A small RNA downregulates LamB maltoporin in Salmonella

In Escherichia coli and Salmonella enterica, activation of sigma(E)-dependent envelope stress response leads to the abrupt decline in the synthesis of all major outer membrane proteins (OMPs). Recent studies found that two sigma(E)-controlled small RNAs (sRNAs), MicA and RybB, downregulate a number of OMPs. While RybB targets several different mRNAs, including ompC and ompD, MicA was up to date thought to act solely on ompA. Here we present evidence showing that MicA downregulates a second Salmonella OMP: LamB maltoporine. In strains overexpressing sigma(E), MicA accumulation leads to a significant decrease in LamB protein and mRNA levels, as well as a reduction in beta-galactosidase activity in a strain carrying a lamB-lacZ translational fusion. The latter findings provided the basis for a genetic screen that allowed isolating point mutations in the micA gene and in its sigma(E) promoter. All alleles obtained displayed their altered regulatory phenotype from their natural chromosomal location. LamB downregulation by MicA requires a functional Hfq protein. Besides this role, confined to sigma(E)-activated conditions, we show that loss of Hfq results in the accumulation of a lamB-malM dimeric precursor and of malM mRNA during unchallenged growth. This suggests that Hfq normally intervenes in a mechanism that uncouples expression of the malK-lamB-malM operon, causing the distal portion of the transcript to be clipped off and degraded.