Competition among small RNAs in Escherichia coli

Many small RNAs (sRNAs) in bacteria are induced during adaptation to environmental stress and regulate gene expression through direct base pairing with mRNA targets. In E. coli, this family of sRNAs requires Hfq, an RNA binding protein. Hfq binds to and stabilizes sRNAs in vivo and stimulates base pairing in vitro. We asked if Hfq is limiting by inducing one sRNA and monitoring the levels and Hfq binding of others. We also examined the ability of one induced sRNA to interfere with regulation of specific targets by other sRNAs. The sRNA OxyS has previously been shown to negatively regulate RpoS; we found a decrease in accumulation of DsrA, an sRNA that positively regulates RpoS, as well as decreased levels and decreased Hfq binding for other sRNAs after OxyS induction. Increased expression of Hfq reduced or abolished the effect of OxyS in reducing other sRNAs. Similarly, high‐level expression of some but not all sRNAs interfered with negative regulation of a number of tested targets. Therefore, Hfq is limiting for regulation by sRNAs and there is competition among small RNAs for Hfq; some sRNAs compete more effectively than others. This work suggests that, under conditions leading to induction of an sRNA, there will be a hierarchy of competition among sRNAs present in the cell, so that induction of one sRNA may negatively impinge on the action of other sRNAs, creating a complex response to different stresses.