Outside of the human host the pathogen Vibrio cholerae is commonly found in aquatic environments as biofilms attached to chitinous surfaces, which serve as an environmental niche and as a food source. Chitin sensing induces various physiological changes through the activation of multiple genetic pathways, one of which is natural competence, a state during which bacteria are able to acquire exogenous DNA from the environment to be used for nutrition, horizontal gene transfer, and DNA repair. While there are various processes known to induce competence in V. cholerae, the regulatory process leading to competence are still not fully explored. One key regulator is the chitin-induced, Hfq-dependent small RNA (sRNA) TfoR, which activates tfoX mRNA, encoding the master regulator of competence in V. cholerae [1]. Usually regulatory sRNAs have multiple targets, yet for TfoR just a small number of partners have been identified [2], suggesting there might be more to uncover.

To better understand the regulatory role of TfoR in V. cholerae and its role in DNA uptake, we explored the global RNA-RNA network using RIL-seq (RNA-interaction-by-ligation-and-sequencing) approach under competence-inducing conditions to uncover new RNA-RNA interactions. Our RIL-seq results show dozens of new interacting partners, with TfoR occupying approximately 23% of all Hfq mediated interactions under chitin conditions. We have also confirmed many targets, which are related to carbon metabolism or transporters. Additionally, our results revealed TfoR is cleaved by RNase E producing two sRNA isoforms with apparently different regulatory functions.

References

[1] Yamamoto, S., et al., (2011). Identification of a chitin-induced small RNA that regulates translation of the tfoX gene, encoding a positive regulator of natural competence in Vibrio cholerae. Journal of bacteriology, 193(8), 1953-1965.

[2] Huber, M., et al., (2022). An RNA sponge controls quorum sensing dynamics and biofilm formation in Vibrio cholerae. Nature Communications, 13(1), 7585.