Distribution of F- and A/V-type ATPases in Thermus scotoductus and other closely related species

Systematic and Applied Microbiology

Volumn 29, Issue 1, 2006, Pages 15-23

  Lapierre, Pascal ^a   Shial, Reshma ^a   Gogarten, J Peter ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

ATP synthase; ATPase; Deinococci; Horizontal gene transfer; Thermus scotoductus

Indexed keywords

ADENOSINE TRIPHOSPHATASE; GENOMIC DNA;

ARTICLE; BACILLUS; BACTERIAL STRAIN; DEINOCOCCUS RADIODURANS; GENE AMPLIFICATION; HORIZONTAL GENE TRANSFER; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SOUTHERN BLOTTING; THERMUS; THERMUS SCOTODUCTUS;

ARCHAEA; BACILLUS (BACTERIUM); BACTERIA (MICROORGANISMS); DEINOCOCCI; DEINOCOCCUS; DEINOCOCCUS RADIODURANS; MEIOTHERMUS RUBER; THERMUS; THERMUS FILIFORMIS; THERMUS SCOTODUCTUS;

EID: 30744474732     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2005.06.004     Document Type: Article

References (42)

1. D.L. Balkwill, T.L. Kieft, T. Tsukuda, H.M. Kostandarithes, T.C. Onstott, S. Macnaughton, J. Bownas, and J.K. Fredrickson Identification of iron-reducing Thermus strains as Thermus scotoductus Extremophiles 8 2004 37 44
2. H. Bruggemann, S. Baumer, W.F. Fricke, A. Wiezer, H. Liesegang, I. Decker, C. Herzberg, R. Martinez-Arias, R. Merkl, A. Henne, and G. Gottschalk The genome sequence of Clostridium tetani, the causative agent of tetanus disease Proc. Natl. Acad. Sci. USA 100 2003 1316 1321
3. A.M. Cerdeno-Tarraga, S. Patrick, L.C. Crossman, G. Blakely, V. Abratt, N. Lennard, I. Poxton, B. Duerden, B. Harris, M.A. Quail, A. Barron, L. Clark, C. Corton, J. Doggett, M.T. Holden, N. Larke, A. Line, A. Lord, H. Norbertczak, D. Ormond, C. Price, E. Rabbinowitsch, J. Woodward, B. Barrell, and J. Parkhill Extensive DNA inversions in the B. fragilis genome control variable gene expression Science 307 2005 1463 1465
4. D. Cossar, and R.J. Sharp Loss of Pigmentation in Thermus sp. M.S. DaCosta J.C. Duarte R.A.D. Williams Microbiology of Extreme Environments and its Potential for Biotechnology 1989 Elsevier Applied Science London 385
5. J. Felsenstein PHYLIP (Phylogeny Inference Package) version 3.6 Distributed by the author 1993 Department of Genetics, University of Washington Seattle
6. J.J. Ferretti, W.M. McShan, D. Ajdic, D.J. Savic, G. Savic, K. Lyon, C. Primeaux, S. Sezate, A.N. Suvorov, S. Kenton, H.S. Lai, S.P. Lin, Y. Qian, H.G. Jia, F.Z. Najar, Q. Ren, H. Zhu, L. Song, J. White, X. Yuan, S.W. Clifton, B.A. Roe, and R. McLaughlin Complete genome sequence of an M1 strain of Streptococcus pyogenes Proc. Natl. Acad. Sci. USA 98 2001 4658 4663
7. P. Forterre, N. Benachenhou-Lahfa, F. Confalonieri, M. Duguet, C. Elie, and B. Labedan The nature of the last universal ancestor and the root of the tree of life, still open questions Biosystems 28 1992 15 32
8. C.M. Fraser, S. Casjens, W.M. Huang, G.G. Sutton, R. Clayton, R. Lathigra, O. White, K.A. Ketchum, R. Dodson, E.K. Hickey, M. Gwinn, B. Dougherty, J.F. Tomb, R.D. Fleischmann, D. Richardson, J. Peterson, A.R. Kerlavage, J. Quackenbush, S. Salzberg, M. Hanson, R. van Vugt, N. Palmer, M.D. Adams, J. Gocayne, and J.C. Venter Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi Nature 390 1997 580 586
9. C.M. Fraser, S.J. Norris, G.M. Weinstock, O. White, G.G. Sutton, R. Dodson, M. Gwinn, E.K. Hickey, R. Clayton, K.A. Ketchum, E. Sodergren, J.M. Hardham, M.P. McLeod, S. Salzberg, J. Peterson, H. Khalak, D. Richardson, J.K. Howell, M. Chidambaram, T. Utterback, L. McDonald, P. Artiach, C. Bowman, M.D. Cotton, and J.C. Venter Complete genome sequence of Treponema pallidum, the syphilis spirochete Science 281 1998 375 388
10. J.E. Galagan, C. Nusbaum, A. Roy, M.G. Endrizzi, P. Macdonald, W. FitzHugh, S. Calvo, R. Engels, S. Smirnov, D. Atnoor, A. Brown, N. Allen, J. Naylor, N. Stange-Thomann, K. DeArellano, R. Johnson, L. Linton, P. McEwan, K. McKernan, J. Talamas, A. Tirrell, W. Ye, A. Zimmer, R.D. Barber, I. Cann, D.E. Graham, D.A. Grahame, A.M. Guss, R. Hedderich, C. Ingram-Smith, H.C. Kuettner, J.A. Krzycki, J.A. Leigh, W. Li, J. Liu, B. Mukhopadhyay, J.N. Reeve, K. Smith, T.A. Springer, L.A. Umayam, O. White, R.H. White, E. Conway de Macario, J.G. Ferry, K.F. Jarrell, H. Jing, A.J. Macario, I. Paulsen, M. Pritchett, K.R. Sowers, R.V. Swanson, S.H. Zinder, E. Lander, W.W. Metcalf, and B. Birren The genome of M. acetivorans reveals extensive metabolic and physiological diversity Genome Res. 12 2002 532 542
11. J.P. Gogarten, W.F. Doolittle, and J.G. Lawrence Prokaryotic evolution in light of gene transfer Mol. Biol. Evol. 19 2002 2226 2238
12. J.P. Gogarten, H. Kibak, P. Dittrich, L. Taiz, E.J. Bowman, B.J. Bowman, M.F. Manolson, R.J. Poole, T. Date, and T. Oshima Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes Proc. Natl. Acad. Sci. USA 86 1989 6661 6665
13. C. Gruber, and H. Stan-Lotter Western blot of stained proteins from dried polyacrylamide gels Anal. Biochem. 253 1997 125 127
14. W.R. Harvey Physiology of V-ATPases J. Exp. Biol. 172 1992 1 17
15. E. Hilario, and J.P. Gogarten Horizontal transfer of ATPase genes - the tree of life becomes a net of life Biosystems 31 1993 111 119
16. H. Imamura, M. Nakano, H. Noji, E. Muneyuki, S. Ohkuma, M. Yoshida, and K. Yokoyama Evidence for rotation of V1-ATPase Proc. Natl. Acad. Sci. USA 100 2003 2312 2315
17. J.K. Kristjansson, S. Hjorleifsdottir, V.T. Marteinsson, and G.A. Alfredsson Thermus scotoductus, sp. nov., a pigment-producing thermophilic bacterium from hot tap water in Iceland and including Thermus sp. X-1 System. Appl. Microbiol. 1994 44 50
18. C.L. Moyer, F.C. Dobbs, and D.M. Karl Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii Appl. Environ. Microbiol. 60 1994 871 879
19. Y. Mukohata, K. Ihara, M. Yoshida, J. Konishi, and Y. Sugiyama The halobacterial H+-translocating ATP synthase relates to the eukaryotic anion-sensitive H+-ATPase Arch. Biochem. Biophys. 259 1987 650 653
20. K.E. Nelson, R.D. Fleischmann, R.T. DeBoy, I.T. Paulsen, D.E. Fouts, J.A. Eisen, S.C. Daugherty, R.J. Dodson, A.S. Durkin, M. Gwinn, D.H. Haft, J.F. Kolonay, W.C. Nelson, T. Mason, L. Tallon, J. Gray, D. Granger, H. Tettelin, H. Dong, J.L. Galvin, M.J. Duncan, F.E. Dewhirst, and C.M. Fraser Complete genome sequence of the oral pathogenic Bacterium Porphyromonas gingivalis strain W83 J. Bacteriol. 185 2003 5591 5601
21. N. Nelson Structure, molecular genetics, and evolution of vacuolar H+-ATPases J. Bioenerg. Biomembr. 21 1989 553 571
22. C.L. Nesbo, K.E. Nelson, and W.F. Doolittle Suppressive subtractive hybridization detects extensive genomic diversity in Thermotoga maritima J. Bacteriol. 184 2002 4475 4488
23. L. Olendzenski, L. Liu, O. Zhaxybayeva, R. Murphey, D.G. Shin, and J.P. Gogarten Horizontal transfer of archaeal genes into the Deinococcaceae: detection by molecular and computer-based approaches J. Mol. Evol. 51 2000 587 599
24. C. Radax, O. Sigurdsson, G.O. Hreggvidsson, N. Aichinger, C. Gruber, J.K. Kristjansson, and H. Stan-Lotter F- and V-ATPases in the genus Thermus and related species System. Appl. Microbiol. 21 1998 12 22
25. A. Roger, M. Holder, PUZZLEBOOT, script available through the TreePuzzle homepage at http://tree-puzzle.de
26. G. Schafer M. Meyering-Vos, F-type or V-type? The chimeric nature of the archaebacterial ATP synthase Biochim. Biophys. Acta 1101 1992 232 235
27. H. Schmidt, K. Strimmer, M. Vingron, and A. von Haeseler TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing Bioinformatics 18 2002 502 504
28. T. Shimizu, K. Ohtani, H. Hirakawa, K. Ohshima, A. Yamashita, T. Shiba, N. Ogasawara, M. Hattori, S. Kuhara, and H. Hayashi Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater Proc. Natl. Acad. Sci. USA 99 2002 996 1001
29. R.S. Stephens, S. Kalman, C. Lammel, J. Fan, R. Marathe, L. Aravind, W. Mitchell, L. Olinger, R.L. Tatusov, Q. Zhao, E.V. Koonin, and R.W. Davis Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis Science 282 1998 754 759
30. M. Sumi, M. Yohda, Y. Koga, and M. Yoshida F0F1-ATPase genes from an archaebacterium Methanosarcina barkeri Biochem. Biophys. Res. Commun. 241 1997 427 433
31. D. Swofford PAUP* 4.0 beta version, Phylogenetic Analysis Using Parsimony (and Other Methods) 1998 Sinauer Associates, Inc. Sunderland, MA, USA
32. K. Takase, I. Yamato, and Y. Kakinuma Cloning and sequencing of the genes coding for the A and B subunits of vacuolar-type Na(+)-ATPase from Enterococcus hirae. Coexistence of vacuolar- and F0F1-type ATPases in one bacterial cell J. Biol. Chem. 268 1993 11,610 11,616
33. S. Tenreiro, M.F. Nobre, B. Hoste, M. Gillis, J.K. Kristjansson, and M.S. da Costa DNA:DNA hybridization and chemotaxonomic studies of Thermus scotoductus Res. Microbiol. 146 1995 315 324
34. H. Tettelin, K.E. Nelson, I.T. Paulsen, J.A. Eisen, T.D. Read, S. Peterson, J. Heidelberg, R.T. DeBoy, D.H. Haft, R.J. Dodson, A.S. Durkin, M. Gwinn, J.F. Kolonay, W.C. Nelson, J.D. Peterson, L.A. Umayam, O. White, S.L. Salzberg, M.R. Lewis, D. Radune, E. Holtzapple, H. Khouri, A.M. Wolf, T.R. Utterback, C.L. Hansen, L.A. McDonald, T.V. Feldblyum, S. Angiuoli, T. Dickinson, E.K. Hickey, I.E. Holt, B.J. Loftus, F. Yang, H.O. Smith, J.C. Venter, B.A. Dougherty, D.A. Morrison, S.K. Hollingshead, and C.M. Fraser Complete genome sequence of a virulent isolate of Streptococcus pneumoniae Science 293 2001 498 506
35. J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucl. Acids Res. 25 1997 4876 4882
36. S. Tsutsumi, K. Denda, K. Yokoyama, T. Oshima, T. Date, and M. Yoshida Molecular cloning of genes encoding major two subunits of a eubacterial V-Type ATPase from Thermus thermophilus Biochim. Biophys. Acta 1098 1991 13 20
37. O. White, J.A. Eisen, J.F. Heidelberg, E.K. Hickey, J.D. Peterson, R.J. Dodson, D.H. Haft, M.L. Gwinn, W.C. Nelson, D.L. Richardson, K.S. Moffat, H. Qin, L. Jiang, W. Pamphile, M. Crosby, M. Shen, J.J. Vamathevan, P. Lam, L. McDonald, T. Utterback, C. Zalewski, K.S. Makarova, L. Aravind, M.J. Daly, and C.M. Fraser Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1 Science 286 1999 1571 1577
38. R.A.D. Williams The Genus Thermus J.K. Kristjansson Thermophilic Bacteria 1992 CRC Press Inc Boca Raton, Ann Arbor, London 51 62
39. C.R. Woese Bacterial evolution Microbiol. Rev. 51 1987 221 271
40. C.R. Woese On the evolution of cells Proc. Natl. Acad. Sci. USA 99 2002 8742 8747
41. K. Yokoyama, T. Oshima, and M. Yoshida Thermus thermophilus membrane-associated ATPase - indication of a eubacterial V-Type ATPase J. Biol. Chem. 265 1990 21946 21950
42. L. Zimniak, P. Dittrich, J.P. Gogarten, H. Kibak, and L. Taiz The cDNA sequence of the 69-kDa subunit of the carrot vacuolar H+-ATPase. Homology to the beta-chain of F0F1-ATPases J. Biol. Chem. 263 1988 9102 9112