# Patent

## Title
Microorganisms providing novel gene products forming or decomposing polyamino acids

## Abstract

The invention relates to five or four novel genes and the gene products thereof from Bacillus licheniformis and sufficiently similar genes and proteins which are involved in vivo in the formation of polyamino acids. The gene in question is ywsC, ywsC′, ywtA, ywtB and ywtD or proteins coded thereby. The gene ywsC, ywsC′, ywtA and ywtB can be used to improve biotechnological production methods by microorganisms, wherein they are functionally inactivated; the gene ywtD which codes for a peptide decomposing poly-gamma glutamate can, inversely, contribute to the improvement of biotechnological production methods by increased expression. Said genes can be used positively, preferably to result in a modification or decomposition of poly-gamma glutamate.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
The present application is a Section 365(c) continuation of International Application No. PCT/EP2005/006289 filed 11 Jun. 2005, which in turn claims the priority of DE Application 10 2004 030 938.8 filed Jun. 26, 2004, each of which is incorporated herein by reference.


FIELD OF THE INVENTION
The present invention relates to five or four novel genes and their gene products from Bacillus licheniformis and sufficiently similar genes and proteins which are involved in vivo in the formation, the modification and/or the degradation of polyamino acids, and can be used for this purpose, and, based thereon, improved biotechnological production methods by microorganisms which are characterized by an inactivation or activation of these genes.
BACKGROUND OF THE INVENTION
The present invention is in the area of biotechnology, in particular the preparation of viable products by fermentation of microorganisms able to form the viable products of interest. This includes for example the preparation of low molecular weight compounds, for instance of dietary supplements or pharmaceutically relevant compounds, or of proteins for which, because of their diversity, there is in turn a large area of industrial uses. In the first case, the metabolic properties of the relevant microorganisms are utilized and/or modified to prepare the viable products; in the second case, cells which express the genes of the proteins of interest are employed. Thus in both cases, genetically modified organisms (GMO) are mostly involved.
There is an extensive prior art on the fermentation of microorganisms, especially also on the industrial scale; it extends from the optimization of the relevant strains in relation to the formation rate and the nutrient utilization via the technical design of the fermenters and up to the isolation of the valuable products from the relevant cells themselves and/or the fermentation medium. Both genetic and microbiological, and process engineering and biochemical approaches are applied thereto. The aim of the present invention is to improve this process in relation to a common property of the microorganisms employed, which impairs the actual fermentation step, specifically at the level of the genetic properties of the strains employed.
For industrial biotechnological production, the relevant microorganisms are cultured in fermenters which are configured appropriate for their metabolic properties. During the culturing, they metabolize the substrate offered and, besides the actual product, normally form a large number of other substances in which there is ordinarily no interest and/or which—as explained hereinafter—may lead to difficulties in the fermentation or the working up.
Fermentations are normally very complicated processes in which a large number of different parameters must be adjusted and monitored. Thus, for example, aerobic processes are very often involved, meaning that the microorganisms employed must be supplied adequately with oxygen throughout the fermentation (control of the aeration rate). Further examples of such parameters are the reactor geometry, the continuously changing composition of the nutrient medium, the pH or the CO2 formation rate. A particularly important parameter both in terms of the economics and in relation to the process management per se is the necessary energy input, for example via agitation systems which ensure that the reactor content is mixed as thoroughly as possible. In addition, besides the substrate distribution, also an adequate supply of oxygen to the organisms is ensured.
After completion of the fermentation it is normally necessary, besides the removal of the producer organisms, for the valuable product of interest to be purified and/or concentrated from the so-called fermenter slurry. The working up process can include for example various chromatographic and/or filtration steps. Thus, besides the content of valuable products, also decisive for the success of the overall working up process are the biophysical properties of the fermenter slurry, especially its viscosity immediately after completion of the fermentation.
The properties thereof are also influenced by the metabolic activities of the chosen microorganisms, it also being possible for unwanted effects to occur. These include for example a frequent increase in the viscosity of the nutrient medium during the fermentation. This impairs the mixing and thus the transport of matter and the oxygen supply inside the reactor. Additional difficulties mostly arise during the subsequent working up because increased viscosities considerably impair for example the efficiency of filtration processes.
It is known in particular that species of the genus Bacillus produce slime which consists essentially of poly-gamma-glutamate (PGA) and/or -aspartate, meaning polyamino acids linked via the relevant gamma peptide bonds. In scientific studies on Bacillus subtilis it is mainly the three genes ywsC, ywtA and ywtB and the gene products derived therefrom which are connected with the production of poly-gamma-glutamate; the gene product of ywtD is involved in the degradation. The general designation “ywt” for genes is in this connection synonymous with the abbreviations “cap” and “pgs” which are in common use for the same functions. This is explained below.
The publication “Physiological and biochemical characteristics of poly gamma-glutamate synthetase complex of Bacillus subtilis” (2001) by M. Ashiuchi et al., in Eur. J. Biochem., volume 268, pages 5321-5328, describes the PgsBCA (poly-gamma-glutamate synthetase complex BCA) enzyme complex, which consists of the three subunits PgsB, PgsC and PgsA, from B. subtilis. This complex is, according to this, an atypical amide ligase which converts both the D and the L enantiomer of glutamate into the corresponding polymer. According to this publication, a gene disruption experiment described therein is to be regarded as proof that this complex is the only one catalyzing this reaction in B. subtilis. 
Y. Urushibata et al. demonstrate in the publication “Characterization of the Bacillus subtilis ywsC gene, involved in gamma-polyglutamic acid production” (2002), in J. Bacteriol., volume 184, pages 337-343, inter alia via deletion mutations in the three genes ywsC, ywtA and ywtB, that the three gene products responsible in B. subtilis for the formation of PGA are encoded by these three genes. They form in this sequence and together with the subsequent gene ywtC a coherent operon in this microorganism.
The fact that a further gene relevant for the metabolism of PGA is located in the genome of B. subtilis downstream from ywtC in its own operon is shown by T. Suzuki and Y. Tahara in the publication “Characterization of the Bacillus subtilis ywtD gene, whose product is involved in gamma-polyglutamic acid degradation” (2003), J. Bacteriol., volume 185, pages 2379-2382. This gene codes for a DL-endopeptidase which is able to hydrolyze PGA and thus can be referred to as gamma-DL-glutamyl hydrolase.
An up-to-date survey of these enzymes is additionally provided by the article “Biochemistry and molecular genetics of poly-gamma-glutamate synthesis” by M. Ashiuchi and H. Misono in Appl. Microbiol. Biotechnol., volume 59, pages 9-14 of 2002. The genes homologous to pgsB, pgsC and pgsA and coding for the PGA synthase complex in B. anthracis are referred to therein as capB, capC and capA. The gene located downstream is referred to according to this article as dep (for “D-PGA depolymerase”) in B. anthracis and as pgdS (for “PGA depolymerase”) in B. subtilis. 
In the current state of the art, these enzymic activities are already in positive use mainly for preparing poly-gamma-glutamate as raw material, for example for use in cosmetics, although their exact DNA sequences and amino acid sequences have not to date been known—especially from B. licheniformis. Thus, for example, the application JP 08308590 A discloses the preparation of PGA by fermentation of the PGA-producing strains itself, namely of Bacillus species such as B. subtilis and B. licheniformis; the isolation of this raw material from the culture medium is also described therein. B. subtilis var. chunkookjang represents, according to the application WO 02/055671 A1, a microorganism which is particularly suitable therefor.
Thus, in some fermentations there is an interest in GLA as the valuable product to be produced by the fermentation.
However, the interest in all other fermentations is to prepare other valuable products; in this connection, the formation of polyamino acids means, for the reasons stated above, a negative side effect. A typical procedure for mastering the increased viscosity of the fermentation medium attributable to the formation thereof is to increase the agitator speed. However, this has an effect on the energy input. In addition, the fermented microorganisms are exposed thereby to increasing shear forces representing a considerable stress factor for them. In the end, very high viscosities cannot be overcome even thereby, so that premature termination of the fermentation may be necessary, although production could otherwise be continued.
Slime formation, as a negative side effect of numerous fermentation processes, may thus have negative effects on the overall result of fermentation for diverse reasons. Conventional methods for successfully continuing fermentations in progress despite an increasing viscosity of the nutrient medium can be designated only as inadequate, especially because they do not represent a causal control.
SUMMARY OF THE INVENTION
The more pressing problem was thus to suppress as far as possible an unwanted formation of slime, especially a slime attributable to poly-gamma-amino acids such as poly-gamma-glutamate, during the fermentation of microorganisms. It was intended in particular to find a solution representing a causal control. A further aspect of this problem is the provision of the relevant genes for a positive utilization of the GLA-synthesizing gene products and for the degradation and/or modification thereof.
Each of the following proteins involved in the formation or degradation of polyamino acids represents in each case a partial solution of in principle equal value for this problem:

    YwsC (CapB, PgsB) which is encoded by a nucleotide sequence ywsC which shows at least 80% identity to the nucleotide sequence indicated in SEQ ID NO. 1;
    YwsC′ (as truncated variant of YwsC) which is encoded by a nucleotide sequence ywsC′ which shows at least 83% identity to the nucleotide sequence indicated in SEQ ID NO. 3;
    YwtA (CapC, PgsC) which is encoded by a nucleotide sequence ywtA which shows at least 82% identity to the nucleotide sequence indicated in SEQ ID NO. 5;
    YwtB (CapA, PgdA) which is encoded by a nucleotide sequence ywtB which shows at least 72% identity to the nucleotide sequence indicated in SEQ ID NO. 7; and
    YwtD (Dep, PgdS) which is encoded by a nucleotide sequence ywtD which shows at least 67% identity to the nucleotide sequence indicated in SEQ ID NO. 9.


As is evident for example from the mentioned publication by Urushibata et al., the four or three genes involved in GLA formation are present in B. subtilis in succession on the same operon. ywtD is located there directly downstream. It is to be expected that this organization of these components acting together in vivo in a complex, and of the downstream component acting on the polyamino acid formed thereby will also be found in many further microorganisms, in particular of the genus Bacillus. Thus, besides the common biochemical function, there also exists at the genetic level an aspect producing unity of the invention.
Further partial solutions are represented by the relevant nucleic acids ywsC, ywsC′, ywtA, ywtB and ywtD and, based thereon, the use of relevant nucleic acids for reducing the formation of slime attributable to polyamino acids during the fermentation of the microorganism, and corresponding methods for fermentation of microorganisms. In the reduction according to the invention of the formation of slime at the genetic level, at least one of the genes ywsC, ywsC′, ywtA or ywtB is functionally inactivated and/or the activity of ywtD is enhanced. In addition, there is the positive use of these genes or of the derived gene products for the preparation, modification or degradation of poly-gamma-glutamate.
This invention which is applicable in principle to all fermentable microorganisms, especially to those of the genus Bacillus, leads to the microorganisms employed for the fermentative production of valuable products other than polyamino acids, in particular of pharmaceutically relevant low molecular weight compounds or of proteins, being prevented at the genetic level from forming polyamino acids, especially GLA, or immediately degrading them again. On the one hand, this has an advantageous effect on the viscosity of the culture medium and additionally on the mixability, the oxygen input and the energy to be expended, and on the other hand the working up of the product of interest is considerably facilitated. In addition, most of the raw materials employed, for instance the N source, is not converted into a product of no interest, so that overall a higher fermentation yield is to be expected.
According to a further aspect of this invention, said genes are now available for a positive use of the GLA-synthesizing gene products or for their degradation and/or modification, specifically by the derived proteins YwsC, YwsC′, YwtA, YwtB and/or YwtD being produced biotechnologically and being introduced in the cells producing them or independently thereof as catalysts into appropriate reaction mixtures.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1: Alignment of the gene ywsC (SEQ ID NO. 1) from B. licheniformis DSM 13 (B.I. ywsC) with the homologous gene ywsC (SEQ ID NO. 11) from B. subtilis (B.s. ywsC).
FIG. 2: Alignment of the gene ywsC′ (SEQ ID NO. 3) from B. licheniformis DSM 13 (B.I. ywsC′) with the homologous gene ywsC (SEQ ID NO. 11) from B. subtilis (B.s. ywsC).
FIG. 3: Alignment of the gene ywtA (SEQ ID NO. 5) from B. licheniformis DSM 13 (B.I. ywtA) with the homologous gene ywtA (SEQ ID NO. 13) from B. subtilis (B.s. ywtA).
FIG. 4: Alignment of the gene ywtB (SEQ ID NO. 7) from B. licheniformis DSM 13 (B.I. ywtB) with the homologous gene ywtB (SEQ ID NO. 15) from B. subtilis (B.s. ywtB).
FIG. 5: Alignment of the gene ywtD (SEQ ID NO. 9) from B. licheniformis DSM 13 (B.I. ywtD) with the homologous gene ywtD (SEQ ID NO. 17) from B. subtilis (B.s. ywtD).
FIG. 6: Alignment of the protein YwsC (SEQ ID NO. 2) from B. licheniformis DSM 13 (B.I. YwsC) with the homologous protein YwsC (SEQ ID NO. 12) from B. subtilis (B.s. YwsC).
FIG. 7: Alignment of the protein YwsC′ (SEQ ID NO. 4) from B. licheniformis DSM 13 (B.I. YwsC′) with the homologous protein YwsC (SEQ ID NO. 12) from B. subtilis (B.s. YwsC).
FIG. 8: Alignment of the protein YwtA (SEQ ID NO. 6) from B. licheniformis DSM 13 (B.I. YwtA) with the homologous protein YwtA (SEQ ID NO. 14) from B. subtilis (B.s. YwtA).
FIG. 9: Alignment of the protein YwtB (SEQ ID NO. 8) from B. licheniformis DSM 13 (B.I. YwtB) with the homologous protein YwtB (SEQ ID NO. 16) from B. subtilis (B.s. YwtB).
FIG. 10: Alignment of the protein YwtD (SEQ ID NO. 10) from B. licheniformis DSM 13 (B.I. YwtD) with the homologous protein YwtD (SEQ ID NO. 18) from B. subtilis (B.s. YwtD).



DETAILED DESCRIPTION OF THE INVENTION
The first partial solution represents a protein YwsC (CapB, PgsB) which is involved in the formation of polyamino acids and which is encoded by a nucleotide sequence ywsC which shows at least 80% identity to the nucleotide sequence indicated in SEQ ID NO. 1.
This specific enzyme was obtained by analysis of the genome of B. licheniformis DSM 13 (see Example 1). This protein is made reproducibly available through the nucleotide and amino acid sequences indicated in SEQ ID NO. 1 and 2 of the present application (see Example 1).
This takes the form, in agreement with the literature information mentioned in the introduction, of a subunit of the poly-gamma-glutamate synthetase complex. The protein known in the state of the art and most similar thereto has been found to be the homolog YwsC from B. subtilis which is noted in the GenBank database (National Center for Biotechnology Information NCBI, National Institutes of Health, Bethesda, Md., USA) under the accession number AB046355.1 and has a homology of 75.4% identity at the nucleic acid level, while the agreement is 86.1% identity at the amino acid level (see Example 2). These significant agreements suggest not only the same biochemical function, but also the presence within the claimed range of a large number of related proteins having the same function which is likewise included in the protection conferred by the present application.
The following embodiments are to be allocated to this first partial solution:

    Any corresponding protein YwsC which is encoded by a nucleotide sequence which shows with increasing preference at least 85%, 90%, 92%, 94%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the nucleotide sequence indicated in SEQ ID NO. 1. This is because the conclusion to be drawn from an increase in agreement of the sequence is that there is an increase in agreement in the function and mutual replaceability at the genetic level.
    Any protein YwsC (CapB, PgsB) involved in the formation of polyamino acids and having an amino acid sequence which shows at least 91% identity, with increasing preference at least 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the amino acid sequence indicated in SEQ ID NO. 2.


In connection with the present application, an expression of the form “at least X %” means “X % to 100%, including the extreme values X and 100 and all integral and non-integral percentages between them”.
The specific protein obtained from B. licheniformis DSM13 is most preferred in each case, because this is specifically described in the present application and is made available 100% reproducibly.
The second partial solution represents a protein YwsC′ (as truncated variant of YwsC) which is involved in the formation of polyamino acids and is encoded by a nucleotide sequence ywsC′, which shows at least 83% identity to the nucleotide sequence indicated in SEQ ID NO. 3.
This specific enzyme was obtained by analysis of the genome of B. licheniformis DSM 13 (see Example 1). This protein is made reproducibly available through the nucleotide and amino acid sequences indicated in SEQ ID NO. 3 and 4 in the present application (see Example 1).
As additionally explained in Example 1, the comparison, shown in FIG. 6, of the sequences between YwsC from B. licheniformis and B. subtilis suggests that the first 16 amino acids of YwsC from B. licheniformis are immaterial for its function as subunit C of the poly-gamma-glutamate synthetase complex. The present invention is thus also implemented with this truncated variant.
Mentioned in connection with the present application of “five or four genes” means that ywsC and ywsC′ are treated according to the invention as two genes and the derived proteins are treated as two proteins. On the other hand, it is probably to be assumed that both these “genes” are not in each case present in vivo in the relevant organisms, but in each case only one thereof, so that only one corresponding gene product YwsC or YwsC′ is also likely to be present. Thus, the first and the second partial solution represent to a certain extent two aspects of the same subject matter. Separation into two partial solutions does, however, appear justified because of the differences at the amino acid level.
The protein known in the state of the art and most similar thereto has again been found to be the homolog YwsC from B. subtilis which is noted in the GenBank database under the accession number AB046355.1 and has a homology of 78.5% identity at the nucleic acid level; the agreement at the amino acid level is 89.6% identity (see Example 2).
In accordance with the statements above, the following embodiments are to be allocated to this second partial solution:

    Any corresponding protein YwsC′ which is encoded by a nucleotide sequence which shows with increasing preference at least 85%, 90%, 92%, 94%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the nucleotide sequence indicated in SEQ ID NO. 3.
    Any protein YwsC′ (as truncated variant of YwsC) which is involved in the formation of polyamino acids and has an amino acid sequence which shows at least 94% identity, with increasing preference at least 95%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the amino acid sequence indicated in SEQ ID NO. 4.


The specific protein obtained from B. licheniformis DSM13 is most preferred in each case because this is specifically described in the present application and is made available 100% reproducibility.
The third partial solution represents a protein YwtA (CapC, PgsC) which is involved in the formation of polyamino acids and which is encoded by a nucleotide sequence ywtA which shows at least 82% identity to the nucleotide sequence indicated in SEQ ID NO. 5.
This specific enzyme was obtained by analysis of the genome of B. licheniformis DSM13 (see Example 1). This protein is made reproducibly available through the nucleotide and amino acid sequences indicated in SEQ ID NO. 5 and 6 in the present application (see Example 1).
This takes the form, in agreement with the literature information mentioned in the introduction, of a further subunit of the poly-gamma-glutamate synthetase complex. The protein known in the state of the art and most similar thereto has been found to be the homolog YwsA from B. subtilis which is noted in the GenBank database under the accession number AB046355.1 and has a homology of 77.8% identity at the nucleic acid level, while the agreement is 89.9% identity at the amino acid level (see Example 2). These significant agreements suggest not only the same biochemical function, but also the presence within the claimed range of a large number of related proteins having the same function which is likewise included in the protection conferred by the present application.
The following embodiments are to be allocated to this third partial solution:

    Any corresponding protein YwtA which is encoded by a nucleotide sequence which shows with increasing preference at least 85%, 90%, 92%, 94%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the nucleotide sequence indicated in SEQ ID NO. 5.
    Any protein YwtA (CapC, PgsC) involved in the formation of polyamino acids and having an amino acid sequence which shows at least 94% identity, with increasing preference at least 95%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the amino acid sequence indicated in SEQ ID NO. 6.


The specific protein obtained from B. licheniformis DSM13 is most preferred in each case, because this is specifically described in the present application and is made available 100% reproducibly.
The fourth partial solution represents a protein YwtB (CapA, PgsA) which is involved in the formation of polyamino acids and is encoded by a nucleotide sequence ywtB, which shows at least 72% identity to the nucleotide sequence indicated in SEQ ID NO. 7.
This specific enzyme was obtained by analysis of the genome of B. licheniformis DSM 13 (see Example 1). This protein is made reproducibly available through the nucleotide and amino acid sequences indicated in SEQ ID NO. 7 and 8 in the present application (see Example 1).
This takes the form, in agreement with the literature information mentioned in the introduction, of the third subunit of the poly-gamma-glutamate synthetase complex. The protein known in the state of the art and most similar thereto has been found to be the homolog YwsA from B. subtilis which is noted in the GenBank database under the accession number AB046355.1 and has a homology of 67.1% identity at the nucleic acid level, while the agreement is 65.8% identity at the amino acid level (see Example 2). These significant agreements suggest not only the same biochemical functional but also the presence within the claimed range of a large number of related proteins having the same function which is likewise included in the protection conferred by the present application.
The following embodiments are to be allocated to this fourth partial solution:

    Any corresponding protein YwtB which is encoded by a nucleotide sequence which shows with increasing preference at least 75%, 80%, 85%, 90%, 92%, 94%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the nucleotide sequence indicated in SEQ ID NO. 7.
    Any protein YwtB (CapA, PgsA) involved in the formation of polyamino acids and having an amino acid sequence which shows at least 70% identity, with increasing preference at least 75%, 80%, 90%, 95%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the amino acid sequence indicated in SEQ ID NO. 8.


The specific protein obtained from B. licheniformis DSM13 is most preferred in each case, because this is specifically described in the present application and is made available 100% reproducibly.
The fifth partial solution represents a protein YwtD (Dep, PgdS) which is involved in the degradation of polyamino acids and is encoded by a nucleotide sequence ywtD, which shows at least 67% identity to the nucleotide sequence indicated in SEQ ID NO. 9.
This specific enzyme was obtained by analysis of the genome of B. licheniformis DSM 13 (see Example 1). This protein is made reproducibly available through the nucleotide and amino acid sequences indicated in SEQ ID NO. 9 and 10 in the present application (see Example 1).
This takes the form, in agreement with the literature information mentioned in the introduction, of the gamma-DL-glutamyl hydrolase, D-PGA depolymerase or PGA depolymerase. The protein known in the state of the art and most similar thereto was found to be the homolog YwtD from B. subtilis which is noted in the GenBank database under the accession number AB080748 and has a homology of 62.3% identity at the nucleic acid level; the agreement at the amino acid level is 57.3% identity (see Example 2). These significant agreements suggest not only the same biochemical function, but also the presence within the claimed range of a large number of related proteins having the same function which is likewise included in the protection conferred by the present application.
The following embodiments are to be allocated to this fifth partial solution:

    Any corresponding protein YwtD which is encoded by a nucleotide sequence which shows with increasing preference at least 70%, 75%, 80%, 85%, 90%, 92%, 94%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the nucleotide sequence indicated in SEQ ID NO. 9.
    Any protein YwtD (Dep, PgdS) involved in the degradation of polyamino acids and having an amino acid sequence which shows at least 62% identity, with increasing preference at least 65%, 70%, 75%, 80%, 90%, 95%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the amino acid sequence indicated in SEQ ID NO. 10.


The specific protein obtained from B. licheniformis DSM13 is most preferred in each case, because this is specifically described in the present application and is made available 100% reproducibly.
Preference is given in each case among these in each case to a previously described protein of the invention which is involved in the formation or degradation of polyamino acids and which is naturally produced by a microorganism, preferably by a bacterium, particularly preferably by a Gram-positive bacterium, preferably among these by one of the genus Bacillus, particularly preferably among these by one of the species B. licheniformis and very particularly preferably among these by B. licheniformis DSM13.
This is because, in accordance with the problem, there was interest in improving the fermentation of microorganisms, for which bacteria from among these particularly Gram-positive ones, are frequently used, especially those which, like Bacillus, are able to secrete produced valuable products and proteins. In addition, there is a wealth of clinical experience concerning this. In addition, it was possible to detect, as mentioned, the proteins indicated in the sequence listing for B. licheniformis, specifically B. licheniformis DSM13. It is to be expected that an increasing degree of relationship of the relevant organisms will be associated with an increasing extent of agreement of the nucleotide and amino acid sequences and thus their exchangeability.
In accordance with that stated hitherto, the following in each case relevant nucleic acids are to be allocated as further expressions of the present invention to the stated partial solutions:

    Nucleic acid ywsC (capB, pgsB) which codes for a gene product involved in the formation of polyamino acids and has a nucleotide sequence which shows at least 80% identity to the nucleotide sequence indicated in SEQ ID NO. 1;
    a corresponding nucleic acid ywsC having a nucleotide sequence which shows with increasing preference at least 85%, 90%, 92%, 94%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the nucleotide sequence indicated in SEQ ID NO. 1;
    nucleic acid ywsC′ (as truncated variant of ywsC) which codes for a gene product involved in the formation of polyamino acids and has a nucleotide sequence which shows at least 83% identity to the nucleotide sequence indicated in SEQ ID NO. 3;
    a corresponding nucleic acid ywsC′ having a nucleotide sequence which shows with increasing preference at least 85%, 90%, 92%, 94%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the nucleotide sequence indicated in SEQ ID NO. 3;
    nucleic acid ywtA (capC, pgsC) which codes for a gene product involved in the formation of polyamino acids and has a nucleotide sequence which shows at least 82% identity to the nucleotide sequence indicated in SEQ ID NO. 5;
    a corresponding nucleic acid ywtA having a nucleotide sequence which shows with increasing preference at least 85%, 90%, 92%, 94%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the nucleotide sequence indicated in SEQ ID NO. 5;
    nucleic acid ywtB (capA, pgsA), which codes for a gene product involved in the formation of polyamino acids and has a nucleotide sequence which shows at least 72% identity to the nucleotide sequence indicated in SEQ ID NO. 7;
    a corresponding nucleic acid ywtB having a nucleotide sequence which shows with increasing preference at least 75%, 80%, 85%, 90%, 92%, 94%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the nucleotide sequence indicated in SEQ ID NO. 7;
    nucleic acid ywtD (dep, pgdS) which codes for a gene product involved in the degradation of polyamino acids and has a nucleotide sequence which shows at least 67% identity to the nucleotide sequence indicated in SEQ ID NO. 9; and
    a corresponding nucleic acid ywtD having a nucleotide sequence which shows with increasing preference at least 70%, 75%, 80%, 85%, 90%, 92%, 94%, 96%, 97%, 98%, 99% and particularly preferably 100% identity to the nucleotide sequence indicated in SEQ ID NO. 9.


The nucleic acids provided herewith can be employed by methods of molecular biology known per se for inactivating or enhancing the activity of the relevant proteins. Thus, inactivations are possible for example via appropriate deletion vectors (see below); enhancement of the activity advantageously takes place by an overexpression which can be achieved with the aid of an expression vector (see below). Thus, the problem posed is implemented via these nucleic acids through inactivation of ywsC, ywsC′, ywtA and/or ywtB and/or by enhanced ywtD gene activity.
The corresponding genes falling within the homology ranges indicated in each case can be obtained from the organisms of interest for example with the aid of probes which can be prepared on the basis of sequences 1, 3, 5, 7, or 9. These complete genes may also serve as model for generating PCR primers via which the relevant genes can be rendered accessible from corresponding total DNA preparations; these genes in turn provide the proteins described previously. The success rate in this connection usually increases with the closeness of the relationship of the relevant strain to that which has served to construct the probe or the PCR primers, and thus in the present case to B. licheniformis. 
Preference is given in each case among these in each case to a nucleic acid of the invention which is naturally present in a microorganism, preferably a bacterium, particularly preferably a Gram-positive bacterium, and among these preferably one of the genus Bacillus, particularly preferably among these one of the species B. licheniformis and very particularly preferably among these B. licheniformis DSM13.
This is because, as stated above, there is a particular interest in utilizing these genes for fermentations of such microorganisms. On the other hand, the present invention is also linked to the possibility of adjusting, via the genes and/or proteins described herein, the metabolism of the polyamino acids, especially gamma-glutamic acid, at least in parts when they are to be synthesized, modified and/or degraded. The success rate for this generally, especially in appropriate transgenic host cells, increases with the degree of agreement of the relevant genes with those of the natural cells.
It is additionally possible to isolate alternative embodiments of the genes and proteins easily from in principle all natural organisms.
A further embodiment of the present invention represents all nucleic acids which code for a protein of the invention described above.
Thus, differences exist, particularly between remotely related species, in the usage of synonymous codons coding for the respective amino acids, with which the protein biosynthesis apparatus also conforms, for instance via the available number of appropriate loaded tRNAs. Transfer of one of said genes into a less related species can be used particularly successfully for example for deletion mutation or for synthesis of the relevant protein if it is appropriately optimized in terms of the codons. It is possible thereby to introduce increasing percentage differences at the DNA level which, however, have no consequence at the amino acid level. For this reason, such nucleic acids also represent implementations of the present invention.
The invention further relates to vectors which comprise a previously designated nucleic acid region of the invention.
This is because in order to handle the nucleic acids relevant to the invention, and thus in particular to prepare for the production of proteins of the invention, they are suitably ligated into vectors. Such vectors and the relevant working methods are described in detail in the prior art. Vectors are commercially available in large number and range of variation, both for cloning and for expression. These include for example vectors derived from bacterial plasmids, from bacteriophages or from viruses, or predominantly synthetic vectors. They are also distinguished according to the nature of the cell types in which they are able to establish themselves, for example into vectors for Gram-negative, for Gram-positive bacteria, for yeasts or for higher eukaryotes. They form suitable starting points for example for molecular biological and biochemical investigations and for the expression of the relevant gene or associated protein. They are virtually indispensable—as is evident from the prior art relevant thereto—in particular for the preparation of constructs for deletion or enhancement of expression.
Vectors preferred among these are those comprising two or more of the nucleic acids of the invention described above.
This is because in addition on the one hand the relevant genes can at the same time be stored or can be expressed under the control of the same promoter. According to another application, a vector which simultaneously comprises two or more intact copies of the genes of the invention can serve to keep alive (rescue) a deletion mutant which is simultaneously deleted in a plurality of these genes. Targeted removal of this vector then results in this plurality of genes being simultaneously switched off.
In another embodiment, the vectors of the invention are cloning vectors.
This is because cloning vectors are, besides the storage, the biological amplification or the selection of the gene of interest, suitable for its molecular biological characterization. At the same time, they represent transportable and storable forms of the claimed nucleic acids and are also starting points for molecular biological techniques which are not linked to cells, such as, for example, PCR or in vitro mutagenesis methods.
The vectors of the invention are preferably expression vectors.
This is because such expression vectors are the basis for implementing the corresponding nucleic acids in biological production systems and thus producing the relevant proteins. Preferred embodiments of this subject matter of the invention are expression vectors which are by genetic elements necessary for expression, for example the natural promoter originally located in front of this gene, or a promoter from a different organism. These elements may be disposed for example in the form of a so-called expression cassette. An alternative possibility is for one or all regulatory elements also to be provided by the respective host cell. Expression vectors are particularly preferred in relation to further properties such as, for example, the optimum copy number matched to the chosen expression system, especially the host cell (see below).
The possibility of forming intact gene products on the basis of a vector existing as a replicon is particularly important for the rescue described above and the switching off of particular genes. Conversely, the provision of an expression vector is the best possibility for enhanced formation of a protein of the invention and thus an increase in the relevant activity.
Cells which, after genetic modification, comprise one of the nucleic acids of the invention designated above form a separate subject matter of the invention.
This is because these cells comprise the genetic information for synthesizing a protein of the invention. By these are meant in particular cells which have been provided with the nucleic acids of the invention by methods known per se, or which are derived from such cells. The host cells suitably selected for this purpose are those which can be cultured relatively simply and/or provide high product yields.
It is necessary in principle in countries where human embryonic stem cells may not be placed under patent protection for such human embryonic stem cells of the invention to be excluded from the protection conferred.
Cells of the invention make it possible for example to amplify the corresponding genes, but also for them to be mutagenized or transcribed and translated and eventually for the relevant proteins to be produced biotechnologically. This genetic information may be present either extrachromosomally as separate genetic element, meaning located in plasmids in the case of bacteria, or be integrated into a chromosome. The choice of a suitable system depends on questions such as, for example, the nature and duration of the storage of the gene or of the organism or the nature of the mutagenesis or selection.
These include, besides the cells which overexpress in particular YwtD, in particular those which comprise one of the genes ywsC, ywsC′, ywtA and ywtB via a vector in trans and can thus be used for corresponding deletions (see below).
This explains the preferred embodiment in which said nucleic acid is part of a vector, in particular of a previously described vector, in such a cell.
Host cells which are bacteria are preferred among these.
This is because bacteria are distinguished by short generation times and low demands on the culturing conditions. It is possible thereby to establish cost-effective methods. In addition, there is a wealth of experience in the techniques of fermentation of bacteria. Gram-negative or Gram-positive bacteria may be suitable for a specific production for a wide variety of reasons which are to be ascertained experimentally in the individual case, such as nutrient sources, product formation rate, time required etc.
A preferred embodiment involves a Gram-negative bacterium, in particular one of the genera Escherichia coli, Klebsiella, Pseudomonas or Xanthomonas, in particular strains of E. coli K12, E. coli B or Klebsiella planticola, and very especially derivatives of the strain Escherichia coli BL21 (DE3), E. coli RV308, E. coli DH5α, E. coli JM109, E. coli XL-1 or Klebsiella planticola (Rf).
This is because a large number of proteins are secreted into the periplasmic space with Gram-negative bacteria such as, for example, E. coli. This may be advantageous for specific applications. The application WO 01/81597 A1 discloses a method which achieves expulsion of the expressed proteins by Gram-negative bacteria too. The Gram-negative bacteria mentioned as preferred are usually available easily, meaning commercially or through public collections of strains, and can be optimized for specific preparation conditions in association with other components such as, for instance, vectors which are likewise available in large number.
An alternative, not less preferred embodiment involves a Gram-positive bacterium, in particular one of the genera Bacillus, Staphylococcus or Corynebacterium, very particularly of the species Bacillus lentus, B. licheniformis, B. amyloliquefaciens, B. subtilis, B. globigii or B. alcalophilus, Staphylococcus carnosus or Corynebacterium glutamicum, and among these in turn very particularly preferably a derivative of B. licheniformis DSM 13.
This is because Gram-positive bacteria have the fundamental difference from Gram-negative ones of immediately releasing secreted proteins into the nutrient medium which surrounds the cells and from which if desired the expressed proteins of the invention can be directly purified from the nutrient medium. In addition, they are related or identical to most of the organisms of origin of industrially important enzymes and mostly themselves produce comparable enzymes, so that they have a similar codon usage and their protein synthesis apparatus is naturally configured appropriately. Derivatives of B. licheniformis DSM 13 are very particularly preferred because they on the one hand are likewise widely used as biotechnological producer strains in the state of the art and because on the other hand the present application makes exactly the genes and proteins of the invention from B. licheniformis DSM 13 available, so that implementation of the present invention ought most likely to be successful in such strains.
A further embodiment of the present invention is formed by methods for preparing one or more of the gene products YwsC, YwsC′, YwtA, YwtB and YwtD described above.
This includes any method for preparing a protein of the invention described above, for example chemical synthetic methods. However, in relation thereto, all molecular biological, microbiological and biotechnological preparation methods which have been discussed above in individual aspects and are established in the state of the art are preferred. The aim thereof is primarily to obtain the proteins of the invention in order to make them available for appropriate applications, for example for the synthesis, modification or degradation of poly-gamma-glutamate.
Methods preferred in this connection are those taking place with use of a nucleic acid of the invention designated above, preferably taking place with use of a vector of the invention designated above and particularly preferably with use of a cell of the invention designated above.
This is because said nucleic acids, especially the nucleic acids indicated in the sequence listing under SEQ ID NO. 1, 3, 5, 7 and 9, makes the correspondingly preferred genetic information available in microbiologically utilizable form, i.e. for genetic production methods. It is increasingly preferred to provide on a vector which can be utilized particularly successfully by the host cell, or such cells themselves. The relevant production methods are known per se to the skilled worker.
Embodiments of the present invention may on the basis of the relevant nucleic acid sequences also be cell-free expression systems in which the protein biosynthesis is duplicated in vitro. All the elements already mentioned may also be combined to novel methods in order to prepare proteins of the invention. A large number of possible combinations of method steps is conceivable for each protein of the invention moreover, so that optimal methods need to be ascertained experimentally for each specific individual case.
Methods of the invention of such types are further preferred when the nucleotide sequence has been adapted in one or, preferably, more codons to the codon usage of the host strain.
This is because, in accordance with that stated above, transfer of one of said genes into a less related species can be used particularly successfully for synthesizing the relevant protein if it is appropriately optimized in relation to the codon usage.
A further expression of the present invention is the use of a nucleic acid ywsC of the invention described above, of a nucleic acid ywsC′ of the invention described above, of a nucleic acid ywtA of the invention described above, of a nucleic acid ywtB of the invention described above or of a corresponding nucleic acid which codes for one of the proteins of the invention described above or in each case parts thereof for the functional inactivation of the respectively relevant gene ywsC, ywsC′, ywtA or ywtB in a microorganism.
Functional inactivation means in the context of the present application any type of modification or mutation by which the function of the relevant protein as an enzyme involved in the formation of polyamino acids, or as subunit of such an enzyme, is suppressed. This includes the embodiment where a virtually complete but inactive protein is formed, where inactive parts of such a protein are present in the cell, up to the possibilities where the relevant gene is no longer translated or is even completely deleted. Thus, a specific “use” of these factors or genes in this embodiment consists of them no longer acting in their natural manner precisely in the relevant cell. This is achieved according to the subject matter of the invention at the genetic level by switching off the relevant gene.
An alternative embodiment for inactivating the genes ywsC, ywsC′, ywtA or ywtB is the use of a nucleic acid ywtD of the invention described above or of a corresponding nucleic acid which codes for one of the proteins of the invention described above for increasing the activity of the relevant gene ywtD in a microorganism.
This is because, as described in the introduction, the in vivo function of this enzyme is to degrade GLA. Enhancement of this activity thus leads to a reduction in the concentration of polyamino acids in the culture medium and has a positive effect according to the invention on the industrial fermentation of the relevant microorganisms. This enhancement of activity advantageously takes place at the genetic level. Methods for this are known per se. For example, mention may be made of the transfer of this gene to an expression vector: Such a vector can be introduced by transformation into the cells used for the fermentation and where appropriate be activated under certain conditions, so that the derived protein then acts in addition to the endogenously formed YwtD.
In preferred embodiments, both uses are those where the functional inactivation or increase in activity takes place during the fermentation of the microorganism, preferably with a reduction of the slime attributable to polyamino acids to 50%, particularly preferably to less than 20%, very particularly preferably to less than 5%, once again all intermediate integral or fractional percentages being understood in appropriately preferred gradation.
To determine these values, cells of an untreated strain and of a treated strain are fermented under conditions which are otherwise identical and suitably the viscosity of the respective medium is determined during the fermentation. Since the strains are otherwise identical, the differences in viscosity are attributable to the different contents of polyamino acids. Every reduction in viscosity is desired according to the invention. Comparable values as percentages are obtained by taking samples from both fermentations and determining the content of polyamino acid-containing slime by methods known per se. It is increasingly preferred for the value which can be determined in the sample of the invention to be at the transition into the stationary growth phase less than 50%, 40%, 30%, 20%, 10%, 5% and very especially less than 1% of the corresponding value for the comparative fermentation.
This is because the intention according to the problem was to improve the fermentation of the microorganisms employed for biotechnological production. Thus, it is worthwhile or, especially when a plurality of genes is affected, usually necessary to carry out the relevant molecular biological constructs on the laboratory scale and, where appropriate, on host cells which merely represent intermediate stages, for example construction of a deletion vector in E. coli. However, it is desired according to the invention for the inactivation of the genes ywsC, ywsC′, ywtA or ywtB to show the hoped-for effects especially during the fermentation. The increase in the activity of the ywtD gene can be controlled for example via inducible promoters which are for example of the relevant transgene. The activity of this gene can thus be switched on deliberately by adding an inducer at a time which appears suitable during the fermentation. As an alternative thereto, this gene can also be coupled to a promoter which responds to stress signals, for instance to an oxygen content which is too low, as also occurs when mixing is inadequate in a fermenter which is blocked by slime.
In further preferred embodiments, these uses of the invention are such that, with increasing preference, 2, 3 or 4 of the genes ywsC, ywsC′, ywtA and ywtB are inactivated, preferably in combination with an enhancement of the activity mediated by the ywtD gene.
It may be recalled at this point that in vivo in the relevant organisms it is probable that both the genes ywsC and ywsC′ may not be present simultaneously, but in each case only one thereof. In these cases it is possible for a maximum of 3 of said genes to be inactivated, so that this then represents the most preferred embodiment in this respect.
This embodiment serves as safeguard in the event that the molecular biological form of the inactivation chosen for inactivation of one of these genes is incomplete and the cell still has corresponding residual activities. This applies in particular to host cells other than B. subtilis for which, according to Ashiuchi et al. (see above), it has been demonstrated that these genes are present in only one copy in each case. It appears to be particularly worthwhile to combine the deletion approach with that of enhancement of the activity mediated by the ywtD, because two systems which act differently in principle are thereby combined together.
In one embodiment of the use for functional inactivation of one or more of the genes ywsC, ywsC′, ywtA and ywtB, a nucleic acid coding for an inactive protein and having a point mutation is employed.
Nucleic acids of this type can be generated by methods of point mutagenesis known per se. Such methods are described for example in relevant handbooks such as that of Fritsch, Sambrook and Maniatis “Molecular cloning: a laboratory manual”, Cold Spring Harbor Laboratory Press, New York, 1989. In addition, numerous commercial construction kits are now available therefor, for instance the QuickChange® kit from Stratagene, La Jolla, USA. The principle thereof is for oligonucleotides having single exchanges (mismatch primers) to be synthesized and hybridized with the gene in single-stranded form; subsequent DNA polymerization then affords corresponding point mutants. It is possible to use for this purpose the respective species-specific sequences of these genes. Owing to the high homologies, it is possible and particularly advantageous according to the invention to carry out this reaction on the basis of the sequences provided by SEQ ID NO. 1, 3, 5 and 7. These sequences can also serve to design appropriate mismatch primers for related species, especially on the basis of the conserved regions identifiable in the alignments of FIGS. 6 to 10 and 1 to 5.
In one embodiment of this use, in each case a nucleic acid with a deletion mutation or insertion mutation is employed for the functional inactivation, preferably including the border sequences, in each case comprising at least 70 to 150 nucleic acid positions, of the region coding for the protein.
These methods are also familiar per se to the skilled worker. It is thus possible to prevent the formation of one or more of the factors YwsC, YwsC′, YwtA and YwtB by the host cell by cutting out part of the relevant gene on an appropriate transformation vector via restriction endonucleases, and subsequently transforming the vector into the host of interest, where the active gene is replaced by the inactive copy via the homologous recombination which is still possible until then. In the embodiment of insertion mutation it is possible merely to introduce the intact gene interruptingly or, instead of a gene portion, another gene, for example a selection marker. Phenotypical checking of the mutation event is possible thereby in a manner known per se.
In order to enable these recombination events which are necessary in each case between the defective gene introduced into the cell and the intact gene copy which is endogenously present for example on the chromosome, it is necessary according to the current state of knowledge that in each case there is agreement in at least 70 to 150 connected nucleic acid positions, in each case in the two border sequences to the non-agreeing part, with the part lying between being immaterial. Accordingly, preferred embodiments are those including only two flanking regions with at least one of these sizes.
In an alternative embodiment of this use, nucleic acids having a total of two nucleic acid segments which in each case comprise at least 70 to 150 nucleic acid positions, and thus flank at least partly, preferably completely, the region coding for the protein, are employed. The flanking regions can in this connection be ascertained starting from the known sequences by methods known per se, for example with the aid of outwardly directed PCR primers and a preparation of genomic DNA as template (anchored PCR). This is because it is not obligatory for the segments to be protein-encoding in order to make it possible to exchange the two gene copies by homologous recombination. According to the present invention it is possible to design the primers required for this on the basis of SEQ ID NO. 1, 3, 5 and 7 also for other species of Gram-positive bacteria and, among these, in particular for those of the genus Bacillus. As an alternative to this experimental approach it is possible to take such regions which are at least in part non-coding for many of these genes from related species, for example from B. subtilis database entries, for example the SubtiList database of the Institute Pasteur, Paris, France.
A further preferred embodiment involves one of the described uses according to the invention in which an expression vector is employed for said enhancement of the activity mediated by the ywtD gene, preferably a vector which comprises this gene together with nucleic acid segments for regulating this gene.
As already stated above, the increased activity of this gene and thus of the derived protein can be deliberately regulated from outside thereby, or adapts automatically via the conditions prevailing in the fermentation medium to the need for a reduction in the polyamino acid concentration. It is particularly advantageous to use here for the nucleic acids of the invention described which code for ywtD, and very especially that according to SEQ ID NO. 9.
The present invention is also implemented in the form of genetically modified microorganisms, to which that stated above applies correspondingly.
These are very generally microorganisms in which at least one of the genes ywsC, ywsC′, ywtA or ywtB is functionally inactivated or ywtD has enhanced activity.
These are preferably microorganisms in which, with increasing preference, 2, 3 or 4 of the genes ywsC, ywsC′, ywtA or ywtB are inactivated, preferably in combination with an enhancement of the activity mediated by the ywtD gene.
These are preferably microorganisms in the form of bacteria.
The microorganisms among these which are preferred according to the statements hitherto are Gram-negative bacteria, especially those of the genera Escherichia coli, Klebsiella, Pseudomonas or Xanthomonas, especially strains of E. coli K12, E. coli B or Klebsiella planticola, and very especially derivatives of the strains Escherichia coli BL21 (DE3), E. coli RV308, E. coli DH5α, E. coli JM109, E. coli XL-1 or Klebsiella planticola (Rf).
Microorganisms which are not less preferred according to statements hitherto are Gram-positive bacteria, especially those of the genus Bacillus, Staphylococcus or Corynebacterium, very particularly of the species Bacillus lentus, B. licheniformis, B. amyloliquefaciens, B. subtilis, B. globigii or B. alcalophilus, Staphylococcus carnosus or Corynebacterium glutamicum and, among these, very especially B. licheniformis DSM 13.
According to the problem on which the present application is based, the intention was primarily to improve industrial fermentation methods. Accordingly, the invention is implemented especially in corresponding fermentation methods of the invention.
These are very generally methods for the fermentation of a microorganism of the invention described above.
According to statements hitherto, the methods characterized thereby are correspondingly preferred. These include in particular the embodiment of one or more of the genes ywsC, ywsC′, ywtA or ywtB being functionally inactivated or the activity of ywtD being enhanced, in particular combinations of the two approaches. For this purpose, recourse is particularly preferably had to the nucleic acids of the invention described above, especially those indicated under SEQ ID NO. 1, 3, 5, 7, or 9. This applies correspondingly also to the species selected as suitable for the respective fermentation. According to the statements above, those among these which are increasingly preferred have an increasing extent of relationship to B. licheniformis DSM13, because the prospects of success on use of the stated nucleic acids increase thereby.
Among the fermentation methods of the invention, those for preparing a valuable product are preferred, especially for preparing a low molecular weight compound or a protein.
This is because this is the most important area of application of industrial fermentations.
These are preferably methods where the low molecular weight compound is a natural product, a dietary supplement or a pharmaceutically relevant compound.
In this way for example amino acids or vitamins which are used in particular as dietary supplements are produced. Pharmaceutically relevant compounds may be precursors or intermediates for medicaments or even the latter themselves. In all these cases, the term biotransformation is also used, according to which the metabolic properties of the microorganisms are utilized to replace, entirely or at least in individual steps, the otherwise elaborate chemical synthesis.
No less preferred are corresponding methods in which the protein produced in this way is an enzyme, in particular one from the group of α-amylases, proteases, cellulases, lipases, oxidoreductases, peroxidases, laccases, oxidases and hemicellulases.
Industrial enzymes prepared by such methods are used for example in the food industry. Thus, α-amylases are used for example to prevent bread becoming stale or to clarify fruit juices. Proteases are used for the lysis of proteins. All these enzymes have been described for use in detergent and cleaner compositions, a prominent place being occupied in particular by the Subtilisin proteases prepared naturally by Gram-positive bacteria. They are used in particular in the textile and leather industries for processing the natural raw materials. A further possibility is for all these enzymes in turn to be employed in the context of biotransformation as catalysts for chemical reactions.
Many of these enzymes are originally derived from Bacillus species and are therefore produced particularly successfully in Gram-positive organisms, especially those of the genus Bacillus, including in many cases also derivatives of B. licheniformis DSM13. Production methods based on these microbial systems in particular can be improved with the aid of the present invention, because the sequences indicated in particular in SEQ ID NO. 1, 3, 5, 7 and 9 are derived from precisely this organism.
Finally, the factors made available with the present application can also be employed positively, meaning in the sense of their natural function, meaning in connection with a targeted preparation, modification or degradation of poly-gamma-glutamate.
One embodiment is thus formed by microbial methods for the preparation, modification or degradation of poly-gamma-glutamate in which one of the nucleic acids ywsC, ywsC′, ywtA, ywtB and/or ywtD of the invention described above or a corresponding nucleic acid which codes a protein of the invention described above is employed transgenically, preferably to form the corresponding protein of the invention described above.
Preferred methods among these are those in which a microorganism from the genus Bacillus, in particular B. subtilis or B. licheniformis, is employed.
It is thus possible, as described for example in the applications JP 08308590 A or WO 02/055671 A1, to produce GLA microbially, specifically in B. subtilis and B. licheniformis. The DNA sequences made available with the present application can be utilized for example to increase the respective gene activities in appropriate cells, and thus to increase the yield.
As alternative thereto, cell-free methods for the preparation, modification or degradation of poly-gamma-glutamate are now also possible, involving a gene product YwsC, YwsC′, YwtA, YwtB and/or YwtD of the invention described above, which is involved in the formation of polyamino acids, preferably with use of a corresponding nucleic acid of the invention described above.
Thus, these factors can be reacted for example in a bioreactor. The design of such enzyme bioreactors is known from the prior art.
Corresponding methods of this type which are particularly preferred among these are those where 2, preferably 3, particularly preferably 4, different ones of said gene products or nucleic acids are employed.
This is because the factors YwsC, YwtA and YwtB in particular usually form, as described in the introduction, a coherent complex, so that it is necessary to speak of a joint activity. Simultaneous or subsequent activity of YwtD might serve for example to influence the biophysical properties of the formed polyamino acid and, for example, for adaptation for use in cosmetic preparations.
The following examples illustrate the present invention further.
EXAMPLES
All molecular biological working steps follow standard methods as indicated for example in the handbook by Fritsch, Sambrook and Maniatis “Molecular cloning: a laboratory manual”, Cold Spring Harbour Laboratory Press, New York, 1989, or comparable relevant works. Enzymes, construction kits and apparatuses were employed in accordance with the respective manufacturer's instructions.
Example 1
Identification of the Genes ywsC, ywsC′, ywtA, ywtB and ywtD from B. licheniformis DSM 13
The genomic DNA was prepared by standard methods from the strain B. licheniformis DSM 13, which is available to anyone from the Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, mechanically fractionated and fractionated by electrophoresis in a 0.8% agarose gel. For a shotgun cloning of the smaller fragments, the fragments 2 to 2.5 kb in size were eluted from the agarose gel, dephosphorylated and ligated as blunt-ended fragments into the SmaI restriction cleavage site of the vector pTZ19R-Cm. This is a derivative which confers chloramphenicol resistance of the plasmid pTZ19R which is obtainable from Fermentas (St. Leon-Rot). A gene library of the smaller fragments was obtained thereby. As second shotgun cloning, the genomic fragments obtained by a partial restriction with the enzyme SauIIIal were ligated into the SuperCos 1 vector system (“Cosmid Vector Kit”) from Stratagene, La Jolla, USA, resulting in a gene library over the predominantly larger fragments.
The relevant recombinant plasmids were isolated and sequenced from the bacteria E. coli DH5α (D. Hannahan (1983): “Studies on transformation on Escherichia coli”; J Mol. Microbiol., volume 166, pages 557-580) obtainable by transformation with the relevant gene libraries. The dye termination method (dye terminator chemistry) was employed in this case, carried out by the automatic sequencers MegaBACE 1000/4000 (Amersham Bioscience, Piscataway, USA) and ABI Prism 377 (Applied Biosystems, Foster City, USA).
In this way, inter alia the sequences SEQ ID NO. 1, 3, 5, 7 and 9 which are indicated in the sequence listing of the present application were obtained and stand in this sequence for the genes ywsC, ywsC′ (as truncated variant of ywsC), ywtA, ywtB and ywtD. The amino acid sequences derived therefrom are indicated in the corresponding sequence in SEQ ID NO. 2, 4, 6, 8 and 10, respectively. A truncated variant ywsC′ (or YwsC′) is indicated for the gene or protein ywsC (or YwsC) because the comparison, shown in FIG. 6, of the amino acid sequences for the homologous protein in B. subtilis shows a polypeptide which is N-terminally shorter by 16 amino acids with otherwise quite high homology and therefore comparable activity.
Reproducibility
These genes and gene products can now be artificially synthesized by methods known per se, and without the need to reproduce the described sequencing, in a targeted manner on the basis of these sequences. It is possible, as further alternative thereto, to isolate the relevant genes from a Bacillus strain, in particular the strain B. licheniformis DSM 13 which is obtainable from the DSMZ, via PCR, it being possible to use the respective border sequences indicated in the sequence listing for synthesizing primers. If further strains are used, the genes homologous thereto in each case are obtained, and the success of the PCR should increase with the closeness of the relationship of the selected strains to B. licheniformis DSM 13, because this is likely to be associated with an increasing agreement of sequences also within the primer binding regions.
Example 2
Sequence Homologies
After ascertaining the DNA and amino acid sequences as in Example 1, in each case the most similar homologs disclosed to date were ascertained by a search in the databases GenBank (National Center for Biotechnology Information NCBI, National Institutes of Health, Bethesda, Md., USA) and Subtilist of the Institute Pasteur, Paris, France.
The ascertained DNA and amino acid sequences were compared with one another via the alignments depicted in FIGS. 1 to 10; the computer program used for this was Vector NTI® Suite Version 7 which is obtainable from Informax Inc., Bethesda, USA. In this case, the standard parameters of this program were used, meaning for comparison of the DNA sequences: K-tuple size: 2; Number of best Diagonals: 4; Window size: 4; Gap penalty: 5; Gap opening penalty: 15 and Gap extension penalty: 6.66. The following standard parameters applied to the comparison of the amino acid sequences: K-tuple size: 1; Number of best Diagonals: 5; Window size: 5; Gap penalty: 3; Gap opening penalty: 10 and Gap extension penalty: 0.1. The results of these sequence comparisons are compiled in Table 1 below, the accession numbers indicated being those from the NCBI database.







TABLE 1







Genes and proteins of greatest similarity to


the genes and proteins found in Example 1.










Gene or protein

Database entry of



found in B.
Most closely
the most closely


licheniformis/
related gene
related gene or
Homology in


SEQ ID NO.
or protein
protein
% identity





ywsC/1
ywsC from B. subtilis
AB046355.1
75.4


ywsC′/3
ywsC from B. subtilis
AB046355.1
78.5


ywtA/5
ywsA from B. subtilis
AB046355.1
77.8


ywtB/7
ywsB from B. subtilis
AB046355.1
67.1


ywtD/9
ywtD from B. subtilis
AB080748
62.3


YwsC/2
YwsC from B. subtilis
AB046355.1
86.1


YwsC′/4
YwsC from B. subtilis
AB046355.1
89.6


YwtA/6
YwsA from B. subtilis
AB046355.1
89.9


YwtB/8
YwsB from B. subtilis
AB046355.1
65.8


YwtD/10
YwsD from B. subtilis
AB046355.1
57.3









It is evident that the found genes and the gene products derived therefrom are novel genes and proteins with a distinct difference from the prior art disclosed hitherto.
Example 3
Functional Inactivation of One or More of the Genes ywsC, ywsC′, ywtA and ywtB in B. Licheniformis 
Principle of the Preparation of a Deletion Vector
Each of these genes can be functionally inactivated, for example, by means of a so-called deletion vector. This procedure is described per se for example by J. Vehmaanperä et al. (1991) in the publication “Genetic manipulation of Bacillus amyloliquefaciens”; J. Biotechnol., volume 19, pages 221-240.
A suitable vector for this is pE194 which is characterized in the publication “Replication and incompatibility properties of plasmid pE194 in Bacillus subtilis” by T. J. Gryczan et al. (1982), J. Bacteriol., volume 152, pages 722-735. The advantage of this deletion vector is that it possesses a temperature-dependent origin of replication. pE194 is able to replicate in the transformed cell at 33° C., so that initial selection for successful transformation takes place at this temperature. Subsequently, the cells comprising the vector are incubated at 42° C. The deletion vector no longer replicates at this temperature, and a selection pressure is exerted on the integration of the plasmid via a previously selected homologous region into the chromosome. A second homologous recombination via a second homologous region then leads to excision of the vector together with the intact gene copy from the chromosome and thus to deletion of the gene which is located in the chromosome in vivo. Another possibility as second recombination would be the reverse reaction to integration, meaning recombination of the vector out of the chromosome, so that the chromosomal gene would remain intact. The gene deletion must therefore be detected by methods known per se, for instance in a Southern blot after restriction of the chromosomal DNA with suitable enzymes or with the aid of the PCR technique on the basis of the size of the amplified region.
It is thus necessary to select two homologous regions of the gene to be deleted, each of which should include 70 base pairs in each case, for example the 5′ region and the 3′ region of the selected gene. These are cloned into the vector in such a way that they flank a part coding for an inactive protein, or are in direct succession, omitting the region in between. The deletion vector is obtained thereby.
Deletion of the Genes ywsC, ywsC′, ywtA and ywtB Considered Here
A deletion vector of the invention is constructed by PCR amplification of the 5′ and 3′ regions of one of these four or three genes. The sequences SEQ ID NO. 1, 3, 5 and 7 indicated in the sequence listing are available for designing suitable primers and originate from B. licheniformis, but ought also to be suitable, because of the homologies to be expected, for other species, especially of the genus Bacillus. 
The two amplified regions suitably undergo intermediate cloning in direct succession on a vector useful for these operations, for example on the vector pUC18 which is suitable for cloning steps in E. coli. 
The next step is a subcloning into the vector pE194 selected for deletion, and transformation thereof into B. subtilis DB104, for instance by the method of protoplast transformation according to Chang & Cohen (1979; “High Frequency Transformation of Bacillus subtilis Protoplasts by Plasmid DNA”; Molec. Gen. Genet. (1979), volume 168, pages 111-115). All working steps must be carried out at 33° C. in order to ensure replication of the vector.
In a next step, the vector which has undergone intermediate cloning is likewise transformed by the method of protoplast transformation into the desired host strain, in this case B. licheniformis. The transformants obtained in this way and identified as positive by conventional methods (selection via the resistance marker of the plasmid; check by plasmid preparation and PCR for the insert) are subsequently cultured at 42° C. under selection pressure for presence of the plasmid through addition of erythromycin. The deletion vector is unable to replicate at this temperature, and the only cells to survive are those in which the vector is integrated into the chromosome, and this integration most probably takes place in homologous or identical regions. Excision of the deletion vector can then be induced subsequently by culturing at 33° C. without erythromycin selection pressure, the chromosomally encoded gene being completely deleted from the chromosome. The success of the deletion is subsequently checked by Southern blotting after restriction of the chromosomal DNA with suitable enzymes or with the aid of the PCR technique.
Such transformants in which the relevant gene is deleted are additionally distinguished by a limitation or even complete inability to form GLA.

## Claims

1. An isolated microorganism of the genus Bacillus having at least one gene selected from the group consisting of:
(a) functionally inactivated ywsC genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 1,
(b) functionally inactivated ywsC′ genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 3,
(c) functionally inactivated ywtA genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 5,
(d) functionally inactivated ywtB genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 7, and
(e) functionally enhanced Bacillus ywtD genes coding for a gene product involved in the degradation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 9,
wherein the ywsC, ywsC′, ywtA and ywtB genes are functionally inactivated by introducing an insertion, deletion or point mutation in said gene, and the ywtD gene is functionally enhanced by placing the ywtD gene under control of a heterologous promoter or by increasing its copy number, and
wherein the isolated microorganism is able to form polyamino acids prior to functional inactivation of the ywsC, ywsC′, ywtA and ywtB genes and/or functional enhancement of the ywtD gene.

2. The microorganism according to claim 1, wherein said microorganism has a functionally enhanced Bacillus ywtD gene coding for a gene product involved in the degradation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 9, and wherein said microorganism further comprises at least one gene selected from the group consisting of:
(a) functionally inactivated ywsC genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 1,
(b) functionally inactivated ywsC′ genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 3,
(c) functionally inactivated ywtA genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 5, and
(d) functionally inactivated ywtB genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 7,
wherein the ywsC, ywsC′, ywtA and ywtB genes are functionally inactivated by introducing an insertion, deletion or point mutation in said gene, and the ywtD gene is functionally enhanced by placing the ywtD gene under control of a heterologous promoter or by increasing its copy number,
wherein the ywsC, ywsC′, ywtA and ywtB genes, prior to functional inactivation, encode a protein involved in the formation of polyamino acids.

3. The microorganism according to claim 1, wherein said microorganism is a Gram-positive bacterium selected from the group consisting of the species B. lentus, B. licheniformis, B. amyloliquefaciens, B. globigii, and B. alcalophilus.

4. The microorganism according to claim 1, wherein said microorganism is a Gram-positive bacterium which is a derivative of B. licheniformis DSM 13.

5. An isolated B. licheniformis DSM13 microorganism having at least one gene selected from the group consisting of:
(a) functionally inactivated ywsC genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 1,
(b) functionally inactivated ywsC′ genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 3,
(c) functionally inactivated ywtA genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 5,
(d) functionally inactivated ywtB genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 7, and
(e) functionally enhanced Bacillus ywtD genes coding for a gene product involved in the degradation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleic acid sequence of SEQ ID NO. 9,
wherein the ywsC, ywsC′, ywtA and ywtB genes are functionally inactivated by introducing an insertion, deletion or point mutation in said gene, and the ywtD gene is functionally enhanced by placing the ywtD gene under control of a heterologous promoter or by increasing its copy number.

6. The isolated microorganism according to claim 5, wherein said microorganism has a functionally enhanced Bacillus ywtD gene coding for a gene product involved in the degradation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleic acid sequence of SEQ ID NO. 9, and wherein said microorganism further comprises at least one functionally inactivated gene selected from the group consisting of:
(a) functionally inactivated ywsC genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 1,
(b) functionally inactivated ywsC′ genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 3,
(c) functionally inactivated ywtA genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 5, and
(d) functionally inactivated ywtB genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 90% identical to the nucleotide sequence of SEQ ID NO. 6,
wherein the ywsC, ywsC′, ywtA and ywtB genes are functionally inactivated by introducing an insertion, deletion or point mutation in said gene, and the ywtD gene is functionally enhanced by placing the ywtD gene under control of a heterologous promoter or by increasing its copy number,
wherein the ywsC, ywsC′, ywtA and ywtB genes, prior to functional inactivation, encode a protein involved in the formation of polyamino acids.

7. The isolated microorganism according to claim 1 wherein the at least one gene is selected from the group consisting of:
(a) functionally inactivated ywsC genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 96% identical to the nucleotide sequence of SEQ ID NO. 1,
(b) functionally inactivated ywsC′ genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 96% identical to the nucleotide sequence of SEQ ID NO. 3,
(c) functionally inactivated ywtA genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 96% identical to the nucleotide sequence of SEQ ID NO. 5,
(d) functionally inactivated ywtB genes coding for a gene product involved in the formation of polyamino acids and having a nucleotide sequence which is at least 96% identical to the nucleotide sequence of SEQ ID NO. 7, and
(e) functionally enhanced Bacillus ywtD genes coding for a gene product involved in the degradation of polyamino acids and having a nucleotide sequence which is at least 96% identical to the nucleotide sequence of SEQ ID NO. 9.

8. The isolated microorganism according to claim 1 wherein the at least one gene is a functionally inactivated gene inactivated by at least one point mutation, and wherein the functionally inactivated gene is selected from the group consisting of functionally inactivated ywsC, ywsC′, ywtA and ywtB genes.

9. The isolated microorganism according to claim 8 wherein the at least one gene is a functionally inactivated gene inactivated by a single point mutation, and wherein the functionally inactivated gene is selected from the group consisting of functionally inactivated ywsC, ywsC′, ywtA and ywtB genes.

10. The isolated microorganism according to claim 1 wherein the at least one gene is a functionally inactivated gene inactivated by at least one deletion mutation, and wherein the functionally inactivated gene is selected from the group consisting of functionally inactivated ywsC, ywsC′, ywtA and ywtB genes.

11. The isolated microorganism according to claim 10 wherein the at least one gene is a functionally inactivated gene inactivated by a single deletion mutation, and wherein the functionally inactivated gene is selected from the group consisting of functionally inactivated ywsC, ywsC′, ywtA and ywtB genes.

12. The isolated microorganism according to claim 1 wherein the at least one gene is a functionally inactivated gene inactivated by at least one insertion mutation, and wherein the functionally inactivated gene is selected from the group consisting of functionally inactivated ywsC, ywsC′, ywtA and ywtB genes.

13. The isolated microorganism according to claim 12 wherein the at least one gene is a functionally inactivated gene inactivated by a single insertion mutation.

14. The isolated microorganism according to claim 1 wherein the at least one gene is the functionally enhanced Bacillus ywtD gene, and wherein the Bacillus ywtD gene is functionally enhanced by placing the ywtD gene under the control of an inducible promoter.

15. The isolated microorganism according to claim 1 wherein the at least one gene is the functionally enhanced Bacillus ywtD gene, and wherein the Bacillus ywtD gene is functionally enhanced by placing the ywtD gene under the control of a stress-signal responsive promoter.

16. The isolated microorganism according to claim 15 wherein the at least one gene is a functionally inactivated gene inactivated by at least one point mutation, and wherein the functionally inactivated gene is selected from the group consisting of functionally inactivated ywsC, ywsC′, ywtA and ywtB genes.

17. The isolated microorganism according to claim 16 wherein the functionally inactivated gene is inactivated by a single point mutation.

18. The isolated microorganism according to claim 5 wherein the at least one gene is a functionally inactivated gene inactivated by at least one deletion mutation, and wherein the functionally inactivated gene is selected from the group consisting of functionally inactivated ywsC, ywsC′, ywtA and ywtB genes.

19. The isolated microorganism according to claim 18 wherein the functionally inactivated gene is inactivated by a single deletion mutation.

20. The isolated microorganism according to claim 5 wherein the at least one gene is a functionally inactivated gene inactivated by at least one insertion mutation, and wherein the functionally inactivated gene is selected from the group consisting of functionally inactivated ywsC, ywsC′, ywtA and ywtB genes.

21. The isolated microorganism according to claim 20 wherein the functionally inactivated gene is inactivated by a single insertion mutation.

22. The isolated microorganism according to claim 5 wherein the at least one gene is the functionally enhanced Bacillus ywtD gene, and wherein the Bacillus ywtD gene is functionally enhanced by placing the ywtD gene under the control of an inducible promoter.

23. The isolated microorganism according to claim 5 wherein the at least one gene is the functionally enhanced Bacillus ywtD gene and wherein the Bacillus ywtD gene is functionally enhanced by placing the ywtD gene under the control of a stress-signal responsive promoter.