1887

Abstract

is a marine bacterium bearing 11 copies of ribosomal operons. In some strains, such as RIMD2210633, the genome includes identical copies of 16S rRNA genes (). However, it is known that other strains of the species, such as strains ATCC 17802 and RIMD2210856, show conspicuous intragenomic heterogeneity. The extent and diversity of the heterogeneity in were studied in further detail by characterization of the copies in environmental isolates belonging to 21 different genotype groups. Thirteen of these groups showed intragenomic heterogeneity, containing altogether 16 sequences differing within a 25 bp segment of their . These sequences grouped into four clusters differing in at least four nucleotide sites. Some isolates contained alleles from up to three different clusters. Each segment sequence conserved the stem–loop characteristic of the 16S rRNA structure of this 25 bp sequence. The double-stranded stem sequence was quite variable, but almost every variation had a compensatory change to maintain seven to eight paired bases. Conversely, the single-strand loop sequence was conserved. The results may be explained as a consequence of recombination among evolving in different bacteria. The results suggest that intergenomic recombination is very high in and that it occurs solely among species. This high homologous intergenomic recombination could be an effective mechanism to maintain intragenomic cohesion, mediating the dispersal of the most abundant version among the 11 intragenomic loci.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2007/009175-0
2007-08-01
2019-10-14
Loading full text...

Full text loading...

/deliver/fulltext/micro/153/8/2640.html?itemId=/content/journal/micro/10.1099/mic.0.2007/009175-0&mimeType=html&fmt=ahah

References

  1. Acinas, S. G., Marcelino, L. A., Klepac-Ceraj, V. & Polz, M. F. ( 2004; ). Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186, 2629–2635.[CrossRef]
    [Google Scholar]
  2. Beumer, A. & Robinson, J. B. ( 2005; ). A broad-host-range, generalized transducing phage (SN-T) acquires 16S rRNA genes from different genera of bacteria. Appl Environ Microbiol 71, 8301–8304.[CrossRef]
    [Google Scholar]
  3. Cannone, J. J., Subramanian, S., Schnare, M. N., Collett, J. R., D'Souza, L. M., Du, Y., Feng, B., Lin, N., Madabusi, L.V. & other authors ( 2002; ). The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3, 2 [CrossRef]
    [Google Scholar]
  4. Chang, B., Taniguchi, H., Miyamoto, H. & Yoshida, S. ( 1998; ). Filamentous bacteriophages of Vibrio parahaemolyticus as a possible clue to genetic transmission. J Bacteriol 180, 5094–5101.
    [Google Scholar]
  5. Cole, J. R., Chai, B., Farris, R. J., Wang, Q., Kulam, S. A., McGarrell, D. M. & Tiedje, J. M. ( 2005; ). The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33, D294–D296.
    [Google Scholar]
  6. Espejo, R. T., Feijoo, C. G., Romero, J. & Vasquez, M. ( 1998; ). PAGE analysis of the heteroduplexes formed between PCR-amplified 16S rRNA genes: estimation of sequence similarity and rDNA complexity. Microbiology 144, 1611–1617.[CrossRef]
    [Google Scholar]
  7. Feil, E. J., Maiden, M. C., Achtman, M. & Spratt, B. G. ( 1999; ). The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis. Mol Biol Evol 16, 1496–1502.[CrossRef]
    [Google Scholar]
  8. Feil, E. J., Enright, M. C. & Spratt, B. G. ( 2000; ). Estimating the relative contributions of mutation and recombination to clonal diversification: a comparison between Neisseria meningitidis and Streptococcus pneumoniae. Res Microbiol 151, 465–469.[CrossRef]
    [Google Scholar]
  9. Feil, E. J., Holmes, E. C., Bessen, D. E., Chan, M. S., Day, N. P., Enright, M. C., Goldstein, R., Hood, D. W., Kalia, A. & other authors ( 2001; ). Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc Natl Acad Sci U S A 98, 182–187.[CrossRef]
    [Google Scholar]
  10. Fuenzalida, L., Hernandez, C., Toro, J., Rioseco, M. L., Romero, J. & Espejo, R. T. ( 2006; ). Vibrio parahaemolyticus in shellfish and clinical samples during two large epidemics of diarrhoea in southern Chile. Environ Microbiol 8, 675–683.[CrossRef]
    [Google Scholar]
  11. González-Escalona, N., Cachicas, V., Acevedo, C., Rioseco, M. L., Vergara, J. A., Cabello, F., Romero, J., Espejo, R. T. & other authors ( 2005a; ). Vibrio parahaemolyticus diarrhea, Chile, 1998 and 2004. Emerg Infect Dis 11, 129–131.[CrossRef]
    [Google Scholar]
  12. González-Escalona, N., Romero, J. & Espejo, R. T. ( 2005b; ). Polymorphism and gene conversion of the 16S rRNA genes in the multiple rRNA operons of Vibrio parahaemolyticus. FEMS Microbiol Lett 246, 213–219.[CrossRef]
    [Google Scholar]
  13. Hall, T. A. ( 1999; ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95–98.
    [Google Scholar]
  14. Iida, T., Suthienkul, O., Park, K. S., Tang, G. Q., Yamamoto, R. K., Ishibashi, M., Yamamoto, K. & Honda, T. ( 1997; ). Evidence for genetic linkage between the ure and trh genes in Vibrio parahaemolyticus. J Med Microbiol 46, 639–645.[CrossRef]
    [Google Scholar]
  15. Jiang, S. C. & Paul, J. H. ( 1998; ). Gene transfer by transduction in the marine environment. Appl Environ Microbiol 64, 2780–2787.
    [Google Scholar]
  16. 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.
    [Google Scholar]
  17. Liu, S. L., Hessel, A. & Sanderson, K. E. ( 1993; ). Genomic mapping with I-Ceu I, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc Natl Acad Sci U S A 90, 6874–6878.[CrossRef]
    [Google Scholar]
  18. Majewski, J. & Cohan, F. M. ( 1999; ). DNA sequence similarity requirements for interspecific recombination in Bacillus. Genetics 153, 1525–1533.
    [Google Scholar]
  19. Makino, K., Oshima, K., Kurokawa, K., Yokoyama, K., Uda, T., Tagomori, K., Iijima, Y., Najima, M., Nakano, M. & other authors ( 2003; ). Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae. Lancet 361, 743–749.[CrossRef]
    [Google Scholar]
  20. Morandi, A., Zhaxybayeva, O., Gogarten, J. P. & Graf, J. ( 2005; ). Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strains. J Bacteriol 187, 6561–6564.[CrossRef]
    [Google Scholar]
  21. Moreno, C., Romero, J. & Espejo, R. T. ( 2002; ). Polymorphism in repeated 16S rRNA genes is a common property of type strains and environmental isolates of the genus Vibrio. Microbiology 148, 1233–1239.
    [Google Scholar]
  22. Nei, M. & Li, W. H. ( 1979; ). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76, 5269–5273.[CrossRef]
    [Google Scholar]
  23. Sapag, A., Vartikar, J. V. & Draper, D. E. ( 1990; ). Dissection of the 16S rRNA binding site for ribosomal protein S4. Biochim Biophys Acta 1050, 34–37.[CrossRef]
    [Google Scholar]
  24. Sneath, P. H. ( 1993; ). Evidence from Aeromonas for genetic crossing-over in ribosomal sequences. Int J Syst Bacteriol 43, 626–629.[CrossRef]
    [Google Scholar]
  25. Ueda, K., Seki, T., Kudo, T., Yoshida, T. & Kataoka, M. ( 1999; ). Two distinct mechanisms cause heterogeneity of 16S rRNA. J Bacteriol 181, 78–82.
    [Google Scholar]
  26. 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]
  27. Yap, W. H., 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.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2007/009175-0
Loading
/content/journal/micro/10.1099/mic.0.2007/009175-0
Loading

Data & Media loading...

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