1. Biochemistry and Chemical Biology
  2. Chromosomes and Gene Expression

The elemental mechanism of transcriptional pausing

  1. Jason Saba
  2. Xien Yu Chua
  3. Tatiana V Mishanina
  4. Dhananjaya Nayak
  5. Tricia A Windgassen
  6. Rachel Anne Mooney
  7. Robert Landick  Is a corresponding author
  1. University of Wisconsin-Madison, United States
https://doi.org/10.7554/eLife.40981
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  1. Jason Saba
  2. Xien Yu Chua
  3. Tatiana V Mishanina
  4. Dhananjaya Nayak
  5. Tricia A Windgassen
  6. Rachel Anne Mooney
  7. Robert Landick
(2019)
The elemental mechanism of transcriptional pausing
eLife 8:e40981.
https://doi.org/10.7554/eLife.40981
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Abstract

Transcriptional pausing underlies regulation of cellular RNA biogenesis. A consensus pause sequence that acts on RNA polymerases (RNAPs) from bacteria to mammals halts RNAP in an elemental paused state from which longer-lived pauses can arise. Although the structural foundations of pauses prolonged by backtracking or nascent RNA hairpins are recognized, the fundamental mechanism of the elemental pause is less well-defined. Here we report a mechanistic dissection that establishes the elemental pause signal (i) is multipartite; (ii) causes a modest conformational shift that puts g-proteobacterial RNAP in an off-pathway state in which template base loading but not RNA translocation is inhibited; and (iii) allows RNAP to enter pretranslocated and one-base-pair backtracked states easily even though the half-translocated state observed in paused cryo-EM structures rate-limits pause escape. Our findings provide a mechanistic basis for the elemental pause and a framework to understand how pausing is modulated by sequence, cellular conditions, and regulators.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 2 and 7.

Article and author information

Author details

  1. Jason Saba

    Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7273-2970

  2. Xien Yu Chua

    Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2455-9493

  3. Tatiana V Mishanina

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

  4. Dhananjaya Nayak

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

  5. Tricia A Windgassen

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

  6. Rachel Anne Mooney

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

  7. Robert Landick

    Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
    For correspondence
    landick@bact.wisc.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5042-0383

Funding

National Institute of General Medical Sciences (R01 GM38660)

  • Robert Landick

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

Reviewing Editor

  1. Jerry L Workman, Stowers Institute for Medical Research, United States

Publication history

  1. Received: September 19, 2018
  2. Accepted: December 19, 2018
  3. Accepted Manuscript published: January 8, 2019 (version 1)
  4. Version of Record published: January 17, 2019 (version 2)

Copyright

© 2019, Saba 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. Jason Saba
  2. Xien Yu Chua
  3. Tatiana V Mishanina
  4. Dhananjaya Nayak
  5. Tricia A Windgassen
  6. Rachel Anne Mooney
  7. Robert Landick
(2019)
The elemental mechanism of transcriptional pausing
eLife 8:e40981.
https://doi.org/10.7554/eLife.40981

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