A Heterodimeric DNA Polymerase: Evidence That Members of Euryarchaeota Possess a Distinct DNA Polymerase

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1998 Nov 25

PMID 9826686

Citations 59

Authors

I K Cann

K Komori

H Toh

S Kanai

Y Ishino

Affiliations

Soon will be listed here.

Abstract

We describe here a DNA polymerase family highly conserved in Euryarchaeota, a subdomain of Archaea. The DNA polymerase is composed of two proteins, DP1 and DP2. Sequence analysis showed that considerable similarity exists between DP1 and the second subunit of eukaryotic DNA polymerase delta, a protein essential for the propagation of Eukarya, and that DP2 has conserved motifs found in proteins with nucleotide-polymerizing activity. These results, together with our previous biochemical analyses of one of the members, DNA polymerase II (DP1 + DP2) from Pyrococcus furiosus, implicate the DNA polymerases of this family in the DNA replication process of Euryarchaeota. The discovery of this DNA-polymerase family, aside from providing an opportunity to enhance our knowledge of the evolution of DNA polymerases, is a significant step toward the complete understanding of DNA replication across the three domains of life.

Citing Articles

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References

Kiefer J, Mao C, Hansen C, Basehore S, Hogrefe H, Braman J . Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution. Structure. 1997; 5(1):95-108. DOI: 10.1016/s0969-2126(97)00169-x. View

Lee S, Hurwitz J . Mechanism of elongation of primed DNA by DNA polymerase delta, proliferating cell nuclear antigen, and activator 1. Proc Natl Acad Sci U S A. 1990; 87(15):5672-6. PMC: 54389. DOI: 10.1073/pnas.87.15.5672. View

Hashimoto K, Nakashima N, Ohara T, Maki S, Sugino A . The second subunit of DNA polymerase III (delta) is encoded by the HYS2 gene in Saccharomyces cerevisiae. Nucleic Acids Res. 1998; 26(2):477-85. PMC: 147283. DOI: 10.1093/nar/26.2.477. View

Kelman Z, ODonnell M . DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annu Rev Biochem. 1995; 64:171-200. DOI: 10.1146/annurev.bi.64.070195.001131. View

Smith D, DeLoughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R . Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol. 1997; 179(22):7135-55. PMC: 179657. DOI: 10.1128/jb.179.22.7135-7155.1997. View

NEEDLEMAN S, Wunsch C . A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970; 48(3):443-53. DOI: 10.1016/0022-2836(70)90057-4. View

Woese C, Fox G . Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A. 1977; 74(11):5088-90. PMC: 432104. DOI: 10.1073/pnas.74.11.5088. View

Kohlstaedt L, Wang J, Friedman J, Rice P, Steitz T . Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science. 1992; 256(5065):1783-90. DOI: 10.1126/science.1377403. View

Uemori T, Sato Y, Kato I, Doi H, Ishino Y . A novel DNA polymerase in the hyperthermophilic archaeon, Pyrococcus furiosus: gene cloning, expression, and characterization. Genes Cells. 1997; 2(8):499-512. DOI: 10.1046/j.1365-2443.1997.1380336.x. View

10.

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

11.

Tratner I, Piard K, Grenon M, Perderiset M, Baldacci G . PCNA and DNA polymerase delta catalytic subunit from Schizosaccharomyces pombe do not interact directly. Biochem Biophys Res Commun. 1997; 231(2):321-8. DOI: 10.1006/bbrc.1997.6082. View

12.

Olsen G, Woese C . Archaeal genomics: an overview. Cell. 1997; 89(7):991-4. DOI: 10.1016/s0092-8674(00)80284-6. View

13.

Edgell D, Doolittle W . Archaea and the origin(s) of DNA replication proteins. Cell. 1997; 89(7):995-8. DOI: 10.1016/s0092-8674(00)80285-8. View

14.

Kim Y, Eom S, Wang J, Lee D, Suh S, Steitz T . Crystal structure of Thermus aquaticus DNA polymerase. Nature. 1995; 376(6541):612-6. DOI: 10.1038/376612a0. View

15.

Bult C, White O, Olsen G, Zhou L, Fleischmann R, Sutton G . Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996; 273(5278):1058-73. DOI: 10.1126/science.273.5278.1058. View

16.

Stillman B . Smart machines at the DNA replication fork. Cell. 1994; 78(5):725-8. DOI: 10.1016/s0092-8674(94)90362-x. View

17.

Hansen J, Long A, SCHULTZ S . Structure of the RNA-dependent RNA polymerase of poliovirus. Structure. 1997; 5(8):1109-22. DOI: 10.1016/s0969-2126(97)00261-x. View

18.

Pearson W, Lipman D . Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988; 85(8):2444-8. PMC: 280013. DOI: 10.1073/pnas.85.8.2444. View

19.

Ishino Y, Komori K, Cann I, Koga Y . A novel DNA polymerase family found in Archaea. J Bacteriol. 1998; 180(8):2232-6. PMC: 107154. DOI: 10.1128/JB.180.8.2232-2236.1998. View

20.

Zhou J, He H, Tan C, Downey K, So A . The small subunit is required for functional interaction of DNA polymerase delta with the proliferating cell nuclear antigen. Nucleic Acids Res. 1997; 25(6):1094-9. PMC: 146557. DOI: 10.1093/nar/25.6.1094. View