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The  Escherichia coli  RNA chaperone Hfq was discovered originally as an accessory factor of the phage Qβ replicase. More recent work suggested a role of Hfq in cellular physiology through its interaction with  ompA  mRNA and small RNAs (sRNAs), some of which are involved in translational regulation. Despite their stability under certain conditions,  E. coli  sRNAs contain putative RNase E recognition sites, that is, A/U-rich sequences and adjacent stem–loop structures. We show herein that an RNase E cleavage site coincides with the Hfq-binding site in the 5′-untranslated region of  E. coli ompA  mRNA as well as with that in the sRNA, DsrA. Likewise, Hfq protects RyhB RNA from in vitro cleavage by RNase E. These in vitro data are supported by the increased abundance of DsrA and RyhB sRNAs in an RNase E mutant strain as well as by their decreased stability in a  hfq  −  strain. It is commonly believed that the RNA chaperone Hfq facilitates or promotes the interaction between sRNAs and their mRNA targets. This study reveals another role for Hfq, that is, protection of sRNAs from endonucleolytic attack.

Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs