High-Throughput Genomic and Proteomic Interpretation of Gene Duplication in Vibrio Cholera Genomes: An in Silico Study Publisher



Noori Goodarzi N¹ ; Badmasti F^{2, 3} ; Haririzadeh Jouriani F² ; Fereshteh S²
Source: Informatics in Medicine Unlocked Published:2023

Abstract

Background: Vibrio cholerae leads to severe acute watery diarrhea with a high mortality rate; owing to several virulence factors, especially the cholera toxin. Generally, gene duplication is a major evolutionary process that affects the environmental adaptation of bacteria. In this study, we aimed to investigate the repetitive virulence factors in V. cholera genomes. Method: Totally, 1530 genomes were collected and the possible duplication of 25 known virulence factors was assessed. Next, the genomes carrying duplicated cholera toxins (e.g. ctxA and ctxB) were further analyzed for the identification of novel repetitive virulence factors. All duplicated potential virulence proteins were classified based on clusters of orthologous groups (COGs) and their functions in different pathways were assessed. Results: Genome-wide analysis showed eight repetitive known virulence factors including rstA, ctxA, ctxB, zot, ace, espA, VC_RS09110, and mshA in V. cholerae genomes. It seems that the majority of the duplicated virulence factors are encoded on the CTXφ such as cholera toxin. Interestingly, our analysis revealed that fourteen genomes had simultaneously two copy numbers of ctxA and ctxB. The proteome of these strains harbored some repetitive proteins that resembled virulence factors of other bacteria. These duplicated proteins were mainly involved in replication, transcription, metabolism, and pathogenesis including Elongation factor Tu, Transketolase, Methyl-accepting chemotaxis protein, GNAT family N-acetyltransferases, cGAMP-activated phospholipase of Vibrio (CapV), HigA, and Helix-turn-helix transcriptional regulator. Conclusion: Surprisingly, a considerable number of duplicated genes have essential roles in the virulence and pathogenesis of V. cholerae. Moreover, it seems that novel duplicated genes had different roles in cellular processes or metabolic pathways. © 2023 The Authors