Skip to main content

Some NLM-NCBI services and products are experiencing heavy traffic, which may affect performance and availability. We apologize for the inconvenience and appreciate your patience. For assistance, please contact our Help Desk at info@ncbi.nlm.nih.gov.

Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 Feb 25;21(4):787–802. doi: 10.1093/nar/21.4.787

Compilation, alignment, and phylogenetic relationships of DNA polymerases.

D K Braithwaite 1, J Ito 1
PMCID: PMC309208  PMID: 8451181

Full text

PDF
787

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Akhmetzjanov A. A., Vakhitov V. A. Molecular cloning and nucleotide sequence of the DNA polymerase gene from Thermus flavus. Nucleic Acids Res. 1992 Nov 11;20(21):5839–5839. doi: 10.1093/nar/20.21.5839. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Albrecht J. C., Fleckenstein B. Structural organization of the conserved gene block of Herpesvirus saimiri coding for DNA polymerase, glycoprotein B, and major DNA binding protein. Virology. 1990 Feb;174(2):533–542. doi: 10.1016/0042-6822(90)90107-3. [DOI] [PubMed] [Google Scholar]
  3. 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]
  4. 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]
  5. Bjornson R. M., Rohrmann G. F. Nucleotide sequence of the polyhedron envelope protein gene region of the Lymantria dispar nuclear polyhedrosis virus. J Gen Virol. 1992 Jun;73(Pt 6):1499–1504. doi: 10.1099/0022-1317-73-6-1499. [DOI] [PubMed] [Google Scholar]
  6. Blanco L., Bernad A., Salas M. MIP1 DNA polymerase of S. cerevisiae: structural similarity with the E. coli DNA polymerase I-type enzymes. Nucleic Acids Res. 1991 Feb 25;19(4):955–955. doi: 10.1093/nar/19.4.955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chan B. S., Court D. A., Vierula P. J., Bertrand H. The kalilo linear senescence-inducing plasmid of Neurospora is an invertron and encodes DNA and RNA polymerases. Curr Genet. 1991 Aug;20(3):225–237. doi: 10.1007/BF00326237. [DOI] [PubMed] [Google Scholar]
  8. Chung D. W., Zhang J. A., Tan C. K., Davie E. W., So A. G., Downey K. M. Primary structure of the catalytic subunit of human DNA polymerase delta and chromosomal location of the gene. Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11197–11201. doi: 10.1073/pnas.88.24.11197. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Court D. A., Bertrand H. Genetic organization and structural features of maranhar, a senescence-inducing linear mitochondrial plasmid of Neurospora crassa. Curr Genet. 1992 Nov;22(5):385–397. doi: 10.1007/BF00352440. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Davison A. J. Channel catfish virus: a new type of herpesvirus. Virology. 1992 Jan;186(1):9–14. doi: 10.1016/0042-6822(92)90056-u. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Dunn J. J., Studier F. W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J Mol Biol. 1983 Jun 5;166(4):477–535. doi: 10.1016/s0022-2836(83)80282-4. [DOI] [PubMed] [Google Scholar]
  14. 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]
  15. Elliott R., Clark C., Jaquish D., Spector D. H. Transcription analysis and sequence of the putative murine cytomegalovirus DNA polymerase gene. Virology. 1991 Nov;185(1):169–186. doi: 10.1016/0042-6822(91)90765-4. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Foury F. Cloning and sequencing of the nuclear gene MIP1 encoding the catalytic subunit of the yeast mitochondrial DNA polymerase. J Biol Chem. 1989 Dec 5;264(34):20552–20560. [PubMed] [Google Scholar]
  18. Gibbs J. S., Chiou H. C., Hall J. D., Mount D. W., Retondo M. J., Weller S. K., Coen D. M. Sequence and mapping analyses of the herpes simplex virus DNA polymerase gene predict a C-terminal substrate binding domain. Proc Natl Acad Sci U S A. 1985 Dec;82(23):7969–7973. doi: 10.1073/pnas.82.23.7969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. 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]
  21. Hahn S., Rüger W. Organization of the bacteriophage T4 genome between map positions 150.745 and 145.824. Nucleic Acids Res. 1989 Aug 25;17(16):6729–6729. doi: 10.1093/nar/17.16.6729. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hammond R. A., Barnes M. H., Mack S. L., Mitchener J. A., Brown N. C. Bacillus subtilis DNA polymerase III: complete sequence, overexpression, and characterization of the polC gene. Gene. 1991 Feb 1;98(1):29–36. doi: 10.1016/0378-1119(91)90100-p. [DOI] [PubMed] [Google Scholar]
  23. 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]
  24. Hishinuma F., Hirai K. Genome organization of the linear plasmid, pSKL, isolated from Saccharomyces kluyveri. Mol Gen Genet. 1991 Apr;226(1-2):97–106. doi: 10.1007/BF00273592. [DOI] [PubMed] [Google Scholar]
  25. Hollingsworth H. C., Nossal N. G. Bacteriophage T4 encodes an RNase H which removes RNA primers made by the T4 DNA replication system in vitro. J Biol Chem. 1991 Jan 25;266(3):1888–1897. [PubMed] [Google Scholar]
  26. 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]
  27. Ito J., Braithwaite D. K. Yeast mitochondrial DNA polymerase is related to the family A DNA polymerases. Nucleic Acids Res. 1990 Nov 25;18(22):6716–6716. doi: 10.1093/nar/18.22.6716. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. 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]
  29. Joyce C. M., Kelley W. S., Grindley N. D. Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I. J Biol Chem. 1982 Feb 25;257(4):1958–1964. [PubMed] [Google Scholar]
  30. 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]
  31. Kaliman A. V., Krutilina A. I., Kryukov V. M., Bayev A. A. Cloning and DNA sequence of the 5'-exonuclease gene of bacteriophage T5. FEBS Lett. 1986 Jan 20;195(1-2):61–64. doi: 10.1016/0014-5793(86)80130-2. [DOI] [PubMed] [Google Scholar]
  32. 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]
  33. 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]
  34. Lancy E. D., Lifsics M. R., Munson P., Maurer R. Nucleotide sequences of dnaE, the gene for the polymerase subunit of DNA polymerase III in Salmonella typhimurium, and a variant that facilitates growth in the absence of another polymerase subunit. J Bacteriol. 1989 Oct;171(10):5581–5586. doi: 10.1128/jb.171.10.5581-5586.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Lawyer F. C., Stoffel S., Saiki R. K., Myambo K., Drummond R., Gelfand D. H. Isolation, characterization, and expression in Escherichia coli of the DNA polymerase gene from Thermus aquaticus. J Biol Chem. 1989 Apr 15;264(11):6427–6437. [PubMed] [Google Scholar]
  36. Leavitt M. C., Ito J. T5 DNA polymerase: structural--functional relationships to other DNA polymerases. Proc Natl Acad Sci U S A. 1989 Jun;86(12):4465–4469. doi: 10.1073/pnas.86.12.4465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Leegwater P. A., Strating M., Murphy N. B., Kooy R. F., van der Vliet P. C., Overdulve J. P. The Trypanosoma brucei DNA polymerase alpha core subunit gene is developmentally regulated and linked to a constitutively expressed open reading frame. Nucleic Acids Res. 1991 Dec 11;19(23):6441–6447. doi: 10.1093/nar/19.23.6441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Lopez P., Martinez S., Diaz A., Espinosa M., Lacks S. A. Characterization of the polA gene of Streptococcus pneumoniae and comparison of the DNA polymerase I it encodes to homologous enzymes from Escherichia coli and phage T7. J Biol Chem. 1989 Mar 5;264(7):4255–4263. [PubMed] [Google Scholar]
  39. Maki H., Horiuchi T., Sekiguchi M. Structure and expression of the dnaQ mutator and the RNase H genes of Escherichia coli: overlap of the promoter regions. Proc Natl Acad Sci U S A. 1983 Dec;80(23):7137–7141. doi: 10.1073/pnas.80.23.7137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. 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]
  41. 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]
  42. 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]
  43. Morrison A., Sugino A. Nucleotide sequence of the POL3 gene encoding DNA polymerase III (delta) of Saccharomyces cerevisiae. Nucleic Acids Res. 1992 Jan 25;20(2):375–375. doi: 10.1093/nar/20.2.375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Mustafa A., Yuen L. Identification and sequencing of the Choristoneura biennis entomopoxvirus DNA polymerase gene. DNA Seq. 1991;2(1):39–45. doi: 10.3109/10425179109008437. [DOI] [PubMed] [Google Scholar]
  45. 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]
  46. 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]
  47. 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]
  48. 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]
  49. 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]
  50. 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]
  51. Ridley R. G., White J. H., McAleese S. M., Goman M., Alano P., de Vries E., Kilbey B. J. DNA polymerase delta: gene sequences from Plasmodium falciparum indicate that this enzyme is more highly conserved than DNA polymerase alpha. Nucleic Acids Res. 1991 Dec 25;19(24):6731–6736. doi: 10.1093/nar/19.24.6731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Robison M. M., Royer J. C., Horgen P. A. Homology between mitochondrial DNA of Agaricus bisporus and an internal portion of a linear mitochondrial plasmid of Agaricus bitorquis. Curr Genet. 1991 Jun;19(6):495–502. doi: 10.1007/BF00312742. [DOI] [PubMed] [Google Scholar]
  53. Rådén B., Rutberg L. Nucleotide sequence of the temperate Bacillus subtilis bacteriophage SPO2 DNA polymerase gene L. J Virol. 1984 Oct;52(1):9–15. doi: 10.1128/jvi.52.1.9-15.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Savilahti H., Bamford D. H. The complete nucleotide sequence of the left very early region of Escherichia coli bacteriophage PRD1 coding for the terminal protein and the DNA polymerase. Gene. 1987;57(1):121–130. doi: 10.1016/0378-1119(87)90183-1. [DOI] [PubMed] [Google Scholar]
  55. Scarlato V., Gargano S. The DNA polymerase-encoding gene of Bacillus subtilis bacteriophage SPO1. Gene. 1992 Sep 1;118(1):109–113. doi: 10.1016/0378-1119(92)90256-o. [DOI] [PubMed] [Google Scholar]
  56. 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]
  57. 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]
  58. 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]
  59. Telford E. A., Watson M. S., McBride K., Davison A. J. The DNA sequence of equine herpesvirus-1. Virology. 1992 Jul;189(1):304–316. doi: 10.1016/0042-6822(92)90706-u. [DOI] [PubMed] [Google Scholar]
  60. 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]
  61. 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]
  62. Tomasiewicz H. G., McHenry C. S. Sequence analysis of the Escherichia coli dnaE gene. J Bacteriol. 1987 Dec;169(12):5735–5744. doi: 10.1128/jb.169.12.5735-5744.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. 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]
  64. Wheelis M. L., Kandler O., Woese C. R. On the nature of global classification. Proc Natl Acad Sci U S A. 1992 Apr;89:2930–2934. doi: 10.1073/pnas.89.7.2930. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. 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]
  66. 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]
  67. 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]
  68. 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]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES