RNA-mediated adaptation to a new chromosome

Approximately 10% of bacterial species possess more than one main chromosome, an architecture named multipartite genome. Such arrangement enables quicker adaptation to new environmental niches. Vibrio cholerae, for example, has two chromosomes: Chr1 and Chr2. While genes encoding for essential cell functions and pathogenicity are located on Chr1, Chr2 encodes genes involved in specialized metabolism and pathogenicity. A novel giant replicon (named hereafter Chr3) has been found in a recent isolate of Vibrio cholerae. Despite being present in various Vibrionaceae, the function of Chr3 remains elusive.

To shed light on the impact of Chr3 on its host, we performed transcriptional and post-transcriptional analysis. Comparative transcriptomics showed that Chr3 is conditionally expressed, influencing Chr1 and Chr2 gene expression mostly in the exponential growth phase. Global analysis of RNA duplex formation using RIL-Seq (RNA-interaction-by-ligation-and-sequencing) revealed a vast network of Hfq-assisted interactions between Chr3 and the other two chromosomes. In combination with RIP-Seq (RNA immunoprecipitation and sequencing) analysis, we found 74 sRNAs (small regulatory RNA) encoded on Chr3. Whilst the majority of the newly annotated sRNAs target genes encoded on Chr3, Vcr313 targets genes on primary chromosomes involved in tRNA metabolism. We further show that Chr3 impacts quorum sensing, possesses a functional typeI-F CRISPR-Cas, and contains a more specialized Hfq-like RNA-binding protein. Overall, our data shows ample interactions between all three chromosomes suggesting they are equally involved in post transcriptional gene control. Moreover, the new set of advantageous genes encoded on Chr3 makes it an important entity to expand the adaptation capacities of Vibrio cholerae.