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

Anustup Poddar, Muhammad S. Azam, Tunc Kayikcioglu, Maksym Bobrovskyy, Jichuan Zhang, Xiangqian Ma, Piyush Labhsetwar, Jingyi Fei, Digvijay Singh, Zaida Luthey-Schulten, Carin K. Vanderpool () and Taekjip Ha ()
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Anustup Poddar: Johns Hopkins University School of Medicine
Muhammad S. Azam: University of Illinois at Urbana-Champaign
Tunc Kayikcioglu: Johns Hopkins University School of Medicine
Maksym Bobrovskyy: University of Illinois at Urbana-Champaign
Jichuan Zhang: Johns Hopkins University School of Medicine
Xiangqian Ma: University of Illinois at Urbana-Champaign
Piyush Labhsetwar: University of Illinois at Urbana-Champaign
Jingyi Fei: University of Chicago
Digvijay Singh: Johns Hopkins University School of Medicine
Zaida Luthey-Schulten: University of Illinois at Urbana-Champaign
Carin K. Vanderpool: University of Illinois at Urbana-Champaign
Taekjip Ha: Johns Hopkins University School of Medicine

Nature Communications, 2021, vol. 12, issue 1, 1-15

Abstract: 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.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21144-0

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DOI: 10.1038/s41467-021-21144-0

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