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Analysis of the Three Yersinia pestis CRISPR Loci Provides New Tools for Phylogenetic Studies and Possibly for the Investigation of Ancient DNA

  • Gilles Vergnaud
  • Dongsheng Zhou
  • Mikhail E. Platonov
  • Christine Pourcel
  • Ruifu Yang
  • Andrey P. Anisimov
  • Heinrich Neubauer
  • Sergey V. Balakhonov
  • Alexander Rakin
  • Svetlana V. Dentovskaya
  • Ibtissem Grissa
  • Yajun Song
  • Yujun Cui
  • Olivier Gorgé
  • Yanjun Li
Part of the Advances In Experimental Medicine And Biology book series (AEMB, volume 603)

The precise nature of the pathogen having caused early plague pandemics is uncertain. Although Yersinia pestis is a likely candidate for all three plague pandemics, the very rare direct evidence that can be deduced from ancient DNA (aDNA) analysis is controversial. Moreover, which of the three biovars, Antiqua, Medievalis or Orientalis, was associated with these pandemics is still debated. There is a need for phylogenetic analysis performed on Y. pestis strains isolated from countries from which plague probably arose and is still endemic. In addition there exist technical difficulties inherent to aDNA investigations and a lack of appropriate genetic targets. The recently described CRISPRs (clustered regularly interspaced short palindromic repeats) may represent such a target. CRISPR loci consist of a succession of highly conserved regions separated by specific “spacers” usually of viral origin. To be of use, data describing the mechanisms of evolution and diversity of CRISPRs in Y. pestis, its closest neighbors, and other species which might contaminate ancient DNA, are necessary.

Keywords

Yersinia Pestis Short Palindromic Repeat Genetic Target Mycobacterium Tuberculosis Complex CRISPR Locus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. Achtman, M., Morelli G., Zhu, P., Wirth, T., Diehl, I., Kusecek, B., Vogler, A.J., Wagner, D.M., Allender, C.J., Easterday, W.R., Chenal-Francisque, V., Worsham, P., Thomson, N.R., Parkhill, J., Lindler, L.E., Carniel, E. and Keim, P. (2004) Microevolution and his-tory of the plague bacillus, Yersinia pestis. Proc. Natl. Acad. Sci. USA 101, 17837-17842.CrossRefPubMedPubMedCentralGoogle Scholar
  2. Achtman, M., Zurth, K., Morelli, G., Torrea, G., Guiyoule, A. and Carniel, E. (1999) Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis [published erratum appears in Proc. Natl. Acad. Sci. USA 2000 97, 8192]. Proc. Natl. Acad. Sci. USA 96, 14043-14048.Google Scholar
  3. Anisimov, A.P., Lindler, L.E. and Pier, G.B. (2004) Intraspecific diversity of Yersinia pestis. Clin. Microbiol. Rev. 17, 434-464.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Brudey, K., Driscoll, J.R., Rigouts, L., Prodinger, W.M., Gori, A., Al-Hajoj, S.A., Allix, C., Aristimuno, L., Arora, J., Baumanis, V., Binder, L., Cafrune, P., Cataldi, A., Cheong, S., Diel, R., Ellermeier, C., Evans, J.T., Fauville-Dufaux, M., Ferdinand, S., Garcia de Viedma, D., Garzelli, C., Gazzola, L., Gomes, H.M., Guttierez, M.C., Hawkey, P.M., van Helden, P.D., Kadival, G.V., Kreiswirth, B.N., Kremer, K., Kubin, M., Kulkarni, S.P., Liens, B., Lillebaek, T., Ho, M.L., Martin, C., Martin, C., Mokrousov, I., Narvskaia, O., Ngeow, Y.F., Naumann, L., Niemann, S., Parwati, I., Rahim, Z., Rasolofo-Razanamparany, V., Rasolonavalona, T., Rossetti, M.L., Rusch-Gerdes, S., Sajduda, A., Samper, S., Shemyakin, I.G., Singh, U.B., Somoskovi, A., Skuce, R.A., van Soolingen, D., Streicher, E.M., Suffys, P.N., Tortoli, E., Tracevska, T., Vincent, V. Victor, T.C. Warren, R.M., Yap, S.F., Zaman, K., Portaels, F., Rastogi, N. and Sola, C. (2006) Myco-bacterium tuberculosis complex genetic diversity: mining the fourth international spoligo-typing database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 6, 23.Google Scholar
  5. Drancourt, M., Roux, V., Dang, L.V., Tran-Hung, L., Castex, D., Chenal-Francisque, V., Ogata, H., Fournier, P-E., Crubézy, E. and Raoult, D. (2004) Genotyping, Orientalis-like Yersinia pestis, and plague pandemics. Emerg. Infect. Dis. 10, 1585-1592.CrossRefPubMedPubMedCentralGoogle Scholar
  6. Gilbert, M.T., Cuccui, J., White, W., Lynnerup, N., Titball, R.W., Cooper, A. and Prentice, M.B. (2004) Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims. Microbiology 150, 341-354.CrossRefPubMedGoogle Scholar
  7. Jansen, R., Embden, J.D., Gaastra, W. and Schouls, L.M. (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43, 1565-1575.CrossRefPubMedGoogle Scholar
  8. Le Flèche, P., Hauck, Y., Onteniente, L., Prieur, A., Denoeud, F., Ramisse, V., Sylvestre, P., Benson, G., Ramisse, F. and Vergnaud, G. (2001) A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis. BMC Microbiol. 1, 2.CrossRefPubMedPubMedCentralGoogle Scholar
  9. Lillestol, R.K., Redder, P., Garrett, R.A. and Brugger, K. (2006) A putative viral defence mechanism in archaeal cells. Archaea 2, 59-72.CrossRefPubMedPubMedCentralGoogle Scholar
  10. Makarova, K.S., Grishin, N.V., Shabalina, S.A., Wolf, Y.I. and Koonin, E.V. (2006) A puta-tive RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1, 7.CrossRefPubMedPubMedCentralGoogle Scholar
  11. Mojica, F.J., Diez-Villasenor, C., Garcia-Martinez, J. and Soria, E. (2005) Intervening se-quences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60, 174-182.CrossRefPubMedGoogle Scholar
  12. Pourcel, C., Andre-Mazeaud, F., Neubauer, H., Ramisse, F. and Vergnaud, G. (2004) Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis. BMC Mi-crobiol. 4, 22.CrossRefGoogle Scholar
  13. Pourcel, C., Salvignol, G. and Vergnaud, G. (2005) CRISPR elements in Yersinia pestis ac-quire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151, 653-663.CrossRefPubMedGoogle Scholar
  14. Prentice, M.B., Gilbert, T. and Cooper, A. (2004) Was the Black Death caused by Yersinia pestis? Lancet Infect. Dis. 4, 72.CrossRefPubMedGoogle Scholar
  15. Shapiro, B., Rambaut, A. and Gilbert, M.T. (2006) No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al.). Int. J. Infect. Dis. 10, 334-335; author reply 335-336.CrossRefPubMedGoogle Scholar
  16. Song, Y., Tong, Z., Wang, J., Wang, L., Guo, Z., Han, Y., Zhang, J., Pei, D., Zhou, D., Qin, H., Pang, X., Zhai, J., Li, M., Cui, B., Qi, Z., Jin, L., Dai, R., Chen, F., Li, S., Ye, C., Du, Z., Lin, W., Yu, J., Yang, H., Huang, P. and Yang, R. (2004) Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans. DNA Res. 11, 179-197.CrossRefPubMedGoogle Scholar
  17. Tang, T.H., Bachellerie, J.P., Rozhdestvensky, T., Bortolin, M.L., Huber, H., Drungowski, M., Elge, T., Brosius, J. and Huttenhofer, A. (2002) Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc. Natl. Acad. Sci. USA 99, 7536-7541.CrossRefPubMedPubMedCentralGoogle Scholar
  18. Vergnaud, G. (2005) Yersinia pestis genotyping. Emerg. Infect. Dis. 11: 1317-1318; author reply 1318-1319.CrossRefPubMedPubMedCentralGoogle Scholar
  19. Zhou, D., Han Y., Song, Y., Huang, P. and Yang, R. (2004a) Comparative and evolutionary genomics of Yersinia pestis. Microbes Infect. 6, 1226-1234.CrossRefPubMedGoogle Scholar
  20. Zhou, D., Han, Y., Song, Y., Tong, Z., Wang, J., Guo, Z., Pei, D., Pang, X., Zhai, J., Li, M., Cui, B., Qi, Z., Jin, L., Dai, R., Du, Z., Bao, J., Zhang, X., Yu, J., Wang, J., Huang, P. and Yang, R. (2004b) DNA microarray analysis of genome dynamics in Yersinia pestis: in-sights into bacterial genome microevolution and niche adaptation. J. Bacteriol. 186, 5138-5146.CrossRefPubMedPubMedCentralGoogle Scholar
  21. Zink, A.R., Sola, C., Reischl, U., Grabner, W., Rastogi, N., Wolf, H. and Nerlich, A.G. (2003) Characterization of Mycobacterium tuberculosis complex DNAs from Egyptian mummies by spoligotyping. J. Clin. Microbiol. 41, 359-367.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Gilles Vergnaud
    • 1
  • Dongsheng Zhou
    • 3
  • Mikhail E. Platonov
    • 2
  • Christine Pourcel
    • 1
  • Ruifu Yang
    • 5
  • Andrey P. Anisimov
    • 2
  • Heinrich Neubauer
    • 4
  • Sergey V. Balakhonov
    • 5
  • Alexander Rakin
    • 6
  • Svetlana V. Dentovskaya
    • 2
  • Ibtissem Grissa
    • 1
  • Yajun Song
    • 3
  • Yujun Cui
    • 3
  • Olivier Gorgé
    • 7
  • Yanjun Li
    • 3
  1. 1.Institut de Génétique et MicrobiologieUniv Paris-SudFrance
  2. 2.State Research Center for Applied Microbiology and BiotechnologyObolenskRussia
  3. 3.Academy of Military Medical SciencesInstitute of Microbiology and EpidemiologyChina
  4. 4.Friedrich-Loeffler InstituteGerman Reference Center for Human and Animal BrucellosisGermany
  5. 5.Antiplague Research Institute of Siberia and Far EastRussia
  6. 6.Max von Pettenkofer Institute for Hygiene and Medical MicrobiologyGermany
  7. 7.Division of Analytical MicrobiologyCentre d'Etudes du BouchetFrance

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