sRNA-dependent control of curli biosynthesis in Escherichia coli: McaS directs endonucleolytic cleavage of csgD mRNA

Production of curli, extracellular protein structures important for Escherichia coli biofilm formation, is governed by a highly complex regulatory mechanism that integrates multiple environmental signals through the involvement of numerous proteins and small non-coding RNAs (sRNAs). No less than seven sRNAs (McaS, RprA, GcvB, RydC, RybB, OmrA and OmrB) are known to repress the expression of the curli activator CsgD. Many of the sRNAs repress CsgD production by binding to the csgD mRNA at sites far upstream of the ribosomal binding site. The precise mechanism behind sRNA-mediated regulation of CsgD synthesis is largely unknown. In this study, we identify a conserved A/U-rich region in the csgD mRNA 5' untranslated region, which is cleaved upon binding of the small RNAs, McaS, RprA or GcvB, to sites located more than 30 nucleotides downstream. Mutational analysis shows that the A/U-rich region as well as an adjacent stem-loop structure are required for McaS-stimulated degradation, also serving as a binding platform for the RNA chaperone Hfq. Prevention of McaS-activated cleavage completely relieves repression, suggesting that endoribonucleolytic cleavage of csgD mRNA is the primary regulatory effect exerted by McaS. Moreover, we find that McaS-mediated degradation of the csgD 5' untranslated region requires RNase E.