Cluster of type IV secretion genes in Helicobacter pylori's plasticity zone

Journal of Bacteriology

Volumn 185, Issue 13, 2003, Pages 3764-3772

  Kersulyte, Dangeruta ^a   Velapatiño, Billie ^a,b   Mukhopadhyay, Asish K ^a,c   Cahuayme, Lizbeth ^b   Bussalleu, Alejandro ^b   Combe, Juan ^b   Gilman, Robert H ^b   Berg, Douglas E ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSIDAD PERUANA CAYETANO HEREDIA   (Peru)

^c NATIONAL INSTITUTE OF CHOLERA AND ENTERIC DISEASES   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; CELL SECRETION; CHROMOSOME WALKING; CONTROLLED STUDY; DNA SEQUENCE; DNA TRANSPOSITION; EVOLUTION; GENE CLUSTER; GENE DELETION; GENE INSERTION; GENETIC CONSERVATION; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; HELICOBACTER PYLORI; HUMAN; HUMAN TISSUE; HYBRIDIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHENOTYPE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; STOMACH DISEASE; TFS3 GENE; VIRB10 GENE; VIRB11 GENE; VIRB4 GENE; VIRB7 GENE; VIRB8 GENE; VIRB9 GENE; VIRD4 GENE;

BACTERIAL PROTEINS; BASE SEQUENCE; CHROMOSOME WALKING; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; GENES, BACTERIAL; HELICOBACTER PYLORI; HUMANS; INDIA; JAPAN; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NUCLEIC ACID HYBRIDIZATION; OPEN READING FRAMES; PERU; SEQUENCE ANALYSIS, DNA; SPAIN;

BACTERIA (MICROORGANISMS); HELICOBACTER; HELICOBACTER PYLORI; INSERTION SEQUENCES;

EID: 0038039237     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.13.3764-3772.2003     Document Type: Article

References (54)

1. Akopyants, N. S., S. W. Clifton, D. Kersulyte, J. E. Crabtree, B. E. Youree, C. A. Reece, N. O. Bukanov, E. S. Drazek, B. A. Roe, and D. E. Berg. 1998. Analyses of the cag pathogenicity island of Helicobacter pylori. Mol. Microbiol. 28:37-53.
2. Akopyants, N. S., A. Fradkov, L. Diatchenko, P. D. Siebert, S. Lukyanov, E. D. Sverdlov, and D. E. Berg. 1998. PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori. Proc. Natl. Acad. Sci. USA 95:13108-13113.
3. Alm, R. A., L. S. Ling, D. T. Moir, B. L. King, E. D. Brown, P. C. Doig, D. R. Smith, B. Noonan, B. C. Guild, B. L. deJonge, G. Carmel, P. J. Tummino, A. Caruso, M. Uria-Nickelsen, D. M. Mills, C. Ives, R. Gibson, D. Merberg, S. D. Mills, Q. Jiang, D. E. Taylor, G. F. Vovis, and T. J. Trust. 1999. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176-180.
4. Amieva, M. R., N. R. Salama, L. S. Tompkins, and S. Falkow. 2002. Helicobacter pylori enter and survive within multivesicular vacuoles of epithelial cells. Cell Microbiol. 4:677-690.
5. Amundsen, S. K., and G. R. Smith. 2003. Interchangeable parts of the Escherichia coli recombination machinery. Cell 112:741-744.
6. Anonymous. 1995. The Gold Bug: Helicobacter pylori. Science 267:173.
7. Arnold, D. A., N. Handa, I. Kobayashi, and S. C. Kowalczykowski. 2000. A novel, 11 nucleotide variant of chi, chi*: one of a class of sequences defining the Escherichia coli recombination hotspot chi. J. Mol. Biol. 300:469-479.
8. Ashizawa, Y., T. Yokochi, Y. Ogata, Y. Shubuike, J. Kato, and H. Ikeda. 1999. Mechanism of DNA gyrase-mediated illegitimate recombination: characterization of Escherichia coli gyrA mutations that confer hyper-recombination phenotype. J. Mol. Biol. 289:447-458.
9. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A., Smith, and K. A. Struhl. 1994. Current protocols in molecular biology; supplement 27 CPMB, p. 2.4.1. Greene Publishing and Wiley Interscience, New York, N.Y.
10. Bacon, D. J., R. A. Alm, L. Hu, T. E. Hickey, C. P. Ewing, R. A. Batchelor, T. J. Trust, and P. Guerry. 2002. DNA sequence and mutational analyses of the pVir plasmid of Campylobacter jejuni 81-176. Infect. Immun. 70:6242-6250.
11. Berg, D. E., R. H. Gilman, J. Lelwala-Guruge, K. Srivaalava, Y. Valdez, J. Watanabe, J. Miyagi, N. S. Akopyants, A. Ramirez-Ramos, T. H. Yoshiwara, S. Recavarren, and R. Leon-Barua. 1997. Helicobacter pylori populations in individual Peruvian patients. Clin. Infect. Dis. 25:996-1002.
12. Blackwell, L. J., K. P. Bjornson, D. J. Allen, and P. Modrich. 2001. Distinct MutS DNA-binding modes that are differentially modulated by ATP binding and hydrolysis. J. Biol. Chem. 276:34339-34347.
13. Bourniquel, A. A., and T. A. Bickle. 2002. Complex restriction enzymes: NTP-driven molecular motors. Biochimie 84:1047-1059.
14. Cao, T. B., and M. H. Saier, Jr. 2001. Conjugal type IV macromolecular transfer systems of gram-negative bacteria: organismal distribution, structural constraints and evolutionary conclusions. Microbiology 147:3201-3214.
15. Chalkauskas, H., D. Kersulyte, I. Cepuliene, V. Urbonas, D. Ruzeviciene, A. Barakauskiene, A. Raudonikiene, and D. E. Berg. 1998. Genotypes of Helicobacter pylori in Lithuanian families. Helicobacter 3:296-302.
16. Chalker, A. F., H. W. Minehart, N. J. Hughes, K. K. Koretke, M. A. Lonetto, K. K. Brinkman, P. V. Warren, A. Lupas, M. J. Stanhope, J. R. Brown, and P. S. Hoffman. 2001. Systematic identification of selective essential genes in Helicobacter pylori by genome prioritization and allelic replacement mutagenesis. J. Bacteriol. 183:1259-1268.
17. Chedin, F., and S. C. Kowalczykowski. 2002. A novel family of regulated helicases/nucleases from gram-positive bacteria: insights into the initiation of DNA recombination. Mol. Microbiol. 43:823-834.
18. Christie, P. J. 2001. Type IV secretion: intercellular transfer of macromolecules by systems ancestrally related to conjugation machines. Mol. Microbiol. 40:294-305.
19. Cover, T. L., D. E. Berg, M. J. Blaser, and H. L. T. Mobley. 2001. H. pylori pathogenesis, p. 509-558. In E. A. Groisman (ed.), Principles of bacterial pathogenesis. Academic Press, New York, N.Y.
20. Dailidiene, D., M. T. Bertoli, J. Miciuleviciene, A. K. Mukhopadhyay, G. Dailide, M. A. Pascasio, L. Kupcinskas, and D. E. Berg. 2002. Emergence of tetracycline resistance in Helicobacter pylori: multiple mutational changes in 16S ribosomal DNA and other genetic loci. Antimicrob. Agents Chemother. 46:3940-3946.
21. Doolittle, W. F., and C. Sapienza. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601-603.
22. Dover, G., and W. F. Doolittle. 1980. Modes of genome evolution. Nature 88:646-647.
23. Dubreuil, J. D., G. Dei Giudice, and R. Rappuoli. 2002. Helicobacter pylori interactions with host serum and extracellular matrix proteins: potential role in the infectious process. Microbiol. Mol. Biol. Rev. 66:617-629.
24. Ehrlich, S. D., H. Bierne, E. d'Alencon, D. Vilette, M. Petranovic, P. Noirot, and M. Michel. 1993. Mechanisms of illegitimate recombination. Gene 135:161-166.
25. Ernst, P. B., and B. D. Gold. 2000. The disease spectrum of Helicobacter pylori: the immunopathogenesis of gastroduodenal ulcer and gastric cancer. Annu. Rev. Microbiol. 54:615-640.
26. Falush, D., C. Kraft, N. S. Taylor, P. Correa, J. G. Fox, M. Achlman, and S. Suerbaum. 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. USA 98:15056-15061.
27. Fischer, W., R. Haas, and S. Odenbreit. 2002. Type IV secretion systems in pathogenic bacteria. Int. J. Med. Microbiol. 292:159-168.
28. Fischer, W., J. Puls, R. Buhrdorf, B. Gebert, S. Odenbreit, and R. Haas. 2001. Systematic mutagenesis of the Helicobacter pylori cag pathogenicity island: essential genes for CagA translocation in host cells and induction of interleukin-8. Mol. Microbiol. 42:1337-1348.
29. Garcia, L. R., and I. J. Molineux. 1999. Translocation and specific cleavage of bacteriophage T7 DNA in vivo by EcoK1. Proc. Natl. Acad. Sci. USA 96:12430-12435.
30. Hofreuter, D., S. Odenbreit, and R. Haas. 2001. Natural transformation competence in Helicobacter pylori is mediated by the basic components of a type IV secretion system. Mol. Microbiol. 41:379-391.
31. Israel, D. A., N. Salama, U. Krishna, U. M. Rieger, J. C. Atherton, S. Falkow, and R. M. Peek, Jr. 2001. Helicobacter pylori genetic diversity within the gastric niche of a single human host. Proc. Natl. Acad. Sci. USA 98:14625-14630.
32. Jilk, R. A., J. C. Makris, L. Borchardt, and W. S. Reznikoff. 1993. Implications of Tn5-associated adjacent deletions. J. Bacteriol. 175:1264-1271.
33. Juhala, R. J., M. E. Ford, R. L. Dude, A. Youlton, G. F. Hatfull, and R. W. Hendrix. 2000. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J. Mol. Biol. 299:27-51.
34. Kersulyte, D., H. Chalkauskas., and D. E. Berg. 1999. Emergence of recombinant strains of Helicobacter pylori during human infection. Mol. Microbiol. 31:31-43.
35. Kersulyte, D., B. Velapatiño, G. Dailide, A. K. Mukhopadhyay, Y. Ito, L. Cahuayme, A. J. Parkinson, R. H. Gilman, and D. E. Berg. 2002. Transposable element ISHp608 of Helicobacter pylori: nonrandom geographic distribution, functional organization, and insertion specificity. J. Bacteriol. 184:192-1002
36. Kulpers, E. J., D. A. Israel, J. G. Kusters, and M. J. Blaser. 1998. Evidence for a conjugation-like mechanism of DNA transfer in Helicobacter pylori. J. Bacteriol. 180:2901-2905.
37. Kwok, T., S. Backert, H. Schwarz, J. Berger, and T. F. Meyer. 2002. Specific entry of Helicobacter pylori into cultured gastric epithelial cells via a zipper-like mechanism. Infect. Immun. 70:2108-2120.
38. Lee, V. T., and O. Schneewind. 2001. Protein secretion and the pathogenesis of bacterial infections. Genes Dev. 15:1725-1752.
39. Mahdavi, J. B. Sonden, M. Hurtig, F. O. Olfat, L. Forsberg, N. Roche, J. Angstrom, T. Larsson, S. Teneberg, K. A. Karlsson, S. Altraja, T. Wadstrom, D. Kersulyte, D. E. Berg, A. Dubois, C. Petersson, K. E. Magnusson, T. Norberg, F. Lindh, B. B. Lundskog, A. Arnqvist, L. Hammarstrom, and T. Boren. 2002. Helicobacter pylori SabA adhesin in persistent infection and chronic inflammation. Science 297:573-578.
40. Mobley, H. L. T., G. L. Mendez, and S. L. Hazell (ed.). 2001. Helicobacter pylori: physiology and genetics. ASM Press, Washington, D.C.
41. Mukhopadhyay, A. K., D. Kersulyte, J.-Y. Jeong, S. Datta, Y. Ito, A. Chowdhury, S. Chowdhury, A. Santra, S. K. Bhattacharya, T. Azuma, G. B. Nair, and D. E. Berg. 2000. Distinctiveness of genotypes of Helicobacter pylori in Calcutta, India. J. Bacteriol. 182:3219-3227.
42. Murray, N. E. 2000. Type 1 restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle). Microbiol. Mol. Biol. Rev. 64:412-434
43. Occhialini, A., A. Marais, R. Alm, F. Garcia, R. Sierra, and F. Mégraud. 2000. Distribution of open reading frames of plasticity region of strain J99 in Helicobacter pylori strains isolated from gastric carcinoma and gastritis patients in Costa Rica. Infect. Immun. 68:6240-6249.
44. Rhen, M., S. Eriksson, M. Clements, S. Bergström, and S. J. Normark. 2003. The basis of persistent bacterial infections. Trends Microbiol. 11:80-86.
45. Salama, N., K. Guillemin, T. K. McDaniel, G. Sherlock, L. Tompkins, and S. Falkow. 2000. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc. Natl. Acad. Sci. USA 97:14668-14673.
46. Sexton, J. A., and J. P. Vogel. 2002. Type IVB secretion by intracellular pathogens. Traffic 3:178-185.
47. Studier, F. W., and P. K. Bandyopadhyay. 1988. Model for how type 1 restriction enzymes select cleavage sites in DNA. Proc. Natl. Acad. Sci. USA 85:4677-4681.
48. Tomb, J. F., O. White, A. R. Kerlavage, R. A. Clayton, G. G. Sutton, R. D. Fleischmann, K. A. Ketchum, H. P. Klenk, S. Gill, B. A. Dougherty, K. Nelson, J. Quackenbush, L. Zhou, E. F. Kirkness, S. Peterson, B. Loftus, D. Richardson, R. Dodson, H. G. Khalak, A. Glodek, K. McKenney, L. M. Fitzgerald, N. Lee, M. D. Adams, E. K. Hickey, D. E. Berg, J. D. Gocayne, T. R. Utterback, J. D. Peterson, J. M. Kelley, M. D. Cotton, J. M. Weidman, C. Fujii, C. Bowman, L. Watthey, E. Wallin, W. S. Hayes, M. Borodovsky, P. D. Karp, H. O. Smith, C. M. Fraser, and J. C. Venter. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539-547.
49. Tomcsanyi, T., C. M. Berg, S. H. Phadnis, and D. E. Berg. 1990. Intramolecular transposition by a synthetic IS50 (Tn5) derivative. J. Bacteriol. 172:6348-6354.
50. Trieber, C. A., and D. E. Taylor. 2002. Mutations in the 16S rRNA genes of Helicobacter pylori mediate resistance to tetracycline. J. Bacteriol. 184:2131-2140.
51. Trieu-Cuot, P., G. Gerbaud, T. Lambert, and P. Courvalin. 1985. In vivo transfer of genetic information between gram-positive and gram-negative bacteria. EMBO J. 4:3583-3587.
52. Turlan, C., and M. Chandler. 1995. 1S1-mediated intramolecular rearrangements: formation of excised transposon circles and replicative deletions. EMBO J. 14:5410-5421.
53. van der Ende, A., E. A. Rauws, M. Feller, C. J. Mulder, G. N. Tytgat, and J. Dankert. 1996. Heterogeneous Helicobacter pylori isolates from members of a family with a history of peptic ulcer disease. Gastroenterology 111:638-647.
54. Wang, G., R. W. Blakesley, D. E. Berg, and C. M. Berg. 1993. pDUAL: a transposon-based cosmid cloning vector for generating nested deletions and DNA sequencing templates in vivo. Proc. Natl. Acad. Sci. USA 90:7874-7878.