Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs

Abstract

Integrating and conjugative elements (ICEs) are one of the three principal types of self-transmissible mobile genetic elements in bacteria. ICEs, like plasmids, transfer via conjugation; but unlike plasmids and similar to many phages, these elements integrate into and replicate along with the host chromosome. Members of the SXT/R391 family of ICEs have been isolated from several species of gram-negative bacteria, including Vibrio cholerae, the cause of cholera, where they have been important vectors for disseminating genes conferring resistance to antibiotics. Here we developed a plasmid-based system to capture and isolate SXT/R391 ICEs for sequencing. Comparative analyses of the genomes of 13 SXT/R391 ICEs derived from diverse hosts and locations revealed that they contain 52 perfectly syntenic and nearly identical core genes that serve as a scaffold capable of mobilizing an array of variable DNA. Furthermore, selection pressure to maintain ICE mobility appears to have restricted insertions of variable DNA into intergenic sites that do not interrupt core functions. The variable genes confer diverse element-specific phenotypes, such as resistance to antibiotics. Functional analysis of a set of deletion mutants revealed that less than half of the conserved core genes are required for ICE mobility; the functions of most of the dispensable core genes are unknown. Several lines of evidence suggest that there has been extensive recombination between SXT/R391 ICEs, resulting in re-assortment of their respective variable gene content. Furthermore, our analyses suggest that there may be a network of phylogenetic relationships among sequences found in all types of mobile genetic elements.

Author Summary

Integrative and conjugative elements (ICEs) are a class of mobile genetic elements that are key mediators of horizontal gene flow in bacteria. These elements integrate into the host chromosome, yet are able to excise and transfer via conjugation. Our understanding of ICE evolution is rudimentary. Here, we developed a method to capture ICEs on plasmids, thus facilitating their sequencing. Comparative analyses of the DNA sequences of ICEs from the same family revealed that they have an identical genetic structure consisting of syntenous, highly conserved core genes that are interrupted by clusters of diverse variable genes. Unexpectedly, many genes in the core backbone proved non-essential for ICE transfer. Comparisons of the variable gene content in the ICEs analyzed revealed that these elements are mosaics whose genomes have been shaped by inter–ICE recombination. Finally, our work suggests that ICEs contribute to a larger gene pool that connects all types of mobile elements.