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RNA compaction and iterative scanning for small RNA targets by the Hfq chaperone

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  • Ewelina M. Małecka

    (Johns Hopkins University
    International Institute of Molecular and Cell Biology in Warsaw)

  • Sarah A. Woodson

    (Johns Hopkins University)

Abstract

RNA-guided enzymes must quickly search a vast sequence space for their targets. This search is aided by chaperones such as Hfq, a protein that mediates regulation by bacterial small RNAs (sRNAs). How RNA binding proteins enhance this search is little known. Using single-molecule Förster resonance energy transfer, we show that E. coli Hfq performs a one-dimensional scan in which compaction of the target RNA delivers sRNAs to sites distant from the location of Hfq recruitment. We also show that Hfq can transfer an sRNA between different target sites in a single mRNA, favoring the most stable duplex. We propose that compaction and segmental transfer, combined with repeated cycles of base pairing, enable the kinetic selection of optimal sRNA targets. Finally, we show that RNA compaction and sRNA transfer require conserved arginine patches. We suggest that arginine patches are a widespread strategy for enabling the movement of RNA across protein surfaces.

Suggested Citation

  • Ewelina M. Małecka & Sarah A. Woodson, 2024. "RNA compaction and iterative scanning for small RNA targets by the Hfq chaperone," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46316-6
    DOI: 10.1038/s41467-024-46316-6
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    References listed on IDEAS

    as
    1. Jorjethe Roca & Andrew Santiago-Frangos & Sarah A. Woodson, 2022. "Diversity of bacterial small RNAs drives competitive strategies for a mutual chaperone," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    2. Debora Lika Makino & Marc Baumgärtner & Elena Conti, 2013. "Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex," Nature, Nature, vol. 495(7439), pages 70-75, March.
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