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Nucleotide Correspondence between Protein-Coding Sequences of Helicobacter pylori Strains 26695 and J99

  • Genomics. Transcriptomics. Proteomics
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Abstract

Comparison of ORFs between H. pylori strains 26695 and J99 showed that transitions (more than 3%) prevail over transversions (less than 1%). The predominance of transitions was explained by the high rates of cytosine replacement by thymine in the coding (3.5–5.3%) and noncoding (2.9–3.9%) DNA strands. The proportion of transversion-type correspondences (A → C, A → T, C → A, C → G, G → C, G → T, T → A, and T → G) did not exceed 0.84%. The highest proportion (28.3%) was observed for correspondences between C and T in ACGT-ATGT, the target site of active methyltransferase of H. pylori J99 (M.Hpy99XI). It was assumed that C → T mutations due to cytosine methylation-deamination are prevalent in H. pylori.

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REFERENCES

  1. Marais A., Mendz G.L., Hazell S.L., Megraud F. 1999. Metabolism and genetics of Helicobacter pylori: The genome era. Microb. Mol. Biol. Rev. 63, 642–674.

    CAS  Google Scholar 

  2. Alm R.A., Ling L.S., Moir D.T., King B.L. et al. 1999. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature. 397, 176–180.

    PubMed  Google Scholar 

  3. Tomb J.F., White O., Kerlavage A.R., Clayton R.A., et al. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 388, 539–547.

    Article  PubMed  CAS  Google Scholar 

  4. Alm R.A., Trust T.J. 1999. Analysis of the genetic diversity of Helicobacter pylori: The tale of two genomes. J. Mol. Med. 77, 834–846.

    Article  PubMed  CAS  Google Scholar 

  5. Boucher Y., Nesbo C.L., Doolittle W.F. 2001. Microbial genomes: Dealing with diversity. Curr. Opin. Microbiol. 4, 285–289.

    Article  PubMed  CAS  Google Scholar 

  6. Kuipers E., Israel D.A., Kusters J.G., Gerrits M.M., et al. 2000. Quasispecies development of Helicobacter pylori observed in paired isolates obtained years apart from the same host. J. Infect. Dis. 181, 273–282.

    Article  PubMed  CAS  Google Scholar 

  7. Israel D.A. Salama N., Krishna U., Rieger U.M., et al. 2001. Helicobacter pylori genetic diversity within the gastric niche of a single human host. Proc. Natl. Acad. Sci. USA. 98, 14625–14630.

    Article  PubMed  CAS  Google Scholar 

  8. Momynaliev K.T., Smirnova O.V., Kudryavtseva L.V., Govorun V.M. 2003. Comparative genome analysis of Helicobacter pylori strains. Mol. Biol. 37, 625–633.

    Article  CAS  Google Scholar 

  9. Salama N., Guillemin K., McDaniel T.K., Sherlock G., Tompkins L., Falkow S. 2000. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc. Natl. Acad. Sci. USA. 97, 14668–14673.

    Article  PubMed  CAS  Google Scholar 

  10. Kansau I., Raymond J., Bingen E., Courcoux P., et al. 1996. Genotyping of Helicobacter pylori isolates by sequencing of PCR products and comparison with the RAPD technique. Res. Microbiol. 147, 661–669.

    Article  PubMed  CAS  Google Scholar 

  11. Hook-Nikanne J., Berg D.E., Peek R.M. Jr., Kersulyte D., Tummuru M.K., Blaser M.J. 1998. DNA sequence conservation and diversity in transposable element IS605 of Helicobacter pylori. Helicobacter. 3, 79–85.

    PubMed  CAS  Google Scholar 

  12. Suerbaum S, Smith J.M., Bapumia K., Morelli G., Smith N.H., et al. 1998. Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. USA. 95, 12619–12624.

    Article  PubMed  CAS  Google Scholar 

  13. Garner J.A., Cover T.L. 1995. Analysis of genetic diversity in cytotoxin-producing and non-cytotoxin-producing Helicobacter pylori strains. J. Infect. Dis. 172, 290–293.

    PubMed  CAS  Google Scholar 

  14. Evans Jr. D.J, Queiroz D.M., Mendes E.N., Evans D.G. 1998. Diversity in the variable region of Helicobacter pylori cagA gene involves more than simple repetition of a 102-nucleotide sequence. Biochem. Biophys. Res. Commun. 245, 780–784.

    PubMed  CAS  Google Scholar 

  15. Aras R.A., Kang J., Tschumi A.I., Harasaki Y., Blaser M.J. 2003. Extensive repetitive DNA facilitates prokaryotic genome plasticity. Proc. Natl. Acad. Sci. USA. 100, 13579–13584.

    Article  PubMed  CAS  Google Scholar 

  16. Wang G., Humayun M.Z., Taylor D.E. 1999. Mutation as an origin of genetic variability in Helicobacter pylori. Trends Microbiol. 7, 488–493.

    Article  PubMed  CAS  Google Scholar 

  17. Frederico L.A., Kunkel T.A., Shaw B.R. 1990. A sensitive genetic assay for the detection of cytosine deamination: Determination of rate constants and the activation energy. Biochemistry. 29, 2532–2537.

    Article  PubMed  CAS  Google Scholar 

  18. Shen J.-C., Rideout WM., Jones P.A. 1994. The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res. 22, 972–976.

    PubMed  CAS  Google Scholar 

  19. Coulondre C., Miller J.H., Farabaugh P.J., Gilbert W. 1978. Molecular basis of base substitution hotspots in Escherichia coli. Nature. 274, 775–780.

    Article  PubMed  CAS  Google Scholar 

  20. De Jong P.J., Grosvosky A.J. & Glickman B.W. 1988. Spectrum of spontaneous mutation at the APRT locus of Chinese hamster ovary cells: An analysis at the DNA sequence level. Proc. Natl. Acad. Sci. USA. 85, 3499–3503.

    PubMed  Google Scholar 

  21. Halliday J.A., Glickman B.W. 1991. Mechanisms of spontaneous mutation in DNA repair-proficient Escherichia coli. Mutat. Res. 250, 55–71.

    PubMed  CAS  Google Scholar 

  22. Douglas G.R., Gingerich J.D., Gossen J.A., Bartlett S.A. 1994. Sequence spectra of spontaneous lacZ gene mutations in transgenic mouse somatic and germline tissues. Mutagenesis. 9, 451–458.

    PubMed  CAS  Google Scholar 

  23. Lindahl T., Nyberg B. 1974. Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry. 13, 3405–3410.

    Article  PubMed  CAS  Google Scholar 

  24. Gromova E.S., Khoroshaev A.V. 2003. Prokaryotic DNA methyltransferases: Structure and mechanism of interaction with DNA. Mol. Biol. 37, 300–314.

    Article  CAS  Google Scholar 

  25. Bell D.C., Cupples C.G. 2001. Very-short-patch repair in Escherichia coli requires the dam adenine methylase. J. Bacteriol. 183, 3631–3635.

    Article  PubMed  CAS  Google Scholar 

  26. Bhagwat A.S., Lieb M. 2002. Cooperation and competition in mismatch repair: Very short-patch repair and methyl-directed mismatch repair in Escherichia coli. Mol. Microbiol. 44, 1421–1428.

    Article  PubMed  CAS  Google Scholar 

  27. Suerbaum S., Smith J.M., Bapumia K., et al. 1998. Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. USA. 95, 12619–12624.

    Article  PubMed  CAS  Google Scholar 

  28. Suerbaum S., Achtman M. 1999. Evolution of Helicobacter pylori: The role of recombination. Trends Microbiol. 7, 182–184.

    Article  PubMed  CAS  Google Scholar 

  29. Suerbaum S. 2000. Genetic variability within Helicobacter pylori. Int. J. Med. Microbiol. 290, 175–181.

    PubMed  CAS  Google Scholar 

  30. Achtman M., Suerbaum S. 2000. Sequence variation in Helicobacter pylori. Trends Microbiol. 8, 57–58.

    Article  PubMed  CAS  Google Scholar 

  31. Suerbaum S., Achtman M. 2004. Helicobacter pylori: Recombination, population structure and human migrations. Int. J. Med. Microbiol. 294, 133–139.

    Article  PubMed  CAS  Google Scholar 

  32. Francino M.P., Ochman H. 1997. Strand asymmetries in DNA evolution. Trends Genet. 13, 240–245.

    Article  PubMed  CAS  Google Scholar 

  33. Cebrat S., Dudek M.R., Mackiewicz P., et al. 1997. Asymmetry of coding versus noncoding strand in coding sequences of different genomes. Microb. Comp. Genomics. 2, 259–268.

    PubMed  CAS  Google Scholar 

  34. Rogerson A.C. 1989. The sequence asymmetry of the Escherichia coli chromosome appears to be independent of strand or function and may be evolutionarily conserved. Nucleic Acids Res. 17, 5547–5563.

    PubMed  CAS  Google Scholar 

  35. Kowalczuk M., Mackiewicz P., Mackiewicz D., et al. 2001. DNA asymmetry and the replicational mutational pressure. J. Appl. Genet. 42, 553–577.

    PubMed  CAS  Google Scholar 

  36. Nikolaou C., Almirantis Y. 2003. Mutually symmetric and complementary triplets: Differences in their use distinguish systematically between coding and non-coding genomic sequences. J. Theor. Biol. 223, 477–487.

    Article  PubMed  CAS  Google Scholar 

  37. Karlin S., Doerfler W., Cardon L.R. 1994. Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses? J. Virol. 68, 2889–2897.

    PubMed  CAS  Google Scholar 

  38. Karlin S., Mrazek J., Campbell A.M. 1997. Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol. 179, 3899–3913.

    PubMed  CAS  Google Scholar 

  39. Breslauer K.J., Frank E., Blocker H., Marky L.A. 1986. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA. 83, 3746–3750.

    PubMed  CAS  Google Scholar 

  40. Delcourt S.G., Blake R.D. 1991. Stacking energies in DNA. J. Biol. Chem. 266, 15160–15169.

    PubMed  CAS  Google Scholar 

  41. Karlin S. Global dinucleotide signatures and analysis of genomic heterogeneity. 1998. Curr Opin. Microbiol. 1, 598–610.

    Article  PubMed  CAS  Google Scholar 

  42. Xia X. DNA methylation and Mycoplasma genomes. 2003. J. Mol. Evol. 57, 21–28.

    Article  Google Scholar 

  43. Lin L.F., Posfai J., Roberts R.J., Kong H. 2001. Comparative genomics of the restriction-modification systems in Helicobacter pylori. Proc. Natl. Acad. Sci. USA. 98, 2740–2745.

    PubMed  CAS  Google Scholar 

  44. Kusano K., Naito T., Handa N., Kobayashi I. 1995. Restriction-modification systems as genomic parasites in competition for specific sequences. Proc. Natl. Acad. Sci. USA. 92, 11095–11099.

    PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Institute of Physico-Chemical Medicine, Ministry of Health and Social Development of the Russian Federation, Moscow, 119992, Russia

    K. T. Momynaliev, S. I. Rogov & V. M. Govorun

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  1. K. T. Momynaliev
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  2. S. I. Rogov
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  3. V. M. Govorun
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__________

Translated from Molekulyarnaya Biologiya, Vol. 39, No. 6, 2005, pp. 945–951.

Original Russian Text Copyright © 2005 by Momynaliev, Rogov, Govorun.

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Momynaliev, K.T., Rogov, S.I. & Govorun, V.M. Nucleotide Correspondence between Protein-Coding Sequences of Helicobacter pylori Strains 26695 and J99. Mol Biol 39, 826–832 (2005). https://doi.org/10.1007/s11008-005-0101-1

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