1. Biochemistry and Chemical Biology
  2. Structural Biology and Molecular Biophysics
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The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand

  1. Philipp Konrad Zuber
  2. Irina Artsimovitch
  3. Monali NandyMazumdar
  4. Zhaokun Liu
  5. Yuri Nedialkov
  6. Kristian Schweimer
  7. Paul Rösch
  8. Stefan H Knauer  Is a corresponding author
  1. Universität Bayreuth, Germany
  2. Ohio State University, United States
Research Article
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Cite this article as: eLife 2018;7:e36349 doi: 10.7554/eLife.36349

Abstract

RfaH, a transcription regulator of the universally conserved NusG/Spt5 family, utilizes a unique mode of recruitment to elongating RNA polymerase to activate virulence genes. RfaH function depends critically on an ops sequence, an exemplar of a consensus pause, in the non-template DNA strand of the transcription bubble. We used structural and functional analyses to elucidate the role of ops in RfaH recruitment. Our results demonstrate that ops induces pausing to facilitate RfaH binding and establishes direct contacts with RfaH. Strikingly, the non-template DNA forms a hairpin in the RfaH:ops complex structure, flipping out a conserved T residue that is specifically recognized by RfaH. Molecular modeling and genetic evidence support the notion that ops hairpin is required for RfaH recruitment. We argue that both the sequence and the structure of the non-template strand are read out by transcription factors, expanding the repertoire of transcriptional regulators in all domains of life.

Article and author information

Author details

  1. Philipp Konrad Zuber

    Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Irina Artsimovitch

    Department of Microbiology, Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Monali NandyMazumdar

    Department of Microbiology, Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Zhaokun Liu

    Department of Microbiology, Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Yuri Nedialkov

    Department of Microbiology, Ohio State University, Columbus, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Kristian Schweimer

    Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Paul Rösch

    Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Stefan H Knauer

    Lehrstuhl Biopolymere und Forschungszentrum für Bio-Makromoleküle, Universität Bayreuth, Bayreuth, Germany
    For correspondence
    stefan.knauer@uni-bayreuth.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4143-0694

Funding

Deutsche Forschungsgemeinschaft (Ro 617/21-1)

  • Paul Rösch

National Institutes of Health (GM67153)

  • Irina Artsimovitch

Deutsche Forschungsgemeinschaft (Ro 617/17-1)

  • Paul Rösch

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

Reviewing Editor

  1. Andrés Aguilera, CABIMER, Universidad de Sevilla, Spain

Publication history

  1. Received: March 2, 2018
  2. Accepted: May 5, 2018
  3. Accepted Manuscript published: May 9, 2018 (version 1)
  4. Version of Record published: June 11, 2018 (version 2)

Copyright

© 2018, Zuber 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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