Patent Application
20130084621
The present application claims priority from Japanese Patent Application No. 2010-81774 filed on Mar. 31, 2010, the entire disclosures of which are incorporated herein by reference.
The present invention relates to a technique that contributes to improving a function of a microorganism with the use of genetic engineering techniques. More specifically, the present invention relates to a plasmid vector derived from bacteria of the genus Kocuria.
Many bacteria of the family Micrococcaceae have been recognized to be effective in food industry, pharmaceutical industry, chemical industry, environmental cleanup, and other fields. For example, in producing dairy products such as cheese or in other fields, propionibacteria are used. As L-glutamine-producing microorganisms, bacteria of the genus Brevibacteria are known.
However, wild-type strains of the above bacteria have various problems such as the lower ability to generate products and the difficulty to culture the bacteria. To solve such problems, attempts have been made to obtain variant strains that have the improved ability to generate products and adjust to the environment, among other things, through genetic manipulation of the bacteria. Among those used for the manipulation are vectors such as plasmids, which are autonomously replicable in the bacteria. For example, one of the vectors available to propionibacteria is disclosed in Patent Publication 1, JP 2002-112790 A (the disclosures of Patent Publication 1 are incorporated herein by reference).
Among the bacteria belonging to the family Micrococcaceae, bacteria of the genus Kocuria are known. Bacteria of the genus Kocuria show high levels of organic solvent tolerance, heavy metal resistance, and proliferating ability, and are expected to be used in various fields, such as production of fuel and pharmaceutical chemical products, and environmental cleanup.
However, the techniques to retain a foreign gene in a stable manner in bacteria of the genus Kocuria remain unknown. There is no case of successfully modifying microorganisms with the use of the above bacteria by means of genetic engineering techniques. As a result, it is not possible to add new biological functions, or to optimize the original functionality. Therefore, few bacteria of the genus Kocuria are used in the industrial world.
In the present invention, the problem to be solved by the invention is therefore to provide a technique to modify bacteria of the genus Kocuria in a genetic engineering manner in order to make possible effectively industrial use of bacteria of the genus Kocuria.
As a result of intensive studies to solve the above problem, the present inventors have succeeded in isolating, from bottom sediment at a depth of about 2,000 meters in Sagami Bay, Kocuria sp. strain MBE131 (FERN P-21885; also referred to as strain MBE131, hereinafter), which is a new bacterium of the genus Kocuria having a circular plasmid that is relatively small in size and easy to handle.
The present inventors named a plasmid acquired from the strain MBE 131 pKR100, and combined pKR100 with a foreign gene and a plasmid that is autonomously replicable in Escherichia coli to constitute a shuttle vector for the strain MBE 131 and Escherichia coli. After the shuttle vector was introduced into the strain MBE 131 and Escherichia coli, the foreign gene was expressed in each of them.
As a result of further studies on plasmid pKR100, the present inventors discovered a region (replication region) that is predicted to play a role in DNA replication in plasmid pKR100. Then, the present inventors prepared recombinant plasmids that have a foreign gene inserted into a different region from the replication region of plasmid pKR100, and introduced the recombinant plasmids into Kocuria rhizophila DC2201 strain (NBRC103217), which is a bacterium of the genus Kocuria different from the strain MBE 131. As a result, the recombinant plasmids expressed the foreign gene and were autonomously replicable even in Kocuria rhizophila DC2201 strain.
The present invention has been successfully accomplished based on the above findings. According to the present invention, there is provided a circular plasmid that is autonomously replicable in bacteria, having a replication region comprising a base sequence of a DNA-binding protein-like protein gene; a base sequence of a replicase-like protein gene; and a base sequence disclosed in Sequence Number 45, or a base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence.
According to another aspect of the present invention, there is provided a circular plasmid that is autonomously replicable in bacteria, having a replication region comprising a base sequence of a DNA-binding protein-like protein gene; a base sequence of a replicase-like protein gene; and at least one sequence selected from a group consisting of a DNA-binding protein binding sequence and a repeat motif sequence.
According to another aspect of the present invention, there is provided a circular plasmid that is autonomously replicable in bacteria, having a replication region comprising a base sequence of a DNA-binding protein-like protein gene; a base sequence of a replicase-like protein gene; and a base sequence comprising at least one sequence selected from a group consisting of a DNA-binding protein binding sequence and a repeat motif sequence, an oxidant sensitive sequence, and an inverted repeat sequence.
Preferably, the plasmid of the present invention comprises, in the replication region, one or more DNA-binding protein binding sequences and two or more repeat motif sequences for at least one sequence selected from the group consisting of a DNA-binding protein binding sequence and a repeat motif sequence.
Preferably, the DNA-binding protein binding sequence is selected from a group consisting of CACCGGTG, ACCGGTG, CCGGTG, ACCGGT, CACCGGT, CACCGGT, CACCGG, GTGCGCAC, GGCCGGCC, TCGGAGCTCCGA (Sequence Number 46), TCCCGGGA, TGCCGGCA, TGATCGATCA (Sequence Number 47), and GCACGTGC.
Preferably, a repeat unit of the repeat motif sequence is selected from a group consisting of TGGCGTGGTCGTTG (Sequence Number 48), GCGCTGGGGTG (Sequence Number 49), TGGGGCTGTGGTGG (Sequence Number 50), GCGGTGGTG, GCGGTGGTGTG (Sequence Number 51), GGGCCGGGGTTG (Sequence Number 52), GCCGGGGTTGT (Sequence Number 53), TGGTCGTGTTG (Sequence Number 54), TGTTGCTGGGGTG (Sequence Number 55), TGGCGGTGTTGTGG (Sequence Number 56), and GGGGTGCCGGTGG (Sequence Number 57).
Preferably, the plasmid of the present invention comprises one or more oxidant sensitive sequences in the replication region.
Preferably, the oxidant sensitive sequence is selected from a group consisting of TGTGGGGTGGCCCCTCAGCGAAATA (Sequence Number 58), GGCCTCTCAGC (Sequence Number 59), CTGCGGGCACCTCCTAC (Sequence Number 60), TTCGATGAG, GGTGAGGGGTAACCC (Sequence Number 61), GTGGGGTGGC (Sequence Number 62), GGGGGGTGGCTTCCTATCG (Sequence Number 63), GTGGGGTGGCCC (Sequence Number 64), TGTGGCGGCGGCACGTGCGCTAA (Sequence Number 65), GCGGGGGCACCCGA (Sequence Number 66), and CTGAGGGTCCTC (Sequence Number 67).
Preferably, the plasmid of the present invention comprises one or more inverted repeat sequences in a replication region.
Preferably, the inverted repeat sequence is selected from a group consisting of GAAAAAGCCGGGCTGCTGCCCGGCTTTTTC (Sequence Number 68) and CACAGAAAAAGCCGGGTGGTAGAGCCCGGCTTTTTCCGTG (Sequence Number 69).
Preferably, the base sequence of a replicase-like protein gene is a base sequence of RepA protein gene.
Preferably, the base sequence of a replicase-like protein gene is a base sequence disclosed in Sequence Number 2, or a base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence and codes a protein with replicase activity.
Preferably, the base sequence of a DNA-binding protein-like protein gene is abase sequence of a helix-turn-helix protein gene.
Preferably, the base sequence of a DNA-binding protein-like protein gene is a base sequence disclosed in Sequence Number 1, or a base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence and codes a helix-turn-helix protein.
Preferably, the replication region is a base sequence disclosed in Sequence Number 3, or a base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence.
Preferably, the bacteria are the bacteria of the genus Kocuria.
According to another aspect of the present invention, there is provided a circular plasmid that is autonomously replicable in bacteria of the genus Kocuria, comprising, as for restriction enzyme recognition sites and the number thereof (Restriction enzyme recognition site: Number), SmaI: 2, SphI: 1, SalI: 1, XhoI: 1, and BamHI: 1.
Preferably, the plasmid of the present invention comprises restriction enzyme recognition sites SmaI, SmaI, SphI, SalI, XhoI, BamHI and SacI in that order.
Preferably, in the plasmid of the present invention, the number of base pairs is 3.0×103 to 3.4×103.
Preferably, the plasmid of the present invention is represented by the following restriction enzyme map (I):
Preferably, the plasmid of the present invention comprises a base sequence disclosed in Sequence Number 3 or 4.
Preferably, the plasmid of the present invention is derived from Kocuria sp. strain MBE131 (FERN P-21885).
According to another aspect of the present invention, there is provided a DNA fragment comprising a base sequence disclosed in Sequence Number 3, or a base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence.
According to another aspect of the present invention, there is provided a vector comprising a base sequence of the DNA fragment of the present invention.
According to another aspect of the present invention, there is provided a transformant comprising the plasmid of the present invention, the DNA fragment of the present invention, or the vector of the present invention.
According to a plasmid of the present invention, a vector can be constituted to introduce and express a foreign gene in bacteria of the genus Kocuria. Therefore, the use of the plasmid of the present invention makes it possible to introduce Useful genes into host cells such as bacteria of the genus Kocuria. Thus, it is possible to add new biological functions to host cells, as well as to improve original functions of host cells.
The use of a DNA fragment and vector of the present invention makes it possible to produce shuttle vectors that are autonomously replicable in bacteria of the genus Kocuria and other bacteria. Among the transformants of the present invention are those created by adding new biological functions to host cells, as well as those created by improving original functions of host cells; the transformants may be used in various fields depending on how the transformants are used.
Hereinafter, details of the present invention will be described.
First, a circular plasmid that is autonomously replicable in bacteria of the genus Kocuria that is one of embodiments of a plasmid of the present invention will be described. Incidentally, the phrase “autonomously replicable” in the present application means that a plasmid exists in cytoplasm of a host cell, and replicates and/or proliferates independently of chromosomal DNA of the host.
Bacteria of the genus Kocuria are one type of gram-positive coccus that does not produce hyphae, belonging to the family Micrococcaceae of the suborder Micrococcineae. Bacteria of the genus Kocuria are separated from various separation sources, and are isolated for example from mammalian skin, soil, mycorrhizal fungi, fermented food, clinical specimens, fresh water, marine sediment and the like. As for a method of identifying bacteria of the genus Kocuria, already-known methods are available without any restriction. For example, the following can be used: genetic-engineering phylogenetic analysis based on 16S rRNA region of a microbial genome, and an identification method based on physiological and biochemical characteristics of microorganisms.
A plasmid of the present invention can be, for example, represented by a restriction enzyme recognition site and the number of restriction enzyme recognition sites. As for a restriction enzyme recognition site and the number of restriction enzyme recognition sites (Restriction enzyme recognition site: Number), one preferred embodiment of a plasmid of the present invention comprises SmaI: 2, SphI : 1, SalI : 1, XhoI: 1, and BamHI: 1. According to the above embodiment, two sites are recognized by restriction enzyme SmaI; one site by SphI; one site by SalI; one site by XhoI; and one site by BamHI.
A more preferred embodiment of a plasmid of the present invention comprises restriction enzyme recognition sites SmaI, SmaI, SphI, SalI, XhoI, and BamHI in that order.
A method of confirming restriction enzyme recognition sites in a plasmid of the present invention is not specifically restricted. For example, the following methods may be employed: a method of confirming restriction enzyme recognition sites by determining a base sequence of a plasmid and then matching restriction enzyme recognition sites; and a method of carrying out restriction enzyme digestion of a plasmid to confirm restriction enzyme recognition sites from a pattern of bands that appear after agarose gel electrophoresis.
It is preferred that the amount of GC contained in a plasmid of the present invention be 60 to 70%. Incidentally, in plasmid pKR100 shown in
A plasmid of the present invention is not specifically restricted as long as the plasmid is autonomously replicable in bacteria of the genus Kocuria. Various embodiments are conceivable. As for the overall size thereof, the number of base pairs is about 3.2×103, or more preferably 3.0×103 to 3.4×103. The phrase “about 3.2×103” refers to the number of base pairs in a natural plasmid that is isolated from bacteria of the genus Kocuria. The number of base pairs thereof can vary by extracting any region other than a region (also referred to as replication region, hereinafter) that is predicted to have a function of autonomously replicating and/or proliferating in bacteria of the genus Kocuria, or by inserting a foreign gene.
A preferred embodiment of a plasmid of the present invention, for example, comprises restriction enzyme recognition sites shown in the following restriction enzyme map (I):
A more specific embodiment of such a plasmid is plasmid pKR100 shown in
In
A protein (ORF2) coded by orf2 includes 385 amino acids; the molecular weight and the isoelectric point thereof are estimated to be 41 kDa and 11.1, respectively. ORF2 has 31 percent homology (80/257 amino acids, E-value 6e-6) with replication protein RepA (Accession Number YP—345164) derived from Rhodococcus rhodochrous. In the present application, such a protein that is estimated to have 30 percent or more homology with RepA and have similar activity to RepA is referred to as a replicase-like protein. A base sequence that codes the replicase-like protein is referred to as a replicase-like protein gene.
The plasmid shown in
The base sequence of the plasmid shown in
A base sequence shown in
The base sequence shown in
The base sequence shown in
For example, it is predicted that in pAL5000, repeat motif sequence (iteron), repA gene, and repB gene may be sequences that play a role in autonomous replication of pAL5000. There is a report that, if a plasmid that has neither repA gene nor repB gene derived from pAL5000 but has a repeat motif sequence derived from pAL5000 is supplied in trans with RepA and RepB proteins derived from other plasmids, then the plasmid that has the repeat motif sequence derived from pAL5000 becomes replicable (See “Stolt P, Stoker N G., Microbiology. 1996, 142 (Pt 10): 2795-802.”; the disclosures of the document are incorporated herein by reference). As reported in the document, it is estimated that the repeat motif sequence is a cis-element that is involved in the incompatibility, copy number, and stability of plasmid.
As described in Example 8, the present inventors prepared plasmid pKR141 that has a region of the 1,031st to 3,170th of the base sequence (Sequence Number 3), comprising one set of a plurality of repeat motif sequences and one inverted repeat sequence, in the base sequence shown in
The base sequence disclosed in Sequence Number 3 is a unique base sequence. For example, when a homology search is performed as to the base sequence disclosed in Sequence Number 3 by the FASTA search at DDBJ, what appears at the top is Actinosynnema mirum DSM43827 strain, which has about 54-percent sequence similarity (http://fasta.ddbj.nig.ac.jp/top-j.html; Regarding the FASTA search, see “Pearson W R, Lipman D J., (1998), Proc Natl Acad Sci USA. 85(8): 2444-8, Lipman D J, Pearson W R., (1985), Science. 227(4693): 1435-41,” and “Wilbur W J, Lipman D J., (1983), Proc Natl Acad Sci USA. 80(3): 726-30”; the disclosures of the documents are incorporated herein by reference). The results of alignment between the base sequence disclosed in Sequence Number 3 and the base sequence of Actinosynnema mirum DSM43827 strain are shown in
The base sequence disclosed in Sequence Number 3 is a unique base sequence. Therefore, the possibility is high that the following plasmid autonomously replicates in bacteria of the genus Kocuria: a plasmid that is derived from bacteria of the genus Kocuria, is in the form of being linearly single-stranded, and hybridizes under stringent conditions to a DNA fragment comprising a base sequence complementary to a base sequence consisting of successive 500 or more bases out of the base sequence disclosed in Sequence Number 3, or preferably 1,000 or more bases, or more preferably 1,500 or more bases, or still more preferably 1,700 or more bases, or even more preferably 1,900 or more bases. Accordingly, such a plasmid is also among the plasmids of the present invention.
The phrase “hybridize under stringent conditions” in the present application means a DNA base sequence obtained by colony hybridization method, plaque hybridization method, Southern blot hybridization method, or any other method with the use of DNA as a probe. For example, the DNA identified by the following procedure and other DNAs can be included: with the use of a filter to which a DNA derived from a colony or plaque, or a fragment of the DNA, has been fixed, in the presence of 0.5 to 2.0M NaCl, hybridization is carried out at 40 to 75 degrees Celsius; preferably in the presence of 0.7 to 1.0M NaCl, hybridization is carried out at 65 degrees Celsius; then, with the use of 0.1 to 2×SSC solution (1×SSC solution is prepared from 150 mM of sodium chloride and 15 mM of sodium citrate), the filter is cleaned under a 65-degree-Celsius condition. The preparation of the probe and hybridization may be performed in a way that complies with the methods disclosed in the following documents or other documents (the disclosures of the documents are incorporated herein by reference): “Molecular Cloning: A laboratory Manual, 2nd ED., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989 (simply referred to as “Molecular Cloning 2nd Edition,” hereinafter)”; “Current Protocols in Molecular Biology, Supplement 1 to 38, John Wiley & Sons (1987-1997) (simply referred to as “Current Protocols in Molecular Biology,” hereinafter).” Incidentally, a person of ordinary skill in the art can set a condition for acquiring a replication region in a plasmid of the present invention by taking into consideration various factors including factors such as the salt concentration and temperature of such a buffer as well as other factors, such as the concentration of the probe, the length of the probe, and reaction time.
As for the DNA fragment containing a base sequence that hybridizes under stringent conditions, the following DNA can be included: a DNA having a predetermined level of homology (similarity) with a base sequence of a DNA that is used as a probe. For example, what can be included is a DNA fragment that has 70% or more homology, or preferably 80% or more homology, or more preferably 90% or more homology, or still more preferably 93% or more homology, or particularly preferably 95% or more homology, or most preferably 98% or more homology.
The base sequences that hybridize under stringent conditions to a base sequence complementary to the base sequence disclosed in Sequence Number 3, for example, include abase sequence that is obtained as the deletion, replacement, and/or addition of one or more bases is performed on the base sequence disclosed in Sequence Number 3: the number of bases deleted, replaced and/or added is one to several, preferably 1 to 50, or more preferably 1 to 30, or still more preferably 1 to 20, or even more preferably 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
The phrase “deletion of a base” means that a base in a sequence is lost or deleted. The phrase “replacement of a base” means that a base in a sequence is replaced with another base. The phrase “addition of a base” means that a base is added.
According to a method disclosed in examples, it is possible to confirm whether or not a plasmid comprising a base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence disclosed in Sequence Number 3 is autonomously replicable in bacteria of the genus Kocuria. The method, when briefly described, includes the processes of: preparing a recombinant plasmid, which is constituted by connecting a drug resistance gene to a base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence disclosed in Sequence Number 3; producing a transformant by introducing the recombinant plasmid into bacteria of the genus Kocuria; culturing the transformant in the presence of a drug associated with the drug resistance gene; and then confirming proliferation of the transformant.
A plasmid having a base sequence shown in
A method of extracting the plasmid from bacteria of the genus Kocuria is not specifically restricted. For example, the following method can be included: a method of using a suitable culture medium such as YTNM medium and proliferating bacteria of the genus Kocuria under conditions suitable for proliferation of the bacteria of the genus Kocuria, i.e. at 15 to 30 degrees Celsius for one to three days by means of static culture or shaking culture for example; recovering bacterial cells by performing centrifugal separation or other operations; dissolving cell walls of the bacterial cells by performing lysozyme treatment and other operations; and then recovering plasmids with the use of a plasmid extraction kit such as High pure plasmid purification kit (manufactured by Roche).
A method of confirming whether or not a plasmid extracted from bacteria of the genus Kocuria comprises the base sequence disclosed in Sequence Number 3 or 4 is not specifically restricted. For example, the following and other methods can be included: a hybridization method that uses a DNA or RNA probe prepared based on information regarding the base sequence disclosed in Sequence Number 3 or 4; a method of performing restriction enzyme digestion on the basis of a restriction enzyme map of pKR100 followed by confirming the size of a DNA that appears after the digestion through agarose gel electrophoresis.
As for another method of acquiring a plasmid of the present invention, for example, the plasmid can be isolated from among the plasmids extracted from the strain MBE 131 or other bacteria of the genus Kocuria by using a probe or a PCR primer set synthesized on the basis of information regarding the base sequence disclosed in Sequence Number 3 or 4 so as to be able to hybridize to the base sequence.
The plasmids of the present invention are connected to a foreign gene, and are then introduced into host cells such as bacteria of the genus Kocuria by an already-known DNA introduction method such as an electroporation method, a protoplast method, or a method with the use of calcium ions. Therefore, the plasmids of the present invention are available to prepare a transformant that expresses a foreign gene.
When being connected to a DNA replication region of a plasmid that is autonomously replicable in host cells different from bacteria of the genus Kocuria, the plasmids of the present invention are available to constitute a shuttle vector that is autonomously replicable in bacteria of the genus Kocuria and in host cells different from the bacteria of the genus Kocuria. A method of constituting a shuttle vector with the use of a plasmid of the present invention is not specifically restricted. For example, it is possible to constitute a shuttle vector whose host cells are bacteria of the genus Kocuria and Escherichia coli by connecting all of the plasmid of the present invention, or part thereof that comprises a region playing a role in DNA replication, to a multicloning site of a plasmid that is autonomously replicable in Escherichia coli such as pHY300PLK.
[2] Plasmid (2)
According to another embodiment of the present invention, a circular plasmid can be included that has one of replication regions of the following (A) to (C), which is estimated to have a function of autonomously replicating in bacteria, or preferably bacteria of the genus Kocuria or other bacteria of the family Micrococcaceae:
DNA-binding proteins are proteins that have a structure able to bind to DNA, and are classified in terms of structure into the following and other groups: homeodomain, Zinc finger domain, winged helix, Leucine zipper protein, helix-loop-helix (HLH) protein, and helix-turn-helix (HTH) protein. As for a base sequence of a DNA-binding protein-like protein gene in the replication regions (A) to (C) of a plasmid of the present invention, for example, base sequences of the gene of the DNA-binding protein can be included without limitation. However, the base sequence is preferably a base sequence of helix-turn-helix protein gene, or more preferably the base sequence disclosed in Sequence Number 1 or a base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence and codes a helix-turn-helix protein.
A replicase-like protein is a protein having replicase activity to dissociate the double helix or secondary structure of nucleic acid along a phosphoric acid ester skeleton of nucleic acid, and may be structured in various ways. As for the functions of a replication protein (or replicase), there is the following document: “Hiraga S, Sugiyama T, Itoh T., J Bacteriol. 1994 December; 176(23): 7233-43” (the disclosures of the document are incorporated herein by reference). For example, the document states that “The Rep protein specifically binds to the origin and synthesizes a unique primer RNA at the origin.”
As for a base sequence of a replicase-like protein gene in the replication regions (A) to (C) of a plasmid of the present invention, for example, abase sequence of the gene of RepA protein can be included. Preferably, the base sequence is the base sequence disclosed in Sequence Number 2 or a base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence and codes a protein having replicase activity.
The replication region (A) of a plasmid of the present invention comprises a base sequence disclosed in Sequence Number 45 or a base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence, as well as a base sequence of DNA-binding protein gene and a base sequence of replicase-like protein gene. The base sequence disclosed in Sequence Number 45 or the base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence comprises the following and other sequences, which are regions that are estimated to be involved in autonomous replication in bacteria of the genus Kocuria of a plasmid of the present invention: a DNA-binding protein binding sequence, a repeat motif sequence, an oxidant sensitive sequence, and an inverted repeat sequence. The base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence disclosed in Sequence Number 45 preferably comprises at least one sequence selected as a DNA-binding protein binding sequence from a group consisting of TGCCGGCA, TGATCGATCA (Sequence Number 47), GCACGTGC, and CACCGGT; at least one type of sequence selected as a repeat motif sequence from a group consisting of GGGCCGGGGTTG (Sequence Number 52), TGGTCGTGTTG (Sequence Number 54), TGTTGCTGGGGTG (Sequence Number 55), TGGCGGTGTTGTGG (Sequence Number 56), and GGGGTGCCGGTGG (Sequence Number 57); at least one type of sequence selected as an oxidant sensitive sequence from a group consisting of GGGGGGTGGCTTCCTATCG (Sequence Number 63), GTGGGGTGGCCC (Sequence Number 64), TGTGGCGGCGGCACGTGCGCTAA (Sequence Number 65), GCGGGGGCACCCGA (Sequence Number 66), and CTGAGGGTCCTC (Sequence Number 67); and, as an inverted repeat sequence, GAAAAAGCCGGGCTGCTGCCCGGCTTTTTC (Sequence Number 68) or CACAGAAAAAGCCGGGTGGTAGAGCCCGGCTTTTTCCGTG (Sequence Number 69).
Examples of a DNA-binding protein binding sequence in the replication regions (B) and (C) of a plasmid of the present invention can include CACCGGTG, ACCGGTG, CCGGTG, ACCGGT, CACAGGT, CACCGGT, CACCGG, GTGCGCAC, GGCCGGCC, TCGGAGCTCCGA (Sequence Number 46), TCCCGGGA, TGCCGGCA, TGATCGATCA (Sequence Number 47), and GCACGTGC.
Examples of a repeat unit of a repeat motif sequence in the replication regions (B) and (C) of a plasmid of the present invention can include TGGCGTGGTCGTTG (Sequence Number 48), GCGCTGGGGTG (Sequence Number 49), TGGGGCTGTGGTGG (Sequence Number 50), GCGGTGGTG, GCGGTGGTGTG (Sequence Number 51), GGGCCGGGGTTG (Sequence Number 52), GCCGGGGTTGT (Sequence Number 53), TGGTCGTGTTG (Sequence Number 54), TGTTGCTGGGGTG (Sequence Number 55), TGGCGGTGTTGTGG (Sequence Number 56), and GGGGTGCCGGTGG (Sequence Number 57).
Examples of an oxidant sensitive sequence in the replication region (C) of a plasmid of the present invention can include TGTGGGGTGGCCCCTCAGCGAAATA (Sequence Number 58), GGCCTCTCAGC (Sequence Number 59), CTGCGGGCACCTCCTAC (Sequence Number 60), TTCGATGAG, GGTGAGGGGTAACCC (Sequence Number 61), GTGGGGTGGC (Sequence Number 62), GGGGGGTGGCTTCCTATCG (Sequence Number 63), GTGGGGTGGCCC (Sequence Number 64), TGTGGCGGCGGCACGTGCGCTAA (Sequence Number 65), GCGGGGGCACCCGA (Sequence Number 66), and CTGAGGGTCCTC (Sequence Number 67).
Examples of an inverted repeat sequence in the replication region (C) of a plasmid of the present invention can include GAAAAAGCCGGGCTGCTGCCCGGCTTTTTC (Sequence Number 68) and CACAGAAAAAGCCGGGTGGTAGAGCCCGGCTTTTTCCGTG (Sequence Number 69).
As described below in Example 2, a region that comprises either the DNA-binding protein binding sequence or the repeat motif sequence, or both of them, is estimated to be involved in the replication and stable retention of a plasmid in the replication region. Accordingly, the replication regions (B) and (C) of a plasmid of the present invention comprises the DNA-binding protein binding sequence, the repeat motif sequence or DNA-binding protein binding sequence, and the repeat motif sequence. Moreover, the replication regions (B) and (C) of a plasmid of the present invention may comprise either two or more DNA-binding protein binding sequences or two or more repeat motif sequences, or comprise both two or more DNA-binding protein binding sequences and two or more repeat motif sequences.
The replication region (C) of a plasmid of the present invention comprises an oxidant sensitive sequence and an inverted repeat sequence. As described above, the oxidant sensitive sequence is a sequence that is estimated to be involved in the initiation of replication; and the inverted repeat sequence is a sequence to which a replicase-like protein binds and which is able to control the copy number of a plasmid as a result. The replication region (C) of a plasmid of the present invention comprises the above sequences, it is possible to control autonomous replication of the plasmid. Incidentally, it is preferred that an inverted repeat sequence be comprised in the replication regions (A) and (B) of a plasmid of the present invention.
The number of sequences of each type in the replication regions (A) to (C) of a plasmid of the present invention, as well as the order the sequences are arranged, is not specifically restricted as long as the plasmid of the present invention is autonomously replicable in bacteria; and thus various embodiments are possible.
One embodiment of the replication regions (A) to (C) in a plasmid of the present invention is the base sequence disclosed in Sequence Number 3 or a base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence.
[3] DNA Fragment, Vector, and Transformant
According to another aspect of the present invention, there is provided a DNA fragment having the base sequence disclosed in Sequence Number 3 or a base sequence that hybridizes under stringent conditions to a base sequence complementary to the base sequence. By introducing those obtained by connecting the DNA fragment of the present invention to a foreign gene into chromosomes of host cells such as bacteria of the genus Kocuria or into cytoplasm of host cells as cyclized plasmids, it is possible to obtain a transformant that expresses the foreign gene.
The DNA fragment of the present invention can be synthesized by the above PCR or any other already-known DNA synthesis method without restriction. Examples of DNA synthesis can include (the disclosures of the following documents are incorporated herein by reference): a method of chemically synthesizing the DNA fragment on the basis of information regarding the base sequence disclosed in Sequence Number 3 by means of a phosphotriester method, a phosphoamidite method, or the like [J. Am. Chem. Soc., 89, 4801 (1967) ; J. Am. Chem. Soc., 91, 3350 (1969) ; Science, 150, 178 (1968) ; Tetrahedron Lett., 22, 1859 (1981); Tetrahedron Lett., 24, 245 (1983)]; genetic-engineering methods, such as a method of introducing site-specific mutation into the base sequence disclosed in Sequence Number 3 [Methods in Enzymology, 154, 350, 367-382 (1987); Methods in Enzymology, 100, 468 (1983); Nucleic Acids Res., 12, 9441 (1984); Sequel of Biochemical Experiment Course 1 “Genetic Research Method II,” Japanese Biochemical Society, p105 (1986)]; and a combination of the methods described above. For example, the DNA synthesis may be achieved by chemosynthesis due to a phosphoramidite method or a triester method. Moreover, a commercially-available automated oligonucleotide synthesis device may also be used.
The DNA fragment of the present invention may be inserted into an already-known vector and then introduced into a target cell corresponding to the vector. For example, such a vector may be one which is autonomously replicable, or one which is integrated into the chromosome of a target cell when being introduced into the target cell followed by being replicated together with the chromosome. A preferred example of the vector is an expression vector. Examples of the expression vector can include plasmid vector, phage vector, virus vector, and the like. The DNA fragment of the present invention is functionally linked along with an element (e.g. promoter or the like) required for transcription in an expression vector. The promoter is a DNA sequence that shows transcriptional activity in a target cell, and can be appropriately selected according to the type of the target cell.
A vector comprising the DNA fragment of the present invention is among other embodiments of the present invention. A preferred embodiment of a vector of the present invention is a plasmid of the present invention. A transformant comprising a plasmid or vector of the present invention is also among other embodiments of the present invention.
In the present application, the preparation of primers and probes, extraction of plasmid DNA, ligation, introduction of DNA, cloning, and other operations are already known to a person of ordinary skill in the art. For example, the above operations can be carried out in a way that complies with the methods described in Molecular Cloning 2nd Edition, Current Protocols in Molecular Biology, and the like.
The following describes the present invention in more detail through examples. However, the present invention is not limited to the examples.
About 250 strains of bacteria of the suborder Actinomyces were isolated from the bottom sediment at a depth of about 2,000 meters in Sagami Bay. Among the strains, it was confirmed as described in the following that Kocuria sp. strain MBE131, which was a bacterium of the genus Kocuria, retained plasmid DNA. Strain MBE131 was cultured in YTNM medium (1.6% of bacto-tryptone, 0.5% of yeast extract, 1% of sodium chloride, and 0.1% of magnesium sulfate) at 25 degrees Celsius for two days by means of shaking culture. Bacterial cells were obtained by centrifugation from the culture. The bacterial cells were incubated in a 20 mM Tris-HCl buffer containing lysozyme (2 mg/mL) at 37 degrees Celsius for one hour so that cell walls of the bacterial cells were lysed. The plasmid DNA was then prepared from the lysate using High pure plasmid purification kit (manufactured by Roche).
The fragments that were obtained by digesting the plasmid prepared in Example 1 with restriction enzyme BamHI or SalI were each cloned to plasmid vector pUC18, and the entire base sequence of each was determined. As a result, it was found that the clones were circular plasmids that had an insert fragment made up of completely identical base sequence, respectively. The plasmid was named pKR100. The base sequence thereof is disclosed in Sequence Number 4 and shown in
Among the region represented by the 1st to 1,751st of Sequence Number 1, a plurality of the following structures were detected (See
Across the entire length of pKR100, a search for the inverted repeat & complementary sequences was carried out by GENETYX. As a result, the inverted repeat sequences were detected at the 806th to 835th and 1,322nd to 1,361st bases.
In pKR100, among the region represented by the 1st to 1,751st, the following sequence (indicated by lower-case letters in FIG. 1) was detected: a sequence that had homology with a sequence called GCbox in High affinity site (H-site), which was known as a replication protein binding site that existed in a replication initiation region of plasmid pAL5000 derived from Mycobacterium fortuitum. Moreover, across the entire length of pKR100, a homology search was performed by gene analysis software GENETYX-MAC ver. 12.1.0 (manufactured by GENETYX CORPORATION) with the use of the sequence CACCGGTG, which was called GCbox consisting of the most important 8 base pairs out of H-site (DNA-binding protein binding sequence). As a result, a portion in which the successive seven bases were completely consistent with the GCbox was detected in the base sequence of the 442nd to 448th of pKR100 and in the base sequence of the 1,399th to 1,405th. Therefore, it was predicted that the above portions of H-site-like seq would be a base sequence that took an important role in binding of RepB protein to plasmids. Thus, it was assumed that one of the H-site-like seq portions, or both of them, would be involved in the replication of pKR100.
As for the oxidant sensitive sequence that was estimated to be involved in the initiation of replication, a homology search with the use of TGTGGGGTGGCCCCTCAGCGAAATA (Sequence Number 58) was performed for the overall length of pKR100 by means of GENETYX-MAC. As a result, a site that showed homology with the above sequence was detected in a non-orf region of pKR100. It was estimated that it was highly possible that one out of the sequence portions showing homology with TGTGGGGTGGCCCCTCAGCGAAATA (Sequence Number 58) would function as a replication origin of pKR100. In particular, as for TGTGGGG, high levels of homology were found in the 1,200th to 1,211th bases (GTGGGGTGGCCC (Sequence Number 64)) and in the 370th to 379th bases (GTGGGGTGGC (Sequence Number 62)). Moreover, a plurality of other sequences showing homology were also detected. It was estimated that it was highly possible that one or a plurality of the above sequences would be involved in the initiation of replication as dissociation points of DNA.
As described above, it was estimated that, among the non-orf regions of pKR100, a region comprising either the direct repeat made up of approximate repeat motif sequences or the H-site-like sequence, or both of them, had a function related to the replication and stable retention of plasmids.
Then, an analysis of open reading frame was performed, and the results suggested that two open reading frames (orf1 and orf2) could exist (See
With the use of the amino acid sequence of ORF1, a secondary-structure prediction was performed by APSSP2: Advanced Protein Secondary Structure Prediction Server (http://www.imtech.res.in/raghava/apssp2/) (See “Raghava, G. P. S. (2002) APSSP2: A combination method for protein secondary structure prediction based on neural network and example based learning. CASP5. A-132.”; the disclosures of the document are incorporated herein by reference). As a result, it was predicted that ORF1 had two helix structures separated by a random coil structure. It is suggested that ORF1 would be a DNA-binding protein forming a unique helix-turn-helix (HTH) structure that could be typically found in a DNA-binding protein. The protein (ORF2) coded by orf2 included 385 amino acids; the molecular weight thereof was estimated to be 41 kDa, and the isoelectric point thereof 11.1 as a result of calculation. A search for a protein matching ORF2 was conducted by the BLAST program provided by NCBI. As a result, ORF2 was found to have homology with a replicase superfamily protein. However, as for those with highest levels of homology, only replication proteins (Accession Number YP—345164) derived from Rhodococcus rhodochrous were found to be only 31% (80/257 amino acids, E-value 6e-6) identical. It was suggested that ORF2 was a protein involved in the replication of plasmid pKR100.
From the entire DNA of the strain MBE 131 obtained in Example 1, the 16S rRNA gene was amplified with the use of primer sets made up of the base sequences disclosed in Sequence Numbers 7 and 8. An amplified fragment was purified using Wizard PCR purification kit (manufactured by Promega KK.), and the base sequence thereof was determined. The 16S rRNA gene sequence of the strain MBE 131 showed 99% base sequence similarity to the 16S rRNA gene sequence (Accession Number X87756) of a standard strain of Kocuria rosea registered in the database. Therefore, in terms of phylogenetic systematics, the strain MBE 131 was assumed to be the most closely-related species to Kocuria rosea.
The strain MBE 131 was cultured for two days in YTMN medium at 25 degrees Celsius. In a similar way to Example 1, from the bacterial cells obtained, an extraction operation of plasmids was conducted with the use of a plasmid purification kit. Meanwhile, the standard strain of Kocuria rosea (NBRC15588), which was a bacterium of the genus Kocuria reserved by a bacterial-cell preservation organization, was cultured under the same conditions, and the same operation was conducted on the bacterial cells obtained from the culture. Then, each of the DNA solutions extracted from the above two strains was loaded into agarose gel electrophoresis (See
Furthermore, with each of the extracted DNA solutions as a template, the PCR was carried out with the use of primer sets A to F (Table 1) of forward and reverse primers that had a sequence complementary to the base sequence of pKR100.
In the PCR, LA taq polymerase (manufactured by TAKARA BIO INC.) was used. One cycle was a reaction with a thermal denaturation condition of 98 degrees Celsius for 30 seconds, an annealing condition of 62 degrees Celsius for 60 seconds, and a elongation condition of 72 degrees Celsius for two minutes. The cycle was repeated 30 times in total. The obtained PCR reactant was loaded into agarose gel electrophoresis. When the DNA solution obtained from the strain MBE 131 was used as a template, an amplified fragment was detected that was equal in size to what was calculated based on Sequence Number 1. However, when the DNA solution obtained from the standard strain of Kocuria rosea was used as a template, no amplified fragment was detected (See FIG.6). Incidentally, Table 2 shows the relationship between lanes, primer sets, and DNAs employed as templates in the case of
Furthermore, the strain MBE 131 or the standard strain of Kocuria rosea was suspended in the 0.1% TritonX solution containing 0.1 mg/mL of protease K; incubated at 65 degrees Celsius for 20 minutes; and then heated at 100 degrees Celsius for 10 minutes.
In this manner, a cell lysis solution was prepared. The cell lysis solution, which was obtained from each bacterial strain, was employed as a template DNA solution. The PCR was carried out with the use of the above-described primer sets A-F (Table 1). In the PCR, LA tag polymerase (manufactured by TAKARA BIO INC.) was used. One cycle was a reaction with a thermal denaturation condition of 98 degrees Celsius for 30 seconds, an annealing condition of 62 degrees Celsius for 60 seconds, and a elongation condition of 72 degrees Celsius for two minutes. The cycle was repeated 30 times in total. The obtained PCR reactant was loaded into agarose gel electrophoresis. When the cell lysis solution obtained from the strain MBE 131 was employed as a template DNA solution, an amplified fragment was detected, which was equal in size to what was calculated based on Sequence Number 1. However, when the cell lysis solution obtained from the standard strain of Kocuria rosea was employed as a template DNA solution, no amplified fragment was detected (See
A DNA fragment comprising a base sequence represented by the 7th to 3,170th of Sequence Number 4 of plasmid pKR100 and a chloramphenicol resistance gene derived from Staphyrococcus aureus were linked to a multicloning site of pHY300PLK, thereby constituting shuttle vector pR6632 with respect to Escherichia coli bacteria. The transformation of Kocuria bacteria strain MBE131 was carried out by electroporation under the following conditions with the use of a plasmid prepared from a transformant of Escherichia coli bacteria HB101 having pR6632: Plasmid DNA 0.1 to 10 pg; Electric field intensity 6 to 25 kV/cm; Resistance 50 to 900 Q. The incubation time after pulse processing of cells was three hours at 30 degrees Celsius.
On the YTNM agar medium containing 2 pg/mL of chloramphenicol or 4 μg/mL of tetracycline, the above transformant was cultured at 30 degrees Celsius for five to seven days. A colony that had grown was suspended in the 0.1% TritonX solution containing 0.1 mg/mL of protease K; incubated at 65 degrees Celsius for 20 minutes; and then heated at 100 degrees Celsius for 10 minutes. In this manner, a cell lysis solution was prepared. With the obtained cell lysis solution as a template DNA solution, the PCR was carried out with the use of primer sets (primer sets made up of the base sequences disclosed in Sequence Numbers 21 and 22) complementary to the base sequence of a chloramphenicol resistance gene that pR6632 had. In the PCR here, a chloramphenicol resistance gene did not exist in wild-type strains of MBE131 and plasmid pHY300PLK. Therefore, it was possible to selectively detect the introduced pR6632. In the PCR, LA taq polymerase (manufactured by TAKARA BIO INC.) was used. One cycle was a reaction with a thermal denaturation condition of 98 degrees Celsius for 30 seconds, an annealing condition of 60 degrees Celsius for 60 seconds, and a elongation condition of 72 degrees Celsius for one minute. The cycle was repeated 30 times in total. The obtained PCR reactant was loaded into agarose gel electrophoresis. When the cell lysis solution obtained from the strain MBE 131 transformant was employed as a template DNA solution, an amplified fragment was detected, which was calculated from the base sequence of pR6632 (See Lane 2 of
Meanwhile, the MBE131 transformant was cultured at 30 degrees Celsius on the YTNM medium for one day. A plasmid extraction operation was carried out with the use of a plasmid purification kit in a similar way to that in Example 1. With the use of the obtained DNA solution, Escherichia coli bacteria HB101 were transformed. From the transformant of Escherichia coli bacteria, a plasmid was prepared with the use of the same plasmid purification kit, and then loaded into agarose gel electrophoresis after being digested with restriction enzyme HindIII (See
It was seen from the above results that plasmid pR6632 was replicated and retained in the strain MBE 131. The chloramphenicol resistance of the strain MBE 131 containing pKR100 was less than 1 μg/mL on the YTNM solid medium. On the other hand, the strain MBE 131 transformed by pR6632 showed resistance to 50 μg/mL of chloramphenicol. Moreover, pR6632 includes a tetracycline gene derived from Enterococcus faecalis. The strain MBE 131 containing pKR100 had a tetracycline resistance of less than 3 μg/mL. On the other hand, the strain MBE 131 transformed by pR6632 showed resistance to 100 μg/mL of tetracycline. Accordingly, it was considered that a plasmid containing pKR100 would function as a vector serving to hold and express heterologous foreign genes in the strain MBE 131.
Various DNA fragments comprising part of plasmid pKR100 were amplified by PCR. The above chloramphenicol resistance gene was linked to a multicloning site of pHY300PLK. Furthermore, the fragments shown in
In the PCR, LA tag polymerase (manufactured by TAKARA BIO INC.) was used. One cycle was a reaction with a thermal denaturation condition of 94 to 98 degrees Celsius for 15 to 30 seconds, an annealing condition of 55 to 68 degrees Celsius for 15 to 60 seconds, and a elongation condition of 72 degrees Celsius for two to five minutes. The cycle was repeated 30 times in total.
With the use of plasmid pR6632, Kocuria rhizophila DC2201 (NBRC103217), a different species of bacteria of the genus Kocuria, was transformed. The transformant was cultured on the YTNM agar medium containing 2 μg/mL of chloramphenicol or 4 μg/mL of tetracycline at 30 degrees Celsius for five to seven days. A colony that had grown was suspended in the 0.1% TritonX solution containing 0.1 mg/mL of protease K; incubated at 65 degrees Celsius for 20 minutes; and then heated at 100 degrees Celsius for 10 minutes. In this manner, a cell lysis solution was prepared. With the obtained cell lysis solution as a template DNA solution, the PCR was carried out with the use of primer sets (forward and reverse primers made up of the base sequences disclosed in Sequence Numbers 21 and 22) complementary to the base sequence of a chloramphenicol resistance gene that pR6632 had, and primer sets (forward and reverse primers made up of the base sequences disclosed in Sequence Numbers 43 and 44) complementary to the base sequence of a tetracycline resistance gene.
The chloramphenicol resistance gene and the tetracycline resistance gene did not exist on the DC2201 strain genome. Therefore, it was possible to selectively detect pR6632. In the PCR, LA taq polymerase (manufactured by TAKARA BIO INC.) was used. One cycle was a reaction with a thermal denaturation condition of 98 degrees Celsius for 30 seconds, an annealing condition of 60 degrees Celsius for 60 seconds, and a elongation condition of 72 degrees Celsius for one minute. The cycle was repeated 30 times in total. The obtained PCR reactant was loaded into agarose gel electrophoresis. When the cell lysis solution obtained from the DC2201 transformant was employed as a template DNA solution, an amplified fragment was detected, which was calculated from the base sequence of pR6632 (See Lanes 1 and 2 of
Therefore, it was considered that plasmid pR6632 could be replicated and retained even in other different species of bacteria of the genus Kocuria. The chloramphenicol resistance of the DC2201 strain containing no plasmid was less than 1 μg/mL on the YTNM solid medium. On the other hand, the DC2201 strain transformed by pR6632 showed resistance to 10 μg/mL of chloramphenicol. Accordingly, it was considered that a plasmid that comprised a region playing a role in the replication of pKR100 functioned as a vector serving to hold and express heterologous foreign genes even in different species of bacteria of the genus Kocuria.
In order to confirm a function of a DNA base sequence that did not code a protein that pKR100 had, the experiment as described below was performed. Plasmids pKR111, pKR121, and pKR141 comprising a DNA fragment which lacked part of pKR100 were constituted. The plasmids had a chloramphenicol resistance gene as a selection marker in the same manner as pR6632. pKR111 comprised a DNA fragment derived from the 312th to 3,170th of pKR100. pKR121 comprised a DNA fragment derived from the 559th to 3,170th of pKR100. pKR141 comprised a DNA fragment derived from the 1,031st to 3,170th of pKR100. As in the case of pR6632, pKR111 and pKR121 had two sets of unique sequences made up of the direct repeat and the inverted repeat, which were made up of approximate repeat motif sequences. However, pKR141 had only one set of them. The transformants that each contained each of the plasmids, MBE131(pR6632), MBE131(pKR111), MBE131 (pKR121), and MBE131(pKR141), were cultured at 25 degrees Celsius for 20 generations in the YTNM medium containing no antibiotic. After the culturing, the culture solution was applied to the YTNM agar medium containing no antibiotic, and was cultured at 25 degrees Celsius for three days to form a single colony. Each of the colonies that had grown on the solid agar media was simultaneously picked up on the YTNM agar media containing no antibiotic and the solid agar media containing chloramphenicol. Relative to the number of colonies that had grown on the solid agar media containing no antibiotic, the number of colonies that had grown on the solid agar media containing chloramphenicol was calculated as plasmid retention rate (%) (See
The Kocuria sp. strain MBE131 has been deposited in the International Patent Organism Depositary of the National Institute of Advanced Industrial Science and Technology (Tsukuba Central 6, 1-1, Higashi 1-chome Tukuba-shi, Ibaraki-ken 305-8566 Japan) with Receipt Number FERM P-21885 on Jan. 6, 2010.
The base sequences disclosed in the present application are listed below:
The present invention can be used to introduce a useful gene into bacteria of the genus Kocuria that serve as host cells, thereby obtaining a transformant to which a useful biological function has been added. Such a transformant can further improve the original, high-level functions that the host cells have, such as organic solvent tolerance, heavy metal resistance, and proliferating ability, and may be used in an advantageous manner in various fields, such as food industry, production of fuel and pharmaceutical chemical products, and environmental cleanup.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2010-081774 | Mar 2010 | JP | national |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/JP2011/056635 | 3/18/2011 | WO | 00 | 9/27/2012 |
