Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs and mRNAs in live bacterial cells

  1. Seongjin Park
  2. Karine Prévost
  3. Emily M Heideman
  4. Marie-Claude Carrier
  5. Muhammad S Azam
  6. Matthew A Reyer
  7. Wei Liu
  8. Eric Massé  Is a corresponding author
  9. Jingyi Fei  Is a corresponding author
  1. University of Chicago, United States
  2. University of Sherbrooke, Canada

Abstract

RNA-binding proteins play myriad roles in regulating RNAs and RNA-mediated functions. In bacteria, the RNA chaperone Hfq is an important post-transcriptional gene regulator. Using live-cell super-resolution imaging, we can distinguish Hfq binding to different sizes of cellular RNAs. We demonstrate that under normal growth conditions, Hfq exhibits widespread mRNA-binding activity, with the distal face of Hfq contributing mostly to the mRNA binding in vivo. In addition, sRNAs can either co-occupy Hfq with the mRNA as a ternary complex, or displace the mRNA from Hfq in a binding face-dependent manner, suggesting mechanisms through which sRNAs rapidly access Hfq to induce sRNA-mediated gene regulation. Finally, our data suggest that binding of Hfq to certain mRNAs through its distal face can recruit RNase E to promote turnover of these mRNAs in an sRNA-independent manner, and such regulatory function of Hfq can be decoyed by sRNA competitors that bind strongly at the distal face.

Data availability

All the numeric data for each plot/graph and fitting results are provided in Supplementary file 1 or as source data. The MATLAB scripts for analysis are provided as source code.

Article and author information

Author details

  1. Seongjin Park

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Karine Prévost

    RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Emily M Heideman

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Marie-Claude Carrier

    RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
    Competing interests
    The authors declare that no competing interests exist.
  5. Muhammad S Azam

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Matthew A Reyer

    Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Wei Liu

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Eric Massé

    RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
    For correspondence
    eric.masse@usherbrooke.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5253-1415
  9. Jingyi Fei

    Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
    For correspondence
    jingyifei@uchicago.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9775-3820

Funding

National Institutes of Health (1DP2GM128185-01)

  • Jingyi Fei

Searle Scholars Program

  • Jingyi Fei

National Institutes of Health (R01 GM092830-06A1)

  • Eric Massé

Canadian Institutes of Health Research (MOP69005)

  • Eric Massé

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Gisela Storz, National Institute of Child Health and Human Development, United States

Publication history

  1. Received: October 21, 2020
  2. Accepted: February 19, 2021
  3. Accepted Manuscript published: February 22, 2021 (version 1)
  4. Version of Record published: March 23, 2021 (version 2)

Copyright

© 2021, Park et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Seongjin Park
  2. Karine Prévost
  3. Emily M Heideman
  4. Marie-Claude Carrier
  5. Muhammad S Azam
  6. Matthew A Reyer
  7. Wei Liu
  8. Eric Massé
  9. Jingyi Fei
(2021)
Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs and mRNAs in live bacterial cells
eLife 10:e64207.
https://doi.org/10.7554/eLife.64207

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