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. 1993 Jan 25;21(2):259–265. doi: 10.1093/nar/21.2.259

Organization and nucleotide sequence of the DNA polymerase gene from the archaeon Pyrococcus furiosus.

T Uemori 1, Y Ishino 1, H Toh 1, K Asada 1, I Kato 1
PMCID: PMC309101  PMID: 8441634

Abstract

We cloned the gene encoding the thermostable DNA polymerase from the archaeon Pyrococcus furiosus. The DNA fragment of 2785 base pair (bp) containing the structural gene for DNA polymerase was sequenced. DNA polymerase (Pfu polymerase), as deduced from the DNA sequence, consisted of 775 amino acids, had a molecular weight of 90, 109, and was structurally homologous to the alpha-like DNA polymerases (family B) represented by human DNA polymerase alpha and Escherichia coli DNA polymerase II. An unrooted phylogenetic tree of the alpha-like DNA polymerases based on the amino acid sequence alignment was constructed. Pfu polymerase, with two other archaeon polymerases, constitutes a group with some animal viruses. The transcription initiation sites of the pol gene were identified by analysis of in vivo transcripts of both from P. furiosus and E. coli, and the promoters were assigned upstream of the pol coding region. A typical promoter sequence for the archaeon was found at a reasonable distance from the transcription initiation site in P. furiosus.

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Selected References

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  1. Baer R., Bankier A. T., Biggin M. D., Deininger P. L., Farrell P. J., Gibson T. J., Hatfull G., Hudson G. S., Satchwell S. C., Séguin C. DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature. 1984 Jul 19;310(5974):207–211. doi: 10.1038/310207a0. [DOI] [PubMed] [Google Scholar]
  2. Binns M. M., Stenzler L., Tomley F. M., Campbell J., Boursnell M. E. Identification by a random sequencing strategy of the fowlpoxvirus DNA polymerase gene, its nucleotide sequence and comparison with other viral DNA polymerases. Nucleic Acids Res. 1987 Aug 25;15(16):6563–6573. doi: 10.1093/nar/15.16.6563. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Boulet A., Simon M., Faye G., Bauer G. A., Burgers P. M. Structure and function of the Saccharomyces cerevisiae CDC2 gene encoding the large subunit of DNA polymerase III. EMBO J. 1989 Jun;8(6):1849–1854. doi: 10.1002/j.1460-2075.1989.tb03580.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cubellis M. V., Rozzo C., Montecucchi P., Rossi M. Isolation and sequencing of a new beta-galactosidase-encoding archaebacterial gene. Gene. 1990 Sep 28;94(1):89–94. doi: 10.1016/0378-1119(90)90472-4. [DOI] [PubMed] [Google Scholar]
  5. Damagnez V., Tillit J., de Recondo A. M., Baldacci G. The POL1 gene from the fission yeast, Schizosaccharomyces pombe, shows conserved amino acid blocks specific for eukaryotic DNA polymerases alpha. Mol Gen Genet. 1991 Apr;226(1-2):182–189. doi: 10.1007/BF00273602. [DOI] [PubMed] [Google Scholar]
  6. Davison A. J., Scott J. E. The complete DNA sequence of varicella-zoster virus. J Gen Virol. 1986 Sep;67(Pt 9):1759–1816. doi: 10.1099/0022-1317-67-9-1759. [DOI] [PubMed] [Google Scholar]
  7. Dekker B. M., van Ormondt H. The nucleotide sequence of fragment HindIII-C of human adenovirus type 5 DNA (map positions 17.1-31.7). Gene. 1984 Jan;27(1):115–120. doi: 10.1016/0378-1119(84)90244-0. [DOI] [PubMed] [Google Scholar]
  8. Earl P. L., Jones E. V., Moss B. Homology between DNA polymerases of poxviruses, herpesviruses, and adenoviruses: nucleotide sequence of the vaccinia virus DNA polymerase gene. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3659–3663. doi: 10.1073/pnas.83.11.3659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Elie C., De Recondo A. M., Forterre P. Thermostable DNA polymerase from the archaebacterium Sulfolobus acidocaldarius. Purification, characterization and immunological properties. Eur J Biochem. 1989 Jan 2;178(3):619–626. doi: 10.1111/j.1432-1033.1989.tb14490.x. [DOI] [PubMed] [Google Scholar]
  10. Engler J. A., Hoppe M. S., van Bree M. P. The nucleotide sequence of the genes encoded in early region 2b of human adenovirus type 7. Gene. 1983 Jan-Feb;21(1-2):145–159. doi: 10.1016/0378-1119(83)90156-7. [DOI] [PubMed] [Google Scholar]
  11. Fox B. A., Bzik D. J. The primary structure of Plasmodium falciparum DNA polymerase delta is similar to drug sensitive delta-like viral DNA polymerases. Mol Biochem Parasitol. 1991 Dec;49(2):289–296. doi: 10.1016/0166-6851(91)90072-e. [DOI] [PubMed] [Google Scholar]
  12. Gingeras T. R., Sciaky D., Gelinas R. E., Bing-Dong J., Yen C. E., Kelly M. M., Bullock P. A., Parsons B. L., O'Neill K. E., Roberts R. J. Nucleotide sequences from the adenovirus-2 genome. J Biol Chem. 1982 Nov 25;257(22):13475–13491. [PubMed] [Google Scholar]
  13. Grabherr R., Strasser P., Van Etten J. L. The DNA polymerase gene from chlorella viruses PBCV-1 and NY-2A contains an intron with nuclear splicing sequences. Virology. 1992 Jun;188(2):721–731. doi: 10.1016/0042-6822(92)90527-v. [DOI] [PubMed] [Google Scholar]
  14. Hirose F., Yamaguchi M., Nishida Y., Masutani M., Miyazawa H., Hanaoka F., Matsukage A. Structure and expression during development of Drosophila melanogaster gene for DNA polymerase alpha. Nucleic Acids Res. 1991 Sep 25;19(18):4991–4998. doi: 10.1093/nar/19.18.4991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Ishino Y. Rapid and reliable DNA sequencing with a dideoxy sequencing kit. Am Biotechnol Lab. 1992 Sep;10(9):47–47. [PubMed] [Google Scholar]
  16. Ito J., Braithwaite D. K. Compilation and alignment of DNA polymerase sequences. Nucleic Acids Res. 1991 Aug 11;19(15):4045–4057. doi: 10.1093/nar/19.15.4045. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Iwasaki H., Ishino Y., Toh H., Nakata A., Shinagawa H. Escherichia coli DNA polymerase II is homologous to alpha-like DNA polymerases. Mol Gen Genet. 1991 Apr;226(1-2):24–33. doi: 10.1007/BF00273583. [DOI] [PubMed] [Google Scholar]
  18. Jung G. H., Leavitt M. C., Hsieh J. C., Ito J. Bacteriophage PRD1 DNA polymerase: evolution of DNA polymerases. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8287–8291. doi: 10.1073/pnas.84.23.8287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kempken F., Meinhardt F., Esser K. In organello replication and viral affinity of linear, extrachromosomal DNA of the ascomycete Ascobolus immersus. Mol Gen Genet. 1989 Sep;218(3):523–530. doi: 10.1007/BF00332419. [DOI] [PubMed] [Google Scholar]
  20. Klimczak L. J., Grummt F., Burger K. J. Purification and characterization of DNA polymerase from the archaebacterium Sulfolobus acidocaldarius. Nucleic Acids Res. 1985 Jul 25;13(14):5269–5282. doi: 10.1093/nar/13.14.5269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kouzarides T., Bankier A. T., Satchwell S. C., Weston K., Tomlinson P., Barrell B. G. Sequence and transcription analysis of the human cytomegalovirus DNA polymerase gene. J Virol. 1987 Jan;61(1):125–133. doi: 10.1128/jvi.61.1.125-133.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Larder B. A., Kemp S. D., Darby G. Related functional domains in virus DNA polymerases. EMBO J. 1987 Jan;6(1):169–175. doi: 10.1002/j.1460-2075.1987.tb04735.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lundberg K. S., Shoemaker D. D., Adams M. W., Short J. M., Sorge J. A., Mathur E. J. High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus. Gene. 1991 Dec 1;108(1):1–6. doi: 10.1016/0378-1119(91)90480-y. [DOI] [PubMed] [Google Scholar]
  24. Mathur E. J., Adams M. W., Callen W. N., Cline J. M. The DNA polymerase gene from the hyperthermophilic marine archaebacterium, Pyrococcus furiosus, shows sequence homology with alpha-like DNA polymerases. Nucleic Acids Res. 1991 Dec 25;19(24):6952–6952. doi: 10.1093/nar/19.24.6952. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Matsudaira P. Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J Biol Chem. 1987 Jul 25;262(21):10035–10038. [PubMed] [Google Scholar]
  26. Matsumoto K., Takano H., Kim C. I., Hirokawa H. Primary structure of bacteriophage M2 DNA polymerase: conserved segments within protein-priming DNA polymerases and DNA polymerase I of Escherichia coli. Gene. 1989 Dec 14;84(2):247–255. doi: 10.1016/0378-1119(89)90498-8. [DOI] [PubMed] [Google Scholar]
  27. Morrison A., Araki H., Clark A. B., Hamatake R. K., Sugino A. A third essential DNA polymerase in S. cerevisiae. Cell. 1990 Sep 21;62(6):1143–1151. doi: 10.1016/0092-8674(90)90391-q. [DOI] [PubMed] [Google Scholar]
  28. Morrison A., Bell J. B., Kunkel T. A., Sugino A. Eukaryotic DNA polymerase amino acid sequence required for 3'----5' exonuclease activity. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9473–9477. doi: 10.1073/pnas.88.21.9473. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Morrison A., Christensen R. B., Alley J., Beck A. K., Bernstine E. G., Lemontt J. F., Lawrence C. W. REV3, a Saccharomyces cerevisiae gene whose function is required for induced mutagenesis, is predicted to encode a nonessential DNA polymerase. J Bacteriol. 1989 Oct;171(10):5659–5667. doi: 10.1128/jb.171.10.5659-5667.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Nishikawa K., Nakashima H., Kanehisa M., Ooi T. Detection of weak sequence homology of proteins for tertiary structure prediction. Protein Seq Data Anal. 1987;1(2):107–116. [PubMed] [Google Scholar]
  31. Oeser B., Tudzynski P. The linear mitochondrial plasmid pClK1 of the phytopathogenic fungus Claviceps purpurea may code for a DNA polymerase and an RNA polymerase. Mol Gen Genet. 1989 May;217(1):132–140. doi: 10.1007/BF00330952. [DOI] [PubMed] [Google Scholar]
  32. Paillard M., Sederoff R. R., Levings C. S. Nucleotide sequence of the S-1 mitochondrial DNA from the S cytoplasm of maize. EMBO J. 1985 May;4(5):1125–1128. doi: 10.1002/j.1460-2075.1985.tb03749.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Perler F. B., Comb D. G., Jack W. E., Moran L. S., Qiang B., Kucera R. B., Benner J., Slatko B. E., Nwankwo D. O., Hempstead S. K. Intervening sequences in an Archaea DNA polymerase gene. Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5577–5581. doi: 10.1073/pnas.89.12.5577. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Pignède G., Bouvier D., de Recondo A. M., Baldacci G. Characterization of the POL3 gene product from Schizosaccharomyces pombe indicates inter-species conservation of the catalytic subunit of DNA polymerase delta. J Mol Biol. 1991 Nov 20;222(2):209–218. doi: 10.1016/0022-2836(91)90207-m. [DOI] [PubMed] [Google Scholar]
  35. Pisani F. M., De Martino C., Rossi M. A DNA polymerase from the archaeon Sulfolobus solfataricus shows sequence similarity to family B DNA polymerases. Nucleic Acids Res. 1992 Jun 11;20(11):2711–2716. doi: 10.1093/nar/20.11.2711. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Pizzagalli A., Valsasnini P., Plevani P., Lucchini G. DNA polymerase I gene of Saccharomyces cerevisiae: nucleotide sequence, mapping of a temperature-sensitive mutation, and protein homology with other DNA polymerases. Proc Natl Acad Sci U S A. 1988 Jun;85(11):3772–3776. doi: 10.1073/pnas.85.11.3772. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Reiter W. D., Palm P., Zillig W. Analysis of transcription in the archaebacterium Sulfolobus indicates that archaebacterial promoters are homologous to eukaryotic pol II promoters. Nucleic Acids Res. 1988 Jan 11;16(1):1–19. doi: 10.1093/nar/16.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Reiter W. D., Palm P., Zillig W. Transcription termination in the archaebacterium Sulfolobus: signal structures and linkage to transcription initiation. Nucleic Acids Res. 1988 Mar 25;16(6):2445–2459. doi: 10.1093/nar/16.6.2445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Rella R., Raia C. A., Pisani F. M., D'Auria S., Nucci R., Gambacorta A., De Rosa M., Rossi M. Purification and properties of a thermophilic and thermostable DNA polymerase from the archaebacterium Sulfolobus solfataricus. Ital J Biochem. 1990 Mar-Apr;39(2):83–99. [PubMed] [Google Scholar]
  40. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  41. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Shu L. M., Hong J. S., Wei Y. F., Engler J. A. Nucleotide sequence of the genes encoded in early region 2b of human adenovirus type 12. Gene. 1986;46(2-3):187–195. doi: 10.1016/0378-1119(86)90403-8. [DOI] [PubMed] [Google Scholar]
  43. Simon M., Giot L., Faye G. The 3' to 5' exonuclease activity located in the DNA polymerase delta subunit of Saccharomyces cerevisiae is required for accurate replication. EMBO J. 1991 Aug;10(8):2165–2170. doi: 10.1002/j.1460-2075.1991.tb07751.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Spicer E. K., Rush J., Fung C., Reha-Krantz L. J., Karam J. D., Konigsberg W. H. Primary structure of T4 DNA polymerase. Evolutionary relatedness to eucaryotic and other procaryotic DNA polymerases. J Biol Chem. 1988 Jun 5;263(16):7478–7486. [PubMed] [Google Scholar]
  45. Stark M. J., Mileham A. J., Romanos M. A., Boyd A. Nucleotide sequence and transcription analysis of a linear DNA plasmid associated with the killer character of the yeast Kluyveromyces lactis. Nucleic Acids Res. 1984 Aug 10;12(15):6011–6030. doi: 10.1093/nar/12.15.6011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Teo I. A., Griffin B. E., Jones M. D. Characterization of the DNA polymerase gene of human herpesvirus 6. J Virol. 1991 Sep;65(9):4670–4680. doi: 10.1128/jvi.65.9.4670-4680.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Thomm M., Wich G. An archaebacterial promoter element for stable RNA genes with homology to the TATA box of higher eukaryotes. Nucleic Acids Res. 1988 Jan 11;16(1):151–163. doi: 10.1093/nar/16.1.151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Tomalski M. D., Wu J. G., Miller L. K. The location, sequence, transcription, and regulation of a baculovirus DNA polymerase gene. Virology. 1988 Dec;167(2):591–600. [PubMed] [Google Scholar]
  49. Tommasino M., Ricci S., Galeotti C. L. Genome organization of the killer plasmid pGK12 from Kluyveromyces lactis. Nucleic Acids Res. 1988 Jul 11;16(13):5863–5878. doi: 10.1093/nar/16.13.5863. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Treisman R., Proudfoot N. J., Shander M., Maniatis T. A single-base change at a splice site in a beta 0-thalassemic gene causes abnormal RNA splicing. Cell. 1982 Jul;29(3):903–911. doi: 10.1016/0092-8674(82)90452-4. [DOI] [PubMed] [Google Scholar]
  51. Tsurumi T., Maeno K., Nishiyama Y. Nucleotide sequence of the DNA polymerase gene of herpes simplex virus type 2 and comparison with the type 1 counterpart. Gene. 1987;52(2-3):129–137. doi: 10.1016/0378-1119(87)90039-4. [DOI] [PubMed] [Google Scholar]
  52. Wong S. W., Wahl A. F., Yuan P. M., Arai N., Pearson B. E., Arai K., Korn D., Hunkapiller M. W., Wang T. S. Human DNA polymerase alpha gene expression is cell proliferation dependent and its primary structure is similar to both prokaryotic and eukaryotic replicative DNA polymerases. EMBO J. 1988 Jan;7(1):37–47. doi: 10.1002/j.1460-2075.1988.tb02781.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Yang C. L., Chang L. S., Zhang P., Hao H., Zhu L., Toomey N. L., Lee M. Y. Molecular cloning of the cDNA for the catalytic subunit of human DNA polymerase delta. Nucleic Acids Res. 1992 Feb 25;20(4):735–745. doi: 10.1093/nar/20.4.735. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Yoshikawa H., Ito J. Nucleotide sequence of the major early region of bacteriophage phi 29. Gene. 1982 Mar;17(3):323–335. doi: 10.1016/0378-1119(82)90149-4. [DOI] [PubMed] [Google Scholar]
  55. Zhang J., Chung D. W., Tan C. K., Downey K. M., Davie E. W., So A. G. Primary structure of the catalytic subunit of calf thymus DNA polymerase delta: sequence similarities with other DNA polymerases. Biochemistry. 1991 Dec 24;30(51):11742–11750. doi: 10.1021/bi00115a002. [DOI] [PubMed] [Google Scholar]

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