Molecular insights into the genome dynamics and interactions between core and acquired genomes of <i>Vibrio cholerae</i>.

Abstract

Bacterial species are hosts to horizontally acquired mobile genetic elements (MGEs), which encode virulence, toxin, antimicrobial resistance, and other metabolic functions. The bipartite genome of <i>Vibrio cholerae</i> harbors sporadic and conserved MGEs that contribute in the disease development and survival of the pathogens. For a comprehensive understanding of dynamics of MGEs in the bacterial genome, we engineered the genome of <i>V. cholerae</i> and examined in vitro and in vivo stability of genomic islands (GIs), integrative conjugative elements (ICEs), and prophages. Recombinant vectors carrying the integration module of these GIs, ICE and CTXΦ, helped us to understand the efficiency of integrations of MGEs in the <i>V. cholerae</i> chromosome. We have deleted more than 250 acquired genes from 6 different loci in the <i>V. cholerae</i> chromosome and showed contribution of CTX prophage in the essentiality of SOS response master regulator LexA, which is otherwise not essential for viability in other bacteria, including <i>Escherichia coli</i> In addition, we observed that the core genome-encoded RecA helps CTXΦ to bypass <i>V. cholerae</i> immunity and allow it to replicate in the host bacterium in the presence of similar prophage in the chromosome. Finally, our proteomics analysis reveals the importance of MGEs in modulating the levels of cellular proteome. This study engineered the genome of <i>V. cholerae</i> to remove all of the GIs, ICEs, and prophages and revealed important interactions between core and acquired genomes.