PMC:3091627 / 21558-24119 JSONTXT

{"project":"2_test","denotations":[{"id":"20537153-14742532-10781745","span":{"begin":337,"end":339},"obj":"14742532"},{"id":"20537153-9157493-10781746","span":{"begin":1678,"end":1680},"obj":"9157493"}],"text":"Specific properties associated with the genomes of strains belonging to the MALT lymphoma PAI minus cluster\nOf the 19 strains belonging to the MALT lymphoma PAI minus cluster, all 19 contained the vacAm2 allele; 16 exhibited an s2m2 genotype, indicating that they encode a non-functional cytotoxin, and three exhibited an s1m2 genotype [18]. We then investigated whether the properties found to be unique to strain B38 are shared by the strains belonging to the cluster of the MALT lymphoma PAI-minus cluster. The search for the presence of the HacII-like prophage was done through hybridization using internal fragments of HELPY1521, HELPY1525, and HELPY1526 as probes. Four of the 19 strains (21%, including B38) of the MALT lymphoma PAI minus cluster, contained HacII prophage-like sequences. By contrast, 1/24 (4%) strains isolated from patients with MALT lymphoma containing cagPAI, 2/33 (6%) strains from patients suffering from gastritis and 2/27 strains (7.4%) from those with duodenal ulcers contained HacII prophage-like sequences. Furthermore, the presence of the two adjacent HELPY0989 and HELPY0990 genes encoding a helicase and a serine kinase, respectively, not previously found in the other sequenced genomes as functional proteins were found in three of the 19 strains (16%) of the B38 cluster. These two genes were not detected in the other MALT lymphoma strains (cagPAI positive), nor within the 22 isolates associated with gastritis and peptic ulcers. Finally, three clustered conservative mutations in glmM (HELPY0072 - Ala332, Leu333), leading to the absence of amplification of the 294-bp internal fragment of the phosphoglucosamine mutase-encoding gene [36], were observed in five of the 19 MALT lymphoma PAI minus isolates (26%). However, these mutations were not found in any of the 120 clinical isolates of this study, nor were they found in more than 400 H. pylori isolates associated with gastritis, peptic ulcers or metaplasia that were tested with identical oligonucleotides (personal data). These conservative mutations may be indicative of a selective pressure to maintain these mutations, together with a property encoded by a gene present in close proximity to glmM, a property that has yet to be identified. Thus, although none of the unique properties of B38 were shared by all MALT strains of the cluster, characterizing a cagPAI minus isolate containing either glmM mutations or HELPY0989-0990 genes may be predictive of MALT lymphoma, as these two characteristics were found exclusively among the strains of this cluster."}