Genome Engineering in Vibrio cholerae: A Feasible Approach to Address Biological Issues

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Abstract
Although bacteria with multipartite genomes are prevalent, our knowledge of the mechanisms maintaining their genome is very limited, and much remains to be learned about the structural and functional interrelationships of multiple chromosomes. Owing to its bi-chromosomal genome architecture and its importance in public health, Vibrio cholerae, the causative agent of cholera, has become a preferred model to study bacteria with multipartite genomes. However, most in vivo studies in V. cholerae have been hampered by its genome architecture, as it is difficult to give phenotypes to a specific chromosome. This difficulty was surmounted using a unique and powerful strategy based on massive rearrangement of prokaryotic genomes. We developed a site-specific recombination-based engineering tool, which allows targeted, oriented, and reciprocal DNA exchanges. Using this genetic tool, we obtained a panel of V. cholerae mutants with various genome configurations: one with a single chromosome, one with two chromosomes of equal size, and one with both chromosomes controlled by identical origins. We used these synthetic strains to address several biological questions—the specific case of the essentiality of Dam methylation in V. cholerae and the general question concerning bacteria carrying circular chromosomes—by looking at the effect of chromosome size on topological issues. In this article, we show that Dam, RctB, and ParA2/ParB2 are strictly essential for chrII origin maintenance, and we formally demonstrate that the formation of chromosome dimers increases exponentially with chromosome size. Vibrio cholerae, the causative agent of cholera in humans, has two circular chromosomes of uneven size, each with distinct maintenance requirements. This is in contrast to classical, Escherichia coli–centric bacterial models of a single chromosome. In this study, we took advantage of V. cholerae's atypical genome structure to address important biological issues related to the maintenance of multipartite genomes. We further used V. cholerae to determine how genome architecture and genetic organization affects the odds of topological difficulties arising during replication. Our approach consisted of performing massive genome rearrangements to create various synthetic mutants of V. cholerae with nearly identical genetic backgrounds. We created mutants of V. cholerae with a single chromosome, with two chromosomes of equal size, or with identical origins of replication. To do so, we developed a genetic engineering tool based on the multiplexing of two site-specific recombination systems to allow efficient and directional manipulations of any DNA segment. In this study, we show that Dam, RctB, and ParA2/ParB2 are only essential for chrII origin maintenance, and we demonstrate that the odds of forming chromosome dimers exponentially increases with chromosome size.

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