Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA
Open Access
- 8 February 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Communications
- Vol. 12 (1), 1-15
- https://doi.org/10.1038/s41467-021-21144-0
Abstract
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, kon, and increase the dissociation rate, koff, showing that Hfq directly facilitates sRNA–mRNA annealing in vivo. Single base-pair mismatches in the annealing region reduce kon by 24–31% and increase koff 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.Funding Information
- Howard Hughes Medical Institute
This publication has 76 references indexed in Scilit:
- RNA-guided genetic silencing systems in bacteria and archaeaNature, 2012
- Molecular call and response: The physiology of bacterial small RNAsBiochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2011
- Regulation by Small RNAs in Bacteria: Expanding FrontiersMolecular Cell, 2011
- PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq actionProceedings of the National Academy of Sciences of the United States of America, 2011
- Structural basis for RNA 3′-end recognition by HfqProceedings of the National Academy of Sciences of the United States of America, 2011
- Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequenceProceedings of the National Academy of Sciences of the United States of America, 2010
- RNA, but not protein partners, is directly responsible for translational silencing by a bacterial Hfq-binding small RNAProceedings of the National Academy of Sciences of the United States of America, 2008
- A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptideProceedings of the National Academy of Sciences of the United States of America, 2007
- Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)Nature Methods, 2006
- Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulatorThe EMBO Journal, 2004