1. Biochemistry and Chemical Biology
  2. Structural Biology and Molecular Biophysics
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Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation

  1. Hannah Steinert
  2. Florian Sochor
  3. Anna Wacker
  4. Janina Buck
  5. Christina Helmling
  6. Fabian Hiller
  7. Sara Keyhani
  8. Jonas Noeske
  9. Steffen Kaspar Grimm
  10. Martin M Rudolph
  11. Heiko Keller
  12. Rachel Anne Mooney
  13. Robert Landick
  14. Beatrix Suess
  15. Boris Fürtig  Is a corresponding author
  16. Jens Wöhnert  Is a corresponding author
  17. Harald Schwalbe  Is a corresponding author
  1. Johann Wolfgang Goethe-University Frankfurt am Main, Germany
  2. Goethe University Frankfurt, Germany
  3. Technical University Darmstadt, Germany
  4. University of Wisconsin - Madison, United States
Research Article
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Cite this article as: eLife 2017;6:e21297 doi: 10.7554/eLife.21297

Abstract

In bacteria, the regulation of gene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of messenger RNA requires the temporal synchronization of RNA synthesis and ligand binding-dependent conformational refolding. Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA synthesis of ligand-associated genes due to the coupled formation of 3'-structural elements acting as terminators. To date, there has been no high resolution structural description of the concerted process of synthesis and ligand-induced restructuring of the regulatory RNA element. Here, we show that for the guanine-sensing xpt-pbuX riboswitch from Bacillus subtilis, the conformation of the full-length transcripts is static: it exclusively populates the functional off-state but cannot switch to the on-state, regardless of the presence or absence of ligand. We show that only the combined matching of transcription rates and ligand binding enables transcription intermediates to undergo ligand-dependent conformational refolding.

Article and author information

Author details

  1. Hannah Steinert

    Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Florian Sochor

    Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Anna Wacker

    Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Janina Buck

    Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Christina Helmling

    Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Fabian Hiller

    Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Sara Keyhani

    Johann Wolfgang Goethe-University Frankfurt am Main, Goethe University Frankfurt, Frankfurt am Main, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Jonas Noeske

    Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
    Competing interests
    The authors declare that no competing interests exist.
  9. Steffen Kaspar Grimm

    Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. Martin M Rudolph

    Department of Biology, Technical University Darmstadt, Darmstadt, Germany
    Competing interests
    The authors declare that no competing interests exist.
  11. Heiko Keller

    Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
    Competing interests
    The authors declare that no competing interests exist.
  12. Rachel Anne Mooney

    Department of Biochemistry, University of Wisconsin - Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Robert Landick

    Department of Biochemistry, University of Wisconsin - Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Beatrix Suess

    Department of Biology, Technical University Darmstadt, Darmstadt, Germany
    Competing interests
    The authors declare that no competing interests exist.
  15. Boris Fürtig

    Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
    For correspondence
    fuertig@nmr.uni-frankfurt.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6443-7656
  16. Jens Wöhnert

    Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt, Germany
    For correspondence
    woehnert@bio.uni-frankfurt.de
    Competing interests
    The authors declare that no competing interests exist.
  17. Harald Schwalbe

    Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
    For correspondence
    schwalbe@nmr.uni-frankfurt.de
    Competing interests
    The authors declare that no competing interests exist.

Funding

Deutsche Forschungsgemeinschaft (SFB902)

  • Harald Schwalbe

State of Hesse (BMRZ)

  • Harald Schwalbe

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

Reviewing Editor

  1. Lewis E Kay, University of Toronto, Canada

Publication history

  1. Received: September 6, 2016
  2. Accepted: May 24, 2017
  3. Accepted Manuscript published: May 25, 2017 (version 1)
  4. Version of Record published: June 5, 2017 (version 2)

Copyright

© 2017, Steinert 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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