1887

Abstract

The partial nucleotide sequences encoding the elongation factor Tu ( gene) (652 bp) and transfer-mRNA (tmRNA or gene) (340 bp) were determined to assess the suitability of these two genes as phylogenetic markers for the classification of mycobacteria, and thus as alternative target molecules for identifying mycobacteria. A total of 125 reference strains of the genus and 74 clinical isolates were amplified by PCR and sequenced. Phylogenies of the two genes constructed by the neighbour-joining method were created and compared to a concatenated tree of 16S rDNA, , and genes. The phylogenetic trees revealed the overall natural relationships among species. The tmRNA phylogeny was similar to that of 16S rDNA, with low resolving power. The gene provided better resolution of each mycobacterial species, with a phylogeny close to that of . However, none of these methods differentiated between the members of the complex or the subspecies of the complex. The correct identification of clinical isolates confirms the interest of these genes, especially . It is suggested from these findings that tmRNA might be useful as another housekeeping gene in a polyphyletic approach to species, but not as a first-line marker of species. gene analysis suggests that this gene could be used effectively for phylogenetic analysis and to identify mycobacteria.

Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.47105-0
2007-08-01
2019-10-14
Loading full text...

Full text loading...

/deliver/fulltext/jmm/56/8/1033.html?itemId=/content/journal/jmm/10.1099/jmm.0.47105-0&mimeType=html&fmt=ahah

References

  1. Adekambi, T. & Drancourt, M. ( 2004; ). Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA, rpoB gene sequencing. Int J Syst Evol Microbiol 54, 2095–2105.[CrossRef]
    [Google Scholar]
  2. Afghani, B. & Stutman, H. R. ( 1996; ). Polymerase chain reaction for diagnosis of M. tuberculosis: comparison of simple boiling and a conventional method for DNA extraction. Biochem Mol Med 57, 14–18.[CrossRef]
    [Google Scholar]
  3. Andersen, E. S., Rosenblad, M. A., Larsen, N., Westergaard, J. C., Burks, J., Wower, I. K., Wower, J., Gorodkin, J., Samuelsson, T. & Zwieb, C. ( 2006; ). The tmRDB and SRPDB resources. Nucleic Acids Res 34, D163–D168.[CrossRef]
    [Google Scholar]
  4. Blackwood, K. S., He, C., Gunton, J., Turenne, C. Y., Wolfe, J. & Kabani, A. M. ( 2000; ). Evaluation of recA sequences for identification of Mycobacterium species. J Clin Microbiol 38, 2846–2852.
    [Google Scholar]
  5. Devulder, G., Perriere, G., Baty, F. & Flandrois, J. P. ( 2003; ). BIBI, a bioinformatics bacterial identification tool. J Clin Microbiol 41, 1785–1787.[CrossRef]
    [Google Scholar]
  6. Devulder, G., Pérouse de Montclos, M. & Flandrois, J. P. ( 2005; ). A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model. Int J Syst Evol Microbiol 55, 293–302.[CrossRef]
    [Google Scholar]
  7. Dobner, P., Feldmann, K., Rifai, M., Loscher, T. & Rinder, H. ( 1996; ). Rapid identification of mycobacterial species by PCR amplification of hypervariable 16S rRNA gene promoter region. J Clin Microbiol 34, 866–869.
    [Google Scholar]
  8. Edgar, R. C. ( 2004; ). muscle: multiple sequence alignment with accuracy and high throughput. Nucleic Acids Res 32, 1792–1797.[CrossRef]
    [Google Scholar]
  9. Felsenstein, J. ( 1993; ). phylip (phylogeny inference package), version 3.5c. Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  10. Galtier, N., Gouy, M. & Gautier, C. ( 1996; ). SeaView and Phylo_win: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12, 543–548.
    [Google Scholar]
  11. Haebel, P. W., Gutmann, S. & Ban, N. ( 2004; ). Dial tm for rescue: tmRNA engages ribosomes stalled on defective mRNAs. Curr Opin Struct Biol 14, 58–65.[CrossRef]
    [Google Scholar]
  12. Kasai, H., Ezaki, T. & Harayama, S. ( 2000; ). Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences. J Clin Microbiol 38, 301–308.
    [Google Scholar]
  13. Kazda, J., Cooney, R., Monaghan, M., Quinn, P. J., Stackebrandt, E., Dorsch, M., Daffe, M., Muller, K., Cook, B. R. & Tarnok, Z. S. ( 1993; ). Mycobacterium hiberniae sp.nov. Int J Syst Bacteriol 43, 352–357.[CrossRef]
    [Google Scholar]
  14. Keiler, K. C., Waller, P. R. & Sauer, R. T. ( 1996; ). Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271, 990–993.[CrossRef]
    [Google Scholar]
  15. Kim, B. J., Lee, S. H., Lyu, M. A., Kim, S. J., Bai, G. H., Kim, S. J., Chae, G. T., Kim, E. C., Cha, C. Y. & Kook, Y. H. ( 1999; ). Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J Clin Microbiol 37, 1714–1720.
    [Google Scholar]
  16. Kim, H., Kim, S. H., Shim, T. S., Kim, M., Bai, G. H., Park, Y. G., Lee, S. H., Chae, G. T., Cha, C. Y. & other authors ( 2005; ). Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65). Int J Syst Evol Microbiol 55, 1649–1656.[CrossRef]
    [Google Scholar]
  17. Kimura, M. ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotides sequences. J Mol Evol 16, 111–120.[CrossRef]
    [Google Scholar]
  18. Kirschner, P., Springer, B., Vogel, U., Meier, A., Wrede, A., Kiekenbeck, M., Bange, F. C. & Bottger, E. C. ( 1993; ). Genotypic identification of mycobacteria by nucleic acid sequence determination: report of a 2-year experience in a clinical laboratory. J Clin Microbiol 31, 2882–2889.
    [Google Scholar]
  19. Kox, L. F. F., Van Leeuwen, J., Jansen, H. M. & Kolk, A. H. J. ( 1995; ). PCR assay based on DNA coding for 16S rRNA for detection and identification of mycobacteria in clinical samples. J Clin Microbiol 33, 3225–3233.
    [Google Scholar]
  20. McNabb, A., Eisler, D., Adie, K., Amos, M., Rodrigues, M., Stephens, G., Black, W. A. & Isaac-Renton, J. ( 2004; ). Assessment of partial sequencing of the 65-kilodalton heat shock protein gene (hsp65) for routine identification of Mycobacterium species isolated from clinical sources. J Clin Microbiol 42, 3000–3011.[CrossRef]
    [Google Scholar]
  21. Picard, F. J., Ke, D., Boudreau, D. K., Boissinot, M., Huletsky, A., Richard, D., Ouellette, M., Roy, P. H. & Bergeron, M. G. ( 2004; ). Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species. J Clin Microbiol 42, 3686–3695.[CrossRef]
    [Google Scholar]
  22. Picardeau, M., Prod'hom, G., Raskine, L., LePennec, M. P. & Vincent, V. ( 1997; ). Genotypic characterization of five subspecies of Mycobacterium kansasii. J Clin Microbiol 35, 25–32.
    [Google Scholar]
  23. Portaels, F., Aguiar, J., Fissette, K., Fonteyne, P. A., de Beenhouwer, H., de Rijk, P., Guedenon, A., Leman, R., Steunou, C. & other authors ( 1997; ). Direct detection and identification of Mycobacterium ulcerans in clinical specimens by PCR and oligonucleotide-specific capture plate hybridization. J Clin Microbiol 35, 1097–1100.
    [Google Scholar]
  24. Ringuet, H., Akoua-Koffi, C., Honore, S., Varnerot, A., Vincent, V., Berche, P., Gaillard, J. L. & Pierre-Audigier, C. ( 1999; ). hsp65 sequencing for identification of rapidly growing mycobacteria. J Clin Microbiol 37, 852–857.
    [Google Scholar]
  25. Roth, A., Fisher, M., Hamid, M. E., Michalke, S., Ludwig, W. & Mauch, H. ( 1998; ). Differentiation of phylogenetically related slowly growing mycobacteria based on 16S–23S rRNA gene internal transcribed spaces sequences. J Clin Microbiol 36, 139–147.
    [Google Scholar]
  26. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  27. Schonhuber, W., le Bourhis, G., Tremblay, J., Amann, R. & Kulakauskas, S. ( 2001; ). Utilization of tmRNA sequences for bacterial identification. BMC Microbiol 1, 20 [CrossRef]
    [Google Scholar]
  28. Sela, S., Yogev, D., Razin, S. & Bervovier, H. ( 1989; ). Duplication of the tuf gene: a new insight into the phylogeny of eubacteria. J Bacteriol 171, 581–584.
    [Google Scholar]
  29. Stahl, D. A. & Urbance, J. W. ( 1990; ). The division between fast- and slow-growing species corresponds to natural relationships among the mycobacteria. J Bacteriol 172, 116–124.
    [Google Scholar]
  30. Takewaki, S. I., Okuzumi, K., Ishiko, H., Nakahara, K. I., Ohkubo, A. & Nagai, R. ( 1993; ). Genus-specific polymerase chain reaction or the mycobacterial dnaJ gene and species-specific oligonucleotide probes. J Clin Microbiol 31, 446–450.
    [Google Scholar]
  31. Telenti, A., Marchesi, F., Balz, M., Bally, F., Bottger, E. C. & Bodmer, T. ( 1993; ). Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol 31, 175–178.
    [Google Scholar]
  32. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmongin, F. & Higgins, D. G. ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
  33. Van Soolingen, D., Hoogenboezem, T., de Haas, P. E. W., Hermans, P. W. M., Koedam, M. A., Teppema, K. S., Brennan, P. J., Besra, G. S., Portaels, F. & other authors ( 1997; ). A novel pathogenic taxon of the Mycobacterium tuberculosis complex, Canetti: characterization of an exceptional isolate from Africa. Int J Syst Bacteriol 47, 1236–1245.[CrossRef]
    [Google Scholar]
  34. Withey, J. H. & Friedman, D. I. ( 2003; ). A salvage pathway for protein synthesis: tmRNA and trans-translation. Annu Rev Microbiol 57, 101–123.[CrossRef]
    [Google Scholar]
  35. Zolg, J. W. & Philippi-Schulz, S. ( 1994; ). The superoxide dismutase gene as a target for detection and identification of mycobacteria by PCR. J Clin Microbiol 32, 2801–2812.
    [Google Scholar]
  36. Zwieb, C., Wower, I. & Wower, J. ( 1999; ). Comparative sequence analysis of tmRNA. Nucleic Acids Res 27, 2063–2071.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.47105-0
Loading
/content/journal/jmm/10.1099/jmm.0.47105-0
Loading

Data & Media loading...

vol. , part 8, pp. 1033 - 1041

Mycobacterial strains and GenBank accession numbers. [ PDF file] (68 KB)



PDF
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