any grass producing this grain such as but not limited to any one of wheat, milled wheat, barley, maize, sorghum, rye, oats, triticale and rice or combinations thereof. In one preferred embodiment, the cereal is a wheat cereal.
The xylan in the food and/or feed supplement is modified by contacting the xylan with the variant xylanase of the present invention.
As used herein, the term “contacting” includes but is not limited to spraying, coating, impregnating or layering the food and/or feed supplement with the variant xylanase enzyme of the present invention.
In one embodiment, the food and/or feed supplement of the present invention may be prepared by mixing the variant xylanase enzyme directly with a food and/or feed supplement. By way of example, the variant xylanase enzyme may be contacted (for example, by spraying) onto a cereal-based food and/or feed supplement such as milled wheat, maize or soya flour.
It is also possible to incorporating the variant xylanase enzyme it into a second (and different) food and/or feed or drinking water which is then added to the food and/or feed supplement of the present invention. Accordingly, it is not essential that the variant xylanase enzyme provided by the present invention is incorporated into the cereal-based food and/or feed supplement itself, although such incorporation forms a particularly preferred aspect of the present invention.
In one embodiment of the present invention, the food and/or feed supplement may be combined with other food and/or feed components to produce a cereal-based food and/or feed. Such other food and/or feed components may include one or more other (preferably thermostable) enzyme supplements, vitamin food and/or feed supplements, mineral food and/or feed supplements and amino acid food and/or feed supplements. The resulting (combined) food and/or feed supplement comprising possibly several different types of compounds can then be mixed in an appropriate amount with the other food and/or feed components such as cereal and protein supplements to form a human food and/or an animal feed.
In one preferred embodiment, the food and/or feed supplement of the present invention can be prepared by mixing different enzymes having the appropriate activities to produce an enzyme mix. By way of example, a cereal-based food and/or feed supplement formed from e.g. milled wheat or maize may be contacted (e.g. by spraying) either simultaneously or sequentially with the xylanase enzyme and other enzymes having appropriate activities. These enzymes may include but are not limited to any one or more of an amylase, a glucoamylase, a mannanase, an a galactosidase, a phytase, a lipase, a glucanase, an-arabinofuranosidase, a pectinase, a protease, a glucose oxidase, a hexose oxidase and a xylanase. Enzymes having the desired activities may for instance be mixed with the xylanase of the present invention either before contacting these enzymes with a cereal-based food and/or feed supplement or alternatively such enzymes may be contacted simultaneously or sequentially on such a cereal based supplement. The food and/or feed supplement is then in turn mixed with a cereal-based food and/or feed to prepare the final food and/or feed. It is also possible to formulate the food and/or feed supplement as a solution of the individual enzyme activities and then mix this solution with a food and/or feed material prior to processing the food and/or feed supplement into pellets or as a mash.
Bakery Products
The present invention provides the use of a variant xylanase polypeptide of the invention in a process for preparing a foodstuff. Typical bakery (baked) products in accordance with the present invention include bread—such as loaves, rolls, buns, pizza bases etc.—pretzels, tortillas, cakes, cookies, biscuits, crackers etc. The preparation of foodstuffs such as bakery products is well know in the art. Dough production, for example, is described in example 2. The use of variant xylanases of the invention to alter the viscosity of a flour slurry in described in the example 5.
Starch Production
A variant xylanase of the invention may also be used in starch production from plant materials derived from cereals and tubers, such as potatoes.
Processing of Wood Pulp
A variant xylanase of the invention may also be used in processing wood pulp, for example in the preparation of paper.
As discussed above, we have shown that a major determinant of xylanase functionality is the presence of endogenous inhibitors in plant material. Consequently, although one method for altering xylanase functionality is to modify a xylanase to change its sensitivity to endogenous inhibitors, another method would be to vary the amount and/or type of inhibitor present in the plant material. Thus, the present invention also provides the use of a xylanase inhibitor to alter the functionality of a xylanase and consequently the use of a xylanase inhibitor in the methods of processing plant materials described above.
The present invention will now be further described with reference to the following examples which are intended to be illustrative only and non-limiting.
EXAMPLES
Example 1
Purification and Characterisation of Wheat Endogenous Xylanase Inhibitor
2 kg wheat flour (Danish reform, batch 99056) was extracted with water, using a flour:water ratio of 1:2, during 10 minutes of stirring. The soluble endogenous xylanase inhibitor was separated from the flour-water slurry by centrifugation. The extraction and centrifugation was performed at 4° C. The inhibitor was purified from the water extract by the following chromatographic techniques and concentration techniques: HPLC-SEC, HPLC-CIEC, rotary evaporation, HPLC-HIC, HPLC-SEC and rotary evaporation. The xylanase inhibitor could be monitored and quantified during purification, using the following quantification method.
Inhibitor Quantification Method
1 XIU (Xylanase Inhibitor Unit) is defined as the amount of inhibitor that decreases 1 TXU to 0.5 TXU under the conditions described below.
The xylanase used in this assay is Bacillus subtilis wild type xylanase.
250 μl xylanase solution containing 12 TXU/ml, approx. 100 μl xylanase inhibitor solution and citric acid (0.1 M)-di-sodium-hydrogen phosphate (0.2 M) buffer, pH 5, to react a reaction volume of 1000 μl is pre-incubated for 5 minutes at 40° C. At t=5 minutes, 1 Xylazyme (Megazyme, Ireland) tablet is added to the reaction mixture. At t=15 minutes the reaction is terminated, by addition of 10 ml 2% TRIS/NaOH, pH 12. The solution is filtered and the absorbency of the supernatant is measured at 590 nm. By choosing several different concentrations of inhibitor in the above assay, it is possible to create a plot of OD versus inhibitor concentration. Using the slope (a) and intercept (b) from this plot and the concentration of the xylanase it is possible to calculate the amount of XIU in a given inhibitor solution (equation 1).

amount of XIU in solution=((b/2)/−a)/TXU  Equation 1

From the endogenous xylanase inhibitor purification, the following inhibitor yield was recovered (table 1).







TABLE 1







Wheat endogenous xylanase inhibitor recovery after purification.











Sample
Amount
XIU
XIU, total
Recovery, %














Flour
2000 g
 590/g  
1.180.000
100


Purified inhibitor
   90 ml
4658/ml
  419.220
35.5









The inhibitor sample was pure and free from wheat endogenous xylanolytic activities.
Example 2
Fractionation and Reconstruction of Wheat Flour Free of Xylanase Inhibitor and Xylanases Functionality in this Flour as a Function of Added Xylanase Inhibitor
Flour Fractionation and Reconstitution
The flour used was: Danish Reform flour, batch No 99056. The fractionation, inhibitor inactivation and reconstitution were as follows:
A simple dough was made by mixing 1600 gram flour, with optimal water addition, according to a baker's absorption at 500 BU and mixing time according to Farinograph results. This resulted in 2512 gram dough. The gluten was manually washed out from the dough, using a water dough ratio of approx. 5:1. The water used was pre-chilled to 4° C. to prevent further enzyme activity in the dough. The resulting wash-water contained the soluble proteins (including the xylanase inhibitor), lipids, non-starch polysaccharides and starch. The starch and other non-soluble components were separated from the wash-water by centrifugation (5000 g, 10 minutes, 10° C.). To inactivate the endogenous xylanase inhibitor in the wash-water, the supernatant from the centrifugation was boiled for three minutes using a heat-evaporator.
All three fractions (gluten, starch and solubles) were frozen in flasks and placed in a freeze dryer. After drying, the fractions were weighed, grounded using a mortar and pestle, coffee mill and sieved through a 250 μm sieve. All fractions were weighed again and flour was reconstituted, based on the ratios obtained after fractionation.
Enzymes
The xylanases listed in table 2 have been used in the study. The xylanases are purified, meaning no other xylonolytic activity is present in the sample.







TABLE 2







Xylanases used in the study and activity, TXU.











ID
Origin
TXU







B. sub
B. subtilis.
5100



A. nig
A. niger
8800










Xylanase Assay (Endo-β-1,4-Xylanase Activity)

Xylanase samples are diluted in citric acid (0.1 M)-di-sodium-hydrogen phosphate (0.2 M) buffer, pH 5.0, to obtain approx. OD=0.7 in the final assay. Three dilutions of the sample and an internal standard with a defined activity are thermostated for 5 minutes at 40° C. At time=5 minutes, 1 Xylazyme tab (crosslinked, dyed xylan substrate) is added to the enzyme solution. At time=15 minutes (or in some cases longer, depending on the xylanase activity present in the sample) the reaction is terminated, by adding 10 ml of 2% TRIS. The reaction mixture is centrifuged and the OD of the supernatant is measured at 590 nm. Taking into account the dilutions and the amount of xylanase, the activity (TXU, Total-Xylanase-Units) of the sample can be calculated relative to the standard.
Baking Trials
Baking trials were done with (1.44× initial inhibitor level in Danish Reform flour, batch No 99056) and without addition of purified endogenous xylanase inhibitor to the reconstituted flour, respectively. The baking trials were done using the xylanases listed in table 2 and the compositions listed in table 3.







TABLE 3







Composition of dough made within the baking trials.










Dough No
ID
TXU
Inh. add, XIU/50 g













1
Control
0
0


2
B. sub
7500
0


3
A. nig
7500
0


4
B. sub
7500
850


5
A. nig
7500
850


6
Control
0
850









Dough Analysis

The dough were analysed with respect to:
Stickiness
Dough stickiness was measured on a TX-XT2 system (Stable Micro Systems) using a SMS Dough Stickiness Cell according to the method described by Chen And Hoseney (Lebensmittel Wiss u.-Technol., 28, 467-473. 1995).
Viscosity Analysis of Dough Liquid
The viscosity of extracted dough liquid was measured using a Brookfield viscosimeter after extraction.
Pentosan Analysis of Dough Liquid
Solubilised pentosan was measured in the dough liquid using the method of Rouau and Surget (Carbohydrate polymers, 24, 123-132, 1994).
Results
Flour Fractionation and Reconstitution
The fractionation and reconstitution of the dough resulted in 168.15 grams of freeze dried gluten, 111.13 grams of freeze dried soluble fraction and 1143.56 grams of freeze dried starch.
Inhibitor Quantification in Flour
Using the inhibitor quantification method, the inhibitor level in the 99056 flour and the reconstituted flour could be detected. The results from these analyses are listed in table 4.







TABLE 4







Results from inhibitor quantification in native flour (99056)


and reconstituted flour.










Flour
Inhibitor concentration, XIU/g flour














99056
590



Reconstituted flour
42










Comparing the inhibitor level in the two portions of flour a 93% (100−(42XIU/590XIU)×100%)) decrease of inhibitor level in the reconstituted flour is shown.
Baking Trials
The results from the baking trial are listed in tables 5 and 6.







TABLE 5







Data from baking trials with reconstituted flour, xylanase


and +/− xylanase inhibitor addition.


Std. dev., % represents the standard deviation


over two days of baking.














Avg. spec. vol,



ID
TXU
Inh., XIU/50 g
ml/gram
Std. dev., %














Control
0
42
3.04
4.06


B. sub
7500
42
3.23
12.51


A. nig.
7500
42
3.44
5.24


B. sub
7500
850
3.22
4.26


A. nig.
7500
850
3.38
0.70


Control
0
850
2.94
0.05









The standard deviation shown in table 5 reflects the dough handling properties of the tested dough. The dough made without the endogenous xylanase inhibitor (42 XIU), were very difficult to handle. The standard deviation for these doughs are in the area of 3 to 12.5%. Compared to the dough with the inhibitor added, this is quite high. If these standard deviations are compared with the actual changes in the bread volume, it can be seen that the figures are approximately the same value. This means that we can not conclude anything about the absence of the inhibitor's influence on the bread volume. If we look at the dough made with addition of the endogenous xylanase inhibitor (850 XIU) in table 5, we can see that we were able to produce bread from the reconstituted flour in a reproducible way over a two day period. The standard deviation was within the area of 0.05 to 4.2%, which is acceptable. From table 6 it can be seen, that the xylanases all increased the volume of the baked bread.







TABLE 6







Volume increase in bread baked from reconstituted


flour as a function of xylanase and


xylanase inhibitor addition.













Inh.,
Avg. spec. vol,
Volume increase as


ID
TXU
XIU/50 g
ml/gram
function of xylanase, %














Control
0
42
3.04
0.0


B. sub
7500
42
3.23
6.2


A. nig.
7500
42
3.44
13.3


B. sub
7500
850
3.22
9.7


A. nig.
7500
850
3.38
15.0


Control
0
850
2.94
0.0









What can be deduced from table 5 and table 6, is that the absence of the xylanase inhibitor in the flour made the handling of the dough very difficult. Therefore, what may seem as a positive response in volume by addition of inhibitor in table 6, probably can be explained by the high standard deviation in the dough lacking the inhibitor, due to difficult handling properties. Furthermore, it can be concluded that all the xylanases tested increased the bread volume significantly compared to the blank control.
Stickiness
The same dough, that was used for the baking trials, was used for stickiness measurements. The results are listed in table 7.







TABLE 7







Data representing stickiness as a function of time,


xylanase and xylanase inhibitor addition


to reconstituted flour.













Inh.,
Avg. stickiness after
Avg. stickiness


ID
TXU
XIU/50 g
10 min, g × s
after 60 min, g × s














Control
0
42
4.71
4.79


B. sub.
7500
42
12.20
13.39


A. nig.
7500
42
9.22
12.58


B. sub.
7500
850
2.51
3.66


A. nig.
7500
850
5.24
6.45


Control
0
850
4.10
4.15









The results in table 7 clearly indicate the influence of the inhibitor that was observed in the experiment. The dough with a low level of xylanase inhibitor in combination with xylanase, was very difficult to handle and mould. However, when the inhibitor was added, the dough became dry and very easy to handle. As can be seen from table 7, addition of the 990202 xylanase in combination with the inhibitor decreased the stickiness. The dough became drier.
Table 7 also shows that there is only a small effect of time on the stickiness. It seems that the xylanases act very rapidly. Within the first 10 minutes most of the arabinoxylan is modified when the first xylanase (B. sub) is added. The second xylanase tested (A. nig), seems to act less rapidly. A function of time can easily be observed using this xylanase. This is also the xylanase that shows the least effect as a function of inhibitor level when analysed on stickiness.
Dough Viscosity
The dough viscosity and the pentosan analysis results were obtained from the same extraction of dough prepared from reconstituted flour added xylanase and xylanase inhibitor. This dough was analysed after two proofing times, 30 and 120 minutes.
The results of the viscosity analysis are presented in table 8.







TABLE 8







Data representing dough liquid viscosity as a function of time,


xylanase and xylanase inhibitor addition


to reconstituted flour.














Avg. dough





Inh.,
viscosity, cP,
Avg. dough viscosity,


ID
TXU
XIU/50 g
30 min proofing
cP, 120 min proofing














Control
0
42
5.21
5.56


B. sub.
7500
42
5.07
4.55


A. nig.
7500
42
5.78
4.14


B. sub.
7500
850
9.03
11.09


A. nig.
7500
850
8.44
8.55


Control
0
850
5.96
6.95









As can be seen from table 8 the inhibitor has a significant effect on the functionality of the xylanases. Without addition of the inhibitor, the arabinoxylan is being de-polymerised to Low Molecular Weight (LMW) arabinoxylan with a low viscosity. Addition of inhibitor prevents this very extensive de-polymerisation of the arabinoxylan.
Pentosan Analysis of Dough Liquid
The results from the pentosan (arabinoxylan) analysis of the dough liquid are presented in table 9.







TABLE 9







Data representing pentosan solubilisation as a function of time, xylanase


and xylanase inhibitor addition to reconstituted flour.













Inh.,
Avg. Pentosan, %,
Avg. Pentosan, %,


ID
TXU
XIU/50 g
30 min proofing
120 min proofing














Control
0
42
0.387
0.458


B. sub.
7500
42
0.766
0.819


A. nig.
7500
42
0.719
0.798


B. sub.
7500
850
0.410
0.544


A. nig.
7500
850
0.560
0.673


Control
0
850
0.400
0.528









As can be seen from the results in table 9, the addition of endogenous xylanase inhibitor decreased the solubilisation of the arabinoxylan. When evaluated after 30 minutes proofing time, the amount of arabinoxylan solubilised in absence of the inhibitor is almost twice the amount as in presence of the inhibitor. Calculated on the basis of the relating control samples, the solubilisation is much higher in absence of the inhibitor, as illustrated in the following example:

(0.766−0.387)/(0.410−0.400)=37.9 times higher solubilisation

The above example was calculated on basis of solubilisation of arabinoxylan using the Bacillus xylanase, 30 minutes proofing and +/−inhibitor.
Example 3
Site-Directed Mutagenesis on Xylanases
Specific mutants of Bacillus subtilis xylanase may be obtained by site directed mutagenesis of the wild type enzyme, by the use of any of a number of commercially available mutagenesis kits. An example of how to obtain the D11F mutant using the Quick Exchange kit, available from Stratagene Cloning Systems, 11011 North Torrey Pines Road, La Jolla, Calif. 92037, USA is given below:
The DNA sequence encoding Bacillus subtilis xylanase A has been published by Paice et al., 1986.
The sequence of the coding region is as follows, with the sequence encoding the mature part of the protein shown in capitals: (SEQ ID NO: 10)








catatgtttaagtttaaaaagaatttcttagttggattatcggcagcttt



 


aatgagtattagcttgttttcggcaaccgcctctgcaGCTAGCACAGACT


 


ACTGGCAAAATTGGACTGATGGGGGCGGTATAGTAAACGCTGTCAATGGG


 


TCTGGCGGGAATTACAGTGTTAATTGGTCTAATACCGGAAATTTTGTTGT


 


TGGTAAAGGTTGGACTACAGGTTCGCCATTTAGGACGATAAACTATAATG


 


CCGGAGTTTGGGCGCCGAATGGCAATGGATATTTAACTTTATATGGTTGG


 


ACGAGATCACCTCTCATAGAATATTATGTAGTGGATTCATGGGGTACTTA


 


TAGACCTACTGGAACGTATAAAGGTACTGTAAAAAGTGATGGGGGTACAT


 


ATGACATATATACAACTACACGTTATAACGCACCTTCCATTGATGGCGAT


 


CGCACTACTTTTACGCAGTACTGGAGTGTTCGCCAGTCGAAGAGACCAAC


 


CGGAAGCAACGCTACAATCACTTTCAGCAATCATGTGAACGCATGGAAGA


 


GCCATGGAATGAATCTGGGCAGTAATTGGGCTTACCAAGTCATGGCGACA


 


GAAGGATATCAAAGTAGTGGAAGTTCTAACGTAACAGTGTGGTAA






The part of the gene encoding the mature part of the wild type enzyme may be expressed intracellularly in E. coli by methods well known to people skilled in the art of molecular biology. For example:

    1. Generating a copy of the capitalised part of the above described gene by use of the Polymerase Chain Reaction (PCR) with an added Nde1 restriction enzyme site (CATATG) before the GCTAGCACA and an added HindIII restriction site (AAGCTT) after the GTGTGGTAA.
    2. Inserting the resultant modified copy of the gene by use of the above mentioned enzymes into the expression vector pET24a(+), which can be obtained from Novagen, Inc. 601 Science Drive, Madison, Wis. 53711, USA.
    3. Transforming into a suitable E. coli strain and expression by fermentation as described by the vendor of pET24a(+).


Our D11F mutant enzyme may be obtained by using the “Quick Exchange” mutagenesis kit according to the manufacturer, and using the above described Bacillus subtilis wild type xylanase-pET24a(+) construct and the following PCR mutagenesis primers:
Sense primer: (SEQ ID NO: 12)
CTACTGGCAAAATTGGACTTTTGGAGGAGGTATAGTAAACGCTG
Antisense primer: (SEQ ID NO: 13)
CAGCGTTTACTATACCTCCTCCAAAAGTCCAATTTTGCCAGTAG
The mutant enzyme is expressed and purified using the same protocols as for the wild type enzyme.
Example 4
Inhibition Studies of Xylanase Mutants
Xylanase mutants expressed in E. coli (see Example 3) were fermented and purified (meaning no other xylanolytic activity was present in the purified preparation) using a de-salting step and a cation exchange chromatography step.
These pure xylanase mutant preparations were diluted to 12 TXU/ml using 0.1 M citric acid-0.2 M di-sodium-hydrogen phosphate, pH 5.0 and used in the following assay.
A stable inhibitor preparation was made according to the protocol described in Example 1. This stable inhibitor preparation is used as stock for all xylanase-xylanase inhibitor studies. Using the inhibitor quantification method described in example 1, the inhibitor preparation was analysed to contain 126 XIU/ml.
Assay
To 250 μl diluted xylanase mutant preparations, are added 0, 10, 25, 50 or 100 μl inhibitor preparation, respectively. To these inhibitor-xylanase mixtures were added 0.1 M citric acid-0.2 M di-sodium-hydrogen phosphate, pH 5.0 making the end-volume 1000 μl. These reaction mixtures were pre-incubated for 5 minutes at 40° C. Hereafter 1 xylazyme tablet (Megazyme, Ireland) were added to all inhibitor-xylanase mixtures. After 10 minutes of incubation at 40° C., the reactions were terminated, by adding 10 ml 2% Tris/NaOH, pH 12.0. The mixtures were centrifuged and the liberated blue colour from the substrate was measured at 590 nm.
The results are presented in table 10.







TABLE 10







Relative inhibition of xylanase mutants and parent


xylanase (here wildtype enzyme)


as a function of xylanase inhibitor.









Mutant ID













0
1, 26
3, 15
6, 3
12, 6










Relative inhibition, %













Wildtype
100
77
48
29
23















D11Y
100
120
114
126
124


D11N
100
93
72
53
32


D11F
100
114
119
116
115


D11K
100
109
112
113
116


D11S
100
98
81
60
38


D11W
100
101
88
70
50


G34D
100
94
83
70
53


G34F
100
76
53
34
29


G34T
100
99
99
93
86


Y113A
100
96
80
62
43


Y113D
100
96
81
63
45


Y113K
100
103
85
63
47


N114A
100
80
49
28
22


N114D
100
84
57
39
29


N114F
100
84
54
39
34


N114K
100
87
56
33
24


D121N
100
80
36
16
14


D121K
100
104
95
85
75


D121F
100
101
89
72
60


D121A
100
81
50
27
21


R122D
100
85
59
41
28


R122F
100
93
74
58
58


R122A
100
78
46
33
26


Q175E
100
87
59
40
31


Q175S
100
88
59
30
19


Q175L
100
78
42
25
23


G12F
100
110
106
100
92


G13F
100
104
95
87
84


I15K
100
84
47
28
23


N32K
100
82
42
19
14


G120K
100
85
52
29
22


G120D
100
84
47
24
18


G120F
100
71
35
18
15


G120Y
100
81
40
18
16


G120N
100
84
49
29
23


D119K
100
94
67
40
26


D119Y
100
87
50
28
22


D119N
100
91
74
44
22


T123K
100
80
46
30
25


T123Y
100
80
47
28
27


T123D
100
83
36
20
17


T124K
100
110
92
73
57


T124Y
100
101
76
49
33


T124D
100
87
52
32
25


N17K
100
88
48
31
26


N17Y
100
79
42
23
19


N17D
100
90
81
50
22


N29K
100
83
50
30
23


N29Y
100
85
49
30
24


N29D
100
74
44
26
20


S31K
100
77
42
23
23


S31Y
100
83
50
27
22


S31D
100
79
52
30
24


D11F/R122D
100
109
111
110
109


D11F/G34D
100
104
106
103
104









From the results in table 10, it can be seen the xylanase mutants D11Y, D11F, D11K, D11F/R122D and D11F/G34D are uninhibited by the wheat endogenous xylanase inhibitor. These xylanase mutants would be expected to act more aggressively/specifically on the soluble arabinoxylan, compared to the other xylanase mutants or other xylanases. They would therefore be superior in applications where a decrease in viscosity (as a function of HMW arabinoxylan) is wanted.
Example 5
Functionality Studies of Xylanase Mutants
Xylanase mutants expressed in E. Coli (see Example 3) were fermented and purified (meaning no other xylanolytic activity were present in the purified preparation).
These pure xylanase mutant preparations were diluted to 400 TXU/ml using water and used in the following assay.
Assay
200 ml 30% (w/w) flour slurry was made using water (thermostated to 25° C.), by stirring for 5 minutes. 60.0 ml of this flour slurry is poured into a Ford-cup, and the time for drainage of 50.0 ml is measured. This measurement is the blank measurement. The 60.0 ml flour slurry is poured back and 1000 μl diluted xylanase mutant preparation is added to the flour slurry under stirring. After 2, 5, 10 and 20 minutes, 60.0 ml is poured into the Ford-cup, and the drainage time for 50.0 ml is recorded. Each measurement were done in triplicate.
The results are presented in table 11.







TABLE 11







Relative viscosity of flour slurry as a function of


xylanase mutant and parent xylanase


(here wild type xylanase)









Incubation time,



minutes



Mutant ID













0
2
5
10
20









Relative viscosity



change, %












Wildtype
100
112
120
131
141















D11Y
100
97
93
83
75


D11N
100
112
125
130
136


D11F
100
93
87
78
69


D11K
100
105
95
88
78


D11S
100
102
110
113
117


D11W
100
106
115
121
122


G34D
100
110
120
128
124


G34F
100
111
126
128
146


G34T
100
100
108
111
106


Y113A
100
118
129
130
124


Y113D
100
116
127
124
114


Y113K
100
118
123
121
115


N114A
100
117
128
127
131


N114D
100
125
144
162
170


N114F
100
113
119
131
150


N114K
100
119
129
141
147


D121N
100
104
103
106
104


D121K
100
122
132
141
162


D121F
100
107
117
128
147


D121A
100
101
102
103
107


R122D
100
120
119
124
115


R122F
100
127
144
150
160


R122A
100
123
138
144
153


Q175E
100
116
134
142
149


Q175S
100
110
113
121
129


Q175L
100
111
111
119
126


G12F
100
127
132
122
101


G13F
100
106
119
124
113


I15K
100
109
108
113
118


N32K
100
97
98
101
101


G120K
100
103
111
115
121


G120D
100
112
122
120
126


G120F
100
103
111
117
130


G120Y
100
106
106
108
126


G120N
100
119
123
130
141


D119K
100
118
119
127
125


D119Y
100
102
102
111
110


D119N
100
126
137
145
146


T123K
100
106
109
121
120


T123Y
100
101
106
108
116


T123D
100
113
123
125
126


T124K
100
117
131
128
127


T124Y
100
112
123
132
135


T124D
100
103
110
111
118


N17K
100
114
119
119
132


N17Y
100
102
102
108
108


N17D
100
120
131
135
143


N29K
100
98
100
100
104


N29Y
100
115
117
132
143


N29D
100
104
104
113
111


S31K
100
119
115
124
134


S31Y
100
110
118
122
137


S31D
100
99
103
109
110


D11F/R122D
100
91
89
82
77


D11F/G34D
100
96
93
84
80









Example 6
Site-Directed Mutation in the Active Site of Bacillus subtilis Xylanase A, Does not Influence the Xylanase: Xylanase Inhibitor Interaction
A residue in the active site of the Bacillus subtilis wildtype xylanase A enzyme was altered by a site-directed mutation (see ex. 3) In the mutated residue (Y166F) a potential hydrogen bond is lost. The mutant xylanase, was expressed in E. coli, fermented and purified. Hereafter, the mutant was investigated for its interaction with the xylanase inhibitor (see example 4).
As can be seen below (table 12), the exchange of an amino acid in the active site, did surprisingly not have any effect on interactions with the xylanase inhibitor as compared to the Bacillus subtilis wildtype xylanase enzyme.







TABLE 12







Relative inhibition of Bacillus subtilis wildtype xylanase


and the xylanase mutant Y166F.









XIU/ml



Xylanase ID













0
1, 26
3, 15
6, 3
12, 6









Relative inhibition, %












Wildtype
100
75
40
24
20















Y166F
100
74
39
22
20









Hence, in summary the experiment described above shows a site-directed mutation in the active site of the Bacillus subtilis xylanase A, which mutation does not influence the xylanase's interactions with the xylanase inhibitor.
Example 7
Site-Directed Mutation in Family 11 Xylanases Other than the Bacillus subtilis Xylanase A, Influencing the Xylanase—Xylanase Inhibitor Interactions
D19 residue of the Thermomyces lanuginosus xylanase A enzyme was mutated to F19 by site-directed mutagenesis. D19 corresponds to D11 residue in the Bacillus subtilis xylanase (SEQ ID NO. 1). Thermomyces lanuginosus xylanase A gene is described as SEQ ID NO. 9.
The primers for PCR construction of the D19F mutant may be the following:
Sense primer: (SEQ ID NO: 14)
GGTTATTACTATTCCTGGTGGAGTTTTGGAGGAGCGCAGGCCACG
Antisense primer: (SEQ ID NO: 15)
CGTGGCCTGCGCTCCTCCAAAACTCCACCAGGAATAGTAATAACC
The obtained mutant xylanase (D19F), was expressed in E. coli, fermented and purified. Hereafter, the mutant and the Thermomyces lanuginosus wildtype xylanase A was investigated for to its interaction with the xylanase inhibitor (see example 4). As can be seen from the results in table 13, the D19F mutant of the Thermomyces lanuginosus xylanase A is significantly less inhibited by the xylanase inhibitor as compared to the Thermomyces lanuginosus wildtype xylanase A.







TABLE 13







Relative inhibition of Thermomyces lanoginosus wildtype


xylanase A (TLX) and the Thermomyces lanoginosus


mutant xylanase, D19F (D19F).









XIU/ml



Xylanase ID













0
1, 26
3, 15
6, 3
12, 6









Relative inhibition, %














TLX
100
45
24
17
14


















D19F
100
73
38
24
20










Hence, in summary the experiment described above shows a site-directed mutation in the Thermomyces lanuginosus xylanase A. The results show that a mutation introducing a substitution of an amino acid on the surface of the xylanase molecule (analogue to the D11F in B. subtilis) changes the xylanase:xylanase inhibitor interactions. Thus, our invention (i.e. that surface residues control the level of inhibition of xylanase) holds true for xylanases that are homologous to the B. subtilis xylanase.
SUMMARY
In summary, the present invention provides a means for altering the sensitivity of a xylanase enzyme to a xylanase inhibitor.
All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described methods and system of the present invention will be apparent to those skilled in the art without departing from the scope and spirit of the present invention. Although the present invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in biochemistry and biotechnology or related fields are intended to be within the scope of the following claims.
REFERENCES


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## Claims

1. An isolated variant polypeptide or fragment thereof having at least 80% homology to SEQ ID NO: 1 as determined by using the GCG Wisconsin Bestfit package, and having xylanase activity, comprising two or more amino acid modifications, wherein said amino acid modifications are at two or more of positions 11, 12, 13, 15, 17, 29, 31, 32, 34, 113, 114, 119, 120, 121, 122, 123, 124 and 175 of the B. subtilis amino acid sequence shown as SEQ ID NO: 1, or their equivalent positions in other family 11 xylanases, such that the polypeptide or fragment thereof has altered sensitivity to a xylanase inhibitor as compared with the parent xylanase, wherein one of said modifications is at position 11, wherein the variant polypeptide is a family 11 xylanase, wherein said inhibitor is an inhibitor found naturally in wheat extract wherein said amino acid modifications are any of: D11Y, D11N, D11F, D11K, D11S, D11W, G12F, G13F, I15K, N17K, N17Y, N17D, N29K, N29Y, N29D, S31K, S31Y, S31D, N32K, G34D, G34F, G34T, Y113A, Y113D, Y113K, N114A, N114D, N114F, N114K, D119K, D119Y, D119N, G120K, G120D, G120F, G120Y, G120N, D121N, D121K, D121F, D121A, R122D, R122F, R122A, T123K, T123Y, T123D, T124K, T124Y, T124D, Q175E, Q175S and Q175L.

2. An isolated variant polypeptide according to claim 1 wherein the sensitivity of the variant polypeptide is reduced as compared to the parent xylanase enzyme.

3. A composition comprising an isolated variant polypeptide according to claim 1.

4. An isolated variant polypeptide according to claim 1, wherein two of said amino acid modifications are D11F and R122D.

5. An isolated variant polypeptide or fragment thereof having at least 80% homology to SEQ ID NO: 1 as determined by using the GCG Wisconsin Bestfit package, xylanase activity, comprising two or more amino acid modifications, wherein said amino acid modifications are at two or more of positions 11, 12, 13, 15, 17, 29, 31, 32, 34, 113, 114, 119, 120, 121, 122, 123, 124 and 175 of the B. subtilis amino acid sequence shown as SEQ ID NO: 1, such that the polypeptide or fragment thereof has altered sensitivity to a xylanase inhibitor found naturally in wheat plant tissues as compared with the parent xylanase, wherein one of said modifications is at position 11 and wherein the variant polypeptide is a family 11 xylanase.

6. An isolated variant polypeptide according to claim 5, wherein one of said amino acid modifications is D11Y, D11N, D11F, D11K, D11S or D11W.

7. The isolated variant polypeptide according to claim 6, wherein one of said amino acid modifications is D11F.