Intra-chromosomal heterogeneity between the four 16S rRNA gene copies in the genus Veillonella: Implications for phylogeny and taxonomy

Microbiology

Volumn 149, Issue 6, 2003, Pages 1493-1501

  Marchandin, Hélène ^a   Teyssier, Corrine ^b   Siméon de Buochberg, Michèle ^b   Jean Pierre, Hélène ^a   Carriere, Christian ^a   Jumas Bilak, Estelle ^b  

^a HÔPITAL ARNAUD DE VILLENEUVE   (France)

^b UNIV MONTPELLIER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S; RNA 16S;

ARTICLE; BACTERIAL FLORA; BACTERIAL STRAIN; BACTERIUM ISOLATION; CONTROLLED STUDY; GENE LOCUS; GENETIC HETEROGENEITY; GENETIC VARIABILITY; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RNA STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; STRAIN DIFFERENCE; STRAIN IDENTIFICATION; TAXONOMY; VEILLONELLA;

ALEUTIAN MINK DISEASE PARVOVIRUS (STRAIN G); BACTERIA (MICROORGANISMS); NEGIBACTERIA; PROKARYOTA; VEILLONELLA; VEILLONELLA ATYPICA; VEILLONELLA DISPAR; VEILLONELLA PARVULA;

EID: 0037804236     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.26132-0     Document Type: Article

References (33)

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.
2. Bascunana, C. R., Mattsson, J. G., Bolske, G. & Johansson, K. E. (1994). Characterization of the 16S rRNA genes from Mycoplasma sp. strain F38 and development of an identification system based on PCR. J Bacteriol 176, 2577-2586.
3. Carlier, J. P., Marchandin, H., Lorin, V., Henry, C., Jumas-Bilak, E., Carrière, C. & Jean-Pierre, H. (2002). Anaeroglobus geminatus gen. nov., sp. nov., a novel member of the Veillonellaceae family. Int J Syst Evol Microbiol 52, 983-986.
4. Cilia, B., 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.
5. Clayton, R. A., Sutton, G., Hinkle, P. S., Jr, Bult, C. & Fields, C. (1995). Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45, 595-599.
6. Heldtander, M., Pettersson, B., Tully, J. G. & Johansson, K. E. (1998). Sequences of the 16S rRNA genes and phylogeny of the goat mycoplasmas Mycoplasma adleri, Mycoplasma auris, Mycoplasma cottewii, and Mycoplasma yeatsii. Int J Syst Bacteriol 48, 263-268.
7. Houston, S., Taylor, D. & Rennie, R. (1997). Prosthetic valve endocarditis due to Veillonella dispar: successful medical treatment following penicillin desensitization. Clin Infect Dis 24, 1013-1014.
8. Jumas-Bilak, E., Michaux-Charachon, S., Bourg, G., O'Callaghan, D. & Ramuz, M. (1998). Differences in chromosome number and genome rearrangements in the genus Brucella. Mol Microbiol 27, 99-106.
9. Kolenbrander, P. E. & Moore, L. V. H. (1992). The genus Veillonella. In The Prokaryotes, 2nd edn, pp. 2034-2047. Edited by H. G. Balows, M. Trüper, W. Dworkin, W. Harder & K.-H. Schleifer. New York: Springer.
10. Liao, D. (2000). Gene conversion drives within genic sequences: concerted evolution of ribosomal RNA genes in bacteria and archaea. J Mol Evol 51, 305-317.
11. Liefting, L. W., Andersen, M. T., Beever, R. E., Gardner, R. C. & Forster, R. L. S. (1996). Sequence heterogeneity in the two 16S rRNA genes of Phormium yellow leaf phytoplasma. Appl Environ Microbiol 62, 3133-3139.
12. Liu, S. L. & Sanderson, K. E. (1998). Homologous recombination between rrn operons rearranges the chromosome in host-specialized species of Salmonella. FEMS Microbiol Lett 164, 275-281.
13. Liu, J. W., Wu, J. J., Wang, L. R., Teng, L. J. & Huang, T. C. (1998). Two fatal cases of Veillonella bacteremia. Eur J Clin Microbiol Dis 17, 62-64.
14. Marchandin, H., Jean-Pierre, H., Carrière, C., Canovas, F., Darbas, H. & Jumas-Bilak, E. (2001). Prosthetic joint infection due to Veillonella dispar. Eur J Clin Microbiol Infect Dis 20, 340-342.
15. Martinez-Murcia, A. J., Anton, A. I. & Rodriguez-Valera, F. (1999). Patterns of sequence variation in two regions of the 16S rRNA mulltigene family of Escherichia coli. Int J Syst Bacteriol 49, 601-610.
16. Mays, T. D., Holdeman, L. V., Moore, W. E. C., Rogosa, M. & Johnson, J. L. (1982). Taxonomy of the genus Veillonella. Int J Syst Bacteriol 32, 28-36.
17. Murray, R. G. E., Brenner, D. J., Colwell, R. R., De Vos, P., Goodfellow, M., Grimont, P. A. D., Pfennig, N., Stackebrandt, E. & Zavarzin, G. A. (1990). International Committee on Systematic Bacteriology. Report of the ad hoc committee on approaches to taxonomy within the Proteobacteria. Int J Syst Bacteriol 40, 213-215.
18. Ninet, B., Monod, M., Emler, S., Pawlowski, J., Metral, C., Rohner, P., Auckenthaler, R. & Hirschel, B. (1996). Two different 16S rRNA genes in a mycobacterial strain. J Clin Microbiol 34, 2531-2536.
19. Nubel, U., Engelen, B., Felske, A., Snaidr, J., Wieshuber, A., Amann, R. I., Ludwig, W. & Backhaus, H. (1996). Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 178, 5636-5643.
20. Pettersson, B., Leitner, T., Ronaghi, M., Bolske, G., Uhlen, M. & Johansson. K. E. (1996). Phylogeny of the Mycoplasma mycoides cluster as determined by sequence analysis of the 16S rRNA genes from the two rRNA operons. J Bacteriol 178, 4131-4142.
21. Reischl, K., Feldmann, K., Naumann, L., Gaugler, B. J. M., Ninet, B., Hirschel, B. & Emler, S. (1998). 16S rRNA sequence diversity in Mycobacterium celatum strains caused by presence of two different copies of 16S rRNA gene. J Clin Microbiol 36, 1767-1784.
22. Rogosa, M. (1965). The genus Veillonella, IV. Serological groupings, and genus and species emendations. J Bacteriol 90, 704-709.
23. Rogosa, M. (1984). Anaerobic Gram negative cocci. Veillonellaceae. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 680-685. Edited by N. R. Krieg & J. G. Holt. Baltimore, MD: Williams & Wilkins.
24. Sato, T., Matsuyama, J., Sato, M. & Hoshino, E. (1997). Differentiation of Veillonella atypica, Veillonella dispar and Veillonella parvula using restricted fragment-length polymorphism analysis of 16S rDNA amplified by polymerase chain reaction. Oral Microbiol Immunol 12, 350-353.
25. Sato, T., Sato, M., Matsuyama, J., & Hoshino, E. (1997). PCR-restriction fragment length polymorphism analysis of genes coding for 16S rRNA in Veillonella spp. Int J Syst Bacteriol 47, 1268-1270.
26. Singh, N & Yu, V. L. (1992). Osteomyelitis due to Veillonella parvula: case report and review. Clin Infect Dis 14, 361-363.
27. Stackebrandt, E., Frederiksen, W., Garrity, G. M. & 10 other authors (2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043-1047.
28. Tanner, A., Maiden, M. F. J., Paster, B. J. & Dewhirst, F. E (2000). The impact of 16S ribosomal RNA-based phylogeny on the taxonomy of oral bacteria. Periodontology 2000 5, 26-51.
29. Ueda, K., Seki, T., Kudo, T., Yoshida, T. & Kataoka, M. (1999). Two distinct mechanisms cause heterogeneity of 16S rRNA. J Bacteriol 181, 78-82.
30. Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K. & Swings, J. (1996). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60, 407-438.
31. Walter, A. E., Turner, D. H., Kim, J., Lyttle, M. H., Muller, P., Matthews D. H. & Zuker, M. (1994). Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci U S A 91, 9218-9222.
32. Wang, Y., Zhang, Z. & Ramanan, N. (1997). The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J Bacteriol 179, 3270-3276.
33. Yap, W. O., Zhang, Z. & Wang, Y. (1999). Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J Bacteriol 181, 5201-5209.