1887

Abstract

The remarkable repetitive elements called CRISPRs (clustered regularly interspaced short palindromic repeats) consist of repeats interspaced with non-repetitive elements or ‘spacers’. CRISPRs are present in both archaea and bacteria, in association with genes involved in DNA recombination and repair. In the genome, three such elements are found at three distinct loci, one of them being highly polymorphic. The authors have sequenced a total of 109 alleles of the three CRISPRs and they describe 29 new spacers, most being specific to one isolate. In nine strains of , 132 spacers were found, of which only three are common to isolates. In of the Orientalis biovar investigated in detail here, deletion of motifs is observed but it appears that addition of new motifs to a common ancestral element is the most frequent event. This takes place at the three different loci, although at a higher rate in one of the loci, and the addition of new motifs is polarized. Interestingly, the most recently acquired spacers were found to have a homologue at another locus in the genome, the majority of these inside an inactive prophage. This is believed to be the first time that the origin of the spacers in CRISPR elements has been explained. The CRISPR structure provides a new and robust identification tool.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.27437-0
2005-03-01
2020-02-25
Loading full text...

Full text loading...

/deliver/fulltext/micro/151/3/mic1510653.html?itemId=/content/journal/micro/10.1099/mic.0.27437-0&mimeType=html&fmt=ahah

References

  1. Achtman M., Zurth K., Morelli G., Torrea G., Guiyoule A., Carniel E. 1999; Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A96:14043–14048[CrossRef]
    [Google Scholar]
  2. Anisimov A. P., Lindler L. E., Pier G. B. 2004; Intraspecific diversity of Yersinia pestis. Clin Microbiol Rev17:434–464[CrossRef]
    [Google Scholar]
  3. Beres S. B., Sylva G. L., Barbian K. D. & 13 other authors. 2002; Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Proc Natl Acad Sci U S A99:10078–10083[CrossRef]
    [Google Scholar]
  4. Deng W., Burland V., Plunkett G.. 3rd & 18 other authors. 2002; Genome sequence of Yersinia pestis. KIM. J Bacteriol184:4601–4611[CrossRef]
    [Google Scholar]
  5. Denoeud F., Vergnaud G. 2004; Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains: a Web-based resource. BMC Bioinformatics5:4[CrossRef]
    [Google Scholar]
  6. Devignat R. 1951; Variétés de l'espèce Pasteurella pestis. Nouvelle hypothèse. Bull W H O4:247–263
    [Google Scholar]
  7. Embley T. M. 1991; The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett Appl Microbiol13:171–174[CrossRef]
    [Google Scholar]
  8. Fabre M., Koeck J. L., Simon F., Vergnaud G., Pourcel C, Le Flèche P., Hervé V.. 2004; High genetic diversity revealed by variable-number tandem repeat genotyping and analysis of hsp65 gene polymorphism in a large collection of ‘Mycobacterium canettii’strains indicates that the M. tuberculosis complex is a recently emerged clone of ‘M. canettii’. . J Clin Microbiol42:3248–3255[CrossRef]
    [Google Scholar]
  9. Groenen P. M., Bunschoten A. E., van Soolingen D, van Embden J. D. 1993; Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method. Mol Microbiol10:1057–1065[CrossRef]
    [Google Scholar]
  10. Hernandez E., Girardet M., Ramisse F., Vidal D., Cavallo J. D. 2003; Antibiotic susceptibilities of 94 isolates of Yersinia pestis to 24 antimicrobial agents. J Antimicrob Chemother52:1029–1031[CrossRef]
    [Google Scholar]
  11. Hinchliffe S. J., Isherwood K. E., Stabler R. A.. 7 other authors 2003; Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis. Genome Res13:2018–2029[CrossRef]
    [Google Scholar]
  12. Hoe N., Nakashima K., Grigsby D.. 7 other authors 1999; Rapid molecular genetic subtyping of serotype M1 group A Streptococcus strains. Emerg Infect Dis5:254–263[CrossRef]
    [Google Scholar]
  13. Jansen R., Embden J. D., Gaastra W., Schouls L. M. 2002; Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol43:1565–1575[CrossRef]
    [Google Scholar]
  14. Kamerbeek J., Schouls L., Kolk A.. 8 other authors 1997; Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol35:907–914
    [Google Scholar]
  15. Le Flèche P., Hauck Y., Onteniente L. 7 other authors 2001; A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis. BMC Microbiol1:2[CrossRef]
    [Google Scholar]
  16. Makarova K. S., Aravind L., Grishin N. V., Rogozin I. B., Koonin E. V. 2002; A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res30:482–496[CrossRef]
    [Google Scholar]
  17. Mojica F. J., Ferrer C., Juez G., Rodriguez-Valera F. 1995; Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Mol Microbiol17:85–93[CrossRef]
    [Google Scholar]
  18. Mojica F. J., Diez-Villasenor C., Soria E., Juez G. 2000; Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol36:244–246[CrossRef]
    [Google Scholar]
  19. Motin V. L., Georgescu A. M., Elliott J. M. & 8 other authors. 2002; Genetic variability of Yersinia pestis isolates as predicted by PCR-based IS100 genotyping and analysis of structural genes encoding glycerol-3-phosphate dehydrogenase (glpD. J Bacteriol184:1019–1027[CrossRef]
    [Google Scholar]
  20. Parkhill J., Wren B. W., Thomson N. R. & 32 other authors. 2001; Genome sequence of Yersinia pestis, the causative agent of plague. Nature413:523–527[CrossRef]
    [Google Scholar]
  21. Pourcel C., Neubauer H., Ramisse F., Vergnaud G, André-Mazeaud F.. 2004; Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis. BMC Microbiol4:22[CrossRef]
    [Google Scholar]
  22. Radnedge L., Agron P. G., Worsham P. L., Andersen G. L. 2002; Genome plasticity in Yersinia pestis. Microbiology148:1687–1698
    [Google Scholar]
  23. Schouls L. M., Reulen S., Duim B., Wagenaar J. A., Willems R. J., Dingle K. E., Colles F. M., Van Embden J. D. 2003; Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: strain diversity, host range, and recombination. J Clin Microbiol41:15–26[CrossRef]
    [Google Scholar]
  24. Skurnik M., Peippo A., Ervela E. 2000; Characterization of the O-antigen gene clusters of Yersinia pseudotuberculosis and the cryptic O-antigen gene cluster of Yersinia pestis shows that the plague bacillus is most closely related to and has evolved fromY. pseudotuberculosis serotype O : 1b. Mol Microbiol37:316–330[CrossRef]
    [Google Scholar]
  25. Sola C., Filliol I., Legrand E., Lesjean S., Locht C., Supply P., Rastogi N. 2003; Genotyping of the Mycobacterium tuberculosis complex using MIRUs: association with VNTR and spoligotyping for molecular epidemiology and evolutionary genetics. Infect Genet Evol3:125–133[CrossRef]
    [Google Scholar]
  26. van Embden J. D., van Gorkom T., Kremer K., Jansen R., van Der Zeijst B. A., Schouls L. M. 2000; Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. J Bacteriol182:2393–2401[CrossRef]
    [Google Scholar]
  27. Yersin A. 1894; La peste bubonique à Hong-Kong. Ann Inst Pasteur2:428–430
    [Google Scholar]
  28. Zhou D., Tong Z., Song Y. & 14 other authors. 2004; Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus. J Bacteriol186:5147–5152[CrossRef]
    [Google Scholar]
  29. Zivanovic Y., Lopez P., Philippe H., Forterre P. 2002; Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. Nucleic Acids Res30:1902–1910[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.27437-0
Loading
/content/journal/micro/10.1099/mic.0.27437-0
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