# Patent

## Title
Method for secretory production of protein

## Abstract

A novel technique for improving ability for secretory production of a multimeric protein of a coryneform bacterium is provided, and thereby a method for secretory production of a multimeric protein is provided. A multimeric protein is produced by secretory production utilizing a coryneform bacterium having an ability to produce a multimeric protein by secretory production and modified so that expression of a gene coding for a metallopeptidase is increased as an expression host.

## Background
This application is a Continuation of, and claims priority under 35 U.S.C. §120 to, International Application No. PCT/JP2012/078285, filed Nov. 1, 2012, and claims priority therethrough under 35 U.S.C. §119 to Japanese Patent Application No. 2011-240745, filed Nov. 2, 2011, the entireties of which are incorporated by reference herein. Also, the Sequence Listing filed electronically herewith is hereby incorporated by reference (File name: 2014-04-29T_US-512_Seq_List; File size: 63 KB; Date recorded: Apr. 29, 2014).


BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates to a coryneform bacterium that is able to efficiently produce a heterologous protein by secretory production and a method for secretory production of a heterologous protein. Specifically, the heterologous protein produced by secretory production according to the present invention is a multimeric protein.
2. Brief Description of the Related Art
To date, secretory production of heterologous proteins by microorganisms has been reported in Bacillus bacterium (Microbiol. Rev., 57, 109-137 (1993)), methanol-assimilating yeast, Pichia pastoris (Biotechnol., 11, 905-910 (1993)), filamentous fungi of the genus Aspergillus (Biotechnol., 6, 1419-1422 (1988) and Biotechnol., 9, 976-981 (1991)), and so forth.
Secretory production of heterologous proteins by coryneform bacteria has also been reported, specifically secretion of a nuclease and a lipase by Corynebacterium glutamicum (henceforth also abbreviated as C. glutamicum) (U.S. Pat. No. 4,965,197, J. Bacteriol., 174, 1854-1861 (1992)), secretion of a protease such as subtilisin (Appl. Environ. Microbiol., 61, 1610-1613 (1995)), secretion of a protein using signal peptides of cell surface layer proteins PS1 and PS2 (also referred to as CspB) of coryneform bacteria (Japanese Patent Laid-open (Kohyo) No. 6-502548), secretion of a fibronectin-binding protein using the signal peptide of PS2 (CspB) (Appl. Environ. Microbiol., 63, 4392-4400 (1997)), secretion of protransglutaminase using signal peptides of cell surface layer proteins PS2 (CspB) and SlpA (also referred to as CspA) of coryneform bacteria (Japanese Patent No. 4320769), secretion of a protein using a variant type secretion system (Japanese Patent Laid-open (Kokai) No. 11-169182), secretion of a protransglutaminase by a variant strain (Japanese Patent No. 4362651), secretion of a protein using a Tat-dependent signal peptide (Japanese Patent No. 4730302), and so forth.
Various proteins have been suggested as proteins that could be produced by secretory production; however, in coryneform bacteria, there are no reports of secretory production of any multimeric protein such as, for example, antibody-related molecules.
Metallopeptidases are a class of protease that requires various metal ions, such as zinc and calcium, for activation, and have an activity of decomposing various kinds of proteins. Among the metallopeptidases, metallopeptidases belonging to the M23/M37 family (also referred to as M23/M37 metallopeptidases) require zinc ion. It has already been elucidated that the Cgl0858 gene of C. glutamicum is a gene coding for a protein that includes a region homologous to a motif of M23/M37 metallopeptidases on the basis of the sequence information. However, the function of the protein encoded by the Cgl0858 gene in C. glutamicum is still elusive. Moreover, the ability to improve the production amount of an objective heterologous protein due to high expression of a gene coding for a region homologous to this motif of the M23/M37 metallopeptidases has not been reported for any biological species.
Penicillin-binding protein (PBP) is a generic term which describes proteins that bind with β-lactam type antibiotics, and as a result, inhibit binding with β-lactam type antibiotics. PBPs are generally membrane-binding proteins, and they are considered essential for cell wall synthesis of eubacteria. PBPs are classified as high molecular weight PBPs (HMW-PBPs) or low molecular weight PBPs (LMW-PBPs), according to the molecular weights thereof. HMW-PBPs are further classified as class A high molecular weight PBPs (class A HMW-PBPs), which have both a transpeptidase activity domain for crosslinking peptidoglycan moieties, and a transglycosylase activity domain for forming a polysaccharide chain from disaccharides, and class B high molecular weight PBPs (class B HMW-PBPs) which have only a transpeptidase activity domain.
The findings about PBPs of C. glutamicum are detailed in Mol. Microbiol., 66, 643-57 (2007), Antonie Van Leeuwenhoek, 94, 99-109 (2008), and so forth. In C. glutamicum, at least nine PBP homologues have been found so far. Five of them are HMW-PBPs including two class A HMW-PBPs (PBP1a, PBP1b) and three class B HMW-PBPs (FtsI, PBP2a, PBP2b). It is known that the class A HMW-PBPs of C. glutamicum are responsible for cell extension, and the class B HMW-PBPs are responsible for formation of peptidoglycan of septal walls at the time of cell division.
However, the relationship between penicillin-binding protein and the secretory production of a heterologous protein has not been previously reported.
SUMMARY OF THE INVENTION
Aspects to be Achieved by the Invention
An aspect of the present invention is to develop a novel technique for improving the ability of a coryneform bacterium to produce a multimeric protein by secretory production, and thereby to provide a coryneform bacterium that produces a multimeric protein by secretory production and a method for secretory production of a multimeric protein using such a bacterium.
A method for producing a heterologous protein utilizing a coryneform bacterium as an expression host is described, wherein the ability of the coryneform bacterium to produce a multimeric protein by secretory production is improved by modifying the coryneform bacterium so that the expression of a gene coding for a metallopeptidase is increased.
It is an aspect of the present invention to provide a coryneform bacterium having an ability to produce a multimeric protein by secretory production, which is modified so that expression of a gene coding for a metallopeptidase is increased.
It is a further aspect of the present invention to provide the bacterium as described above, wherein the expression of the gene is increased by increasing copy number of the gene or by modifying an expression control sequence of the gene.
It is a further aspect of the present invention to provide the bacterium as described above, wherein the metallopeptidase is an M23/M37 metallopeptidase or a protein comprising a region homologous to a motif of an M23/M37 metallopeptidase.
It is a further aspect of the present invention to provide the bacterium as described above, wherein the metallopeptidase is a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence shown in SEQ ID NO: 4,
(B) a protein comprising the amino acid sequence shown in SEQ ID NO: 4, but which includes substitution, deletion, insertion, or addition of 1 to 10 amino acid residues, and wherein said protein has a property that if expression thereof is increased in the coryneform bacterium, the secretory production amount of the multimeric protein is increased compared with that observed for a non-modified strain.
It is a further aspect of the present invention to provide the bacterium as described above, which is further modified so that the activity of a penicillin-binding protein is reduced.
It is a further aspect of the present invention to provide the bacterium as described above, wherein the activity of a cell surface layer protein is reduced.
It is a further aspect of the present invention to provide the bacterium as described above, which belongs to the genus Corynebacterium or Brevibacterium. 
It is a further aspect of the present invention to provide the bacterium as described above, which is Corynebacterium glutamicum. 
It is a further aspect of the present invention to provide the bacterium as described above, wherein the coryneform bacterium has a genetic construct for secretory expression of the multimeric protein, and wherein the genetic construct comprises a promoter sequence that functions in the coryneform bacterium, a nucleic acid sequence coding for a signal peptide that functions in the coryneform bacterium, which is ligated downstream from the promoter sequence, and a nucleic acid sequence coding for the multimeric protein, which is ligated downstream from the nucleic acid sequence coding for the signal peptide.
It is a further aspect of the present invention to provide the bacterium as described above, wherein the multimeric protein is an antibody-related molecule.
It is a further aspect of the present invention to provide the bacterium as described above, wherein the antibody-related molecule is a protein selected from the group consisting of Fab, F(ab′)2, Fc fusion protein, and combinations thereof.
It is a further aspect of the present invention to provide the bacterium as described above, wherein the multimeric protein is the vascular endothelial cell growth factor A (VEGF-A).
It is a further aspect of the present invention to provide a method for producing a multimeric protein comprising: culturing the coryneform bacterium as mentioned above; and collecting the protein produced by secretory production.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows an alignment of the amino acid sequences of the protein encoded by Cgl0858 of C. glutamicum ATCC 13032 (SEQ ID NO: 98) and the protein encoded by the Cgl0858 homologue of C. glutamicum ATCC 13869 (SEQ ID NO: 4).
FIG. 2 is a photograph showing the results of non-reduced SDS-PAGE of the H chain region and the L chain region of the Fab fragment of trastuzumab coexpressed in the C. glutamicum YDK010 strain and a metallopeptidase expression-enhanced strain thereof.
FIG. 3 is a photograph showing the results of Western blotting of the F(ab′)2 fragment of trastuzumab expressed in the C. glutamicum YDK010 strain and a metallopeptidase expression-enhanced strain thereof.
FIG. 4 is a photograph showing the results of non-reduced SDS-PAGE of the H chain region and the L chain region of the Fab fragment of trastuzumab coexpressed in the C. glutamicum YDK010 strain and a metallopeptidase expression-enhanced strain thereof, and a metallopeptidase expression-enhanced strain of the C. glutamicum YDK010ΔPBP1a strain.
FIG. 5 is a photograph showing the results of non-reduced SDS-PAGE of the vascular endothelial cell growth factor A (VEGF-A) expressed in the C. glutamicum YDK010 strain and a metallopeptidase expression-enhanced strain thereof.
FIG. 6 is a photograph showing the results of non-reduced SDS-PAGE of the Fab(H&L) fragment of adalimumab expressed in the C. glutamicum YDK010ΔPBP1a strain and a metallopeptidase expression-enhanced strain thereof.
FIG. 7 is a photograph showing the results of non-reduced SDS-PAGE of the Fab(H&L) fragment of trastuzumab expressed in the C. glutamicum ATCC 13869 strain (wild-type strain) and a metallopeptidase expression-enhanced strain thereof.



DESCRIPTION OF THE PREFERRED EMBODIMENTS
<1> Coryneform Bacterium of the Present Invention
The present invention provides a coryneform bacterium having an ability to produce a multimeric protein by secretory production, which is modified so that the expression of a gene coding for a metallopeptidase is increased (henceforth also referred to as the “bacterium of the present invention” or the “coryneform bacterium of the present invention”).
The expression that a protein is “secreted” can mean that the protein is transported out of the bacterial cell, that is, extracellularly transported. The expression that a protein is “secreted” of course can include when all the protein molecules eventually are present in a medium in completely free forms, when all the protein molecules are present in the cell surface layer, and/or when some of the protein molecules are present in the medium and some are present in the cell surface layer.
That is, the “ability to produce a multimeric protein by secretory production” can refer to an ability of the bacterium of the present invention to secrete the multimeric protein into a medium or the cell surface layer, and allow it to accumulate there to such an extent that the multimeric protein can be collected from the medium or the cell surface layer, when the bacterium is cultured in the medium. The accumulation amount may be, for example, in terms of the accumulation amount in the medium, 10 μg/L or more, 1 mg/L or more, 100 mg/L or more, 1 g/L or more. Also, the accumulation amount may be, for example, in terms of the accumulation amount in the cell surface layer, such an amount that if the multimeric protein in the cell surface layer is collected and suspended in a liquid of the same volume as the medium, the concentration of the multimeric protein in the suspension is 10 μg/L or more, 1 mg/L or more, 100 mg/L or more. In addition, the term “protein” to be produced by secretory production can refer to molecules called a peptide or polypeptide.
The multimeric protein to be produced by secretory production is not particularly limited so long as it is a heterologous multimeric protein. The “heterologous protein” can refer to an exogenous protein relative to the coryneform bacterium that expresses and secretes that protein. The heterologous protein may be, for example, a protein derived from a microorganism, a protein derived from a plant, a protein derived from an animal, a protein derived from a virus, or even a protein with an artificially designed amino acid sequence. The multimeric protein can contain two or more subunits. In the multimer, the subunits may be linked by covalent bonds such as disulfide bonds, linked by non-covalent bonds such as hydrogen bonds and hydrophobic interaction, or linked by a combination thereof. The multimer can include one or more intermolecular disulfide bonds. The multimer can be a homo-multimer consisting of a single kind of subunit, or may be a hetero-multimer consisting of two or more kinds of subunits. For the hetero-multimer, it is sufficient that at least one subunit is a heterologous protein. That is, all the subunits may be heterologous, or only a part of subunits may be heterologous. Although the multimeric protein may be a secretory protein in nature, or may be a non-secretory protein in nature, it is preferably a secretory protein in nature. Specific examples of the “multimeric protein” are described herein.
The multimeric protein to be produced by secretory production can be a single kind of protein, or two or more kinds of proteins. When the multimeric protein is a hetero-multimer, all the subunits of the hetero-multimer are produced by secretory production.
The coryneform bacteria are aerobic gram-positive bacilli, and include Corynebacterium bacteria, Brevibacterium bacteria, Microbacterium bacteria, and so forth. The coryneform bacteria include bacteria which have previously been classified into the genus Brevibacterium but are presently united into the genus Corynebacterium (Int. J. Syst. Bacteriol., 41, 255 (1991)). The coryneform bacteria also include bacteria which have previously been classified into Corynebacterium ammoniagenes but are presently reclassified into Corynebacterium stationis by nucleotide sequence analysis of 16S rRNA and so forth (Int. J. Syst. Evol. Microbiol., 60, 874-879 (2010)). Advantages of using coryneform bacteria include that they inherently secrete an extremely small amount of proteins to the outside of cells compared with fungi, yeasts, Bacillus bacteria, etc., which are conventionally used for secretory production of proteins, and therefore the purification process of a heterologous protein produced by secretory production is expected to be simplified or eliminated. Another advantage is that they can grow well in a simple medium containing a saccharide, ammonia, mineral salts, etc., and therefore they are excellent in view of cost of medium, culture method, and culture productivity, and so forth.
Specific examples of coryneform bacteria include the following species:
Corynebacterium acetoacidophilum 
Corynebacterium acetoglutamicum 
Corynebacterium alkanolyticum 
Corynebacterium callunae 
Corynebacterium glutamicum 
Corynebacterium lilium 
Corynebacterium melassecola 
Corynebacterium thermoaminogenes (Corynebacterium efficiens)
Corynebacterium herculis 
Brevibacterium divaricatum 
Brevibacterium flavum 
Brevibacterium immariophilum 
Brevibacterium lactofermentum (Corynebacterium glutamicum)
Brevibacterium roseum 
Brevibacterium saccharolyticum 
Brevibacterium thiogenitalis 
Corynebacterium ammoniagenes (Corynebacterium stationis)
Brevibacterium album 
Brevibacterium cerinum 
Microbacterium ammoniaphilum 
Specific examples of coryneform bacteria include the following strains:
Corynebacterium acetoacidophilum ATCC 13870
Corynebacterium acetoglutamicum ATCC 15806
Corynebacterium alkanolyticum ATCC 21511
Corynebacterium callunae ATCC 15991
Corynebacterium glutamicum ATCC 13020, ATCC 13032, ATCC 13060, ATCC 13869, FERM BP-734
Corynebacterium lilium ATCC 15990
Corynebacterium melassecola ATCC 17965
Corynebacterium thermoaminogenes AJ12340 (FERM BP-1539)
Corynebacterium herculis ATCC 13868
Brevibacterium divaricatum ATCC 14020
Brevibacterium flavum ATCC 13826, ATCC 14067, AJ12418 (FERM BP-2205)
Brevibacterium immariophilum ATCC 14068
Brevibacterium lactofermentum ATCC 13869
Brevibacterium roseum ATCC 13825
Brevibacterium saccharolyticum ATCC 14066
Brevibacterium thiogenitalis ATCC 19240
Corynebacterium ammoniagenes (Corynebacterium stationis) ATCC 6871, ATCC 6872
Brevibacterium album ATCC 15111
Brevibacterium cerinum ATCC 15112
Microbacterium ammoniaphilum ATCC 15354
These strains are available from, for example, the American Type Culture Collection (Address: P.O. Box 1549, Manassas, Va. 20108, United States of America). That is, registration numbers are assigned to the respective strains, and the strains can be ordered by using these registration numbers (refer to atcc.org). The registration numbers of the strains are listed in the catalogue of the American Type Culture Collection.
In particular, the Corynebacterium glutamicum (C. glutamicum) AJ12036 strain (FERM BP-734), which was isolated as a streptomycin (Sm) resistant mutant strain from the wild-type strain, C. glutamicum ATCC 13869, is predicted to have a mutation in the functional gene responsible for secretion of proteins, and shows an extremely high secretory production ability for heterologous proteins as high as about 2 to 3 times in terms of accumulation the amount of proteins under optimum culture conditions, compared with the parent strain (wild-type strain), and therefore it is preferred as a host bacterium. The AJ12036 strain was originally deposited at the National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology (currently, the incorporated administrative agency, National Institute of Technology and Evaluation, International Patent Organism Depositary, Tsukuba Central 6, 1-1, Higashi 1-Chome, Tsukuba-shi, Ibaraki-ken, 305-8566, Japan) on Mar. 26, 1984 as an international deposit, and assigned an accession number of FERM BP-734.
Moreover, a strain having an enhanced ability to produce a protein by secretory production may be selected from such coryneform bacteria as mentioned above as a parent strain by using a mutagenesis method or a genetic recombination method, and used as a host. For example, after a parent strain is treated with ultraviolet irradiation or a chemical mutation agent such as N-methyl-N′-nitrosoguanidine, a strain having an enhanced ability to produce a protein by secretory production can be selected.
Furthermore, if a strain obtained by modifying such a strain as mentioned above so that it does not produce a cell surface layer protein is used as the host, purification of the heterologous protein secreted in the medium or on the cell surface layer becomes easy, and therefore it is particularly preferred. Such modification can be carried out by introducing a mutation into the coding region of the cell surface layer protein or an expression control region thereof, on the chromosome by mutagenesis or genetic recombination. Examples of coryneform bacterium modified so that it does not produce a cell surface layer protein can include the C. glutamicum YDK010 strain (WO2004/029254), which is a cell surface layer protein PS2 (CspB) deficient strain of the C. glutamicum AJ12036 strain (FERM BP-734).
The coryneform bacterium having an ability to produce a multimeric protein by secretory production can be obtained by introducing a genetic construct for secretory expression of the multimeric protein into such a coryneform bacterium as mentioned above so that the bacterium harbors the genetic construct. That is, the bacterium of the present invention has a genetic construct for secretory expression of a multimeric protein. The “genetic construct for secretory expression of a multimeric protein” and a method for introducing it is described herein.
The bacterium of the present invention is modified so that the expression of a gene coding for a metallopeptidase is increased. The bacterium of the present invention can be obtained by modifying a coryneform bacterium having an ability to produce a multimeric protein by secretory production so that the expression of a gene coding for a metallopeptidase is increased. Alternatively, the bacterium of the present invention can also be obtained by modifying a coryneform bacterium so that the expression of a gene coding for a metallopeptidase is increased, and then imparting an ability to produce a multimeric protein by secretory production to it. In the present invention, the modification and impartation of the ability for constructing the bacterium of the present invention can be carried out in an arbitrary order. The bacterium of the present invention may be a bacterium obtained from a bacterium that can produce a multimeric protein by secretory production even before it is modified so that the expression of a gene coding for a metallopeptidase is increased. Alternatively, the bacterium of the present invention may also be a bacterium obtained from a bacterium that cannot produce a multimeric protein by secretory production even when it has a genetic construct for secretory expression of a multimeric protein before it is modified so that the expression of a gene coding for a metallopeptidase is increased, which comes to be able to produce the multimeric protein by secretory production as a result of such modification that the expression of a gene coding for a metallopeptidase is increased.
Hereafter, metallopeptidases and genes coding for them will be explained.
Metallopeptidases are a class of protease that requires various metal ions such as zinc and calcium for activation thereof, and have an activity of decomposing various kinds of proteins. This activity can also be referred to as metallopeptidase activity. Although the metallopeptidase with enhanced expression is not particularly limited, it can be an M23/M37 metallopeptidase. The M23/M37 metallopeptidase is a metalloendopeptidase that requires zinc ion. Specific examples of the M23/M37 metallopeptidase can include, for example, the protein encoded by the ale-1 gene of the Staphylococcus capitis EPK1 strain.
Furthermore, the metallopeptidase with enhanced expression can be a protein that includes a region homologous to a motif of a metallopeptidase as described above. For example, the metallopeptidase with enhanced expression can be a protein that includes a region homologous to a motif of an M23/M37 metallopeptidase. Specific examples of the protein containing a region homologous to a motif of an M23/M37 metallopeptidase can include, for example, the protein encoded by the Cgl0858 gene of C. glutamicum ATCC 13032 and the protein encoded by the Cgl0858 homologue gene of C. glutamicum ATCC 13869. Specific examples of the protein containing a region homologous to a motif of an M23/M37 metallopeptidase can also include, for example, the protein encoded by the nlpD gene of the Escherichia coli (E. coli) K12 MG1655 strain.
The metallopeptidase with enhanced expression has a property that if the expression thereof is increased in a coryneform bacterium, the secretory production amount of the multimeric protein is increased compared with that observed for a non-modified strain. In addition, the metallopeptidase with enhanced expression may have or may not have the metallopeptidase activity.
The phrase “property that if the expression thereof is increased in a coryneform bacterium, the secretory production amount of a multimeric protein is increased compared with that observed for a non-modified strain” can refer to a property of imparting an ability to produce a multimeric protein by secretory production in an amount larger than that observed for a non-modified strain, such as wild-type strain or parent strain to a coryneform bacterium when the expression thereof is increased in the coryneform bacterium. The expression “to produce a multimeric protein by secretory production in an amount larger than that observed for a non-modified strain” may mean, but is not particularly limited to, so long as the secretory production amount of the multimeric protein increases compared with that observed for a non-modified strain, for example, that the multimeric protein is produced by secretory production in an amount larger than that observed for a non-modified strain by 10% or more, 20% or more, 30% or more, 100% or more, in terms of the accumulation amount in the medium and/or the cell surface layer. In addition, the expression “to produce a multimeric protein by secretory production in an amount larger than that observed for a non-modified strain” may also mean that whereas the multimeric protein cannot be detected when a non-concentrated culture supernatant of a non-modified strain is applied to SDS-PAGE and stained with CBB, the multimeric protein can be detected when a non-concentrated culture supernatant of a modified strain is applied to SDS-PAGE and stained with CBB.
Whether a protein has a property that if the expression thereof is increased in a coryneform bacterium, the secretory production amount of a multimeric protein is increased compared with that observed for a non-modified strain can be confirmed by preparing a strain from a strain belonging to the coryneform bacteria by modification so that the expression of the gene thereof is increased, quantifying the secretory production amount of the multimeric protein observed when the modified strain is cultured in a medium, and comparing the quantified amount with the secretory production amount of the multimeric protein observed when the strain before being modified (non-modified strain) is cultured in the medium. As the non-modified strain referred to above, for example, a coryneform bacterium having the genetic construct for secretory expression of a multimeric protein can be used. Specifically, as the non-modified strain, for example, a strain obtained by introducing the genetic construct for secretory expression of a multimeric protein into the C. glutamicum AJ12036 (FERM BP-734) or C. glutamicum YDK010 strain can be used.
Further, the phrase “property that if the expression thereof is increased in a coryneform bacterium, the secretory production amount of the multimeric protein is increased compared with that observed for a non-modified strain” of the metallopeptidase may be, specifically, the metallopeptidase activity.
Whether a protein has the metallopeptidase activity can be confirmed by measuring that activity. The metallopeptidase activity can be measured by a method well known to those skilled in the art. Specifically, the metallopeptidase activity can be measured with, for example, a metalloprotease assay kit (Oxford Biomedical Research), or the like.
The ale-1 gene of the Staphylococcus capitis (S. capitis) EPK1 strain is registered in the NCBI database as GenBank accession BAA13069 (VERSION BAA13069.1 GI: 1890068).
The Cgl0858 gene of C. glutamicum ATCC 13032 corresponds to a sequence complementary to the sequence of the positions 916,967 to 917,680 in the genomic sequence registered in the NCBI database as GenBank accession BA000036 (VERSION BA000036.3 GI: 42602314). The amino acid sequence of the protein encoded by the Cgl0858 gene of C. glutamicum ATCC 13032 is shown in SEQ ID NO: 98. Further, the nucleotide sequence of the Cgl0858 homologue gene of C. glutamicum ATCC 13869 and the amino acid sequence of the protein encoded by this gene are shown in SEQ ID NOS: 3 and 4, respectively.
The nlpD gene of the Escherichia coli (E. coli) K12 MG1655 strain corresponds to a sequence complementary to the sequence of the positions 2,865,636 to 2,866,775 in the genomic sequence registered in the NCBI database as GenBank accession NC_000913 (VERSION NC_000913.2 GI: 49175990). The nlpD gene of the E. coli K12 MG1655 strain is synonymous with ECK2737 or JW2712.
Since the nucleotide sequence of the gene coding for a metallopeptidase may differ depending on the genus, species, or strain to which the bacterium belongs, the gene coding for a metallopeptidase may be a variant of the aforementioned nucleotide sequence, so long as it codes for a protein having a property that if the expression thereof is increased in a coryneform bacterium, the secretory production amount of the multimeric protein is increased compared with that observed for a non-modified strain. The variants of the Cgl0858 gene, the nlpD gene, and the ale-1 gene can include homologues of the genes. Homologues of the Cgl0858 gene, the nlpD gene, and the ale-1 gene can be easily obtained from public databases by BLAST search or FASTA search using the aforementioned wild-type Cgl0858 gene of C. glutamicum, the wild-type nlpD gene of E. coli, or the wild-type ale-1 gene of S. capitis as a query sequence, and can also be obtained by PCR using a chromosome of a bacterium belonging to the family Enterobacteriaceae or a coryneform bacterium as a template and oligonucleotides prepared on the basis of a known gene sequence such as those mentioned above as primers.
The gene coding for a metallopeptidase may be a gene coding for a protein having the aforementioned amino acid sequence including substitution, deletion, insertion, or addition of one or several amino acid residues at one or several positions, so long as it codes for a protein having a property that if the expression thereof is increased in a coryneform bacterium, the secretory production amount of the multimeric protein is increased compared with that observed for a non-modified strain. In such a case, usually 70% or more, 80% or more, 90% or more of the property that if the expression thereof is increased in a coryneform bacterium, the secretory production amount of the multimeric protein is increased compared with that observed for a non-modified strain is maintained against that of the protein not introduced with substitution, deletion, insertion, or addition of one or several amino acid residues. Although the number of “one or several” may differ depending on the position in the three-dimensional structure of the protein or types of amino acid residues, specifically, it is 1 to 20, 1 to 10, or 1 to 5.
The aforementioned substitution, deletion, insertion, or addition of one or several amino acid residues can be a conservative mutation that maintains the normal function of the protein. Typical examples of conservative mutations are conservative substitutions. The conservative substitution is a mutation wherein substitution takes place mutually among Phe, Trp, and Tyr, if the substitution site is an aromatic amino acid; among Leu, Ile, and Val, if it is a hydrophobic amino acid; between Gln and Asn, if it is a polar amino acid; among Lys, Arg, and H is, if it is a basic amino acid; between Asp and Glu, if it is an acidic amino acid; and between Ser and Thr, if it is an amino acid having a hydroxyl group. Examples of substitutions considered as conservative substitutions include, specifically, substitution of Ser or Thr for Ala, substitution of Gln, His, or Lys for Arg, substitution of Glu, Gln, Lys, His, or Asp for Asn, substitution of Asn, Glu, or Gln for Asp, substitution of Ser or Ala for Cys, substitution of Asn, Glu, Lys, His, Asp, or Arg for Gln, substitution of Gly, Asn, Gln, Lys, or Asp for Glu, substitution of Pro for Gly, substitution of Asn, Lys, Gln, Arg, or Tyr for H is, substitution of Leu, Met, Val, or Phe for Ile, substitution of Ile, Met, Val, or Phe for Leu, substitution of Asn, Glu, Gln, His, or Arg for Lys, substitution of Ile, Leu, Val, or Phe for Met, substitution of Trp, Tyr, Met, Ile, or Leu for Phe, substitution of Thr or Ala for Ser, substitution of Ser or Ala for Thr, substitution of Phe or Tyr for Trp, substitution of His, Phe, or Trp for Tyr, and substitution of Met, Ile, or Leu for Val. Further, such substitution, deletion, insertion, addition, inversion or the like of amino acid residues as mentioned above includes a naturally occurring mutation due to an individual difference, or a difference of species of a bacterium from which the gene is derived (mutant or variant).
Furthermore, the gene having such a conservative mutation as mentioned above may be a gene coding for a protein showing a homology of 80% or more, 90% or more, 95% or more, 97% or more, 99% or more, to the total encoded amino acid sequence, and having a property that if the expression of the protein is increased in a coryneform bacterium, the secretory production amount of the multimeric protein is increased compared with that observed for a non-modified strain. In addition, in this specification, “homology” may mean “identity”.
Moreover, the gene coding for a metallopeptidase may be a DNA that is able to hybridize with a probe that can be prepared from a known gene sequence, such as a sequence complementary to a part or the whole of the aforementioned nucleotide sequence, under stringent conditions, and codes for a protein having a property that if the expression of the protein is increased in a coryneform bacterium, the secretory production amount of the multimeric protein is increased compared with that observed for a non-modified strain. The “stringent conditions” can refer to conditions under which a so-called specific hybrid is formed, and a non-specific hybrid is not formed. Examples of the stringent conditions can include those under which highly homologous DNAs hybridize to each other, for example, DNAs not less than 80% homologous, not less than 90% homologous, not less than 95% homologous, not less than 97% homologous, not less than 99% homologous, hybridize to each other, and DNAs less homologous than the above do not hybridize to each other, or conditions of washing of typical Southern hybridization, i.e., conditions of washing once, preferably 2 or 3 times, at a salt concentration and temperature corresponding to 1×SSC, 0.1% SDS at 60° C., 0.1×SSC, 0.1% SDS at 60° C., 0.1×SSC, 0.1% SDS at 68° C.
The probe used for the aforementioned hybridization may be a part of a sequence that is complementary to the gene as described above. Such a probe can be prepared by PCR using oligonucleotides prepared on the basis of a known gene sequence as primers and a DNA fragment containing the nucleotide sequence as a template. For example, when a DNA fragment having a length of about 300 bp is used as the probe, the washing conditions of the hybridization may be, for example, 50° C., 2×SSC and 0.1% SDS.
Furthermore, although a naturally occurring gene coding for a metallopeptidase can be used as it is, a gene coding for a metallopeptidase in which an arbitrary codon is replaced with an equivalent codon may also be used. For example, the gene coding for a metallopeptidase may be modified so that it has optimal codons according to codon frequencies in a host to be used.
The above descriptions concerning variants of the genes and proteins can also be applied mutatis mutandis to arbitrary proteins such as cell surface layer proteins, penicillin-binding proteins, and multimeric proteins to be produced by secretory production according to the present invention, and genes coding for them.
The method for increasing the expression of a gene will be explained below.
The phrase “the expression of a gene is increased” can mean that the expression amount of the target gene is increased compared with that observed in a non-modified strain such as wild-type strain or parent strain. Although the degree of the increase of the expression of the gene is not particularly limited so long as the expression is increased compared with that observed in a non-modified strain, it can be increased 1.5 times or more, 2 times or more, 3 times or more, compared with that observed in a non-modified strain. Further, the phrase “the expression of a gene is increased” can include not only a case where the expression amount of a target gene is increased in a strain in which the target gene is originally expressed, but also a case where a target gene is expressed in a strain that does not originally express the gene. That is, the phrase “expression of a gene is increased” can include, for example, the case where the target gene is introduced into a strain that does not have the gene, and expressed in it.
The expression of a gene can be increased by, for example, increasing the copy number of the gene.
The copy number of a target gene can be increased by introducing the gene into the chromosome of a host microorganism. A gene can be introduced into a chromosome by a method of randomly introducing it into a chromosome using a transposon or Mini-Mu (Japanese Patent Laid-open (Kokai) No. 2-109985, U.S. Pat. No. 5,882,888, European Patent Publication No. 805867 B1), or by homologous recombination using a sequence present on a chromosomal DNA in a multiple copy number as a target. As a sequence present on a chromosomal DNA in a multiple copy number, a repetitive DNA, and inverted repeats located at the both ends of a transposon can be used. Alternatively, a gene can also be introduced into a chromosome by using the Red driven integration method (WO2005/010175). Moreover, a gene can also be introduced into a chromosome by transduction using a phage, or by using a conjugative transfer vector. Furthermore, a gene can also be introduced using a gene unnecessary for production of a heterologous protein on a chromosome as a target, as described in WO03/040373. One or plural copies of a gene can be introduced into a target sequence by such methods as described above.
Introduction of a target gene into a chromosome can be confirmed by Southern hybridization using a probe having a sequence complementary to the whole or a part of the gene, PCR using primers prepared on the basis of the sequence of the gene, or the like.
Furthermore, the copy number of a target gene can also be increased by introducing a vector containing the gene into a host bacterium. For example, copy number of a target gene can be increased by ligating a DNA fragment containing the target gene with a vector that functions in a host bacterium to construct an expression vector of the gene, and transforming the host bacterium with the expression vector. As the vector, a vector autonomously replicable in the cell of the host bacterium can be used. The vector can be a multi-copy vector. Further, the vector preferably includes a marker such as an antibiotic resistance gene for selection of transformants. The vector may be, for example, a vector derived from a bacterial plasmid, a vector derived from a yeast plasmid, a vector derived from a bacteriophage, cosmid, phagemid, or the like. Specific examples of vector autonomously replicable in coryneform bacteria include pHM1519 (Agric. Biol. Chem., 48, 2901-2903 (1984)); pAM330 (Agric. Biol. Chem., 48, 2901-2903 (1984)); plasmids obtained by improving these and having a drug resistance gene; plasmid pCRY30 described in Japanese Patent Laid-open (Kokai) No. 3-210184; plasmids pCRY21, pCRY2KE, pCRY2KX, pCRY31, pCRY3KE, and pCRY3KX described in Japanese Patent Laid-open (Kokai) No. 2-72876 and U.S. Pat. No. 5,185,262; plasmids pCRY2 and pCRY3 described in Japanese Patent Laid-open (Kokai) No. 1-191686; pAM330 described in Japanese Patent Laid-open (Kokai) No. 58-67679; pHM1519 described in Japanese Patent Laid-open (Kokai) No. 58-77895; pAJ655, pAJ611, and pAJ1844 described in Japanese Patent Laid-open (Kokai) No. 58-192900; pCG1 described in Japanese Patent Laid-open (Kokai) No. 57-134500; pCG2 described in Japanese Patent Laid-open (Kokai) No. 58-35197; pCG4 and pCG11 described in Japanese Patent Laid-open (Kokai) No. 57-183799; pVK7 described in Japanese Patent Laid-open (Kokai) No. 10-215883; pVC7 described in Japanese Patent Laid-open (Kokai) No. 9-070291; and so forth.
Furthermore, the expression of a gene can also be increased by improving the transcription efficiency of the gene. The transcription efficiency of a gene can be improved by, for example, substituting a stronger promoter for the promoter of the gene on the chromosome. The “stronger promoter” can mean a promoter providing improved transcription of a gene compared with the native wild-type promoter. As a stronger promoter, for example, known high expression promoters, such as T7 promoter, trp promoter, lac promoter, tac promoter, and PL promoter, can be used. Further, as the stronger promoter, a highly-active type of an existing promoter can be obtained by using various reporter genes. For example, by making the −35 and −10 regions in a promoter region closer to the consensus sequence, the activity of the promoter can be enhanced (International Patent Publication WO00/18935). Methods for evaluating the strength of promoters and examples of strong promoter are described in the paper of Goldstein et al. (Prokaryotic Promoters in Biotechnology, Biotechnol. Annu. Rev., 1, 105-128 (1995)), and so forth.
Furthermore, expression of a gene can also be increased by improving the translation efficiency of the gene. The translation efficiency of a gene can be improved by, for example, replacing the Shine-Dargarno (SD) sequence (also referred to as ribosome binding site (RBS)) of the gene on a chromosome with a stronger SD sequence. The “stronger SD sequence” can mean a SD sequence that provides improved translation of mRNA compared with the originally existing wild-type SD sequence. Examples of the stronger SD sequence include, for example, RBS of the gene 10 derived from phage T7 (Olins P. O. et al, Gene, 1988, 73, 227-235). Further, it is known that substitution, insertion, or deletion of several nucleotides in a spacer region between RBS and the start codon, especially in a sequence immediately upstream of the start codon (5′-UTR), significantly affects the stability and translation efficiency of mRNA, and the translation efficiency of a gene can also be improved by modifying them.
Sites affecting gene expression, such as promoter, SD sequence, and spacer region between RBS and the start codon, are also collectively called an “expression control region”. An expression control region can be determined by using a promoter-search vector or gene analysis software such as GENETYX. Such an expression control region can be modified by, for example, a method using a temperature sensitive vector or the Red driven integration method (WO2005/010175).
Furthermore, the expression of a target gene can also be increased by amplifying a regulator that increases the expression of the gene, or deleting or attenuating a regulator that reduces the expression of the gene.
Such methods for increasing the expression of a gene as mentioned above may be used independently or in an arbitrary combination.
The method for the transformation is not particularly limited, and conventionally known methods can be used. There can be used, for example, a method of treating recipient cells with calcium chloride so as to increase permeability thereof for DNA, which has been reported for Escherichia coli K-12 strain (Mandel, M. and Higa, A., J. Mol. Biol., 1970, 53, 159-162), and a method of preparing competent cells from cells which are in the growth phase, followed by transformation with DNA, which has been reported for Bacillus subtilis (Duncan, C. H., Wilson, G. A. and Young, F. E., Gene, 1977, 1:153-167). Alternatively, there can also be used a method of making DNA-recipient cells into protoplasts or spheroplasts, which can easily take up recombinant DNA, followed by introducing a recombinant DNA into the cells, which is known to be applicable to Bacillus subtilis, actinomycetes and yeasts (Chang, S, and Choen, S. N., 1979, Mol. Gen. Genet., 168:111-115; Bibb, M. J., Ward, J. M. and Hopwood, O. A., 1978, Nature, 274:398-400; Hinnen, A., Hicks, J. B. and Fink, G. R., 1978, Proc. Natl. Acad. Sci. USA, 75:1929-1933). Further, a coryneform bacterium can also be transformed by the electric pulse method (Japanese Patent Laid-open (Kokai) No. 2-207791).
An increase in the expression of a target gene can be confirmed by, for example, confirming the increase in the activity of the target protein expressed from the gene. An increase in the activity of the target protein can be confirmed by measuring the activity of the protein. The activity of the protein can be increased 1.5 times or more, 2 times or more, or 3 times or more, compared with that observed in a non-modified strain. The metallopeptidase activity can be measured by a method well known to those skilled in the art. Specifically, the metallopeptidase activity can be measured with, for example, a metalloproteinase assay kit (Oxford Biomedical Research), or the like.
An increase in the expression of a target gene can be confirmed by confirming increase in the transcription amount of the gene, or by confirming increase in the amount of the target protein expressed from the gene.
An increase in the transcription amount of a target gene can be confirmed by comparing the amount of mRNA transcribed from the gene with that of a non-modified strain such as wild-type strain or parent strain. Examples of the method for evaluating the amount of mRNA include Northern hybridization, RT-PCR, and so forth (Sambrook, J., et al., Molecular Cloning A Laboratory Manual/Third Edition, Cold spring Harbor Laboratory Press, Cold Spring Harbor (USA), 2001). The amount of mRNA can increase, for example, 1.5 times or more, 2 times or more, or 3 times or more, compared with that of a non-modified strain.
An increase in the amount of a target protein can be confirmed by Western blotting using an antibody (Molecular Cloning, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (USA), 2001). The amount of the protein can be increased, for example, 1.5 times or more, 2 times or more, or 3 times or more, compared with that of a non-modified strain.
The bacterium of the present invention may further have a property of improving secretory production ability for a heterologous protein. For example, the bacterium of the present invention may be modified so that the activity of a penicillin-binding protein is reduced. Further, the bacterium of the present invention may be, for example, a bacterium in which the activity of a cell surface layer protein is reduced.
Hereafter, penicillin-binding proteins and genes coding for them will be explained.
In general, the penicillin-binding proteins (PBPs) can refer to proteins that bind with β-lactam type antibiotics, and as a result, inhibit their enzymatic function. The penicillin-binding proteins include high molecular weight PBPs (HMW-PBPs) and low molecular weight PBPs (LMW-PBPs). The high molecular weight PBPs include class A high molecular weight PBPs (class A HMW-PBPs) and class B high molecular weight PBPs (class B HMW-PBPs). The class A HMW-PBPs have both a transpeptidase activity domain for crosslinking peptidoglycan moieties and a transglycosylase activity domain for forming a polysaccharide chain from disaccharides. The class B HMW-PBPs have a transpeptidase activity domain. For example, as for C. glutamicum, PBP1a and PBP1b can be mentioned as the class A HMW-PBPs. As for C. glutamicum, FtsI, PBP2a, and PBP2b can be mentioned as the class B HMW-PBPs.
When the activity of a penicillin-binding protein is reduced in a coryneform bacterium, the secretory production amount of a heterologous protein is increased compared with that observed for a non-modified strain. Examples of a penicillin-binding protein, for example, include PBP1a, class B HMW-PBPs, and LMW-PBPs, specifically include PBP1a and class B HMW-PBPs, or more specifically include PBP1a.
The “property that if the activity thereof is reduced in a coryneform bacterium, the secretory production amount of a heterologous protein is increased compared with that observed for a non-modified strain” can refer to a property imparting an ability to produce a heterologous protein by secretory production in an amount larger than that observed for a non-modified strain such as wild-type strain or parent strain to a coryneform bacterium when the activity thereof is reduced in the coryneform bacterium. The expression “to produce a heterologous protein by secretory production in an amount larger than that observed for a non-modified strain” may mean, but is not particularly limited to, so long as the secretory production amount of the heterologous protein increases compared with that observed for a non-modified strain, for example, that the heterologous protein is produced by secretory production in an amount larger than that observed for a non-modified strain by 10% or more, 20% or more, 30% or more, 100% or more, in terms of the accumulation amount in the medium and/or the cell surface layer. In addition, the expression “to produce a heterologous protein by secretory production in an amount larger than that observed for a non-modified strain” may also mean that whereas the heterologous protein cannot be detected when a non-concentrated culture supernatant of a non-modified strain is applied to SDS-PAGE and stained with CBB, the heterologous protein can be detected when a non-concentrated culture supernatant of a modified strain is applied to SDS-PAGE and stained with CBB.
Whether a protein has a property that if the activity thereof is reduced in a coryneform bacterium, the secretory production amount of a heterologous protein is increased compared with that observed for a non-modified strain can be confirmed by modifying a coryneform bacterium so that the activity of the protein is reduced, quantifying the secretory production amount of the heterologous protein observed when the modified strain is cultured in a medium, and comparing the quantified amount with the secretory production amount of the heterologous protein observed when an un-modified strain is cultured in the medium.
The Cgl0278 gene coding for the PBP1a protein of the C. glutamicum ATCC 13032 corresponds to a sequence complementary to the sequence of the positions 294001 to 296388 in the genome sequence registered in the NCBI database as GenBank accession BA000036 (VERSION BA000036.3 GI: 42602314). Also, the PBP1a protein of the C. glutamicum ATCC 13032 is registered as GenBank accession NP_599531 (version NP_599531.1 GI: 19551529, locus_tag=“NCgl0274”). The nucleotide sequence of the Cgl0278 gene of C. glutamicum ATCC 13032 and the amino acid sequence of the PBP1a protein encoded by this gene are shown as SEQ ID NOS: 99 and 100, respectively.
Since the nucleotide sequence of a gene coding for a penicillin-binding protein may differ depending on species or strain to which the coryneform bacterium belongs, the gene coding for a penicillin-binding protein may be a variant of the aforementioned nucleotide sequence, so long as it codes for a protein having a property that if the activity thereof is reduced in a coryneform bacterium, the secretory production amount of a heterologous protein is increased compared with that observed for a non-modified strain. For example, the gene coding for a penicillin-binding protein may be a gene coding for a protein having the aforementioned amino acid sequence including substitution, deletion, insertion, or addition of one or several amino acid residues at one or several positions, so long as the gene codes for a protein having a property that if the activity thereof is reduced in a coryneform bacterium, the secretory production amount of a heterologous protein is increased compared with that observed for a non-modified strain. The above descriptions concerning variants of the metallopeptidases and genes coding for them can be applied mutatis mutandis to variants of the penicillin-binding proteins and genes coding for them.
Hereafter, cell surface layer proteins and genes coding for them will be explained.
The cell surface layer proteins are present in the cell surface layers (S-layer) of bacteria and archaea. Examples of the cell surface layer proteins of coryneform bacteria include PS1 and PS2 (also referred to as CspB) of C. glutamicum and SlpA (also referred to as CspA) of C. stationis. Among them, it is preferred that the activity of PS2 protein is reduced.
The nucleotide sequence of the cspB gene of C. glutamicum ATCC 13869 and the amino acid sequence of the PS2 protein encoded by the gene are shown in SEQ ID NOS: 114 and 115, respectively.
Further, for example, amino acid sequences of CspB homologues were reported for 28 strains of C. glutamicum (J. Biotechnol., 112, 177-193 (2004)). These 28 strains of C. glutamicum and the GenBank accession numbers of the cspB gene homologues in NCBI database are exemplified below (the GenBank accession numbers are shown in the parentheses).
C. glutamicum ATCC 13058 (AY524990)
C. glutamicum ATCC 13744 (AY524991)
C. glutamicum ATCC 13745 (AY524992)
C. glutamicum ATCC 14017 (AY524993)
C. glutamicum ATCC 14020 (AY525009)
C. glutamicum ATCC 14067 (AY524994)
C. glutamicum ATCC 14068 (AY525010)
C. glutamicum ATCC 14747 (AY525011)
C. glutamicum ATCC 14751 (AY524995)
C. glutamicum ATCC 14752 (AY524996)
C. glutamicum ATCC 14915 (AY524997)
C. glutamicum ATCC 15243 (AY524998)
C. glutamicum ATCC 15354 (AY524999)
C. glutamicum ATCC 17965 (AY525000)
C. glutamicum ATCC 17966 (AY525001)
C. glutamicum ATCC 19223 (AY525002)
C. glutamicum ATCC 19240 (AY525012)
C. glutamicum ATCC 21341 (AY525003)
C. glutamicum ATCC 21645 (AY525004)
C. glutamicum ATCC 31808 (AY525013)
C. glutamicum ATCC 31830 (AY525007)
C. glutamicum ATCC 31832 (AY525008)
C. glutamicum LP-6 (AY525014)
C. glutamicum DSM20137 (AY525015)
C. glutamicum DSM20598 (AY525016)
C. glutamicum DSM46307 (AY525017)
C. glutamicum 22220 (AY525005)
C. glutamicum 22243 (AY525006)
Since the nucleotide sequence of a gene coding for a cell surface layer protein may differ depending on species or strain to which the coryneform bacterium belongs, the gene coding for a cell surface layer protein may be a variant of the aforementioned nucleotide sequence, so long as it codes for a protein having a property that if the activity thereof is reduced in a coryneform bacterium, the secretory production amount of a heterologous protein is increased compared with that observed for a non-modified strain. For example, the gene coding for a cell surface layer protein may be a gene coding for a protein having the aforementioned amino acid sequence including substitution, deletion, insertion, or addition of one or several amino acid residues at one or several positions, so long as the gene codes for a protein having a property that if the activity thereof is reduced in a coryneform bacterium, the secretory production amount of a heterologous protein is increased compared with that observed for a non-modified strain. The above descriptions concerning variants of the metallopeptidases and genes coding for them can be applied to variants of the cell surface layer proteins and genes coding for them.
The expression “activity of a cell surface layer protein is reduced” includes when a coryneform bacterium has been modified so that the activity of a cell surface layer protein is reduced and a case where the activity of a cell surface layer protein is inherently reduced in a coryneform bacterium. The “activity of a cell surface layer protein is inherently reduced in a coryneform bacterium” includes a case where a coryneform bacterium is inherently deficient in a cell surface layer protein. That is, examples of a coryneform bacterium in which the activity of a cell surface layer protein is reduced include a coryneform bacterium that is inherently deficient in a cell surface layer protein. Examples of the “case where a coryneform bacterium is inherently deficient in a cell surface layer protein” include a case where a coryneform bacterium is inherently deficient in the gene encoding a cell surface layer protein. The expression “a coryneform bacterium is inherently deficient in a cell surface layer protein” may mean that a coryneform bacterium is inherently deficient in one or more proteins selected from cell surface layer protein(s) found in other strain(s) of the species to which the coryneform bacterium belongs. For example, “C. glutamicum is inherently deficient in a cell surface layer protein” may mean that a C. glutamicum strain is inherently deficient in one or more proteins selected from cell surface layer protein(s) found in other C. glutamicum strain(s), i.e. for example, deficient in PS1 and/or PS2 (CspB). Examples of the coryneform bacterium that is inherently deficient in a cell surface layer protein include C. glutamicum ATCC 13032, which is inherently deficient in the cspB gene.
Hereafter, means for reducing the activity of a protein will be explained.
The expression “activity of a protein is reduced” can mean that the activity of the target protein is decreased compared with that of a non-modified strain such as a wild-type strain or parent strain, which includes a case where the activity completely disappears. Specifically, the expression “activity of a protein is reduced” can mean that the number of molecules of the protein per cell is reduced, and/or the function of each molecule of the protein is reduced compared with those of a non-modified strain. That is, the term “activity” regarding the expression “activity of a protein is reduced” can mean the transcription amount (the amount of mRNA) of a gene encoding the protein or the amount of the protein, as well as the catalytic activity of the protein. In addition, the case where “number of molecules of the protein per cell is reduced” can include a case where the protein does not exist at all. Further, the case where “function of each molecule of the protein is reduced” can include a case where function of each molecule of the protein completely disappears.
The modification for reducing the activity of a protein can be attained by, for example, reducing expression of a gene coding for the protein. “Reduction of gene expression” is also referred to as “attenuation of gene expression”. The reduction of gene expression may be induced by, for example, reduction of transcription efficiency, reduction of translation efficiency, or a combination of these. Reduction of expression of a gene can be attained by modifying an expression control sequence of the gene such as a promoter and the Shine-Dalgarno (SD) sequence. When an expression control sequence is modified, preferably one nucleotide or more, more preferably two nucleotides or more, particularly preferably three nucleotides or more, of the expression control sequence are modified. Moreover, a part or all of the expression control sequence may be deleted. Reduction of gene expression can also be attained by, for example, manipulating a factor responsible for expression control. Examples of the factor responsible for expression control include low molecules responsible for transcription or translation control (inducers, inhibitors, etc.), proteins responsible for transcription or translation control (transcription factors etc.), nucleic acids responsible for transcription or translation control (siRNA etc.), and so forth.
The modification for reducing the activity of a protein can also be attained by, for example, disrupting the gene coding for the protein. Disruption of a gene can be attained by, for example, deleting a part or all of the coding region of the gene on a chromosome. Furthermore, the total gene including sequences upstream and downstream from the gene on a chromosome may be deleted. The region to be deleted may be any region such as an N-terminal region, an internal region, or a C-terminal region, so long as reduction of the activity of the protein is to be attained. Deletion of a longer region can usually more surely inactivate the gene. Further, it is preferred that the reading frames of the sequences upstream and downstream from the region to be deleted are not the same.
Disruption of a gene can also be attained by, for example, introduction of a mutation for an amino acid substitution (missense mutation), a stop codon (nonsense mutation), a frame shift mutation which adds or deletes one or two nucleotides into the coding region of the gene on a chromosome, or the like (Journal of Biological Chemistry, 272:8611-8617 (1997); Proceedings of the National Academy of Sciences, USA, 95 5511-5515 (1998); Journal of Biological Chemistry, 26 116, 20833-20839 (1991)).
Disruption of a gene can also be attained by, for example, inserting another sequence into the coding region of the gene on a chromosome. Site of the insertion may be at any region of the gene, and insertion of a longer region can usually more surely inactivate the gene. It is preferred that the reading frames of the sequences upstream and downstream from the insertion site are not the same. The other sequence is not particularly limited so long as a sequence that reduces or eliminates the activity of the encoded protein is chosen, and examples include, for example, a marker gene such as an antibiotic resistance gene, a gene useful for production of a heterologous protein, and so forth.
Such modification of a gene on a chromosome as described above can be attained by, for example, preparing a deficient type gene in which a partial sequence of the gene is deleted so that it cannot produce a protein that can normally function, and transforming a bacterium with a recombinant DNA containing the deficient type gene to cause homologous recombination between the deficient type gene and the gene on a chromosome and thereby substitute the deficient type gene for the gene on the chromosome. In such a case, if a marker gene selected according to the characteristics of the host such as auxotrophy is included in the recombinant DNA, the operation becomes easy. The protein encoded by the deficient type gene has a conformation different from that of a wild-type protein, even if it is produced, and thus the function thereof is reduced or eliminated. Such gene disruption based on gene substitution utilizing homologous recombination has been already established, and such methods include “Red driven integration” (Datsenko, K. A, and Wanner, B. L., Proc. Natl. Acad. Sci. USA, 97:6640-6645 (2000)), a method of using a linear DNA such as a method utilizing the Red driven integration in combination with an excision system derived from λ phage (Cho, E. H., Gumport, R. I., Gardner, J. F., J. Bacteriol., 184:5200-5203 (2002)), a method of using a plasmid containing a temperature sensitive replication origin, a method of using a plasmid capable of conjugative transfer, a method of using a suicide vector not having replication origin which functions in a host (U.S. Pat. No. 6,303,383, Japanese Patent Laid-open (Kokai) No. 05-007491), and so forth.
The modification for reducing the activity of a protein can also be attained by, for example, a mutagenesis treatment. Examples of the mutagenesis treatment include usual mutagenesis treatments such as irradiation of X-ray or ultraviolet radiation and mutagenesis treatment with a mutation agent such as N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), ethyl methanesulfonate (EMS), and methyl methanesulfonate (MMS).
Reduction of the activity of a target protein can be confirmed by measuring the activity of the protein. Specifically, the activity of a protein is decreased to, for example, 50% or less, 20% or less, 10% or less, 5% or less, or even 0%, of that observed in a non-modified strain. In the case of a penicillin-binding protein, whether activity of the protein has been reduced can be confirmed by, for example, measuring the transpeptidase activity and/or the transglycosylase activity depending on the class to which the protein belongs. The transpeptidase activity and/or the transglycosylase activity can be measured by, for example, a method well known to those skilled in the art. Specifically, for example, the transpeptidase and transglycosylase activities of PBP1a can be measured by measuring the reaction of oligomerizing lipid II to glycan strands and forming peptide cross-links (Born P, et al., J Biol. Chem. 2006 Sep. 15; 281(37): 26985-93.). Specifically, activity of a protein is decreased to, for example, 50% or less, 20% or less, 10% or less, 5% or less, or even 0%, of that observed in a non-modified strain.
Reduction of expression of a target gene can be confirmed by confirming reduction of the transcription amount of the gene or reduction of the amount of the target protein expressed from the gene.
Reduction of the transcription amount of a target gene can be confirmed by comparing the amount of mRNA transcribed from the gene with that observed in a non-modified strain. Examples of the method for measuring the amount of mRNA include Northern hybridization, RT-PCR, and so forth (Molecular Cloning, Cold spring Harbor Laboratory Press, Cold Spring Harbor (USA), 2001). The amount of mRNA can be decreased to, for example, 50% or less, 20% or less, 10% or less, 5% or less, or 0%, of that observed in a non-modified strain.
Reduction of the amount of a target protein can be confirmed by Western blotting using antibodies (Molecular Cloning, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (USA) 2001). The amount of the protein can be decreased to, for example, 50% or less, 20% or less, 10% or less, 5% or less, or 0%, of that observed in a non-modified strain.
Disruption of a target gene can be confirmed by determining the nucleotide sequence of a part or all of the gene, restriction enzyme map, full length of the gene, or the like depending on the means used for the disruption.
The methods mentioned above for reducing the activity of a protein can also be applied mutatis mutandis to arbitrary proteins and genes coding for them as well as for reducing the activity of a penicillin-binding protein and reducing the activity of a cell surface layer protein.
Hereafter, the “genetic construct for secretory expression of a multimeric protein” and introduction method therefor will be explained. This genetic construct is also referred to as “genetic construct used for the present invention”.
It is known that a secretory protein is generally translated as a preprotein (also referred to as prepeptide) or a preproprotein (also referred to as prepropeptide), and then becomes a mature protein through processing. Specifically, a secretory protein is generally translated as a preprotein or preproprotein, then a signal peptide as the pre-moiety is cleaved with a protease (generally called signal peptidase), and the secretory protein is thereby converted into a mature protein or proprotein. As for the proprotein, the pro-moiety thereof is further cleaved by a protease, and the proprotein thereby becomes a mature protein. Therefore, a signal peptide is preferably used for the secretory production of a multimeric protein in the method of the present invention. In the present invention, a preprotein and a preproprotein of a secretory protein may be collectively referred to as “secretory protein precursor”. The “signal peptide” (also referred to as “signal sequence”) can refer to an amino acid sequence present at the N-terminus of a secretory protein precursor, and usually not present in a natural mature protein.
Although the genetic construct is not particularly limited so long as secretory production of a multimeric protein can be attained, it can include a promoter sequence that functions in a coryneform bacterium, a nucleic acid sequence coding for a signal peptide that functions in the coryneform bacterium, which is ligated downstream from the promoter sequence, and a nucleic acid sequence coding for a multimeric protein, which is ligated downstream from the nucleic acid sequence coding for the signal peptide. The nucleic acid sequence coding for a signal peptide may be ligated downstream from the promoter sequence so that the signal peptide is expressed under the control of the promoter. The nucleic acid sequence coding for the multimeric protein may be ligated downstream from the nucleic acid sequence coding for the signal peptide so that the multimeric protein is expressed as a fusion protein with the signal peptide. The genetic construct can also comprise a control sequence (operator, terminator, etc.) effective for expression of the multimeric protein gene in a coryneform bacterium at such an appropriate position that it can function.
The promoter is not particularly limited so long as a promoter that functions in a coryneform bacterium is chosen, and it may be a promoter derived from a coryneform bacterium, or a heterologous promoter. The “promoter that functions in a coryneform bacterium” can refer to a promoter that possesses promoter activity in a coryneform bacterium. Specific examples of the heterologous promoter include, for example, promoters derived from E. coli such as tac promoter, lac promoter, trp promoter, and araBAD promoter. Among these, potent promoters such as tac promoter are preferred, and inducible promoters such as araBAD promoter are also preferred.
Examples of the promoter derived from a coryneform bacterium can include, for example, promoters of the genes coding for the cell surface layer proteins PS1, PS2 (also referred to as CspB), and SlpA (also referred to as CspA), and promoters of various amino acid biosynthesis system genes. Specific examples of the promoters of various amino acid biosynthesis system genes can include, for example, promoters of the glutamate dehydrogenase gene of the glutamic acid biosynthesis system, the glutamine synthetase gene of the glutamine synthesis system, the aspartokinase gene of the lysine biosynthesis system, the homoserine dehydrogenase gene of the threonine biosynthesis system, the acetohydroxy acid synthetase gene of the isoleucine and valine biosynthesis system, 2-isopropylmalate synthetase gene of the leucine biosynthesis system, the glutamate kinase gene of the proline and arginine biosynthesis system, the phosphoribosyl-ATP pyrophosphorylase gene of the histidine biosynthesis system, the deoxyarabinoheptulonate phosphate (DAHP) synthetase gene of the aromatic amino acid biosynthesis systems such as those for tryptophan, tyrosine, and phenylalanine, the phosphoribosyl pyrophosphate (PRPP) amidotransferase gene of the nucleic acid biosynthesis systems such as those for inosinic acid and guanylic acid, the inosinic acid dehydrogenase gene, and the guanylic acid synthetase gene.
As the promoter, a high activity type of an existing promoter may be obtained by using various reporter genes, and used. For example, by making the −35 and −10 regions in a promoter region closer to a consensus sequence, the activity of the promoter can be enhanced (International Patent Publication WO00/18935). Examples of the method for evaluating strength of a promoter and strong promoters are described in the paper of Goldstein et al. (Prokaryotic promoters in biotechnology, Biotechnol. Annu. Rev., 1, 105-128 (1995)) and so forth. Further, it is known that substitution, insertion, or deletion of several nucleotides in a spacer region between the ribosome-binding site (RBS) and the start codon, especially in a sequence immediately upstream of the start codon (5′-UTR), significantly affects stability and translation efficiency of mRNA, and these sequences can also be modified.
The signal peptide is not particularly limited so long as a signal peptide that functions in a coryneform bacterium is chosen, and it may be a signal peptide derived from a coryneform bacterium, or it may be a heterologous signal peptide. The “signal peptide that functions in a coryneform bacterium” can refer to a peptide that when it is ligated to the N-terminus of an objective protein, allows the coryneform bacterium to secrete the protein. The signal peptide can be a signal peptide of a secretory protein of the coryneform bacterium as the host, or a signal peptide of a cell surface layer protein of the coryneform bacterium. Examples of the cell surface layer protein of coryneform bacteria include PS1 and PS2 (CspB) derived from C. glutamicum (Japanese Patent Laid-open (Kohyo) No. 6-502548), and SlpA (CspA) derived from C. ammoniagenes (C. stationis) (Japanese Patent Laid-open (Kokai) No. 10-108675). The amino acid sequence of the signal peptide of PS1 is shown in SEQ ID NO: 101, the amino acid sequence of the signal peptide of PS2 (CspB) is shown in SEQ ID NO: 102, and the amino acid sequence of the signal peptide of SlpA (CspA) is shown in SEQ ID NO: 103. Moreover, U.S. Pat. No. 4,965,197 describes that there are signal peptides for DNases derived from coryneform bacteria, and such signal peptides can also be used for the present invention.
Although signal peptides have a certain characteristic of sequence common over biological species, a signal peptide that exhibits a secretory function in a certain biological species does not necessarily exhibit a secretory function in another biological species. Therefore, when a heterologous signal peptide is used, a signal peptide that functions in a coryneform bacterium may be appropriately chosen. Whether a certain signal peptide functions in a coryneform bacterium can be confirmed by, for example, expressing the objective protein as a fusion protein with that signal peptide, and confirming whether the protein is secreted or not.
The signal peptide may include a part of the N-terminal amino acid sequence of the secretory protein from which the signal peptide is derived. The signal sequence is generally cleaved by a signal peptidase, when the translation product is secreted out of the cell. As a gene coding for a signal peptide, although a naturally occurring gene may be used as it is, it may be modified so that it has the optimal codons according to codon frequencies in the chosen host.
Examples of the multimeric protein to be produced by secretory production can include, for example, physiologically active proteins, receptor proteins, antigen proteins which can be used as vaccines, and enzymes, which are multimeric proteins. Examples of the physiologically active proteins can include, for example, growth factors, hormones, cytokines, and antibody-related molecules.
The antibody-related molecule can refer to a protein that includes a single domain or a combination of two or more domains, such as domains that constitute a complete antibody. Examples of the domains that constitute a complete antibody include VH, CH1, CH2, and CH3, which are domains of a heavy chain, and VL and CL, which are domains of a light chain. The antibody-related molecule may be a monomer protein or a multimeric protein so long as it includes the above-mentioned molecular species. In the case where the antibody-related molecule is a multimeric protein, the antibody-related molecule may be a homo-multimer consisting of a single kind of subunit, or may be a hetero-multimer consisting of two or more kinds of subunits. Specific examples of the antibody-related molecules can include, for example, complete antibodies, Fab, F(ab′), F(ab′)2, Fc, dimer consisting of the heavy chain (H chain) and the light chain (L chain), Fc-fusion proteins, the heavy chain (H chain), the light chain (L chain), single chain Fv (scFv), sc(Fv)2, disulfide-linked Fv (sdFv), and diabody.
Examples of the antibody-related molecules that are multimeric proteins can include, for example, complete antibodies, Fab, F(ab′), F(ab′)2, Fc, dimer consisting of the heavy chain (H chain) and the light chain (L chain), Fc-fusion proteins, sc(Fv)2, and diabody. Among these, Fab, F(ab′)2, and Fc-fusion proteins are preferred.
Fab (fragment, antigen binding) is a part of a complete antibody except for the Fc region of the H chain, and it is an antibody fragment consisting only of the antigen-binding region. Fab is a dimer consisting of one molecule of the Fab moiety of the H chain and one molecule of the L chain, and they are linked via a disulfide bond at the C-terminus. The complete antibody is a H2L2 tetramer, and is a huge molecule having a molecular weight of about 150 kDa. In contrast, Fab has a smaller molecular weight of about 50 kDa, and therefore it is considered that Fab shows superior permeability for objective tissues. Since Fab does not have the Fc region, it does not have the complement activity or crystallization ability. However, since Fab has an antigen-binding ability, it is mainly used for the purpose of neutralizing antigens. Fab attracts attention in recent years among the antibody drugs.
F(ab′) is a part of a complete antibody except for the Fc′ region of the H chain. F(ab′) is a dimer consisting of one molecule of the F(ab′) moiety of the H chain and one molecule of the L chain, and they are linked via a disulfide bond at the C-terminus. The remaining moiety of the H chain in F(ab′) is longer than the remaining moiety of the H chain in Fab, and hence, the disulfide bond moiety linking the H chains remains. Therefore, two molecules of F(ab′) can form F(ab′)2 with a disulfide bond. F(ab′) and F(ab′)2 can also be used as antibody drugs like the Fab fragment.
Fc (fragment, crystallizable) is an antibody fragment consisting only of the Fc region, which is responsible for the complement activity or crystallization ability. A protein consisting of the Fc region of the H chain fused with another functional protein is called Fc fusion protein.
Specific examples of the growth factors that are multimeric proteins can include, for example, vascular endothelial growth factor (VEGF).
Specific examples of the hormones that are multimeric proteins can include, for example, insulin.
Specific examples of the cytokines that are multimeric proteins can include, for example, interleukin 5, interferon γ, and tumor necrosis factors (TNFs).
The growth factors, hormones, and cytokines may not be strictly distinguished from one another. For example, a physiologically active protein may be a protein such as a growth factor, hormone, or cytokine, or may be a protein that is classified in more than one of these.
The receptor proteins are not particularly limited, so long as they are multimeric proteins. A receptor protein may be, for example, a receptor protein for any of physiologically active proteins and other physiologically active substances. Examples of the other physiologically active substances can include, for example, neurotransmitters such as dopamine. Further, a receptor protein may be an orphan receptor of which the corresponding ligand is not known.
The antigen proteins which can be used as vaccines are not particularly limited, so long as they are multimeric proteins that can induce an immune response. An antigen protein can be appropriately selected depending on the intended object of the immune response.
Specific examples of the enzymes that are multimeric proteins can include, for example, reverse transcriptase.
Genes coding for these proteins can be modified according to the chosen host and to obtain a desired activity. For example, the genes coding for these proteins may be modified so that the proteins include addition, deletion, substitution, or the like of one or several amino acid residues. The above descriptions concerning variants of the metallopeptidases and the genes coding for them can also be applied mutatis mutandis to the multimeric protein to be produced by secretory production by the method of the present invention and the gene coding for it. Further, in the genes coding for these proteins, arbitrary codons may be replaced with equivalent codons. For example, in the genes coding for these proteins, codons may be optimized as required according to codon frequencies observed in the host.
The N-terminal region of the multimeric protein eventually obtained by the method of the present invention may be the same as that of the natural protein, or may not be the same as that of the natural protein. For example, the N-terminal region of the eventually obtained multimeric protein may be that of the natural protein including addition or deletion of one or several amino acid residues. Although the number of the “one or several” amino acid residues may differ depending on the full length or structure of the objective multimeric protein, specifically, it can be 1 to 20, 1 to 10, or 1 to 5.
Furthermore, the multimeric protein to be produced by secretory production may be a protein comprising a pro-structure moiety (proprotein). When the multimeric protein to be produced by secretory production is a proprotein, the multimeric protein to be eventually obtained may be the proprotein or may not be the proprotein. That is, the proprotein may be processed into the mature protein by cleavage of the pro-structure moiety. The cleavage can be attained with, for example, a protease. When a protease is used, generally, the proprotein is preferably cleaved at a position substantially the same as that of the natural protein, or more preferably at exactly the same position as that of the natural protein so that the same mature protein as the natural mature protein is obtained, in view of the activity of the eventually obtained protein. Therefore, generally, a specific protease that cleaves the proprotein at such a position that the same protein as the naturally occurring mature protein is generated is most preferred. However, the N-terminal region of the multimeric protein to be eventually obtained may not be the same as that of the natural protein as described above. For example, depending on type, purpose of use etc. of the multimeric protein to be produced, a protein having an N-terminus longer or shorter by one to several amino acid residues compared with the natural protein may have more appropriate activity. Proteases that can be used in the present invention can include, for example, commercially available proteases such as Dispase (produced by Boehringer Mannheim) as well as those obtainable from culture broth of a microorganism such as culture broth of actinomycetes. Such proteases may be used in an un-purified state, or may be used after purification to an appropriate purity as required.
The method for introducing the genetic construct into the coryneform bacterium is not particularly limited. In the bacterium of the present invention, the genetic construct may be present on a vector that autonomously replicates out of the chromosome such as a plasmid, or may be incorporated into the chromosome. In addition, as described above, for constructing the bacterium of the present invention, modifications such as the introduction of the genetic construct, impartation or enhancement of the ability to produce a protein by secretory production, increase of the expression of a gene coding for a metallopeptidase, reduction of the activity of a penicillin-binding protein, and reduction of the activity of a cell surface layer protein can be performed in an arbitrary order.
The genetic construct can be introduced into a host by using, for example, a vector including the genetic construct. The vector is not particularly limited so long as a vector autonomously replicable in a coryneform bacterium is chosen, and may be, for example, a vector derived from a bacterial plasmid, a vector derived from a yeast plasmid, a vector derived from a bacteriophage, cosmid, phagemid, or the like. As the vector, for example, a plasmid derived from a coryneform bacterium is preferred. Specific examples of vector autonomously replicable in coryneform bacteria include pHM1519 (Agric. Biol. Chem., 48, 2901-2903 (1984)); pAM330 (Agric. Biol. Chem., 48, 2901-2903 (1984)); plasmids obtained by improving these and having a drug resistance gene; plasmid pCRY30 described in Japanese Patent Laid-open (Kokai) No. 3-210184; plasmids pCRY21, pCRY2KE, pCRY2KX, pCRY31, pCRY3KE, and pCRY3KX described in Japanese Patent Laid-open (Kokai) No. 2-72876 and U.S. Pat. No. 5,185,262; plasmids pCRY2 and pCRY3 described in Japanese Patent Laid-open (Kokai) No. 1-191686; pAJ655, pAJ611, and pAJ1844 described in Japanese Patent Laid-open (Kokai) No. 58-192900; pCG1 described in Japanese Patent Laid-open (Kokai) No. 57-134500; pCG2 described in Japanese Patent Laid-open (Kokai) No. 58-35197; pCG4 and pCG11 described in Japanese Patent Laid-open (Kokai) No. 57-183799; pVK7 described in Japanese Patent Laid-open (Kokai) No. 10-215883; pVC7 described in Japanese Patent Laid-open (Kokai) No. 9-070291; and so forth.
Further, an artificial transposon and so forth can also be used. When a transposon is used, a multimeric protein gene is introduced into a chromosome by homologous recombination or translocation ability of the transposon itself. Other examples of the introduction method utilizing homologous recombination include, for example, the methods utilizing a linear DNA, a plasmid having a temperature sensitive replication origin, a plasmid capable of conjugative transfer, a suicide vector not having a replication origin that functions in a host, and so forth. In addition, when a multimeric protein gene is introduced into a chromosome, so long as the genetic construct is present on the chromosome, either one or both of the promoter sequence and the nucleic acid sequence coding for a signal peptide present in the genetic construct may be native to the host chromosome. Specifically, for example, by using a promoter sequence native to the host chromosome and a nucleic acid sequence coding for a signal peptide native to the host chromosome and ligated downstream from the promoter sequence as they are, and replacing only the gene ligated downstream from the nucleic acid sequence coding for the signal peptide with a gene of an objective multimeric protein, the genetic construct used for the present invention can be present on the chromosome, and the bacterium of the present invention can be thereby constructed.
Furthermore, when two or more kinds of subunits are expressed, it is sufficient that the genetic constructs for secretory expression of the subunits are harbored by the bacterium of the present invention so that secretory expression of the objective multimeric protein can be attained. Specifically, for example, all the genetic constructs for secretory expression of the subunits may be carried by a single expression vector, or carried by the chromosome. Alternatively, the genetic constructs for secretory expression of the subunits may be separately carried by two or more expression vectors, or may be separately carried by one or more expression vectors and the chromosome. The “case where two or more kinds of subunits are expressed” refers to, for example, a case where two or more kinds of multimeric proteins are produced by secretory production, or a case where a hetero-multimeric protein is produced by secretory production.
The method for introducing the genetic construct used for the present invention into the coryneform bacterium is not particularly limited, and a generally used method, for example, the protoplast method (Gene, 39, 281-286 (1985)), the electroporation method (Bio/Technology, 7, 1067-1070 (1989)), and so forth can be used.
<2> Method for Producing Multimeric Protein of the Present Invention
The present invention provides a method for producing a multimeric protein by culturing the bacterium of the present invention, and collecting the multimeric protein produced by secretory production (henceforth referred to as the “method of the present invention” or “method for producing a multimeric protein of the present invention”). That is, by culturing the bacterium of the present invention obtained as described above to express a multimeric protein, a large amount of the multimeric protein secreted out of the cells is obtained.
The bacterium of the present invention can be cultured according to a usually used method and conditions. For example, the bacterium of the present invention can be cultured in a usual medium containing a carbon source, a nitrogen source, and inorganic ions. In order to obtain still higher proliferation, organic micronutrients such as vitamins and amino acids can also be added as required.
As the carbon source, carbohydrates such as glucose and sucrose, organic acids such as acetic acid, alcohols, and others can be used. As the nitrogen source, ammonia gas, aqueous ammonia, ammonium salts, and others can be used. As the inorganic ions, calcium ions, magnesium ions, phosphate ions, potassium ions, iron ions, and so forth are appropriately used as required. The culture is performed within appropriate ranges of pH 5.0 to 8.5 and 15 to 37° C. under aerobic conditions for 1 to 7 days. Further, the culture conditions for L-amino acid production by coryneform bacteria and other conditions described for the methods for producing a protein using a signal peptide of the Sec type or the Tat type can be used (refer to WO01/23591 and WO2005/103278). Further, when an inducible promoter is used for expression of the multimeric protein, culture may also be performed with adding a promoter-inducing agent to the medium. By culturing the bacterium of the present invention under such conditions, a large amount of the objective protein is produced in cells and efficiently secreted out of the cells. In addition, according to the method of the present invention, the produced multimeric protein is secreted out of the cells, and therefore a protein that is generally lethal if it is accumulated in a large amount in cells of microorganisms can also be continuously produced without lethal effect.
The protein secreted in the medium according to the method of the present invention can be separated and purified from the medium after the culture by a method well known to those skilled in the art. For example, after the cells are removed by centrifugation or the like, the protein can be separated and purified by a known appropriate method such as salting out, ethanol precipitation, ultrafiltration, gel filtration chromatography, ion exchange column chromatography, affinity chromatography, medium or high pressure liquid chromatography, reverse phase chromatography, and hydrophobic chromatography, or a combination of these. Further, in a certain case, culture or culture supernatant may be used as it is. The protein secreted in the cell surface layer according to the method of the present invention can also be separated and purified in the same manner as that for the case where the protein is secreted in the medium, after solubilizing it by a method well known to those skilled in the art such as elevation of salt concentration and use of a surfactant. Further, in a certain case, the protein secreted in the cell surface layer may be used as, for example, an immobilized enzyme, without solubilizing it.
Secretory production of the objective multimeric protein can be confirmed by performing SDS-PAGE for the culture supernatant and/or a fraction containing the cell surface layer as a sample, and confirming the molecular weights of the separated protein bands. Secretory production of the objective multimeric protein can also be confirmed by performing Western blotting using antibodies for the culture supernatant and/or a fraction containing the cell surface layer as a sample (Molecular Cloning, Cold spring Harbor Laboratory Press, Cold Spring Harbor (USA), 2001). Secretory production of the objective multimeric protein can also be confirmed by determining the N-terminal amino acid sequences of the constituents of the obtained objective multimeric protein using a protein sequencer. Further, secretory production of the objective multimeric protein can also be confirmed by determining mass of the constituents of the obtained objective multimeric protein using a mass spectrometer. Furthermore, when the objective multimeric protein is an enzyme or a protein having a certain measurable physiological activity, secretory production of the objective multimeric protein can be confirmed by measuring enzymatic activity or the physiological activity of the objective multimeric protein in the culture supernatant and/or a fraction containing the cell surface layer as a sample.
EXAMPLES
The present invention will be further specifically explained with reference to the following non-limiting examples.
Reference Example 1
Construction of Corynebacterium glutamicum Deficient in Penicillin-Binding Protein PBP1a
(1) Construction of Vector pBSΔCgl0278 for Deleting Cgl0278 Gene Coding for PBP1a
The genome sequence of C. glutamicum ATCC 13032 and the nucleotide sequence of the Cgl0278 gene coding for the penicillin-binding protein PBP1a thereof have already been determined (Genbank Accession No. BA000036, NCBI gene entry NCgl0274). With reference to this sequence, the primers shown in SEQ ID NOS: 26, 27, 28, and 29 were synthesized. By PCR using the chromosomal DNA of the C. glutamicum ATCC 13869 strain prepared in a conventional manner (method of Saito and Miura [Biochim. Biophys. Acta, 72, 619 (1963)]) as the template, and the primers of SEQ ID NOS: 26 and 27, and the primers of SEQ ID NOS: 28 and 29, about 1 kbp of 5′ side upstream region and about 1 kbp of 3′ side downstream region of Cgl0278 coding for PBP1a were amplified, respectively. Then, by PCR using both the amplified DNA fragments as the template and DNAs shown as SEQ ID NOS: 26 and 29 as the primers, a DNA fragment of about 2 kbp consisting of both the fragments fused together was obtained. In the primers of SEQ ID NOS: 26 and 29, recognition sequences for the restriction enzymes BamHI and XbaI were designed, respectively. For PCR, Pyrobest DNA Polymerase (produced by Takara Bio) was used, and the reaction conditions were according to the protocol recommended by the manufacturer. This DNA fragment was treated with the restriction enzymes BamHI and XbaI, and inserted into pBS4 described in WO2005/113744 at the BamHI-XbaI site to obtain a vector pBSΔCgl0278 for deleting the Cgl0278 gene. For the ligation reaction, DNA Ligation Kit Ver. 2.1 (produced by Takara Bio) was used, and the reaction conditions were according to the protocol recommended by the manufacturer.
(3) Construction of PBP1a-Deficient Strain
Then, the C. glutamicum YDK010 strain described in WO2004/029254 was transformed with the constructed pBSΔCgl0278. The C. glutamicum YDK010 strain is a cell surface layer protein PS2-deficient strain of C. glutamicum AJ12036 (FERM BP-734) (WO2004/029254). Strains were selected from the obtained transformants according to the methods described in WO2005/113744 and WO2006/057450 to obtain YDK010ΔPBP1a strain deficient in the Cgl0278 gene.
Example 1
Cloning of Metalloendopeptidase-Like Gene Cgl0858 Homologue Derived from C. Glutamicum ATCC 13869
The genomic sequence of C. glutamicum ATCC 13032 and the nucleotide sequence of the Cgl0858 gene coding for the metalloendopeptidase-like protein thereof have already been determined (Genbank Accession No. BA000036, NCBI gene entry NCgl0824). With reference to this sequence, the primers shown in SEQ ID NOS: 01 and 02 were synthesized. By PCR using the chromosomal DNA of the C. glutamicum ATCC 13869 strain prepared in a conventional manner (method of Saito and Miura [Biochim. Biophys. Acta, 72, 619 (1963)]) as the template, and the primers of SEQ ID NOS: 01 and 02, a region of about 1.1 kbp which includes a Cgl0858 homologue coding for a metalloendopeptidase-like protein was amplified. For PCR, Pyrobest DNA Polymerase (produced by Takara Bio) was used, and the reaction conditions were according to the protocol recommended by the manufacturer.
Then, the amplified DNA fragment of about 1.1 kbp was collected by agarose gel electrophoresis using Wizard (registered trademark) SV Gel and PCR Clean-Up System (Promega). The collected fragment was introduced into pVC7 (shuttle vector replicable in both Escherichia coli and coryneform bacteria described in Japanese Patent Laid-open (Kokai) No. 9-070291) at the SmaI site, and then the result was introduced into competent cells of Escherichia coli JM109 (Takara Bio) to obtain a strain harboring a plasmid in which the Cgl0858 homologue was cloned. The plasmid was collected from this strain, and designated as pVMEP1. The nucleotide sequencing of the fragment cloned in pVMEP1 was performed by using BigDye (registered trademark) Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) and 3130 Genetic Analyzer (Applied Biosystems). As a result of the nucleotide sequencing, it was revealed that the nucleotide sequence of the cloned Cgl0858 homologue of C. glutamicum ATCC 13869 partially differed from the nucleotide sequence of Cgl0858 of C. glutamicum ATCC 13032. The nucleotide sequence of the Cgl0858 homologue derived from C. glutamicum ATCC 13869 is shown in SEQ ID NO: 3, and the total encoded amino acid sequence is shown in SEQ ID NO: 4. FIG. 1 shows an alignment of the amino acid sequences of the protein encoded by Cgl0858 of C. glutamicum ATCC 13032 and the protein encoded by the Cgl0858 homologue of C. glutamicum ATCC 13869. The homology for the full length of the amino acid sequences between the protein encoded by Cgl0858 of C. glutamicum ATCC 13032 and the protein encoded by the Cgl0858 homologue of C. glutamicum ATCC 13869 was 97.9%. The preparation of the alignment and calculation of the homology were performed by using Genetyx_Version9 (Genetyx).
Example 2
Secretory Expression of Fab(H&L) Fragments of Antibody Trastuzumab Using C. Glutamicum with Enhanced Expression of Cgl0858 Homologue
(1) Construction of Plasmids for Secretory Expression of H Chain Region of Fab Fragments of Antibody Trastuzumab
The gene sequence for the variable region of the H chain of the breast carcinoma cell-specific antibody trastuzumab has already been determined (Genbank Accession No. AY513484). With reference to this sequence and the sequence for the non-variable region of the H chain of a general antibody and in consideration of the codon frequencies in C. glutamicum, DNAs shown in SEQ ID NOS: 30 to 63 were synthesized. By PCR using these DNAs as the template and the separately synthesized primer DNAs shown in SEQ ID NOS: 64 and 65, the region for the full length H chain of trastuzumab was amplified to obtain a DNA fragment of about 1.4 kbp shown in the ID NO: 66. The amino acid sequence of the H chain of the antibody trastuzumab encoded by DNA shown in SEQ ID NO: 66 is shown in SEQ ID NO: 104.
Then, by PCR using pPKSPTG1 described in WO01/23591 (pPKSPTG1 is a vector for secretory expression of protransglutaminase (transglutaminase having a pro-structure moiety), and includes the promoter derived from the PS2 gene of the C. glutamicum ATCC 13869 strain, a DNA coding for the signal peptide derived from SlpA of the C. ammoniagenes ATCC 6872 strain and expressibly ligated downstream from the promoter, and a protransglutaminase gene derived from S. mobaraense ligated so that the protransglutaminase is expressed as a fusion protein with the signal peptide) as the template and the primers shown in SEQ ID NOS: 67 and 68, a region that includes the aforementioned promoter region and the aforementioned signal peptide region was amplified to obtain a DNA fragment of about 0.7 kbp.
Then, by PCR using both the amplified DNA fragments (i.e. the fragment that includes the region for the full length H chain of trastuzumab and the fragment that includes the promoter region and the signal peptide region) as the template and DNAs shown in SEQ ID NO: 65 and 67 as the primers, a DNA fragment of about 2.0 kbp consisting of both the DNA fragments fused together was obtained.
Then, by PCR using this fusion DNA fragment as the template, and DNAs shown in SEQ ID NOS: 67 and 69, SEQ ID NOS: 67 and 70, SEQ ID NOS: 67 and 71, SEQ ID NOS: 67 and 72, SEQ ID NOS: 67 and 73, SEQ ID NOS: 67 and 74, and SEQ ID NOS: 67 and 75 as the primers, DNA fragments of about 1.4 kbp each were obtained. In the primer of SEQ ID NO: 67, the recognition sequence for the restriction enzyme KpnI was designed. In the primers of SEQ ID NOS: 69, 70, 71, 72, 73, 74, and 75, a stop codon and the recognition sequence for the restriction enzyme KpnI were designed. For PCR, Pyrobest DNA Polymerase (produced by Takara Bio) was used, and the reaction conditions were according to the protocol recommended by the manufacturer. These DNA fragments were treated with the restriction enzyme KpnI, and inserted into pPK4 described in Japanese Patent Laid-open (Kokai) No. 9-322774 at the KpnI site to obtain plasmids for secretory expression of the H chain region of the Fab moiety of trastuzumab, pPKStrast-FabH(1-223C), pPKStrast-FabH(1-228T), pPKStrast-FabH(1-229C), pPKStrast-FabH(1-230P), pPKStrast-FabH(1-231P), pPKStrast-FabH(1-232C), and pPKStrast-FabH(1-233P). Specifically, with these plasmids, the amino acid sequence of the H chain of trastuzumab from the first amino acid residue to 223rd, 228th, 229th, 230th, 231st, 232nd or 233rd amino acid residue can be expressed according to the numbers included in the plasmid names, respectively. As a result of the nucleotide sequencing of the inserted fragments, it was confirmed that the expected genes were constructed. The nucleotide sequencing was performed by using BigDye (registered trademark) Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) and 3130 Genetic Analyzer (Applied Biosystems).
(2) Construction of Plasmid for Secretory Expression of L Chain Region of Fab Fragment of Antibody Trastuzumab
The gene sequence for the variable region of the L chain of the breast carcinoma cell-specific antibody trastuzumab has already determined (Genbank Accession No. AY513485). With reference to this sequence and the sequence of the non-variable region of the L chain of a general antibody and in consideration of the codon frequencies in C. glutamicum, DNAs shown in SEQ ID NOS: 76 to 91 were synthesized. By PCR using these DNAs as the template, and the separately synthesized DNAs shown in SEQ ID NOS: 92 and 93 as the primers, the region for the full length L chain of trastuzumab was amplified to obtain a DNA fragment of about 0.6 kbp shown in the SEQ ID NO: 94. The amino acid sequence of the L chain of the antibody trastuzumab encoded by DNA shown in SEQ ID NO: 94 is shown in SEQ ID NO: 105. Then, by PCR using pPKSPTG1 described in WO01/23591 (including the promoter region derived from the C. glutamicum ATCC 13869 strain and the region for the signal peptide derived from the C. ammoniagenes ATCC 6872 strain) as the template, and the primers shown in SEQ ID NO: 95 and 96, a region that includes the aforementioned promoter region and the aforementioned region for signal peptide was amplified to obtain a DNA fragment of about 0.7 kbp. Then, by PCR using both the amplified DNA fragments (i.e. the fragment that includes the region for the L chain of trastuzumab and the fragment including the promoter region and the region for signal peptide) as the template and DNAs shown in SEQ ID NOS: 95 and 97 as the primers, a DNA fragment of about 1.3 kbp consisting of both the DNA fragments fused together was obtained. In the primers of SEQ ID NOS: 95 and 97, the recognition sequence for the restriction enzyme BamHI was designed. For PCR, Pyrobest DNA Polymerase (produced by Takara Bio) was used, and the reaction conditions were according to the protocol recommended by the manufacturer. This fusion DNA fragment was treated with the restriction enzyme BamHI, and then inserted into pPK4 described in Japanese Patent Laid-open (Kokai) No. 9-322774 at the BamHI site to obtain a plasmid for secretory expression of the L chain region of the Fab moiety of trastuzumab, pPKStrast-FabL. As a result of the nucleotide sequencing of the inserted fragment, it was confirmed that the expected gene was constructed. The nucleotide sequencing was performed by using BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) and 3130 Genetic Analyzer (Applied Biosystems).
(3) Construction of Plasmids for Secretory Expression of Fab(H&L) Fragment of Antibody Trastuzumab
DNA fragments of about 1.4 kb obtained by digesting the expression plasmids for the H chain region of the Fab fragment of antibody trastuzumab constructed in Example 2(1) with the restriction enzyme KpnI each were inserted into the expression plasmid for the L chain region of the Fab fragment of antibody trastuzumab constructed in Example 2(2), pPKStrast-FabL, at the KpnI site to obtain plasmids for coexpression of the H chain region and the L chain region of the Fab fragment of trastuzumab, pPKStrast-FabH(1-223C)+L, pPKStrast-FabH(1-228T)+L, pPKStrast-FabH(1-229C)+L, pPKStrast-FabH(1-230P)+L, pPKStrast-FabH(1-231P)+L, pPKStrast-FabH(1-232C)+L, and pPKStrast-FabH(1-233P)+L.
(4) Secretory Expression of Fab(H&L) Fragment of Antibody Trastuzumab Using C. Glutamicum with Enhanced Expression of Cgl0858 Homologue
By using the expression plasmid pVMEP1 for Cgl0858 homologue constructed in Example 1, as well as the plasmids for secretory expression of Fab(H&L) fragment of the antibody trastuzumab constructed in Example 2(3), pPKStrast-FabH(1-223C)+L, pPKStrast-FabH(1-228T)+L, pPKStrast-FabH(1-229C)+L, pPKStrast-FabH(1-230P)+L, pPKStrast-FabH(1-231P)+L, pPKStrast-FabH(1-232C)+L, and pPKStrast-FabH(1-233P)+L, the C. glutamicum YDK010 strain described in WO2004/029254 was transformed. Each of the obtained transformants was cultured in the MM liquid medium (120 g of glucose, 3 g of magnesium sulfate heptahydrate, 30 g of ammonium sulfate, 1.5 g of potassium dihydrogenphosphate, 0.03 g of iron sulfate heptahydrate, 0.03 g of manganese sulfate pentahydrate, 450 μg of thiamine hydrochloride, 450 μg of biotin, 0.15 g of DL-methionine, and 50 g of calcium carbonate made into a volume of 1 L with water, and adjusted to pH 7.0) containing 5 mg/l of chloramphenicol and 25 mg/l of kanamycin at 30° C. for 96 hours. After completion of the culture, the culture supernatant obtained by centrifuging each culture broth was subjected to non-reduced SDS-PAGE, and then staining was performed with SYPRO Orange (Invitrogen) to perform comparison of the secretion amounts of the Fab(H&L) fragments of the antibody trastuzumab. As a result, it was found that the secretion amount of the heterodimer Fab(H&L) fragment of the antibody trastuzumab was significantly increased for all the strains introduced with pVMEP1, compared with that observed for the control strains introduced with pVC7, when using any of the plasmids for secretory expression of the Fab(H&L) fragments of the antibody trastuzumab (FIG. 2).
(5) Secretory Expression of Antibody Trastuzumab F(Ab′)2 Using C. Glutamicum with Enhanced Expression of Cgl0858 Homologue
Each of the culture supernatants obtained in Example 2(4) was subjected to non-reduced SDS-PAGE, and then the proteins were transferred onto a PVDF membrane by using iBlot (registered trademark) Gel Transfer Stacks PVDF, Mini (Invitrogen) and iBlot (registered trademark) Gel Transfer System (Invitrogen). Western blotting was performed for this PVDF membrane by using alkaline phosphatase-labeled anti-human IgG[H&L] antibody (ROCKLAND) and Alkaline Phosphatase Conjugate Substrate Kit (Bio-Rad) to detect F(ab′)2 of the antibody trastuzumab. As a result, a protein band of the molecular weight of F(ab′)2 fragment of the antibody trastuzumab was detected for the culture supernatant of the transformant harboring each of pPKStrast-FabH(1-229C)+L, pPKStrast-FabH(1-230P)+L, pPKStrast-FabH(1-231P)+L, pPKStrast-FabH(1-232C)+L, and pPKStrast-FabH(1-233P)+L, which are plasmids for coexpression of the gene for the H chain region including a Cys residue which forms a disulfide bond linking the H chains, and the gene for the L chain. Further, the protein band of the molecular weight of the hetero-tetramer F(ab′)2 was significantly enhanced for all the strains introduced with pVMEP1, compared with that observed for the control strains introduced with pVC7, when using any of these plasmids for secretory expression (FIG. 3).
(6) Secretory Expression of Fab(H&L) Fragment of Antibody Trastuzumab Using C. Glutamicum with Enhanced Expression of Cgl0858 Homologue and Deficient in PBP1a
By using the expression plasmid pVMEP1 for Cgl0858 homologue constructed in Example 1, as well as the plasmids for secretory expression of the Fab(H&L) fragment of antibody trastuzumab constructed in Example 2(3), pPKStrast-FabH(1-223C)+L, pPKStrast-FabH(1-228T)+L, pPKStrast-FabH(1-229C)+L, pPKStrast-FabH(1-230P)+L, pPKStrast-FabH(1-231P)+L, pPKStrast-FabH(1-232C)+L, and pPKStrast-FabH(1-233P)+L, the C. glutamicum YDK010ΔPBP1a strain constructed in Reference Example 1 was transformed. Each of the obtained transformants was cultured in the MM liquid medium (120 g of glucose, 3 g of magnesium sulfate heptahydrate, 30 g of ammonium sulfate, 1.5 g of potassium dihydrogenphosphate, 0.03 g of iron sulfate heptahydrate, 0.03 g of manganese sulfate pentahydrate, 450 μg of thiamine hydrochloride, 450 μg of biotin, 0.15 g of DL-methionine, and 50 g of calcium carbonate made into a volume of 1 L with water, and adjusted to pH 7.0) containing 5 mg/l of chloramphenicol and 25 mg/l of kanamycin at 30° C. for 96 hours. After completion of the culture, each culture broth was centrifuged to obtain a culture supernatant.
Then, the culture supernatant samples obtained in Example 2(4) and Example 2(6) were subjected to non-reduced SDS-PAGE using the same gel, and then staining was performed with CBB-R250 (Bio-Rad) to perform comparison of the secretory production amounts of the Fab(H&L) fragment of the antibody trastuzumab. As a result, it was confirmed that the secretory production amount of the hetero-dimer Fab(H&L) fragment of the antibody trastuzumab further increased synergistically in the strains in which the enhanced expression of the Cgl0858 homologue was performed in combination with the deletion of PBP1a, compared with the strains in which the enhancement of the expression of the Cgl0858 homologue was performed solely (FIG. 4). Specifically, for the strains in which the only enhancement was the expression of the Cgl0858 homologue, SYPRO Orange showing high detection sensitivity was preferred for the detection of the bands, but for the strains in which the expression of the Cgl0858 homologue was enhanced in combination with the deletion of PBP1a, the expression amounts were at such a level that the bands could be easily detected by staining with CBB-R250, of which detection sensitivity is low.
Example 3
Secretory Expression of VEGF-A Using Corynebacterium glutamicum with Enhanced Expression of Cgl0858 Homologue
(1) Construction of Plasmid for Secretory Expression of VEGF-A
The sequence of the gene for the vascular endothelial growth factor A (VEGF-A) has already been determined (Genbank Accession No. NP_001165097). With reference to this sequence and in consideration of the codon frequencies in C. glutamicum, DNAs shown in SEQ ID NOS: 05 to 18 were synthesized. By PCR using these DNAs as the template and the separately synthesized DNAs shown in SEQ ID NOS: 19 and 20 as the primers, the full length of the VEGF-A gene sequence was amplified to obtain a DNA fragment of about 0.6 kbp shown in the ID NO: 21. Then, by PCR using this DNA fragment as the template and DNAs shown in SEQ ID NOS: 22 and 23 as the primers, the gene sequence for mature VEGF-A was amplified to obtain a DNA fragment of about 0.5 kbp. The amino acid sequence of the full length VEGF-A encoded by DNA shown in SEQ ID NO: 21 is shown in SEQ ID NO: 106, and the amino acid sequence of the mature VEGF-A is shown in SEQ ID NO: 107. Then, by PCR using pPKSPTG1 described in WO01/23591 (including the promoter region of CspB (PS2) derived from the C. glutamicum ATCC 13869 strain, and DNA coding for the signal peptide of CspA (SlpA) derived from the C. ammoniagenes ATCC 6872 strain) as the template and the primers shown in SEQ ID NOS: 24 and 25, the promoter region and the region for signal peptide were amplified to obtain a DNA fragment of about 0.7 kbp. Then, by PCR using both the amplified DNA fragments (i.e. the fragment of the mature VEGF gene sequence and the fragment of the promoter region and the region for signal peptide) as the template and DNAs shown in SEQ ID NO: 24 and 23 as the primers, a DNA fragment of about 1.2 kbp consisting of both the DNA fragments fused together was obtained. In the primers of SEQ ID NOS: 24 and 23, the recognition sequences for the restriction enzymes KpnI and XbaI were designed, respectively. For PCR, PrimeSTAR (registered trademark) HS DNA Polymerase (Takara Bio) was used, and the reaction conditions were according to the protocol recommended by the manufacturer. This fused DNA fragment was treated with the restriction enzymes KpnI and XbaI, and then inserted into pPK4 described in Japanese Patent Laid-open (Kokai) No. 9-322774 at the KpnI-XbaI site to obtain a plasmid pPKSVEGF for expression of VEGF-A. As a result of the nucleotide sequencing of the inserted fragment, it was confirmed that the expected gene was constructed. The nucleotide sequencing was performed by using BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) and 3130 Genetic Analyzer (Applied Biosystems).
(2) Secretory Expression of VEGF-A Using C. Glutamicum with Enhanced Expression of Cgl0858 Homologue
By using the expression plasmid pVMEP1 for Cgl0858 homologue constructed in Example 1(1) and the plasmid for secretory expression of VEGF-A, pPKSVEGF, constructed in Example 3(1), the C. glutamicum YDK010 strain described in WO2004/029254 was transformed. The obtained transformant was cultured in the MM liquid medium (120 g of glucose, 3 g of magnesium sulfate heptahydrate, 30 g of ammonium sulfate, 1.5 g of potassium dihydrogenphosphate, 0.03 g of iron sulfate heptahydrate, 0.03 g of manganese sulfate pentahydrate, 450 μg of thiamine hydrochloride, 450 μg of biotin, 0.15 g of DL-methionine, and 50 g of calcium carbonate made into a volume of 1 L with water, and adjusted to pH 7.0) containing 5 mg/l of chloramphenicol and 25 mg/l of kanamycin at 30° C. for 96 hours. After completion of the culture, the culture supernatant obtained by centrifuging each culture broth was subjected to non-reduced SDS-PAGE, and then staining was performed with SYPRO Orange (Invitrogen) to perform comparison of the secretion amounts of VEGF-A. As a result, the intensity of the protein band of the same molecular weight as that of the objective homodimer VEGF-A was observed for the strain introduced with pVMEP1, compared with that observed for the control strain introduced with pVC7 (FIG. 5). When the N-terminal sequence of this protein band was determined by using a protein sequencer PPSQ-21A (Shimadzu), it agreed with the N-terminal sequence of VEGF-A, and therefore secretory expression of the homodimer VEGF-A in the culture supernatant could be confirmed. As described above, the secretory production amount of the VEGF-A homodimer could be increased by increasing the expression of the Cgl0858 homologue.
Example 4
Secretory Expression of Fab(H&L) Fragment of Antibody Adalimumab Using C. Glutamicum with Enhanced Expression of Cgl0858 Homologue
Construction of Plasmids for Secretory Expression of Fab(H&L) Fragments of Antibody Adalimumab
The amino acid sequence of the tumor necrosis factor α (TNF-α)-specific antibody adalimumab has already been determined (The independent administrative agency, Pharmaceuticals and Medical Devices Agency, Examination report (Feb. 14, 2008)). With reference to this sequence, the total DNA fragment shown in SEQ ID NO: 108 was synthesized, including the promoter derived from the PS2 gene of the C. glutamicum ATCC 13869 strain, a DNA coding for the signal peptide derived from SlpA of the C. stationis ATCC 6872 strain expressibly ligated downstream from the promoter, and a DNA coding for the amino acid sequence of the 1st to 230th cysteine residue of the H chain of adalimumab ligated so that the amino acid sequence is expressed as a fusion protein with the signal peptide, and further including in the downstream thereof the promoter derived from the PS2 gene of the C. glutamicum ATCC 13869 strain, a DNA coding for the signal peptide derived from SlpA of the C. stationis ATCC 6872 strain expressibly ligated downstream from the promoter, and a DNA coding for the L chain of adalimumab ligated so that the L chain is expressed as a fusion protein with the signal peptide. Similarly, the total DNA fragment shown in SEQ ID NO: 109 was synthesized, including the promoter derived from the PS2 gene of the C. glutamicum ATCC 13869 strain, a DNA coding for the signal peptide derived from SlpA of the C. stationis ATCC 6872 strain expressibly ligated downstream from the promoter, and a DNA coding for the L chain of adalimumab ligated so that the L chain is expressed as a fusion protein with the signal peptide, and further including in the downstream thereof the promoter derived from the PS2 gene of the C. glutamicum ATCC 13869 strain, a DNA coding for the signal peptide derived from SlpA of the C. stationis ATCC 6872 strain expressibly ligated downstream from the promoter, and a DNA coding for the amino acid sequence of the 1st to 230th cysteine residue of the H chain of adalimumab ligated so that the amino acid sequence is expressed as a fusion protein with the signal peptide. The synthetic DNAs of SEQ ID NOS: 108 and 109 comprise the recognition sequence for the restriction enzyme BamHI at the 5′ end and the recognition sequence for the restriction enzyme XbaI at the 3′ end. In addition, the DNAs coding for the H chain and L chain of adalimumab comprised in the synthetic DNAs were designed in consideration of the codon frequencies in C. glutamicum. The DNA sequence coding for the amino acid sequence of the 1st to 230th cysteine residue of the H chain of adalimumab the 1st to the 230th amino acid residues of the H chain of adalimumab in the synthetic DNA is shown in SEQ ID NO: 110, and the amino acid sequence is shown in SEQ ID NO: 111. Further, the DNA sequence coding for the L chain of adalimumab in the synthetic DNA is shown in SEQ ID NO: 112, and the amino acid sequence of the L chain of adalimumab is shown in SEQ ID NO: 113. The synthesized total DNA fragments of about 2.7 kbp each were digested with the restriction enzymes BamHI and XbaI, and inserted into pPK4 described in Japanese Patent Laid-open (Kokai) No. 9-322774 at the BamHI-XbaI site to obtain plasmids for coexpression of the H chain (1-230C) and the L chain of the Fab fragment of the antibody adalimumab, pPKSada-FabHL and pPKSada-FabLH. “FabHL” and “FabLH” in the plasmid names indicate the carrying orders of the genes for the H chain and the L chain of adalimumab in the expression plasmids.
(2) Secretory Expression of Fab(H&L) Fragment of Antibody Adalimumab Using C. Glutamicum with Enhanced Expression of Cgl0858 Homologue
By using the expression plasmid pVMEP1 for Cgl0858 homologue constructed in Example 1, as well as the plasmids for secretory expression of Fab(H&L) fragment of the antibody adalimumab constructed in Example 4(1), pPKSada-FabHL and pPKSada-FabLH, the YDK010ΔPBP1a strain constructed in Reference Example 1 was transformed. Each of the obtained transformants was cultured in the MM liquid medium (120 g of glucose, 3 g of magnesium sulfate heptahydrate, 30 g of ammonium sulfate, 1.5 g of potassium dihydrogenphosphate, 0.03 g of iron sulfate heptahydrate, 0.03 g of manganese sulfate pentahydrate, 450 μg of thiamine hydrochloride, 450 μg of biotin, 0.15 g of DL-methionine, and 50 g of calcium carbonate made into a volume of 1 L with water, and adjusted to pH 7.0) containing 5 mg/l of chloramphenicol and 25 mg/l of kanamycin at 30° C. for 96 hours. After completion of the culture, the culture supernatant obtained by centrifuging each culture broth was subjected to non-reduced SDS-PAGE, and then staining was performed with CBB-R250 (Bio-Rad) to perform comparison of the secretory production amounts of the Fab(H&L) fragment of the antibody adalimumab. As a result, it was found that the secretion amount of the heterodimer Fab(H&L) fragment of the antibody adalimumab was significantly increased for both the strains introduced with pVMEP1, compared with that observed for the control strains introduced with pVC7, when using any of these plasmids for secretory expression (FIG. 6). On the basis of these results, it was revealed that the secretion amount of the antibody Fab(H&L) fragment is increased by enhancing expression of the Cgl0858 homologue not only in the case of expressing the Fab(H&L) fragment of trastuzumab, but also in the case of expressing the Fab(H&L) fragment of adalimumab.
Example 5
Secretory Expression of Fab(H&L) Fragment of Antibody Trastuzumab in C. Glutamicum ATCC 13869 Strain with Enhanced Expression of Cgl0858 Homologue
By using the expression plasmid pVMEP1 for Cgl0858 homologue constructed in Example 1, and the plasmid for secretory expression of the Fab(H&L) fragment of the antibody trastuzumab constructed in Example 2(3), pPKStrast-FabH(1-229C)+L, the C. glutamicum ATCC 13869 strain, which is the wild-type strain of the YDK010 strain (the cell surface layer protein PS2 (CspB)-deficient strain of C. glutamicum AJ12036 (FERM BP-734) (WO2004/029254)), was transformed. The obtained transformant was cultured in the MM liquid medium (120 g of glucose, 3 g of magnesium sulfate heptahydrate, 30 g of ammonium sulfate, 1.5 g of potassium dihydrogenphosphate, 0.03 g of iron sulfate heptahydrate, 0.03 g of manganese sulfate pentahydrate, 450 μg of thiamine hydrochloride, 450 μg of biotin, 0.15 g of DL-methionine, and 50 g of calcium carbonate made into a volume of 1 L with water, and adjusted to pH 7.0) containing 25 mg/l of kanamycin at 30° C. for 96 hours. After completion of the culture, the culture supernatant obtained by centrifuging each culture broth was subjected to non-reduced SDS-PAGE, and then staining was performed with SYPRO Orange (Invitrogen) to perform comparison of the secretion amounts of the Fab(H&L) fragment of the antibody trastuzumab. As a result, it was found that the secretion amount of the heterodimer Fab(H&L) fragment of the antibody trastuzumab was significantly increased for the strain introduced with pVMEP1 compared with that observed for the control strain introduced with pVC7 (FIG. 7). On the basis of this result, it was found that, even when the ATCC 13869 strain, which is a wild-type strain, was used as an expression host, the secretion amount of the antibody Fab(H&L) fragment was improved by enhancing the expression of the Cgl0858 homologue.
INDUSTRIAL APPLICABILITY
According to the present invention, a coryneform bacterium that can efficiently produce a multimeric protein by secretory production can be provided. Further, by using the coryneform bacterium provided by the present invention as an expression host, a multimeric protein such as industrially useful multimeric proteins can be efficiently produced by secretory production.
While the invention has been described in detail with reference to preferred embodiments thereof, it will be apparent to one skilled in the art that various changes can be made, an equivalents employed, without departing from the scope of the invention. Each of the aforementioned documents is incorporated by reference herein in its entirety.
EXPLANATION OF SEQUENCE LISTING
SEQ ID NOS: 1 and 2: Primers
SEQ ID NO: 3: Nucleotide sequence of Cgl0858 homologue of C. glutamicum ATCC 13869
SEQ ID NO: 4: Amino acid sequence of protein encoded by Cgl0858 homologue of C. glutamicum ATCC 13869
SEQ ID NOS: 5 to 18: Nucleotide sequences of DNAs for total synthesis of VEGF-A
SEQ ID NOS: 19 and 20: Primers
SEQ ID NO: 21: Nucleotide sequence of VEGF-A gene
SEQ ID NOS: 22 to 25: Primers
SEQ ID NOS: 26 to 29: Primers
SEQ ID NOS: 30 to 63: Nucleotide sequences of DNAs for total synthesis of H chain of trastuzumab
SEQ ID NOS: 64 and 65: Primers
SEQ ID NO: 66: Nucleotide sequence of trastuzumab H chain gene
SEQ ID NOS: 67 to 75: Primers
SEQ ID NOS: 76 to 91: Nucleotide sequences of DNAs for total synthesis of trastuzumab L chain
SEQ ID NOS: 92 and 93: Primers
SEQ ID NO: 94: Nucleotide sequence of trastuzumab L chain gene
SEQ ID NOS: 95 to 97: Primers
SEQ ID NO: 98: Amino acid sequence of protein encoded by Cgl0858 of C. glutamicum ATCC 13032
SEQ ID NO: 99: Nucleotide sequence of Cgl0278 of C. glutamicum ATCC 13032
SEQ ID NO: 100: Amino acid sequence of protein encoded by Cgl0278 of C. glutamicum ATCC 13032
SEQ ID NO: 101: Amino acid sequence of signal peptide of PS1 derived from C. glutamicum 
SEQ ID NO: 102: Amino acid sequence of signal peptide of PS2 (CspB) derived from C. glutamicum 
SEQ ID NO: 103: Amino acid sequence of signal peptide of SlpA (CspA) derived from C. ammoniagenes 
SEQ ID NO: 104: Amino acid sequence of trastuzumab H chain
SEQ ID NO: 105: Amino acid sequence of trastuzumab L chain
SEQ ID NO: 106: Amino acid sequence of VEGF-A
SEQ ID NO: 107: Amino acid sequence of mature VEGF-A
SEQ ID NOS: 108 and 109: Nucleotide sequences of totally synthesized DNAs for expression of Fab(H&L) fragment of adalimumab
SEQ ID NO: 110: Nucleotide sequence of adalimumab H chain gene (1-230C coding region)
SEQ ID NO: 111: Amino acid sequence of adalimumab H chain (1-230C)
SEQ ID NO: 112: Nucleotide sequence of adalimumab L chain gene
SEQ ID NO: 113: Amino acid sequence of adalimumab L chain
SEQ ID NO: 114: Nucleotide sequence of cspB gene of C. glutamicum ATCC 13869
SEQ ID NO: 115: Amino acid sequence of protein encoded by cspB gene of C. glutamicum ATCC 13869

## Claims

1. A coryneform bacterium having an ability to produce a multimeric protein by secretory production, which is modified so that expression of a gene coding for a metallopeptidase is increased as compared with that in a non-modified strain,
wherein the metallopeptidase is a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence shown in SEQ ID NO: 4,
(B) a protein comprising the amino acid sequence shown in SEQ ID NO: 4, but which includes substitution, deletion, insertion, or addition of 1 to 10 amino acid residues, and wherein said protein has a property that if activity thereof is increased in the coryneform bacterium, the secretory production amount of the multimeric protein is increased compared with that observed for a non-modified strain; and
wherein the multimeric protein is an antibody-related molecule.

2. The coryneform bacterium according to claim 1, wherein the expression of the gene is increased by increasing copy number of the gene or by modifying an expression control sequence of the gene.

3. The coryneform bacterium according to claim 1, which is further modified so that the activity of a penicillin-binding protein is reduced as compared with that in a non-modified strain.

4. The coryneform bacterium according to claim 1, wherein the activity of a cell surface layer protein is reduced as compared with that in a non-modified strain.

5. The coryneform bacterium according to claim 1, which belongs to the genus Corynebacterium or Brevibacterium.

6. The coryneform bacterium according to claim 1, which is Corynebacterium glutamicum.

7. The coryneform bacterium according to claim 1, wherein the coryneform bacterium has a genetic construct for secretory expression of the multimeric protein, and wherein the genetic construct comprises a promoter sequence that functions in the coryneform bacterium, a nucleic acid sequence coding for a signal peptide that functions in the coryneform bacterium, which is ligated downstream from the promoter sequence, and a nucleic acid sequence coding for the multimeric protein, which is ligated downstream from the nucleic acid sequence coding for the signal peptide.

8. The coryneform bacterium according to claim 1, wherein the antibody-related molecule is selected from the group consisting of Fab, F(ab′)2, Fc fusion protein, and combinations thereof.

9. A method for producing a multimeric protein comprising:
A) culturing the coryneform bacterium according to claim 1; and
B) collecting the protein produced by secretory production.