This website does readability filtering of other pages. All styles, scripts, forms and ads are stripped. If you want your website excluded or have other feedback, use this form.

Microbiology Society Journals | Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data


  1. Home
  2. Publications
  3. International Journal of Systematic and Evolutionary Microbiology
  4. Volume 54, Issue 3
  5. Article

f Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data

Access full text Article HTML 52.64 Kb PDF 300.54 Kb
  • Cover date: 01/05/2004
Preview this:

Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data, Page 1 of 1

< Previous page | Next page > /docserver/preview/fulltext/ijsem/54/3/871-1.gif
  • The phylogenetic position of the Mollicutes has been re-examined by using phosphoglycerate kinase (Pgk) amino acid sequences. Hitherto unpublished sequences from Mycoplasma mycoides subsp. mycoides, Mycoplasma hyopneumoniae and Spiroplasma citri were included in the analysis. Phylogenetic trees based on Pgk data indicated a monophyletic origin for the Mollicutes within the Firmicutes, whereas Bacilli (Firmicutes) and Clostridia (Firmicutes) appeared to be paraphyletic. With two exceptions, i.e. Thermotoga (Thermotogae) and Fusobacterium (Fusobacteria), which clustered within the Firmicutes, 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.

  • Published online ahead of print on 12 December 2003 as DOI 10.1099/ijs.0.02868-0.

  • The GenBank/EMBL/DDBJ accession numbers for the Pgk sequences of Mycoplasma mycoides subsp. mycoides, Spiroplasma citri and Mycoplasma hyopneumoniae are BX293980, AJ580006 and AY319328, respectively.

SGM | Published by the Microbiology Society

  • 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]
  • 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.
  • Brochier, C. & Philippe, H. ( 2002; ). Phylogeny: a non-hyperthermophilic ancestor for Bacteria. Nature 417, 244.[CrossRef] [Google Scholar]
  • 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]
  • Chattopadhyay, S. & Chakrabarti, J. ( 2003; ). Temporal changes in phosphoglycerate kinase coding sequences: a quantative measure. J Comput Biol 10, 83–93.[CrossRef] [Google Scholar]
  • 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]
  • 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.
  • 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]
  • Felsenstein, J. ( 1993; ). phylip (phylogeny inference package), version 3.6. Department of Genetics, University of Washington, Seattle, USA.
  • 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.
  • Fothergill-Gilmore, L. A. & Michels, P. A. ( 1993; ). Evolution of glycolysis. Prog Biophys Mol Biol 59, 105–235.[CrossRef] [Google Scholar]
  • Hepperle, D. ( 2002; ). Align: a multicolor sequence alignment editor (available at []).
  • 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.
  • 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]
  • 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]
  • 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]
  • 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.
  • 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.
  • 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.
  • 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]
  • Page, R. D. M. ( 1996; ). treeview: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12, 357–358. [Google Scholar]
  • 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.
  • 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]
  • Razin, S., Yogev, D. & Naot, Y. ( 1998; ). Molecular biology and pathogenicity of mycoplasmas. Microbiol Mol Biol Rev 62, 1094–1156. [Google Scholar]
  • Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  • 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]
  • Swofford, D. L. ( 2002; ). paup*: Phylogenetic Analysis Using Parsimony (*and other methods), version 4.0b10 win32. Sunderland, MA: Sinauer Associates.
  • 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]
  • 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]
  • 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]

Supplementary Data

 Data loading....

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.02868-0 2004-05-01 2018-12-19

Full text loading...


Author and Article Information

 Figure data loading....


Validated antibodies in this article

This is a required field Please enter a valid email address Please check the format of the address you have entered. Approval was a Success Invalid data An Error Occurred Approval was partially successful, following selected items could not be processed due to error