New DNA polymerase from the hyperthermophilic marine archaeon Thermococcus thioreducens

Extremophiles

Volumn 12, Issue 6, 2008, Pages 775-788

  Marsic, Damien ^a,b   Flaman, Jean Michel ^c   Ng, Joseph D ^a,b  

^a HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^b UNIVERSITY OF ALABAMA IN HUNTSVILLE   (United States)

^c INSERM   (France)

Author keywords

Archaea; DNA polymerase; Hyperthermophilic; PCR; Thermococcus

Indexed keywords

DNA DIRECTED DNA POLYMERASE; PRIMER DNA; RECOMBINANT PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; ENZYME STABILITY; ENZYMOLOGY; ESCHERICHIA COLI; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROTEIN CONFORMATION; THERMOCOCCUS;

AMINO ACID SEQUENCE; BASE SEQUENCE; CLONING, MOLECULAR; DNA PRIMERS; DNA-DIRECTED DNA POLYMERASE; ENZYME STABILITY; ESCHERICHIA COLI; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; THERMOCOCCUS;

ARCHAEA; ESCHERICHIA COLI; THERMOCOCCALES; THERMOCOCCUS; THERMOCOCCUS GORGONARIUS;

EID: 55949087929     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-008-0181-7     Document Type: Article

References (50)

1. S Agrawal J Goodchild MP Civeira AH Thornton PS Sarin PD Zamecnik 1988 Oligodeoxynucleoside phophoramidates and phosphorothioates as inhibitiors of human immunodeficiency virus Proc Natl Acad Sci USA 85 7079 7083
2. T Blöndal SH Thorbjarnardóttir J Kieleczawa S Hjörleifsdóttir JK Kristjánsson JM Einarsson G Eggertsson 2001 Cloning, sequence analysis and functional characterization of DNA polymerase I from the thermophilic eubacterium Rhodothermus marinus Biotechnol Appl Biochem 34 37 45
3. Bonch-Osmolovskaya E, Svetlichny V, Ankenbauer W, Schmitz-Agheguian G, Angerer B, Ebenbichler C, Laue F (1996) Eur Patent Appl EP 0 834 570 A1
4. MM Bradford 1976 A rapid and sensitive method for the quantitation of microgram qualities of protein using the principle of protein-dye binding Anal Biochem 72 248 254
5. AT Brunger PD Adams GM Clore WL DeLano P Gros RW Grosse-Kunstleve J-S Jiang J Kuszewski M Nilges NS Pannu RJ Read LM Rice 1998 Crystallography & NMR System: a new solftware suite for macromolecular structure determination Acta Cryst D 54 905 921
6. MA Cambon-Bonavita P Schmitt M Zeiger JM Flaman F Lesongeur G Raguenes D Bindel N Frisch Z Lakkis D Dupret G Barbier J Querellou 2000 Cloning, expression, and characterization of DNA polymerase I from the hyperthermophilic archaea Thermococcus fumicolans Extremophiles 4 215 225
7. IKO Cann Y Ishino 1999 Archael DNA replication: identifying the pieces to solve a puzzle Genetics 152 1249 1267
8. J Cline JC Braman HH Hogrefe 1996 PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases Nucleic Acids Res 15 3546 3551
9. J Dietrich P Schmitt M Zeiger B Preve JL Rolland H Chaabihi Y Gueguen 2002 PCR performance of the highly thermostable proof-reading B-type DNA polymerase from Pyrococcus abyssi FEMS Microbiol Lett 217 89 94
10. JM Flaman T Frebourg V Moreau F Charbonnier C Martin C Ishioka SH Friend R Iggo 1994 A rapid PCR fidelity assay Nucleic Acids Res 22 3259 3260
11. JM Flaman T Frebourg V Moreau F Charbonnier C Martin P Chappuis AP Sappino IM Limacher L Bron J Benhattar 1995 A simple functional assay for screening cell lines, blood and tumors Proc Natl Acad Sci USA 92 3963 3967
12. MR Goddard A Burt 1999 Recurrent invasion and extinction of a selfish gene Proc Natl Acad Sci USA 96 13880 13885
13. Y Gueguen JL Rolland O Lecompte P Azam G Le Romancer D Flament JP Raffin J Dietrich 2001 Characterization of two DNA polymerases from the hyperthermophilic euyarchaeon Pyrococcus abyssi Eur J Biochem 268 5961 5969
14. H Hashimoto M Nishioka S Fujiwara M Takagi T Imanaka T Inoue Y Kai 2001 Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 J Mol Biol 306 469 477
15. G Henneke D Flament U Hübscher J Querellou JP Raffin 2005 The hyperthermophilic eurychaeota Pyrococcus abyssi likely requires the two DNA polymerases D and B for DNA replication J Mol Biol 350 53 64
16. R Hirata Y Ohsumi A Nakano H Kawasaki K Suzuki Y Anraku 1990 Molecular structure of gene, VMA1, encoding the catalytic subunit of H (+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae J Biol Chem 265 6726 6733
17. HH Hogrefe J Cline AE Lovejoy KB Nielson 2001 DNA polymerases from hyperthermophiles Methods Enzymol 334 91 116
18. KP Hopfner A Eichinger RA Engh F Laue B Angerer 1999 Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius Proc Natl Acad Sci USA 96 3600 3605
19. RM Horton HD Hunt SN Ho JK Pullen LR Pease 1989 Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension Gene 77 61 68
20. J Ito DK Braithwaite 1991 Compilation and alignment of DNA polymerase sequences Nucleic Acids Res 19 4045 4057
21. M Kahler G Antranikian 2000 Cloning and characterization of a family B DNA polymerase from the hyperthermophilic crenarchaeon Pyrobavulum islandicum J Bacteriol 182 655 663
22. PM Kane CT Yamashiro DF Wolczyk N Neff M Goebl TH Stevens 1990 Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase Science 250 651 657
23. Z Kelman S Pietrokovski J Hurwitz 1999 Isolation and characterization of a split B-type DNApolymerase from the archaeon Methanobacterium thermoautotrophicum deltaH J Biol Chem 274 28751 28761
24. H Kong RB Kucera WE Jack 1993 Characterization of a DNA polymerase from the hyperthermophile archaea Thermococcus litoralis. Vent DNA polymerase, steady state kinetics, thermal stability, processivity, strand displacement, and exonuclease activities J Biol Chem 268 1965 1975
25. S Kumar K Tamura IB Jakobsen M Nei 2001 MEGA2: molecular evolutionary genetics analysis software Bioinformatics 17 1244 1245
26. TA Kunkel F Eckstein AS Mildvan RM Koplitz LA Loeb 1981 Deoxynucleoside [1-thio] triphosphates prevent proofreading during in vitro DNA synthesis Proc Natl Acad Sci USA 78 6734 6738
27. H Lineweaver D Burk 1934 The determination of enzyme dissociation constants J Am Chem Soc 56 658 666
28. KS Lundberg DD Shoemaker MW Adams JM Short JA Soge EJ Mathur 1991 High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus Gene 108 1 6
29. Y Nakamura T Gojobori T Ikemura 2000 Codon usage tabulated from the international DNA sequence databases: status for the year 2000 Nucleic Acids Res 28 292
30. F Niehaus B Frey G Antranikian 1997 Cloning and characterization of a thermostable alphaa-DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. TY Gene 204 153 158
31. CM de Noronha JI Mullins 1992 Amplimers with 3′-terminal phosphorothioate linkages resist degradation by vent polymerase and reduce Taq polymerase mispriming PCR Methods 2 131 136
32. H Ohmori EC Friedberg RP Fuchs MF Goodman F Hanaoka D Hinkle TA Kundel CW Lawrence Z Livneh T Nohmi L Prakash S Prakash 2001 The Y-family of DNA polymerases Mol Cell 8 7 8
33. FB Perler 2002 InBase: the intein database Nucleic Acids Res 30 383 384
34. S Pietrokovski 2001 Intein spread and extinction in evolution Trends Genet 17 465 472
35. EV Pikuta D Marsic T Itoh AK Bej J Tang WB Whitman JD Ng OK Garriott RB Hoover 2007 Thermococcus thioreducens sp. nov., a novel hyperthermophilic, obligately sulfur-reducing archaeon from a deep-sea hydrothermal vent Int J Syst Evol Microbiol 57 1612 1618
36. SD Putney SJ Benkovic PR Schimmel 1981 A DNA fragment with an alpha-phosphorothiate nucleotide at one end is assymmetrically blocked from digestion by exonuclease III and can be replicated in vivo Proc Natl Acad Sci USA 78 7350 7354
37. J Riley R Butler D Ogilvie R Finniear D Jenner S Powell R Anand JC Smith AF Markham 1990 A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones Nucleic Acids Res 18 2887 2890
38. AC Rodriguez HW Park C Mao LS Beese 2000 Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9° N-7 J Mol Biol 299 447 462
39. N Saitou M Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425
40. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor, NY
41. G Sarkar RT Turner ME Bolander 1993 Restriction-site PCR: a direct method of unknown sequence retrieval adjacent to a known locus by using universal primers PCR Methods Appl 2 18 322
42. M Seville AB West AG Cull CS McHenry 1996 Fluorometeric assay for DNA polymerases and reverse transcriptases BioTechniques 21 664 672
43. A Skerra 1992 Phosphorothioate primers improve the amplification of DNA sequences by DNA polymerases with proofreading activity Nucleic Acids Res 20 3551 3554
44. MW Southworth H Kong RB Kucera J Ware HW Jannasch FB Perler 1996 Cloning of thermostable DNA polymerases from hyperthermophilic marine Archaea with emphasis on Thermococcus sp. 9° N-7 and mutations affecting 3′-5′ exonuclease activity Proc Natl Acad Sci USA 93 5281 5285
45. P Stothard 2000 The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences BioTechniques 28 1102 1104
46. M Takagi M Nishioka H Kakihara M Kitabayashi H Inoue B Kawakami M Oka T Imanaka 1997 Charaterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR Appl Environ Microbiol 63 4504 4510
47. JD Thompson DG Higgins TJ Gibson 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 22 4673 4680
48. H Tveit T Kristensen 2001 Fluorescence-based DNA polymerase assay Anal Biochem 289 96 98
49. J Wang AK Sattar CC Wang JD Karam WH Konigsberg TA Steitz 1997 Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69 Cell 89 1087 1099
50. KL Weber ME Bolander G Sarkar 1998 Rapid acquisition of unknown DNA sequence adjacent to a known segment by multiplex restriction site PCR BioTechniques 25 415 419