1. Biochemistry and Chemical Biology
  2. Structural Biology and Molecular Biophysics
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Homology sensing via non-linear amplification of sequence dependent pausing by RecQ helicase

  1. Yeonee Seol
  2. Gábor M Harami
  3. Mihály Kovács  Is a corresponding author
  4. Keir C Neuman  Is a corresponding author
  1. National Heart, Lung and Blood Institute, National Institutes of Health, United States
  2. Eötvös Loránd University, Hungary
Research Article
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Cite this article as: eLife 2019;8:e45909 doi: 10.7554/eLife.45909

Abstract

RecQ helicases promote genomic stability through their unique ability to suppress illegitimate recombination and resolve recombination intermediates. These DNA structure-specific activities of RecQ helicases are mediated by the helicase-and-RNAseD like C-terminal (HRDC) domain, via unknown mechanisms. Here, employing single-molecule magnetic tweezers and rapid kinetic approaches we establish that the HRDC domain stabilizes intrinsic, sequence-dependent, pauses of the core helicase (lacking the HRDC) in a DNA geometry-dependent manner. We elucidate the core unwinding mechanism in which the unwinding rate depends on the stability of the duplex DNA leading to transient sequence-dependent pauses. We further demonstrate a non-linear amplification of these transient pauses by the controlled binding of the HRDC domain. The resulting DNA sequence- and geometry-dependent pausing may underlie a homology sensing mechanism that allows rapid disruption of unstable (illegitimate) and stabilization of stable (legitimate) DNA strand invasions, which suggests an intrinsic mechanism of recombination quality control by RecQ helicases.

Data availability

The single molecule experimental data analysis codes in this study were previously published and referenced in the manuscript. The Kerssemakers step-finder routine (J. W. J. Kerssemakers et. al., (2006) Nature, 442:709-712) is available from the authors. Alternative step-finding routines (Wiggins, P. A. (2015). Biophys J 109: 346-354; Hill, F. R., et al. (2018) J Chem Phys 148: 123317) are available here (http://mtshasta.phys.washington.edu/website/steppi/, or here https://github.com/duderstadt-lab/Julia_KCP_Notebooks). Source data for all of the figures and graphs are provided in the main and supplemental data.

Article and author information

Author details

  1. Yeonee Seol

    Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Gábor M Harami

    Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
    Competing interests
    The authors declare that no competing interests exist.
  3. Mihály Kovács

    Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
    For correspondence
    mihaly.kovacs@ttk.elte.hu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1200-4741
  4. Keir C Neuman

    Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
    For correspondence
    neumankc@mail.nih.gov
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0863-5671

Funding

Human Frontier Science Program (RGY0072/2010)

  • Yeonee Seol
  • Gábor M Harami
  • Mihály Kovács
  • Keir C Neuman

National Institutes of Health (HL001056-12)

  • Yeonee Seol
  • Keir C Neuman

Hungarian Academy of Sciences (LP2011-006/2011)

  • Gábor M Harami
  • Mihály Kovács

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

Reviewing Editor

  1. Maria Spies, University of Iowa, United States

Publication history

  1. Received: February 8, 2019
  2. Accepted: August 28, 2019
  3. Accepted Manuscript published: August 29, 2019 (version 1)
  4. Version of Record published: October 1, 2019 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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