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An In Silico Approach for Identification of the Pathogenic Species, Helicobacter pylori and Its Relatives.

ABSTRACT: Helicobacter is an economically important genus within the phylum Proteobacteria and include many species which cause many diseases in humans. With the conventional methods, it is difficult to identify them easily due to the high genetic similarity among its species. In the present study, 361 16S rRNA (rrs) gene sequences belonging to 45 species of genus Helicobacter were analyzed. Out of these, 264 sequences of 10 clinically relevant species (including Helicobacter pylori) were used. rrs gene sequences were analyzed to obtain a phylogenetic framework tree, in silico restriction enzyme analysis and species-specific conserved motifs. Protein sequences of another housekeeping gene, hsp60 were also subjected to phylogenetic analysis to supplement the data obtained using rrs sequences. Using these approaches, six out of ten species (including H. pylori) were easily segregated, whereas four species namely H. bilis, H. cinaedi, H. felis and Candidatus H. heilmannii were found to be heterogeneous. The above approaches have also helped in segregating unclassified sequences, thus proving them as an easy diagnostic method for identifying members of genus Helicobacter up to species level.

SUBMITTER: Puri A

PROVIDER: S-EPMC4920758 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

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An In Silico Approach for Identification of the Pathogenic Species, Helicobacter pylori and Its Relatives.

Puri Ayush A Rai Arshiya A Dhanaraj P S PS Lal Rup R Patel Dev Dutt DD Kaicker Anju A Verma Mansi M

Indian journal of microbiology 20160430 3

Helicobacter is an economically important genus within the phylum Proteobacteria and include many species which cause many diseases in humans. With the conventional methods, it is difficult to identify them easily due to the high genetic similarity among its species. In the present study, 361 16S rRNA (rrs) gene sequences belonging to 45 species of genus Helicobacter were analyzed. Out of these, 264 sequences of 10 clinically relevant species (including Helicobacter pylori) were used. rrs gene s ...[more]

PMID: 27407291

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Project description:BACKGROUND:Helicobacter pylori is associated with inflammation of different areas, such as the duodenum and stomach, causing gastritis and gastric ulcers leading to lymphoma and cancer. Pathogenic islands are a type of clustered mobile elements ranging from 10-200 Kb contributing to the virulence of the respective pathogen coding for one or more virulence factors. Virulence factors are molecules expressed and secreted by pathogen and are responsible for causing disease in the host. Bacterial genes/virulence factors of the pathogenic islands represent a promising source for identifying novel drug targets. OBJECTIVE:The study aimed at identifying novel drug targets from pathogenic islands in H. pylori. MATERIAL & METHODS:The genome of 23 H. pylori strains were screened for pathogenic islands and bacterial genes/virulence factors to identify drug targets. Protein-protein interactions of drug targets were predicted for identifying interacting partners. Further, host-pathogen interactions of interacting partners were predicted to identify important molecules which are closely associated with gastric cancer. RESULTS:Screening the genome of 23 H. pylori strains revealed 642 bacterial genes/virulence factors in 31 pathogenic islands. Further analysis identified 101 genes which were non-homologous to human and essential for the survival of the pathogen, among them 31 are potential drug targets. Protein-protein interactions for 31 drug targets predicted 609 interacting partners. Predicted interacting partners were further subjected to host-pathogen interactions leading to identification of important molecules like TNF receptor associated factor 6, (TRAF6) and MAPKKK7 which are closely associated with gastric cancer. CONCLUSION:These provocative studies enabled us to identify important molecules in H. pylori and their counter interacting molecules in the host leading to gastric cancer and also a pool of novel drug targets for therapeutic intervention of gastric cancer.

Dataset Information

An In Silico Approach for Identification of the Pathogenic Species, Helicobacter pylori and Its Relatives.

Publications

An In Silico Approach for Identification of the Pathogenic Species, Helicobacter pylori and Its Relatives.

Similar Datasets

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