ppGpp synthetase and expression systems for improved production of protein of interest

FIELD OF THE INVENTION

[0002] This invention relates to a novel ppGpp synthetase and expression systems for improved production of proteins of interest in gram-positive bacteria, involving use of said novel ppGpp synthetase.

DESCRIPTION OF THE RELATED ART

[0003] In gram-positive bacteria secreted proteins are exported across a cell membrane and a cell wall, and are then subsequently released into the external medium.

[0004] Gram-positive bacteria such as B. subtilis, B. amyloliquefaciens, and B. licheniformis have a high capacity for secreting proteins, and indeed, many bacillar extracellular enzymes are used industrially.

[0005] A number of proteins are involved in the secretion machinery in gram-positive cells.

[0006] WO 94/19471 describes a PrsA protein involved in the secretion machinery of Bacillus, and further describe an expression system for enhancing secretion of exoproteins of interest involving over-expression of the PrsA protein.

[0007] Dedhia et al. (Biotechnology and Bioengineering 53:379-386 (1997)) describe gram-negative E coli strains which express smaller than wild-type amounts of ppGpp synthetase (relA). Such gram-negative E coli strains give improved production of a chloramphenicol acetyltransferase (CAT) protein.

SUMMARY OF THE INVENTION

[0008] The problem to be solved, by the present invention is to provide an expression system for improved production of a protein of interest in a Gram-positive bacterium, e.g. in a Bacillus strain.

[0009] The solution is based on cloned novel DNA sequences from Bacillus species B. subtilis (SEQ ID NO:1) and B. amyloliquefaciens (SEQ ID NO:3) which both encode a polypeptide having ppGpp synthetase activity.

[0010] The novel DNA sequence information disclosed herein can be used to clone similar DNA sequences from Gram positive bacteria by e.g. standard PCR technology. See e.g. a working example herein (vide infra).

[0011] This DNA sequence information provides the possibility of constructing an expression system for improved production of at least one protein of interest in a gram-positive bacterium, wherein said gram-positive bacterium is expressing smaller than wild-type amounts of a polypeptide having ppGpp synthetase activity.

[0012] Accordingly, in a first aspect, the present invention provides an isolated polynucleotide molecule selected from the group consisting of (a) polynucleotide molecules encoding a polypeptide having ppGpp synthetase activity and comprising a sequence of nucleotides as shown in SEQ ID NO:1 from nucleotide 21 to nucleotide 2225; (b) species homologs of (a); (c) polynucleotide molecules that encode a polypeptide having ppGpp synthetase activity that is at least 70% identical to the amino acid sequence of SEQ ID NO:2 from amino acid residue 1 to amino acid residue 734; (d) molecules complementary to (a), (b) or (c); and (e) degenerate nucleotide sequences of (a), (b), (c) or (d).

[0013] Within a second aspect of the invention there is provided an expression vector comprising the following operably linked elements: a transcription promoter; a DNA segment selected from the group consisting of (a) polynucleotide molecules encoding a polypeptide having ppGpp synthetase activity and comprising a sequence of nucleotides as shown in SEQ ID NO:1 from nucleotide 21 to nucleotide 2225; (b) species homologs of (a); (c) polynucleotide molecules that encode a polypeptide having ppGpp synthetase activity that is at least 70% identical to the amino acid sequence of SEQ ID NO:2 from amino acid residue 1 to amino acid residue 734; and (d) degenerate nucleotide sequences of (a), (b), or (c); and a transcription terminator.

[0014] Within a third aspect of the present invention there is provided a cultured cell into which has been introduced an expression vector as disclosed above, wherein said cell expresses the polypeptide encoded by the DNA segment.

[0015] A fourth aspect of the present invention provides an isolated polypeptide having ppGpp synthetase activity selected from the group consisting of (a) polypeptide molecules comprising a sequence of amino acid residues as shown in SEQ ID NO:2 from amino acid residue 1 to amino acid residue 734; (b) species homologs of (a).

[0016] Within another aspect of the present invention there is provided a composition comprising a purified polypeptide according to the invention in combination with other polypeptides.

[0017] Within yet another aspect of the present invention there are provided methods for producing a polypeptide according to the invention comprising culturing a cell into which has been introduced an expression vector as disclosed above, whereby said cell expresses a polypeptide encoded by the DNA segment and recovering the polypeptide.

[0018] In a further aspect, the present invention relates to an expression system for improved production of at least one protein of interest in gram-positive bacteria, which expression system comprises a gram-positive bacterium expressing smaller than wild-type amounts of a polypeptide according to the invention.

[0019] In a final aspect the present invention relates to a method for improved production of at least one protein of interest in a gram-positive bacterium, which method comprises:

[0020] i) culturing an expression system according to the invention; and

[0021] ii) purifying said protein of interest from the resulting culture broth or expression system.

DEFINITIONS

[0022] Prior to discussing this invention in further detail, the following terms will first be defined

[0023] The term “species homolog” is intended to include “ortholog” and/or “paralog”.

[0024] The term “ortholog” denotes a polypeptide or protein obtained from one species that has homology to an analogous polypeptide or protein from a different species.

[0025] The term “paralog” denotes a polypeptide or protein obtained from a given species that has homology to a distinct polypeptide or protein from that same species.

[0026] The term “expression vector” denotes a DNA molecule, linear or circular, that comprises a segment encoding a polypeptide of interest operably linked to additional segments that provide for its transcription. Such additional segments may include promoter and terminator sequences, and may optionally include one or more origins of replication, one or more selectable markers, an enhancer, a polyadenylation signal, and the like. Expression vectors are generally derived from plasmid or viral DNA, or may contain elements of both. The expression vector of the invention may be any expression vector that is conveniently subjected to recombinant DNA procedures, and the choice of vector will often depend on the host cell into which the vector it is to be introduced. Thus, the vector may be an autonomously replicating vector, i.e. a vector which exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g. a plasmid. Alternatively, the vector may be one which, when introduced into a host cell, is integrated into the host cell genome and replicated together with the chromosome(s) into which it has been integrated.

[0027] The term “recombinant expression” or “recombinantly expressed” used herein in connection with expression of a polypeptide or protein is defined according to the standard definition in the art. Recombinant expression of a protein is generally performed by using an expression vector as described immediately above.

[0028] The term “isolated”, when applied to a polynucleotide molecule, denotes that the polynucleotide has been removed from its natural genetic environment and is thus free of other extraneous or unwanted coding sequences, and is in a form suitable for use within genetically engineered protein production systems. Such isolated molecules are those that are separated from their natural environment and include cDNA and genomic clones. Isolated DNA molecules of the present invention are free of other genes with which they are ordinarily associated, but may include naturally occurring 5′ and 3′ untranslated regions such as promoters and terminators. The identification of associated regions will be evident to one of ordinary skill in the art (see for example, Dynan and Tijan, Nature 316:774-78, 1985). The term “an isolated polynucleotide” may alternatively be termed “a cloned polynucleotide”.

[0029] When applied to a protein, the term “isolated” indicates that the protein is found in a condition other than its native environment. In a preferred form, the isolated protein is substantially free of other proteins, particularly other homologous proteins (i.e. “homologous impurities” (see below)). It is preferred to provide the protein in a highly purified form, i.e., greater than 80% pure, more preferably greater than 95% pure, and even more preferably greater than 99% pure, as determined by SDS-PAGE.

[0030] The term “homologous impurities” means any impurity (e.g. another polypeptide than the polypeptide of the invention) which originate from the homologous cell where the polypeptide of the invention is originally obtained from.

[0031] The term “obtained from” as used herein in connection with a specific microbial source, means that the polynucleotide and/or polypeptide produced by the specific source, or by a cell in which a gene from the source have been inserted.

[0032] The term “operably linked”, when referring to DNA segments, denotes that the segments are arranged so that they function in concert for their intended purposes, e.g. transcription initiates in the promoter and proceeds through the coding segment to the terminator.

[0033] The term “polynucleotide” denotes a single- or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5′ to the 3′ end. Polynucleotides include RNA and DNA, and may be isolated from natural sources, synthesized in vitro, or prepared from a combination of natural and synthetic molecules.

[0034] The term “complements of polynucleotide molecules” denotes polynucleotide molecules having a complementary base sequence and reverse orientation as compared to a reference sequence. For example, the sequence 5′ ATGCACGGG 3′ is complementary to 5′ CCCGTGCAT 3′.

[0035] The term “degenerate nucleotide sequence” denotes a sequence of nucleotides that includes one or more degenerate codons (as compared to a reference polynucleotide molecule that encodes a polypeptide). Degenerate codons contain different triplets of nucleotides, but encode the same amino acid residue (i.e., GAU and GAC triplets each encode Asp).

[0036] The term “promoter” denotes a portion of a gene containing DNA sequences that provide for the binding of RNA polymerase and initiation of transcription. Promoter sequences are commonly, but not always, found in the 5′ non-coding regions of genes.

[0037] The term “secretory signal sequence” denotes a DNA sequence that encodes a polypeptide (a “secretory peptide”) that, as a component of a larger polypeptide, directs the larger polypeptide through a secretory pathway of a cell in which it is synthesized. The larger peptide is commonly cleaved to remove the secretory peptide during transit through the secretory pathway.

[0038] The term “expression system” for improved production of a protein of interest in gram-positive bacteria, denotes a gram-positive bacterium which express smaller than wild-type amounts of a polypeptide having ppGpp synthetase activity according to the invention. The protein of interest may e.g. be a recombinantly expressed protein.

[0039] The term “wildtype amounts” used herein in connection with an expression system as described immediately above, denotes the wild-type (native) amounts of expression level of the polypeptide according to the invention, i.e. the amount of expression level before the gram-positive strain has been modified to express smaller amounts of said polypeptide.

[0040] The term “exoprotein” denotes a protein which is secreted from a cell of interest. An exoprotein generally comprise a secretory signal sequence as described above.

[0041] The term “ppGpp synthetase” denotes a ppGpp synthetase enzyme defined according to the art.

[0042] Synthesis of ppGpp is in E coli governed by at least two ways (Dedhia et al. (Biotechnology and Bioengineering 53:379-386 (1997)). The enzyme ppGpp synthetase I (PSI) (EC 2.7.6.5) encoded by the relA gene in E coli is responsible for ppGpp synthesis during the stringent response to amino acid deprivation (Block, R., Haseltine, W. A. 1974. In vitro synthesis of ppGpp and ppGppp, pp. 747-761. In: M. Nomura, A. Tissieres, and P. Lengyel (eds.), Ribosomes. Cold Spring Harbor Press, Cold Spring Harbor N.Y.). When growth of the bacterium is slowed by the depletion of a primary carbon source, the stringent response is activated by a pathway that is independent of the relA gene (Hernandez, V. J., Bremer, H. 1991. E coli ppGpp synthetase II activity requires spoT. J. Biol. Chem. 266:5991-5999). A second enzyme, ppGpp synthetase II (PSII), encoded by the spoT gene, is responsible for catalyzing ppGpp synthesis (Hernandez, V. J., Bremer, H. 1991. E coli ppGpp synthetase II activity requires spoT. J. Biol. Chem. 266:5991-5999).

[0043] In the present context “ppGpp synthetase” is intended to cover both an enzyme having ppGpp synthetase I activity (EC 2.7.6.5) and/or an enzyme having ppGpp synthetase II activity as described above.

[0044] Alternatively the term “ppGpp synthetase” may be termed “(p)ppGpp synthetase”.

[0045] The term “ppGpp synthetase gene” is intended to cover a DNA sequence encoding a polypeptide with ppGpp synthetase activity.

DETAILED DESCRIPTION OF THE INVENTION

How to Use a Sequence of the Invention to Get Other Related Sequences

[0046] The disclosed sequence information herein relating to a polynucleotide sequence encoding a ppGpp synthetase of the invention can be used as a tool to identify other homologous ppGpp synthetases. For instance, polymerase chain reaction (PCR) can be used to amplify sequences encoding other homologous ppGpp synthetases from a variety of microbial sources, in particular of different Bacillus species.

[0047] For further details reference is made to a working example herein (vide infra).

Assay for Activity Test

[0048] A polypeptide of the invention having ppGpp synthetase activity may be tested for ppGpp synthetase activity according to standard test procedures known in the art, such as by using UV absorbance at 254 nm after nucleotide separation by ion-pair reversed phase high-performance liquid chromatography. For further details reference is made to Baracchini et al (Mol Gen Genet (1988) 213:379-387).

[0049] A protein of interest produced by use of an expression system of the invention may be tested for activity by standard activity assays relating to said protein of interest. In particular when the protein of interest is an enzyme a number of relevant enzyme activity assays are described in the art. For a person skilled in the art it is routine work, in particular for enzymes, to identify a useful assay relating to the protein of interest.

Polynucleotides

[0050] Within preferred embodiments of the invention an isolated polynucleotide of the invention will hybridize to similar sized regions of SEQ ID NO:1, or a sequence complementary thereto, under at least medium stringency conditions.

[0051] In particular polynucleotides of the invention will hybridize to a double-stranded DNA probe comprising the sequence shown in positions 21-2225 in SEQ ID NO:1, under at least medium stringency conditions, but preferably at high stringency conditions as described in detail below.

[0052] Suitable experimental conditions for determining hybridization at medium or high stringency between a nucleotide probe and a homologous DNA or RNA sequence involves presoaking of the filter containing the DNA fragments or RNA to hybridize in 5×SSC (Sodium chloride/Sodium citrate, Sambrook et al. 1989) for 10 min, and prehybridization of the filter in a solution of 5×SSC, 5×Denhardt's solution (Sambrook et al. 1989), 0.5 % SDS and 100 μg/ml of denatured sonicated salmon sperm DNA (Sambrook et al. 1989), followed by hybridization in the same solution containing a concentration of 10 ng/ml of a random-primed (Feinberg, A. P. and Vogelstein, B. (1983) Anal. Biochem. 132:6-13), 32P-dCTP-labeled (specific activity>1×109 cpm/μg ) probe for 12 hours at ca. 45° C. The filter is then washed twice for 30 minutes in 2×SSC, 0.5% SDS at least 60° C. (medium stringency), still more preferably at least 65° C. (medium/high stringency), even more preferably at least 70° C. (high stringency), and even more preferably at least 75° C. (very high stringency).

[0053] Molecules to which the oligonucleotide probe hybridizes under these conditions are detected using an x-ray film.

[0054] As previously noted, the isolated polynucleotides of the present invention include DNA and RNA. Methods for isolating DNA and RNA are well known in the art.

[0055] Total RNA can be prepared using guanidine HCl extraction followed by isolation by centrifugation in a CsCl gradient (Chirgwin et al., Biochemistry 18:52-94, 1979). Poly (A)+RNA is prepared from total RNA using the method of Aviv and Leder (Proc. Natl. Acad. Sci. USA 69:1408-1412, 1972). Complementary DNA (cDNA) is prepared from poly(A)+RNA using known methods. Polynucleotides encoding polypeptides having ppGpp synthetase activity of the invention are then identified and isolated by, for example, hybridization or PCR.

[0056] The present invention further provides counterpart polypeptides and polynucleotides from different bacterial strains (orthologs or paralogs). Of particular interest are ppGpp synthetase polypeptides from gram-positive strains, including species of Bacillus such as Bacillus subtilis, Bacillus lentus, Bacillus brevis, Bacillus stearothermophilus, Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus coagulans, Bacillus circulans, Bacillus lautus, Bacillus thuringiensis, Bacillus clausii, or in particular Bacillus licheniformis.

[0057] The polynucleotide of the invention shown in SEQ ID NO:1 is obtained from the Bacillus subtilis strain 168 (NCIB 10106). The polynucleotide of SEQ ID NO:1 encodes a polypeptide exhibiting ppGpp snthetase activity of SEQ ID NO:2. The polypeptide of SEQ ID NO:2 is designated herein relA-Bac.

[0058] Species homologs of a polypeptides having ppGpp synthetase activity of the invention can be cloned using information and compositions provided by the present invention in combination with conventional cloning techniques. For example, a cDNA can be cloned using mRNA obtained from cell type that expresses the protein. Suitable sources of mRNA can be identified by probing Northern blots with probes designed from the sequences disclosed herein. A library is then prepared from mRNA of a positive cell. A cDNA encoding a polypeptide having ppGpp synthetase activity of the invention can then be isolated by a variety of methods, such as by probing with a complete or partial cDNA or with one or more sets of degenerate probes based on the disclosed sequences. A cDNA can also be cloned using the polymerase chain reaction, or PCR (Mullis, U.S. Pat. No. 4,683,202), using primers designed from the sequences disclosed herein. Within an additional method, the cDNA library can be used to transform or transfect host cells, and expression of the cDNA of interest can be detected with an antibody to relA-bac or by an activity test relating to a polypeptide having ppGpp synthetase activity. Similar techniques can also be applied to the isolation of genomic clones.

Polypeptides

[0059] The present invention also provides isolated ppGpp synthetase polypeptides that are substantially homologous to the polypeptides of SEQ ID NO:2 and their species homologs (paralogs or orthologs). The term “substantially homologous” is used herein to denote polypeptides having 70%, more preferably at least 80%, sequence identity to the sequences shown in SEQ ID NO: 2 or their orthologs or paralogs. Such polypeptides will more preferably be at least 90% identical, and most preferably 95% or more identical to SEQ ID NO:2 or its orthologs or paralogs. Percent sequence identity is determined by conventional methods, by means of computer programs known in the art such as GAP provided in the GCG program package (Program Manual for the Wisconsin Package, Version 8, August 1994, Genetics Computer Group, 575 Science Drive, Madison, Wis., USA 53711) (Needleman, S. B. and Wunsch, C. D., (1970), Journal of Molecular Biology, 48, 443-453). GAP is used with the following settings for polypeptide sequence comparison: GAP creation penalty of 3.0 and GAP extension penalty of 0.1.

[0060] Sequence identity of polynucleotide molecules is determined by similar methods using GAP with the following settings for DNA sequence comparison: GAP creation penalty of 5.0 and GAP extension penalty of 0.3.

[0061] Substantially homologous proteins and polypeptides are characterized as having one or more amino acid substitutions, deletions or additions. These changes are preferably of a minor nature, that is conservative amino acid substitutions (see Table 2) and other substitutions that do not significantly affect the folding or activity of the protein or polypeptide; small deletions, typically of one to about 30 amino acids; and small amino- or carboxyl-terminal extensions, such as an amino-terminal methionine residue, a small linker peptide of up to about 20-25 residues, or a small extension that facilitates purification (an affinity tag), such as a poly-histidine tract, protein A (Nilsson et al., EMBO J. 4:1075, 1985; Nilsson et al., Methods Enzymol. 198:3, 1991. See, in general Ford et al., Protein Expression and Purification 2: 95-107, 1991, which is incorporated herein by reference. DNAs encoding affinity tags are available from commercial suppliers (e.g., Pharmacia Biotech, Piscataway, N.J.; New England Biolabs, Beverly, Mass.)

1TABLE 2Conservative amino acid substitutionsBasic:argininelysinehistidineAcidic:glutamic acidaspartic acidPolar:glutamineasparagineHydrophobic:leucineisoleucinevalineAromatic:phenylalaninetryptophantyrosineSmall:glycinealanineserinethreoninemethionine

[0062] In addition to the 20 standard amino acids, non-standard amino acids (such as 4-hydroxyproline, 6-N-methyl lysine, 2-aminoisobutyric acid, isovaline and a-methyl serine) may be substituted for amino acid residues of a polypeptide according to the invention. A limited number of non-conservative amino acids, amino acids that are not encoded by the genetic code, and unnatural amino acids may be substituted for amino acid residues. “Unnatural amino acids” have been modified after protein synthesis, and/or have a chemical structure in their side chain(s) different from that of the standard amino acids. Unnatural amino acids can be chemically synthesized, or preferably, are commercially available, and include pipecolic acid, thiazolidine carboxylic acid, dehydroproline, 3- and 4-methylproline, and 3,3-dimethylproline.

[0063] Essential amino acids in the ppGpp synthetase polypeptides of the present invention can be identified according to procedures known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (Cunningham and Wells, Science 244: 1081-1085, 1989). In the latter technique, single alanine mutations are introduced at every residue in the molecule, and the resultant mutant molecules are tested for biological activity (i.e., ppGpp synthetase activity) to identify amino acid residues that are critical to the activity of the molecule. See also, Hilton et al., J. Biol. Chem. 271:4699-4708, 1996. Sites of ligand-receptor or other biological interaction can also be determined by physical analysis of structure, as determined by such techniques as nuclear magnetic resonance, crystallography, electron diffraction or photoaffinity labeling, in conjunction with mutation of putative contact site amino acids. See, for example, de Vos et al., Science 255:306-312, 1992; Smith et al., J. Mol. Biol. 224:899-904, 1992; Wlodaver et al., FEBS Lett. 309:59-64, 1992. The identities of essential amino acids can also be inferred from analysis of homologies with polypeptides which are related to a polypeptide according to the invention.

[0064] Multiple amino acid substitutions can be made and tested using known methods of mutagenesis, recombination and/or shuffling followed by a relevant screening procedure, such as those disclosed by Reidhaar-Olson and Sauer (Science 241:53-57, 1988), Bowie and Sauer (Proc. Natl. Acad. Sci. USA 86:2152-2156, 1989), W095/17413, or WO 95/22625. Briefly, these authors disclose methods for simultaneously randomizing two or more positions in a polypeptide, or recombination/shuffling of different mutations (WO95/17413, W095/22625), followed by selecting for functional a polypeptide, and then sequencing the mutagenized polypeptides to determine the spectrum of allowable substitutions at each position. Other methods that can be used include phage display (e.g., Lowman et al., Biochem. 30:10832-10837, 1991; Ladner et al., U.S. Pat. No. 5,223,409; Huse, WIPO Publication WO 92/06204) and region-directed mutagenesis (Derbyshire et al., Gene 46:145, 1986; Ner et al., DNA 7:127, 1988).

[0065] Mutagenesis/shuffling methods as disclosed above can be combined with high-throughput, automated screening methods to detect activity of cloned, mutagenized polypeptides in host cells. Mutagenized DNA molecules that encode active polypeptides can be recovered from the host cells and rapidly sequenced using modern equipment. These methods allow the rapid determination of the importance of individual amino acid residues in a polypeptide of interest, and can be applied to polypeptides of unknown structure.

[0066] Using the methods discussed above, one of ordinary skill in the art can identify and/or prepare a variety of polypeptides that are substantially homologous to residues 1 to 734 of SEQ ID NO:2 and retain the ppGpp synthetase activity of the wild-type protein.

Protein Production

[0067] The polypeptides of the present invention, including full-length proteins, fragments thereof and fusion proteins, can be produced in genetically engineered host cells according to conventional techniques. Suitable host cells are those cell types that can be transformed or transfected with exogenous DNA and grown in culture, and include bacteria, fungal cells, and cultured higher eukaryotic cells. Bacterial cells, particularly cultured cells of gram-positive organisms, are preferred. Gram-positive cells from the genus of Bacillus are especially preferred, such as Bacillus subtilis, Bacillus lentus, Bacillus brevis, Bacillus stearothermophilus, Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus coagulans, Bacillus circulans, Bacillus lautus, Bacillus thuringiensis, Bacillus clausii, or in particular Bacillus licheniformis.

[0068] Techniques for manipulating cloned DNA molecules and introducing exogenous DNA into a variety of host cells are disclosed by Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989; Ausubel et al. (eds.), Current Protocols in Molecular Biology, John Wiley and Sons, Inc., NY, 1987; and (Bacillus subtilis and Other Gram-Positive Bacteria, Sonensheim et al., 1993, American Society for Microbiology, Washington D.C.), which are incorporated herein by reference.

[0069] In general, a DNA sequence encoding a ppGpp synthetase polypeptide of the present invention is operably linked to other genetic elements required for its expression, generally including a transcription promoter and terminator within an expression vector. The vector will also commonly contain one or more selectable markers and one or more origins of replication, W although those skilled in the art will recognize that within certain systems selectable markers may be provided on separate vectors, and replication of the exogenous DNA may be provided by integration into the host cell genome. Selection of promoters, terminators, selectable markers, vectors and other elements is a matter of routine design within the level of ordinary skill in the art. Many such elements are described in the literature and are available through commercial suppliers.

[0070] To direct a polypeptide into the secretory pathway of a host cell, a secretory signal sequence (also known as a leader sequence, prepro sequence or pre sequence) is provided in the expression vector. The secretory signal sequence may be that of the polypeptide, or may be derived from another secreted protein or synthesized de novo. The secretory signal sequence is joined to the DNA sequence in the correct reading frame. Secretory signal sequences are commonly positioned 5′ to the DNA sequence encoding the polypeptide of interest, although certain signal sequences may be positioned elsewhere in the DNA sequence of interest (see, e.g., Welch et al., U.S. Pat. No. 5,037,743; Holland et al., U.S. Pat. No. 5,143,830).

[0071] Transformed or transfected host cells are cultured according to conventional procedures in a culture medium containing nutrients and other components required for the growth of the chosen host cells. A variety of suitable media, including defined media and complex media, are known in the art and generally include a carbon source, a nitrogen source, essential amino acids, vitamins and minerals. Media may also contain such components as growth factors or serum, as required. The growth medium will generally select for cells containing the exogenously added DNA by, for example, drug selection or deficiency in an essential nutrient which is complemented by the selectable marker carried on the expression vector or co-transfected into the host cell.

Protein Isolation

[0072] Expressed recombinant polypeptides (or chimeric polypeptides) can be purified using fractionation and/or conventional purification methods and media. Ammonium sulfate precipitation and acid or chaotrope extraction may be used for fractionation of samples. Exemplary purification steps may include hydroxyapatite, size exclusion, FPLC and reverse-phase high performance liquid chromatography. Suitable anion exchange media include derivatized dextrans, agarose, cellulose, polyacrylamide, specialty silicas, and the like. PEI, DEAE, QAE and Q derivatives are preferred, with DEAE Fast-Flow Sepharose (Pharmacia, Piscataway, N.J.) being particularly preferred. Exemplary chromatographic media include those media derivatized with phenyl, butyl, or octyl groups, such as Phenyl-Sepharose FF (Pharmacia), Toyopearl butyl 650 (Toso Haas, Montgomeryville, Pa.), Octyl-Sepharose (Pharmacia) and the like; or polyacrylic resins, such as Amberchrom CG 71 (Toso Haas) and the like. Suitable solid supports include glass beads, silica-based resins, cellulosic resins, agarose beads, cross-linked agarose beads, polystyrene beads, cross-linked polyacrylamide resins and the like that are insoluble under the conditions in which they are to be used. These supports may be modified with reactive groups that allow attachment of proteins by amino groups, carboxyl groups, sulfhydryl groups, hydroxyl groups and/or carbohydrate moieties. Examples of coupling chemistries include cyanogen bromide activation, N-hydroxysuccinimide activation, epoxide activation, sulfhydryl activation, hydrazide activation, and carboxyl and amino derivatives for carbodiimide coupling chemistries. These and other solid media are well known and widely used in the art, and are available from commercial suppliers.

[0073] Selection of a particular method is a matter of routine design and is determined in part by the properties of the chosen support. See, for example, Affinity Chromatography: Principles & Methods, Pharmacia LKB Biotechnology, Uppsala, Sweden, 1988.

[0074] It is preferred to purify the protein to >80% purity, more preferably to >90% purity, even more preferably >95%, and particularly preferred is a nearly complete pure state, that is greater than 99.9% pure with respect to contaminating macromolecules, particularly other proteins and nucleic acids, and free of infectious and pyrogenic agents. Preferably, a purified protein is substantially free of other proteins, particularly other proteins of bacterial origin, and especially of gram-positive bacterial origin. The degree of purity is determined by SDS-PAGE.

[0075] Polypeptides of the invention or fragments thereof may also be prepared through chemical synthesis. Polypeptides of the invention may be monomers or multimers; glycosylated or non-glycosylated; pegylated or non-pegylated; and may or may not include an initial methionine amino acid residue.

Uses of Polynucleotide/Polypeptide

[0076] The information disclosed herein relating to a polypeptide having ppGpp synthetase activity of the invention is essential to construct an expression system for improved production of a protein of interest in gram-positive bacteria as described in further details below.

Expressing System for Enhancing Secretion of Exoproteins in Gram-Positive Bacteria

[0077] An aspect of the present invention relates to an expression system for improved production of at least one protein of interest in gram-positive bacteria, which expression system comprises a gram-positive bacterium expressing smaller than wild-type amounts of a polypeptide according to the invention.

[0078] Preferably the protein of interest in an exoprotein.

[0079] Preferably, the term “expression system for improved production of at least one protein of interest” is an expression system having one or more of the improved properties described immediately below.

[0080] Improved properties for an expression system of the invention include properties such as an improved ability to utilize growth media, an ability to grow to higher cell densities, an ability to grow in minimal medium, sporulation deficiency of the production hosts, increased expression of the protein of interest, measured either in terms of the amount of the protein of interest accumulated in the fermentation broth or as the production of the protein of interest per cell mass per time unit, reduced tendency of the fermentation broths to form foam, reduced viscosity of the fermentation broth, reduced degradation of the protein product produced by the production host, reduced tendency of the producer organism to lyse (reduced autolysis), a higher fraction of highly producing cells in the producing culture, a reduced formation of pigments or colored compounds during fermentation, and improved fermentation broths allowing more easy and efficient recovery steps and thus result in improved recovery yields.

[0081] As described above a relA-Bac polypeptide of the invention is a polypeptide which is having ppGpp synthetase activity.

[0082] Advantages of having smaller than wildtype amounts of ppGpp in the production organism:

[0083] ppGpp is a true alarmone, i.e., its concentration is very low under normal growth conditions (P. Neubauer et al (J. of Biotechnology (1995) 43:195-204)) and the intracellular concentration of ppGpp increases rapidly when the organism is exposed to starvation or other stress factors. When the intra cellular ppGpp concentration is increasing the ribosomal RNA (rRNA) concentration is decreasing which again may result in:

[0084] Decrease in translation and thereby a decrease in the desired protein production.

[0085] Higher instability of a given mRNA because the number of ribosomes loaded on the mRNA is reduced resulting in a less protected mRNA that could lead to a higher nuclease activity.

[0086] Reduced elongation rate of messenger RNA chains (U. Vogel et al. (J. of Biological Chemistry (1997) 272:12265-12271)).

[0087] Accordingly, in order to obtain an expression system for improved production of a protein of interest, it is advantageously to express smaller than wildtype amount of a ppGpp synthetase in the production cell used to express said protein of interest.

[0088] A number of techniques to be able to express smaller amounts of a polypeptide of interest in gram-positive bacteria are known in the art, in particular for a preferred gram-positive bacterium of the genus of Bacillus (Bacillus subtilis and other Gram-Positive Bacteria, Sonensheim et al., 1993, American Society for Microbiology, Washington D.C.).

[0089] Suitable techniques to express smaller amounts of a polypeptide having ppGpp synthetase activity of the invention include techniques such as deletion or otherwise destruction (e.g. by destroying the correct reading frame) of a ppGpp synthetase gene (some or all copies thereof) of the invention (e.g. on the chromosome of the gram-positive bacterium), truncation of a ppGpp synthetase gene (e.g. by introduction of STOP-codons), using anti-sense mRNA against the transcribed mRNA from a ppGpp synthetase gene, and/or altering the regulatory elements to increase expression, e.g. use of weak promoters, and so forth. For further details reference is made to (Sambrook et al. (1989) Molecular cloning: A laboratory manual, Cold Spring Harbor lab., Cold Spring Harbor, N.Y.; Ausubel, F. M. et al. (eds.) “Current protocols in Molecular Biology”. John Wiley and Sons, 1995; Harwood, C. R., and Cutting, S. M. (eds.) “Molecular Biological Methods for Bacillus”. John Wiley and Sons, 1990).

[0090] Based on the DNA and/or amino acid sequence information provided herein, selection of a particular strategy to express smaller than wild-type amounts of a polypeptide having ppGpp synthetase activity of the invention in a gram-positive bacterium is a matter of routine for a person skilled in the art.

[0091] To determine the degree of decreased expression of a polypeptide having ppGpp synthetase activity of the invention any relevant ppGpp synthetase activity assay/test may be used (suitable assays are described herein (vide supra)). The amount of a polypeptide of the invention having ppGpp synthetase activity produced before and after modification of the gram-positive cell is measured, and the degree of decreased expression may be measured relative to the unmodified wild-type (control) cell.

[0092] The degree of decreased expression of a polypeptide having ppGpp synthetase activity according to the invention is preferably a two fold decreased expression, more preferably a four fold decreased expression, and even more preferably a ten fold decreased expression, and most preferably the expression of a polypeptide, according to the invention, having ppGpp synthetase activity is completely disrupted.

[0093] Preferably a polypeptide having ppGpp synthetase activity of the invention is a polypeptide obtained from a species of Bacillus, such as Bacillus lentus, Bacillus brevis, Bacillus stearothermophilus, Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus coagulans, Bacillus circulans, Bacillus lautus, Bacillus thuringiensis, Bacillus licheniformis, Bacillus clausii, or in particular from Bacillus subtilis.

[0094] The gram-positive bacteria in the expression system of the invention may be cultured by conventional methods as described for host cells in the section “PROTEIN PRODUCTION” (vide supra).

[0095] Preferably the gram-positive bacterium is a species of Bacillus such as Bacillus subtilis, Bacillus lentus, Bacillus brevis, Bacillus stearothermophilus, Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus coagulans, Bacillus circulans, Bacillus lautus, Bacillus thuringiensis, Bacillus clausii, or Bacillus licheniformis.

[0096] Relatively to the gram-positive bacterium, the protein of interest may be both a homologous protein, or a heterologous protein.

[0097] Preferably, the protein of interest is recombinantly expressed.

[0098] The protein of interest may be any protein of interest. However preferably the protein of interest is an exoprotein, and in particular a protease, a lipase, an amylase, a galactosidase, a pullanase, a cellulase, a glucose isomerase, a protein disulphide isomerase, a CGTàse (cyclodextrin gluconotransferase), a phytase, a glucose oxidase, a glucosyl transferase, a laccase, a xylanase, a bacterial protein toxin, a microbial surface protein, a viral protein, or a pharmaceuticical protein.

[0099] To determine the degree of improved production of a protein of interest, preferably an exoprotein of interest, any relevant activity assay/test, corresponding to the protein (e.g. exoprotein) of interest, may be used.

[0100] The degree of improved production of a protein of interest may be determined relative to the production level of the protein in the gram-positive strain before the strain has been modified to express smaller amounts of a polypeptide according to the invention.

[0101] Use of the expression system of the invention results in at least 2 fold improved production of at least one protein of interest, more preferably at least 4 fold improved production of at least one protein of interest, and even more preferably at least 10 fold improved production of at least one protein of interest

[0102] The protein of interest may be isolated by standard procedures as e.g. described in the section “PROTEIN ISOLATION” (vide supra).

[0103] Further the present invention relates to a method for improved production of at least one protein of interest in a gram-positive bacterium, which method comprises:

[0104] i) culturing an expression system according to the invention; and

[0105] ii) purifying said protein of interest from the resulting culture broth or expression system.

[0106] In a preferred embodiment said culturing is done as a fed-batch fermentation.

[0107] A fed-batch fermentation is a standard fermentation procedure especially for large scale industrial production of a protein of interest.

[0108] Fed-batch fermentation is generally described in BASIC Biochemical Engineering (Bungay, Henry R. BASIC Biochemical Engineering (2nd ed.).Troy: BiLine Associates, 1993.) as the type of system where “nutrient is added when its concentration falls below some set point.” Usually the addition of the nutrient is controlled by a computer for precision. A preferred way to control the addition of the feed is to monitor the concentration of the nutrient itself in the fermenter or reactor vessel.

[0109] The nutrient is added in several doses, to ensure that there is not too much of the nutrient present in the fermenter at any time. If too much of a nutrient is present, it may inhibit the growth of the cells. By adding the nutrient in a controlled manner, the reaction can proceed at a high rate of production without getting overloaded.

[0110] An example of a suitable fed-batch fermentation is described by Neubauer, P. et al. (1995. Journal of Biotechnology 43 p.197-198).

[0111] The theory behind this preferred embodiment is that the cellular content of many direct participants in protein synthesis such as RNA polymerase, elongation factors and initiation factors are decreased as a result of nutrient and energy starvation and mediated by the (p)ppGpp synthetase encoded by the relA gene Dedhia, N. et. al. (1997) Biotechnology and Bioengineering 53 (4) p 379-386.

[0112] Thereby, by using a gram-positive bacteria with decreased expression of a polypeptide having ppGpp synthetase activity according to the invention, the production of a protein of interest will improve in such a fed-batch fermentation.

[0113] Alternatively, said culturing may e.g. be done by using one of below mentioned standard fermentation techniques:

[0114] Batch fermentation: In a batch fermentation the cells will grow, after inoculation, until one of the substrate components is exhausted or an inhibitor is accumulated; or

[0115] Continuous Cultivation, by of one following standard techniques;

[0116] chemostat nutrient is fed at constant rate;

[0117] turbidostat employing feedback control of pumping rate to maintain a fixed turbidity of the culture. The controller of a turbidostat slows feeding when the cell concentration is below the set point so that growth can restore the turbidity. If the set point is exceeded, the pump speeds up to dilute the cell concentration; or

[0118] nustat, nutritstat, or auxostat (names are synonymous) feeding medium to hold a factor constant.

[0119] The invention is further illustrated by the following non-limiting examples.

Materials and Methods

General Molecular Biology Methods

[0120] Unless otherwise mentioned the DNA manipulations and transformations were performed using standard methods of molecular biology (Sambrook et al. (1989) Molecular cloning: A laboratory manual, Cold Spring Harbor lab., Cold Spring Harbor, N.Y.; Ausubel, F. M. et al. (eds.) “Current protocols in Molecular Biology”. John Wiley and Sons, 1995; Harwood, C. R., and Cutting, S. M. (eds.) “Molecular Biological Methods for Bacillus”. John Wiley and Sons, 1990).

[0121] Enzymes for DNA manipulations were used according to the specifications of the suppliers.

Enzymes for DNA Manipulations

[0122] Unless otherwise mentioned all enzymes for DNA manipulations, such as e.g. restiction endonucleases, ligases etc., are obtained from New England Biolabs, Inc.

EXAMPLES

Example 1

Identification of others ppGpp synthethases obtained from different Bacillus

[0123] PCR reactions.

[0124] On colonies:

[0125] A reisolated colony which had been incubated 18 hours on LB agar plates containing 10 μg/ml kanamycin, 10 mM pottasium phosphate pH 7,0 and 0,4% glucose was suspended in 10 μl 1×PCR buffer (Super Taq™ DNA polymerase) heated to 96° C. for 5 minutes, spun 20,000×g for 2 minutes. From the supernatant, 5 μl was used as template in a PCR reaction (30 cycles) using the different primers below and the Super Taq™ DNA polymerase following the manufactures' instructions (Enzyme technologies Ltd.).

[0126] Primers for PCR reactions. DNA primers (primer:#104775 to #104780) with a oligo nucleotide composition with identity to the B. subtilis relA-Bac sequence shown in SEQ ID NO:1 (underlined) has been used for amplifying DNA fragments from B. subtilis, B. amyloliquefaciens, B. lentus and B. licheniformis.

[0127] Positions relates to the DNA sequence shown in SEQ ID NO:1.

[0128] Non-underline primer sequence is a linker sequence for cloning purpose, which comprise a suitable site for restriction enzyme digestion.

[0129] Primers for the 5′-end of the relA-Bac gene from B. subtilis: (sense primers)

2#104775: 5′-CCG AAT TCA AAG GTG ATT CCA TGG CGA ACG-3′(Pos: 9 to 30) (SEQ ID NO: 5)#104776: 5′-CCG AAT TCG GTG ATT CCA TGG CGA ACG-3′ (Pos: 12to 30) (SEQ ID NO: 6)Primers for the 3′-end of internal parts of the relA-Bacgene of B. subtilis. (anti-sense primers)#104777: 5′-GCG GAT CCG CTT TAG GCC C-3′ (Pos: 987 to969) (SEQ ID NO: 7)#104778: 5′-CAT GCA TTT CAA AGG TGC GG-3′ (Pos: 1020 to1001) (SEQ ID NO: 8)Primers for the 3′-end of the relA-Bac gene of B. subtilis.(anti-sense primers)#104779: 5′-CCT TTA GTT CAT GAC GCG GCG C-3′ (Pos: 2228to 2207) (SEQ ID NO: 9)#104780: 5′-GTG TTT AGC GGC CGC TGA ACAACT AAT CTC-3′(Pos: 2277 to 2256) (SEQ ID NO: 10)#113554: 5′-ATA AGC ATG CGC TGA ACA ACT AAT CTC-3′ (Pos:2256 to 2239) (SEQ ID NO: 11)

[0130] Analyses of PCR products.

[0131] PCR products from B. subtilis, B. amyloliquefaciens, B. licheniformis, and B. lentus were analyzed on a 0.7% agarose gel containing Ethidium bromide to determine if DNA was present and if present an estimate of the size of the DNA.

[0132] The expected size PCR product was obtained.

[0133]

B. amyloliquefaciens:
PCR fragment size approximately 980 bp, with primers 104775, 104777.

[0134]

B. lentus:
PCR fragment size approximately 980 bp and 680, with primers 104775, 104777. Both PCR fragment may be used further to clone a B. lentus ppGpp synthetase.

[0135]

B. licheniformis:
PCR fragment size approximately 800 bp, with primers 104776, 104778; and PCR fragment size approximately 1900 bp, with primers 104776, 104779.

[0136] The PCR amplified DNA fragments are sequenced and this sequence information is used to clone B. amyloliquefaciens, B. licheniformis, and B. lentus ppGpp synthethases according to the invention. The cloning is performed according to standard procedure in the art.

Cloning of B.amyloliquefaciens full length ppGpp Synthethases

[0137] Using the B.amyloliquefaciens PCR fragment sized approximately 980 bp amplified with primers 104775, 104777 (see above) together with PCR (anti-sense) primer #113554 A PCR fragment from a B.amyloliquefaciens strain was obtained and DNA sequenced on an automatic DNA sequencer according to the manufactures protocol.

[0138] This DNA sequence and corresponding mature protein sequence are shown in SEQ ID NOS:3 and 4. The polypeptide has been designated relA-BacII and is obtained from a Bacillus amyloliquefaciens strain.

Example 2

Homology/Basis for Prediction

[0139] The present invention is based in part upon the discovery of a novel polynucleotide sequence obtained form a Bacillus subtilis strain that encodes a polypeptide having ppGpp synthetase activity and having homology to other microbial ppGpp syntheases. The polypeptide has been designated relA-Bac.

[0140] The criteria for defining novel polypeptides having ppGpp synthetase activity of the present invention were initially identified by querying to the public known database Genebank (EMBL, Heidelberg) for homologous sequences to the novel relA-Bac sequence of the invention.

[0141] Using a conventional percent sequence identity program as described in further details herein (vide infra) the DNA sequence identity of relA-Bac (SEQ ID NO:1) to prior art known ppGpp syntheases are shown in table I below, and the corresponding amino acid sequence identity are shown in Table II.

Table II

[0142] Homology between DNA sequences. The sequences used for similarity is the coding DNA sequences (CDS) from the GeneBank entries at EMBLwith the locus listed in the scheme.

[0143] GB13BA:SEDEXB ! X72832 S.equisimilis

[0144] GB13BA:VSU13769 ! U13769 Vibrio sp.

[0145] GB13BA:ECOSPOT ! M24503 E.coli

[0146] GB13BA:ECORELA ! J04039 E.coli

3bsrela.ecorelaecospotsedexb.vsu13769GB_BA:orf.orf.orforf.orfrelA-Bac100 50515950Ecorela.orf50100 484962Ecospot.orf5148100 5145sedexb.orf594951100 49vsu13769.orf50624549100

[0147] Homology between peptide sequences encoded by the above DNA sequences.

4Bsrela.ecorelaecospotSedexb.vsu13769pep.pep.peppep.peprelA-Bac100 38415337ecorela.pep38100 323665ecospot.pep4132100 4232sedexb.pep533642100 34vsu13769.pep37653234100

[0148] From the foregoing, it will be appreciated that, although specific embodiments of the invention have been described herein for purposes of illustration, various modifications may be made without deviating from the spirit and scope of the invention. Accordingly, the invention is not limited except as by the appended claims.

	Number	Date	Country
Parent	09442055	Nov 1999	US
Child	09946931	Sep 2001	US

	Number	Date	Country
Parent	PCT/DK98/00261	Jun 1998	US
Child	09442055	Nov 1999	US

ppGpp synthetase and expression systems for improved production of protein of interest

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