Fitzgerald JR, Musser JM: Evolutionary genomics of pathogenic bacteria. Trends Microbiol. 2001, 9: 547-553. 10.1016/S0966-842X(01)02228-4.
Article
PubMed
CAS
Google Scholar
Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC, Smith DR, Noonan B, Guild BC, deJonge BL, Carmel G, Tummino PJ, Caruso A, Uria-Nickelsen M, Mills DM, Ives C, Gibson R, Merberg D, Mills SD, Jiang Q, Taylor DE, Vovis GF, Trust TJ: Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature. 1999, 397: 176-180. 10.1038/16495.
Article
PubMed
CAS
Google Scholar
Mobley HLT, Mendz GL, Hazell SL: Helicobacter pylori: physiology and genetics. 2001, Amer Society for Microbiology
Google Scholar
Yamaoka Y: Helicobacter pylori: molecular genetics and cellular biology. 2008, Caister Academic Pr
Google Scholar
Honda S, Fujioka T, Tokieda M, Satoh R, Nishizono A, Nasu M: Development of Helicobacter pylori-induced gastric carcinoma in Mongolian gerbils. Cancer Res. 1998, 58: 4255-4259.
PubMed
CAS
Google Scholar
Watanabe T, Tada M, Nagai H, Sasaki S, Nakao M: Helicobacter pylori infection induces gastric cancer in mongolian gerbils. Gastroenterology. 1998, 115: 642-648. 10.1016/S0016-5085(98)70143-X.
Article
PubMed
CAS
Google Scholar
Fukase K, Kato M, Kikuchi S, Inoue K, Uemura N, Okamoto S, Terao S, Amagai K, Hayashi S, Asaka M: Effect of eradication of Helicobacter pylori on incidence of metachronous gastric carcinoma after endoscopic resection of early gastric cancer: an open-label, randomised controlled trial. Lancet. 2008, 372: 392-397. 10.1016/S0140-6736(08)61159-9.
Article
PubMed
Google Scholar
Kraft C, Suerbaum S: Mutation and recombination in Helicobacter pylori: mechanisms and role in generating strain diversity. Int J Med Microbiol. 2005, 295: 299-305. 10.1016/j.ijmm.2005.06.002.
Article
PubMed
CAS
Google Scholar
Falush D, Wirth T, Linz B, Pritchard JK, Stephens M, Kidd M, Blaser MJ, Graham DY, Vacher S, Perez-Perez GI, Yamaoka Y, Megraud F, Otto K, Reichard U, Katzowitsch E, Wang X, Achtman M, Suerbaum S: Traces of human migrations in Helicobacter pylori populations. Science. 2003, 299: 1582-1585. 10.1126/science.1080857.
Article
PubMed
CAS
Google Scholar
Moodley Y, Linz B, Yamaoka Y, Windsor HM, Breurec S, Wu JY, Maady A, Bernhoft S, Thiberge JM, Phuanukoonnon S, Jobb G, Siba P, Graham DY, Marshall BJ, Achtman M: The peopling of the Pacific from a bacterial perspective. Science. 2009, 323: 527-530. 10.1126/science.1166083.
Article
PubMed
CAS
PubMed Central
Google Scholar
Higashi H, Tsutsumi R, Fujita A, Yamazaki S, Asaka M, Azuma T, Hatakeyama M: Biological activity of the Helicobacter pylori virulence factor CagA is determined by variation in the tyrosine phosphorylation sites. Proc Natl Acad Sci USA. 2002, 99: 14428-14433. 10.1073/pnas.222375399.
Article
PubMed
CAS
PubMed Central
Google Scholar
Satomi S, Yamakawa A, Matsunaga S, Masaki R, Inagaki T, Okuda T, Suto H, Ito Y, Yamazaki Y, Kuriyama M, Keida Y, Kutsumi H, Azuma T: Relationship between the diversity of the cagA gene of Helicobacter pylori and gastric cancer in Okinawa, Japan. J Gastroenterol. 2006, 41: 668-673. 10.1007/s00535-006-1838-6.
Article
PubMed
CAS
Google Scholar
Pride DT, Meinersmann RJ, Blaser MJ: Allelic Variation within Helicobacter pylori babA and babB. Infect Immun. 2001, 69: 1160-1171. 10.1128/IAI.69.2.1160-1171.2001.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ghose C, Perez-Perez GI, Dominguez-Bello MG, Pride DT, Bravi CM, Blaser MJ: East Asian genotypes of Helicobacter pylori strains in Amerindians provide evidence for its ancient human carriage. Proc Natl Acad Sci USA. 2002, 99: 15107-15111. 10.1073/pnas.242574599.
Article
PubMed
CAS
PubMed Central
Google Scholar
Salaün L, Saunders NJ: Population-associated differences between the phase variable LPS biosynthetic genes of Helicobacter pylori. BMC Microbiol. 2006, 6: 79-10.1186/1471-2180-6-79.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ogura M, Perez JC, Mittl PRE, Lee HK, Dailide G, Tan S, Ito Y, Secka O, Dailidiene D, Putty K: Helicobacter pylori evolution: lineage-specific adaptations in homologs of eukaryotic Sel1-like genes. PLoS Comput Biol. 2007, 3: e151-10.1371/journal.pcbi.0030151.
Article
PubMed
PubMed Central
CAS
Google Scholar
Oleastro M, Cordeiro R, Menard A, Yamaoka Y, Queiroz D, Megraud F, Monteiro L: Allelic diversity and phylogeny of homB, a novel co-virulence marker of Helicobacter pylori. BMC Microbiol. 2009, 9: 248-10.1186/1471-2180-9-248.
Article
PubMed
PubMed Central
CAS
Google Scholar
H. pylori MLST database. [http://pubmlst.org/helicobacter/]
Linz B, Balloux F, Moodley Y, Manica A, Liu H, Roumagnac P, Falush D, Stamer C, Prugnolle F, van der Merwe SW, Yamaoka Y, Graham DY, Perez-Trallero E, Wadstrom T, Suerbaum S, Achtman M: An African origin for the intimate association between humans and Helicobacter pylori. Nature. 2007, 445: 915-918. 10.1038/nature05562.
Article
PubMed
PubMed Central
Google Scholar
Jolley KA, Chan MS, Maiden MC: mlstdbNet - distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics. 2004, 5: 86-10.1186/1471-2105-5-86.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kersulyte D, Kalia A, Gilman RH, Mendez M, Herrera P, Cabrera L, Velapatiño B, Balqui J, Paredes Puente de la Vega F, Rodriguez Ulloa CA, Cok J, Hooper CC, Dailide G, Tamma S, Berg DE: Helicobacter pylori from Peruvian amerindians: traces of human migrations in strains from remote Amazon, and genome sequence of an Amerind strain. PLoS One. 2010, 5: e15076-10.1371/journal.pone.0015076.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mane SP, Dominguez-Bello MG, Blaser MJ, Sobral BW, Hontecillas R, Skoneczka J, Mohapatra SK, Crasta OR, Evans C, Modise T, Shallom S, Shukla M, Varon C, Megraud F, Maldonado-Contreras AL, Williams KP, Bassaganya-Riera J: Host-interactive genes in Amerindian Helicobacter pylori diverge from their Old World homologs and mediate inflammatory responses. J Bacteriol. 2010, 192: 3078-3092. 10.1128/JB.00063-10.
Article
PubMed
CAS
PubMed Central
Google Scholar
Uchiyama I: Multiple genome alignment for identifying the core structure among moderately related microbial genomes. BMC Genomics. 2008, 9: 515-10.1186/1471-2164-9-515.
Article
PubMed
PubMed Central
CAS
Google Scholar
Uchiyama I: Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes. Nucleic Acids Res. 2006, 34: 647-658. 10.1093/nar/gkj448.
Article
PubMed
CAS
PubMed Central
Google Scholar
Furuta Y, Kawai M, Yahara K, Takahashi N, Handa N, Tsuru T, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I: Birth and death of genes linked to chromosomal inversion. Proc Natl Acad Sci USA. 2011, 108: 1501-1506. 10.1073/pnas.1012579108.
Article
PubMed
CAS
PubMed Central
Google Scholar
Yamaoka Y, Alm RA: Helicobacter pylori Outer Membrane Proteins. Helicobacter pylori Molecular Genetics and Cellular Biology. Edited by: Yamaoka Y. 2008, Norfolk, UK: Caister Academic Press, 37-60.
Google Scholar
Alm RA, Bina J, Andrews BM, Doig P, Hancock RE, Trust TJ: Comparative genomics of Helicobacter pylori: analysis of the outer membrane protein families. Infect Immun. 2000, 68: 4155-4168. 10.1128/IAI.68.7.4155-4168.2000.
Article
PubMed
CAS
PubMed Central
Google Scholar
Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK, Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM, et al: The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 1997, 388: 539-547. 10.1038/41483.
Article
PubMed
CAS
Google Scholar
Schwarz G, Mendel RR, Ribbe MW: Molybdenum cofactors, enzymes and pathways. Nature. 2009, 460: 839-847. 10.1038/nature08302.
Article
PubMed
CAS
Google Scholar
Oh JD, Kling-Backhed H, Giannakis M, Xu J, Fulton RS, Fulton LA, Cordum HS, Wang C, Elliott G, Edwards J, Mardis ER, Engstrand LG, Gordon JI: The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression. Proc Natl Acad Sci USA. 2006, 103: 9999-10004. 10.1073/pnas.0603784103.
Article
PubMed
CAS
PubMed Central
Google Scholar
Gressmann H, Linz B, Ghai R, Pleissner KP, Schlapbach R, Yamaoka Y, Kraft C, Suerbaum S, Meyer TF, Achtman M: Gain and loss of multiple genes during the evolution of Helicobacter pylori. PLoS Genet. 2005, 1: e43-10.1371/journal.pgen.0010043.
Article
PubMed
PubMed Central
CAS
Google Scholar
Erickson RP: Autosomal recessive diseases among the Athabaskans of the southwestern United States: recent advances and implications for the future. Am J Med Genet A. 2009, 149A: 2602-2611. 10.1002/ajmg.a.33052.
Article
PubMed
Google Scholar
Wolfe AJ: The acetate switch. Microbiol Mol Biol Rev. 2005, 69: 12-10.1128/MMBR.69.1.12-50.2005.
Article
PubMed
CAS
PubMed Central
Google Scholar
Doig P, de Jonge BL, Alm RA, Brown ED, Uria-Nickelsen M, Noonan B, Mills SD, Tummino P, Carmel G, Guild BC, Moir DT, Vovis GF, Trust TJ: Helicobacter pylori physiology predicted from genomic comparison of two strains. Microbiol Mol Biol Rev. 1999, 63: 675-707.
PubMed
CAS
PubMed Central
Google Scholar
Kratzer R, Wilson DK, Nidetzky B: Catalytic mechanism and substrate selectivity of aldo-keto reductases: insights from structure-function studies of Candida tenuis xylose reductase. IUBMB Life. 2006, 58: 499-507. 10.1080/15216540600818143.
Article
PubMed
CAS
Google Scholar
Eppinger M, Baar C, Linz B, Raddatz G, Lanz C, Keller H, Morelli G, Gressmann H, Achtman M, Schuster SC: Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PLoS Genet. 2006, 2: e120-10.1371/journal.pgen.0020120.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dundon WG, Marshall DG, Moráin CA, Smyth CJ: A novel tRNA-associated locus (trl) from Helicobacter pylori is co-transcribed with tRNA(Gly) and reveals genetic diversity. Microbiology. 1999, 145 (Pt 6): 1289-1298.
Article
PubMed
CAS
Google Scholar
Bocs S, Danchin A, Medigue C: Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes. BMC Bioinformatics. 2002, 3: 5-10.1186/1471-2105-3-5.
Article
PubMed
PubMed Central
Google Scholar
Chase JW, Rabin BA, Murphy JB, Stone KL, Williams KR: Escherichia coli exonuclease VII. Cloning and sequencing of the gene encoding the large subunit (xseA). J Biol Chem. 1986, 261: 14929-14935.
PubMed
CAS
Google Scholar
Chase JW, Richardson CC: Escherichia coli mutants deficient in exonuclease VII. J Bacteriol. 1977, 129: 934-947.
PubMed
CAS
PubMed Central
Google Scholar
Burdett V, Baitinger C, Viswanathan M, Lovett ST, Modrich P: In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair. Proc Natl Acad Sci USA. 2001, 98: 6765-6770. 10.1073/pnas.121183298.
Article
PubMed
CAS
PubMed Central
Google Scholar
Fassbinder F, van Vliet AH, Gimmel V, Kusters JG, Kist M, Bereswill S: Identification of iron-regulated genes of Helicobacter pylori by a modified fur titration assay (FURTA-Hp). FEMS Microbiol Lett. 2000, 184: 225-229. 10.1111/j.1574-6968.2000.tb09018.x.
Article
PubMed
CAS
Google Scholar
Stoof J, Belzer C, van Vliet A: Metal Metabolism and Transport in Helicobacter pylori. Helicobacter pylori: molecular genetics and cellular biology. 2008, 165-177.
Google Scholar
Peck B, Ortkamp M, Diehl KD, Hundt E, Knapp B: Conservation, localization and expression of HopZ, a protein involved in adhesion of Helicobacter pylori. Nucleic Acids Res. 1999, 27: 3325-3333. 10.1093/nar/27.16.3325.
Article
PubMed
CAS
PubMed Central
Google Scholar
Cao P, Lee KJ, Blaser MJ, Cover TL: Analysis of hopQ alleles in East Asian and Western strains of Helicobacter pylori. FEMS Microbiol Lett. 2005, 251: 37-43. 10.1016/j.femsle.2005.07.023.
Article
PubMed
CAS
Google Scholar
Chalk PA, Roberts AD, Blows WM: Metabolism of pyruvate and glucose by intact cells of Helicobacter pylori studied by 13C NMR spectroscopy. Microbiology. 1994, 140 (Pt 8): 2085-2092.
Article
PubMed
CAS
Google Scholar
Fujitani Y, Yamamoto K, Kobayashi I: Dependence of frequency of homologous recombination on the homology length. Genetics. 1995, 140: 797-809.
PubMed
CAS
PubMed Central
Google Scholar
Kersulyte D, Lee W, Subramaniam D, Anant S, Herrera P, Cabrera L, Balqui J, Barabas O, Kalia A, Gilman RH, Berg DE: Helicobacter Pylori's plasticity zones are novel transposable elements. PLoS One. 2009, 4: e6859-10.1371/journal.pone.0006859.
Article
PubMed
PubMed Central
CAS
Google Scholar
Fischer W, Windhager L, Rohrer S, Zeiller M, Karnholz A, Hoffmann R, Zimmer R, Haas R: Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer. Nucleic Acids Res. 2010, 38: 6089-6101. 10.1093/nar/gkq378.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ilyina TV, Gorbalenya AE, Koonin EV: Organization and evolution of bacterial and bacteriophage primase-helicase systems. J Mol Evol. 1992, 34: 351-357. 10.1007/BF00160243.
Article
PubMed
CAS
Google Scholar
Thiberge JM, Boursaux-Eude C, Lehours P, Dillies MA, Creno S, Coppee JY, Rouy Z, Lajus A, Ma L, Burucoa C, Ruskone-Foumestraux A, Courillon-Mallet A, De Reuse H, Boneca IG, Lamarque D, Megraud F, Delchier JC, Medigue C, Bouchier C, Labigne A, Raymond J: From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma. BMC Genomics. 2010, 11: 368-10.1186/1471-2164-11-368.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hofler C, Fischer W, Hofreuter D, Haas R: Cryptic plasmids in Helicobacter pylori: putative functions in conjugative transfer and microcin production. Int J Med Microbiol. 2004, 294: 141-148. 10.1016/j.ijmm.2004.06.021.
Article
PubMed
CAS
Google Scholar
Hosaka Y, Okamoto R, Irinoda K, Kaieda S, Koizumi W, Saigenji K, Inoue M: Characterization of pKU701, a 2.5-kb plasmid, in a Japanese Helicobacter pylori isolate. Plasmid. 2002, 47: 193-200. 10.1016/S0147-619X(02)00003-3.
Article
PubMed
CAS
Google Scholar
Song JY, Choi SH, Byun EY, Lee SG, Park YH, Park SG, Lee SK, Kim KM, Park JU, Kang HL, Baik SC, Lee WK, Cho MJ, Youn HS, Ko GH, Bae DW, Rhee KH: Characterization of a small cryptic plasmid, pHP51, from a Korean isolate of strain 51 of Helicobacter pylori. Plasmid. 2003, 50: 145-151. 10.1016/S0147-619X(03)00059-3.
Article
PubMed
CAS
Google Scholar
Hofreuter D, Haas R: Characterization of two cryptic Helicobacter pylori plasmids: a putative source for horizontal gene transfer and gene shuffling. J Bacteriol. 2002, 184: 2755-2766. 10.1128/JB.184.10.2755-2766.2002.
Article
PubMed
CAS
PubMed Central
Google Scholar
Baltrus DA, Amieva MR, Covacci A, Lowe TM, Merrell DS, Ottemann KM, Stein M, Salama NR, Guillemin K: The complete genome sequence of Helicobacter pylori strain G27. J Bacteriol. 2009, 191: 447-448. 10.1128/JB.01416-08.
Article
PubMed
CAS
PubMed Central
Google Scholar
Farnbacher M, Jahns T, Willrodt D, Daniel R, Haas R, Goesmann A, Kurtz S, Rieder G: Sequencing, annotation and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8. BMC Genomics. 2010, 11: 335-10.1186/1471-2164-11-335.
Article
PubMed
PubMed Central
CAS
Google Scholar
GIB-IS. [http://gib-is.genes.nig.ac.jp/]
Nesic D, Miller MC, Quinkert ZT, Stein M, Chait BT, Stebbins CE: Helicobacter pylori CagA inhibits PAR1-MARK family kinases by mimicking host substrates. Nat Struct Mol Biol. 2010, 17: 130-132. 10.1038/nsmb.1705.
Article
PubMed
CAS
Google Scholar
Zhang J, Nielsen R, Yang Z: Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 2005, 22: 2472-2479. 10.1093/molbev/msi237.
Article
PubMed
CAS
Google Scholar
Gangwer KA, Mushrush DJ, Stauff DL, Spiller B, McClain MS, Cover TL, Lacy DB: Crystal structure of the Helicobacter pylori vacuolating toxin p55 domain. Proc Natl Acad Sci USA. 2007, 104: 16293-16298. 10.1073/pnas.0707447104.
Article
PubMed
CAS
PubMed Central
Google Scholar
Wang HJ, Wang WC: Expression and binding analysis of GST-VacA fusions reveals that the C-terminal approximately 100-residue segment of exotoxin is crucial for binding in HeLa cells. Biochem Biophys Res Commun. 2000, 278: 449-454. 10.1006/bbrc.2000.3820.
Article
PubMed
CAS
Google Scholar
Seif E, Hallberg BM: RNA-protein mutually induced fit: structure of Escherichia coli isopentenyl-tRNA transferase in complex with tRNA(Phe). J Biol Chem. 2009, 284: 6600-6604.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kaminska KH, Baraniak U, Boniecki M, Nowaczyk K, Czerwoniec A, Bujnicki JM: Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA. Proteins. 2008, 70: 1-18.
Article
PubMed
CAS
Google Scholar
Cover TL, Blaser MJ: Purification and characterization of the vacuolating toxin from Helicobacter pylori. J Biol Chem. 1992, 267: 10570-10575.
PubMed
CAS
Google Scholar
Jang JY, Yoon HJ, Yoon JY, Kim HS, Lee SJ, Kim KH, Kim dJ, Jang S, Han BG, Lee BI, Suh SW: Crystal structure of the TNF-alpha-Inducing protein (Tipalpha) from Helicobacter pylori: Insights into Its DNA-binding activity. J Mol Biol. 2009, 392: 191-197. 10.1016/j.jmb.2009.07.010.
Article
PubMed
CAS
Google Scholar
Chung C, Olivares A, Torres E, Yilmaz O, Cohen H, Perez-Perez G: Diversity of VacA intermediate region among Helicobacter pylori strains from several regions of the world. J Clin Microbiol. 2010, 48: 690-696. 10.1128/JCM.01815-09.
Article
PubMed
CAS
PubMed Central
Google Scholar
Testerman T, McGee D, Mobley H: Adherence and colonization. Helicobacter pylori: physiology and genetics. 2001, 381-417.
Chapter
Google Scholar
Carlsohn E, Nystrom J, Bolin I, Nilsson CL, Svennerholm AM: HpaA is essential for Helicobacter pylori colonization in mice. Infect Immun. 2006, 74: 920-926. 10.1128/IAI.74.2.920-926.2006.
Article
PubMed
CAS
PubMed Central
Google Scholar
Yamaoka Y, Kwon DH, Graham DY: A M(r) 34,000 proinflammatory outer membrane protein (oipA) of Helicobacter pylori. Proc Natl Acad Sci USA. 2000, 97: 7533-7538. 10.1073/pnas.130079797.
Article
PubMed
CAS
PubMed Central
Google Scholar
Aspholm-Hurtig M, Dailide G, Lahmann M, Kalia A, Ilver D, Roche N, Vikstrom S, Sjostrom R, Linden S, Backstrom A, Lundberg C, Arnqvist A, Mahdavi J, Nilsson UJ, Velapatino B, Gilman RH, Gerhard M, Alarcon T, Lopez-Brea M, Nakazawa T, Fox JG, Correa P, Dominguez-Bello MG, Perez-Perez GI, Blaser MJ, Normark S, Carlstedt I, Oscarson S, Teneberg S, Berg DE, et al: Functional adaptation of BabA, the H. pylori ABO blood group antigen binding adhesin. Science. 2004, 305: 519-522. 10.1126/science.1098801.
Article
PubMed
CAS
Google Scholar
Ilver D, Arnqvist A, Ogren J, Frick IM, Kersulyte D, Incecik ET, Berg DE, Covacci A, Engstrand L, Boren T: Helicobacter pylori adhesin binding fucosylated histo-blood group antigens revealed by retagging. Science. 1998, 279: 373-377. 10.1126/science.279.5349.373.
Article
PubMed
CAS
Google Scholar
Odenbreit S, Till M, Hofreuter D, Faller G, Haas R: Genetic and functional characterization of the alpAB gene locus essential for the adhesion of Helicobacter pylori to human gastric tissue. Mol Microbiol. 1999, 31: 1537-1548. 10.1046/j.1365-2958.1999.01300.x.
Article
PubMed
CAS
Google Scholar
Lu H, Wu JY, Beswick EJ, Ohno T, Odenbreit S, Haas R, Reyes VE, Kita M, Graham DY, Yamaoka Y: Functional and intracellular signaling differences associated with the Helicobacter pylori AlpAB adhesin from Western and East Asian strains. J Biol Chem. 2007, 282: 6242-6254.
Article
PubMed
CAS
PubMed Central
Google Scholar
Moran AP, Trent MS: Helicobacter pylori Lipopolysaccharides and Lewis Antigens. Helicobacter pylori: molecular genetics and cellular biology. 2008, Caister Academic Pr, 7-
Google Scholar
Rasko DA, Wang G, Palcic MM, Taylor DE: Cloning and characterization of the alpha(1,3/4) fucosyltransferase of Helicobacter pylori. J Biol Chem. 2000, 275: 4988-4994. 10.1074/jbc.275.7.4988.
Article
PubMed
CAS
Google Scholar
Bergman M, Del Prete G, van Kooyk Y, Appelmelk B: Helicobacter pylori phase variation, immune modulation and gastric autoimmunity. Nat Rev Microbiol. 2006, 4: 151-159. 10.1038/nrmicro1344.
Article
PubMed
CAS
Google Scholar
Nilsson C, Skoglund A, Moran AP, Annuk H, Engstrand L, Normark S: Lipopolysaccharide diversity evolving in Helicobacter pylori communities through genetic modifications in fucosyltransferases. PLoS One. 2008, 3: e3811-10.1371/journal.pone.0003811.
Article
PubMed
PubMed Central
CAS
Google Scholar
Skoglund A, Bäckhed HK, Nilsson C, Björkholm B, Normark S, Engstrand L: A changing gastric environment leads to adaptation of lipopolysaccharide variants in Helicobacter pylori populations during colonization. PLoS One. 2009, 4: e5885-10.1371/journal.pone.0005885.
Article
PubMed
PubMed Central
CAS
Google Scholar
Driessen AJ, Nouwen N: Protein translocation across the bacterial cytoplasmic membrane. Annu Rev Biochem. 2008, 77: 643-667. 10.1146/annurev.biochem.77.061606.160747.
Article
PubMed
CAS
Google Scholar
Kato Y, Nishiyama K, Tokuda H: Depletion of SecDF-YajC causes a decrease in the level of SecG: implication for their functional interaction. FEBS Lett. 2003, 550: 114-118. 10.1016/S0014-5793(03)00847-0.
Article
PubMed
CAS
Google Scholar
Smeets LC, Bijlsma JJ, Boomkens SY, Vandenbroucke-Grauls CM, Kusters JG: comH, a novel gene essential for natural transformation of Helicobacter pylori. J Bacteriol. 2000, 182: 3948-3954. 10.1128/JB.182.14.3948-3954.2000.
Article
PubMed
CAS
PubMed Central
Google Scholar
Fath MJ, Mahanty HK, Kolter R: Characterization of a purF operon mutation which affects colicin V production. J Bacteriol. 1989, 171: 3158-3161.
PubMed
CAS
PubMed Central
Google Scholar
Rust M, Schweinitzer T, Josenhans C: Helicobacter Flagella, Motility and Chemotaxis. Helicobacter pylori: molecular genetics and cellular biology. 2008, 61-
Google Scholar
Ryan KA, Karim N, Worku M, Penn CW, O'Toole PW: Helicobacter pylori flagellar hook-filament transition is controlled by a FliK functional homolog encoded by the gene HP0906. J Bacteriol. 2005, 187: 5742-5750. 10.1128/JB.187.16.5742-5750.2005.
Article
PubMed
CAS
PubMed Central
Google Scholar
Logan SM: Flagellar glycosylation - a new component of the motility repertoire?. Microbiology. 2006, 152: 1249-1262. 10.1099/mic.0.28735-0.
Article
PubMed
CAS
Google Scholar
Kelly DJ, Hughes NJ, Poole RK: Microaerobic physiology: aerobic respiration, anaerobic respiration, and carbon dioxide metabolism. Helicobacter pylori: physiology and genetics. 2001, 113-124.
Chapter
Google Scholar
Kohanski MA, Dwyer DJ, Collins JJ: How antibiotics kill bacteria: from targets to networks. Nat Rev Microbiol. 2010, 8: 423-435. 10.1038/nrmicro2333.
Article
PubMed
CAS
PubMed Central
Google Scholar
Ingelman M, Ramaswamy S, Nivière V, Fontecave M, Eklund H: Crystal structure of NAD(P)H:flavin oxidoreductase from Escherichia coli. Biochemistry. 1999, 38: 7040-7049. 10.1021/bi982849m.
Article
PubMed
CAS
Google Scholar
Kwon DH, El-Zaatari FA, Kato M, Osato MS, Reddy R, Yamaoka Y, Graham DY: Analysis of rdxA and involvement of additional genes encoding NAD(P)H flavin oxidoreductase (FrxA) and ferredoxin-like protein (FdxB) in metronidazole resistance of Helicobacter pylori. Antimicrob Agents Chemother. 2000, 44: 2133-2142. 10.1128/AAC.44.8.2133-2142.2000.
Article
PubMed
CAS
PubMed Central
Google Scholar
Watanabe S, Matsumi R, Arai T, Atomi H, Imanaka T, Miki K: Crystal structures of [NiFe] hydrogenase maturation proteins HypC, HypD, and HypE: insights into cyanation reaction by thiol redox signaling. Mol Cell. 2007, 27: 29-40. 10.1016/j.molcel.2007.05.039.
Article
PubMed
CAS
Google Scholar
Benoit S, Mehta N, Wang G, Gatlin M, Maier RJ: Requirement of hydD, hydE, hypC and hypE genes for hydrogenase activity in Helicobacter pylori. Microb Pathog. 2004, 36: 153-157. 10.1016/j.micpath.2003.11.001.
Article
PubMed
CAS
Google Scholar
Hazell S, Harris A, Trend M: Evasion of the toxic effects of oxygen. Helicobacter pylori: physiology and genetics. Edited by: Mobley H, Mendz G, Hazell S. 2001, ASM Press, 167-175.
Chapter
Google Scholar
Giró M, Carrillo N, Krapp AR: Glucose-6-phosphate dehydrogenase and ferredoxin-NADP(H) reductase contribute to damage repair during the soxRS response of Escherichia coli. Microbiology. 2006, 152: 1119-1128. 10.1099/mic.0.28612-0.
Article
PubMed
CAS
Google Scholar
Urbonavicius J, Qian Q, Durand JM, Hagervall TG, Bjork GR: Improvement of reading frame maintenance is a common function for several tRNA modifications. Embo J. 2001, 20: 4863-4873. 10.1093/emboj/20.17.4863.
Article
PubMed
CAS
PubMed Central
Google Scholar
Nakanishi K, Bonnefond L, Kimura S, Suzuki T, Ishitani R, Nureki O: Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Nature. 2009, 461: 1144-1148. 10.1038/nature08474.
Article
PubMed
CAS
Google Scholar
Suzuki T, Miyauchi K: Discovery and characterization of tRNAIle lysidine synthetase (TilS). FEBS Lett. 2010, 584: 272-277. 10.1016/j.febslet.2009.11.085.
Article
PubMed
CAS
Google Scholar
Cai J, Han C, Hu T, Zhang J, Wu D, Wang F, Liu Y, Ding J, Chen K, Yue J, Shen X, Jiang H: Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation. Protein Sci. 2006, 15: 2071-2081. 10.1110/ps.062238406.
Article
PubMed
CAS
PubMed Central
Google Scholar
Demirci H, Gregory ST, Dahlberg AE, Jogl G: Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA. Embo J. 2007, 26: 567-577. 10.1038/sj.emboj.7601508.
Article
PubMed
CAS
PubMed Central
Google Scholar
Amundsen SK, Fero J, Hansen LM, Cromie GA, Solnick JV, Smith GR, Salama NR: Helicobacter pylori AddAB helicase-nuclease and RecA promote recombination-related DNA repair and survival during stomach colonization. Mol Microbiol. 2008, 69: 994-1007. 10.1111/j.1365-2958.2008.06336.x.
Article
PubMed
CAS
PubMed Central
Google Scholar
Sourice S, Biaudet V, El Karoui M, Ehrlich SD, Gruss A: Identification of the Chi site of Haemophilus influenzae as several sequences related to the Escherichia coli Chi site. Mol Microbiol. 1998, 27: 1021-1029. 10.1046/j.1365-2958.1998.00749.x.
Article
PubMed
CAS
Google Scholar
Handa N, Ohashi S, Kusano K, Kobayashi I: Chi-star, a chi-related 11-mer sequence partially active in an E. coli recC1004 strain. Genes Cells. 1997, 2: 525-536. 10.1046/j.1365-2443.1997.1410339.x.
Article
PubMed
CAS
Google Scholar
Tadokoro T, Kanaya S: Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes. FEBS J. 2009, 276: 1482-1493. 10.1111/j.1742-4658.2009.06907.x.
Article
PubMed
CAS
Google Scholar
Kogoma T: Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription. Microbiol Mol Biol Rev. 1997, 61: 212-238.
PubMed
CAS
PubMed Central
Google Scholar
Adams DW, Errington J: Bacterial cell division: assembly, maintenance and disassembly of the Z ring. Nat Rev Microbiol. 2009, 7: 642-653. 10.1038/nrmicro2198.
Article
PubMed
CAS
Google Scholar
Lock RL, Harry EJ: Cell-division inhibitors: new insights for future antibiotics. Nat Rev Drug Discov. 2008, 7: 324-338. 10.1038/nrd2510.
Article
PubMed
CAS
Google Scholar
Moran AP: Relevance of fucosylation and Lewis antigen expression in the bacterial gastroduodenal pathogen Helicobacter pylori. Carbohydr Res. 2008, 343: 1952-1965. 10.1016/j.carres.2007.12.012.
Article
PubMed
CAS
Google Scholar
Broadberry RE, Lin-Chu M: The Lewis blood group system among Chinese in Taiwan. Hum Hered. 1991, 41: 290-294. 10.1159/000154015.
Article
PubMed
CAS
Google Scholar
Anstee DJ: The relationship between blood groups and disease. Blood. 2010, 115: 4635-4643. 10.1182/blood-2010-01-261859.
Article
PubMed
CAS
Google Scholar
Rajagopalan KV: Molybdenum: an essential trace element in human nutrition. Annual review of nutrition. 1988, 8: 401-427. 10.1146/annurev.nu.08.070188.002153.
Article
PubMed
CAS
Google Scholar
Ezraty B, Bos J, Barras F, Aussel L: Methionine sulfoxide reduction and assimilation in Escherichia coli: new role for the biotin sulfoxide reductase BisC. J Bacteriol. 2005, 187: 231-237. 10.1128/JB.187.1.231-237.2005.
Article
PubMed
CAS
PubMed Central
Google Scholar
Alamuri P, Maier RJ: Methionine sulphoxide reductase is an important antioxidant enzyme in the gastric pathogen Helicobacter pylori. Molecular microbiology. 2004, 53: 1397-1406. 10.1111/j.1365-2958.2004.04190.x.
Article
PubMed
CAS
Google Scholar
Wang G, Alamuri P, Maier RJ: The diverse antioxidant systems of Helicobacter pylori. Mol Microbiol. 2006, 61: 847-860. 10.1111/j.1365-2958.2006.05302.x.
Article
PubMed
CAS
Google Scholar
Alamuri P, Maier RJ: Methionine sulfoxide reductase in Helicobacter pylori: interaction with methionine-rich proteins and stress-induced expression. J Bacteriol. 2006, 188: 5839-5850. 10.1128/JB.00430-06.
Article
PubMed
CAS
PubMed Central
Google Scholar
Sachs G, Weeks D, Melchers K, Scott D: The gastric biology of Helicobacter pylori. Helicobacter pylori: molecular genetics and cellular biology. 2008, 137-
Google Scholar
McColl KE: Helicobacter pylori and acid secretion: where are we now?. Eur J Gastroenterol Hepatol. 1997, 9: 333-335.
Article
PubMed
CAS
Google Scholar
El-Mansi M, Cozzone AJ, Shiloach J, Eikmanns BJ: Control of carbon flux through enzymes of central and intermediary metabolism during growth of Escherichia coli on acetate. Curr Opin Microbiol. 2006, 9: 173-179. 10.1016/j.mib.2006.02.002.
Article
PubMed
CAS
Google Scholar
Moura GR, Carreto LC, Santos MA: Genetic code ambiguity: an unexpected source of proteome innovation and phenotypic diversity. Curr Opin Microbiol. 2009, 12: 631-637. 10.1016/j.mib.2009.09.004.
Article
PubMed
CAS
Google Scholar
Denamur E, Lecointre G, Darlu P, Tenaillon O, Acquaviva C, Sayada C, Sunjevaric I, Rothstein R, Elion J, Taddei F, Radman M, Matic I: Evolutionary implications of the frequent horizontal transfer of mismatch repair genes. Cell. 2000, 103: 711-721. 10.1016/S0092-8674(00)00175-6.
Article
PubMed
CAS
Google Scholar
Jenks PJ, Edwards DI: Metronidazole resistance in Helicobacter pylori. Int J Antimicrob Agents. 2002, 19: 1-7. 10.1016/S0924-8579(01)00468-X.
Article
PubMed
CAS
Google Scholar
Ito Y, Azuma T, Ito S, Suto H, Miyaji H, Yamazaki Y, Kohli Y, Kuriyama M: Full-length sequence analysis of the vacA gene from cytotoxic and noncytotoxic Helicobacter pylori. J Infect Dis. 1998, 178: 1391-1398. 10.1086/314435.
Article
PubMed
CAS
Google Scholar
Azuma T, Yamakawa A, Yamazaki S, Ohtani M, Ito Y, Muramatsu A, Suto H, Yamazaki Y, Keida Y, Higashi H, Hatakeyama M: Distinct diversity of the cag pathogenicity island among Helicobacter pylori strains in Japan. J Clin Microbiol. 2004, 42: 2508-2517. 10.1128/JCM.42.6.2508-2517.2004.
Article
PubMed
CAS
PubMed Central
Google Scholar
National Center for Biotechnology Information. [http://www.ncbi.nlm.nih.gov]
Besemer J, Lomsadze A, Borodovsky M: GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001, 29: 2607-2618. 10.1093/nar/29.12.2607.
Article
PubMed
CAS
PubMed Central
Google Scholar
Delcher AL, Bratke KA, Powers EC, Salzberg SL: Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007, 23: 673-679. 10.1093/bioinformatics/btm009.
Article
PubMed
CAS
PubMed Central
Google Scholar
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25: 955-964. 10.1093/nar/25.5.955.
Article
PubMed
CAS
PubMed Central
Google Scholar
Katoh K, Asimenos G, Toh H: Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol. 2009, 537: 39-64. 10.1007/978-1-59745-251-9_3.
Article
PubMed
CAS
Google Scholar
Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, 17: 540-552.
Article
PubMed
CAS
Google Scholar
Bryant D, Moulton V: Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol. 2004, 21: 255-265.
Article
PubMed
CAS
Google Scholar
Huson DH, Bryant D: Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006, 23: 254-267.
Article
PubMed
CAS
Google Scholar
Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH: CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 2002, 30: 281-283. 10.1093/nar/30.1.281.
Article
PubMed
CAS
PubMed Central
Google Scholar
Cvetkovic A, Menon AL, Thorgersen MP, Scott JW, Poole FL, Jenney FE, Lancaster WA, Praissman JL, Shanmukh S, Vaccaro BJ, Trauger SA, Kalisiak E, Apon JV, Siuzdak G, Yannone SM, Tainer JA, Adams MW: Microbial metalloproteomes are largely uncharacterized. Nature. 2010, 466: 779-782. 10.1038/nature09265.
Article
PubMed
CAS
Google Scholar
Vernikos GS, Parkhill J: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics. 2006, 22: 2196-2203. 10.1093/bioinformatics/btl369.
Article
PubMed
CAS
Google Scholar
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673.
Article
PubMed
CAS
PubMed Central
Google Scholar
Loytynoja A, Goldman N: An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci USA. 2005, 102: 10557-10562. 10.1073/pnas.0409137102.
Article
PubMed
PubMed Central
CAS
Google Scholar
R Development Core Team: R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2010, [http://www.R-project.org/]
Google Scholar
Ren S, Higashi H, Lu H, Azuma T, Hatakeyama M: Structural basis and functional consequence of Helicobacter pylori CagA multimerization in cells. J Biol Chem. 2006, 281: 32344-32352. 10.1074/jbc.M606172200.
Article
PubMed
CAS
Google Scholar
Devi SH, Taylor TD, Avasthi TS, Kondo S, Suzuki Y, Megraud F, Ahmed N: Genome of Helicobacter pylori strain 908. J Bacteriol. 2010, 192: 6488-6489. 10.1128/JB.01110-10.
Article
PubMed
CAS
PubMed Central
Google Scholar
Xia Y, Yamaoka Y, Zhu Q, Matha I, Gao X: A comprehensive sequence and disease correlation analyses for the C-terminal region of CagA protein of Helicobacter pylori. PLoS One. 2009, 4: e7736-10.1371/journal.pone.0007736.
Article
PubMed
PubMed Central
CAS
Google Scholar
van Doorn LJ, Figueiredo C, Rossau R, Jannes G, van Asbroek M, Sousa JC, Carneiro F, Quint WG: Typing of Helicobacter pylori vacA gene and detection of cagA gene by PCR and reverse hybridization. J Clin Microbiol. 1998, 36: 1271-1276.
PubMed
CAS
PubMed Central
Google Scholar
Rhead JL, Letley DP, Mohammadi M, Hussein N, Mohagheghi MA, Eshagh Hosseini M, Atherton JC: A new Helicobacter pylori vacuolating cytotoxin determinant, the intermediate region, is associated with gastric cancer. Gastroenterology. 2007, 133: 926-936. 10.1053/j.gastro.2007.06.056.
Article
PubMed
CAS
Google Scholar
McClain MS, Shaffer CL, Israel DA, Peek RM, Cover TL: Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer. BMC Genomics. 2009, 10: 3-10.1186/1471-2164-10-3.
Article
PubMed
PubMed Central
CAS
Google Scholar
Xie W, Zhou C, Huang RH: Structure of tRNA dimethylallyltransferase: RNA modification through a channel. J Mol Biol. 2007, 367: 872-881. 10.1016/j.jmb.2007.01.048.
Article
PubMed
CAS
PubMed Central
Google Scholar
Blokesch M, Albracht SP, Matzanke BF, Drapal NM, Jacobi A, Bock A: The complex between hydrogenase-maturation proteins HypC and HypD is an intermediate in the supply of cyanide to the active site iron of [NiFe]-hydrogenases. J Mol Biol. 2004, 344: 155-167. 10.1016/j.jmb.2004.09.040.
Article
PubMed
CAS
Google Scholar
Blokesch M, Bock A: Properties of the [NiFe]-hydrogenase maturation protein HypD. FEBS Lett. 2006, 580: 4065-4068. 10.1016/j.febslet.2006.06.045.
Article
PubMed
CAS
Google Scholar
Comments
View archived comments (2)