Molecular phylogenetic analysis of archaeal intron-containing genes coding for rRNA obtained from a deep-subsurface geothermal water pool

Applied and Environmental Microbiology

Volumn 65, Issue 12, 1999, Pages 5586-5589

  Takai, Ken ^a,b   Horikoshi, Koki ^a  

^a JAPAN AGENCY FOR MARINE EARTH SCIENCE AND TECHNOLOGY   (Japan)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENDONUCLEASE; RIBOSOME RNA;

ARCHAEBACTERIUM; ARTICLE; BIODIVERSITY; DNA SEQUENCE; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; SEQUENCE ANALYSIS;

PYROBACULUM;

EID: 0032710404     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.65.12.5586-5589.1999     Document Type: Article

References (34)

1. Altschul, S. F., T. L. Madden, A. A. Schäffer, 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.
2. Bakken, L. R., and R. A. Olsen. 1989. DNA content of soil bacteria of different cell size. Soil Biol. Biochem. 21:789-793.
3. Bale, S. J., K. Goodman, P. A. Rochelle, J. R. Marchesi, J. C. Fry, A. J. Weightman, and R. J. Parkes. 1997. Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. Int. J. Syst. Bacteriol. 47:515-521.
4. 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.
5. Barns, S. M., R. E. Fundyga, M. W. Jeffries, and N. R. Pace. 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91:1609-1613.
6. Benson, D. A., M. S. Boguski, D. J. Lipman, J. Ostell, and B. F. F. Ouellette. 1998. GenBank. Nucleic Acids Res. 26:1-7.
7. Boone, D. R., Y. Liu, Z.-J. Zhao, D. L. Balkwill, G. R. Drake, T. O. Stevens, and H. C. Aldrich. 1995. Bacillus infernus sp. nov., an Fe(III)- and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface. Int. J. Syst. Bacteriol. 45:441-448.
8. Burggraf, S., N. Larsen, C. R. Woese, and K. O. Stetter. 1993. An intron within the 16S ribosomal RNA gene of the archaeon Pyrobaculum aerophilum. Proc. Natl. Acad. Sci. USA 90:2547-2550.
9. Dalgaard, J. Z., and R. A. Garrett. 1992. Protein-coding introns from the 23S rRNA-encoding gene form stable circles in the hyperthermophilic archaeon Pyrobaculum organotrophum. Gene 121:103-110.
10. Fredrickson, J. K. 1992. DOE explores subsurface biosphere. ASM News 58:183.
11. Fredrickson, J. K., F. J. Brockman, D. J. Workman, S. W. Li, and T. O. Stevens. 1991. Isolation and characterization of a subsurface bacterium capable of growth on toluene, naphthalene, and other aromatic compounds. Appl. Environ. Microbiol. 57:796-803.
12. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1992. Novel major archaebacterial group from marine plankton. Nature 356:148-149.
13. Gold, T. 1992. The deep, hot biosphere. Proc. Natl. Acad. Sci. USA 89:6045-6049.
14. Greene, A. C., B. K. C. Patel, and A. J. Sheehy. 1997. Deferribacter thermophilus gen. nov., sp. nov., a novel thermophilic manganese- and iron-reducing bacterium isolated from a petroleum reservoir. Int. J. Syst. Bacteriol. 47: 505-509.
15. Hirowatari, K., E. Nishiyama, and A. Tanaka. 1981. Research in chemical processing of water in geothermal electric power plants. Proc. Res. Kyusyu Electric Power Co. 56:15-27. (In Japanese.)
16. Itoh, T., K. Suzuki, and T. Nakase. 1998. Occurrence of introns in the 16S rRNA genes of members of the genus Thermoproteus. Arch. Microbiol. 170: 155-161.
17. Kieft, T. L., J. K. Fredrickson, T. C. Onstott, Y. A. Gorby, H. M. Kostandarithes, T. J. Bailey, D. W. Kennedy, S. W. Li, A. E. Plymale, C. M. Spadoni, and M. S. Gray. 1999. Dissimilatory reduction of Fe(III) and other electron acceptors by a Thermus isolate. Appl. Environ. Microhiol. 65:1214-1221.
18. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequence. J. Mol. Evol. 16:111-120.
19. Kjems, J., and R. A. Garrett. 1985. An intron in the 23S ribosomal RNA gene of the archaebacterium Desulfurococcus mobilis. Nature 318:675-677.
20. Lane, D.J. 1985. 16S/23S sequencing, p. 115-176. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York, N.Y.
21. Larsen, N., G. J. Olsen, B. L. Maidak, M. J. McCaughey, R. Overbeek, T. J. Macke, T. L. Marsh, and C. R. Woese. 1993. The Ribosomal Database Project. Nucleic Acids Res. 21:3021-3023.
22. L'Haridon, S., A.-L. Reysenbach, P. Glenat, D. Prieur, and C. Jeanthon. 1995. Hot subterranean biosphere in a continental oil reservoir. Nature 377: 223-224.
23. Lykke-Andersen, J., C. Aagaard, M. Semionenkov, and G. A. Garrett. 1997. Archaeal introns: splicing, intercellular mobility and evolution. Trends Biochem. Sci. 22:326-331.
24. Lykke-Andersen, J., and R. A. Garrett. 1994. Structural characteristics of the stable RNA introns of archaeal hyperthermophiles and their splicing junctions. J. Mol. Biol. 243:846-855.
25. Muller, J. E., M. Bryk, N. Loizos, and M. Belfort. 1993. Homing endonucleases, p. 111-143. In S. M. Linn, R. S. Lloyd, and R. J. Roberts (ed.), Nucleases. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
26. Nomura, N., Y. Sako, and A. Uchida. 1998. Molecular characterization and postsplicing fate of three introns within the single rRNA operon of the hyperthermophilic archaeon Aeropyrum pernix K1. J. Bacteriol. 180:3635-3643.
27. Ravot, G., M. Magot, M.-L. Fardeau, B. K. C. Patel, G. Prensier, A. Egan, J.-L. Garcia, and B. Ollivier. 1995. Thermotoga elfii sp. nov., a novel thermophilic bacterium from an African oil-producing well. Int. J. Syst. Bacteriol. 45:308-314.
28. Stetter, K. O., R. Huber, E. Blöchl, M. Kurr, R. D. Eden, M. Fielder, H. Cash, and I. Vance. 1993. Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs. Nature 365:743-745.
29. Stevens, T. O., and J. P. McKinley. 1995. Lithoautotrophic microbial ecosystems in deep basalt aquifers. Science 270:450-454.
30. Takai, K., and K. Horikoshi. 1999. Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152:1285-1297.
31. Takai, K., and Y. Sako. 1999. A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiol. Ecol. 28: 177-188.
32. Tanner, M. A., B. M. Goebel, M. A. Dojka, and N. R. Pace. 1998. Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants. Appl. Environ. Microbiol. 64:3110-3113.
33. Trp intron endonuclease from Halobacterium volcanii: unique substrate recognition properties. J. Biol. Chem. 263:17951-17959.
34. Whitman, W. B., O. C. Coleman, and W. J. Wiebe. 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95:6578-6583.