RNA-RNA interactomes of Hfq and ProQ reveal overlapping and competing roles for RNA chaperones

In many bacteria, the base pairing between most small regulatory RNAs (sRNAs) and their targets is facilitated by the Hfq RNA chaperone. However, recent studies have shown FinO-domain proteins also bind sRNAs. To compare the contributions of Hfq and the FinO-domain ProQ protein in Escherichia coli, we carried out RIL-seq, which allows global identification of two RNAs bound to the same protein. We detected hundreds of RNA pairs on ProQ. Intriguingly, 33% of the ProQ-bound RNA pairs are also found associated with Hfq, suggesting overlapping, complementary or competing roles for the two proteins. Applying RIL-seq to strains carrying chromosomly Hfq-FLAG or ProQ-3XFLAG in the presence or in the absence of the other RNA chaperon.