The Genome

Richard A. Alm; Brian Noonan

doi:10.1128/9781555818005.ch27

Chapter 27 : The Genome

Authors: Richard A. Alm¹, Brian Noonan¹

VIEW AFFILIATIONS HIDE AFFILIATIONS

Affiliations: 1: Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451

Content Type: Monograph

Publication Year: 2001

Category: Bacterial Pathogenesis

Book DOI: 10.1128/9781555818005

Chapter DOI: 10.1128/9781555818005.ch27

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:

The Genome, Page 1 of 2

< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555818005/9781555812133_Chap27-1.gif /docserver/preview/fulltext/10.1128/9781555818005/9781555812133_Chap27-2.gif

Abstract:

A milestone in microbial genomics was set when Helicobacter pylori 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 H. pylori 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 H. pylori 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), Helicobacter pylori. ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch27

Key Concept Ranking

Restriction Fragment Length Polymorphism: 0.42471582
Gene Expression and Regulation: 0.4114848

0.42471582

Highlighted Text: Show | Hide

Full text loading...

Figures

The Genome

[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818005.chap27-1,webId=/content/author/10.1128/9781555818005.chap27-1,properties={foaf_givenname=Richard A., foaf_name=Richard A. Alm, foaf_surname=Alm, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818005.chap27-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818005.chap27-2,webId=/content/author/10.1128/9781555818005.chap27-2,properties={foaf_givenname=Brian, foaf_name=Brian Noonan, foaf_surname=Noonan, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818005.chap27-aff1]]}]]

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

/content/10.1128/9781555818005.chap27.fig27-1

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 ( 8 ). 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 (*).

10.1128/9781555818005/fig27-1_thmb.gif

10.1128/9781555818005/fig27-1.gif

Figure 1

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

/content/10.1128/9781555818005.chap27.fig27-2

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.

10.1128/9781555818005/fig27-2_thmb.gif

10.1128/9781555818005/fig27-2.gif

Figure 2

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

References

/content/book/10.1128/9781555818005.chap27

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

The Genome

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

/content/10.1128/9781555818005.chap27.tab27-1

Table 1

General comparative features of the H. pylori genomes

10.1128/9781555818005/tab27-1_thmb.gif

10.1128/9781555818005/tab27-1.gif

Table 1

General comparative features of the H. pylori genomes

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

/content/10.1128/9781555818005.chap27.tab27-2

Table 2

Genes unique to either H. pylori J99 or 26695

10.1128/9781555818005/tab27-2_thmb.gif

10.1128/9781555818005/tab27-2.gif

Table 2

Genes unique to either H. pylori J99 or 26695

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