This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Ueda, K.
Right arrow Articles by Kataoka, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ueda, K.
Right arrow Articles by Kataoka, M.

 Previous Article  |  Next Article 

Journal of Bacteriology, January 1999, p. 78-82, Vol. 181, No. 1
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Two Distinct Mechanisms Cause Heterogeneity of 16S rRNA

Kumiko Ueda,1,dagger Tatsuji Seki,1 Takuji Kudo,2 Toshiomi Yoshida,1 and Masakazu Kataoka1,3,*

International Center for Biotechnology, Osaka University, Yamada-oka, Suita, Osaka 565,1 Japan Collection of Microorganisms, Institute of Physical and Chemical Research, Hirosawa, Wako, Saitama 351-01,2 and Mitsubishi-kasei Institute of Life Sciences, Minami-ooya, Machida, Tokyo 194-8511,3 Japan

Received 10 April 1998/Accepted 21 October 1998

To investigate the frequency of heterogeneity among the multiple 16S rRNA genes within a single microorganism, we determined directly the 120-bp nucleotide sequences containing the hypervariable alpha  region of the 16S rRNA gene from 475 Streptomyces strains. Display of the direct sequencing patterns revealed the existence of 136 heterogeneous loci among a total of 33 strains. The heterogeneous loci were detected only in the stem region designated helix 10. All of the substitutions conserved the relevant secondary structure. The 33 strains were divided into two groups: one group, including 22 strains, had less than two heterogeneous bases; the other group, including 11 strains, had five or more heterogeneous bases. The two groups were different in their combinations of heterogeneous bases. The former mainly contained transitional substitutions, and the latter was mainly composed of transversional substitutions, suggesting that at least two mechanisms, possibly misincorporation during DNA replication and horizontal gene transfer, cause rRNA heterogeneity.

* Corresponding author. Mailing address: Mitsubishi-kasei Institute of Life Sciences, Minami-ooya 11, Machida, Tokyo 194, Japan. Phone: 88-427-24-6283. Fax: 88-427-24-6314. E-mail: mars{at}libra.ls.m-kagaku.co.jp.

dagger Present address: Institute for Fermentation, Osaka, Juso-honmachi, Yodogawa-ku, Osaka 532, Japan.

Journal of Bacteriology, January 1999, p. 78-82, Vol. 181, No. 1
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Ghosh, D., Roy, K., Williamson, K. E., White, D. C., Wommack, K. E., Sublette, K. L., Radosevich, M. (2008). Prevalence of Lysogeny among Soil Bacteria and Presence of 16S rRNA and trzN Genes in Viral-Community DNA. Appl. Environ. Microbiol. 74: 495-502 [Abstract] [Full Text]  
  • Ueno, R., Huss, V. A. R., Urano, N., Watabe, S. (2007). Direct evidence for redundant segmental replacement between multiple 18S rRNA genes in a single Prototheca strain. Microbiology 153: 3879-3893 [Abstract] [Full Text]  
  • Ventura, M., Canchaya, C., Tauch, A., Chandra, G., Fitzgerald, G. F., Chater, K. F., van Sinderen, D. (2007). Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum. Microbiol. Mol. Biol. Rev. 71: 495-548 [Abstract] [Full Text]  
  • Harth, E., Romero, J., Torres, R., Espejo, R. T. (2007). Intragenomic heterogeneity and intergenomic recombination among Vibrio parahaemolyticus 16S rRNA genes. Microbiology 153: 2640-2647 [Abstract] [Full Text]  
  • Wang, F. Q., Wang, E. T., Liu, J., Chen, Q., Sui, X. H., Chen, W. F., Chen, W. X. (2007). Mesorhizobium albiziae sp. nov., a novel bacterium that nodulates Albizia kalkora in a subtropical region of China. Int. J. Syst. Evol. Microbiol. 57: 1192-1199 [Abstract] [Full Text]  
  • Michel, C., Pelletier, C., Boussaha, M., Douet, D.-G., Lautraite, A., Tailliez, P. (2007). Diversity of Lactic Acid Bacteria Associated with Fish and the Fish Farm Environment, Established by Amplified rRNA Gene Restriction Analysis. Appl. Environ. Microbiol. 73: 2947-2955 [Abstract] [Full Text]  
  • 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 [Abstract] [Full Text]  
  • 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 [Abstract] [Full Text]  
  • Rubin, C.-J., Thollesson, M., Kirsebom, L. A., Herrmann, B. (2005). Phylogenetic relationships and species differentiation of 39 Legionella species by sequence determination of the RNase P RNA gene rnpB. Int. J. Syst. Evol. Microbiol. 55: 2039-2049 [Abstract] [Full Text]  
  • Sacchi, C. T., Alber, D., Dull, P., Mothershed, E. A., Whitney, A. M., Barnett, G. A., Popovic, T., Mayer, L. W. (2005). High Level of Sequence Diversity in the 16S rRNA Genes of Haemophilus influenzae Isolates Is Useful for Molecular Subtyping. J. Clin. Microbiol. 43: 3734-3742 [Abstract] [Full Text]  
  • Rooney, A. P., Ward, T. J. (2005). Evolution of a large ribosomal RNA multigene family in filamentous fungi: Birth and death of a concerted evolution paradigm. Proc. Natl. Acad. Sci. USA 102: 5084-5089 [Abstract] [Full Text]  
  • Miller, S. R., Augustine, S., Olson, T. L., Blankenship, R. E., Selker, J., Wood, A. M. (2005). Discovery of a free-living chlorophyll d-producing cyanobacterium with a hybrid proteobacterial/cyanobacterial small-subunit rRNA gene. Proc. Natl. Acad. Sci. USA 102: 850-855 [Abstract] [Full Text]  
  • Kong, F., Gilbert, G. L. (2004). Postgenomic taxonomy of human ureaplasmas - a case study based on multiple gene sequences. Int. J. Syst. Evol. Microbiol. 54: 1815-1821 [Abstract] [Full Text]  
  • Rooney, A. P. (2004). Mechanisms Underlying the Evolution and Maintenance of Functionally Heterogeneous 18S rRNA Genes in Apicomplexans. Mol Biol Evol 21: 1704-1711 [Abstract] [Full Text]  
  • Kim, B.-J., Kim, C.-J., Chun, J., Koh, Y.-H., Lee, S.-H., Hyun, J.-W., Cha, C.-Y., Kook, Y.-H. (2004). Phylogenetic analysis of the genera Streptomyces and Kitasatospora based on partial RNA polymerase {beta}-subunit gene (rpoB) sequences. Int. J. Syst. Evol. Microbiol. 54: 593-598 [Abstract] [Full Text]  
  • Schouls, L. M., Schot, C. S., Jacobs, J. A. (2003). Horizontal Transfer of Segments of the 16S rRNA Genes between Species of the Streptococcus anginosus Group. J. Bacteriol. 185: 7241-7246 [Abstract] [Full Text]  
  • Marchandin, H., Teyssier, C., Simeon de Buochberg, M., Jean-Pierre, H., Carriere, C., Jumas-Bilak, E. (2003). Intra-chromosomal heterogeneity between the four 16S rRNA gene copies in the genus Veillonella: implications for phylogeny and taxonomy. Microbiology 149: 1493-1501 [Abstract] [Full Text]  
  • Teyssier, C., Marchandin, H., Simeon De Buochberg, M., Ramuz, M., Jumas-Bilak, E. (2003). Atypical 16S rRNA Gene Copies in Ochrobactrum intermedium Strains Reveal a Large Genomic Rearrangement by Recombination between rrn Copies. J. Bacteriol. 185: 2901-2909 [Abstract] [Full Text]  
  • Hashimoto, J. G., Stevenson, B. S., Schmidt, T. M. (2003). Rates and Consequences of Recombination between rRNA Operons. J. Bacteriol. 185: 966-972 [Abstract] [Full Text]  
  • Sacchi, C. T., Whitney, A. M., Reeves, M. W., Mayer, L. W., Popovic, T. (2002). Sequence Diversity of Neisseria meningitidis 16S rRNA Genes and Use of 16S rRNA Gene Sequencing as a Molecular Subtyping Tool. J. Clin. Microbiol. 40: 4520-4527 [Abstract] [Full Text]  
  • Gogarten, J. P., Doolittle, W. F., Lawrence, J. G. (2002). Prokaryotic Evolution in Light of Gene Transfer. Mol Biol Evol 19: 2226-2238 [Abstract] [Full Text]  
  • Metsa-Ketela, M., Halo, L., Munukka, E., Hakala, J., Mantsala, P., Ylihonko, K. (2002). Molecular Evolution of Aromatic Polyketides and Comparative Sequence Analysis of Polyketide Ketosynthase and 16S Ribosomal DNA Genes from Various Streptomyces Species. Appl. Environ. Microbiol. 68: 4472-4479 [Abstract] [Full Text]  
  • Kaplan, J. B., Schreiner, H. C., Furgang, D., Fine, D. H. (2002). Population Structure and Genetic Diversity of Actinobacillus actinomycetemcomitans Strains Isolated from Localized Juvenile Periodontitis Patients. J. Clin. Microbiol. 40: 1181-1187 [Abstract] [Full Text]  
  • 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 [Abstract] [Full Text]  
  • Iteman, I., Rippka, R., Tandeau de Marsac, N., Herdman, M. (2002). rDNA analyses of planktonic heterocystous cyanobacteria, including members of the genera Anabaenopsis and Cyanospira. Microbiology 148: 481-496 [Abstract] [Full Text]  
  • Alber, D., Oberkötter, M., Suerbaum, S., Claus, H., Frosch, M., Vogel, U. (2001). Genetic Diversity of Neisseria lactamica Strains from Epidemiologically Defined Carriers. J. Clin. Microbiol. 39: 1710-1715 [Abstract] [Full Text]  
  • Satokari, R. M., Vaughan, E. E., Akkermans, A. D. L., Saarela, M., de Vos, W. M. (2001). Bifidobacterial Diversity in Human Feces Detected by Genus-Specific PCR and Denaturing Gradient Gel Electrophoresis. Appl. Environ. Microbiol. 67: 504-513 [Abstract] [Full Text]  
  • Ke, D., Boissinot, M., Huletsky, A., Picard, F. J., Frenette, J., Ouellette, M., Roy, P. H., Bergeron, M. G. (2000). Evidence for Horizontal Gene Transfer in Evolution of Elongation Factor Tu in Enterococci. J. Bacteriol. 182: 6913-6920 [Abstract] [Full Text]  
  • 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. Microbiology 146: 2845-2854 [Abstract] [Full Text]  
  • Dahllöf, I., Baillie, H., Kjelleberg, S. (2000). rpoB-Based Microbial Community Analysis Avoids Limitations Inherent in 16S rRNA Gene Intraspecies Heterogeneity. Appl. Environ. Microbiol. 66: 3376-3380 [Abstract] [Full Text]  
  • Pabbaraju, K., Miller, W. L., Sanderson, K. E. (2000). Distribution of Intervening Sequences in the Genes for 23S rRNA and rRNA Fragmentation among Strains of the Salmonella Reference Collection B (SARB) and SARC Sets. J. Bacteriol. 182: 1923-1929 [Abstract] [Full Text]  
  • Poyart, C., Quesnes, G., Trieu-Cuot, P. (2000). Sequencing the Gene Encoding Manganese-Dependent Superoxide Dismutase for Rapid Species Identification of Enterococci. J. Clin. Microbiol. 38: 415-418 [Abstract] [Full Text]  
  • Macario, A. J. L., Lange, M., Ahring, B. K., De Macario, E. C. (1999). Stress Genes and Proteins in the Archaea. Microbiol. Mol. Biol. Rev. 63: 923-967 [Abstract] [Full Text]  
  • Doolittle, W. F. (1999). Phylogenetic Classification and the Universal Tree. Science 284: 2124-2128 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»