1. Biochemistry and Chemical Biology
  2. Chromosomes and Gene Expression
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Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria

  1. Matthew V Kotlajich
  2. Daniel R Hron
  3. Beth A Boudreau
  4. Zhiqiang Sun
  5. Yuri Lyubchenko
  6. Robert Landick  Is a corresponding author
  1. University of Wisconsin-Madison, United States
  2. University of Nebraska Medical Center, United States
Research Article
  • Cited 61
  • Views 2,882
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Cite this article as: eLife 2015;4:e04970 doi: 10.7554/eLife.04970

Abstract

Bacterial H-NS forms nucleoprotein filaments that spread on DNA and bridge distant DNA sites. H-NS filaments co-localize with sites of Rho-dependent termination in Escherichia coli, but their direct effects on transcriptional pausing and termination are untested. Here we report that bridged H-NS filaments strongly increase pausing by E. coli RNA polymerase at a subset of pause sites with high potential for backtracking. Bridged but not linear H-NS filaments promoted Rho-dependent termination by increasing pause dwell times and the kinetic window for Rho action. By observing single H-NS filaments and elongating RNA polymerase molecules using atomic force microscopy, we established that bridged filaments surround paused complexes. Our results favor a model in which H-NS-constrained changes in DNA supercoiling driven by transcription promote pausing at backtracking-susceptible sites. Our findings provide a mechanistic rationale for H-NS stimulation of Rho-dependent termination in horizontally transferred genes and during pervasive antisense and noncoding transcription in bacteria.

Article and author information

Author details

  1. Matthew V Kotlajich

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

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

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

    Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Yuri Lyubchenko

    Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Robert Landick

    Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
    For correspondence
    landick@biochem.wisc.edu
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Nick J Proudfoot, University of Oxford, United Kingdom

Publication history

  1. Received: September 30, 2014
  2. Accepted: January 15, 2015
  3. Accepted Manuscript published: January 16, 2015 (version 1)
  4. Version of Record published: February 20, 2015 (version 2)

Copyright

© 2015, Kotlajich 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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