1887

Abstract

In order to clarify the current phylogeny of the haloarchaea, particularly the closely related genera that have been difficult to sort out using 16S rRNA gene sequences, the DNA-dependent RNA polymerase subunit B′ gene (′) was used as a complementary molecular marker. Partial sequences of the gene were determined from 16 strains of the family . Comparisons of phylogenetic trees inferred from the gene and protein sequences as well as from corresponding 16S rRNA gene sequences suggested that species of the genera , , , , , / and formed a monophyletic group in all trees. In the RpoB′ protein tree, the alkaliphilic species , and formed a tight group, while the neutrophilic species formed a separate group with species of the genera and . Species of the genus were split into two groups in both the ′ gene and protein trees. The most important advantage of the use of the gene over the 16S rRNA gene is that sequences of the former are highly conserved amongst species of the family . All sequences determined so far can be aligned unambiguously without any gaps. On the other hand, gaps are necessary at 49 positions in the inner part of the alignment of 16S rRNA gene sequences. The ′ gene and protein sequences can be used as an excellent alternative molecular marker in phylogenetic analysis of the .

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.65190-0
2007-10-01
2019-10-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/57/10/2289.html?itemId=/content/journal/ijsem/10.1099/ijs.0.65190-0&mimeType=html&fmt=ahah

References

  1. Acinas, S. G., Marcelino, L. A., Klepac-Ceraj, V. & Polz, M. F. ( 2004; ). Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186, 2629–2635.[CrossRef]
    [Google Scholar]
  2. Adékambi, T., Colson, P. & Drancourt, M. ( 2003; ). rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J Clin Microbiol 41, 5699–5708.[CrossRef]
    [Google Scholar]
  3. Baliga, N. S., Bonneau, R., Facciotti, M. T., Pan, M., Glusman, G., Deutsch, E. W., Shanonn, P., Chiu, Y., Weng, R. S. & other authors ( 2004; ). Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res 14, 2221–2234.[CrossRef]
    [Google Scholar]
  4. Bolhuis, H., Palm, P., Wende, A., Falb, M., Rampp, M., Rodriguez-Valera, F., Pfeifer, F. & Oesterhelt, D. ( 2006; ). The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 7, 169 [CrossRef]
    [Google Scholar]
  5. Boucher, Y., Douady, J. C., Sharma, K. A., Kamekura, M. & Doolittle, W. F. ( 2004; ). Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J Bacteriol 186, 3980–3990.[CrossRef]
    [Google Scholar]
  6. Burns, D. G., Janssen, P. H., Itoh, T., Kamekura, M., Li, Z., Jensen, G., Rodríguez-Valera, F. E., Bolhuis, H. & Dyall-Smith, M. L. ( 2007; ). Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain. Int J Syst Evol Microbiol 57, 387–392.[CrossRef]
    [Google Scholar]
  7. Case, R. J., Boucher, Y., Dahllöf, I., Holmström, C., Doolittle, W. F. & Kjelleberg, S. ( 2007; ). Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73, 278–288.[CrossRef]
    [Google Scholar]
  8. Castillo, A. M., Gutiérrez, M. C., Kamekura, M., Ma, Y., Cowan, D. A., Jones, B. E., Grant, W. D. & Ventosa, A. ( 2006; ). Halovivax asiaticus gen. nov., sp. nov., a novel extremely halophilic archaeon isolated from Inner Mongolia, China. Int J Syst Evol Microbiol 56, 765–770.[CrossRef]
    [Google Scholar]
  9. Cilia, V., Lafay, B. & Christen, R. ( 1996; ). Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level. Mol Biol Evol 13, 451–461.[CrossRef]
    [Google Scholar]
  10. Cui, H.-L., Tohty, D., Feng, J., Zhou, P.-J. & Liu, S.-J. ( 2006; ). Natronorubrum aibiense sp. nov., an extremely halophilic archaeon isolated from Aibi salt lake in Xin-Jiang, China, and emended description of the genus Natronorubrum. Int J Syst Evol Microbiol 56, 1515–1517.[CrossRef]
    [Google Scholar]
  11. Dahllöf, I., Baillie, H. & Kjelleberg, S. ( 2000; ). rpoB-based microbial community analysis avoid limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66, 3376–3380.[CrossRef]
    [Google Scholar]
  12. Dennis, P. P., Ziesche, S. & Mylvaganam, S. ( 1998; ). Transcription analysis of two disparate rRNA operons in the halophilic archaeon Haloarcula marismortui. J Bacteriol 180, 4804–4813.
    [Google Scholar]
  13. Enache, M., Itoh, T., Kamekura, M., Teodosiu, G. & Dumitru, L. ( 2007; ). Haloferax prahovense sp. nov., an extremely halophilic archaeon isolated from a Romanian salt lake. Int J Syst Evol Microbiol 57, 393–397.[CrossRef]
    [Google Scholar]
  14. Falb, M., Pfeifer, F., Palm, P., Rodeward, K., Hickmann, V., Tittor, J. & Oesterhelt, D. ( 2005; ). Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis. Genome Res 15, 1336–1343.[CrossRef]
    [Google Scholar]
  15. Fan, H., Xue, Y., Ma, Y., Ventosa, A. & Grant, W. D. ( 2004; ). Halorubrum tibetense sp. nov., a novel haloalkaliphilic archaeon from Lake Zabuye in Tibet, China. Int J Syst Evol Microbiol 54, 1213–1216.[CrossRef]
    [Google Scholar]
  16. Feng, J., Zhou, P., Zhou, Y.-G., Liu, S.-J. & Warren-Rhodes, K. ( 2005; ). Halorubrum alkaliphilum sp. nov., a novel haloalkaliphile isolated from a soda lake in Xinjiang, China. Int J Syst Evol Microbiol 55, 149–152.[CrossRef]
    [Google Scholar]
  17. Grant, W. D., Kamekura, M., McGenity, T. J. & Ventosa, A. ( 2001; ). Order I. Halobacteriales Grant and Larsen 1989b, 495VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 294–299. Edited by D. R. Boone, R. W. Castenholz & G. M. Garrity. New York: Springer.
  18. Gropp, F., Reiter, W.-D., Sentenac, A., Zillig, W., Schnabel, R., Thomm, M. & Stetter, K. O. ( 1986; ). Homologies of components of DNA-dependent RNA polymerases of archaebacteria, eukaryotes and eubacteria. Syst Appl Microbiol 7, 95–101.[CrossRef]
    [Google Scholar]
  19. Horikoshi, K. ( 1999; ). Alkaliphiles: some applications of their products for biotechnology. Microbiol Mol Biol Rev 63, 735–750.
    [Google Scholar]
  20. Itoh, T., Yamaguchi, T., Zhou, P. & Takashina, T. ( 2005; ). Natronolimnobius baerhuensis gen. nov., sp. nov., and Natronolimnobius innermongolicus sp. nov., novel haloalkaliphilic archaea isolated from soda lakes in Inner Mongolia, China. Extremophiles 9, 111–116.[CrossRef]
    [Google Scholar]
  21. Kamekura, M., Dyall-Smith, M. L., Upasani, V., Ventosa, A. & Kates, M. ( 1997; ). Diversity of alkaliphilic halobacteria: proposal for transfer of Natronobacterium vacuolatum, Natronobacterium magadii, and Natronobacterium pharaonis to Halorubrum, Natrialba and Natronomonas gen. nov., respectively, as Halorubrum vacuolatum comb. nov., Natrialba magadii comb. nov., and Natronomonas pharaonis comb. nov., respectively. Int J Syst Bacteriol 47, 853–857.[CrossRef]
    [Google Scholar]
  22. Klenk, H.-P. & Zillig, W. ( 1994; ). DNA-dependent RNA polymerase subunit B as a tool for phylogenetic reconstructions: branching topology of the archaeal domain. J Mol Evol 38, 420–432.[CrossRef]
    [Google Scholar]
  23. Korczak, B., Christensen, H., Elmer, S., Frey, J. & Kuhnert, P. ( 2004; ). Phylogeny of the family Pasteurellaceae based on rpoB sequences. Int J Syst Evol Microbiol 54, 1393–1399.[CrossRef]
    [Google Scholar]
  24. Langer, D., Hain, J., Thuriaux, P. & Zillig, W. ( 1995; ). Transcription in Archaea: similarity to that in Eucarya. Proc Natl Acad Sci U S A 92, 5768–5772.[CrossRef]
    [Google Scholar]
  25. Leffers, H., Gropp, F., Lottspeich, F., Zillig, W. & Garret, R. A. ( 1989; ). Sequence, organization, transcription and evolution of RNA polymerase subunit genes from the archaebacterial extreme halophiles Halobacterium halobium and Halococcus morrhuae. J Mol Biol 206, 1–17.[CrossRef]
    [Google Scholar]
  26. Rees, H. C., Grant, W. D., Jones, B. E. & Heaphy, S. ( 2004; ). Diversity of Kenyan soda lake alkaliphiles assessed by molecular methods. Extremophiles 8, 63–71.[CrossRef]
    [Google Scholar]
  27. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  28. Tamaoka, J. ( 1994; ). Determination of DNA base composition. In Chemical Methods in Prokaryotic Systematics, pp. 463–470. Edited by M. Goodfellow & A. G. O'Donnell. Chichester: Wiley.
  29. Tindall, B. J. ( 2003; ). Taxonomic problems arising in the genera Haloterrigena and Natrinema. Int J Syst Evol Microbiol 53, 1697–1698.[CrossRef]
    [Google Scholar]
  30. Vreeland, R. H., Straight, S., Krammes, J., Dougherty, K., Rosenzweig, W. D. & Kamekura, M. ( 2002; ). Halosimplex carlsbadense gen. nov., sp. nov., a unique halophilic archaeon, with three 16S rRNA genes, that grows only in defined medium with glycerol and acetate or pyruvate. Extremophiles 6, 445–452.[CrossRef]
    [Google Scholar]
  31. Walsh, D. A., Bapteste, E., Kamekura, M. & Doolittle, W. F. ( 2004; ). Evolution of the RNA polymerase B′ subunit gene (rpoB′) in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol Biol Evol 21, 2340–2351.[CrossRef]
    [Google Scholar]
  32. Wright, A.-D. G. ( 2006; ). Phylogenetic relationships within the order Halobacteriales inferred from 16S rRNA gene sequences. Int J Syst Evol Microbiol 56, 1223–1227.[CrossRef]
    [Google Scholar]
  33. Xu, Y., Wang, Z., Xue, Y., Zhou, P., Ma, Y., Ventosa, A. & Grant, W. D. ( 2001; ). Natrialba hulunbeirensis sp. nov. and Natrialba chahannaoensis sp. nov., novel haloalkaliphilic archaea from soda lakes in Inner Mongolia Autonomous Region, China. Int J Syst Evol Microbiol 51, 1693–1698.[CrossRef]
    [Google Scholar]
  34. Xue, Y., Fan, H., Ventosa, A., Grant, W. D., Jones, B. E., Cowan, D. A. & Ma, Y. ( 2005; ). Halalkalicoccus tibetensis gen. nov., sp. nov., representing a novel genus of haloalkaliphilic archaea. Int J Syst Evol Microbiol 55, 2501–2505.[CrossRef]
    [Google Scholar]
  35. Zillig, W., Stetter, K. O. & Tobien, M. ( 1978; ). DNA-dependent RNA polymerase from Halobacterium halobium. Eur J Biochem 91, 193–199.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.65190-0
Loading
/content/journal/ijsem/10.1099/ijs.0.65190-0
Loading

Data & Media loading...

Supplements

vol. , part 10, pp. 2289 - 2295

Aligned deduced amino acid sequences of RpoB′ and RpoB proteins. [PDF](149 KB)



PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error