Hfq proximity and orientation controls RNA annealing.

ABSTRACT: Regulation of bacterial gene networks by small non-coding RNAs (sRNAs) requires base pairing with messenger RNA (mRNA) targets, which is facilitated by Hfq protein. Hfq is recruited to sRNAs and mRNAs through U-rich- and A-rich-binding sites, respectively, but their distance from the sRNA-mRNA complementary region varies widely among different genes. To determine whether distance and binding orientation affect Hfq's chaperone function, we engineered 'toy' RNAs containing strong Hfq-binding sites at defined distances from the complementary target site. We show that RNA annealing is fastest when the distal face of Hfq binds an A-rich sequence immediately 3' of the target. This recruitment advantage is lost when Hfq binds >20 nt away from the target, but is partially restored by secondary str

SUBMITTER: Panja S 

PROVIDER: S-EPMC3458560 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature