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

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

Version 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.

Metrics

  • 1,259
    views
  • 216
    downloads
  • 12
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Yeonee Seol
  2. Gábor M Harami
  3. Mihály Kovács
  4. Keir C Neuman
(2019)
Homology sensing via non-linear amplification of sequence dependent pausing by RecQ helicase
eLife 8:e45909.
https://doi.org/10.7554/eLife.45909

Share this article

https://doi.org/10.7554/eLife.45909

Further reading

    1. Biochemistry and Chemical Biology
    Zheng Ruan, Junuk Lee ... Wei Lü
    Research Article

    Protein phosphorylation is one of the major molecular mechanisms regulating protein activity and function throughout the cell. Pannexin 1 (PANX1) is a large-pore channel permeable to ATP and other cellular metabolites. Its tyrosine phosphorylation and subsequent activation have been found to play critical roles in diverse cellular conditions, including neuronal cell death, acute inflammation, and smooth muscle contraction. Specifically, the non-receptor kinase Src has been reported to phosphorylate Tyr198 and Tyr308 of mouse PANX1 (equivalent to Tyr199 and Tyr309 of human PANX1), resulting in channel opening and ATP release. Although the Src-dependent PANX1 activation mechanism has been widely discussed in the literature, independent validation of the tyrosine phosphorylation of PANX1 has been lacking. Here, we show that commercially available antibodies against the two phosphorylation sites mentioned above—which were used to identify endogenous PANX1 phosphorylation at these two sites—are nonspecific and should not be used to interpret results related to PANX1 phosphorylation. We further provide evidence that neither tyrosine residue is a major phosphorylation site for Src kinase in heterologous expression systems. We call on the field to re-examine the existing paradigm of tyrosine phosphorylation-dependent activation of the PANX1 channel.

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Christopher TA Lewis, Elise G Melhedegaard ... Julien Ochala
    Research Article

    Hibernation is a period of metabolic suppression utilized by many small and large mammal species to survive during winter periods. As the underlying cellular and molecular mechanisms remain incompletely understood, our study aimed to determine whether skeletal muscle myosin and its metabolic efficiency undergo alterations during hibernation to optimize energy utilization. We isolated muscle fibers from small hibernators, Ictidomys tridecemlineatus and Eliomys quercinus and larger hibernators, Ursus arctos and Ursus americanus. We then conducted loaded Mant-ATP chase experiments alongside X-ray diffraction to measure resting myosin dynamics and its ATP demand. In parallel, we performed multiple proteomics analyses. Our results showed a preservation of myosin structure in U. arctos and U. americanus during hibernation, whilst in I. tridecemlineatus and E. quercinus, changes in myosin metabolic states during torpor unexpectedly led to higher levels in energy expenditure of type II, fast-twitch muscle fibers at ambient lab temperatures (20 °C). Upon repeating loaded Mant-ATP chase experiments at 8 °C (near the body temperature of torpid animals), we found that myosin ATP consumption in type II muscle fibers was reduced by 77–107% during torpor compared to active periods. Additionally, we observed Myh2 hyper-phosphorylation during torpor in I. tridecemilineatus, which was predicted to stabilize the myosin molecule. This may act as a potential molecular mechanism mitigating myosin-associated increases in skeletal muscle energy expenditure during periods of torpor in response to cold exposure. Altogether, we demonstrate that resting myosin is altered in hibernating mammals, contributing to significant changes to the ATP consumption of skeletal muscle. Additionally, we observe that it is further altered in response to cold exposure and highlight myosin as a potentially contributor to skeletal muscle non-shivering thermogenesis.