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 gastroduodenal disorders, including gastric cancer and peptic ulcer disease. The virulence and pathogenicity peculiar to H. pylori have 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 the relationship between African-generated vacA genes with genes from other regions with high gastrointestinal disorder prevalence. Nucleotide sequences of 228 vacA genes of H. pylori were retrieved from the National Centre for Biotechnology Information (NCBI). Pairwise and multiple sequence alignment was carried out on 228 vacA nucleotide sequences using MEGA 10.2.4 software to identify regions of similarities. Phylogenetic analysis, also using MEGA software, was carried out to establish the evolutionary relationships between all extracted sequences. Analysis for conserved domain was also performed on the NCBI Conserved Domain Database to better understand each geographical data's properties. After the evolutionary analysis, it was observed that South African vacA genes were more closely related to genes from Mexico, Italy, Spain, and Germany—with Italy having the highest occurring relationship. Conserved domain analysis showed 2 highly conserved 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 the degree of domain conservation across each gene. It also shows the need for a holistic assessment of the virulent genes in H. pylori.