Porin biogenesis activates the sigma(E) response in Salmonella hfq mutants.

In Salmonella enterica, loss of RNA chaperon Hfq promotes proteolytic cleavage of anti-sigma(E) factor RseA leading to the constitutive induction of the sigma(E)-dependent envelope stress response. Seeking to identify the source of the inducing signal, in the present study we measured RseA cleavage and sigma(E)-dependent transcription in strains lacking relevant outer membrane protein (omp) genes. We found removal of the main Salmonella porin, OmpD, to markedly reduce sigma(E) activation in hfq mutant cells. Subsequent removal of LamB and of OmpC further attenuated the response, indicating that different OMPs collectively contribute to the sigma(E)-activated phenotype. Thus, loss of Hfq-mediated regulation might cause unfolded OMPs to accumulate in the periplasm, triggering the sigma(E) response. These findings corroborate the role of Hfq protein as a pleiotropic regulator of OMP biogenesis in Gram-negative bacteria.

Loss of Hfq activates the sigmaE-dependent envelope stress response in Salmonella enterica.

Ubiquitous RNA-binding protein Hfq mediates the regulatory activity of many small RNAs (sRNAs) in bacteria. To identify potential targets for Hfq-mediated regulation in Salmonella, we searched for lacZ translational fusions whose activity varied in the presence or absence of Hfq. Fusions downregulated by Hfq were more common than fusions showing the opposite response. Surprisingly, in a subset of isolates from the major class, the higher activity in the absence of Hfq was due to transcriptional activation by the alternative sigma factor RpoE (sigmaE). Activation of the sigmaE regulon normally results from envelope stress conditions that elicit proteolytic cleavage of the anti-sigmaE factor RseA. Using an epitope tagged variant of RseA, we found that RseA is cleaved at an increased rate in a strain lacking Hfq. This cleavage was dependent on the DegS protease and could be completely prevented upon expressing the hfq gene from an inducible promoter. Thus, loss of Hfq function appears to affect envelope biogenesis in a way that mimics a stress condition and thereby induces the sigmaE response constitutively. In a RseA mutant, activation of the sigmaE response causes Hfq-dependent downregulation of outer membrane protein (OMP) genes including lamB, ompA, ompC and ompF. For ompA, downregulation results in part from sigmaE-dependent accumulation of MicA (SraD), a small RNA recently shown to downregulate ompA transcript levels in stationary phase. We show that the micA gene is under sigmaE control, and that DegS-mediated sigmaE release is required for the accumulation of MicA RNA upon entry into stationary phase. A similar mechanism involving additional, still unidentified, sRNAs, might underlie the growth phase-dependent regulation of other OMP mRNAs.