Helicobacter pylori: Genomic insight into the host-pathogen interaction

International Journal of Genomics

Volumn 2015, Issue , 2015, Pages

  Haley, Kathryn P ^a   Gaddy, Jennifer A ^a,b  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b DEPARTMENT OF VETERANS AFFAIRS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL TOXIN; CARCINOGEN; HOST FACTOR; VIRULENCE FACTOR;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; CHRONIC INFLAMMATION; COEVOLUTION; DIETARY INTAKE; ECOLOGICAL NICHE; ENVIRONMENTAL FACTOR; GENOMICS; GEOGRAPHIC DISTRIBUTION; HELICOBACTER PYLORI; HOST PATHOGEN INTERACTION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; TRANSCRIPTOMICS;

BACTERIA (MICROORGANISMS); HELICOBACTER PYLORI;

EID: 84924064937     PISSN: 2314436X     EISSN: 23144378     Source Type: Journal    
DOI: 10.1155/2015/386905     Document Type: Article

References (73)

1. M. Stolte, "Helicobacter pylori gastritis and gastric MALTlymphoma," The Lancet, vol. 339, no. 8795, pp. 745-746, 1992.
2. S. R. Pernitzsch and C.M. Sharma, "Transcriptome complexity and riboregulation in the human pathogen Helicobacter pylori," Frontiers in Cellular and InfectionMicrobiology, vol. 2, article 14, 2012.
3. D. Makola, D. A. Peura, and S. E. Crowe, "Helicobacter pylori infection and related gastrointestinal diseases," Journal of Clinical Gastroenterology, vol. 41, no. 6, pp. 548-558, 2007.
4. N. D. Lewis, M. Asim, D. P. Barry et al., "Immune evasion by Helicobacter pylori is mediated by induction of macrophage arginase II,"TheJournal of Immunology, vol. 186, no.6,pp. 3632-3641, 2011.
5. L. Pacifico, C. Anania, J. F. Osborn, F. Ferraro, and C. Chiesa, "Consequences of Helicobacter pylori infection in children," World Journal of Gastroenterology, vol. 16, no. 41, pp. 5181-5194, 2010.
6. I. C. Arnold, N. Dehzad, S. Reuter et al., "Helicobacter pylori infection prevents allergic asthma in mousemodels through the induction of regulatory T cells," Journal of Clinical Investigation, vol. 121, no. 8, pp. 3088-3093, 2011.
7. A. Kandulski and P. Malfertheiner, "Helicobacter pylori and gastroesophageal reflux disease," Current Opinion in Gastroenterology, vol. 30, no. 4, pp. 402-407, 2014.
8. T. L. Cover and M. J. Blaser, "Helicobacter pylori in health and disease," Gastroenterology, vol. 136, no. 6, pp. 1863-1873, 2009.
9. J. C. Atherton, "The pathogenesis of Helicobacter pylori-induced gastro-duodenal diseases," Annual Review of Pathology, vol. 1, pp. 63-96, 2006.
10. Y. Moodley, B. Linz, R. P. Bond et al., "Age of the association between Helicobacter pylori and man," PLoS Pathogens, vol. 8, no. 5, Article IDe1002693, 2012.
11. P. Correa and M. B. Piazuelo, "Natural history of Helicobacter pylori infection," Digestive and Liver Disease, vol. 40, no. 7, pp. 490-496, 2008.
12. S. Hellmig, J. Hampe, and S. Schreiber, "Helicobacter pylori infection in Africa and Europe: enigma of host genetics," Gut, vol. 52, no. 12, p. 1799, 2003.
13. V. Misra, R. Pandey, S. P. Misra, and M. Dwivedi, "Helicobacter pylori and gastric cancer: Indian enigma," World Journal of Gastroenterology, vol. 20, no. 6, pp. 1503-1509, 2014.
14. N. R. Hussein, "Helicobacter pylori and gastric cancer in the Middle East: a new enigma?"World Journal of Gastroenterology, vol. 16, no. 26, pp. 3226-3234, 2010.
15. R. Suzuki, S. Shiota, and Y. Yamaoka, "Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori," Infection,Genetics and Evolution, vol. 12,no. 2, pp.203-213,2012.
16. A. Torres-Morquecho, S. Giono-Cerezo, M. Camorlinga-Ponce, C. F. vargas-Mendoza, and J. Torres, "Evolution of bacterial genes: evidences of positive Darwinian selection and fixation of base substitutions in virulence genes of Helicobacter pylori," Infection, Genetics and Evolution, vol. 10, no. 6, pp. 764-776, 2010.
17. M. Camorlinga-Ponce, G. Perez-Perez, G. Gonzalez-valencia et al., "Helicobacter pylori genotyping from american indigenous groups shows novel amerindian vacA and cagA alleles and Asian, African and European admixture," PLoS ONE, vol. 6, no. 11, Article ID e27212, 2011.
18. A. Sheh, R. Chaturvedi, D. S. Merrell, P. Correa, K. T. Wilson, and J. G. Fox, "Phylogeographic origin of Helicobacter pylori determines host-adaptive responses upon coculturewith gastric epithelial cells," Infection and Immunity, vol. 81, no. 7, pp. 2468-2477, 2013.
19. S. P. Mane, M. G. Dominguez-Bello, M. J. Blaser et al., "Hostinteractive genes in Amerindian Helicobacter pylori diverge from their old world homologs and mediate inflammatory responses," Journal of Bacteriology, vol. 192, no. 12, pp. 3078-3092, 2010.
20. S. M. Devi, I. Ahmed, P. Francalacci et al., "Ancestral European roots of Helicobacter pylori in India," BMC Genomics, vol. 8, article 184, 2007.
21. S. M. Devi, I. Ahmed, A. A. Khan et al., "Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cagpathogenicity island," BMC Genomics, vol. 7, article 191, 2006.
22. P. Cao, J. L. Kerry, M. J. Blaser, and T. L. Cover, "Analysis of hopQ alleles in East Asian andWestern strains of Helicobacter pylori," FEMS Microbiology Letters, vol. 251, no. 1, pp. 37-43, 2005.
23. Q.-J. Dong, L.-L. Wang, Z.-B. Tian, X.-J. Yu, S.-J. Jia, and S.-Y. Xuan, "Reduced genome size of Helicobacter pylori originating from East Asia," World Journal of Gastroenterology, vol. 20, no. 19, pp. 5666-5671, 2014.
24. G. Xie, C. A. Bonner, and R. A. Jensen, "Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture," Genome Biology, vol. 3, no. 9, Article IDresearch0051.1, 2002.
25. M. A. Meseguer, A. Álvarez, M. T. Rejas, C. Sánchez, J. C. Pérez- Díaz, and F. Baquero, "Mycoplasma pneumoniae: a reducedgenome intracellular bacterial pathogen," Infection, Genetics and Evolution, vol. 3, no. 1, pp. 47-55, 2003.
26. C. Toft and S. G. E. Andersson, "Evolutionary microbial genomics: insights into bacterial host adaptation," Nature Reviews Genetics, vol. 11, no. 7, pp. 465-475, 2010.
27. W. Fischer, U. Breithaupt, B. I. Kern, S. I. Smith, C. Spicher, and R. Haas, "A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity," BMC Genomics, vol. 15, article 310, 2014.
28. B. Linz, H. M. Windsor, J. J. McGraw et al., "A mutation burst during the acute phase of Helicobacter pylori infection in humans and rhesus macaques," Nature Communications, vol. 5, article 4165, 2014.
29. B. Linz, H. M. Windsor, J. P. Gajewski et al., "Helicobacter pylori genomic microevolution during naturally occurring transmission between adults," PLoS ONE, vol. 8, no. 12, Article IDe82187, 2013.
30. C. M. Sharma, S. Hoffmann, F. Darfeuille et al., "The primary transcriptome of the major human pathogen Helicobacter pylori," Nature, vol. 464, no. 7286, pp. 250-255, 2010.
31. I. Porcelli, M. Reuter, B. M. Pearson, T. Wilhelm, and A. H. M. van vliet, "Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria," BMC Genomics, vol. 14, no. 1, article 616, 2013.
32. Y. Furuta, H. Namba-Fukuyo, T. F. Shibata et al., "Methylome diversification through changes in DNA methyltransferase sequence specificity," PLoS Genetics, vol. 10, no. 4, Article ID e1004272, 2014.
33. J. Krebes, R. D. Morgan, B. Bunk et al., "The complex methylomeof thehumangastricpathogenHelicobacter pylori," Nucleic Acids Research, vol. 42, no. 4, pp. 2415-2432, 2014.
34. T. L. Cover and M. J. Blaser, "Purification and characterization of the vacuolating toxin from Helicobacter pylori," The Journal of Biological Chemistry, vol. 267, no. 15, pp. 10570-10575, 1992.
35. M. K. R. Tummuru, T. L. Cover, and M. J. Blaser, "Cloning and expression of a high-molecular-mass major antigen of Helicobacter pylori: evidence of linkage to cytotoxin production," Infection and Immunity, vol. 61, no. 5, pp. 1799-1809, 1993.
36. M. S. Sundrud, V. J. Torres, D. Unutmaz, and T. L. Cover, "Inhibition of primary human T cell proliferation by Helicobacter pylori vacuolating toxin (vacA) is independent of vacA effects on IL-2 secretion," Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 20, pp. 7727-7732, 2004.
37. J. N. Radin, C. González-Rivera, S. E. Ivie, M. S. McClain, and T. L. Cover, "Helicobacter pylori vacA induces programmed necrosis in gastric epithelial cells," Infection and Immunity, vol. 79, no. 7, pp. 2535-2543, 2011.
38. K. Yahiro, M. Satoh, M. Nakano et al., "Low-density lipoprotein receptor-related protein-1 (LRP1) mediates autophagy and apoptosis caused by Helicobacter pylori vacA," Journal of Biological Chemistry, vol. 287, no. 37, pp. 31104-31115, 2012.
39. M. Höcker and P. Hohenberger, "Helicobacter pylori virulence factors-one part of a big picture," The Lancet, vol. 362, no. 9391, pp. 1231-1233, 2003.
40. K. R. Jones, S. Jang, J. Y. Chang et al., "Polymorphisms in the intermediate region ofvacAimpact Helicobacter pylori-induced disease development," Journal of Clinical Microbiology, vol. 49, no. 1, pp. 101-110, 2011.
41. K. A. Gangwer, C. L. Shaffer, S. Suerbaum, D. B. Lacy, T. L. Cover, and S. R. Bordenstein, "Molecular evolution of the Helicobacter pylori vacuolating toxin gene vacA," Journal of Bacteriology, vol. 192, no. 23, pp. 6126-6135, 2010.
42. E. M. Johnson, J. A. Gaddy, B. J. voss, E. E. Hennig, and T. L. Cover, "Genes required for assembly of pili associated with the Helicobacter pylori cag type Iv secretion system," Infection and Immunity, vol. 82, no. 8, pp. 3457-3470, 2014.
43. M. L. Hutton, M. Kaparakis-Liaskos, L. Turner, A. Cardona, T. Kwok, and R. L. Ferrero, "Helicobacter pylori exploits cholesterol-rich microdomains for induction of NF- κB-dependent responses and peptidoglycan delivery in epithelial cells," Infection and Immunity, vol. 78, no. 11, pp. 4523-4531, 2010.
44. K. Guillemin,N. R. Salama, L. S. Tompkins, and S. Falkow, "Cag pathogenicity island-specific responses of gastric epithelial cells to Helicobacter pylori infection," Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 23, pp. 15136-15141, 2002.
45. N. Tegtmeyer, S. Wessler, and S. Backert, "Role of the cagpathogenicity island encoded type Iv secretion system in Helicobacter pylori pathogenesis," FEBS Journal, vol. 278, no. 8, pp. 1190-1202, 2011.
46. S. Tan, J. M. Noto, J. Romero-Gallo, R. M. Peek Jr., and M. R. Amieva, "Helicobacter pylori perturbs iron trafficking in the epithelium to grow on the cell surface," PLoS Pathogens, vol. 7, no. 5, Article IDe1002050, 2011.
47. C. Y. Chen, F. Y. Wang, H. J. Wan et al., "Amino acid polymorphisms flanking the EPIYA-A motif of Helicobacter pylori CagA C-terminal region is associated with gastric cancer in East China: Experience from a single center," Journal of Digestive Diseases, vol. 14, no. 7, pp. 358-365, 2013.
48. D. Basso, C.-F. Zambon, D. P. Letley et al., "Clinical relevance of Helicobacter pylori cagA and vacA Gene Polymorphisms," Gastroenterology, vol. 135, no. 1, pp. 91-99, 2008.
49. M. S. McClain, C. L. Shaffer, D. A. Israel, R. M. Peek Jr., and T. L. Cover, "Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer," BMC Genomics, vol. 10, article 13, 2009.
50. D. R. Scott, E. A. Marcus, Y. Wen, J. Oh, and G. Sachs, "Gene expression in vivo shows that Helicobacter pylori colonizes an acidic niche on the gastric surface," Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 17, pp. 7235-7240, 2007.
51. L. H. Ta, L. M. Hansen, W. E. Sause et al., "Conserved transcriptional unit organization of the cag pathogenicity island among Helicobacter pylori strains," Frontiers in Cellular and Infection Microbiology, vol. 2, article 46, 2012.
52. M. Contreras, J. M. Thiberge, M. A. Mandrand-Berthelot, and A. Labigne, "Characterization of the roles of NikR, a nickelresponsive pleiotropic autoregulator of Helicobacter pylori," Molecular Microbiology, vol. 49, no. 4, pp. 947-963, 2003.
53. J. M. Noto, J. A. Gaddy, J. Y. Lee et al., "Iron deficiency accelerates Helicobacter pylori-induced carcinogenesis in rodents and humans,"The Journal of Clinical Investigation, vol. 123, no. 1, pp. 479-492, 2013.
54. J. A. Gaddy, J. N. Radin, J. T. Loh et al., "The host protein calprotectin modulates the Helicobacter pylori cag type Iv secretion system via zinc sequestration," PLoS Pathogens, vol. 10, no. 10, Article ID e1004450, 2014.
55. Y.-W. Zhang, S.-Y. Eom, D.-H. Yim et al., "Evaluation of the relationship between dietary factors, CagA-positive Helicobacter pylori infection, and RUNX3 promoter hypermethylation in gastric cancer tissue,"World Journal of Gastroenterology, vol. 19, no. 11, pp. 1778-1787, 2013.
56. D. Pra, S. I. R. Franke, J. A. P. Henriques, and M. Fenech, "A possible link between iron deficiency and gastrointestinal carcinogenesis," Nutrition and Cancer, vol. 61, no. 4, pp. 415-426, 2009.
57. J. A. Gaddy, J. N. Radin, J. T. Loh et al., "High dietary salt intake exacerbates Helicobacter pylori-induced gastric carcinogenesis," Infection and Immunity, vol. 81, no. 6, pp. 2258-2267, 2013.
58. A. Mueller, J. O'Rourke, P. Chu et al., "The role of antigenic drive and tumor-infiltrating accessory cells in the pathogenesis of helicobacter-induced mucosa-associated lymphoid tissue lymphoma," The American Journal of Pathology, vol. 167, no. 3, pp. 797-812, 2005.
59. H. M. Scott Algood, J. Gallo-Romero, K. T. Wilson, R. M. Peek Jr., and T. L. Cover, "Host response to Helicobacter pylori infection before initiation of the adaptive immune response," FEMS Immunology and Medical Microbiology, vol. 51, no. 3, pp. 577-586, 2007.
60. H. M. Algood, S. S. Allen, M. K. Washington, R. M. Peek Jr., G. G. Miller, and T. L. Cover, "Regulation of gastric B cell recruitment is dependent on IL-17 receptor A signaling in a model of chronic bacterial infection," The Journal of Immunology, vol. 183, no. 9, pp. 5837-5846, 2009.
61. S. T. Leach, H. M. Mitchell, C. L. Geczy, P. M. Sherman, and A. S. Day, "S100 calgranulin proteins S100A8, S100A9 and S100A12 are expressed in the inflamed gastric mucosa of Helicobacter pylori-infected children," Canadian Journal of Gastroenterology, vol. 22, no. 5, pp. 461-464, 2008.
62. S. Y. Wang, X. Y. Shen, C. Y. Wu et al., "Analysis of whole genomic expression profiles of Helicobacter pylori related chronic atrophic gastritis with IL-1B-31CC/-511TT genotypes," Journal of Digestive Diseases, vol. 10, no. 2, pp. 99-106, 2009.
63. H. Xue, J. Liu, B. Lin, Z. Wang, J. Sun, and G. Huang, "A meta-analysis of interleukin-8-251 promoter polymorphism associated with gastric cancer risk," PLoS ONE, vol. 7, no. 1, Article ID e28083, 2012.
64. J. Behnsen, S. Jellbauer, C. P. Wong et al., "The cytokine IL-22 promotes pathogen colonization by suppressing related commensal bacteria," Immunity, vol. 40, no. 2, pp. 262-273, 2014.
65. M. Sassone-Corsi and M. Raffatellu, "A hydrogen boost for Salmonella," Cell Host & Microbe, vol. 14, no. 6, pp. 603-604, 2013.
66. N. Kodaman, A. Pazos, B. G. Schneider et al., "Human and Helicobacter pylori coevolution shapes the risk of gastric disease," Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 4, pp. 1455-1460, 2014.
67. N. Kodaman, R. S. Sobota, R. Mera, B. G. Schneider, and S. M. Williams, "Disrupted human-pathogen co-evolution: amodel for disease," Frontiers in Genetics, vol. 5, article 290, 2014.
68. J. Ferreira and S. F. Moss, "Current paradigm and future directions for treatment of Helicobacter pylori infection," Current Treatment Options in Gastroenterology, vol. 12, no. 4, pp. 373-384, 2014.
69. R. Slinger, L. Yan, F. Chan et al., "Pyrosequencing assay to rapidly detect clarithromycin resistance mutations in Canadian Helicobacter pylori isolates," Canadian Journal of Gastroenterology, vol. 23, no. 9, pp. 609-612, 2009.
70. A. Iwamoto, T. Tanahashi, R. Okada et al., "Whole-genome sequencing of clarithromycin resistant Helicobacter pylori characterizes unidentified variants of multidrug resistant efflux pump genes," Gut Pathogens, vol. 6, no. 1, article 27, 2014.
71. N. N. Qureshi, B. Gallaher, and N. L. Schiller, "Evolution of amoxicillin resistance of Helicobacter pylori in vitro : characterization of resistancemechanisms," MicrobialDrug Resistance, vol. 20, no. 6, pp. 509-516, 2014.
72. H. Alfizah, A. Norazah, R. Hamizah, and M. Ramelah, "Resistotype of Helicobacter pylori isolates: the impact on eradication outcome," Journal of Medical Microbiology, vol. 63, no. 5, pp. 703-709, 2014.
73. S. S. Choi, P. T. Chivers, and D. E. Berg, "Point mutations in Helicobacter pylori's fur regulatory gene that alter resistance to metronidazole, a prodrug activated by chemical reduction," PLoS ONE, vol. 6, no. 3,Article ID e18236, 2011.