US20050019789A1

US20050019789A1 - Thermostable DNA polymerase from anaerocellum thermophilum

Info

Publication number: US20050019789A1
Application number: US10/770,989
Authority: US
Inventors: Waltraud Ankenbauer; Gudrun Schmitz-Agheguian; Elizaveta Bonch-Osmolovskaya; Vitaly Svetlichny; Ursula Markau; Bernhard Angerer; Astrid Reiser
Original assignee: Roche Diagnostics GmbH
Current assignee: Roche Diagnostics GmbH
Priority date: 1996-10-03
Filing date: 2004-02-02
Publication date: 2005-01-27
Also published as: NO991567D0; AU4942597A; NZ334654A; RU2002114591A; EP0954583A1; JP4285615B2; AU718256B2; JP2001502169A; CA2267217A1; IL129165A0; RU2198222C2; WO1998014588A1; EP0835935A1; CA2267217C; NO991567L; US6692932B1; RU2297454C2

Abstract

A thermostable enzyme is provided which is derived from the microorganism Anaerocellum thermophilum. The enzyme has a molecular weight of 96 to 100 kDa, shows DNA polymerase activity and reverse transcriptase activity in the presence of magnesium ions. The enzyme may be native or recombinant, and may be used with selected primers and nucleoside triphosphates in a temperature cycling polymerase chain reaction on DNA or RNA as template with or without additional DNA polymerases as an enzyme mixture.

Description

The present invention relates to a thermostable enzyme which is a DNA polymerase obtainable from Anaerocellum thermophilum.
Heat stable DNA polymerases (EC 2.7.7.7. DNA nucleotidyltransferase, DNA-directed) have been isolated from numerous thermophilic organisms (for example: Kaledin et al., 1980, Bio-kimiya Vol. 45, p. 644-651; Kaledin et al., 1981, Biokimiya Vol. 46, p. 1247-1254; Kaledin et al., 1982, Biokimiya Vol. 47, p. 1515-1521; Ruttimann, et al., 1985, Eur. J. Biochem. Vol. 149, p. 41-46; Neuner et al., 1990, Arch. Microbiol. Vol. 153, p. 205-207.)
For some organisms, the polymerase gene has been cloned and expressed (Lawyer et al., 1989, J. Biol. Chem. Vol. 264, p. 6427-6437; Engelke et al., 1990, Anal. Biochem. Vol. 191, p. 396-400; Lundberg et al., 1991, Gene, Vol. 108, p. 1-6; Kaledin et al., 1980 Biokimiya Vol. 44, p. 644-651; Kaledin et al., 1981, Biokimiya Vol. 46, p. 1247-1254; Kaledin et al., 1982, Biokimiya Vol. 47, p. 1515-1521; Ruttimann, et al., 1985, Eur. J. Biochem. Vol. 149, p. 41-46; Neuner et al., 1990, Arch. Microbiol. Vol. 153, p. 205-207; Perler et al., 1992, Proc. Natl. Acad. Sci. USA Vol. 89, p. 5577).
Thermophilic DNA polymerases are increasingly becoming important tools for use in molecular biology and there is growing interest in finding new polymerases which have more suitable properties and activities for use in diagnostic detection of RNA and DNA, gene cloning and DNA sequencing. At present, the thermophilic DNA polymerases mostly used for these purposes are from Thermus species like Taq polymerase from T. aquaticus (Brock et al 1969, J. Bacteriol. Vol. 98, p. 289-297).
Reverse transcription is commonly performed with viral reverse transcriptases like the enzymes isolated from Avian myeloblastosis virus or Moloney murine leukemia virus, which are active in the presence of Magnesium ions but have the disadvantages to possess RNase H-activity, which destroys the template RNA during the reverse transcription reaction and have a temperature optimum at 42° C. or 37° C., respectively.
Alternative methods are described using the reverse transcriptase activity of DNA polymerases of thermophilic organisms which are active at higher temperatures. Reverse transcription at higher temperatures is of advantage to overcome secondary structures of the RNA template which could result in premature termination of products. Thermostable DNA polymerases with reverse transcriptase activities are commonly isolated from Thermus species. These DNA polymerases however, show reverse transcriptase activity only in the presence of Manganese ions. These reaction conditions are suboptimal, because the presence of Manganese ions lowers the fidelity of the DNA polymerase transcribing the template RNA.
Therefore, it is desirable to develop a reverse transcriptase which acts at higher temperatures to overcome secondary structures of the template and is active in the presence of Magnesium ions in order to prepare cDNA from RNA templates with higher fidelity.
The present invention addresses these needs and provides a purified DNA polymerase enzyme (EC 2.7.7.7.) active at higher temperatures which has reverse transcriptase activity in the presence of magnesium ions. The invention comprises a DNA polymerase isolated from Anaerocellum thermophilum DSM 8995, deposited on the Deutsche Sammlung von Mikro-organismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig. In a further aspect the invention comprises a DNA polymerase that catalyses the template directed polymerisation of DNA and posess 5′-3′-polymerase activity, 5′-3′-exonuclease activity and no substantial 3′-5′-exonuclease activity.
The polymerase according to the present invention retains at least 90% of its activity after incubation for 30 Minutes at 80° C. in absence of stabilizing detergents.
In a further aspect the invention comprises a DNA polymerase having a molecular mass of about 96 to 100 kDa as determined by in situ activity PAGE analysis.
In a further aspect the invention comprises a DNA polymerase having reverse transcriptase activity in the presence of magnesiums ions and in the substantial absence of manganese ions. The polymerase according to the present invention exhibits a Mg²⁺ dependent reverse transcriptase activity of more than 30% relative to the DNA polymerase activity which is set to 100%. In a further aspect the present invention comprises a thermostable DNA polymerase wherein said polymerase exhibits a reverse transcriptase activity which is Mn²⁺ dependent. The Mn²⁺ dependent reverse transcriptase activity is more than 60% relative to the DNA polymerase activity.
In a further aspect the invention comprises a thermostable reverse transcriptase. The thermostable reverse transcriptase retains more than 80% after incubation for 60 minutes at 80° C.
Moreover, DNA encoding the 96.000-100.000 daltons thermostable DNA polymerase obtainable from Anearocellum thermophilum has been isolated and which allows to obtain the thermostable enzyme of the present invention by expression in E.coli. The entire Anearocellum thermophilum DNA polymerase coding sequence is depicted below as SEQ ID NO. 7. The recombinant Anearocellum thermophilum DNA polymerase also possesses 5′-3′polymerase activity, no substantial 3′-5′-exonuclease activity, 5′-3′-exonuclease activity and a reverse transcriptase activity which is a Mg²⁺ dependent.
Anaerocellum thermophilum was isolated from a hot spring in the Valley of Geysers in Kamchatka (V. Svetlichny et al. Mikrobilogiya, Vol. 59, No. 5 p. 871-879, 1990). Anaerocellum thermophilum was deposited with the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig under the terms of the Budapest Treaty and received DSM Accession Number 8995. The thermostable polymerase isolated from Anaerocellum thermophilum has a molecular weight of 96 to 100 kDa and retains more than 90% of activity after heating to 80° C. for 30 minutes in absence of stabilizing detergents. The thermostable enzyme possesses a 5′-3′ polymerase activity and a reverse transcriptase activity which is Mn⁺⁺ as well as Mg⁺⁺-dependent. The thermostable enzyme may be native or recombinant and may be used for first and second strand cDNA synthesis, in cDNA cloning, DNA sequencing, DNA labeling and DNA amplification.
The present invention provides improved methods for the replication and amplification of deoxyribonucleic (DNA) and ribonucleic acid (RNA) sequences. These improvements are achieved by the discovery and application of previously unknown properties of thermoactive DNA polymerases. In a preferred embodiment, the invention provides a method for synthesizing a complementary DNA copy from an RNA template with a thermoreactive DNA polymerase. In another aspect, the invention provides methods for amplifying a DNA segment from an RNA or DNA template using a thermostable DNA polymerase (RT-PCR or PCR).
The term “reverse transcriptase” describes a class of polymerases characterized as RNA-dependent DNA polymerases. All known reverse transcriptases require a primer to synthesize a DNA transcript from an RNA template. Historically, reverse transcriptase has been used primarily to transcribe MRNA into cDNA which can then be cloned into a vector for further manipulation.
For recovering the native protein Anaerocellum thermophilum may be grown using any suitable technique, such as the technique described by Svetlichny et al., 1991, System. Appl. Microbiol. Vol. 14, p. 205-208. After cell growth one preferred method for isolation and purification of the enzyme is accomplished using the multi-step process as follows:
The cells are thawed, suspended in buffer A (40 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 7 mM 2-mercaptoethanol, 0.4 M NaCl, 10 mM Pefabloc™ SC (4-(2-Aminoethyl)-benzolsulfonyl-fluorid, Hydrochlorid) and lysed by twofold passage through a Gaulin homogenizer. The raw extract is cleared by centrifugation, the supernatant dialyzed against buffer B (40 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 7 mM 2-mercaptoethanol, 10% Glycerol) and applied onto a column filled with Heparin-Sepharose (Pharmacia). In each case the columns are equilibrated with the starting solvent and after application of the sample the columns are washed with the threefold of their volume with this solvent. Eluation of the first column is performed with a linear gradient of 0 to 0.5 M NaCl in Buffer B. The fractions showing polymerase activity are pooled and ammonium sulfate is added to a final concentration of 20%. This solution is applied to a hydrophobic column containing Butyl-TSK-Toyopearl (TosoHaas). This column is eluted with a falling gradient of 20 to 0% ammonium sulfate. The pool containing the activity is dialyzed and again transferred to a column of DEAE-Sepharose (Pharmacia) and eluted with a linear gradient of 0-0.5 M NaCl in buffer B. The fourth column contains Tris-Acryl-Blue (Biosepra) and is eluted as in the preceding case. Finally the active fractions are dialyzed against buffer C (20 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 7.0 mM 2-mercaptoethanol, 100 mM NaCl, 50% Glycerol).
DNA polymerase activity was either measured by incorporation of ³²P-dCTP or by incorporation of digoxigenin labeled dUTP into the synthesized DNA. Detection and quantification of the incorporated digoxigenin was performed essentially as described in Höltke, H.-J.; Sagner, G. Kessler, C. and Schmitz, G., 1992, Biotechniques Vol. 12, p. 104-113.
Reverse transcriptase activity was measured using oligo dT primed poly A template by incorporation of either ³²P-dTTP or digoxigenin-labeled dUTP into the complementary strand. Detection of the incorporated digoxigenin was perfomed in analogy to the procedure used for detection of DNA polymerase activity.
In situ PAGE analysis of polymerase activity and reverse transcriptase activity was performed essentially according to the method described by Spanos A. and Hübscher U., 1983, Methods in Enzymology Vol. 91 p. 263-277. Some minor, but essential modifications to the original method are, that the renaturation of the SDS-denatured polypeptides is performed in the presence of magnesium ions (3 mM) and dATP (0.5-1 μM) to assist refolding.
The thermostable enzyme of this invention may also be produced by recombinant DNA techniques, as the gene encoding this enzyme has been cloned from Anaerocellum thermophilum genomic DNA. In a further aspect the invention includes a recombinant plasmid comprising the vector pASK75 carrying the Anaerocellum thermophilum DNA polymerase gene and designated pAR10.

The isolation of the recombinant clone expressing DNA polymerase from Anaerocellum thermophilum includes the following steps: chromosomal DNA from Anaerocellum thermophilum is isolated by treating the cells with detergent e.g. SDS and a proteinase e.g. Proteinase K. The solution is extracted with phenol and chloroform and the DNA purified by precipitation with ethanol. The DNA is dissolved in Tris/EDTA buffer and the gene encoding the DNA polymerase is specifically amplified by the PCR technique using two mixed oligonucleotides (primer 1 and 2). These oligonucleotides, described in SEQ ID NO.: 1 and SEQ ID NO.: 2, were designed on the basis of conserved regions of family A DNA polymerases as published by Braithwaite D. K. and Ito J., 1993, Nucl. Acids Res. Vol. 21, p. 787-802. The specifically amplified fragment is ligated into an vector, preferably the pCR™II vector (Invitrogen) and the sequence is determined by cycle-sequencing. Complete isolation of the coding region and the flanking sequences of the DNA polymerase gene can be performed by restriction fragmentation of the Anaerocellum thermophilum DNA with another restriction enzyme as in the first round of screening and by inverse PCR (Innis et al., (1990) PCR Protocols; Academic Press, Inc., p. 219-227). This can be accomplished with synthesized oligonucleotide primers binding at the outer DNA sequences of the gene part but in opposite orientation. These oligonucleotides, described by SEQ ID Nos. 3 and 4, were designed on the basis of the sequences which were determined by the first above described PCR. As template Anaerocellum thermophilum DNA is used which is cleaved by restriction digestion and circularized by contacting with T4 DNA ligase. To isolate the coding region of the whole polymerase gene, another PCR is performed using primers as shown in SEQ ID Nos. 5 and 6 to amplify the complete DNA polymerase gene directly from genomic DNA and introducing ends compatible with the linearized expression vector.


Primer 1:
5′-WSN GAY AAY ATH CCN GGN GT-3′:	SEQ ID NO. 1

Primer 2:
5′-NCC NAC YTC NAC YTC NAR NGG-3′:	SEQ ID NO. 2

Primer 3:
5′-CAA TTC AGG GCA GTG CTG CTG ATA	SEQ ID NO. 3

TC-3′:

Primer 4:
5′-GAG CTT CTG GGC ACT CTT TTC GCC-	SEQ ID NO. 4

3′:

Primer 5:
5′-CGA ATT CGG CCG TCA TGA AAC TGG	SEQ ID NO. 5

TTA TAT TCG ATG GAA ACA G-3′:

Primer 6:
5′-CGA ATT GGA TCC GTT TTG TCT CAT	SEQ ID NO. 6

ACC AGT TCA GTC CTT C-3′:

The gene is operably linked to appropriate control sequences for expression in either prokaryotic or eucaryotic host/vector systems. The vector preferably encodes all functions required for transformation and maintenance in a suitable host, and may encode selectable markers and/or control sequences for polymerase expression. Active recombinant thermostable polymerase can be produced by transformed host cultures either continuously or after induction of expression. Active thermostable polymerase can be recovered either from host cells or from the culture media if the protein is secreted through the cell membrane.
It is also preferable that Anaerocellum thermophilum thermostable polymerase expression is tightly controlled in E. coli during cloning and expression. Vectors useful in practicing the present invention should provide varying degrees of controlled expression of Anaerocellum thermophilum polymerase by providing some or all of the following control features: (1) promoters or sites of initiation of transcription, either directly adjacent to the start of the polymerase gene or as fusion proteins, (2) operators which could be used to turn gene expression on or off, (3) ribosome binding sites for improved translation, and (4) transcription or translation termination sites for improved stability. Appropriate vectors used in cloning and expression of Anaerocellum thermophilum polymerase include, for example, phage and plasmids. Example of phage include lambda gt11 (Promega), lambda Dash (Stratagene) lambda ZapII (Stratagene). Examples of plasmids include pBR322, pBTac2 (Boehringer Mannheim), pBluescript (Stratagene), pET3A (Rosenberg, A. H. et al., (1987) Gene 56:125-135), pASK75 (Biometra) and pET11C (Studier, F. W. et al. (1990) Methods in Enzymology, 185:60-89). According to the present invention the use of a plasmid has shown to be advantageously, particularly pASK75 (Biometra). The Plasmid pASK75 carrying the Anaerocellum thermophilum DNA polymerase gene is then designated pAR10.
Standard protocols exist for transformation, phage infection and cell culture (Maniatis, et al. (1982) Molecular Cloning: A Laboratory Manual, Cold Spring Harbour Laboratory Press). Of the numerous E. coli strains which can be used for plasmid transformation, the preferred strains include JM110 (ATCC 47013), LE392 pUBS 520 (Maniatis et al. supra; Brinkmann et al., (1989) Gene 85:109-114;), JM101 (ATCC No. 33876), XL1 (Stratagene), and RR1 (ATCC no. 31343), and BL21 (DE3) plysS (Studier, F. W. et al., (1990) Methods in Enzymology, supra). According to the present invention the use of the E. coli strain LE392 pUBS 520 has shown to be advantageously. The E. coli strain LE392 pUBS 520 transformed with the plasmid pASK75 carrying the Anaerocellum thermophilum DNA polymerase gene (designated pAR10) is then designated E. coli AR220 (DSM No. 11177). E. coli strain XL1. Blue (Stratagene) is among the strains that can be used for lambda phage, and Y1089 can be used for lambda gt11 lysogeny. The transformed cells are preferably grown at 37° C. and expression of the cloned gene is induced with anhydrotetracycline.
Isolation of the recombinant DNA polymerase can be performed by standard techniques. Separation and purification of the DNA polymerase from the E. coli extract can be performed by standard methods. These methods include, for example, methods utilizing solubility such as salt precipitation and solvent precipitation, methods utilizing the difference in molecular weight such as dialysis, ultra-filtration, gel-filtration, and SDS-polyacrylamide gel electrophoresis, methods utilizing a difference in electric charge such as ion-exchange column chromatography, methods utilizing specific interaction such as affinity chromatography, methods utilizing a difference in hydrophobicity such as reversed-phase high performance liquid chromatography and methods utilizing a difference in isoelectric point such as isoelectric focussing electrophoresis.
The thermostable enzyme of this invention may be used for any purpose in which such enzyme activity is necessary or desired. In a particularly preferred embodiment, the enzyme catalyzes the nucleic acid amplification reaction known as PCR. This process for amplifying nucleic acid sequences is disclosed and claimed in EP 0 201 189. The PCR nucleic acid amplification method involves amplifying at least one specific nucleic acid sequence contained in a nucleic acid or a mixture of nucleic acids and produces double stranded DNA. Any nucleic acid sequence, in purified or nonpurified form, can be utilized as the starting nucleic acid(s), provided it contains or is suspected to contain the specific nucleic acid sequence desired. The nucleic acid to be amplified can be obtained from any source, for example, from plasmids such as pBR322, from cloned DNA or RNA, from natural DNA or RNA from any source, including bacteria, yeast, viruses, organelles, and higher organisms such as plants and animals, or from preparations of nucleic acids made in vitro. DNA or RNA may be extracted from blood, tissue material such as chorionic villi, or amniotic cells by a variety of techniques. See, e.g., Maniatis T. et al., 1982, Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.) pp. 280-281. Thus the process may employ, for example, DNA or RNA, including messenger RNA, which DNA or RNA may be single-stranded or double-stranded. In addition, a DNA-RNA hybrid which contains one strand of each may be utilized.
The amplification of target sequences in DNA or from RNA may be performed to proof the presence of a particular sequence in the sample of nucleic acid to be analyzed or to clone a specific gene. DNA polymerase from Anaerocellum thermophilum is very useful for these processes. Due to the fact that the DNA polymerase from Anaerocellum thermophilum requires Mg⁺⁺ ions as a cofactor instead of Mn⁺⁺ like the other DNA polymerases from thermophilic organisms with reverse transcriptase activity of the state of the art the RNA templates can be copied with higher fidelity. These properties make DNA polymerase from Anaerocellum thermophilum a very useful tool for the molecular biologist.
DNA polymerase from Anaerocellum thermophilum may also be used to simplify and improve methods for detection of RNA target molecules in a sample. In these methods DNA polymerase from Anaerocellum thermophilum catalyzes: (a) reverse transcription, (b) second strand cDNA synthesis, and, if desired, (c) amplification by PCR. The use of DNA polymerase from Anaerocellum thermophilum in the described methods eliminates the previous requirement of two sets of incubation conditions which were necessary due to the use of different enzymes for each step. The use of DNA polymerase from Anaerocellum thermophilum provides RNA reverse transcription and amplification of the resulting complementary DNA with enhanced specificity and with fewer steps than previous RNA cloning and diagnostic methods.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a photograph of a DNA polymerase assay performed in situ. The DNA polymerase activity of DNA polymerase from Anaerocellum thermophilum is analysed in comparison with DNA polymerase I and Klenow fragment of E. coli and DNA polymerase from Thermus thermophilus. A fraction of DNA polymerase from Anaerocellum thermophilum was submitted to electrophoresis on a SDS-polyacrylamide gel containing activated (DNAseI treated) DNA. After electrophoresis the SDS was removed, the proteins were renatured over night and incubated at 72° C. in the presence of magnesium salt, dNTPs and digoxigenin labeled dUTPs to allow synthesis of the complementary strand. The nucleic acid was blotted to a nylon membrane and the newly synthesized DNA detected by a chemiluminescence reaction.
As control proteins DNA polymerase I and Klenow fragment of E. coli and DNA polymerase from Thermus thermophilus were analyzed on the same gel. Using these proteins as standards the apparent molecular weight of DNA polymerase from Anaerocellum thermophilum of 96.000 to 100.000 Daltons can be deduced.
FIG. 2 shows results obtained from assays determining the relative activity of the reverse transcriptase in dependence of varying concentrations of magnesium and manganese ions.
FIG. 3 shows the thermostability of DNA polymerase from Anaerocellum thermophilum. Aliquots of the DNA polymerase were incubated at 80° C. and the activity measured at the times indicated in the figure.
FIG. 4 shows the DNA sequence (SEQ ID No. 7) of the polymerase gene of Anaerocellum thermophilum and the derived peptide sequence (SEQ ID No. 8) for Anaerocellum thermophilum polymerase.
FIG. 5 shows the comparison ot the reverse transcriptase activity of Anaerocellum thermophilum polymerase with Thermus filiformis and Thermus thermophilus.

EXAMPLE 1

Isolation of DNA Polymerase
For recovering the native protein Anaerocellum thermophilum may be grown using any suitable technique, such as the technique described by Svetlichny et al., 1991, System. Appl. Microbiol. Vol. 14, p. 205-208. After cell growth one preferred method for isolation and purification of the enzyme is accomplished using the multi-step process as follows:
The cells are thawed, suspended in buffer A (40 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 7 mM 2-mercaptoethanol, 0.4 M NaCl, 10 mM Pefabloc™ SC (4-(2-Aminoethyl)-benzolsulfonyl-fluorid, Hydrochlorid) and lysed by twofold passage through a Gaulin homogenizer. The raw extract is cleared by centrifugation, the supernatant dialyzed against buffer B (40 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 7 mM 2-mercaptoethanol, 10% Glycerol) and applied onto a column filled with Heparin-Sepharose (Pharmacia). In each case the columns are equilibrated with the starting solvent and after application of the sample the columns are washed with the threefold of their volume with this solvent. Eluation of the first column is performed with a linear gradient of 0 to 0.5 M NaCl in Buffer B. The fractions showing polymerase activity are pooled and ammonium sulfate is added to a final concentration of 20%. This solution is applied to a hydrophobic column containing Butyl-TSK-Toyopearl (TosoHaas). This column is eluted with a falling gradient of 20 to 0% ammonium sulfate. The pool containing the activity is dialyzed and again transferred to a column of DEAE-Sepharose (Pharmacia) and eluted with a linear gradient of 0-0.5 M NaCl in buffer B. The fourth column contains Tris-Acryl-Blue (Biosepra) and is eluted as in the preceding case. Finally the active fractions are dialyzed against buffer C (20 mM Tris-HCl, pH 7.5, 0.1 mM EDTA, 7.0 mM 2-mercaptoethanol, 100 mM NaCl, 50% Glycerol).

EXAMPLE 2

Detection of Endonuclease, Exonuclease and Ribonuclease Activities:
Absence of endonuclease activity: 1 μg of plasmid DNA is incubated for 4 hours with an excess of purified DNA polymerase in 50 μl of test buffer with a paraffin oil overlay at 72° C.
Absence of nonspecific exonuclease activity: 1 μg of EcoRI/HindIII-fragments of lambda DNA are incubated in 50 μl of test buffer in the absence and presence of dNTPs (1 mM final concentration each) with an excess of purified DNA polymerase for 4 hours at 72° C. with a paraffin overlay.
Absence of ribonuclease activity: 3 μg of MS2 RNA are incubated with an excess of DNA polymerase in 20 μl of test buffer for 4 hours at 72° C. The RNA is subsequently analyzed by electrophoresis in a MOPS gel (Maniatis et al., 1982, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y.).

EXAMPLE 3

Determination of DNA Polymerase Activity
DNA polymerase activity was either measured by incorporation of ³²P-dCTP or by incorporation of digoxigenin labeled dUTP into the synthesized DNA.
Detection and quantification of ³²P-dCTP incorporation was measured as follows: The reaction mixture contained 50 mM Tris-HCl, pH 8.5; 12.5 mM (NH₄)₂SO₄; 10 mM KCl; 5 mM MgCl₂; 10 mM 2-mercaptoethanol, 200 μg/ml BSA, 200 μM of dATP, dGTP and dTTP, 100 μM dCTP, 12 μg of DNAse activated DNA from calf thymus and 0.1 μl of ³²P-dCTP (10 mCi/ml, 3000 Ci/mmol). After incubation for 30 min. at 70° C. the samples were placed on ice, 250 μl of 10% trichloroacetic acid were added, the samples mixed and incubated for 10 more min. on ice. 150 μl of the samples were filtrated through nylon membranes, the filters washed four times with 5% trichloroacetic acid. The filters were dried for 30 minutes at 80° C. and the radioactivity bound to the filters determined in a Packard Matrix 96 Direct Beta Counter.
Detection and quantification of the incorporated digoxigenin was performed essentially as described in Höltke, H.-J.; Sagner, G; Kessler, C. and Schmitz, G., 1992, Biotechniques Vol. 12, p. 104-113. Typically, this assay is performed in a total volume of 50 μl of a reaction mixture composed of 1 or 2 μl of diluted (0.05 U-0.01 U) DNA polymerase and 50 mM Tris-HCl, pH 8.5; 12.5 mM (NH₄)₂SO₄; 10 mM KCl; 5 mM MgCl₂; 10 mM 2-mercaptoethanol; 33 μM dNTPs; 200 μg/ml BSA; 12 μg of DNAse activated DNA from calf thymus and 0.036 μM digoxigenin-dUTP.
The samples are incubated for 30 min. at 72° C., the reaction is stopped by addition of 2 μl 0.5 M EDTA and the tubes placed on ice. After addition of 8 μl 5 M NaCl and 150 μl of Ethanol (precooled to −20° C.) the DNA is precipitated by incubation for 15 min. on ice and pelleted by centrifugation for 10 min. at 13000×rpm and 4° C. The pellet is washed with 100 μl of 70% Ethanol (precooled to −20° C.) and 0.2 M NaCl, centrifuged again and dried under vacuum. The pellets are dissolved in 50 μl Tris-EDTA (10 mM/0.1 mM; pH 7.5). 5 μl of the sample are spotted into a well of a nylon membrane bottomed white microwell plate (Pall Filtrationstechnik GmbH, Dreieich, FRG, product no: SM045BWP). The DNA is fixed to the membrane by baking for 10 min. at 70° C. The DNA loaded wells are filled with 100 μl of 0.45 μm-filtrated 1% blocking solution (100 mM maleic acid, 150 mM NaCl, 1% (w/v) casein, pH 7.5). All following incubation steps are done at room temperature. After incubation for 2 min. the solution is sucked through the membrane with a suitable vacuum manifold at −0.4 bar. After repeating the washing step, the wells are filled with 100 μl of a 1:10000-dilution anti-digoxigenin-AP, Fab fragments (Boehringer Mannheim, FRG, no: 1093274) diluted in the blocking solution described above. After incubation for 2 min. and sucking this step is repeated once. The wells are washed twice under vacuum with 200 μl of washing buffer 1 (100 mM maleic acid, 150 mM NaCl, 0.3% (v/v) Tween™ 20, pH7.5). After washing another two times under vacuum with 200 μl washing buffer 2 (10 mM Tris-HCl, 100 mM NaCl, 50 mM MgCl₂, pH 9.5), 50 μl of CSPD™ (Boehringer Mannheim, no: 1655884) diluted 1:100 in washing buffer 2, which serves as a chemiluminescent substrate for the alkaline phosphatase, are added to the wells and the microwell plate is incubated for 5 min. at room temperature. The solution is then sucked through the membrane and after 10 min. further incubation at room temperature the RLU/s (Relative Light Unit per second) are detected in a Luminometer e.g. MicroLumat LB 96 P (EG&G Berthold, Wildbad, FRG).
With a serial dilution of Taq DNA polymerase a standard curve is prepared from which the linear range serves as a standard for the activity determination of the DNA polymerase to be analyzed.

EXAMPLE 4

Determination of Reverse Transcriptase Activity
Reverse transcriptase activity was measured using oligo dT primed poly A template by incorporation of either ³²P-dTTP or digoxigenin-labeled dUTP into the complementary strand. Incorporation of 32P-dTTP was measured in a mixture containing 1 μg of poly A·(dT)₁₅, 500 μM of dTTP, 100 mg/ml BSA, 10 mM Tris-HCl, pH 8.5, 20 mM KCl, 0.5-10 mM MgCl₂or 0.1-5 mM MnCl₂, 10 mM DTE, 0.5 μg, of ³²P-dTTP (10 mM Ci/ml, 3000 Ci/mmol) and various amounts of DNA polymerase. The incubation temperature used was 50° C. The incorporated radioactivity was determined as described in the assay for determination of DNA polymerase activity.
Incorporation of digoxigenin-dUTP was measured in a mixture containing 1 μg of poly A·(dT)₁₅, 330 μM of dTTP, 0.36 μM of digoxigenin-dUTP, 200 mg/ml BSA, 10 mM Tris-HCl, pH 8.5, 20 mM KCl, 0.5-10 mM MgCl₂or 0.1-5 mM MnCl₂, 10 mM DTE and various amounts of DNA polymerase. The incubation temperature used was 50° C. Detection of the radioactivity incorporated was performed in analogy to the procedure used for detection of DNA polymerase activity.

EXAMPLE 5

Detection of DNA Polymerase and Reverse Transcriptase Activity in situ
In situ PAGE analysis of polymerase activity and reverse transcriptase activity was performed essentially according to the method described by Spanos A. and Hübscher U., 1983, Methods in Enzymology Vol. 91 p. 263-277. Some minor, but essential modifications to the original method are, that the renaturation of the SDS-denatured polypeptides is performed in the presence of magnesium ions (3 mM) and dATP (0.5-1 μM) to assist refolding.
In brief the method is as follows:
After separation of polypeptides from either crude cell extracts or purified samples on a denaturing 8% polyacrylamide gel (stacking gel 5% acrylamide) which contains 150 μg activated calf thymus DNA per ml gel volume, the gel is washed four times (15-30 min. each at room temperature with moderate shaking) in excess renaturation buffer (Tris-HCl, 50 mM, pH 8.4; EDTA, 1 mM; 2-mercaptoethanol, 3 mM; KCl, 50 mM; Glycerol, 5-10%) to remove SDS. Then the gel is incubated overnight in the same buffer, including 3 mM MgCl₂and 0.5-1 μM dATP at 4° C. without agitation. The first four washes are repeated the next day with renaturation buffer. After the removal of SDS and renaturation of the proteins the gel is transferred into the reaction mixture consisting of Tris-HCl, 50 mM, pH 8.4; KCl, 50 mM; DTT, 3 mM; MgCl₂, 7 mM; 12 μM of dATP, dCTP, dGTP (each), 8 μM dTTP and 4 μM Dig-dUTP; 10% (v/v) glycerol. The gel is first incubated under shaking at room temperature (30 min.) and then slowly warmed up to 72° C. by temperature increments of 5° C. At each temperature interval DNA synthesis is allowed to proceed for 30 min., in order to detect also polymerase activity of mesophile control polymerases. After DNA synthesis, the DNA is transferred either electrophoretically (0.25×TBE) or by capillary blotting (15×SSC) to nylon membranes (Boehringer Mannheim) and UV crosslinked. Newly synthesized Dig-labeled DNA is detected according to the procedure described for analysis of DNA polymerase activity.

EXAMPLE 6

Cloning of the Anaerocellum Thermophilum DNA Polymerase Gene.
Preparation of chromosomal DNA from Anaerocellum thermophilum. 0.8 g biomass of Anaerocellum thermophilum was suspended in 20 ml 1M KCl and centrifuged. Then the pellet was resuspended in 4.8 ml SET-buffer (150 mM NaCl, 15 mM EDTA, pH 8.0, 60 mM Tris-HCl, pH 8.0, 50 μg/μl RNaseA), after which 1 ml 20% SDS and 50 μl of proteinase K (10 mg/ml) were added. The mixture was kept at 37° C. for 45 min. After extraction with phenol and chloroform the DNA was precipitated with ethanol and dissolved in H₂O. Thus about 3.8 mg of DNA were obtained.
Amplification of Specific DNA by PCR.
For amplification of the gene encoding the DNA polymerase of Anaerocellum thermophilum by the PCR technique two mixed oligonucleotides (primer 1 and 2) were designed on the basis of conserved regions of family A DNA polymerases as published by Braithwaite D. K. and Ito J., 1993, Nucl. Acids Res. Vol.21, p. 787-802.

Primer 1:

5′-WSN GAY AAY ATH CCN GGN GT-3′: SEQ ID NO. 1

Primer 2:

5′-NCC NAC YTC NAC YTC NAR NGG-3′: SEQ ID NO. 2
The PCR amplification was performed in 100 μl buffer containing 750 ng of genomic DNA from Anaerocellum thermophilum, 10 mM Tris-HCl, pH 8.8, 2.5 mM MgCl₂, 50 mM KCl, 200 μM dNTPs, 100 pmoles of each primer and 2.5 units of Taq polymerase (Boehringer Mannheim GmbH). The target sequence was amplified by first denaturing at 95° C. for 2 min. followed by 30 cycles of 95° C. for 0.5 min, 50° C. for 1 min. and 72° C. for 2 min. Thermal cycling was performed in a Perkin Elmer GenAmp 9600 thermal cycler. Agarose gel electrophoresis showed, that a fragment of approximately 1,900 base pairs was amplified specifically. This fragment was ligated into the pCR™II vector (Invitrogen) and the sequence determined by cycle-sequencing. The amino acid sequence deduced from this nucleotide sequence was very similar to that of other known DNA polymerases, so that primer 3 and 4 could be designed for inverse PCR.

Primer 3:

5′-CAA TTC AGG GCA GTG CTG CTG ATA SEQ ID NO. 3

TC-3′:

Primer 4:

5′-GAG CTT CTG GGC ACT CTT TTC GCC- SEQ ID NO. 4

3′:
Inverse PCR was performed essentially as described in Triglia T. et al., 1988, Nucleic Acids Research Vol. 16, p. 8186. 5 μg genomic DNA from Anaerocellum thermophilum were cleaved by EcoRI according to supplier's specifications (Boehringer Mannheim GmbH) and treated with an equal volume of phenol/chloroform mixture. The aqueous phase was removed, the DNA precipitated with ethanol and collected by centrifugation.
For circularization the digested DNA was diluted to a concentration of 50 ng/μl in ligation buffer (Boehringer Mannheim GmbH). The ligation reaction was initiated by the addition of T4 DNA Ligase (Boehringer Mannheim GmbH) to a concentration of 0.2 units/μl and the reaction was allowed to proceed for 15 hrs at 15° C. The ligated DNA was then precipitated with ethanol and collected by centrifugation.
The PCR was performed in 50 μl buffer containing 50 mM Tris-Cl, pH 9.2, 16 mM (NH₄)₂SO₄, 2.25 mM MgCl₂, 2% (v/v) DMSO, 0.1% (v/v) Tween™ 20 (Poly(oxyethylen)_n-sorbitan-mono-laurat), 700 ng of circularized DNA obtained as described above, 50 pmoles of each primer, 500 μM dNTP and 0.75 μl enzyme mix (Expand Long Template PCR System, Boehringer Mannheim GmbH).
The cycle conditions were as follows: $1 \times denaturation of template for 2 \min . at 92 ° C . 10 \times [\begin{matrix} denaturation at 92 ° C . for 10 \sec . \\ annealing at 64 ° C . for 30 \sec . \\ elongation at 68 ° C . for 2 \min . \end{matrix} 20 \times [\begin{matrix} denaturation at 92 ° C . for 10 \sec . \\ annealing at 64 ° C . for 30 \sec . \\ elongation at 68 ° C . for 2 \min . + \\ cycle elongation of 20 \sec . for each cycle \end{matrix}$
Agarose gel electrophoresis revealed a specifically amplified DNA fragment 6,500 base pairs long. The DNA fragment was ligated into the pCR™II vector (Invitrogen) and sequenced. Deduced from this sequence primer 5 and 6 coding for the 5′- and 3′-ends, respectively, of the polymerase region could be designed. Primer 5 contained a EclX1 site and primer 6 contained a BamHI site.

The PCR was performed under the same conditions as described above (inverse PCR) using 750 ng genomic DNA from Anaerocellum thermophilum as template.


Primer 5:
5′-CGA ATT CGG CCG TCA TGA AAC TGG	SEQ ID NO. 5

TTA TAT TCG ATG GAA ACA G-3′:

Primer 6:
5′-CGA ATT GGA TCC GTT TTG TCT CAT	SEQ ID NO. 6

ACC AGT TCA GTC CTT C-3′:

Cloning and Expression.

The PCR product was purified by electrophoresis of 20 μl of the PCR mixture on a 0.8% agarose gel. The 2.552 kb band of the polymerase coding region was purified from the agarose by phenol extraction. The DNA was then treated with chloroform and precipitated with ethanol. The pellet was resuspended and digested with EclXI and BamHI according to supplier's specifications (Boehringer Mannheim GmbH) to give cohesive ends for directional cloning. The DNA was ligated into the expression vector pASK75 (Biometra) that had also been digested with EclXI and BamHI. The ligated products were introduced into E. coli strain LE392 pUBS520 (Brinkmann U., et al., 1989, Gene Vol. 85, p. 109-114) by transformation. Transformants were grown on L-agar containing 100 μg/ml ampicillin and 50 μg/ml kanamycin to allow selection of recombinants. Colonies were picked and grown in L-broth containing 100 μg/ml ampicillin and 50 μg/ml kanamycin, and plasmid DNA was prepared by alkaline lysis. The plasmids were screened for insertions by digestion with BamHI. Those recombinants containing inserts were grown in L-broth containing ampicillin and kanamycin and tested for the expression of thermophilic DNA polymerase by induction of exponentially growing culture with 0.2 μg/ml anhydrotetracycline and assaying the heat-treated extracts for DNA polymerase activity as described above (determination of DNA polymerase activity). A recombinant expressing the DNA polymerase from Anaerocellum thermophilum was obtained. The strain was designated E. coli AR220 (DSM No. 11177) and the plasmid pAR10.

EXAMPLE 7

DNA polymerase from Anaerocellum thermophilum was compared with DNA polymerases from Thermus thermophilus and Thermus filiformis.
Similar amounts (units) of the DNA polymerases were analyzed. Each enzyme was tested for DNA polymerase activity, for reverse transcriptase activity in the presence of Mg++ (5 mM) and reverse transcriptase activity in the presence of Mn++ (1 mM) under the reaction conditions optimal for the individual enzymes. In order to compare the ratio of DNA polymerase to reverse transcriptase activity, the relative light units (RLU) measured in the DNA polymerase assay were set to 100. The RLUs measured in the reverse transcriptase activity tests are expressed as percent of the polymerase activity. Results are shown in FIG. 5.

Claims

1-21. (Cancelled)

22. An isolated DNA encoding a purified thermostable DNA polymerase obtainable from Anaerocellum thermophilum that catalyses the template directed polymerisation of DNA, possesses 5′-3′polymerase activity, lacks 3′-5′-exonuclease activity, has a magnesium-dependent reverse transcriptase activity, and has a manganese-dependent reverse transcriptase activity.

23. The isolated DNA sequence of claim 22 that has the nucleotide sequence shown in SEQ ID NO. 7.

24. A vector containing the isolated DNA sequence of claim 23.

25. A microbial host transformed with the vector of claim 26.