Diversity of radA genes from cultured and uncultured Archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker

Journal of Bacteriology

Volumn 181, Issue 3, 1999, Pages 907-915

  Sandler, Steven J ^a,e   Hugenholtz, Philip ^b   Schleper, Christa ^c   Delong, Edward F ^c,f   Pace, Norman R ^a,b   Clark, Alvin J ^a,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e UNIVERSITY OF MASSACHUSETTS   (United States)

^f MONTEREY BAY AQUARIUM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENE; BACTERIUM CULTURE; BIODIVERSITY; COMPARATIVE STUDY; GENE INSERTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; UNINDEXED SEQUENCE;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 0032942273     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.181.3.907-915.1999     Document Type: Article

References (30)

1. Barns, S. M., C. F. Delwiche, J. D. Palmer, and N. R. Pace. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93:9188-9193.
2. Bishop, D. K., D. Park, L. Xu, and N. Kleckner. 1992. DMC1: a meiosisspecific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression. Cell 69:439-456.
3. Brendel, V., L. Brocchieri, S. J. Sandler, A. J. Clark, and S. Karlin. 1997. Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms. J. Mol. Evol. 44:528-541.
4. Bult, C., O. White, G. J. Olsen, L. Zhou, R. D. Fleischmann, J. D. Gocayne, A. R. Kerlavage, B. A. Dougherty, J. R. Tomb, and M. D. Adams, et al. 1996. Complete genome sequence of the methanogenic archaeon Methanococcus jannaschii. Science 273:1058-1073.
5. Clark, A. J., and A. D. Margulies. 1965. Isolation and characterization of recombination-deficient mutants of Escherichia coli K-12. Proc. Natl. Acad. Sci. USA 53:451.
6. DiRuggiero, J., J. R. Brown, A. P. Bogert, and F. T. Robb. DNA repair systems in archaea: momentos from the last universal common ancestor? J. Mol. Evol., in press.
7. Eisen, J. A. 1995. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of RecAs and 16S rRNAs from the same species. J. Mol. Evol. 41:1105-1123.
8. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package), version 3.5c. Department of Genetics, University of Washington, Seattle.
9. Hecker, K. H., and K. H. Roux. 1996. High and low annealing temperatures increase both specificity and yield in touchdown and stepdown PCR. Bio-Techniques 20:478-485.
10. Horii, T., T. Ogawa, and H. Ogawa. 1980. Organization of the recA gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 77:313-317.
11. Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180:366-376.
12. Karlin, S., and L. Brocchieri. 1996. Evolutionary conservation af recA genes in relation to protein structure and function. J. Bacteriol. 178:1881-1894.
13. Karlin, S., G. M. Weinstock, and V. Brendel. 1995. Bacterial classifications derived from recA protein sequence comparisons. J. Bacteriol. 177:6881-6893.
14. Klenk, H. P., R. A. Clayton, J. F. Tomb, O. White, K. E. Nelson, K. A. Ketchum, R. J. Dodson, M. Gwinn, E. K. Hickey, and J. D. Peterson, et al. 1997. The complete genome sequence of the hypertheromophilic sulphate-reducing archaeon Archeoglobus fulgidus. Nature 390:364-370.
15. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeck, M. J. McCaughey, and C. R. Woese. 1997. The RDP (Rihosomal Database Project). Nucleic Acids Res. 15:109-110.
16. Massana, R., A. E. Murray, C. M. Preston, and E. F. DeLong. 1997. Vertical distribution and phylogenetic characterization of marine planktonic archaea in the Santa Barbara Channel. Appl. Environ. Microbiol. 43:50-56.
17. Miller, R. V., and T. A. Kokjohn. 1990. General microbiology of recA: environmental and evolutionary significance. Annu. Rev. Microbiol. 44:365-394.
18. Olsen, G. Personal communication.
19. Preston, C. M., K. Y. Wu, T. F. Molinski, and E. F. DeLong. 1996. A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum, gen. nov., sp. nov. Proc. Natl. Acad. Sci. USA 93:6241-6246.
20. Rashid, N., M. Morikawa, and T. Imanaka. 1996. A RecA/RAD51 homologue from a hyper-thermophilic archaeon retains the major RecA domain only. Mol. Gen. Genet. 253:397-400.
21. Roca, A. I., and M. M. Cox. 1997. RecA protein: structure, function, and role in recombinational DNA repair. Prog. Nucleic Acid Res. Mol. Biol. 56:129-223.
22. Sandler, S. J., L. H. Satin, H. S. Samra, and A. J. Clark. 1996. recA-like genes from three archaean species with putative protein products similar to Rad51 and Dmc1 proteins of the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 24:2125-2132.
23. Shinohara, A., H. Ogawa, and T. Ogawa. 1992. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein. Cell 69:457-470.
24. Smith, D. R., L. A. Doucette-Stamm, C. Deloughery, H. Lee, J. Dubois, T. Aldredge, R. Rashirzadeh, D. Blakely, R. Cook, and K. Gilbert, et al. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum △ H: functional analysis and comparative genomics. J. Bacteriol. 179:7135-7155.
25. Stassen, N. Y., J. M. Logsdon, Jr., G. J. Vora, H. H. Offenberg, J. D. Palmer, and M. E. Zolan. 1997. Isolation and characterization of rad51 orthologs from Coprinus cinercus and Lycopersicon esculentum and phylogenetic analysis of eukaryotic recA homologs. Curr. Genet. 31:144-157.
26. Stein, J. L. T. L. M., K. Y. Wu, H. Shizuya, and E. F. DeLong. 1996. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol. 178:591-599.
27. Story, R. M., D. K. Bishop, N. Kleckner, and T. A. Steitz. 1993. Structural relationship of bacterial RecA proteins to recombination proteins from bacteriophage T4 and yeast. Science 259:1892-1896.
28. Story, R. M., and T. A. Steitz. 1992. Structure of the recA protein-ADP complex. Nature 355:374-376.
29. Volkl, P., P. Markiewicz, C. Baikalov, S. Fitz-Gibbon, K. O. Stetter, and J. H. Miller. 1996. Genomic and cDNA sequence tags of the hyperthermophilic archaean Pyrobaculum aierophilum. Nucleic Acids Res. 24:4373-1378.
30. 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.