Dynamic Competition for the Proximal RNA Binding Site of Hfq Drives Efficient Annealing of Small Noncoding RNA and mRNA

Abstract

Hfq, a bacterial RNA chaperone, stimulates specific RNA-RNA interactions by inducing RNA unwinding or RNA-RNA annealing. However, it is still unclear how Hfq can selectively achieve two completely opposite functions--annealing, and unwinding--depending on RNA substrates. Also, basic properties like an oligomeric state of an active form is under debate. Here we describe single-molecule fluorescence studies on Hfq-mediated annealing of DsrA, a small noncoding regulatory RNA of E. coli, and its mRNA target rpoS, which encodes the σStranscription factor. Our results reveal that a single hexamer of Hfq stimulates DsrA-rpoS annealing by simultaneously binding both RNAs using same RNA binding site on the proximal surface of Hfq. The competition for the same binding site of the two RNAs makes the RNA-Hfq interaction dynamic, but drives more efficient annealing. When the Hfq-binding sequence exists only in one of the two RNAs, RNA unwinding can occur due to the reduced stability of the RNA caused by the partial unwinding of the RNA upon Hfq binding on the specific binding site.