1887

Abstract

The phylogenetic position of the has been re-examined by using phosphoglycerate kinase (Pgk) amino acid sequences. Hitherto unpublished sequences from subsp. , and were included in the analysis. Phylogenetic trees based on Pgk data indicated a monophyletic origin for the within the , whereas () and () appeared to be paraphyletic. With two exceptions, i.e. () and (), which clustered within the , comparative analyses show that at a low taxonomic level, the resolved phylogenetic relationships that were inferred from both the Pgk protein and 16S rRNA gene sequence data are congruent.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.02868-0
2004-05-01
2019-09-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/54/3/ijs540871.html?itemId=/content/journal/ijsem/10.1099/ijs.0.02868-0&mimeType=html&fmt=ahah

References

  1. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef]
    [Google Scholar]
  2. Balish, M. F. & Krause, D. C. ( 2002; ). Cytadherence and the cytoskeleton. In Molecular Biology and Pathogenicity of Mycoplasmas, pp. 491–519. Edited by S. Razin & R. Herrmann. New York: Kluwer.
  3. Brochier, C. & Philippe, H. ( 2002; ). Phylogeny: a non-hyperthermophilic ancestor for Bacteria. Nature 417, 244.[CrossRef]
    [Google Scholar]
  4. Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E. & Stanhope, M. J. ( 2001; ). Universal trees based on large combined protein sequence data sets. Nat Genet 28, 281–285.[CrossRef]
    [Google Scholar]
  5. Chattopadhyay, S. & Chakrabarti, J. ( 2003; ). Temporal changes in phosphoglycerate kinase coding sequences: a quantative measure. J Comput Biol 10, 83–93.[CrossRef]
    [Google Scholar]
  6. Ciccarese, S., Tommasi, S. & Vonghia, G. ( 1989; ). Cloning and cDNA sequence of the rat X-chromosome linked phosphoglycerate kinase. Biochem Biophys Res Commun 165, 1337–1344.[CrossRef]
    [Google Scholar]
  7. Dandekar, T., Snel, B., Schmidt, S., Lathe, W., Suyama, M., Huynen, M. & Bork, P. ( 2002; ). Comparative genome analysis of the Mollicutes. In Molecular Biology and Pathogenicity of Mycoplasmas, pp. 255–279. Edited by S. Razin & R. Herrmann. New York: Kluwer.
  8. Daubin, V., Gouy, M. & Perrière, G. ( 2002; ). A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 12, 1080–1090.[CrossRef]
    [Google Scholar]
  9. Felsenstein, J. ( 1993; ). phylip (phylogeny inference package), version 3.6. Department of Genetics, University of Washington, Seattle, USA.
  10. Fothergill-Gilmore, L. A. ( 1986; ). Domains of glycolytic enzymes. In Multidomain Proteins: Structure and Function. Edited by D. G. Hardie & J. R. Coggins. Amsterdam: Elsevier.
  11. Fothergill-Gilmore, L. A. & Michels, P. A. ( 1993; ). Evolution of glycolysis. Prog Biophys Mol Biol 59, 105–235.[CrossRef]
    [Google Scholar]
  12. Hepperle, D. ( 2002; ). Align: a multicolor sequence alignment editor (available at http://www.gwdg.de/∼dhepper/software.htm).
  13. Johansson, K.-E. & Pettersson, B. ( 2002; ). Taxonomy of Mollicutes. In Molecular Biology and Pathogenicity of Mycoplasmas, pp. 1–31. Edited by S. Razin & R. Herrmann. New York: Kluwer.
  14. Johansson, K.-E., Heldtander, M. U. K. & Pettersson, B. ( 1998; ). Characterization of mycoplasmas by PCR and sequence analysis with universal 16S rDNA primers. Methods Mol Biol 104, 145–165.
    [Google Scholar]
  15. Jones, D. T., Taylor, W. R. & Thornton, J. M. ( 1992; ). The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8, 275–282.
    [Google Scholar]
  16. Kapatral, V., Anderson, I., Ivanova, N. & 22 other authors ( 2002; ). Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. J Bacteriol 184, 2005–2018.[CrossRef]
    [Google Scholar]
  17. Ludwig, W. & Klenk, H.-P. ( 2001; ). Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 49–65. Edited by D. R. Boone, R. W. Castenholz & G. M. Garrity. New York: Springer.
  18. Maniloff, J. ( 2002; ). Phylogeny and evolution. In Molecular Biology and Pathogenicity of Mycoplasmas, pp. 31–45. Edited by S. Razin & R. Herrmann, R. New York: Kluwer Academic/Plenum Publishers.
  19. Neimark, H. ( 1979; ). Phylogenetic relationships between mycoplasmas and other prokaryotes. In The Mycoplasmas, vol. 1, pp. 43–61. Edited by M. F. Barile & S. Razin. New York: Academic Press.
  20. Nelson, K. E., Clayton, R. A., Gill, S. R. & 26 other authors ( 1999; ). Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399, 323–329.[CrossRef]
    [Google Scholar]
  21. Page, R. D. M. ( 1996; ). treeview: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12, 357–358.
    [Google Scholar]
  22. Pollack, J. D. ( 2002; ). Central carbohydrate pathways: metabolic flexibility and the extra role of some “housekeeping” enzymes. In Molecular Biology and Pathogenicity of Mycoplasmas, pp. 163–201. Edited by S. Razin & R. Herrmann. New York: Kluwer.
  23. Pollack, J. D., Myers, M. A., Dandekar, T. & Herrmann, R. ( 2002; ). Suspected utility of enzymes with multiple activities in the small genome Mycoplasma species: the replacement of the missing “household” nucleoside diphosphate kinase gene and activity by glycolytic kinases. OMICS 6, 247–258.[CrossRef]
    [Google Scholar]
  24. Razin, S., Yogev, D. & Naot, Y. ( 1998; ). Molecular biology and pathogenicity of mycoplasmas. Microbiol Mol Biol Rev 62, 1094–1156.
    [Google Scholar]
  25. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  26. Strimmer, K. & von Haeseler, A. ( 1996; ). Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol 13, 964–969.[CrossRef]
    [Google Scholar]
  27. Swofford, D. L. ( 2002; ). paup*: Phylogenetic Analysis Using Parsimony (*and other methods), version 4.0b10 win32. Sunderland, MA: Sinauer Associates.
  28. Thompson, J. D., Higgins, D. G. & Gibson, T. J. ( 1994; ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef]
    [Google Scholar]
  29. Van de Peer, Y. & De Wachter, R. ( 1994; ). treecon for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10, 569–570.
    [Google Scholar]
  30. Whelan, S. & Goldman, N. ( 2001; ). A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18, 691–699.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.02868-0
Loading
/content/journal/ijsem/10.1099/ijs.0.02868-0
Loading

Data & Media loading...

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