In Silico Comparative Analysis of Different vacA Genes of Helicobacter pylori

Abstract

Helicobacter pylori is a class I carcinogen responsible for 90% of gastrointestinal and gastroduodenaldisorders, including gastric cancer and peptic ulcer disease. The virulence and pathogenicity peculiar to H. pylorihave been associated with several genes, including cytotoxin associated gene (cagA), vacuolating cytotoxin A(vacA), outer inflammatory protein A (oipA), and duodenal ulcer promoting (dupA). This study explored therelationship between African-generated vacA genes with genes from other regions with high gastrointestinaldisorder prevalence. Nucleotide sequences of 228 vacA genes of H. pylori were retrieved from the NationalCentre for Biotechnology Information (NCBI). Pairwise and multiple sequence alignment was carried out on228 vacA nucleotide sequences using MEGA 10.2.4 software to identify regions of similarities. Phylogeneticanalysis, also using MEGA software, was carried out to establish the evolutionary relationships between allextracted sequences. Analysis for conserved domain was also performed on the NCBI Conserved DomainDatabase to better understand each geographical data's properties. After the evolutionary analysis, it wasobserved that South African vacA genes were more closely related to genes from Mexico, Italy, Spain, andGermany—with Italy having the highest occurring relationship. Conserved domain analysis showed 2 highlyconserved superfamilies, cl20029 and cl22877, and 2 protein family models, pfam02691 and pfam03797.The results demonstrate relatedness of vacA genes from the African region to the European region; Italy,Mexico, and Spain. The study shows the biogeographical diversity among vacA genes and emphasizes thedegree of domain conservation across each gene. It also shows the need for a holistic assessment of thevirulent genes in H. pylori.