Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA

Base-pairing interactions mediate many intermolecular target recognition events. Even a single base-pair mismatch can cause a substantial difference in activity but how such changes influence the target search kinetics in vivo is unknown. Here, we use high-throughput sequencing and quantitative super-resolution imaging to probe the mutants of bacterial small RNA, SgrS, and their regulation of ptsG mRNA target. Mutations that disrupt binding of a chaperone protein, Hfq, and are distal to the mRNA annealing region still decrease the rate of target association, k(on), and increase the dissociation rate, k(off), showing that Hfq directly facilitates sRNA-mRNA annealing in vivo. Single base-pair mismatches in the annealing region reduce k(on) by 24-31% and increase k(off) by 14-25%, extending the time it takes to find and destroy the target by about a third. The effects of disrupting contiguous base-pairing are much more modest than that expected from thermodynamics, suggesting that Hfq buffers base-pair disruptions. Bacterial small RNA SgrS binds and regulates its primary target, ptsG mRNA. Here the authors employ Sort-Seq and super resolution imaging to investigate in vivo target recognition and rejection kinetics of SgrS.

Automated summary

Base-pairing interactions are crucial for intermolecular target recognition, with even a single base-pair mismatch causing significant differences in activity. Hfq directly facilitates sRNA-mRNA annealing in vivo. Single base-pair mismatches prolong the time it takes to find and destroy the target.