1887

Abstract

Analysis of the 16S rDNAs obtained from cultures of single colonies of either type collection strains or environmental strains of the genus revealed the presence of polymorphism in every one of the strains examined. Polymorphism was detected by visualization of heteroduplexes produced after 16S rDNA PCR amplification, a procedure that allows for the screening of a large number of isolates. Amplified 16S rDNAs obtained from both and an environmental strain were cloned. Their nucleotide sequences revealed differences of up to 2% among 16S rDNAs from the same strain. Polymorphic sites were concentrated in a recognized variable stem–loop of bacterial 16S rRNA that contained in some cases up to 83% of the total mismatches observed. Most of the substitutions present in the stem–loop region showed compensating base covariation. The accumulation of so many compensating changes in the stem–loop region implies that the divergence of the different versions of this stem–loop is relatively ancient. This divergence could be the result of either a selection process or a lateral transfer of independently evolved genes.

Keyword(s): 16S rDNA , marine and rrn
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2002-04-01
2020-01-25
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References

  1. Amann R. I., Ludwig W., Schleifer K. H. 1995; Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev59:143–169
    [Google Scholar]
  2. Asai T., Zaporojets D., Squires C., Squires C. L. 1999; An Escherichia coli strain with all chromosomal rRNA operons inactivated: Complete exchange of rRNA genes between bacteria. Proc Natl Acad Sci USA96:1971–1976[CrossRef]
    [Google Scholar]
  3. Birnboim D. 1983; A rapid alkaline extraction method for the isolation of plasmid DNA. Methods Enzymol100:243–255
    [Google Scholar]
  4. Cilia V., Laffay B., Christen R. 1996; Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analysis at the species level. Mol Biol Evol13:451–461[CrossRef]
    [Google Scholar]
  5. Dahllof I., Baillie H., Kjelleberg S. 2000; rpoB -based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol66:3376–3380[CrossRef]
    [Google Scholar]
  6. Delwart E. L., Shpaer E. G., Louwagie J., McCutchan F. E., Grez M., Rübsamen-Waigman H., Mullins J. I. 1993; Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes. Science262:1257–1261[CrossRef]
    [Google Scholar]
  7. Dorsch M., Lane D., Stackebrandt E. 1992; Towards a phylogeny of the genus Vibrio based on 16S rRNA sequences. Int J Syst Bacteriol42:58–63[CrossRef]
    [Google Scholar]
  8. Espejo R. T., Feijóo C. G., Romero J., Vásquez M. 1998; PAGE analysis of the heteroduplexes formed between PCR-amplified 16S rRNA genes: estimation of sequence similarity and rDNA complexity. Microbiology144:1611–1617[CrossRef]
    [Google Scholar]
  9. Fegatella F., Lim J., Kjelleberg S., Cavicchioli R. 1998; Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256. Appl Environ Microbiol64:4433–4438
    [Google Scholar]
  10. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution39:783–791[CrossRef]
    [Google Scholar]
  11. Gray M. W., Sankoff K., Cedergren R. J. 1984; On the evolutionary descent of organisms and organelles: A global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA. Nucleic Acids Res12:5837–5852[CrossRef]
    [Google Scholar]
  12. Heidelberg J. F., Eisen J. A., Nelson W. C.. 29 other authors 2000; DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature406:477–483[CrossRef]
    [Google Scholar]
  13. Hu H., Ochi K. 2001; Novel approach for improving the productivity of antibiotic-producing strains by inducing combined resistant mutations. Appl Environ Microbiol67:1885–1892[CrossRef]
    [Google Scholar]
  14. Jensen M. A., Straus N. 1993; Effect of PCR conditions on the formation of heteroduplex and single-stranded DNA products in the amplification of bacterial ribosomal DNA spacer regions. PCR Methods Appl3:186–194[CrossRef]
    [Google Scholar]
  15. Lamfrom H., Sarabhai A., Abelson J. 1978; Cloning of Beneckea genes in Escherichia coli . J Bacteriol133:354–363
    [Google Scholar]
  16. Lawrence J. G. 1999; Gene transfer, speciation, and the evolution of bacterial genomes. Curr Opin Microbiol2:519–523[CrossRef]
    [Google Scholar]
  17. 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 Bacteriol178:5636–5643
    [Google Scholar]
  18. Perez S., Rodriguez F., Lan R., Reeves P. R. 1998; Variation of the ribosomal operon 16S–23S gene spacer region in representatives of Salmonella enterica subspecies. J Bacteriol180:2144–2151
    [Google Scholar]
  19. Recht M. I., Douthwaite S., Puglisi J. D. 1999; Basis for prokaryotic specificity of action of aminoglycoside antibiotics. EMBO J18:3133–3138[CrossRef]
    [Google Scholar]
  20. Reischl U., Feldmann K., Naumann L., Gaugler B. J., Ninet B., Hirschel B. 1998; 16S rRNA sequence diversity in Mycobacterium celatum strains caused by presence of two different copies of 16S rRNA gene. J Clin Microbiol36:1761–1764
    [Google Scholar]
  21. Romero J., Espejo R. T. 2002; The prevalence of non-cultivable bacteria in oysters ( Tiostrea chilensis , Philippi 1845). J Shellfish Res in press
    [Google Scholar]
  22. Ruimy R., Breittmayer V., Elbaze P., Lafay B., Bouseemart O., Gauthier M., Christen R. 1994; Phylogenetic analysis and assessment of the genera Vibrio , Photobacterium , Aeromonas , and Plesiomonas deduced from small-subunit rRNA sequences. Int J Syst Bacteriol44:416–426[CrossRef]
    [Google Scholar]
  23. Sambrook J., Fritsch E. F., Maniatis T. 1989; Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  24. Sapag A., Vartikar J., Draper D. 1990; Dissection of the 16S rRNA binding site for ribosomal protein S4. Biochim Biophys Acta1050:34–37[CrossRef]
    [Google Scholar]
  25. Ueda K., Seki T., Kudo T., Yoshida T., Kataoka M. 1999; Two distinct mechanisms cause heterogeneity of 16S rRNA. J Bacteriol181:78–82
    [Google Scholar]
  26. Wang Y., Zhang Z. 2000; Comparative sequence analyses reveal frequent occurrence of short segments containing an abnormally high number of non-random base variations in bacterial rRNA genes. Microbiology146:2845–2854
    [Google Scholar]
  27. Wang Y., Zhang Z. S., Ramanan N. 1997; The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J Bacteriol179:3270–3276
    [Google Scholar]
  28. Wolfe C. J., Haywood M. G. 1993; Bioluminescent symbionts of the Caribbean flashlight fish ( Kryptophanaron alfredi ) have a single rRNA operon. Mol Mar Biol Biotechnol2:189–197
    [Google Scholar]
  29. Wommack K. E., Colwell R. R. 2000; Viroplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev64:69–114[CrossRef]
    [Google Scholar]
  30. Yamaichi Y., Iida T., Park K.-S., Yamamoto K., Honda T. 1999; Physical and genetic map of the genome of Vibrio parahaemolyticus : presence of two chromosomes in Vibrio species. Mol Microbiol31:1513–1521[CrossRef]
    [Google Scholar]
  31. 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 Bacteriol181:5201–5209
    [Google Scholar]
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