1887

Microbiology Society logo

Volume 148, Issue 6

Genome plasticity in

The GenBank accession numbers for the sequences reported in this paper can be found in Table 1 T1 ; the GenBank accession number for DFR4 is AF426171.

Free

Abstract

, the causative agent of bubonic plague, emerged recently (<20000 years ago) as a clone of . There is scant evidence of genome diversity in , although it is possible to differentiate three biovars (antiqua, mediaevalis or orientalis) based on two biochemical tests. There are a few examples of restriction fragment length polymorphisms (RFLPs) within ; however, their genetic basis is poorly understood. In this study, six difference regions (DFRs) were identified in , by using subtractive hybridization, which ranged from 46 to 19 kb in size. Four of the DFRs are flanked by insertion sequences, and their sequences show similarity to bacterial genes encoding proteins for flagellar synthesis, ABC transport, insect toxicity and bacteriophage functions. The presence or absence of these DFRs (termed the DFR profile) was demonstrated in 78 geographically diverse strains of . Significant genome plasticity was observed among these strains and suggests the acquisition and deletion of these DNA regions during the recent evolution of . biovar orientalis possesses DFR profiles that are different from antiqua and mediaevalis biovars, reflecting the recent origins of this biovar. Whereas some DFR profiles are specific for antiqua and mediaevalis, some DFR profiles are shared by both biovars. Furthermore, the progenitor of , . (an enteric pathogen), possesses its own DFR profile. The DFR profiles detailed here demonstrate genome plasticity within , and they imply evolutionary relationships among the three biovars of , as well as between and . .

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): bacterial genome , comparative genomics , DFR, difference region , RFLP, restriction fragment length polymorphism , SSH, suppression subtractive hybridization , subtractive hybridization and Yersinia pseudotuberculosis
© Microbiology Society
Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-148-6-1687
2002-06-01
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/micro/148/6/1481687a.html?itemId=/content/journal/micro/10.1099/00221287-148-6-1687&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 USA 96:14043–14048 [CrossRef]
     [Google Scholar]
  2. Adair D. M., Worsham P. L., Hill K. K., Klevytska A. M., Jackson P. J., Friedlander A. M., Keim P. 2000; Diversity in a variable-number tandem repeat from Yersinia pestis . J Clin Microbiol 38:1516–1519
     [Google Scholar]
  3. Akopyants N. S., Fradkov A., Diatchenko L., Hill J. E., Siebert P. D., Lukyanov S. A., Sverdlov E. D., Berg D. E. 1998; PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori . Proc Natl Acad Sci USA 95:13108–13113 [CrossRef]
     [Google Scholar]
  4. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [CrossRef]
     [Google Scholar]
  5. Bachellier S., Clément J. M., Hofnung M., Gilson E. 1997; Bacterial interspersed mosaic elements (BIMEs) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence. Genetics 145:551–562
     [Google Scholar]
  6. Bercovier H., Mollaret H. H., Alonso J. M., Brault J., Fanning G. R., Steigerwalt A. G., Brenner D. J. 1980; Intra- and interspecies relatedness of Yersinia pestis by DNA hybridization and its relationship to Y. pseudotuberculosis . Curr Microbiol 4:225–229 [CrossRef]
     [Google Scholar]
  7. Buchrieser C., Prentice M., Carniel E. 1998; The 102-kilobase unstable region of Yersinia pestis comprises a high-pathogenicity island linked to a pigmentation segment which undergoes internal rearrangement. J Bacteriol 180:2321–2329
     [Google Scholar]
  8. Buchrieser C., Rusniok C., Frangeul L., Couve E., Billault A., Kunst F., Carniel E., Glaser P. 1999; The 102-kilobase pgm locus of Yersinia pestis : sequence analysis and comparison of selected regions among different Yersinia pestis and Yersinia pseudotuberculosis strains. Infect Immun 67:4851–4861
     [Google Scholar]
  9. Devignat R. 1951; Variétés de l’espèce Pasteurella pestis . Nouvelle hypothèse. Bull W H O 4:247–253
     [Google Scholar]
  10. Diatchenko L., Lau Y. F., Campbell A. P. 8 other authors 1996; Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93:6025–6030 [CrossRef]
     [Google Scholar]
  11. Ewing B., Green P. 1998; Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194
     [Google Scholar]
  12. Ewing B., Hillier L., Wendl M. C., Green P. 1998; Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185 [CrossRef]
     [Google Scholar]
  13. Fetherston J. D., Perry R. D. 1994; The pigmentation locus of Yersinia pestis KIM6+ is flanked by an insertion sequence and includes the structural genes for pesticin sensitivity and HMWP2. Mol Microbiol 13:697–708 [CrossRef]
     [Google Scholar]
  14. Fetherston J. D., Schuetze P., Perry R. D. 1992; Loss of the pigmentation phenotype in Yersinia pestis is due to the spontaneous deletion of 102 kb of chromosomal DNA which is flanked by a repetitive element. Mol Microbiol 6:2693–2704 [CrossRef]
     [Google Scholar]
  15. Gordon D., Abajian C., Green P. 1998; Consed: a graphical tool for sequence finishing. Genome Res 8:195–202 [CrossRef]
     [Google Scholar]
  16. Guiyoule A., Grimont F., Iteman I., Grimont P. A., Lefèvre M., Carniel E. 1994; Plague pandemics investigated by ribotyping of Yersinia pestis strains. J Clin Microbiol 32:634–641
     [Google Scholar]
  17. Guiyoule A., Rasoamanana B., Buchrieser C., Michel P., Chanteau S., Carniel E. 1997; Recent emergence of new variants of Yersinia pestis in Madagascar. J Clin Microbiol 35:2826–2833
     [Google Scholar]
  18. Hacker J., Kaper J. B. 2000; Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 54:641–679 [CrossRef]
     [Google Scholar]
  19. Hurst M. R., Glare T. R., Jackson T. A., Ronson C. W. 2000; Plasmid-located pathogenicity determinants of Serratia entomophila , the causal agent of amber disease of grass grub, show similarity to the insecticidal toxins of Photorhabdus luminescens . J Bacteriol 182:5127–5138 [CrossRef]
     [Google Scholar]
  20. Jain R., Rivera M. C., Lake J. A. 1999; Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96:3801–3806 [CrossRef]
     [Google Scholar]
  21. Lawrence J. G., Ochman H. 1997; Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 44:383–397 [CrossRef]
     [Google Scholar]
  22. Lawrence J. G., Ochman H. 1998; Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 95:9413–9417 [CrossRef]
     [Google Scholar]
  23. Lucier T. S., Brubaker R. R. 1992; Determination of genome size, macrorestriction pattern polymorphism, and nonpigmentation-specific deletion in Yersinia pestis by pulsed-field gel electrophoresis. J Bacteriol 174:2078–2086
     [Google Scholar]
  24. McCarter L. L., Wright M. E. 1993; Identification of genes encoding components of the swarmer cell flagellar motor and propeller and a sigma factor controlling differentiation of Vibrio parahaemolyticus . J Bacteriol 175:3361–3371
     [Google Scholar]
  25. McDonough K. A., Hare J. M. 1997; Homology with a repeated Yersinia pestis DNA sequence IS100 correlates with pesticin sensitivity in Yersinia pseudotuberculosis . J Bacteriol 179:2081–2085
     [Google Scholar]
  26. 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 Bacteriol 184:1019–1027 [CrossRef]
     [Google Scholar]
  27. Ochman H., Lawrence J. G., Groisman E. A. 2000; Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304 [CrossRef]
     [Google Scholar]
  28. Parkhill J., Wren B. W., Thomson N. R. 32 other authors 2001; Genome sequence of Yersinia pestis , the causative agent of plague. Nature 413:523–527 [CrossRef]
     [Google Scholar]
  29. Perkins J. D., Heath J. D., Sharma B. R., Weinstock G. M. 1993; Xba I and Bln I genomic cleavage maps of Escherichia coli K-12 strain MG1655 and comparative analysis of other strains. J Mol Biol 232:419–445 [CrossRef]
     [Google Scholar]
  30. Perna N. T., Plunkett G. III, Burland V. 25 other authors 2001; Genome sequence of enterohaemorrhagic Escherichia coli O157: H7. Nature 409:529–533 [CrossRef]
     [Google Scholar]
  31. Seeger C., Poulsen C., Dandanell G. 1995; Identification and characterization of genes ( xapA , xapB , and xapR) involved in xanthosine catabolism in Escherichia coli . J Bacteriol 177:5506–5516
     [Google Scholar]
  32. Skowronski E. W., Armstrong N., Andersen G., Macht M., McCready P. M. 2000; Magnetic microplate-format plasmid isolation protocol for high-yield, sequencing-grade DNA. Biotechniques 29:786–790
     [Google Scholar]
  33. Trebesius K., Harmsen D., Rakin A., Schmelz J., Heesemann J. 1998; Development of rRNA-targeted PCR and in situ hybridization with fluorescently labelled oligonucleotides for detection of Yersinia species. J Clin Microbiol 36:2557–2564
     [Google Scholar]
  34. Waterfield N. R., Bowen D. J., Fetherston J. D., Perry R. D., ffrench-Constant R. H. 2001; The tc genes of Photorhabdus : a growing family. Trends Microbiol 9:185–191 [CrossRef]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-148-6-1687
Loading
Genome plasticity in Yersinia pestisThe GenBank accession numbers for the sequences reported in this paper can be found in Table 1T1; the GenBank accession number for DFR4 is AF426171.
Microbiology 148, 1687 (2002); https://doi.org/10.1099/00221287-148-6-1687
/content/journal/micro/10.1099/00221287-148-6-1687
/content/journal/micro/10.1099/00221287-148-6-1687
Loading

Data & Media loading...

Most cited Most Cited RSS feed

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