Intragenomic heterogeneity and intergenomic recombination among Vibrio parahaemolyticus 16S rRNA genes

Microbiology

Volumn 153, Issue 8, 2007, Pages 2640-2647

  Harth, Erika ^a   Romero, Jaime ^a   Torres, Rafael ^a   Espejo, Romilio T ^a  

^a UNIVERSITY OF CHILE   (Chile)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; DOUBLE STRANDED RNA; GENOMIC RNA; RNA 16S; SINGLE STRANDED RNA;

ALLELE; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; GENE CLUSTER; GENE LOCUS; GENETIC VARIABILITY; GENOTYPE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PRIORITY JOURNAL; RNA RECOMBINATION; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; STRAIN DIFFERENCE; VIBRIO PARAHAEMOLYTICUS;

BASE SEQUENCE; CLUSTER ANALYSIS; DNA FINGERPRINTING; GENES, RRNA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; POLYMORPHISM, GENETIC; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RECOMBINATION, GENETIC; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SHELLFISH; VARIATION (GENETICS); VIBRIO PARAHAEMOLYTICUS;

BACTERIA (MICROORGANISMS); VIBRIO; VIBRIO PARAHAEMOLYTICUS;

EID: 34547918923     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.2007/009175-0     Document Type: Article

References (27)

1. Acinas, S. G., Marcelino, L. A., Klepac-Cerej, V. & Polz, M. F. (2004). Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186, 2629-2635.
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.
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.
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.
5. Cole, J. R., Chai, B., Farris, R. J., Wang, O., 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.
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.
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.
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.
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.
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.
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.
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.
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.
14. Iida, T., Suthienkul, O., Park K. S., Tang, G. O., 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.
15. Jiang, S. C. & Paul, J. H. (1998). Gene transfer by transduction in the marine environment. Appl Environ Microbiol 64, 2780-2787.
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.
17. Liu, S. L., Hassel, 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.
18. Majewski, J. & Cohan, F. M. (1999). DNA sequence similarity requirements for interspecific recombination in Bacillus. Genetics 153, 1525-1533.
19. Makino, K., Oshima, K., Kurokewa, 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.
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.
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. Microbioly 148, 1233-1239.
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.
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.
24. Sneath, P. H. (1993). Evidence from Aeromonas for genetic crossing-over in ribosomal sequences. Int J Syst Bacteriol 43, 626-629.
25. Ueda, V., Said, T., Kudo, T., Yoshida, T. & Kataoka, M. (1999). Two distinct mechanisms cause heterogeneity of 16S rRNA. J Bacteriol 181, 78-82.
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.
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.