Europäisches Patentamt *EP000544789B1* (19) European Patent Office Office européen des brevets (11) EP 0 544 789 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.7: C12N 15/54, C12N 9/12 of the grant of the patent: 05.03.2003 Bulletin 2003/10 (86) International application number: PCT/US91/05753 (21) Application number: 91915802.2 (87) International publication number: (22) Date of filing: 13.08.1991 WO 92/003556 (05.03.1992 Gazette 1992/06) (54) PURIFIED THERMOSTABLE NUCLEIC ACID POLYMERASE ENZYME FROM $i(TERMOTOGA MARITIMA) GEREINIGTES THERMOSTABILES NUKLEINSÄURE-POLYMERASEENZYM AUS THERMOTOGA MARITIMA ENZYME D’ACIDE NUCLEIQUE THERMOSTABLE PURIFIEE PROVENANT DE L’EUBACTERIE $i(THERMOTOGA MARITIMA) (84) Designated Contracting States: (74) Representative: Poredda, Andreas et al AT BE CH DE DK ES FR GB GR IT LI LU NL SE Roche Diagnostics GmbH, Patentabteilung, (30) Priority: 13.08.1990 US 567244 Sandhofer Strasse 116 68305 Mannheim (DE) (43) Date of publication of application: 09.06.1993 Bulletin 1993/23 (56) References cited: • CHEMICAL ABSTRACTS, vol. 105, no. 5, 04 (73) Proprietor: F. HOFFMANN-LA ROCHE AG August 1986, Columbus, OH (US); R. HUBER et 4002 Basel (CH) al., p. 386, AN 38901u • JOURNAL OF BIOLOGICAL CHEMISTRY, vol. (72) Inventors: 264, no. 11, 15 April 1989, American Society for • GELFAND, David, H. Biochemistry & Molecular Biology Inc., Oakland, CA 94611 (US) Baltimore, MD (US); F.C. LAWYER et al., pp. • LAWYER, Frances, C. 6427-6437 Oakland, CA 94611 (US) • STOFFEL, Susanne El Cerrito, CA 94530 (US) Note: Within nine months from the publication of the mention of the grant of the European patent, any person may give notice to the European Patent Office of opposition to the European patent granted. Notice of opposition shall be filed in a written reasoned statement. It shall not be deemed to have been filed until the opposition fee has been paid. (Art. 99(1) European Patent Convention). EP 0 544 789 B1 Printed by Jouve, 75001 PARIS (FR) EP 0 544 789 B1 Description Technical Field 5 [0001] The present invention relates to a purified, thermostable DNA polymerase purified from the hyperthermophilic eubacteria Thermotoga maritima and means for isolating and producing the enzyme. Thermostable DNA polymerases are useful in many recombinant DNA techniques, especially nucleic acid amplification by the polymerase chain reaction (PCR). 10 Background Art [0002] In Huber et al., 1986, Arch. Microbiol. 144:324-333, the isolation of the bacterium Thermotoga maritima is described. T. maritima is a eubacterium that is strictly anaerobic, rod-shaped, fermentative, hyperthermophilic, and grows between 55°C and 90°C, with an optimum growth temperature of about 80°C. This eubacterium has been iso- 15 lated from geothermally heated sea floors in Italy and the Azores. T. maritima cells have a sheath-like structure and monotrichous flagellation. T. maritima is classified in the eubacterial kingdom by virtue of having murein and fatty acid- containing lipids, diphtheria-toxin-resistant elongation factor 2, an RNA polymerase subunit pattern, and sensitivity to antibiotics. [0003] Extensive research has been conducted on the isolation of DNA polymerases from mesophilic microorganisms 20 such as E. coli. See, for example, Bessman et al., 1957, J. Biol. Chem. 223:171-177, and Buttin and Kornberg, 1966, J. Biol. Chem. 241:5419-5427. Much less investigation has been made on the isolation and purification of DNA polymer- ases from thermophiles such as Thermotoga maritima. In Kaledin et al., 1980, Biokhymiya 45:644-651, a six-step isolation and enrichment procedure for DNA polymerase activity from cells of a Thermus aquaticus YT-1 strain is disclosed. These steps involve isolation of crude extract, DEAE-cellulose chromatography, fractionation on hydroxya- 25 patite, fractionation on DEAE-cellulose, and chromatography on single-strand DNA-cellulose. The molecular weight of the purified enzyme is reported by Kaledin et al. as 62,000 daltons per monomeric unit. [0004] A second enrichment scheme for a polymerase from Thermus aquaticus is described in Chien et al., 1976, J. Bacteriol. 127:1550-1557. In this process, the crude extract is applied to a DEAE-Sephadex column. The dialyzed pooled fractions are then subjected to treatment on a phosphocellulose column. The pooled fractions are dialyzed, 30 and bovine serum albumin (BSA) is added to prevent loss of polymerase activity. The resulting mixture is loaded on a DNA-cellulose column. The pooled material from the column is dialyzed. The molecular weight of the purified protein is reported to be about 63,000 daltons to 68,000 daltons. [0005] The use of thermostable enzymes, such as those described in Chien et al. and Kaledin et al., to amplify existing nucleic acid sequences in amounts that are large compared to the amount initially present is described in U. 35 S. Patent Nos. 4,683,195; 4,683,202; and 4,965,188, which describe the PCR process, each of which is incorporated herein by reference. Primers, template, nucleoside triphosphates, the appropriate buffer and reaction conditions, and polymerase are used in the PCR process, which involves denaturation of target DNA, hybridization of primers, and synthesis of complementary strands. The extension product of each primer becomes a template for the production of the desired nucleic acid sequence. The patents disclose that, if the polymerase employed is a thermostable enzyme, 40 then polymerase need not be added after every denaturation step, because heat will not destroy the polymerase activity. [0006] U.S. Patent No. 4,889,818, European Patent Publication No. 258,017, Lawyer et al., 1989, J. Biol. Chem. 264:6427-6437, and PCT Publication No. 89/06691, describe the isolation and recombinant expression of an ~94 kDa thermostable DNA polymerase from Thermus aquaticus and the use of that polymerase in PCR. Although T. aquaticus DNA polymerase is especially preferred for use in PCR and other recombinant DNA techniques, there remains a need 45 for other thermostable polymerases. EP-A-359,006 discloses a thermostable DNA polymerase having excellent ther- mostability derived from Thermus thermophilus. [0007] Accordingly, there is a desire in the art to produce a purified, thermostable DNA polymerase that may be used to improve the PCR process described above and to improve the results obtained when using a thermostable DNA polymerase in other recombinant techniques, such as DNA sequencing, nick-tranlation and even reverse transcription 50 (see PCT Publication No. 91/09944). The present invention helps to meet that need by providing recombinant expres- sion vectors and purification protocols for Thermotoga maritima DNA polymerase. Disclosure of Invention 55 [0008] The present invention provides a purified thermostable DNA polymerase I enzyme that catalyzes combination of nucleoside triphosphates to form a nucleic acid strand complementary to a nucleic acid template strand, said enzyme is derived from Thermotoga maritima (Tma) and has 3' to 5' exonuclease activity. The native polymerase has a mo- lecular weight of about 97 kilodaltons (kDa) as measured by SDS-PAGE and an inferred molecular weight, from the 2 EP 0 544 789 B1 nucleotide sequence of the Tma DNA polymerase gene, of 102 kDa. This purified material may be used in PCR to produce a given nucleic acid sequence in amounts that are large compared to the amount initially present so that the sequences can be manipulated and/or analyzed easily. [0009] The gene encoding Tma DNA polymerase enzyme from Thermotoga maritima has also been identified, 5 cloned, sequenced, and expressed at high level and provides yet another means to prepare the thermostable enzyme of the present invention. In addition to the intact gene and the coding sequence for the Tma enzyme, derivatives of the coding sequence for Tma DNA polymerase are also provided. [0010] The invention also encompasses a stable enzyme composition comprising a purified, thermostable Tma en- zyme as described above in a buffer containing one or more non-ionic polymeric detergents. 10 [0011] Finally, the invention provides a method of purification for the thermostable polymerase of the invention. This method involves preparing a crude extract from Thermotoga maritima cells, adjusting the ionic strength of the crude extract so that the DNA polymerase dissociates from nucleic acid in the extract, subjecting the extract to hydrophobic interaction chromatography, subjecting the extract to DNA binding protein affinity chromatography, and subjecting the extract to cation or anion exchange or hydroxyapatite chromatography. In a preferred embodiment, these steps are 15 performed sequentially in the order given above. The nucleotide binding protein affinity chromatography step is pre- ferred for separating the DNA polymerase from endonuclease proteins. Modes for Carrying out the Invention 20 [0012] The present invention provides DNA sequences and expression vectors that encode Tma DNA polymerase, purification protocols for Tma DNA polymerase, preparations of purified Tma DNA polymerase, and methods for using Tma DNA polymerase. To facilitate understanding of the invention, a number of terms are defined below. [0013] The terms "cell," "cell line," and "cell culture" are used interchangeably and all such designations include progeny. Thus, the words "transformants" or "transformed cells" include the primary transformed cell and cultures 25 derived from that cell without regard to the number of transfers. All progeny may not be precisely identical in DNA content, due to deliberate or inadvertent mutations. Mutant progeny that have the same functionality as screened for in the originally transformed cell are included in the definition of transformants. [0014] The term "control sequences" refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for procaryotes, for example, 30 include a promoter, optionally an operator sequence, a ribosome binding site, and possibly other sequences, such as transcription termination sequences. Eucaryotic cells are known to utilize promoters, polyadenylation signals, and en- hancers.