Down-regulation of porins by a small RNA bypasses the essentiality of the regulated intramembrane proteolysis protease RseP in Escherichia coli

Adaptation to extracytoplasmic stress in Escherichia coli depends on the activation of sigma(E), normally sequestered by the membrane protein RseA. sigma(E) is released in response to stress through the successive RseA cleavage by DegS and the RIP protease RseP. sigma(E) and proteases that free it from RseA are essential. We isolated a multicopy suppressor that alleviated RseP and DegS requirement. The suppressor encodes a novel small RNA, RseX. Its activity required the RNA-binding protein Hfq. We used the property that small RNAs are often involved in RNA-RNA interactions to capture RseX putative partners; ompA and ompC mRNA, which encode two major outer membrane proteins, were identified. RseX activity was shown to confer an Hfq-dependent coordinate OmpA and OmpC down-regulation. Because RseP is shown to be no longer essential in a strain lacking OmpA and OmpC, we conclude that RseP, which is required for normal sigma(E) activation, prevents toxicity due to the presence of two specific outer membrane proteins that are down-regulated by RseX.