Small RNA promotes negative feedback of the master virulence regulator PhoP by repressing the PhoQ sensor enhancer UgtL in acidic pH.

Signal transduction allows bacterial pathogens to sense the host environment and regulate gene expression accordingly for adaptation and survival. While the success of infection largely depends on the timely induction of virulence genes, the activity of the regulatory pathways controlling their expression must be tightly regulated for pathogens to cause disease. Here, we establish that a small RNA (sRNA) promotes the negative feedback control of a master virulence regulator in Salmonella enterica serovar Typhimurium (S. Typhimurium) by repressing a signaling protein essential for its induction in response to an intracellular cue. We show that the virulence regulatory PhoP/PhoQ pathway is inhibited by the PhoP-activated sRNA PinT in mildly acidic pH, an infection-relevant condition encountered by S. Typhimurium inside macrophages. PinT directly represses the translation of ugtL mRNA, which encodes the PhoP activator UgtL. This negative feedback regulation reduces PhoP activity, thereby decreasing the expression of PhoP-activated virulence genes like pagC. PinT-mediated repression of ugtL is predicted to be conserved in Salmonella enterica, but not in the nonpathogenic species Salmonella bongori, thus suggesting that the regulation is relevant for virulence. Our findings uncover how pathogens achieve proper levels of induction of their virulence programs through the post-transcriptional negative feedback regulation of factors enhancing the signaling activity of virulence pathways. IMPORTANCE: To cause disease, pathogens must express their virulence genes at the right time and in proper levels. Here, we establish that a small RNA (sRNA) restricts the activation of a regulator critical for the virulence of Salmonella enterica serovar Typhimurium (S. Typhimurium). We show that the sRNA PinT inhibits the activity of the master virulence regulator PhoP by repressing its activator UgtL through a direct interaction with ugtL mRNA. This regulation reduces the expression of PhoP-activated genes. Because PhoP activates PinT and UgtL, the three regulators form a negative feedback loop. That the PinT-mediated repression of ugtL is predicted to occur in Salmonella enterica but not in the nonpathogenic species S. bongori suggests it may be a key virulence determinant. Our results unveil a novel layer of fine-tuning of PhoP activity ensuring that S. Typhimurium induces the proper level of its virulence program in response to an infection-relevant stress condition.