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Elevated levels of adaption in Helicobacter pylori genomes from Japan; a link to higher incidences of gastric cancer?

Soto-Girón MJ, Ospina OE, Massey SE - Evol Med Public Health (2015)

Bottom Line: H.pylori is host dependent and has been carried with human populations around the world after their departure from Africa.Of the identified genes which were annotated, 38% possessed homologs associated with pathogenicity and / or host adaptation, consistent with their involvement in a coevolutionary 'arms race' with the host.Given the efficacy of identifying host interaction factors de novo, in the absence of functionally annotated homologs our evolutionary approach may have value in identifying novel genes which H.pylori employs to interact with the human gut environment.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Lab, Department of Biology, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico.

No MeSH data available.


Related in: MedlinePlus

Gene Ontology enrichment of genes under inferred positive selection. Functional categories for all genes with Ka/Ks > 1 of the pairwise comparisons from Europe (B38 vs G27 and HPAG1 vs 26695) and Japan (F16 vs F57 and 35a vs 83) pairwise comparisons, using the Gene Ontology Database and Blast2Go, described in Methods. The numbers displayed on the y-axis represent the relative enrichment in terms of the proportion of positively selected genes in each GO category compared to the total number present in that category in the genome
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eov005-F3: Gene Ontology enrichment of genes under inferred positive selection. Functional categories for all genes with Ka/Ks > 1 of the pairwise comparisons from Europe (B38 vs G27 and HPAG1 vs 26695) and Japan (F16 vs F57 and 35a vs 83) pairwise comparisons, using the Gene Ontology Database and Blast2Go, described in Methods. The numbers displayed on the y-axis represent the relative enrichment in terms of the proportion of positively selected genes in each GO category compared to the total number present in that category in the genome

Mentions: Positive selection was inferred to be acting on a number of protein coding genes from all H.pylori pairwise comparisons. The Japanese strain 83 presented the highest number of genes with Ka/Ks > 1 (34 genes), while the European strains B38 and 26695 had the least, with 16 genes each. Genes inferred as being under positive selection were significantly elevated in Japanese strains compared to European strains (P < 0.05, two-tailed Mann–Whitney test). Thus, the numbers of genes inferred as being under positive selection in the H.pylori strains may vary by a factor of 2. Strain B38 possesses a phage present in the genome [58], but none of the genes inferred as being under positive selection were phage associated. GO enrichment shows that transport proteins are particularly highly represented, reflecting a major role for membrane proteins in adaptation (Fig. 3).Figure 3.


Elevated levels of adaption in Helicobacter pylori genomes from Japan; a link to higher incidences of gastric cancer?

Soto-Girón MJ, Ospina OE, Massey SE - Evol Med Public Health (2015)

Gene Ontology enrichment of genes under inferred positive selection. Functional categories for all genes with Ka/Ks > 1 of the pairwise comparisons from Europe (B38 vs G27 and HPAG1 vs 26695) and Japan (F16 vs F57 and 35a vs 83) pairwise comparisons, using the Gene Ontology Database and Blast2Go, described in Methods. The numbers displayed on the y-axis represent the relative enrichment in terms of the proportion of positively selected genes in each GO category compared to the total number present in that category in the genome
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4419197&req=5

eov005-F3: Gene Ontology enrichment of genes under inferred positive selection. Functional categories for all genes with Ka/Ks > 1 of the pairwise comparisons from Europe (B38 vs G27 and HPAG1 vs 26695) and Japan (F16 vs F57 and 35a vs 83) pairwise comparisons, using the Gene Ontology Database and Blast2Go, described in Methods. The numbers displayed on the y-axis represent the relative enrichment in terms of the proportion of positively selected genes in each GO category compared to the total number present in that category in the genome
Mentions: Positive selection was inferred to be acting on a number of protein coding genes from all H.pylori pairwise comparisons. The Japanese strain 83 presented the highest number of genes with Ka/Ks > 1 (34 genes), while the European strains B38 and 26695 had the least, with 16 genes each. Genes inferred as being under positive selection were significantly elevated in Japanese strains compared to European strains (P < 0.05, two-tailed Mann–Whitney test). Thus, the numbers of genes inferred as being under positive selection in the H.pylori strains may vary by a factor of 2. Strain B38 possesses a phage present in the genome [58], but none of the genes inferred as being under positive selection were phage associated. GO enrichment shows that transport proteins are particularly highly represented, reflecting a major role for membrane proteins in adaptation (Fig. 3).Figure 3.

Bottom Line: H.pylori is host dependent and has been carried with human populations around the world after their departure from Africa.Of the identified genes which were annotated, 38% possessed homologs associated with pathogenicity and / or host adaptation, consistent with their involvement in a coevolutionary 'arms race' with the host.Given the efficacy of identifying host interaction factors de novo, in the absence of functionally annotated homologs our evolutionary approach may have value in identifying novel genes which H.pylori employs to interact with the human gut environment.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Lab, Department of Biology, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico.

No MeSH data available.


Related in: MedlinePlus