Rate heterogeneity in the evolution of Helicobacter pylori and the behavior of homoplastic sites

Infection, Genetics and Evolution

Volumn 8, Issue 5, 2008, Pages 593-602

  Meinersmann, Richard J ^a   Romero Gallo, Judith ^b   Blaser, Martin J ^c  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b VANDERBILT UNIVERSITY   (United States)

^c NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Helicobacter pylori; Homoplasy; Recombination; Transitions; Transversions

Indexed keywords

AMINO ACID DERIVATIVE; NUCLEOTIDE; OXIDOREDUCTASE; RIBONUCLEASE;

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIUM ISOLATION; CODON; COMPUTER SIMULATION; CONTROLLED STUDY; GENEALOGY; GENETIC DATABASE; GENETIC HETEROGENEITY; GENETIC RECOMBINATION; GENETIC VARIABILITY; HELICOBACTER PYLORI; HOMOPLASY; HOUSEKEEPING GENE; MOLECULAR EVOLUTION; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

COMPUTER SIMULATION; EVOLUTION, MOLECULAR; HELICOBACTER PYLORI; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECOMBINATION, GENETIC; RIBONUCLEOTIDE REDUCTASES;

HELICOBACTER PYLORI;

EID: 50249129211     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2008.04.003     Document Type: Article

References (54)

1. Ando T., Xu Q., Torres M., Kusugami K., Israel D.A., and Blaser M.J. Restriction-modification system differences in Helicobacter pylori are a barrier to interstrain plasmid transfer. Mol. Microbiol. 37 (2000) 1052-1065
2. Bjorkholm B., Sjolund M., Falk P.G., Berg O.G., Engstrand L., and Andersson D.I. Mutation frequency and biological cost of antibiotic resistance in Helicobacter pylori. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 14607-14612
3. Cheng Z.F., Zuo Y., Li Z., Rudd K.E., and Deutscher M.P. The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J. Biol. Chem. 273 (1998) 14077-14080
4. Doig P., de Jonge B.L., Alm R.A., Brown E.D., Uria-Nickelsen M., Noonan B., Mills S.D., Tummino P., Carmel G., Guild B.C., Moir D.T., Vovis G.F., and Trust T.J. Helicobacter pylori physiology predicted from genomic comparison of two strains. Microbiol. Mol. Biol. Rev. 63 (1999) 675-707
5. Donahue J.P., Israel D.A., Peek R.M., Blaser M.J., and Miller G.G. Overcoming the restriction barrier to plasmid transformation of Helicobacter pylori. Mol. Microbiol. 37 (2000) 1066-1074
6. Dunn B.E., Cohen H., and Blaser M.J. Helicobacter pylori. Clin. Micro Rev. 10 (1997) 720-741
7. Falush D., Kraft C., Taylor N.S., Correa P., Fox J.G., Achtman M., and Suerbaum S. 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 (2001) 15056-15061
8. Go M.F., Kapur V., Graham D.Y., and Musser J.M. Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure. J. Bacteriol. 178 (1996) 3934-3938
9. Han S.-R., Zschausch H.-C.E., Meyer H.-G.W., Schneider T., Loos M., Bhakdi S., and Maeurer M.J. Helicobacter pylori: clonal population structure and restricted transmission within families revealed by molecular typing. J. Clin. Microbiol. 38 (2000) 3646-3651
10. Hasegawa M., Kishino H., and Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21 (1985) 160-174
11. Haas R., Meyer T.F., and van Putten J.P. Aflagellated mutants of Helicobacter pylori generated by genetic transformation of naturally competent strains using transposon shuttle mutagenesis. Mol. Microbiol. 8 (1993) 753-760
12. Hey J., and Wakeley J. A coalescent estimator of the population recombination rate. Genetics 145 (1997) 833-846
13. Hillis D.M., Huelsenbeck J.P., and Cunningham C.W. Application and accuracy of molecular phylogenies. Science 264 (1994) 671-677
14. Hirschl A.M., Richter M., Makristathis A., Pruckl P.M., Willinger B., Schutze K., and Rotter M.L. Single and multiple strain colonization in patients with Helicobacter pylori-associated gastritis: detection by macrorestriction DNA analysis. J. Infect. Dis. 170 (1994) 473-475
15. Hofreuter D., Odenbreit S., Puls J., Schwan D., and Haas R. Genetic competence in Helicobacter pylori: mechanisms and biological implications. Res. Microbiol. 151 (2000) 487-491
16. Israel D.A., Lou A.S., and Blaser M.J. Characteristics of Helicobacter pylori natural transformation. FEMS Microbiol. Lett. 186 (2000) 275-280
17. Israel D.A., Salama N., Krishna U., Rieger U.M., Atherton J.C., Falkow S., and Peek R.M. Helicobacter pylori diversity within the gastric niche of a single human host. Proc. Natl. Acad. Sci. 98 (2001) 14625-14630
18. Jakobsen I.B., and Easteal S. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comput. Appl. Biosci. 12 (1996) 291-295
19. Jolley, K.A., Chan, M.S., Maiden, M.C.J., 2004. mlstdbNet-distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics 5:86 (available from: http://www.biomedcentral.com/1471-2105/5/86).
20. Jorgensen M., Daskalopoulos G., Warburton V., Mitchell H.M., and Hazell S.L. Multiple strain colonization and metronidazole resistance in Helicobacter pylori-infected patients: identification from sequential and multiple biopsy specimens. J. Infect. Dis. 174 (1996) 631-635
21. Kimura M. Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles. Genet. Res. 11 (1968) 247-269
22. Kuhner M.K., Yamato J., and Felsenstein J. Maximum likelihood estimation of recombination rates from population data. Genetics 156 (2000) 1393-1401
23. Kuipers E.J., Israel D.A., Kusters J.G., Gerrits M.M., Weel J., van Der Ende A., van Der Hulst R.W., Wirth H.P., Hook-Nikanne J., Thompson S.A., and Blaser M.J. Quasispecies development of Helicobacter pylori observed in paired isolates obtained years apart from the same host. J. Infect. Dis. 181 (2000) 273-282
24. Li W.-H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36 (1993) 96-99
25. Li W.-H. Molecular Evolution (1997), Sinauer Associates, Sunderland, MA pp. 309-334
26. Maddison W.P., and Maddison D.R. MacClade: Analysis of Phylogeny and Character Evolution. Version 3 (1992), Sinauer Associates, Sunderland, MA
27. Martin D., and Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics 16 (2000) 562-563
28. Maynard-Smith J., and Smith N.H. Detecting recombination from gene trees. Mol. Biol. Evol. 15 (1998) 590-599
29. Montecucco C., and Rappuoli R. Living dangerously: how Helicobacter pylori survives in the human stomach. Nat. Rev. Mol. Cell. Biol. 2 (2001) 457-466
30. Morales-Espinosa R., Castillo-Rojas G., Gonzalez-Valencia G., Ponce de Leon S., Cravioto A., Atherton J.C., and Lopez-Vidal Y. Colonization of Mexican patients by multiple Helicobacter pylori strains with different vacA and cagA genotypes. J. Clin. Microbiol. 37 (1999) 3001-3004
31. Nei M. Selectionism and neutralism in molecular evolution. Mol. Biol. Evol. 22 (2005) 2318-2342
32. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substation. Bioinformatics 14 (1998) 817-818
33. Rambaut A., and Grassly M.C. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13 (1997) 235-238
34. Raymond J., Thiberg J.M., Chevalier C., Kalach N., Bergeret M., Labigne A., and Dauga C. Genetic and transmission analysis of Helicobacter pylori strains within a family. Emerg. Infect. Dis. 10 (2004) 1816-1821
35. Rothenbacher D., Bode G., Berg G., Knayer U., Gonser T., Adler G., and Brenner H. Helicobacter pylori among preschool children and their parents: evidence of parent-child transmission. J. Infect. Dis. 179 (1999) 398-402
36. Salama N., Guillemin K., McDaniel T.K., Sherlock G., Tompkins L., and Falkow S. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc. Natl. Acad. Sci. 97 (2000) 14668-14673
37. Salaun L., Audibert C., Le Lay G., Burucoa C., Fauchere J.-L., and Picard B. Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers. FEMS Microbiol. Lett. 161 (1998) 231-239
38. Salminen M.O., Carr J.K., Burke D.S., and McCutchan F.E. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by Bootscanning. AIDS Res. Hum. Retroviruses 11 (1995) 1423-1425
39. Sawyer, S.A., 1999. GENECONV: a computer package for the statistical detection of gene conversion. Distributed by the author, Department of Mathematics, Washington University in St. Louis, available at http://www.math.wustl.edu/∼sawyer.
40. Suerbaum S., Smith J.M., Bapumia K., Morelli G., Smith N.H., Kunstmann E., Dyrek I., and Achtman M. Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 12619-12624
41. Swofford D.L. Paup* 4.0b4. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4 (1998), Sinauer Associates, Sunderland, MA
42. Swofford D.L., Olsen G.J., Waddell P.J., and Hillis D.M. Phylogenetic Inference. In: Hillis D.M., Moritz C., and Mable B.K. (Eds). Molecular Systematics: Second Edition (1996), Sinauer Associates, Inc., Sunderland, MA 407-514
43. Tamura K., and Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10 (1993) 512-526
44. Taylor D.N., and Parsonnet J. Epidemiology and natural history of H. pylori infections. In: Blaser M.J., Smith P.F., Ravdin J., Greenberg H., and Guerrant R.L. (Eds). Infections of the Gastrointestinal Tract (1995), Raven Press, New York, NY 551-564
45. Taylor N.S., Fox J.G., Akopyants N.S., Berg D.E., Thompson N., Shames B., Yan L., Fontham E., Janney F., Hunter F.M., and Correa P. Long-term colonization with single and multiple strains of Helicobacter pylori assessed by DNA fingerprinting. J. Clin. Microbiol. 33 (1995) 918-923
46. Thompson J.D., Higgins D.G., and Gibson T.J. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
47. Tobe T., Sasakawa C., Okada N., Honma Y., and Yoshikawa M. vacB, a novel chromosomal gene required for expression of virulence genes on the large plasmid of Shigella flexneri. J. Bacteriol. 174 (1992) 6359-6367
48. Tsuda M., Karita M., and Nakazawa T. Genetic transformation in Helicobacter pylori. Microbiol. Immunol. 37 (1993) 85-89
49. Wang Y., Roos K.P., and Taylor D.E. Transformation of Helicobacter pylori by chromosomal metronidazole resistance and by a plasmid with a selectable chloramphenicol resistance marker. J. Gen. Microbiol. 139 (1993) 2485-2493
50. Worobey M. A novel approach to detecting and measuring recombination: new insights into evolution in viruses, bacteria, and mitochondria. Mol. Biol. Evol. 18 (2001) 1425-1434
51. Xia, X., 2000a. DAMBE: data analysis in molecular biology and evolution. Department of Ecology and Biodiversity, University of Hong Kong. http://web.hku.hk/∼xxia/software/software.htm.
52. Xia X. Data Analysis in Molecular Biology and Evolution (2000), Kluwer Academic Publishers, Boston, MA
53. Xu Q., Morgan R.D., Roberts R.J., and Blaser M.J. Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 9671-9676
54. Yang Z., Kumar S., and Nei M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141 (1995) 1641-1650