PMC:3091627 / 16246-19428
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{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/3091627","sourcedb":"PMC","sourceid":"3091627","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3091627","text":"Comparative genomics and genome evolution\nWe then analyzed the genomic rearrangements through pair-wise genomic synteny comparisons between B38 and the eight published Helicobacteriaceae genomes. For five of the isolates (namely, 26695, J99, G27, P12, HPAG1), we confirmed the previously reported relative colinearity of the H.pylori genomes. This colinearity is mainly interrupted by insertion elements, the cagPAI, and genes encoding hypothetical proteins [33]. However, unexpectedly, conserved synteny highlighted an almost complete colinearity never described so far, between B38 and Shi470 (Figure 4). Shi470 is a clinical isolate from the gastric antrum of an Amerindian resident of a remote Amazonian village in Peru, and was thought to be related to strains from East Asia [RefSeq:NC_010698]. This unexpected absence of major genomic rearrangements between the two genomes prompted us to compare the genome of these two isolates more closely, as a way of better understanding H. pylori genome evolution. B38 lacks 174 Shi470 genes, of which 70 genes cluster in three insertion blocks: one corresponds to the well characterized cagPAI; another to a block of 33 CDSs, mainly remnants from a conjugative plasmid (presence of TraG, VirB11, toposiomerase I, ComB3, homologs of conjugal plasmid transfer system); and the third corresponds to a block that includes 7 CDSs encoding hypothetical proteins, as well as one CDS encoding an exodeoxyribonuclease subunit which is unique to the Shi 470 isolate.\nFigure 4 Synteny lineplot pair-wise analyses between B38 and the H. pylori strain 26695, J99, HPAG1, Shi470, P12, G27, Helicobacter hepaticus, or Helicobacter acinonychis. Conversely, loss of synteny was also due to the presence of 110 CDSs in B38 that were not present in Shi470. Forty-three of these CDSs appeared as clusters within eight loci. Twenty corresponded to ISHp609 (5 complete and conserved copies of ISHp609 each comprising orf1, orf2, ORFA and ORFB) [31], which interrupts HELPY0571, HELPY0700 (both encoding restriction/modification systems), HELPY0838 (encoding a putative Rad50 ATPase), HELPY1330 (encoding a putative glycosyl-transferase), and HELPY1529 (a HAC prophage II protein homolog). In addition to these five ISHp609 insertions, loss of synteny was also due to the presence of CDSs in four other loci: i) a cluster of seven genes (HELPY1520 to HELPY1525 and HEPLY1527, HELPY1528 to HELPY1533) encoding HacII prophage-like proteins similar to those found in H. acinonychis strain Sheeba [34]; however, the size of the prophage is much larger (32 CDS) in this species, suggesting that the prophage in B38 has been deleted, possibly following the insertion of one copy of ISHp609; ii) a cluster of six genes encoding hypothetical proteins of unknown function (HELPY0051 to HELPY0056); iii) a cluster of three CDSs that are absent in Shi470, HPAG1, J99, P12, and G127, but present in strain 26695, of which two encode alginate-O-acetylation proteins (HELPY0497-498); iv) a cluster of seven CDSs that encode a putative helicase (HELPY0989) and a putative serine kinase (HELPY0990), two functional proteins not found in all of the other sequenced strains.","divisions":[{"label":"title","span":{"begin":0,"end":41}},{"label":"p","span":{"begin":42,"end":1504}},{"label":"figure caption","span":{"begin":1505,"end":1677}},{"label":"p","span":{"begin":1515,"end":1677}}],"tracks":[{"project":"2_test","denotations":[{"id":"20537153-10682319-10781741","span":{"begin":459,"end":461},"obj":"10682319"},{"id":"20537153-15516563-10781742","span":{"begin":1972,"end":1974},"obj":"15516563"},{"id":"20537153-16789826-10781743","span":{"begin":2520,"end":2522},"obj":"16789826"}],"attributes":[{"subj":"20537153-10682319-10781741","pred":"source","obj":"2_test"},{"subj":"20537153-15516563-10781742","pred":"source","obj":"2_test"},{"subj":"20537153-16789826-10781743","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#e093ec","default":true}]}]}}