Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases

Molecular Biology and Evolution

Volumn 15, Issue 9, 1998, Pages 1207-1217

  Edgell, David R ^a,b   Malik, Shehre Banoo ^a,c   Doolittle, W Ford ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

^b STATE UNIVERSITY OF NEW YORK   (United States)

^c UNIVERSITY OF OTTAWA   (Canada)

Author keywords

Archaea; DNA polymerase; Gene duplication; Giardia; Trichomonas

Indexed keywords

DNA DIRECTED DNA POLYMERASE; DNA DIRECTED DNA POLYMERASE ALPHA; DNA DIRECTED DNA POLYMERASE DELTA; DNA POLYMERASE;

ARCHAEBACTERIUM; ARTICLE; DNA SEQUENCE; EUKARYOTE; GENE AMPLIFICATION; GENE DUPLICATION; GIARDIA LAMBLIA; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; TRICHOMONAS VAGINALIS;

ANIMALIA; ARCHAEA; EUKARYOTA; FUNGI; GIARDIA; GIARDIA INTESTINALIS; PROTOZOA; TRICHOMONAS; TRICHOMONAS VAGINALIS;

EID: 0031822199     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026028     Document Type: Article

References (58)

1. ADACHI, J., and M. HASEGAWA. 1992. MOLPHY, programs for molecular phylogenetics I-PROTML, maximum likelihood inference of protein phylogeny. Comput. Sci. Monogr. No. 28.
2. ALTSCHUL, S. F., W. GISH, W. MILLER, E. W. MYERS, and D. J. LIPMAN. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. ALTSCHUL, S. F., T. L. MADDEN, A. A. SCHAFFER, J. ZHANG, Z. ZHANG, W. MILLER, and D. J. LIPMAN. 1997. Gapped BLAST and PSI-BLAST - a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
4. BALDAUF, S., J. D. PALMER, and W. F. DOOLITTLE. 1996. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl. Acad. Sci. USA 93:7749-7754.
5. BONNER, C. A., S. HAYS, K. MCENTEE, and M. F. GOODMAN. 1990. DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 87:7663-7667.
6. BONNER, C. A., P. T. STUKENBERG, M. RAJAGOPALAN, R. ERITJA, M. O'DONNELL, K. MCENTEE, H. ECHOES, and M. F. GOODMAN. 1992. Processive DNA synthesis by DNA polymerase II mediated by DNA polymerase III accessory proteins. J. Biol. Chem. 267:11431-11438.
7. BRAITHWAITE, D. K., and J. ITO. 1993. Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res. 21:787-802.
8. BUDD, M. E., and J. L. CAMPBELL. 1993. DNA polymerases delta and epsilon are required for chromosomal replication in Saccharomyces cerevisiae. Mol. Cell. Biol. 13:496-505.
9. BUDD, M. E., K. D. WITRUP, J. E. BAILEY, and J. L. CAMPBELL. 1989. DNA polymerase I is required for premeiotic DNA replication and sporulation but not X-ray repair in Saccharomyces cerevisiae. Mol. Cell. Biol. 9:365-376.
10. BULT, C. J., O. WHITE, G. J. OLSEN et al. (38 co-authors). 1996. The complete genome sequence of the methanogenic archaeon Methanococcus jannaschii. Science 273:1058-1073.
11. CAVALIER-SMITH, T. 1993. Kindgom protozoa and its 18 phyla. Microbiol. Rev. 57:953-994.
12. CAVALIER-SMITH, T., and E. E. CHAO. 1996. Molecular phylogeny of the free-living archezoan Trepomonas agilis and the nature of the first eukaryote. J. Mol. Evol. 43:551-562.
13. CLAYTON, R. A., O. WHITE, K. A. KETCHUM, and J. C. VENTER. 1997. The first genome from the third domain of life. Nature 387:459-462.
14. EDGELL, D. R., and W. F. DOOLITTLE. 1997. Archaea and the origin(s) of DNA replication proteins. Cell 89:995-998.
15. EDGELL, D. R., H.-P. KLENK, and W. F. DOOLITTLE. 1997. Gene duplications in evolution of archaeal family B DNA polymerases. J. Bacteriol. 179:2632-2640.
16. FELSENSTEIN, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
17. FELSENSTEIN, J. 1996. PHYLIP (phylogeny inference package). Version 3.57c. Department of Genetics, University of Washington, Seattle.
18. FLEISCHMANN, R. D., M. D. ADAMS, O. WHITE et al. (37 co-authors). 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.
19. FORTERRE, P., C. ELIE, and M. KOHIYAMA. 1984. Aphidicolin inhibits growth and DNA synthesis in halophilic archaea. J. Bacteriol. 159:800-802.
20. FRASER, C. M., S. CASJENS, W. M. HUANG et al. (35 co-authors). 1997. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390:580-586.
21. FRASER, C. M., J. D. GOCAYNE, O. WHITE et al. (25 co-authors). 1995. The minimal gene complement of Mycoplasma genitalium. Science 270:397-403.
22. +-ATPase: implications for the origin of eukaryotes. Proc. Natl. Acad. Sci. USA 86:6661-6665.
23. HASEGAWA, M., and M. FUJIWARA. 1993. Relative efficiencies of the maximum-likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogenies. Mol. Phylogenet. Evol. 2:1-5.
24. HIMMELREICH, R., H. HILBER, H. PLAGENS, E. PIRKL, B. C. LI, and R. HERRMANN. 1996. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24:4420-4449.
25. HUELSENBECK, J. P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
26. HUELSENBECK, J. P. 1997. Is the Felsenstein zone a fly trap? Syst. Biol. 46:69-74.
27. HUGHES, A. J. JR., S. K. BRYAN, H. CHEN, R. E. MOSES, and C. S. MCHENRY. 1991. Escherichia coli DNA polymerase II is stimulated by DNA polymerase II holoenzyme auxiliary subunits. J. Biol. Chem. 266:4568-4573.
28. IWABE, N., K. I. KUMA, M. HASEGAWA, S. OSAWA, and T. MIYATA. 1989a. Evolutionary relationships of archaea, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA 86:9355-9399.
29. IWABE, N., K. I. KUMA, H. KISHINO, M. HASEGAWA, and T. MIYATA. 1989b. Evolution of RNA polymerases and branching patterns of the three major groups of archaea. J. Mol. Evol. 32:70-78.
30. IWASAKI, H., Y. ISHINO, H. TOH, A. NAKATA, and H. SHINAGAWA. 1991. Escherichia coli DNA polymerase II is homologous to α-like DNA polymerases. Mol. Gen. Genet. 226:24-33.
31. IWASAKI, H., A. NAKATA, G. C. WALKER, and H. SHINAGAWA. 1990. The Escherichia coli polB gene, which encodes DNA polymerase II, is regulated by the SOS system. J. Bacteriol. 172:6268-6273.
32. KANEKO, T., S. SATO, A. L. KOTANI et al. (21 co-authors). 1996. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3:109-136.
33. KESTI, T., H. FRANTTI, and J. E. SYVAOJA. 1993. Molecular cloning of the cDNA for the catalytic subunit of human DNA polymerase ∈. J. Biol. Chem. 268:10238-10245.
34. KLENK, H.-P., R. A. CLAYTON, J.-F. TOMB et al. (48 co-authors). 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-370.
35. KUHNER, M. K., and J. FELSENSTEIN. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rate. Mol. Biol. Evol. 11:459-468.
36. MORRISON, A., H. ARAKI, A. B. CLARK, R. K. HAMATAKE, and A. SUGINO. 1990. A third essential DNA polymerase in S. cerevisiae. Cell 62:1143-1151.
37. MORRISON, A., R. B. CHRISTENSEN, J. ALLEY, A. K. BECK, E. G. BERNSTINE, J. F. LEMONTT, and C. W. LAWRENCE. 1989. REV3, a Saccharomyces cerevisiae gene whose function is required for mutagenesis, is predicted to encode a nonessential DNA polymerase. J. Bacteriol. 171:5659-5667.
38. NAVAS, T. A., Z. ZHOU, and S. J. ELLEDGE. 1995. DNA polymerase epsilon links the DNA replication machinery to the S-phase checkpoint. Cell 80:29-39.
39. OCHMAN, H., A. S. GERBER, and D. L. HARTL. 1988. Genetic applications of an inverse polymerase chain reaction. Genetics 120:621-623.
40. RANGARAJAN, S., G. GUDMUNDSSON, Z. QIU, P. L. FOSTER, and M. F. GOODMAN. 1997. Escherichia coli DNA polymerase II catalyzes chromosomal and episomal DNA synthesis in vivo. Proc. Natl. Acad. Sci. USA 94:946-951.
41. REYSENBACH, A. L., L. J. GIVER, G. S. WICKHAM, and N. R. PACE. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Envrion. Microbiol. 58: 3417-3418.
42. SAMBROOK, J., E. F. FRITSCH, and T. MANIATIS. 1989. Molecular cloning, a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
43. SANDHU, G. S., J. W. PRECUP, and B. C. KLINE. 1989. Rapid one-step characterization of recombinant vectors by direct analysis of transformed Escherichia coli colonies. BioTechniques 7:689-690.
44. SCHINZEL, R., and K. J. BURGER. 1985. Sensitivity of halobacteria to aphidicolin, an inhibitor of eukaryotic α-type DNA polymerases. FEMS Microbiol. Lett. 25:187-190.
45. SMITH, D. R., L. A. DOUCETTE-SMITH, C. DELOUGHERY et al. (34 co-authors). 1997. Complete genome sequence of Methanobacterium thermoautotrophicum ΔH: Functional analysis and comparative genomics. J. Bacteriol. 179:7135-7155.
46. SOGIN, M. L., J. H. GUNDERSON, H. J. ELWOOD, R. A. ALONSO, and D. A. PEATTIE. 1989. Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia. Science 243:75-77.
47. STRIMMER, K., and A. VON HAESELER. 1996. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
48. SWOFFORD, D. L. 1993. PAUP, phylogenetic analysis using parsimony, Version 3.1. Illinois Natural History Survey, Champaign.
49. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, and D. M. HILLIS. 1996. Phylogenetic inference. Pp. 407-515 in D. M. HILLIS, G. MORITZ, and B. K. MABLE, eds. Molecular systematics. 2nd edition. Sinauer, Sunderland, Mass.
50. THOMPSON, J. D., D. G. HIGGINS, and T. J. GIBSON. 1994. CLUSTALW, improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
51. TOMB, J.-F., O. WHITE, A. R. KERLAVAGE et al. (40 co-authors). 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539-547.
52. UEMORI, T., Y. ISHINO, H. DOI, and I. KAT. 1995. The hyperthermophilic archaeon Pyrodictium occultum has two α-like DNA polymerases. J. Bacteriol. 177:2164-2177.
53. UEMORI, T., Y. ISHINO, K. TOH, I. ADADA, and I. KATO. 1993. Organization and nucleotide sequence of the DNA polymerase gene from the archaeon Pyrococcus furiosus. Nucleic Acids Res. 21:259-265.
54. WANG, J., A. K. SATTAR, C. C. WANG, J. D. KARAM, W. H. KONIGSBERG, and T. A. STEITZ. 1997. Crystal structure of a pol α family replication DNA polymerase from bacteriophage RB69. Cell 89:1087-1099.
55. WOESE, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221-271.
56. WOESE, C. R., L. ACHENBACH, P. ROUVIERE, and L. MANDELCO. 1991. Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst. Appl. Microbiol. 14:364-371.
57. WONG, S. W., A. F. WAHL, P.-M. YUAN, N. ARAI, B. E. PEARSON, K. ARAI, D. KORN, M. W. HUNKAPILLER, and T. S.-F. WANG. 1988. Human DNA polymerase α gene expression is cell proliferation dependent and its primary structure is similar to both prokaryotic and eukaryotic replicative DNA polymerases. EMBO J. 7:37-47.
58. ZABEL, H.-P., H. FISCHER, E. HOLLER, and J. WINTER. 1985. In vivo and in vitro evidence for eucaryotic α-type DNA polymerases in methanogens. Purification of the DNA polymerase of Methanococcus vaneilii. Syst. Appl. Microbiol. 6:111-118.