1887

Abstract

Phase variation is a common mechanism used by pathogenic bacteria to generate intra-strain diversity that is important in niche adaptation and is strongly associated with virulence determinants. Previous analyses of the complete sequences of the strains 26695 and J99 have identified 36 putative phase-variable genes among the two genomes through their association with homopolymeric tracts and dinucleotide repeats. Here a comparative analysis of the two genomes is reported and an updated and expanded list of 46 candidate phase-variable genes in is described. These have been systematically investigated by PCR and sequencing for the presence of the genes, and the presence and variability in length of the repeats in strains 26695 and J99 and in a collection of unrelated strains representative of the main global subdivisions recently suggested. This provides supportive evidence for the phase variability of 30 of the 46 candidates. Other differences in this subset of genes were observed (i) in the repeats, which can be present or absent among the strains, or stabilized in different strains and (ii) in the gene-complements of the strains. Differences between genes were not consistently correlated with the geographic population distribution of the strains. This study extends and provides new evidence for variation of this type in , and of the high degree of diversity of the repertoire of genes which display phase-variable switching within individual strains.

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2004-04-01
2019-10-18
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References

  1. Achtman, M., Azuma, T., Berg, D. E. & 7 other authors ( 1999; ). Recombination and clonal groupings within Helicobacter pylori from different geographical regions. Mol Microbiol 32, 459–470.[CrossRef]
    [Google Scholar]
  2. Akopyants, N. S., Clifton, S. W., Kersulyte, D. & 7 other authors ( 1998; ). Analyses of the cag pathogenicity island of Helicobacter pylori. Mol Microbiol 28, 37–53.
    [Google Scholar]
  3. Alm, R. A., Ling, L. S., Moir, D. T. & 20 other authors ( 1999; ). Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397, 176–180.[CrossRef]
    [Google Scholar]
  4. Appelmelk, B. J., Shiberu, B., Trinks, C. & 10 other authors ( 1998; ). Phase variation in Helicobacter pylori lipopolysaccharide. Infect Immun 66, 70–76.
    [Google Scholar]
  5. Appelmelk, B. J., Martin, S. L., Monteiro, M. A. & 10 other authors ( 1999; ). Phase variation in Helicobacter pylori lipopolysaccharide due to changes in the lengths of poly(C) tracts in alpha3-fucosyltransferase genes. Infect Immun 67, 5361–5366.
    [Google Scholar]
  6. Appelmelk, B. J., Martino, M. C., Veenhof, E. & 7 other authors ( 2000; ). Phase variation in H type I and Lewis a epitopes of Helicobacter pylori lipopolysaccharide. Infect Immun 68, 5928–5932.[CrossRef]
    [Google Scholar]
  7. Atherton, J. C., Peek, R. M., Jr, Tham, K. T., Cover, T. L. & Blaser, M. J. ( 1997; ). Clinical and pathological importance of heterogeneity in vacA, the vacuolating cytotoxin gene of Helicobacter pylori. Gastroenterology 112, 92–99.[CrossRef]
    [Google Scholar]
  8. Björkholm, B. M., Guruge, J. L., Oh, J. D. & 8 other authors ( 2002; ). Colonization of germ-free transgenic mice with genotyped Helicobacter pylori strains from a case-control study of gastric cancer reveals a correlation between host responses and HsdS components of type I restriction-modification systems. J Biol Chem 277, 34191–34197.[CrossRef]
    [Google Scholar]
  9. Blaser, M. J. ( 1997; ). Ecology of Helicobacter pylori in the human stomach. J Clin Invest 100, 759–762.[CrossRef]
    [Google Scholar]
  10. Boneca, I. G., de Reuse, H., Epinat, J. C., Pupin, M., Labigne, A. & Moszer, I. ( 2003; ). A revised annotation and comparative analysis of Helicobacter pylori genomes. Nucleic Acids Res 31, 1704–1714.[CrossRef]
    [Google Scholar]
  11. Bonfield, J. K., Beal, K. F., Betts, M. J. & Staden, R. ( 2002; ). Trev: a DNA trace editor and viewer. Bioinformatics 18, 194–195.[CrossRef]
    [Google Scholar]
  12. Bunn, J. E., MacKay, W. G., Thomas, J. E., Reid, D. C. & Weaver, L. T. ( 2002; ). Detection of Helicobacter pylori DNA in drinking water biofilms: implications for transmission in early life. Lett Appl Microbiol 34, 450–454.[CrossRef]
    [Google Scholar]
  13. De Bolle, X., Bayliss, C. D., Field, D., van de Ven, T., Saunders, N. J., Hood, D. W. & Moxon, E. R. ( 2000; ). The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases. Mol Microbiol 35, 211–222.[CrossRef]
    [Google Scholar]
  14. de Vries, N., Duinsbergen, D., Kuipers, E. J., Pot, R. G., Wiesenekker, P., Penn, C. W., Van Vliet, A. H., Vandenbroucke-Grauls, C. M. & Kusters, J. G. ( 2002; ). Transcriptional phase variation of a type III restriction-modification system in Helicobacter pylori. J Bacteriol 184, 6615–6623.[CrossRef]
    [Google Scholar]
  15. Durbin, R. & Thierry-Mieg, J. T. ( 1991; ). A C. elegans DataBase. Documentation, code and data available from http://www.acedb.org
  16. Falush, D., Kraft, C., Taylor, N. S., Correa, P., Fox, J. G., Achtman, M. & Suerbaum, S. ( 2001; ). Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc Natl Acad Sci U S A 98, 15056–15061.[CrossRef]
    [Google Scholar]
  17. Falush, D., Wirth, T., Linz, B. & 15 other authors ( 2003; ). Traces of human migrations in Helicobacter pylori populations. Science 299, 1582–1585.[CrossRef]
    [Google Scholar]
  18. Go, M. F., Kapur, V., Graham, D. Y. & Musser, J. M. ( 1996; ). Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure. J Bacteriol 178, 3934–3938.
    [Google Scholar]
  19. Hammerschmidt, S., Muller, A., Sillmann, H. & 7 other authors ( 1996; ). Capsule phase variation in Neisseria meningitidis serogroup B by slipped-strand mispairing in the polysialyltransferase gene (siaD): correlation with bacterial invasion and the outbreak of meningococcal disease. Mol Microbiol 20, 1211–1220.[CrossRef]
    [Google Scholar]
  20. Hood, D. W., Deadman, M. E., Jennings, M. P., Bisercic, M., Fleischmann, R. D., Venter, J. C. & Moxon, E. R. ( 1996; ). DNA repeats identify novel virulence genes in Haemophilus influenzae. Proc Natl Acad Sci U S A 93, 11121–11125.[CrossRef]
    [Google Scholar]
  21. Ilver, D., Arnqvist, A., Ogren, J. & 7 other authors ( 1998; ). Helicobacter pylori adhesin binding fucosylated histo-blood group antigens revealed by retagging. Science 279, 373–377.[CrossRef]
    [Google Scholar]
  22. Jennings, M. P., Hood, D. W., Peak, I. R., Virji, M. & Moxon, E. R. ( 1995; ). Molecular analysis of a locus for the biosynthesis and phase-variable expression of the lacto-N-neotetraose terminal lipopolysaccharide structure in Neisseria meningitidis. Mol Microbiol 18, 729–740.[CrossRef]
    [Google Scholar]
  23. Josenhans, C., Eaton, K. A., Thevenot, T. & Suerbaum, S. ( 2000; ). Switching of flagellar motility in Helicobacter pylori by reversible length variation of a short homopolymeric sequence repeat in fliP, a gene encoding a basal body protein. Infect Immun 68, 4598–4603.[CrossRef]
    [Google Scholar]
  24. Lee, A., O'Rourke, J., De Ungria, M. C., Robertson, B., Daskalopoulos, G. & Dixon, M. F. ( 1997; ). A standardized mouse model of Helicobacter pylori infection: introducing the Sydney strain. Gastroenterology 112, 1386–1397.[CrossRef]
    [Google Scholar]
  25. Logan, R. P. & Berg, D. E. ( 1996; ). Genetic diversity of Helicobacter pylori. Lancet 348, 1462–1463.[CrossRef]
    [Google Scholar]
  26. Logan, S. M., Conlan, J. W., Monteiro, M. A., Wakarchuk, W. W. & Altman, E. ( 2000; ). Functional genomics of Helicobacter pylori: identification of a beta-1,4 galactosyltransferase and generation of mutants with altered lipopolysaccharide. Mol Microbiol 35, 1156–1167.[CrossRef]
    [Google Scholar]
  27. Mahdavi, J., Sonden, B., Hurtig, M. & 20 other authors ( 2002; ). Helicobacter pylori SabA adhesin in persistent infection and chronic inflammation. Science 297, 573–578.[CrossRef]
    [Google Scholar]
  28. Majmudar, P., Shah, S. M., Dhunjibhoy, K. R. & Desai, H. G. ( 1990; ). Isolation of Helicobacter pylori from dental plaques in healthy volunteers. Indian J Gastroenterol 9, 271–272.
    [Google Scholar]
  29. Marshall, B. ( 1994; ). Helicobacter pylori. Am J Gastroenterol 89, S116–S118.
    [Google Scholar]
  30. Marshall, B. J. & Warren, J. R. ( 1984; ). Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration. Lancet 1, 1311–1315.
    [Google Scholar]
  31. Martin, P., Van De Ven, T., Mouchel, N., Jeffries, A. C., Hood, D. W. & Moxon, E. R. ( 2003; ). Experimentally revised repertoire of putative contingency loci in Neisseria meningitidis strain MC58: evidence for a novel mechanism of phase variation. Mol Microbiol 50, 245–257.[CrossRef]
    [Google Scholar]
  32. Nomura, A., Stemmermann, G. N., Chyou, P. H., Perez-Perez, G. I. & Blaser, M. J. ( 1994; ). Helicobacter pylori infection and the risk for duodenal and gastric ulceration. Ann Intern Med 120, 977–981.[CrossRef]
    [Google Scholar]
  33. Park, S. R., Mackay, W. G. & Reid, D. C. ( 2001; ). Helicobacter sp. recovered from drinking water biofilm sampled from a water distribution system. Water Res 35, 1624–1626.[CrossRef]
    [Google Scholar]
  34. Parkhill, J., Wren, B. W., Mungall, K. & 18 other authors ( 2000; ). The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403, 665–668.[CrossRef]
    [Google Scholar]
  35. Parsonnet, J. ( 1995; ). The incidence of Helicobacter pylori infection. Aliment Pharmacol Ther 9, 45–51.
    [Google Scholar]
  36. Parsonnet, J., Hansen, S., Rodriguez, L., Gelb, A. B., Warnke, R. A., Jellum, E., Orentreich, N., Vogelman, J. H. & Friedman, G. D. ( 1994; ). Helicobacter pylori infection and gastric lymphoma. N Engl J Med 330, 1267–1271.[CrossRef]
    [Google Scholar]
  37. Peck, B., Ortkamp, M., Diehl, K. D., Hundt, E. & Knapp, B. ( 1999; ). Conservation, localization and expression of HopZ, a protein involved in adhesion of Helicobacter pylori. Nucleic Acids Res 27, 3325–3333.[CrossRef]
    [Google Scholar]
  38. Rocha, E. P., Pradillon, O., Bui, H., Sayada, C. & Denamur, E. ( 2002; ). A new family of highly variable proteins in the Chlamydophila pneumoniae genome. Nucleic Acids Res 30, 4351–4360.[CrossRef]
    [Google Scholar]
  39. Salaün, L., Audibert, C., Le Lay, G., Burucoa, C., Fauchere, J. L. & Picard, B. ( 1998; ). Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers. FEMS Microbiol Lett 161, 231–239.[CrossRef]
    [Google Scholar]
  40. Salaün, L., Snyder, L. A. & Saunders, N. J. ( 2003; ). Adaptation by phase variation in pathogenic bacteria. Adv Appl Microbiol 52, 263–301.
    [Google Scholar]
  41. Saunders, N. J. ( 1999; ). Bacterial phase variation associated with repetitive DNA. PhD thesis, The Open University.
  42. Saunders, N. J. ( 2003; ). Evasion of antibody responses: bacterial phase variation. In Bacterial Evasion of Host Immune Responses, pp. 103–124. Edited by B. Henderson & P. C. F. Oyston. Cambridge: Cambridge University Press.
  43. Saunders, N. J., Peden, J. F., Hood, D. W. & Moxon, E. R. ( 1998; ). Simple sequence repeats in the Helicobacter pylori genome. Mol Microbiol 27, 1091–1098.[CrossRef]
    [Google Scholar]
  44. Saunders, N. J., Jeffries, A. C., Peden, J. F., Hood, D. W., Tettelin, H., Rappuoli, R. & Moxon, E. R. ( 2000; ). Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58. Mol Microbiol 37, 207–215.[CrossRef]
    [Google Scholar]
  45. Snyder, L. A., Butcher, S. A. & Saunders, N. J. ( 2001; ). Comparative whole-genome analyses reveal over 100 putative phase-variable genes in the pathogenic Neisseria spp. Microbiology 147, 2321–2332.
    [Google Scholar]
  46. Suerbaum, S., Smith, J. M., Bapumia, K., Morelli, G., Smith, N. H., Kunstmann, E., Dyrek, I. & Achtman, M. ( 1998; ). Free recombination within Helicobacter pylori. Proc Natl Acad Sci U S A 95, 12619–12624.[CrossRef]
    [Google Scholar]
  47. Tannaes, T., Dekker, N., Bukholm, G., Bijlsma, J. J. & Appelmelk, B. J. ( 2001; ). Phase variation in the Helicobacter pylori phospholipase A gene and its role in acid adaptation. Infect Immun 69, 7334–7340.[CrossRef]
    [Google Scholar]
  48. Tettelin, H., Saunders, N. J., Heidelberg, J. & 39 other authors ( 2000; ). Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287, 1809–1815.[CrossRef]
    [Google Scholar]
  49. Tomb, J. F., White, O., Kerlavage, A. R. & 39 other authors ( 1997; ). The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388, 539–547.[CrossRef]
    [Google Scholar]
  50. van Ham, S. M., van Alphen, L., Mooi, F. R. & van Putten, J. P. ( 1993; ). Phase variation of Haemophilus influenzae fimbriae: transcriptional control of two divergent genes through a variable combined promoter region. Cell 73, 1187–1196.[CrossRef]
    [Google Scholar]
  51. Wang, G., Rasko, D. A., Sherburne, R. & Taylor, D. E. ( 1999; ). Molecular genetic basis for the variable expression of Lewis Y antigen in Helicobacter pylori: analysis of the alpha (1,2) fucosyltransferase gene. Mol Microbiol 31, 1265–1274.[CrossRef]
    [Google Scholar]
  52. Wassenaar, T. M., Wagenaar, J. A., Rigter, A., Fearnley, C., Newell, D. G. & Duim, B. ( 2002; ). Homonucleotide stretches in chromosomal DNA of Campylobacter jejuni display high frequency polymorphism as detected by direct PCR analysis. FEMS Microbiol Lett 212, 77–85.[CrossRef]
    [Google Scholar]
  53. Yamaoka, Y., Kwon, D. H. & Graham, D. Y. ( 2000; ). A M(r) 34,000 proinflammatory outer membrane protein (oipA) of Helicobacter pylori. Proc Natl Acad Sci U S A 97, 7533–7538.[CrossRef]
    [Google Scholar]
  54. Yamaoka, Y., Kikuchi, S., el-Zimaity, H. M., Gutierrez, O., Osato, M. S. & Graham, D. Y. ( 2002a; ). Importance of Helicobacter pylori oipA in clinical presentation, gastric inflammation, and mucosal interleukin 8 production. Gastroenterology 123, 414–424.[CrossRef]
    [Google Scholar]
  55. Yamaoka, Y., Kita, M., Kodama, T., Imamura, S., Ohno, T., Sawai, N., Ishimaru, A., Imanishi, J. & Graham, D. Y. ( 2002b; ). Helicobacter pylori infection in mice: role of outer membrane proteins in colonization and inflammation. Gastroenterology 123, 1992–2004.[CrossRef]
    [Google Scholar]
  56. Yogev, D., Rosengarten, R., Watson-McKown, R. & Wise, K. S. ( 1991; ). Molecular basis of Mycoplasma surface antigenic variation: a novel set of divergent genes undergo spontaneous mutation of periodic coding regions and 5′ regulatory sequences. EMBO J 10, 4069–4079.
    [Google Scholar]
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vol. 150, part 4, pp. 817-830

A table of primers used for amplification and sequencing of the repeat-containing regions is available as an Acrobat PDF file.



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