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Chapter 27 : The Genome

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Abstract:

A milestone in microbial genomics was set when became the first bacterial species to have its genome sequenced and compared from two independent isolates. Studies that sampled the entire genome and addressed nucleotide differences, such as randomly amplified polymorphic DNA (RAPD)-polymerase chain reaction (PCR), also provided a picture of extensive nucleotide diversity and showed that any particular strain could be distinguished from essentially all other strains. Other techniques such as PCR restriction fragment length polymorphism (RFLP), oligofingerprinting, restriction fragment end labeling, and ribotyping supported these observations. As with most microbial genome sequencing projects to date, J99 and 26695 were sequenced using a random shotgun approach from libraries of cloned chromosomal fragments of ~2.5 kb. The transcription and translation processes in appear to bear a lot of similarities to those of other gram-negative bacteria. Bacterial factors such as strain-specific genes (either chromosomally encoded or present on plasmids), differential gene expression (potentially mediated by methylation and pseudogene generation), phase variation (mediated by slippedstrand repair), or allelic variation (such as found in cagA, which plays a role in the level of phosphorylation of the CagA protein) may play a critical role in disease development. The application of techniques such as expression profiling with both human and bacterial microarrays should help answer many of the questions relating to the unique host-pathogen interaction.

Citation: Alm R, Noonan B. 2001. The Genome, p 295-311. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch27

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Restriction Fragment Length Polymorphism
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Figure 1

Comparison of the chromosomal organization of the two sequenced H. pylori genomes. The continuous outer circle represents the H. pylori 26695 genome whereas the inner circle represents the organization of the H. pylori J99 genome relative to that of strain 26695, incorporating artificial breaks to facilitate the alignment as described in the text and elsewhere ( ). The artificial breaks are represented by encircled numbers and represent inversions and/or translocations. The locations of complete (circle) or partial (half-circle) IS605 (filled) and IS606 (open) insertion elements in both chromosomes are indicated, and the five cases of coincident location are indicated by an asterisk (*) between the circles. The location and number of strain-specific genes (found in one strain but not the other) are indicated by vertical marks crossing the respective chromosome. At loci where both genomes possess strain-specific genes at the same position, the vertical mark crosses both genomic circles. The strain-specific genes boxed represent HP1383 and HP1404, which are found at either endpoint of genomic rearrangement 8. In this figure, the mpA and mpB genes of the IS605 and IS606 elements (a total of 2 in J99 and 14 in 26695) are included with the strain-specific genes. The location of the one and two plasticity zone(s) in J99 and 26695, respectively, are represented by stars (*).

Citation: Alm R, Noonan B. 2001. The Genome, p 295-311. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch27
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Figure 2

Genomic location of the conserved orthologous genes between H. pylori J99 and 26695. The nucleotide position of the initiation codon of each orthologous gene-pair (♦) in J99 and 26695 was plotted. The disruption of the conserved gene order of the orthologs is easily detected. The genes affected by the artificial breaks introduced to align the orthologous genes from the two genomes are encircled and numbered according to the inversion and/or translocation number given in Fig. 1 . Due to the resolution, the smallest inversion (number 5) cannot be detected, but its location is indicated with an arrow. The locations of the plasticity zones (PZ) are indicated. Due to their large size, the location of the coincident plasticity zone is represented by a gap in the diagonal “orthologous gene line. ” The other plasticity zone (split by rearrangement 3) in 26695 is located at approximately 0.45 Mb on the 26695 chromosome.

Citation: Alm R, Noonan B. 2001. The Genome, p 295-311. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch27
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References

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1. Achtman, M.,, T. Azuma,, D. E. Berg,, Y. Ito,, G. Morelli,, Z. J. Pan,, S. Suerbaum,, S. A. Thompson,, A. van der Ende,, and L. J. van Doom. 1999. Recombination and clonal groupings within Helicobacter pylori from different geographical regions. Mol. Microbiol. 32: 459 470.
2. Akopyants, N.,, A. Fradkov,, L. Diatchenko,, J. Hill,, P. Siebert,, S. Lukyanov,, E. Sverdlov,, and D. 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. 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.
4. Akopyanz, N.,, N. O. Bukanov,, T. U. Westblom,, and D. E. Berg. 1992. PCR-based RFLP analysis of DNA sequence diversity in the gastric pathogen Helicobacter pylori. Nucleic Acids Res. 20: 6221 6225.
5. Akopyanz, N.,, N. O. Bukanov,, T. U. Westblom,, S. Kresovich,, and D. E. Berg. 1992. DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. Nucleic Acids. Res. 20: 5137 5142.
6. Alarcon, T.,, D. Domingo,, and M. Lopez-Brea. 1999. Antibiotic resistance problems with Helicobacter pylori. Int J. Anti-microb. Agents 12: 19 26.
7. Aim, R. A.,, J. Bina,, B. M. Andrews,, P. Doig,, R. E. W. Hancock,, and T. J. Trust. 2000. Comparative genomics of Helicobacter pylori: analysis of the outer membrane protein families. Infect. Immun. 68: 4155 4168.
8. Aim, R. A.,, L. L. Ling,, D. T. Moir,, B. L. King,, E. D. Brown,, Q. Jiang,, 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,, D. Merberg,, S. D. Mills,, 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: 186 190.
9. Aim, R. A.,, and T. J. Trust. 1999. Analysis of the genetic diversity of Helicobacter pylori—the tale of two genomes. J. Mol. Med. 77: 834 846.
10. Aim, R. A.,, and T. J. Trust,. 2001. Comparative analysis of the Helicobacter pylori genomes. In M. Achtman, and S. Suerbaum (ed.) Helicobacter pylori: Molecular and Cellular Biology. Horizon Scientific Press, Wymondham, United Kingdom.
11. Appelmelk, B. J.,, S. L. Martin,, M. A. Monteiro,, C. A. Clayton,, A. A. McColm,, P. Zheng,, T. Verboom,, J. J. Maaskant,, D. H. van den Eijnden,, C. H. Hokke,, M. B. Perry,, C. M. Vanden broucke-Grauls,, and J. G. Kusters. 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.
12. Appelmelk, B. J.,, R. Negrini,, A. P. Moran,, and E. J. Kipers. 1997. Molecular mimicry between Helicobacter pylori and the host. Trends Microbiol. 5: 70 73.
13. Appelmelk, B. J.,, I. Simoons-Smit,, R. Negrini,, A. P. Moran,, G. O. Aspinall,, J. G. Forte,, T. de Vries,, H. Quan,, T. Verboom,, J. J. Maaskant,, P. Gbiara,, E. J. Kuipers,, E. Bloemena,, T. M. Tadema,, R. R. Townsend,, K. Tyagarajan,, J. M. Crothers, Jr.,, M. A. Monteiro,, A. Savio,, and J. de Graaff. 1996. Potential role of molecular mimicry between Helicobacter pylori lipopolysaccharide and host Lewis blood group antigens in autoimmunity. Infect. Immun. 64: 2031 2040.
14. Berg, D. E.,, R. H. Gilman,, J. Lelwala-Guruge,, K. Srivastava,, 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 Peruvian patients. Clin. Infect. Dis. 25: 996 1002.
15. Bolle, X. D.,, C. D. Bayliss,, D. Field,, T. van de Ven,, N. J. Saunders,, D. W. Hood,, and E. R. Moxon. 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.
16. Chiang, S. L.,, J. J. Mekalanos,, and D. W. Holden. 1999. In vivo genetic analysis of bacterial virulence. Annu. Rev. Microbiol. 53: 129 154.
17. Clemens, J.,, M. J. Albeit,, M. Rao,, F. Qadri,, S. Huda,, B. Kay,, F. P. van Loon,, D. Sack,, B. A. Pradhan,, and R. B. Sack. 1995. Impact of infection by Helicobacter pylori on the risk and severity of endemic cholera. J. Infect. Dis. 171: 1653 1656.
18. Cover, T. L.,, and M. J. Blaser. 1992. Helicobacter pylori and gastroduodenal disease. Annu. Rev. Med. 42: 135 145.
19. Curnow, A. W.,, K. W. Hong,, R. Yuan,, S. I. Kim,, O. Martins,, W. Winkler,, T. M. Henkin,, and D. Soil. 1997. Glu-tRNAGln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc. Natl. Acad. Sci. USA 94: 11819 11826.
20. Dale, A.,, J. E. Thomas,, M. K. Darboe,, W. A. Coward,, M. Harding,, and L. T. Weaver. 1998. Helicobacter pylori infection, gastric acid secretion, and infant growth. J. Pediatr. Gastroenterol. Nutr. 26: 393 397.
21. Doig, P.,, B. L. dejonge,, R. A. Aim,, E. D. Brown,, M. Uria-Nickelsen,, B. Noonan,, S. D. Mills,, P. Turmnino,, G. Carmel,, B. C. Guild,, D. T. Moir,, G. F. Vovis,, and T. J. Trust. 1999. Helicobacter pylori physiology predicted from genomic comparison of two strains. Microbiol. Mol. Biol. Rev. 63: 675 707.
22. Doig, P.,, M. M. Exner,, R. E. W. Hancock,, and T. J. Trust. 1995. Isolation and characterization of a conserved porin protein from Helicobacter pylori. J. Bacterial. 177: 5447 5452.
23. Dunkley, M. L.,, S. J. Harris,, R. J. McCoy,, M. J. Musicka,, F. M. Eyers,, L. G. Beagley,, P. J. Lumley,, K. W. Beagley,, and R. L. Clancy. 1999. Protection against Helicobacter pylori infection by intestinal immunisation with a 50/52-kDa sub-unit protein. PEMS Immunol. Med. Microbiol. 24: 221 225.
24. Eaton, K. A.,, D. R. Morgan,, and S. Krakowka. 1989. Campylobacter pylori virulence factors in gnotobiotic piglets. Infect. Immun. 57: 1119 1125.
25. Evans, D. J.,, D. M. Queiroz,, E. N. Mendes,, and D. G. Evans. 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.
26. Exner, M. M.,, P. Doig,, T. J. Trust,, and R. E. W. Hancock. 1995. Isolation and characterization of a family of porin proteins from Helicobacter pylori. Infect. Immun. 63: 1567 1572.
27. Fassbinder, F.,, A. H. van Vliet,, V. Gimmel,, J. G. Kusters,, M. Kist,, and S. Bereswill. 2000. Identification of iron-regulated genes of Helicobacter pylori by a modified fur titration assay (FURTA-Hp). FEMS Microbiol. Lett. 184: 225 229.
28. Ferrero, R. L.,, J. M. Tbiberge,, I. Kansau,, N. Wuscher,, M. Huerre,, and A. Labigne. 1995. The GroES homolog of Helicobacter pylori confers protective immunity against mucosal infection in mice. Proc. Natl. Acad. Sci. USA 92: 6499 6503.
29. Figura, N. 1997. Helicobacter pylori factors involved in the development of gastroduodenal mucosal damage and ulceration. J. Clin. Gastroenterol. 25: S149 S163.
30. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J. F. Tomb,, B. A. Dougherty,, J. M. Merrick,, K. McKenney,, G. Sutton,, W. FitzHugh,, C. Fields,, J. D. Gocayne,, J. Scott,, R. Shirley,, L.-I. Liu,, A. Glodek,, J. M. Kelley,, J. F. Weidman,, C. A. Phillips,, T. Spriggs,, E. Hedblom,, M. D. Cotton,, T. R. Utterback,, M. C. Hanna,, D. T. Nguyen,, D. M. Saudek,, R. C. Brandon,, L. D. Fine,, J. L. Fritchman,, J. L. Fuhrmann,, N. S. M. Geoghagen,, C. L. Gnehm,, L. A. McDonald,, K. V. Small,, C. M. Fraser,, H. O. Smith,, and J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496 512.
31. Fleischmann, R. D.,, O. White,, E. Hickey,, R. Clayton,, R. Dodson,, M. Gwinn,, J. Heidelberg,, J. Peterson,, L. McDonald,, T. Utterback,, W. Bishai,, A. Delcher,, C. Fraser,, and J. C. Venter. 1998. Sequencing of the M. tuberculosis genome; comparison of a recent clinical isolate with the laboratory strain. Microb. Cotnp. Genotn. 3: C14.
32. Forbes, K. J.,, Z. Fang,, and T. H. Pennington. 1995. Allelic variation in the Helicobacter pylori flagellin genes flaA and flaB: its consequences for strain typing schemes and population structure. Epidemiol. Infect. 114: 257 266.
33. Garner, J. A.,, and T. L. Cover. 1995. Analysis of genetic diversity in cytotoxin-producing and non-cytotoxin-produc-ing Helicobacter pylori strains. J. Infect. Dis. 172: 290 293.
34. Ge, Z.,, N. W. Chan,, M. M. Palcic,, and D. E. Taylor. 1997. Cloning and heterologous expression of an al,3-fucosyl-transferase gene from the gastric pathogen Helicobacter pylori. J. Biol. Chem. 272: 21357 21363.
35. Ghiara, P.,, M. Rossi,, M. Marchetti,, A. D. Tommaso,, C. Vin-digni,, F. Ciampolini,, A. Covacci,, J. L. Telford,, M. T. D. Magistris,, M. Pizza,, R. Rappuoli,, and G. D. Giudice. 1997. Therapeutic intragastric vaccination against Helicobacter pylori in mice eradicates an otherwise chronic infection and confers protection against reinfection. Infect Immun. 65: 4996 5002.
36. Go, M. F.,, V. Kapur,, D. Y. Graham,, and J. M. Musser. 1996. Population genetic analysis of Helicobacter pylori by multilo-cus enzyme electrophoresis: extensive allelic diversity and re-combinational population structure. J. Bacterial. 178: 3934 3938.
37. Graham, D. Y. 1998. Antibiotic resistance in Helicobacter pylori: implications for therapy. Gastroenterology 115: 1272 1277.
38. Guerry, P.,, R. A. Aim,, C. Szymanski,, and T. J. Trust,. 2000. Structure, function, and antigenicity of Campylobacter flagella, p. 405 421. In I. Nachamkin, and M. J. Blaser (ed.), Campylobacter, 2nd ed. ASM Press, Washington, D.C.
39. Han, J.,, E. Yu,, I. Lee,, and Y. Lee. 1997. Diversity among clinical isolates of Helicobacter pylori in Korea. Mol. Cell. 7: 544 547.
40. Hazell, S. L.,, R. H. Andrews,, H. M. Mitchell,, and G. Daskalopoulous. 1997. Genetic relationship among isolates of Helicobacter pylori: evidence for the existence of a Helicobacter pylori species complex. FEMS Microbiol. Lett. 150: 27 32.
41. Hocking, D.,, E. Webb,, F. Radcliff,, L. Rothel,, S. Taylor,, G. Pinczower,, C. Kapouleas,, H. Braley,, A. Lee,, and C. Doidge. 1999. Isolation of recombinant protective Helicobacter pylori antigens. Infect. Immun. 67: 4713 4719.
42. Hook-Nikanne, J.,, D. E. Berg,, R. M. Peek, Jr.,, D. Kersulyte,, M. K. Tummuru,, and M. J. Blaser. 1998. DNA sequence conservation and diversity in transposable element IS605 of Helicobacter pylori. Helicobacter 3: 79 85.
43. Hunt, R. H. 1996. The role of Helicobacter pylori in pathogenesis: the spectrum of clinical outcomes. Scand. J. Gastroenterol. Suppl. 220: 3 9.
44. liver, D.,, A. Arnqvist,, J. Ogren,, I. M. Frick,, D. Kersulyte,, E. T. Incecik,, D. E. Berg,, A. Covacci,, L. Engstrand,, and T. Boren. 1998. Helicobacter pylori adhesin binding fucosylated histo-blood group antigens revealed by retagging. Science 279: 373 377.
45. Ito, A.,, T. Fujioka,, T. Kubota,, and M. Nasu. 1996. Molecular typing of Helicobacter pylori: differences in pathogenicity among diverse strains. J. Gastroenterol. 31: 1 5.
46. Jenks, P. J.,, F. Megraud,, and A. Labigne. 1998. Clinical outcome after infection with Helicobacter pylori does not appear to be reliably predicted by the presence of any of the genes of the cag pathogenicity island. Gut 43: 752 758.
47. Jennings, M. P.,, Y. N. Srikhanta,, E. R. Moxon,, M. Kramer,, J. T. Poolman,, B. Kuipers,, and P. van. der Ley. 1999. The genetic basis of the phase variation repertoire of lipopolysaccharide immunotypes in Neisseria meningitidis. Microbiology 145: 3013 3021.
48. Jiang, Q.,, K. Hiratsuka,, and D. E. Taylor. 1996. Variability of gene order in different Helicobacter pylori strains contributes to genome diversity. Mol. Microbiol. 20: 833 842.
49. Kalman, S.,, W. Mitchell,, R. Marathe,, C. Lammel,, J. Fan,, R. W. Hyman,, L. dinger,, J. Grimwood,, R. W. Davis,, and R. S. Stephens. 1999. Comparative genomes of Chlamydia pneumoniae and C. trachomatis. Nat. Genet. 21: 385 389.
50. Kansau, I.,, J. Raymond,, E. Bingen,, P. Courcoux,, N. Kalach,, M. Bergeret,, N. Braimi,, C. Dupont,, and A. Labigne. 1996. Genotyping of Helicobacter pylori isolates by sequencing of PCR products and comparison with the RAPD technique. Res. Microbiol. 147: 661 669.
51. Karita, M.,, M. K. R. Tummuru,, H.-P. Wirth,, and M. J. Blaser. 1996. Effect of growth phase and acid shock on Helicobacter pylori cagA expression. Infect. Immun. 64: 4501 4507.
52. Kersulyte, D.,, N. S. Akopyants,, S. W. Clifton,, B. A. Roe,, and D. E. Berg. 1998. Novel sequence organization and insertion specificity of IS605 and IS606: chimaeric transposable elements of Helicobacter pylori. Gene 223: 175 186.
53. Kersulyte, D.,, H. Chalkauskas,, and D. E. Berg. 1999. Emergence of recombinant strains of Helicobacter pylori during human infection. Mol. Microbiol. 31: 31 43.
54. Kleanthous, H.,, G. A. Myers,, K. M. Georgakopoulos,, T. J. Tibbitts,, J. W. Ingrassia,, H. L. Gray,, R. Ding,, Z. Z. Zhang,, W. Lei,, R. Nichols,, C. K. Lee,, T. H. Ermak,, and T. P. Mo-nath. 1998. Rectal and intranasal immunizations with recombinant urease induce distinct local and serum immune responses in mice and protect against Helicobacter pylori infection. Infect. Immun. 66: 2879 2886.
55. Labigne, A.,, and H. de Reuse. 1996. Determinants of Helicobacter pylori pathogenicity. Infect. Agents Dis. 5: 191 202.
56. Leying, H.,, S. Suerbaum,, G. Geis,, and R. Haas. 1992. Cloning and genetic characterization of a Helicobacter pylori flagellin gene. Mol. Microbiol. 6: 2863 2874.
57. Lin, L. F.,, N. Porter,, and H. Kong. 2000. Genomes 2000: Int. Conf. Microb. Model Genomes. Institut Pasteur, Paris, France.
58. Logan, S. M.,, J. W. Conlan,, M. A. Monteiro,, W. W. Wakar-chuk,, and E. Altman. 2000. Functional genomics of Helicobacter pylori: identification of a beta-1,4 galactosyltransfer-ase and generation of mutants with altered lipopolysac-charide. Mol. Microbiol. 35: 1156 1167.
59. Maeda, S.,, H. Yoshida,, T. Ikenoue,, K. Ogura,, F. Kanai,, N. Kato,, Y. Shiratori,, and M. Omata. 1999. Structure of cag pathogenicity island in Japanese Helicobacter pylori isolates. Gut 44: 336 341.
60. Marais, A.,, G. L. Mendz,, S. L. Hazell,, and F. Megraud. 1999. Metabolism and genetics of Helicobacter pylori: the genome era. Microbiol. Mol. Biol. Rev. 63: 542 674.
61. Marchetti, M.,, M. Rossi,, V. Giannelli,, M. M. Giuliani,, M. P. M,, S. Censini,, A. Covacci,, P. Massari,, C. Pagliaccia,, R. Manetti,, J. L. Telford,, G. Douce,, G. Dougan,, R. Rappuoli,, and P. Ghiara. 1998. Protection against Helicobacter pylori infection in mice by intragastric vaccination with H. pylori antigens is achieved using a non-toxic mutant of E. coli heat-labile enterotoxin (LT) as adjuvant. Vaccine 16: 33 37.
62. Marshall, B. J.,, and J. R. Warren. 1984. Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration. Lancet i: 1311 1315.
63. Marshall, D. G.,, D. C. Coleman,, D. J. Sullivan,, H. Xia,, C. A. O'Morain,, and C. J. Symth. 1996. Genomic DNA fingerprinting of clinical isolates of Helicobacter pylori using short oligonucleotide probes containing repetitive sequences. J. Appl. Bacteriol. 81: 509 517.
64. Martin, S. L.,, M. R. Edbrooke,, T. C. Hodgman,, D. H. van den Eijnden,, and M. I. Bird. 1997. Lewis X biosynthesis in Helicobacter pylori. Molecular cloning of an alpha( 1,3 )-fucosyltransferase gene. J. Biol. Chem. 272: 21349 21356.
65. McAtee, C. P.,, K. E. Fry, andD. E. Berg. 1998. Identification of potential diagnostic and vaccine candidates of Helicobacter pylori by "proteome" technologies. Helicobacter 3: 163 169.
66. McAtee, C. P.,, M. Y. Lim,, K. Fung,, M. Velligan,, K. Fry,, T. P. Chow,, and D. E. Berg. 1998. Characterization of a Helicobacter pylori vaccine candidate by proteome techniques. J. Chromatogr. B. Biomed. Sci. Appl. 714: 325 333.
67. McGowan, C. C.,, A. Necheva,, S. A. Thompson,, T. L. Cover,, and M. J. Blaser. 1998. Acid-induced expression of an LPS-associated gene in Helicobacter pylori. Mol. Microbiol. 30: 19 31.
68. Meijer, A.,, S. A. Morre,, A. J. van den Brule,, P. H. Savelkoul,, and J. M. Ossewaarde. 1999. Genomic relatedness of Chlamydia isolates determined by amplified fragment length polymorphism analysis. J. Bacteriol. 181: 4469 4475.
69. Nilsson, C. L.,, T. Larsson,, E. Gustafsson,, K. A. Karlsson,, and P. Davidsson. 2000. Identification of protein vaccine candidates from Helicobacter pylori using a preparative two-dimensional electrophoretic procedure and mass spectrometry. Anal. Chem. 72: 2148 2153.
70. Odenbreit, S.,, J. Puis,, B. Sedlmaier,, E. Gerland,, W. Fischer,, and R. Haas. 2000. Translocation of Helicobacter pylori cagA into gastric epithelial cells by type IV secretion. Science 287: 1497 1500.
71. Odenbreit, S.,, M. Till,, D. Hofreuter,, G. Faller,, and R. Haas. 1999. Genetic and functional characterization of the alpAB gene locus essential for the adhesion of Helicobacter pylori to human gastric tissue. Mol. Microbiol. 31: 1537 1548.
72. Owen, R. J.,, C. Hunton,, J. Bickley,, M. Moreno,, and D. Linton. 1992. Ribosomal RNA gene restriction patterns of Helicobacter pylori: analysis and appraisal of HaelXl digests as a molecular typing system. Epidemiol. Infect. 109: 35 47.
73. Pan, Z. J.,, R. W. van der Hulst,, M. Feller,, S. D. Xiao,, G. N. Tytgat,, J. Dankert,, and A. van der Ende. 1997. Equally high prevalences of infection with c agA-positive Helicobacter pylori in Chinese patients with peptic ulcer disease and those with chronic gastritis-associated dyspepsia. J. Clin. Microbiol. 35: 1344 1347.
74. Parkhill, J. 2000. In defense of complete genomes. Nat. Biotechnol. 18: 493 494.
75. Parkhill, J.,, M. Achtman,, K. D. James,, S. D. Bentley,, C. Churcher,, S. R. Klee,, G. Morelli,, D. Basham,, D. Brown,, T. Chillingworth,, R. M. Davies,, P. Davis,, K. Devlin,, T. Feltwell,, N. Hamlin,, S. Holroyd,, K. Jagels,, S. Leather,, S. Moule,, K. Mungall,, M. A. Quail,, M. A. Rajandream,, K. M. Rutherford,, M. Simmonds,, J. Skelton,, S. Whitehead,, B. G. Spratt,, and B. G. Barrell. 2000. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 404: 502 506.
76. Parkhill, J.,, B. W. Wren,, K. Mungall,, J. M. Ketley,, C. Churcher,, D. Basham,, T. Chillingworth,, R. M. Davies,, T. Feltwell,, S. Holroyd,, K. Jagels,, A. V. Karlyshev,, S. Moule,, M. J. Pallen,, C. W. Penn,, M. A. Quail,, M. A. Rajandream,, K. M. Rutherford,, A. H. van Vliet,, S. Whitehead,, and B. G. Barrell. 2000. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403: 665 668.
77. Peak, I. R.,, M. P. Jennings,, D. W. Hood,, M. Bisercic,, and E. R. Moxon. 1996. Tetrameric repeat units associated with virulence factor phase variation in Haemophilus also occur in Neisseria spp. and Moraxella catarrhalis. FEMS Microbiol. Lett. 137: 109 114.
78. Peek, Jr., R. M.,, S. A. Thompson,, J. P. Donahue,, K. T. Tham,, J. C. Atherton,, M. J. Blaser,, and G. G. Miller. 1998. Adherence to gastric epithelial cells induces expression of a Helicobacter pylori gene, iceA, that is associated with clinical outcome. Proc. Assoc. Am. Physicians 110: 531 544.
79. Pizza, M.,, V. Scarlato,, V. Masignani,, M. M. Giuliani,, B. Arico,, M. Comanducci,, G. T. Jennings,, L. Baldi,, E. Bartolini,, B. Capecchi,, C. L. Galeotti,, E. Luzzi,, R. Manetti,, E. Marchetti,, M. Mora,, S. Nuti,, G. Ratti,, L. Santini,, S. Savino,, M. Scarselli,, E. Storni,, P. Zuo,, M. Broeker,, E. Hundt,, B. Knapp,, E. Blair,, T. Mason,, H. Tettelin,, D. W. Hood,, A. C. Jeffries,, N. J. Saunders,, D. M. Granoff,, J. C. Venter,, E. R. Moxon,, G. Grandi,, and R. Rappuoli. 2000. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287: 1816 1820.
80. Radcliff, F. J.,, S. L. Hazell,, T. Kolesnikow,, C. Doidge,, and A. Lee. 1997. Catalase, a novel antigen for Helicobacter pylori vaccination. Infect. Immun. 65: 4668 4674.
81. Raudonikiene, A.,, N. Zakharova,, W. W. Su,, J. Y. Jeong,, L. Bryden,, P. S. Hoffman,, D. E. Berg,, and K. Severinov. 1999. Helicobacter pylori with separate beta- and beta'-subunits of RNA polymerase is viable and can colonize conventional mice. Mol. Microbiol. 32: 131 138.
82. Read, T. D.,, R. C. Brunham,, C. Shen,, S. R. Gill,, J. F. Heidelberg,, O. White,, E. K. Hickey,, J. Peterson,, T. Utterback,, K. Berry,, S. Bass,, K. Linher,, J. Weidman,, H. Khouri,, B. Craven,, C. Bowman,, R. Dodson,, M. Gwinn,, W. Nelson,, R. DeBoy,, J. Kolonay,, G. McClarty,, S. L. Salzberg,, J. Eisen,, and C. M. Fraser. 2000. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae Ar39. Nucleic Acids Res. 28: 1397 1406.
83. Salmela, K. S.,, R. P. Roine,, J. Hook-Nikanne,, T. U. Kosunen,, and M. Salaspuro. 1994. Acetaldehyde and ethanol production by Helicobacter pylori. Scand. J. Gastroenterol. 29: 309 312.
84. Salmela, K. S.,, R. P. Roine,, T. Koivisto,, J. Hook-Nikanne,, T. U. Kosunen,, and M. Salaspuro. 1993. Characteristics of Helicobacter pylori alcohol dehydrogenase. Gastroenterology 105: 325 330.
85. Salzberg, S. L.,, A. J. Salzberg,, A. R. Kerlavage,, and J. F. Tomb. 1998. Skewed oligomers and origins of replication. Gene 217: 57 67.
86. Saunders, N. J.,, J. F. Peden,, D. W. Hood,, and E. R. Moxon. 1998. Simple sequence repeats in the Helicobacter pylori genome. Mol. Microbiol. 27: 1091 1098.
87. Shortridge, V. D.,, G. G. Stone,, R. K. Flamm,, J. Beyer,, J. Versalovic,, D. Y. Graham,, and S. K. Tanaka. 1997. Molecular typing of Helicobacter pylori isolates from a multicenter U.S. clinical trial by ureC restriction fragment length polymorphism. J. Clin. Microbiol. 35: 471 473.
88. Spohn, G.,, and V. Scarlato. 1999. The autoregulatory HspR repressor protein governs chaperone gene transcription in Helicobacter pylori. Mol. Microbiol. 34: 663 674.
89. Stephens, R. S.,, S. Kalman,, C. Lammel,, J. Fan,, R. Marathe,, L. Aravind,, W. Mitchell,, L. Olinger,, R. L. Tatusov,, Q. Zhao,, E. V. Koonin,, and R. W. Davis. 1998. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 282: 754 759.
90. Stone, G. G.,, D. Shortridge,, J. Versalovic,, J. Beyer,, R. K. Flamm,, D. Y. Graham,, A. T. Ghoneim,, and S. K. Tanaka. 1997. A PCR-oligonucleotide ligation assay to determine the prevalence of 23S rRNA gene mutations in clarithromycinresistant Helicobacter pylori. Antimicrob. Agents Chemother. 41: 712 714.
91. Suerbaum, S.,, and M. Achtman. 1999. Evolution of Helicobacter pylori: the role of recombination. Trends Microbiol. 7: 182 184.
92. Suerbaum, S.,, T. Brauer-Steppkes,, A. Labigne,, B. Cameron,, and K. Drlica. 1998. Topoisomerase I of Helicobacter pylori: juxtaposition with a flagellin gene (flaB) and functional requirement of a fourth zinc finger motif. Gene 210: 151 161.
93. Suerbaum, S.,, C. Josenhans,, and A. Labigne. 1993. Cloning and genetic characterization of the Helicobacter pylori and Helicobacter mustelae flaB flagellin genes and construction of H. pylori flaA- and flaB-negative mutants by electroporation-mediated allelic exchange. J. Bacterial. 175: 3278 3288.
94. Suerbaum, S.,, J. M. Smith,, K. Bapumia,, G. Morelli,, N. H. Smith,, E. Kunstmann,, I. Dyrek,, and M. Achtman. 1998. Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. USA 95: 12619 12624.
95. Takami, S.,, T. Hayashi,, Y. Tonokatsu,, T. Shimoyama,, and T. Tamura. 1993. Chromosomal heterogeneity of Helicobacter pylori isolates by pulsed-field gel electrophoresis. Zentralbl. Bakteriol. 280: 120 127.
96. Taylor, D. E.,, M. Eaton,, N. Chang,, and S. M. Salama. 1992. Construction of a Helicobacter pylori genome map and demonstration of diversity at the genome level. J. Bacteriol. 174: 6800 6806.
97. Tee, W.,, J. Lambert,, R. Smallwood,, M. Schembri,, B. C. Ross,, and B. Dwyer. 1992. Ribotyping of Helicobacter pylori from clinical specimens. J. Clin. Microbiol. 30: 1562 1567.
98. Tettelin, H.,, N. J. Saunders,, J. Heidelberg,, A. C. Jeffries,, K. E. Nelson,, J. A. Eisen,, K. A. Ketchum,, D. W. Hood,, J. F. Peden,, R. J. Dodson,, W. C. Nelson,, M. L. Gwinn,, R. DeBoy,, J. D. Peterson,, E. K. Hickey,, D. H. Haft,, S. L. Salzberg,, O. White,, R. D. Fleischmann,, B. A. Dougherty,, T. Mason,, A. Ciecko,, D. S. Parksey,, E. Blair,, H. Cittone,, E. B. Clark,, M. D. Cotton,, T. R. Utterback,, H. Khouri,, H. Qin,, J. Vama-thevan,, J. Gill,, V. Scarlato,, V. Masignani,, M. Pizza,, G. Grandi,, L. Sun,, H. O. Smith,, C. M. Fraser,, E. R. Moxon,, R. Rappuoli,, and J. C. Venter. 2000. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287: 1809 1815.
99. 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. Fitzegerald,, 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. Wat-they,, 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.
100. Torrea, G.,, C. Offredo,, M. Simonet,, B. Gicquel,, P. Berche,, and C. Pierre-Audigier. 1996. Evaluation of tuberculosis transmission in a community by 1 year of systematic typing of Mycobacterium tuberculosis clinical isolates. J. Clin. Microbiol. 34: 1043 1049.
101. van Doom, N. E. M.,, F. Namavar,, J. G. Kusters,, E. P. van Rees,, E. J. Kuipers,, and J. de Graaff. 1998. Genomic DNA fingerprinting of clinical isolates of Helicobacter pylori by REP-PCR and restriction fragment end-labelling. FEMS Microbiol. Lett. 160: 145 150.
102. Wang, G.,, M. Z. Humayun,, and D. E. Taylor. 1999. Mutation as an origin of genetic variability in Helicobacter pylori. Trends Microbiol. 7: 488 493.
103. Wang, G.,, D. A. Rasko,, R. Sherburne,, and D. E. Taylor. 1999. Molecular genetic basis for the variable expression of Lewis Y antigen in Helicobacter pylori: analysis of the alpha(l,2) fucosyltransferase gene. Mol. Microbiol. 31: 1265 1274.
104. Yamaoka, Y.,, D. H. Kwon,, and D. Y. Graham. 2000. A Mr 34,000 proinflammatory outer membrane protein (oipA) of Helicobacter pylori. Proc. Natl. Acad. Sci. USA 97: 7533 7538.
105. Yang, Z. H.,, P. E. de Haas,, D. van Soolingen,, J. D. van Embden,, and A. B. Andersen. 1994. Restriction fragment length polymorphism Mycobacterium tuberculosis strains isolated from Greenland during 1992: evidence of tuberculosis transmission between Greenland and Denmark. J. Clin. Microbiol. 32: 3018 3025.
106. Zakharova, N.,, B. J. Paster,, I. Wesley,, F. E. Dewhirst,, D. E. Berg,, and K. V. Severinov. 1999. Fused and overlapping rpoB and rpoC genes in helicobacters, Campylobacters, and related bacteria. J. Bacteriol. 181: 3857 3859.

Tables

Generic image for table
Table 1

General comparative features of the

Citation: Alm R, Noonan B. 2001. The Genome, p 295-311. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch27
Generic image for table
Table 2

Genes unique to either J99 or 26695

Citation: Alm R, Noonan B. 2001. The Genome, p 295-311. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch27

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