Skip to main content
PMC home page
Journal of Clinical Microbiology logoLink to Journal of Clinical Microbiology
. 1996 Oct;34(10):2531–2536. doi: 10.1128/jcm.34.10.2531-2536.1996

Two different 16S rRNA genes in a mycobacterial strain.

B Ninet 1, M Monod 1, S Emler 1, J Pawlowski 1, C Metral 1, P Rohner 1, R Auckenthaler 1, B Hirschel 1
PMCID: PMC229312  PMID: 8880515

Abstract

Sequencing of the gene coding for 16S rRNA (16S rDNA) is a well-established method used to identify bacteria, particularly mycobacteria. Unique sequences allow identification of a particular genus and species. If more than one 16S rDNA is present on one mycobacterial genome, their sequences are assumed to be strictly or almost identical. We have isolated a slowly growing Mycobacterium strain, "X", identified by conventional biochemical tests as Mycobacterium terrae. Identification by amplification and direct sequencing of 16S rDNA yielded ambiguous results in two variable regions, suggesting the presence of different copies of the sequenced gene. Total DNA was digested by restriction enzymes and hybridized after Southern blotting to a probe representing about two-thirds of the 16S rDNA. Two copies of 16S rDNA were identified and cloned. By sequencing, the clones were of two different types, A and B, differing in 18 positions. Oligonucleotides specific to each copy of the 16S rDNA were used to distinguish the positions of the two genes observed in the Southern blot. We conclude that Mycobacterium strain "X" has two different copies of 16S rDNA. Variations in the sequence between two copies of 16S rDNA gene have been described in archaeobacteria, but not in mycobacteria. When placed in a phylogenetic tree together with other slowly growing mycobacteria gene A shows a common root with M. terrae, whereas gene B is placed separately.

Full Text

The Full Text of this article is available as a PDF (336.1 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bachmann B. J. Linkage map of Escherichia coli K-12, edition 8. Microbiol Rev. 1990 Jun;54(2):130–197. doi: 10.1128/mr.54.2.130-197.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bercovier H., Kafri O., Sela S. Mycobacteria possess a surprisingly small number of ribosomal RNA genes in relation to the size of their genome. Biochem Biophys Res Commun. 1986 May 14;136(3):1136–1141. doi: 10.1016/0006-291x(86)90452-3. [DOI] [PubMed] [Google Scholar]
  3. Bull T. J., Shanson D. C., Archard L. C., Yates M. D., Hamid M. E., Minnikin D. E. A new group (type 3) of Mycobacterium celatum isolated from AIDS patients in the London area. Int J Syst Bacteriol. 1995 Oct;45(4):861–862. doi: 10.1099/00207713-45-4-861. [DOI] [PubMed] [Google Scholar]
  4. Butler W. R., O'Connor S. P., Yakrus M. A., Gross W. M. Cross-reactivity of genetic probe for detection of Mycobacterium tuberculosis with newly described species Mycobacterium celatum. J Clin Microbiol. 1994 Feb;32(2):536–538. doi: 10.1128/jcm.32.2.536-538.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cilia V., Lafay B., Christen R. Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level. Mol Biol Evol. 1996 Mar;13(3):451–461. doi: 10.1093/oxfordjournals.molbev.a025606. [DOI] [PubMed] [Google Scholar]
  6. Clayton R. A., Sutton G., Hinkle P. S., Jr, Bult C., Fields C. Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol. 1995 Jul;45(3):595–599. doi: 10.1099/00207713-45-3-595. [DOI] [PubMed] [Google Scholar]
  7. Domenech P., Menendez M. C., Garcia M. J. Restriction fragment length polymorphisms of 16S rRNA genes in the differentiation of fast-growing mycobacterial species. FEMS Microbiol Lett. 1994 Feb 1;116(1):19–24. doi: 10.1111/j.1574-6968.1994.tb06669.x. [DOI] [PubMed] [Google Scholar]
  8. Emler S., Ninet B., Rohner P., Auckenthaler R., Jäger D., Hirschel B. Molecular basis for cross-reactivity between a strain of Mycobacterium terrae and DNA probes for Mycobacterium tuberculosis complex. Eur J Clin Microbiol Infect Dis. 1995 Jul;14(7):627–629. doi: 10.1007/BF01690741. [DOI] [PubMed] [Google Scholar]
  9. Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet. 1988;22:521–565. doi: 10.1146/annurev.ge.22.120188.002513. [DOI] [PubMed] [Google Scholar]
  10. Ji Y. E., Colston M. J., Cox R. A. The ribosomal RNA (rrn) operons of fast-growing mycobacteria: primary and secondary structures and their relation to rrn operons of pathogenic slow-growers. Microbiology. 1994 Oct;140(Pt 10):2829–2840. doi: 10.1099/00221287-140-10-2829. [DOI] [PubMed] [Google Scholar]
  11. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980 Dec;16(2):111–120. doi: 10.1007/BF01731581. [DOI] [PubMed] [Google Scholar]
  12. Kirschner P., Böttger E. C. Microheterogeneity within rRNA of Mycobacterium gordonae. J Clin Microbiol. 1992 Apr;30(4):1049–1050. doi: 10.1128/jcm.30.4.1049-1050.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kirschner P., Springer B., Vogel U., Meier A., Wrede A., Kiekenbeck M., Bange F. C., Böttger E. C. Genotypic identification of mycobacteria by nucleic acid sequence determination: report of a 2-year experience in a clinical laboratory. J Clin Microbiol. 1993 Nov;31(11):2882–2889. doi: 10.1128/jcm.31.11.2882-2889.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Larsen N., Olsen G. J., Maidak B. L., McCaughey M. J., Overbeek R., Macke T. J., Marsh T. L., Woese C. R. The ribosomal database project. Nucleic Acids Res. 1993 Jul 1;21(13):3021–3023. doi: 10.1093/nar/21.13.3021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lévy-Frébault V. V., Portaels F. Proposed minimal standards for the genus Mycobacterium and for description of new slowly growing Mycobacterium species. Int J Syst Bacteriol. 1992 Apr;42(2):315–323. doi: 10.1099/00207713-42-2-315. [DOI] [PubMed] [Google Scholar]
  16. Monod M., Togni G., Hube B., Sanglard D. Multiplicity of genes encoding secreted aspartic proteinases in Candida species. Mol Microbiol. 1994 Jul;13(2):357–368. doi: 10.1111/j.1365-2958.1994.tb00429.x. [DOI] [PubMed] [Google Scholar]
  17. Mylvaganam S., Dennis P. P. Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics. 1992 Mar;130(3):399–410. doi: 10.1093/genetics/130.3.399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Portaels F., Fonteyene P. A., de Beenhouwer H., de Rijk P., Guédénon A., Hayman J., Meyers M. W. Variability in 3' end of 16S rRNA sequence of Mycobacterium ulcerans is related to geographic origin of isolates. J Clin Microbiol. 1996 Apr;34(4):962–965. doi: 10.1128/jcm.34.4.962-965.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Rogall T., Wolters J., Flohr T., Böttger E. C. Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium. Int J Syst Bacteriol. 1990 Oct;40(4):323–330. doi: 10.1099/00207713-40-4-323. [DOI] [PubMed] [Google Scholar]
  20. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  21. Sechi L. A., Zuccon F. M., Mortensen J. E., Daneo-Moore L. Ribosomal RNA gene (rrn) organization in enterococci. FEMS Microbiol Lett. 1994 Jul 15;120(3):307–313. doi: 10.1111/j.1574-6968.1994.tb07051.x. [DOI] [PubMed] [Google Scholar]
  22. Springer B., Stockman L., Teschner K., Roberts G. D., Böttger E. C. Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods. J Clin Microbiol. 1996 Feb;34(2):296–303. doi: 10.1128/jcm.34.2.296-303.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Stahl D. A., Urbance J. W. The division between fast- and slow-growing species corresponds to natural relationships among the mycobacteria. J Bacteriol. 1990 Jan;172(1):116–124. doi: 10.1128/jb.172.1.116-124.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Woese C. R. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. doi: 10.1128/mr.51.2.221-271.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Clinical Microbiology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES