{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T09:52:09Z","timestamp":1785232329452,"version":"3.55.0"},"reference-count":65,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2012,3,15]],"date-time":"2012-03-15T00:00:00Z","timestamp":1331769600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Bacteriol"],"published-print":{"date-parts":[[2012,3,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Chronic infection with\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Helicobacter pylori<\/jats:named-content>\n            strains expressing the bacterial oncoprotein CagA confers an increased risk of gastric cancer. While much is known about the ancestry and molecular evolution of Western, East Asian, and Amerindian\n            <jats:italic>cagA<\/jats:italic>\n            sequences, relatively little is understood about a fourth group, known as \u201cJ-Western,\u201d which has been detected mainly in strains from Okinawa, Japan. We show here that J-Western\n            <jats:italic>cagA<\/jats:italic>\n            sequences have a more widespread global distribution than previously recognized, occur in strains with multiple different ancestral origins (based on multilocus sequence typing [MLST] analysis), and did not arise recently. As shown by comparisons of Western and J-Western forms of CagA, there are 45 fixed or nearly fixed amino acid differences, and J-Western forms contain a unique 4-amino-acid insertion. The mean nucleotide diversity of synonymous sites (\u03c0\n            <jats:sub>s<\/jats:sub>\n            ) is slightly lower in the J-Western group than in the Western and East Asian groups (0.066, 0.086, and 0.083, respectively), which suggests that the three groups have comparable, but not equivalent, effective population sizes. The reduced \u03c0\n            <jats:sub>s<\/jats:sub>\n            of the J-Western group is attributable to ancestral recombination events within the 5\u2032 region of\n            <jats:italic>cagA.<\/jats:italic>\n            Population genetic analyses suggest that within the\n            <jats:italic>cagA<\/jats:italic>\n            region encoding EPIYA motifs, the East Asian group underwent a marked reduction in effective population size compared to the Western and J-Western groups, in association with positive selection. Finally, we show that J-Western\n            <jats:italic>cagA<\/jats:italic>\n            sequences are found mainly in strains producing m2 forms of the secreted VacA toxin and propose that these functionally interacting proteins coevolved to optimize the gastric colonization capacity of\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">H. pylori<\/jats:named-content>\n            .\n          <\/jats:p>","DOI":"10.1128\/jb.06340-11","type":"journal-article","created":{"date-parts":[[2012,1,14]],"date-time":"2012-01-14T05:42:39Z","timestamp":1326519759000},"page":"1593-1604","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":22,"title":["J-Western Forms of Helicobacter pylori cagA Constitute a Distinct Phylogenetic Group with a Widespread Geographic Distribution"],"prefix":"10.1128","volume":"194","author":[{"given":"Stacy S.","family":"Duncan","sequence":"first","affiliation":[{"name":"Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pieter L.","family":"Valk","sequence":"additional","affiliation":[{"name":"Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carrie L.","family":"Shaffer","sequence":"additional","affiliation":[{"name":"Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seth R.","family":"Bordenstein","sequence":"additional","affiliation":[{"name":"Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA"},{"name":"Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy L.","family":"Cover","sequence":"additional","affiliation":[{"name":"Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA"},{"name":"Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA"},{"name":"Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti263"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1081919"},{"key":"e_1_3_3_4_2","doi-asserted-by":"crossref","first-page":"1062","DOI":"10.1099\/jmm.0.2008\/001818-0","article-title":"Differences in Helicobacter pylori CagA tyrosine phosphorylation motif patterns between western and East Asian strains, and influences on interleukin-8 secretion","volume":"57","author":"Argent RH","year":"2008","unstructured":"ArgentRHHaleJLEl-OmarEMAthertonJC. 2008. 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