A 3UTR-derived small RNA modulates the life-cycle of the cholera toxin-encoding filamentous phage, CTXphi

Bacteriophages (phages) are well known to be one of the major driving forces in bacterial evolution. This also applies to virulent microorganisms, such as the major human pathogen Vibrio cholerae, whose pathogenic potential and epidemic proliferation largely depends on the interaction with environmental phages. Specifically, integration of the CTX{phi} phage genome into the first chromosome of V. cholerae also introduced the ctxAB genes, encoding the primary toxin responsible for the severe acute diarrheal disease, cholera. Whereas the mechanisms underlying CTX{phi}-associated horizontal gene transfer and transcriptional control of the ctxAB genes have been intensively studied over the past years, post-transcriptional regulation affecting the CTX{phi} life-cycle has not been documented. Here, we report the discovery and characterization of the CisR small RNA (sRNA) that is produced from the 3UTR (untranslated region) of the prtV gene and inhibits the expression of the CTX{phi}-encoded cep mRNA. CisR-mediated repression of cep involves Hfq-assisted base-pairing of the two transcripts and results in reduced CTX{phi} production under stress conditions. We further demonstrate that transcription of prtV-cisR requires both the master quorum-sensing regulator HapR and CRP, a global regulator of carbon metabolism. Taken together, our work provides evidence that V. cholerae employs sRNA-mediated post-transcriptional gene regulation to coordinate CTX{phi} activation with both cell density and nutrient availability. SIGNIFICANCE STATEMENTThe integration of the CTX{phi} phage genome, which carries the ctxAB toxin genes, is essential for cholera pathogenesis in humans. While transcriptional control of CTX{phi} and ctxAB has been well-studied, post-transcriptional mechanisms remain unexplored. Here, we identify and characterize CisR, a small RNA derived from the 3' untranslated region of prtV, which inhibits the CTX{phi}-encoded cep mRNA through Hfq-dependent base-pairing. CisR-mediated regulation limits phage production under stress conditions and is co-regulated by the quorum-sensing factor HapR and the metabolic regulator CRP. Our findings reveal a new RNA-based mechanism linking CTX{phi} phage activation to cell density and nutrient status of V. cholerae.