# Patent

## Title
DNA replication factors

## Abstract

A DNA polymerase reaction system which provides high DNA polymerase activity even at a high temperature and at a high salt concentration. A DNA polymerase reaction system that is constructed from a DNA polymerase, a clamp, and a clamp loader without intein sequence, the DNA polymerase being from Pyrococcus horikoshii, a hyperthermophilic archaeon.

## Background
BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates to two DNA replication factors capable of enhancing DNA polymerase activity from Pyrococcus, and to a DNA polymerase reaction system utilizing such factors.
2. Background Art
DNA polymerase is an enzyme useful for DNA sequencing reaction, polymerase chain reaction (PCR), radioactive labeling of DNA, in vitro synthesis of a mutated gene, and the like. DNA polymerases currently known can be generally classified into six families based on their amino acid sequence homology. Among them, DNA polymerases usually used as reagents in gene manipulation experiments belong to Family A polymerases such as typical E. coli DNA pol I and thermophilic bacterium Thermus aquaticus DNA polymerase (i.e., Taq DNA polymerase), and Family B polymerases such as typical T4 phage DNA polymerase. Various DNA polymerases having different optimum temperatures have been discovered from bacteria as well as from animals and plants. However, many of them, derived from mesophilic organisms and thus having low thermostability, are not suitable, for example, for PCR comprising heat denaturation of template DNA at 94° C. or over.
Enzymes from thermophilic bacteria, such as Taq DNA polymerase, are commercially available as thermostable DNA polymerases. However, all of them lack 3′-5′ proofreading exonuclease activity, resulting in higher error rates during polymerase reactions such as PCR, and hence are not suitable for PCR with high fidelity and the like. Further, type B enzymes that are thermostable and have 3′-5′ proofreading exonuclease activity, are isolated from hyperthermophilic archaea such as Pyrococcus and Thermococcus, and are commercially available. However, they have low primer extension activity and so are not suitable for PCR for long-strand DNA.
Examples of PCR techniques developed so far include conventional PCR using commercially available thermostable Pol A or Pol B, and isothermal PCR using φ29 DNA polymerase having high strand-displacement activity. The region replicable by the conventional Pol A or Pol B enzymes is short, the maximum being about 10 kb. In addition, the synthesis rate is as low as 30 b/sec. On the other hand, when φ29 DNA polymerase is used, PCR can be conducted at ambient temperature, so no expensive apparatus for amplification reaction is required and the procedure is simple. However, the use of random primers causes replicated regions to be relatively short, so that it is difficult to synthesize or produce a long DNA strand. Further, it is difficult to amplify DNA directly from the blood, body fluid, etc., by using the above conventional enzymes. This is because any of those conventional enzymes exhibits a reduced activity of DNA synthesis at a high salt concentration, and hence desalting is required to lower the salt concentration in the reaction solution.
The present inventors, for the first time, discovered a DNA polymerase from Pyrococcus horikoshii, which is thermostable and has 3′-5′ proofreading exonuclease activity, and the gene thereof (JP Patent No. 3015878). Moreover, we successfully improved the DNA polymerase activity dramatically by removing an intein sequence from a large subunit of the DNA polymerase (JP Patent Publication (Kokai) No. 2001-299348A). Further, this DNA polymerase has a unique property that its primer extension activity becomes higher as the primer length is longer. However, this DNA polymerase also exhibits a reduced activity at a high salt concentration, although its activity is high at a low salt concentration.
Under these circumstances, the object of the present invention is to construct a new DNA polymerase reaction system utilizing a DNA polymerase, which is highly thermostable, has 3′-5′ exonuclease activity by which mistakes occurring in a newly extended DNA strand are corrected, and also exhibits a high primer extension activity, wherein the high DNA polymerase activity is exerted even at a high salt concentration. Thereby, a novel technology is provided wherein a long-strand DNA region having a length of several Mb can be quickly replicated even under a high salt concentration without pretreatment.
SUMMARY OF THE INVENTION
In order to solve the above-mentioned problems, the present inventors focused on the hyperthermophilic archaeon Pyrococcus horikoshii, which grows at a temperature from 90 to 100° C., and discovered, from its gene sequences, genes expected to encode a clamp and a clamp loader, which are replication factors interacting with DNA polymerase to enhance DNA polymerase activity. Further, the clamp and the clamp loader were produced using E. coli from the discovered genes, and then it was confirmed that these proteins are stable at an elevated temperature (85° C. or higher), and enhance a primer extension activity of the DNA polymerase even at a concentration of sodium chloride as high as 0.2 M, thus the present invention having been completed.
In summary, the present invention comprises:
(1) A method for synthesizing a DNA, in which a primer DNA is extended by a DNA polymerase to synthesize the DNA complementary to a template DNA using deoxynucleotide triphosphates as substrates, wherein the enzyme reaction system comprises the DNA polymerase from Pyrococcus horikoshii and the two protein complexes of the following a) and b):

a) a protein complex composed of three molecules of a subunit and having a clamp function, the subunit being a protein comprising the amino acid sequence of SEQ ID NO: 8 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 8;

b) a protein complex composed of one molecule of a large subunit and four molecules of a small subunit and having a clamp loader function, wherein the large subunit is a protein comprising the amino acid sequence of SEQ ID NO: 10 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 10, and wherein the small subunit is a protein comprising the amino acid sequence of SEQ ID NO: 14 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 14.

(2) The method of the above (1), wherein said enzyme reaction system does not contain ATP.

(3) The method of the above (1) or (2), wherein said enzyme reaction system contains sodium chloride at a concentration of from 0 to 200 mM/L or >0 to 200 mM/L.

(4) A reagent kit for synthesizing a DNA, wherein the kit comprises a DNA polymerase from Pyrococcus horikoshii and the two protein complexes of the following a) and b):

a) a protein complex composed of three molecules of a subunit and having a clamp function, the subunit being a protein comprising the amino acid sequence of SEQ ID NO: 8 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 8;

b) a protein complex composed of one molecule of a large subunit and four molecules of a small subunit and having a clamp loader function, wherein the large subunit is a protein comprising the amino acid sequence of SEQ ID NO: 10 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 10, and wherein the small subunit is a protein comprising the amino acid sequence of SEQ ID NO: 14 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 14.

(5) The reagent kit of the above (4), wherein the kit is used for PCR and optionally contains written instructions, primers and/or ancillary reagents used for PCR.

(6) A protein comprising the amino acid sequence of SEQ ID NO: 8, or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 8, wherein, when three molecules of the protein subunit form a protein complex, the complex has a clamp function.

(7) A protein comprising the amino acid sequence of SEQ ID NO: 10 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 10, wherein, when one molecule of the protein subunit forms a protein complex with four molecules of a small subunit comprising the amino acid sequence of SEQ ID NO: 14 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 14, the complex has a clamp loader function.

(8) A protein comprising the amino acid sequence of SEQ ID NO: 14 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 14, wherein, when four molecules of the subunit form a protein complex with one molecules of a large subunit comprising the amino acid sequence of SEQ ID NO: 10 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 10, the complex has a function as a clamp loader.

(9) A DNA encoding of the protein of any one of the above (6) to (8).

(10) A DNA of the following (i) or (ii):

(i) a DNA comprising the nucleotide sequence of SEQ ID NO: 7, SEQ ID NO: 9, or SEQ ID NO: 13;

(ii) a DNA hybridizing with a DNA comprising a nucleotide sequence complementary to the nucleotide sequence of SEQ ID NO: 7, SEQ ID NO: 9, or SEQ ID NO: 13 under stringent conditions.

(11) A recombinant vector comprising the DNA of the above (9) or (10).

(12) A host cell comprising the recombinant vector of the above (11) is introduced therein.

According to the present invention, two novel DNA replication factors derived from Pyrococcus horikoshii, that is, a clamp and a clamp loader, is provided. Thus, an enzyme reaction system with which a long DNA strand is efficiently and accurately replicated by a DNA polymerase under conditions of a high temperature and a high salt concentration can be constructed. This enzyme reaction system is particularly useful for Long-PCR and the like, and new approaches for gene sequence analysis using such an enzyme reaction system can be developed.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 illustrates the gene sequence of the large subunit of the DNA polymerase D (SEQ ID NO: 1). Underlined is the intein sequence.
FIG. 2 illustrates the amino acid sequence of the large subunit of the DNA polymerase D (SEQ ID NO: 2). Underlined is the intein sequence.
FIG. 3 illustrates the gene sequence of the small subunit of the clamp loader (RFC) (SEQ ID NO: 11). Underlined is an intein sequence.
FIG. 4 illustrates the amino acid sequence of the small subunit of the clamp loader (RFC) (SEQ ID NO: 12). Underlined is an intein sequence.
FIG. 5 illustrates the results determined for optimum pH of the DNA polymerase of the present invention.
FIG. 6 illustrates the results determined for optimum Mg2+ concentration of the DNA polymerase of the present invention.
FIG. 7 illustrates the residual activity of the DNA polymerase of the present invention determined after heat treatment.
FIG. 8 illustrates the results tested for primer extension activity of the DNA polymerase of the present invention. For Lanes 1 to 3, Lanes 4 to 6, and Lanes 7 to 9, 15 mer primers, 34 mer primers, and a 50 mer primers were used, respectively. The reaction was constructed, for Lanes 1, 4, and 7, for 2 min in the presence of the enzyme; and for Lanes 2, 5, and 8, for 10 min in the presence of the enzyme. Lanes 3, 6, and 9 represent control experiments, in which no enzyme was added to the reaction system.
FIG. 9 illustrates the results tested for 3′-5′ exonuclease activity of the DNA polymerase of the present invention. A 50 mer oligonucleotide was used as a substrate. For Lane 1, the reaction was conducted for 30 min in the presence of the enzyme, and Lane 2 represents a control with no enzyme.
FIG. 10 illustrates the results determined by SDS-PAGE for the molecular weight of PCNA of the present invention. Lane 1 shows molecular markers, and Lane 2 shows purified PCNA.
FIG. 11 illustrates the results determined by SDS-PAGE for the molecular weight of RFC complex of the present invention. Lane 1 shows molecular markers, and Lane 2 shows purified RFC complex, wherein L indicates the large subunit and S indicates the small subunit.
FIG. 12 illustrates the results of the pull-down assay of PCNA by RFC complex of the present invention. The interaction between RFC complex and PCNA was analyzed in the presence or absence of ATP by SDS-PAGE.
FIG. 13 illustrates the results tested for the effect of RFC complex and PCNA on enhancement of the activity of DNA polymerase D. ATP was used at the concentration of 10 mM.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
Each of the DNA polymerase, the clamp (proliferating cell nuclear antigen, PCNA), and the clamp loader (replication factor, RFC) used in the present invention is a protein complex that is derived from Pyrococcus (JCM Accession Number 9974) and composed of multiple subunits.
The aforementioned DNA polymerase is a thermostable heterodimer enzyme composed of a small subunit and a large subunit without intein sequence, and has 3′-5′ exonuclease activity and to DNA polymerase activity. This enzyme also has a primer extension activity dependent on primer length and has a property that the primer extension activity increases when the primer length is over 30 mer. A DNA polymerase composed of the small subunit and the large subunit without intein sequence is described in the previous patent application filed by the present inventors (JP Patent Application No. 2000-116257 (JP Patent Publication (Kokai) No. 2001-299348A)), and hence the enzyme without intein sequence itself is well known.
The invention of the previous application is based upon the fact that it was found for the first time that there is an intein sequence in the large subunit of the thermostable heterodimer enzyme, which is derived from Pyrococcus horikoshii and has DNA polymerase activity as well as 3′-5′ exonuclease activity and that, when the intein sequence is removed, the primer extension activity of the enzyme is significantly improved. The amino acid sequence of the small subunit of this thermostable heterodimer enzyme from Pyrococcus horikoshii and the nucleotide sequence of the gene thereof are shown in SEQ ID NO: 6 and SEQ ID NO: 5, respectively. The amino acid sequence of the large subunit and the nucleotide sequence of the gene thereof are shown in SEQ ID NO: 2 and SEQ ID NO: 1 respectively, as well as in FIG. 2 and FIG. 1 respectively. The amino acid sequence of the intein portion corresponds to the region from amino acids 955 to 1120, and the nucleotide sequence thereof to the region from nucleotides 2863 to 3360 (the intein sequence is underlined in FIG. 2 and FIG. 1).
The amino acid sequence of the large subunit with no intein portion and the nucleotide sequence corresponding thereto are shown in SEQ ID NO: 4 and SEQ ID NO: 3, respectively. This enzyme is extremely thermostable and, even after treated at 85° C. for 1 hr., it retains 50% activity when compared to that before treatment. Additionally, after treated at 90° C. for 1 hr., it retains 20% activity. The optimum pH of the activity is pH 8.5.
The clamp (hereinafter, also referred to as PCNA) is a ring-shaped protein complex composed of plural subunits that tethers the DNA polymerase to a primed-template DNA during DNA replication. The clamp loader is a protein complex composed of plural subunits that opens and closes this clamp.
The clamp (PCNA) and the clamp loader (RFC), which are replication factors interacting with the DNA polymerase, a heterodimer, to enhance the DNA polymerase activity, can be obtained from the gene sequences of Pyrococcus horikoshii described above by the following procedures.
The gene of the clamp (PCNA) is amplified by PCR and extracted, which is then inserted into a vector such as a protein expression plasmid. The resulting plasmid is introduced into a host microorganism such as E. coli, which is then cultured to produce the clamp (PCNA). The produced clamp (PCNA) is heated and subsequently subjected to isolation and purification by column chromatography. Thus, the clamp (PCNA) is obtained. The purified PCNA has been revealed to be a homotrimer composed of the subunit having a molecular weight of 28 kDa. The amino acid sequence of the subunit and the nucleotide sequence corresponding thereto are shown in SEQ ID NO: 8 and SEQ ID NO: 7, respectively.
On the other hand, the clamp loader (RFC) from Pyrococcus horikoshii is composed of two subunits having different molecular weights. The subunit having a larger molecular weight has an intein sequence, and the amino acid sequence of this subunit and the nucleotide sequence corresponding thereto are shown in SEQ ID NO: 12 and SEQ ID NO: 11 respectively, as well as in FIG. 4 and FIG. 3 respectively (the intein sequences are underlined in FIG. 4 and FIG. 3). In the present invention, each of the regions upstream and downstream of the intein sequence in the DNA encoding the subunit (SEQ ID NO: 11; FIG. 3) is amplified by PCR, the resulting two DNA fragments are used as templates for amplification by Overlap PCR. Thus, the DNA encoding the subunit from which the intein sequence is removed is obtained. Hereinafter, the subunit without intein sequence is referred to as small subunit, and the subunit that originally contains no intein sequence is referred to as large subunit.
The DNA encoding the large subunit and the DNA encoding the small subunit without intein sequence, which subunits are of the clamp loader (RFC), are inserted into a single expression vector or two separate expression vectors. A host microorganism is then transfected with the resulting vector or vectors for coexpression. Further, the resulting proteins can be heat-treated and subsequently subjected to purification and isolation by column chromatography. Herein, the coexpression refers to the phenomenon wherein two DNAs are expressed in a host simultaneously and respective proteins corresponding to those DNAs are produced therein. The clamp loader having the activity recited in the present invention can be obtained by coexpression. The clamp loader thus obtained is composed of the large subunit having a molecular weight of 54 kDa and the small subunits containing no intein sequence and having a molecular weight of 38 kDa. The clamp loader is a heteropentamer, which is composed of one molecule of the large subunit and four molecules of the small subunit without intein sequence. The amino acid sequence of the 54 kDa large subunit and the corresponding nucleotide sequence are shown in SEQ ID NO: 10 and SEQ ID NO: 9, respectively. The amino acid sequence of the 38 kDa small subunit without intein sequence and the corresponding nucleotide sequence are shown in SEQ ID NO: 14 and SEQ ID NO: 13, respectively.
Each of the subunits composing the DNA polymerase, the clamp, or the clamp loader of the present invention includes a polypeptide comprising an amino acid sequence having at least 80 or 85%, preferably at least 90%, more preferably at least 95, 96, 97, or 98%, still more preferably at least 99% identity with the respective amino acid sequence of SEQ ID NO: 2, 4, or 6 (DNA polymerase subunit), SEQ ID NO: 8 (PCNA subunit), or SEQ ID NO: 10, 12, or 14 (RFC subunit). In particular, each of the subunits composing the above DNA polymerase, the clamp, and the clamp loader of the present invention is not limited to a polypeptide that comprises the amino acid sequence of each of SEQ ID NOS described above, but also includes a polypeptide that comprises an amino acid sequence in which one or more, preferably one or several, amino acids are deleted, substituted or added in any of these amino acid sequences, as long as the DNA polymerase activity, or the clamp function or clamp loader function, is still provided when it forms a respective protein complex as described above.
In the present invention, the term “several” refers to an integer of, for example, from 2 to 20, preferably from 2 to 15, more preferably from 2 to 10, from 2 to 9, from 2 to 8, from 2 to 7, from 2 to 6, from 2 to 5, from 2 to 4, or from 2 to 3.
Herein, in regard to amino acid substitution, amino acid side chains are different one another in terms of chemical properties such as hydrophobicity and electric charge or structural properties. Some highly conservative relationships, wherein the three-dimensional structure (also referred to as conformation) of the entire polypeptide is not essentially affected, are known from experience or actual physicochemical measurements. Substitution between amino acids in the present invention may be conservative substitution between amino acids which are similar to each other in terms of chemical or structural properties, or may be non-conservative substitution between amino acids which are different from each other in terms of such properties. Amino acids can be classified based on similarities in chemical and structural properties into the following groups.
In the hydrophobic amino acid groups, alanine (Ala), leucine (Leu), isoleucine (Ile), valine (Val), methionine (Met), and proline (Pro) are included.
In the polar amino acid group, serine (Ser), threonine (Thr), glycine (Gly), glutamine (Gln), asparagine (Asn), and cysteine (Cys) are included.
In the aromatic amino acid group, phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp) are included.
In the acidic amino acid group, glutamic acid (Glu) and aspartic acid (Asp) are included.
In the basic amino acid group, lysine (Lys), arginine (Arg), and histidine (His) are included.
Examples of conservative substitution include the substitution between the following amino acids: glycine (Gly) and proline (Pro); glycine (Gly) and alanine (Ala) or valine (Val); leucine (Leu) and isoleucine (Ile); glutamic acid (Glu) and aspartic acid (Asp); glutamine (Gln) and asparagine (Asn); cystein (Cys) and threonine (Thr); threonine (Thr) and serine (Ser) or alanine (Ala); lysine (Lys) and arginine (Arg), etc.
Moreover, the DNA encoding each of the subunits composing the clamp or clamp loader of the present invention includes DNA comprising a nucleotide sequence having at least 80 or 85%, preferably at least 90%, more preferably 95, 96, 97, or 98%, still more preferably 99% identity with the respective nucleotide sequence of SEQ ID NO: 7 (PCNA subunit) or SEQ ID NO: 9, 11, or 13 (RFC subunit). In particular, the DNA encoding each of these subunits in the present invention is not limited to a DNA that comprises the nucleotide sequence of each of SEQ ID NOS described above, but also includes a DNA that encodes a protein comprising the amino acid sequence of each of SEQ ID NOS described above or a DNA that encodes a protein comprising an amino acid sequence in which one or more, preferably one or several, amino acids are deleted, substituted, or added in any of such amino acid sequences, wherein, when it forms each of the protein complexes described above, the DNA can encode a subunit capable of providing the respective functions.
The identity ranges and values for polynucleotide and polypeptide sequences herein include all intermediate subranges and values, for example, 80, 81, 82.5, 90, 92.5, 95, 95.1, 95.2, 95.3, 95.5, 99.65 or 99.75% identity to the corresponding sequence.
The DNA encoding each of the subunits composing the clamp or clamp loader of the present invention not only include DNA comprising the respective nucleotide sequence of SEQ ID NO: 7 (the PCNA subunit) or SEQ ID NO: 9, 11, or 13 (the RFC subunits) but also includes DNA comprising a mutated nucleotide sequence of any of these nucleotide sequences based on degeneracy of the genetic code. For example, the most suitable codon for a species different from Pyrococcus horikoshii can be selected based on the degeneracy of the genetic code for incorporation of the DNA into the cells of the species. Such a mutated nucleotide sequence refers to a nucleotide sequence comprising a different codon(s) for a certain amino acid(s).
Alternatively, the DNA encoding each of the subunits composing the clamp (PCNA) or clamp loader (RFC) of the present invention may include an analogue or homologue of the DNA comprising the nucleotide sequence of each SEQ ID NO described above, and is functionally equivalent thereto. As used herein, the term “functionally equivalent” means that the polypeptide encoded by the above analogue or homologue of the DNA has biological and/or biochemical functions that are equivalent to those of the peptide encoded by the DNA consisting of the nucleotide sequence of the respective SEQ ID NOS. More specifically, such a polypeptide has the function of each subunit composing the clamp (PCNA) or the clamp loader (RFC). Such a DNA includes a DNA that hybridizes with a DNA consisting of a nucleotide sequence complementary to the nucleotide sequence of any of SEQ ID NOS described above under stringent conditions. The stringent conditions refer to conditions under which specific hybrid is formed while non-specific hybrid not formed. The stringency comprises high or low stringency, and preferred is high stringent condition. In the low stringent condition, wash after hybridization is carried out, for example, using a solution of 5×SSC and 0.1% SDS at 42° C., and preferably using a solution of 5×SSC and 0.1% SDS at 50° C. In the high stringent condition, wash after hybridization is carried out, for example, using a solution of 0.1×SSC and 0.1% SDS at 65° C. Therefore, even when partial alterations of the full length nucleotide sequence of any SEQ ID NO described above can be generated by various artificial manipulations such as site-directed mutagenesis, random mutation using mutagens, or mutation, deletion or ligation of a DNA fragment cleaved by a restriction enzyme, the DNA variant which hybridizes with a DNA comprising a nucleotide sequence complementary to the nucleotide sequence of any of SEQ ID NOS described above under stringent conditions, and encodes a polypeptide having the function of each of the subunits composing the above clamp (PCNA) or the clamp loader (RFC) is included in the DNA encoding each subunit composing the clamp (PCNA) or the clamp loader (RFC) according to with the present invention, regardless of differences from the nucleotide sequences of SEQ ID NO: 7 (PCNA subunit) or SEQ ID NO: 9, 11, or 13 (RFC subunit).
Alternatively, the DNA encoding each of the subunits composing the clamp (PCNA) or the clamp loader (RFC) of the present invention may also include a DNA comprising a nucleotide sequence having at least 80%, preferably at least 90%, more preferably 95%, still more preferably 99% identity with the respective nucleotide sequence of SEQ ID NO: 7 (PCNA) or SEQ ID NO: 9, 11, or 13 (RFC subunit).
The present invention also relates to a recombinant vector into which the DNA of the present invention has been incorporated. As used herein, the “recombinant vector” refers to a vector engineered to incorporate the DNA of the present invention into it by the recombinant DNA technology well known to person skilled in the art, including an expression vector. The “expression vector” refers to a DNA construct comprising the DNA of the present invention together with a nucleotide sequence(s) that can regulate the expression of the DNA of the present invention. “Regulatory sequences” are nucleotide sequences capable of regulating the expression of the DNA of the present invention, including, for example, a promoter, an enhancer, a polyadenylation signal, a replication initiation site, a ribosome-binding site or a Shine-Dalgarno sequence, a terminator, and the like. Preferred regulatory sequences are a sequence containing a promoter and a sequence containing a terminator. Preferably, such regulatory sequences are from the host organism.
Examples of vectors include a plasmid, a cosmid, a phage, a phagemid, BAC, YAC, a virus, and the like. The preferred vector is a plasmid.
The present invention further relates to a host cell comprising the above recombinant vector. Such a host cell is a transformed cell or a transformant, namely a host cell into which the above recombinant vector is introduced. Examples of host cells include cells derived from microorganisms such as bacteria and fungi, insect cells, and mammalian cells. The preferred host is a microorganism. Preferred microorganisms include E. coli and Saccharomyces. 
The recombinant DNA technology employed in the present invention includes, for example, techniques as described in Sambrook, et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1989; Ausubel, et al., Current Protocols in Molecular Biology, John Wiley & Sons, 1998, etc.
In the presence of PCNA and RFC, the primer extension activity of the heterodimer DNA polymerase is enhanced compared to that in the absence thereof. In particular, this effect is significant at a high salt concentration such as 200 mM NaCl. DNA, thereby, can be amplified without desalting directly from blood, body fluid, etc. Of course, DNA can also be synthesized from a sample containing no salt. Therefore, when the present invention is used in a practical application, no consideration is required for a salt concentration in a sample.
Further, when the RFC (the clamp loader) of the present invention loads the clamp on the DNA, adenosine triphosphate (ATP) is not required as an energy source. The enzyme reaction system of the present invention, in which the above heterodimer DNA polymerase coexists with PCNA and RFC, does not require the addition of adenosine triphosphate (ATP) as an energy source for loading the clamp on DNA in DNA synthesis. This is a further characteristic, because ATP inhibits the action of these DNA replication factors that enhance the DNA polymerase activity at a high salt concentration.
Any of the heterodimer DNA polymerase, PCNA and RFC of the present invention is thermostable, and the reagent kit for DNA synthesis comprising them in combination is suitable as a PCR reagent kit. Further, in the reagent kit, dATP, dTTP, dGTP and dCTP may be incorporated as substrates, and Family B DNA polymerase (Pol B) and the like may also be incorporated.
The reagent kit for synthesizing a DNA of the present invention comprises: a DNA polymerase from Pyrococcus horikoshii as well as (a) a protein complex composed of three molecules of a subunit and having a clamp function, wherein the subunit is a protein comprising the amino acid sequence of SEQ ID NO: 8 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 8; and (b) a protein complex composed of one molecule of a large subunit and four molecules of a small subunit and having a clamp loader function, wherein the large subunit is a protein comprising the amino acid sequence of SEQ ID NO: 10 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 10, and the small subunit being a protein comprising the amino acid sequence of SEQ ID NO: 14 or an amino acid sequence having at least 90% identity with the amino acid sequence of SEQ ID NO: 14. In the reagent kit of the present invention, each of the DNA polymerase, the protein complex (a), and the protein complex (b) may be contained in separate containers. In addition, in the reagent kit of the present invention, all of the DNA polymerase, the protein complex (a), and the protein complex (b) may be contained in the same container, or may be contained in any combination thereof.
Example 1
(1) The Culture of Archaeon
The archaeon JCM 9974 was cultured by the following procedure.
NaCl (13.5 g), Na2SO4 (4 g), KCl (0.7 g), NaHCO3 (0.2 g), KBr (0.1 g), H3BO3 (30 mg), MgCl2.6H2O (10 g), CaCl2 (1.5 g), SrCl2 (25 mg), 1.0 ml of a resazurin solution (0.2 g/L), yeast extract (1.0 g), and bacto peptone (5 g) were dissolved in water to give 1 L of a solution, pH was then adjusted to 6.8 followed by high-pressure sterilization. To the sterilized solution, then, the element sulfur sterilized by dry heat was added at the final concentration of 0.2%. The resulting medium was saturated with argon to render the medium anaerobic, into which JCM 9974 was then inoculated. When a solution of Na2S was added to the medium, the color of resazurin did not change into pink by Na2S in the medium, and thereby the anaerobic condition of the medium was confirmed. This medium was incubated at 95° C. for 2 to 4 days followed by centrifugation to collect the microorganisms.
(2) The Preparation of Chromosomal DNA
The chromosomal DNA of JCM 9974 was prepared by the following procedure. After the incubation was completed, the microorganism was collected by centrifugation at 5,000 rpm for 10 min. The collected microorganism was washed with a 10 mM Tris solution (pH 7.5) containing 1 mM EDTA twice, and then entrapped into a block of InCert Agarose (from FMC). This block was treated in a 1% N-lauroylsarcosine solution containing 1 mg/ml Protease K to separate and prepare the chromosomal DNA in the Agarose block.
(3) The Preparation of Clone Libraries Carrying the Chromosomal DNA
The chromosomal DNA obtained in the above (2) was subjected to partial digestion using the restriction enzyme HindIII followed by agarose gel electrophoresis to give a DNA fragment of about 40 kb in length. This DNA fragment was ligated, by using T4 ligase, with the Bac vector pBAC108L or the fosmid vector pFOS1 completely digested using the restriction enzyme HindIII. When the former vector was used, the DNA was introduced into E. coli immediately after the ligation by electroporation. When the latter vector pFOS1 was used, the DNA after the ligation was packaged into lambda phage particles in vitro using GIGA Pack Gold (from Stratagene), and E. coli was then infected with this packaged particles in order to introduce the DNA into the E. coli. The resulting E. coli population resistant to the antibiotic chloramphenicol was used as the BAC library or fosmid library. From these libraries, clones suitable for covering the chromosome of JCM 9974 were selected for clone alignment.
(4) The Nucleotide Sequencing for the BAC or Fosmid Clone
The nucleotide sequences were determined for the aligned BAC or fosmid clone by the following steps. The DNA of the BAC or fosmid clone collected from E. coli was sonicated to obtain DNA fragments, which were then subjected to agarose gel electrophoresis to give 1 kb or 2 kb DNA fragments. These DNA fragments were inserted into plasmid vector pUC118 at the HincII restriction enzyme site to prepare 500 shotgun clones per BAC or fosmid clone. The nucleotide sequence of each shotgun clone was determined by using an automatic DNA sequencer, Type 373 or Type 377 (PerkinElmer ABI). The nucleotide sequences obtained from the respective shotgun clones were assembled and edited by using an automatic DNA sequence assembly and analysis software, Sequencher, to determine the full-length nucleotide sequence for the BAC clone or the fosmid clone.
(5) The Identification of Genes Encoding DNA Polymerase, Clamp and Clamp Loader
The nucleotide sequences of the BAC clone and the fosmid clone as determined above were analyzed by a large-scale computer, and the following genes were identified: the genes encoding the large subunit (underlined is an intein sequence in FIG. 1; SEQ ID NO: 1) and the small subunit (SEQ ID NO: 5) of the DNA polymerase; the gene encoding the clamp (PCNA) subunit (SEQ ID NO: 7); and the genes encoding the large subunit (SEQ ID NO: 9) and the small subunit (underlined is an intein sequence in FIG. 3; SEQ ID NO: 11) of the clamp loader (RFC).
Example 2
(1) The Construction of an Expression Plasmid for the Small Subunit of the DNA Polymerase D
In order to form restriction enzyme (NdeI and BamHI) sites upstream and downstream of the region of the structural gene coding for the small subunit (SEQ ID NO: 5), DNA primers were synthesized. Using them, the restriction enzyme sites were inserted upstream and downstream of the gene by PCR.










Upper primer: PolS1;











(SEQ ID NO: 15)











5′-TTTTGTCGACGTACATATGGATGAATTCGTAAAG-3′




(NdeI site is underlined)



 



Lower primer: PolS2;










(SEQ ID NO: 16)











5′-TTTTGAGCTCTTTGGATCCTTAGAAGCTCCATCAGCA




CCACCT-3′ (BamHI site is underlined)






After PCR, the extended strands were completely digested (at 37° C. for 2 hr) using the restriction enzymes (NdeI and BamHI), followed by purification of the structural gene. Further, pET11a or pET15b (Novagen) was cleaved using the restriction enzymes NdeI and BamHI and purified, which was then ligated with the above structural gene using T4 ligase at 16° C. for 2 hr. A part of the ligated DNA was introduced into competent E. Coli XL1-BlueMRF′ cells to obtain colonies of transformants. From the resulting colonies, expression plasmids were purified by alkaline lysis. The resulting expression plasmid was abbreviated as pETIla/PoIS or pET15b/PolS, respectively. Absence of a random mutation on the structure gene was confirmed by DNA sequencing.
(2) The Construction of an Expression Plasmid for the Large Subunit of the DNA Polymerase D
The gene coding for the large subunit was cloned into a pGEMEX-1 vector (from Promega) by a two-step procedure. The DNA fragment of upper part of said gene was obtained by PCR using the following two primers.










Upper primer: PolL1;











(SEQ ID NO: 17)











5′-CTCGACTTTAGCATATGGCTCTGATGGAGC-3′




(NdeI site is underlined)



 



Lower primer: PolL2;










(SEQ ID NO: 18)











5′-GCTTGTCGACGCCATAAACTTTGACATTATCCATTG




CGCGCTTAAGCAAC-3′ (SalI site is underlined)






The PCR products were completely digested using NdeI and SalI, and then cloned into a pGEMEX-1 vector, abbreviated as pGEM/PolL1-2.
The DNA fragment of lower part of said gene was obtained by PCR using the following two primers.










Upper primer: PolL3;











(SEQ ID NO: 19)











5′-TTTATGGCGTCGACAAGCTGAAGG-3′




(SalI site is underlined)



 



Lower primer: PolL4;










(SEQ ID NO: 20)











5′-TATAACTTATGCATTGTGGTTATTTCGCTGAGAAG-3′




(NsiI site is underlined)






The PCR products were completely digested using SalI and NsiI and then cloned into the previously prepared pGEM/PolL1-2 to obtain pGEM/PolL carrying the full-length gene coding for the large subunit.
(3) The Construction of an Expression Plasmid for the Large Subunit without Intein
As shown in FIG. 1, the gene coding for the large subunit of the DNA polymerase D from P. horikoshii contains one intein (coding for a proteinous intron). Therefore, the DNA fragment upstream of the intein was amplified by PCR using the primers PolL3 and PolL6, and the DNA fragment downstream of the intein was amplified by PCR using the primers PolL5 and PolL4. The DNA fragment without the intein was amplified by Overlap PCR using these two fragments and the primers PolL3 and PolL4. The products were then completely digested using the restriction enzymes SalI and NsiI, which were then cloned into the previously prepared pGEM/PolL1-2 to obtain pGEM/PolL(-Intein) carrying the gene coding for the large subunit without intein (SEQ ID NO: 3).








(SEQ ID NO: 21)










PolL5:
5′-CACGCTGCAAAGAGGAGAAATTGCGATGGTGATGAAGATGCT-3′



 








(SEQ ID NO: 22)










PolL6:
5′-AGCATCTTCATCACCATCGCAATTTCTCCTCTTTGCAGCGTG-3′







(4) The Construction of a Plasmid Coexpressing the Small Subunit and the Large Subunit without Intein
In order to produce the heterodimer DNA polymerase D of the present invention in a stable manner, a plasmid coexpressing the both subunits was constructed. First, in order to introduce a new multi-cloning site at the immediate upstream of the BamHI site of pET15b/PolS, PCR was performed using the primers PolSI and PolS3. Herein, as described below, the BamHI, NsiI, SalI, and SacII sites were coded in PolS3 from the 5′-terminal in this order. The resulting PCR products were treated with NdeI and BamHI, and then inserted into pET15b to construct pET15b/PolS(M) containing the multi-cloning site between the stop codon of the small subunit and the BamHI site.
Next, PCR was performed using the primers PolL7 and PolL2 with pGEM/PolL(-Intein) as a template. The resulting products contained a new SacII site at the 5′-terminal, and contained the portion from the ribosome-binding site to the SaII site in the coding region of the protein expression unit of pGEM/PolL(-Intein). This products were treated with Sac II and SalI, and then inserted into the multi-cloning site generated in pET15b/PolS(M). This plasmid was abbreviated as pET15b/PolSL1-2. On the other hand, pGEM/PolL(-Intein) was treated with SalI and NsiI to isolate the lower part of the gene of the large subunit (without the intein), which then was inserted into the protein expression unit of the pET15b/PolSL1-2 at the remaining SalI and NsiI sites thereof. The resulting plasmid was abbreviated as pET15b/PolSL(-Intein).
This expression plasmid, pET15b/PolSL(-Intein) enables the coexpression of the small subunit with a histidine tag attached at the N-terminal thereof and the large subunit without intein.








PolS3:









(SEQ ID NO: 23)









5′-CG GGATCC ATGCAT G GTCGAC A CCGCGG



TCAGCACCACCTACT AAAGTCGAG-3′ (BamHI, NsiI, SalI,


and SacII sites from 5′-terminal in this order are


underlined)


 


PolL7:








(SEQ ID NO: 24)









5′-GGTGTCCGCGGCTCACTATAGGGAGACCAC-3′ (SacII site



is underlined)






Example 3
The Construction of an Expression Plasmid for the Clamp (Pcna)
In order to introduce restriction enzyme (NdeI and XhoI) sites upstream and downstream of the region of the structural gene coding for PCNA (SEQ ID NO: 7), DNA primers were synthesized. Using them, the restriction enzyme sites were introduced upstream and downstream of the gene by PCR.










Upper primer: PCNA1;











(SEQ ID NO: 25)











5′-GGGGGCATATGCCATTCGAAATAGTCTTTGAGGG-3′




(NdeI site is underlined)



 



Lower primer: PCNA2;










(SEQ ID NO: 26)











5′-GGGGGCTCGAGTCACTCCTCAACCCTTGG-3′ (XhoI




site is underlined.)






After PCR, the extended strands were completely digested (at 37° C. for 2 hr) using the restriction enzymes (NdeI and XhoI), followed by purification of the fragment of the structural gene. Further, pET11a′, in which the XhoI site was added to the multi-cloning site of pET11a, was newly constructed, which was then cleaved using the restriction enzymes NdeI and XhoI and purified. The purified fragments were then ligated with the above structural gene using T4 ligase at 16° C. for 2 hr. A part of the ligated DNA was introduced into competent E. coli XL1-BlueMRF′ cells to obtain colonies of transformants. From the resulting colonies, expression plasmids were purified by alkaline lysis. The resulting expression plasmid was abbreviated as pET11a′/PCNA. Absence of random mutation in the structure gene was confirmed by DNA sequencing.
Example 4
(1) The Construction of an Expression Plasmid for the Small Subunit of the Clamp Loader (RFC)
As shown in FIG. 3, the gene (RFCS) coding for one of the subunits composing the clamp loader derived from P. horikoshii contains one intein (coding for a proteinous intron; the underlined part in FIG. 3). Therefore, the DNA fragment upstream of the intein was amplified by PCR using the primers RFCS1 and RFCS3, and the DNA fragment downstream of the intein was amplified by PCR using the primers RFCS4 and RFCS2. The DNA fragment without the intein was amplified by Overlap PCR using these two fragments and the primers RFCS1 and RFCS2. Then, the products were completely digested using the restriction enzymes NdeI and BamHI followed by the purification of the structural gene (SEQ ID NO: 13). Further, pET11a (from Novagen) was cleaved using the restriction enzymes NdeI and BamHI followed by purification. The purified fragments were then ligated with the above fragment of the structural gene using T4 ligase at 16° C. for 2 hrs. Competent cells of E Coli XL1-BlueMRF′ was introduced with an aliquot of the ligated DNA to obtain colonies of transformants. From the resulting colonies, expression plasmids were purified by alkaline lysis. The resulting expression plasmid was abbreviated as pET11a/RFCS.








RFCS1:









(SEQ ID NO: 27)









5′-GGGGGGCATATGCATAATATGGAAGAGGTTCGCGAGG-3′ (NdeI



site is underlined)


 


RFCS2:








(SEQ ID NO: 28)









5′-GGGGGATCCTCACTTCTTCTTTCCAACTAAGGTAAA-3′ (BamHI



site is underlined)


 


RFCS3:








(SEQ ID NO: 29)









5′-GCAGGTCCTCCTGGTGTTGGAAAGACTACAGCAGCTTTAGCCCTC



TCA-3′


 


RFCS4:








(SEQ ID NO: 30)









5′-TGAGAGGGCTAAAGCTGCTGTAGTCTTTCCAACACCAGGAGGAC



CTGC-3′






(2) The Construction of an Expression Plasmid for the Large Subunit of the Clamp Loader (RFC)
In order to introduce restriction enzyme (NdeI and BamHI) sites upstream and downstream of the region of the structural gene coding for the large subunit (SEQ ID NO: 9), DNA primers were synthesized. Therewith, the restriction enzyme sites were introduced upstream and downstream of the gene using PCR.










Upper primer: RFCL1;











(SEQ ID NO: 31)











5′-GGGGGGCATATGCCGGATGTTCCATGGATTGAG-3′




(NdeI site is underlined)



 



Lower primer: RFCL2;










(SEQ ID NO: 32)











5′-GGGGGATCCGGGGATGCATGGGGGTCGACCTAAT




TCTTCTTAATAAAGTCAAAGAGTGTG-3′ (BamHI site is



underlined)






After PCR, the extended strands were completely digested (at 37° C. for 2 hr) using the restriction enzymes (NdeI and BamHI) followed by the purification of the fragment of the structural gene. Further, pET15b (from Novagen) was cleaved using the restriction enzymes NdeI and BamHI and purified. The purified fragments were then ligated with the above fragment of the structural gene using T4 ligase at 16° C. for 2 hr. A part of the ligated DNA was introduced into competent E. coli XL1-BlueMRF′ cells to obtain colonies of transformants. From the resulting colonies, expression plasmids were purified by alkaline lysis. The resulting expression plasmid was abbreviated as pET15b/RFCL.
(3) The Construction of a System for Coexpressing the Large and Small Subunits of RFC
In order to construct a system for coexpressing the large and small subunits of RFC by employing co-transformation, the gene coding for the large subunit (RFCL) was inserted between the NcoI site and the BamHI site of the multi-cloning site 2 of pACYCDuet-1 (Novagen) that is compatible (having an Ori sequence from a different origin) with a pET vector. The detailed procedure is explained below.
First, one NcoI recognition sequence in the RFCL gene was subjected to silent mutation using Overlap PCR. More specifically, using pET15b/RFCL as a template, the DNA fragment upstream of the NcoI recognition sequence was amplified by PCR using the primers RFCL3 and RFCL5, and the DNA fragment downstream of the NcoI recognition sequence was amplified by using the primers RFCL6 and RFCL4. The DNA fragment without the NcoI recognition sequence was amplified by Overlap PCR using these two fragments and the primers RFCL3 and RFCL4. The primers RFCL3 and RFCL4 have sequences that can anneal with the upstream and the downstream of the multi-cloning site of the pET15b vector, respectively, and hence the NcoI site and the BamHI site derived from the pET15b were contained in the Overlap PCR products. These products were completely digested using the restriction enzymes NcoI and BamHI followed by the purification of the fragment of the structural gene. On the other hand, pACYCDuet-1 was cleaved using the restriction enzymes NcoI and BamHI, followed by purification. The purified products were then ligated with the above fragment of the structural gene using T4 ligase at 16° C. for 2 hr. Competent cells of E. Coli XL2-Blue were introduced with a part of the ligated DNA to obtain colonies of transformants, which were resistant to chloramphenicol at the final concentration of 500 μg/ml.
From the resulting colonies, expression plasmids were purified by alkaline lysis. The resulting expression plasmid was abbreviated as pACYC/RFCL.








(SEQ ID NO: 33)










RFCL3:
5′-GCAAGGAATGGTGCATGCAAGGAGATGGCG-3′



 








(SEQ ID NO: 34)










RFCL4:
5′-AGCAGCCAACTCAGCTTCCTTTCGGGCTTTGTT-3′



 








(SEQ ID NO: 35)










RFCL5:
5′-CCTGTACTTCTCAATCCAGGGAACATCGGGCAT-3′



 








(SEQ ID NO: 36)










RFCL6:
5′-ATGCCCGATGTTCCCTGGATTGAGAAGTACAGG-3′







Example 5
Expression of the Recombinant Genes
(1) The DNA Polymerase D
Competent E. coli cells (BL21-CodonPlus (DE-3)-RIL; from Stratagene) were thawed, 0.1 ml of which was transferred into a centrifuge tube. To the thawed cells, 0.005 ml of a solution of the expression plasmid was added and kept on ice for 30 min. Then, the cells were subjected to heat shock at 42° C. for 30 sec, to which 0.9 ml of SOC medium was then added followed by shaking at 37° C. for 1 hr. The cultured cells in an appropriate amount were plated onto a 2YT agar plate containing ampicillin, which was incubated at 37° C. overnight to obtain transformants.
The transformants were cultured in 2YT medium (2 L) containing ampicillin until the absorbance at 600 nm reached to 1, and then IPTG (isopropyl-β-D-thiogalactopyranoside) was added thereto and further cultured at 30° C. for 8 hr, followed by centrifugation (6,000 rpm for 20 min.) to collect the microorganisms.
(2) The Clamp (PCNA)
Competent E. coli cells (BL21-CodonPlus (DE-3)-RIL; from Stratagene) were thawed, 0.1 ml of which was transferred into a centrifuge tube. To the thawed cells, 0.005 ml of a solution of the expression plasmid was added and kept on ice for 30 min. Then, the cells were subjected to heat shock at 42° C. for 30 sec., to which then 0.9 ml of SOC medium was added followed by shaking at 37° C. for 1 hr. Subsequently, the cultured cells in an appropriate amount were plated onto a 2YT agar plate containing ampicillin, which was incubated at 37° C. overnight to obtain transformants. The transformant was named E. coli BL21(DE3) CodonPlus RIL/pET11a′/PCNA and deposited under the terms of the Budapest treaty with the International Patent Organism Depositary National Institute of Advanced Industrial Science and Technology (AIST Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan) on Mar. 9, 2007, the assigned Accession Number being FERM BP-10796, which deposit was transferred from the national deposition under Accession Number FERM P-20911 (deposited on May 12, 2006).
The transformants were cultured in 2YT medium (2 L) containing ampicillin until the absorbance at 600 nm reached to 0.5, and then IPTG (at the final concentration of 0.5 mM) was added thereto and further cultured at 37° C. for 4 hr, followed by centrifugation (6,000 rpm for 20 min.) to collect the microorganisms.
(3) The Clamp Loader (RFC)
The large and small subunits of RFC were co-expressed by co-transformation using the two expression vectors. First, competent E. coli cells (BL21 (DE-3); from Stratagene) were thawed, 0.1 ml of which was transferred into a centrifuge tube. To the thawed cells, 0.005 ml of a solution of the expression plasmid pET11a/RFCS was added and kept on ice for 30 min. Then, the cells were subjected to heat shock at 42° C. for 30 sec, to which then 0.9 ml of SOC medium was added followed by shaking at 37° C. for 1 hr. Subsequently, the cultured cells in an appropriate amount were plated onto a 2YT agar plate containing ampicillin, which was incubated at 37° C. overnight to obtain transformants, E. coli BL21 (DE3)/pETIla/RFCS. The transformants were further treated with CaCl2 to prepare competent cells. To the resulting competent cells, 0.005 ml of a solution of the expression plasmid pACYC/RFCL was added and kept on ice for 30 min. Then, the cells were subjected to heat shock at 42° C. for 30 sec., to which then 0.9 ml of SOC medium was added followed by shaking at 37° C. for 1 hr. Subsequently, the cultured cells in an appropriate amount were plated onto a 2YT agar plate containing two antibiotics, ampicillin and chloramphenicol (at the final concentrations of 100 μg/ml and 50 μg/ml, respectively), which was incubated at 37° C. overnight to obtain the transformant E. coli BL21(DE3)/pET11a/RFCS/pACYC/RFCL. This transformant was deposited under the terms of the Budapest treaty with the International Patent Organism Depositary National Institute of Advanced Industrial Science and Technology (AIST Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, Japan) on Mar. 9, 2007, the assigned Accession Number being FERM BP-10797, which deposit was transferred from the national deposition under Accession Number FERM P-20912 (deposited on May 12, 2006).
The transformants were cultured in 2YT medium (200 ml) containing ampicillin and chloramphenicol until the absorbance at 600 nm reached to 0.6, and then IPTG (at the final concentration of 0.3 mM) was added thereto and further cultured at 25° C. for 20 hrs. followed by centrifugation (6,000 rpm for 20 min.) to collect the microorganisms.
Example 6
The Purification of Recombinant Proteins
(1) The Thernostable DNA Polymerase D
The collected microorganisms were frozen at −20° C. and thawed, to which then twice the volume of 10 mM Tris HCl buffer (pH 8.0) and 1 mg of DNase to prepare suspension. The resulting suspension was incubated at 37° C. for 30 min., followed by sonication for 10 min. The suspension was further heated at 85° C. for 30 min. followed by centrifugation (11,000 rpm for 20 min.) to obtain the supernatant. This was used as a solution of the crude enzyme. Next, this solution of the crude enzyme was added to a Ni-column (from Novagen; a His-Bind metal chelation resin & His-Bind buffer kit were used) to carry out affinity chromatography. The 60 mM imidazole eluted fraction obtained thereby was transferred into 100 mM phosphate buffer (pH 6.0) using a Centriprep 30 (from Amicon). Further, this solution was adsorbed in a HiTrap SP column (from Pharmacia) and was then subjected to NaCl gradient elution. Next, SDS-PAGE was done for each fraction to determine a molecular weight of a protein contained therein. The subunits of the DNA polymerase of the present invention were expected to have a molecular weight of 144,000 Da and 70,000 Da, respectively. Hence, fractions having these molecular weights were collected, which were transferred into 50 mM Tris HCl buffer (pH 7.0) using a Centriprep 30 followed by further affinity chromatography using a HiTrap Heparin column (from Pharmacia) and NaCl gradient elution to obtain a purified enzyme.
(2) The Thermostable Clamp (PCNA)
The collected microorganisms were frozen at −20° C. and thawed, to which then twice the volume of 50 mM Tris HCl buffer (pH 8.0), 0.1 M NaCl, 2 mM 2-mercaptoethanol, 0.1 mM EDTA, and 10% glycerol to prepare suspension. The resulting suspension was subjected to sonication for 10 min. followed by centrifugation (30,000 g for 20 min.) to obtain the supernatant. This was further heated at 75° C. for 15 min. followed by centrifugation (30,000 g for 20 min.) to obtain the supernatant. This was still further heated at 80° C. for 10 min. followed by centrifugation to obtain the supernatant. Next, to the resulting supernatant, poly(ethyleneimine) (Sigma) and NaCl were added at the final concentrations of 0.15% and 0.58 M, respectively, which was then stirred at 4° C. for 30 min followed by centrifugation (30,000 g for 20 min.). To the supernatant, (NH4)2SO4 was added until 80% saturation, which was then stirred on ice for 2 hrs. followed by centrifugation (30,000 g for 20 min) to recover the precipitate. This precipitate was dissolved in 50 mM Tris HCl buffer (pH 8.0), 0.1 M NaCl, 2 mM 2-mercaptoethanol, 0.1 mM EDTA, and 10% glycerol. This solution was dialyzed with the same buffer and added to an anion exchange column, HiTrap Q (from Amersham Pharmacia; 5 ml), which had been equilibrated with 50 mM Tris HCl buffer (pH 8.0), followed by from 0 to 1 M NaCl gradient elution in the same buffer. Further, the resulting solution was added to a Superdex 200 column (10/300; Amersham Pharmacia), which had been equilibrated with 50 mM Tris HCl buffer (pH 8.0) and 0.2 M NaCl, followed by elution with the same buffer to obtain purified PCNA.
(3) The Thermostable Clamp Loader (RFC)
The collected microorganisms were frozen at −20° C. and thawed, to which then twice the volume of 50 mM Tris HCl buffer (pH 8.0) containing a protease inhibitor (Complete, EDTA-free; from Roche) was added to prepare a suspension. The resulting suspension was homogenized using a French press, and then heated at 75° C. for 15 min. followed by centrifugation (30,000 g for 20 min) to obtain the supernatant. This supernatant was added to a HiTrap heparin column (from Amersham Pharmacia; 5 ml), which had been equilibrated with 50 mM Tris HCl buffer (pH 8.0), followed by from 0 to 1 M NaCl gradient elution in the same buffer. The eluted fractions were analyzed by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) to identify the elution peak of the RFC complex composed of the large and small subunits. Further, the fractions having these elution peaks were collected and added to a Ni-column (from Novagen; a His-Bind metal chelation resin & His-Bind buffer kit were used) to carry out affinity chromatography. The 200 mM imidazole eluted fraction obtained thereby was concentrated using a Centriprep 30 (Amicon). This concentrated product was added to a Superdex 200 column (10/300; Amersham Pharmacia), which had been equilibrated with 50 mM Tris HCl buffer (pH 8.0) and 0.2 M NaCl, followed by elution with the same buffer to obtain the purified RFC complex.
Example 7
The Evaluations of the Reaction System of the DNA Polymerase
(1) The Test Conditions
(a) PCR
In order to detect the activity of the DNA polymerase D of the present invention, PCR was performed using the aforementioned two DNA oligomers (Upper primer and Lower primer), and the expression vector pET15b/PolS encoding the small subunit of the DNA polymerase of the present invention as a template DNA. One cycle was composed of three steps (94° C. for 1 min.; 61° C. for 2 min.; 70° C. for 3 min.), and 35 cycles were repeated. The reaction solution (100 μl) contained 20 mM Tris HCl buffer (pH 8.8), 10 mM KCl, 4 mM MgSO4, 0.1% Triton X-100, 0.375 mM dNTP mix, 100 pmol Upper primer, 100 pmol Lower primer, and 0.1 μg of the DNA polymerase.
(b) DNA Synthesis
DNA synthesis was based on the method by Kornberg, et al. (J. Biol. Chem., 237, 519-525; J. Biol. Chem., 236, 1487-1493). The reaction solution (200 μl) contained 20 mM Tris HCl buffer (H 8.8), 10 mM KCl, 10 mM (NH4)2SO4, 2 mM MgSO4, 0.1% Triton X-100, 0.25 mM dNTP mix, 0.37 Mbq (α-32P) dATP, 20 μg of salmon testicular DNA treated by heating and chilling, and 0.1 μg of the DNA polymerase. The reaction was performed at 75° C. for 30 min. After the reaction was completed, to the reaction solution, 0.5 mg of the salmon testicular DNA chilled on ice was added, and thereto 500 μl of 1 N perchloric acid and 500 μl of water, both chilled on ice, were added followed by centrifugation (9,000×g for 5 min.) to obtain an acid-insoluble fraction. This precipitate was dissolved in 300 μl of 0.2 N NaOH, and further thereto 300 μl of 1 N perchloric acid and 300 μl of water, both chilled on ice, were added followed by centrifugation to obtain an acid-insoluble fraction. This precipitate was washed with 1 ml of 1 N acetic acid followed by centrifugation. The resulting precipitate was dissolved in 0.4 ml of 2 N ammonia solution. The radioactivity was determined by the Cherenkov effect using a liquid scintillation counter. Herein, the amount of the enzyme that can incorporate 10 nmol of dNTPs in DNA synthesis at 75° C. for 30 min. is defined as 1 Unit.
(c) The Optimum pH
The optimum pH was determined by incorporation of radioactivity into the acid-insoluble fraction, wherein the reaction temperature was held at 75° C. under the above test conditions and pH was changed from 5.8 to 9.5 with a phosphate buffer in the acidic range and with a Tris HCl buffer in the basic range.
(d) The Optimum Concentration of Mg2+
The optimum concentration of Mg2+ was determined by the incorporation of radioactivity into the acid-insoluble fraction, wherein the reaction temperature was fixed at 75° C. under the above test condition and the concentration of MgSO4 was changed from 0 mM to 20 mM.
(e) Thermostability
The enzyme solution (100 μl) for heating contained 20 mM Tris HCl buffer (pH 8.0 at 25° C.), 500 mM NaCl, 10 mM MgSO4, and the enzyme of the present invention at a concentration of 0.1 mg/ml. This solution was heated for 1 hr. in the range of from 60° C. to 95° C. using a GeneAmp PCR System 2400 (PerkinElmer), and then, with the resulting solution, DNA synthesis was performed and the residual activity was determined by the incorporation of radioactivity into the acid-insoluble fraction.
(f) The Primer Extension Activity
The primer extension activity was determined by the following procedure. A single-strand DNA of M13 phage (0.2 μg) and each of the primers (0.5 pmol) (15 mer, 34 mer, and 50 mer), which had been 5′-labeled with 32P, were annealed in 20 mM Tris HCl buffer (pH 8.5), 0.05 Units of the DNA polymerase was added to the DNA mixture in the presence of 10 mM MgCl2, and then the reaction was allowed to proceed at 75° C. The reaction was terminated after 2 min or 10 min by adding the Stop solution thereto. The reaction products were analyzed by electrophoresis with 15% polyacrylamide gel (PAGE) containing 8 M urea.
(g) The 3′-5′ Exonuclease Activity
By using the 50 mer primer 5′-labeled with 32P (0.5 pmol), the 3′-5′ exonuclease activity was determined. The reaction solution (20 μl) contained 20 mM Tris HCl buffer (pH 8.5), 12 mM MgCl2, and 4 ng of the labeled DNA, to which 0.05 Units of the polymerase was added, and the reaction was allowed to proceed at 75° C. The reaction was terminated after 30 min. by adding the Stop solution thereto. The reaction products were analyzed by electrophoresis with 15% polyacrylamide gel (PAGE) containing 8 M urea.
(h) The Interaction Between RFC Complex and PCNA
The binding property of RFC complex and PCNA was examined by the following procedure. In 100 μl of the reaction solution (containing 10 mM MgCl2, 0.5 M NaCl, and ATP at a predetermined concentration), 400 pmol of PCNA and 400 pmol of RFC complex were admixed and kept at room temperature for 20 min. Thereto, 40 μl of Ni2+-chilating resin was added and stirred by shaking at room temperature for 10 min, followed by centrifugation at 5,000 g for 30 sec to recover the resin as the precipitate. This recovered resin was washed with 200 μl of 20 mM Tris HCl buffer (pH 8.0) containing 0.5 M NaCl, 10 mM MgCl2, and 5 mM imidazole four times followed by elution of the target protein complex using 40 μl of 20 mM Tris HCl buffer (pH 8.0) containing 0.5 M NaCl, 10 mM MgCl2, and 500 mM imidazole. The composition of the proteins in the eluted samples was analyzed by SDS-PAGE.
(i) The Effect of RFC Complex and PCNA on the DNA Polymerase Activity
The primed substrate, which would be a substrate of the DNA polymerase D, was prepared by the following procedure. First, the 5′-terminal of the 51 mer oligonucleotide (5′-GTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAAGGACGGCCAGTGCC-3′ (SEQ ID NO: 37)) was labeled with 32P. The reaction solution (20 μl) contained 1× kinase buffer (from Toyobo), 20 pmol of the above 51 mer oligonucleotide, 6 μl of γ-32P ATP (3,000 Ci/mmol), and 2 μl of T4 Kinase. This reaction solution was allowed to react at 37° C. for 3 hrs. followed by heating at 95° C. for 3 min. The oligonucleotide labeled with 32P was purified using QIAquick Nucleotide Removal Kit (QIAGEN). Next, in 100 μl of 1×M buffer (from Toyobo), 2 nmol of M13 ssDNA and 4 pmol of the 51 mer oligonucleotide labeled with 32P were admixed and then boiled for 5 min. followed by allowing the solution to cool gradually for annealing.
Using the above primed M13 ssDNA as a template, DNA polymerase reaction was carried out. To the reaction system, RFC complex and PCNA were added, and thereby the effect of these DNA replication factors to enhance the DNA polymerase activity was evaluated. The composition and the final concentrations of the reaction solution (20 μl) were as follows:
20 mM Tris HCl buffer (pH 8.8)
10 mM KCl
10 mM (NH4)2SO4 
0.1% Triton X-100
6 mM MgSO4 
0.25 mM dNTPs
400 ng of the DNA polymerase
2 μg of PCNA
2 μg of the RFC complex
0.04 pmol of the 32P-labeled primed M13 ssDNA
50-200 mM NaCl
10 mM ATP
This reaction solution (20 μl) was kept at 60° C. for 5 min. After the reaction was completed, 4 μl of the reaction termination solution (0.3 M NaOH, 60 mM EDTA, 0.1% Bromophenol Blue, and 10% glycerol) was added thereto. This solution was then boiled for 5 min. followed by analysis of molecular species in the reaction product by 1.2% alkaline agarose gel electrophoresis, with the electrode solutions of 50 mM NaOH and 1 mM EDTA.
(2) The Results of the Evaluations
(a) The Properties of the DNA Polymerase D
1) The Protein Chemical Properties
The large subunit of the enzyme of the present invention was composed of 1,434 amino acid residues before the removal of the intein and 1,268 amino acid residues after the removal of the intein, and the respective molecular weights were 163,000 Da and 144,000 Da. The small subunit thereof was composed of 623 amino acid residues, the molecular weight being 70,000 Da.
2) The Improved Activity of the Active Enzyme by Coexpressing the Small Subunit and the Large Subunit without the Intein
When expressed individually, each of the subunits was extremely unstable, and hence stable expression was not possible. Therefore, the coexpression system was constructed. Thereby, it was possible to express the active enzyme at a high level, and the physicochemical properties thereof and the mechanism of thermostability were able to be explored.
3) The Detection of DNA Synthesizing Activity and PCR
By using a solution of the crude enzyme from recombinant E. coli, the DNA synthesizing activity was examined. As shown in Table 1, no activity was detected with each of the subunits itself. The combination of the small subunit and the large subunit containing intein also exhibited no activity. From these results, it was evident that the heterodimer structure composed of the small subunit and the large subunit without intein is essential to exhibiting the activity. Further, the heterodimer enzyme pET15b/PolSL(-Intein) composed of the small subunit and the large subunit without intein was purified. This purified enzyme (0.1 μg) and 10 mM MgSO4 were used to determine the activity to synthesize DNA. In the system with the enzyme, an increased radioactivity, 175 times or more, was detected when compared to that without the enzyme. Next, the purified enzyme of the present invention was used for PCR and it was confirmed that the amplified product had the same length as the target DNA fragment (1.9 kb) by agarose gel electrophoresis. On the other hand, in the system without the enzyme of the present invention, no PCR product was detected. From the above findings, it was further evident that the heterodimer DNA polymerase D of the present invention composed of the small subunit and the large subunit without intein has sufficiently activity.







TABLE 1







The detection of the DNA synthesizing activity using a solution of the


crude enzyme (2 ml) obtained from the recombinant E. coli










Enzyme source
Activity (CPM)














Negative control (distilled water only)
2,567



pET15b/PolS
1,181



pGEM/PolL
4,777



pGEM/PolL(-Intein)
3,827



pET15b/PolSL
3,237



pET15b/PolSL (-Intein)
12,323



Positive control (Deep Vent polymerase,
86,189



1 Unit)










4) Optimum pH

The optimum pH at 75° C. was 8.5 (FIG. 5).
5) Optimum Mg2+ Concentration
The optimum Mg2+ concentration of the enzyme of the present invention was 12 mM (FIG. 6).
6) Thermostability
As shown in FIG. 7, the enzyme of the present invention retained 50% of the activity after heating at 85° C. for 1 hr. Further, it retained 20% of the activity even after heating at 90° C. for 1 hr.
7) Primer Extension Activity
As shown in FIG. 8, while no primer extension activity was detected with the 15 mer primer by the enzyme of the present invention, when the primer was lengthened up to, for example, 34 mer or 50 mer long, the primer extension activity became greater. Such a primer extension activity dependent on primer length has not been reported with any other DNA polymerase.
8) 3′-5′ Exonuclease Activity
As shown in FIG. 9, the enzyme of the present invention exhibited great 3′-5′ exonuclease activity on the 50 mer oligonucleotide. From these findings, it was revealed that the enzyme of the present invention is a DNA-dependent DNA polymerase; is a heterodimer protein composed of two subunits having molecular weights of 144 kDa and 70 kDa, respectively; uses DNA as a template to synthesize a complementary strand; and has 3′-5′ exonuclease activity.
(b) Properties of PCNA
PCNA was expressed in a large quantity in recombinant E. coli. Most of the proteins derived from the E. coli were removed by heating, the nucleic acids were removed with polyethyleneimine, and ammonium sulfate precipitation was carried out for concentration followed by anion exchange chromatography and gel filtration column chromatography for complete purification. As shown in FIG. 10, the apparent molecular weight of the PCNA subunit estimated by SDS-PAGE matched with the molecular weight of 28 kDa predicted from the gene. Further, the molecular weight of the native form thereof was predicted to be 110 kDa from the elution position in the gel filtration chromatography of the purified sample, and hence PCNA was revealed to be a homotrimer.
(c) Properties of RFC Complex
1) SDS-PAGE for RFC Complex
RFC complex was expressed in a large quantity in recombinant E. coli. Most of the proteins derived from the E. coli were removed by heating, and then affinity chromatography using heparin, affinity chromatography using nickel resin for the histidine tag present at the N-terminal of the large subunit, and gel filtration column chromatography were carried out for complete purification. As shown in FIG. 11, the apparent molecular weights of the large subunit (L) and the small subunit (S) of RFC complex estimated by SDS-PAGE were 60 kDa and 36 kDa, respectively, which approximately matched with the respective molecular weights of 54 kDa and 38 kDa predicted from the gene. Further, the molar ratio of the large subunit and the small subunit was 1:4, which was calculated from the dye-coupling intensities of the bands of the large and small subunit proteins, and hence the native form thereof was revealed to be a heteropentamer.
(d) Recognition of PCNA by RFC Complex in the Absence of ATP
PCNA that bound to RFC complex was pulled down by using the histidine tag of RFC complex and nickel resin, which then was analyzed by SDS-PAGE. The results were shown in FIG. 12. From these results, it was revealed that both of RFC complex and PCNA were purified as active forms, and that RFC complex and PCNA recognize each other and have an activity to be bound together. Further, it was shown that this binding is not dependent on ATP.
(e) Requirement of ATPp for RFC Complex and PCNA to Enhance the Activity of the DNA Polymerase at a High Salt Concentration
As shown in FIG. 13, it was revealed that while the DNA polymerase D by itself was not able to exhibit DNA polymerase activity in the presence of 200 mM NaCl, when PCNA was added thereto, the enzyme was able to synthesize DNA up to 0.75 kb. On the other hand, it was revealed that when RFC complex and PCNA were added to the DNA polymerase D in the presence of 200 mM NaCl, the enzyme was able to synthesize the full-length complementary strand of M13ssDNA (7.2 kb) at 60° C. for 5 min. At this time, the addition of ATP was not required. On the contrary, it was found that, when 10 mM ATP was present, the effect of RFC complex and PCNA to enhance the DNA polymerase activity at a high salt concentration was significantly inhibited.
From the above results, it was revealed that the primer extension activity of the heterodimer DNA polymerase of the present invention at a high salt concentration can be significantly enhanced in the presence of PCNA and RFC, when compared to that in the absence thereof.

## Claims

1. A method for synthesizing deoxyribonucleic acid (DNA) comprising:
synthesizing a complement of a template DNA by contacting the template DNA with a primer and a DNA polymerase in the presence of deoxynucleotide triphosphates within an enzyme reaction system;
wherein said enzyme reaction system comprises a DNA polymerase from Pyrococcus horikoshii, protein complex (a), and protein complex (b), where
(a) is a protein complex having a clamp function composed of three molecules of a subunit comprising SEQ ID NO: 8, and
(b) is a protein complex having a clamp loader function composed of one molecule of a large subunit comprising SEQ ID NO: 10 and four molecules of a small subunit comprising SEQ ID NO: 14.

2. The method according to claim 1, wherein the enzyme reaction system does not contain ATP.

3. The method according to claim 1, wherein the enzyme reaction system contains sodium chloride at a concentration ranging from 0 to 200 mM.

4. The method according to claim 1, which is performed at a pH ranging from 6.0 to 7.5.

5. The method according to claim 1, which is performed at a pH ranging from 7.5 to 9.5.

6. The method according to claim 1, which is performed at a Mg2+ concentration ranging from 2.5 to 12.5 mM.

7. The method according to claim 1, which is performed at a Mg2+ concentration ranging from 12.5 to 20 mM.

8. The method according to claim 1, which is performed at a temperature ranging from 60 to 70° C.

9. The method according to claim 1, which is performed at a temperature ranging from 70 to 85° C.

10. The method according to claim 1, which is performed at a temperature ranging from 85 to 95° C.