DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome

  1. Alessandro Costa  Is a corresponding author
  2. Ludovic Renault
  3. Paolo Swuec
  4. Tatjana Petojevic
  5. Jim Pesavento
  6. Ivar Ilves
  7. Kirsty MacLellan-Gibson
  8. Roland A Fleck
  9. Michael R Botchan
  10. James M Berger
  1. London Research Institute, Cancer Research UK, United Kingdom
  2. University of California, Berkeley, United States
  3. University of California, Berkeley, United Kingdom
  4. University of Tartu, Estonia
  5. National Institute for Biological Standards and Control, United Kingdom
  6. King's College London, United Kingdom
  7. Johns Hopkins University School of Medicine, United States

Abstract

The Cdc45/Mcm2-7/GINS (CMG) helicase separates DNA strands during replication in eukaryotes. How the CMG is assembled and engages DNA substrates remains unclear. We have determined the electron-microscopy structure of the CMG in the presence of ATPγS and a DNA duplex bearing a 3' single-stranded tail. The structure shows that the MCM subunits of the CMG bind preferentially to single-stranded DNA, establishes the polarity by which DNA enters into the Mcm2-7 pore, and explains how Cdc45 helps prevent DNA from dissociating from the helicase. The Mcm2-7 subcomplex forms a cracked-ring, right-handed spiral when DNA and nucleotide are bound, revealing unexpected congruencies between the CMG and both bacterial DnaB helicases and the AAA+ motor of the eukaryotic proteasome. The existence of a subpopulation of dimeric CMGs establishes the subunit register of Mcm2-7 double hexamers and highlights how Mcm2-7 transitions through different conformational and assembly states as it matures into a functional helicase.

Article and author information

Author details

  1. Alessandro Costa

    London Research Institute, Cancer Research UK, London, United Kingdom
    For correspondence
    alessandro.costa@cancer.org.uk
    Competing interests
    No competing interests declared.
  2. Ludovic Renault

    London Research Institute, Cancer Research UK, London, United Kingdom
    Competing interests
    No competing interests declared.
  3. Paolo Swuec

    London Research Institute, Cancer Research UK, London, United Kingdom
    Competing interests
    No competing interests declared.
  4. Tatjana Petojevic

    University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  5. Jim Pesavento

    University of California, Berkeley, Berkeley, United Kingdom
    Competing interests
    No competing interests declared.
  6. Ivar Ilves

    University of Tartu, Tartu, Estonia
    Competing interests
    No competing interests declared.
  7. Kirsty MacLellan-Gibson

    National Institute for Biological Standards and Control, Potters Bar, United Kingdom
    Competing interests
    No competing interests declared.
  8. Roland A Fleck

    King's College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  9. Michael R Botchan

    University of California, Berkeley, Berkeley, United States
    Competing interests
    Michael R Botchan, Reviewing editor, eLife.
  10. James M Berger

    Johns Hopkins University School of Medicine, Baltimore, United States
    Competing interests
    No competing interests declared.

Reviewing Editor

  1. Stephen C Kowalczykowski, University of California, Davis, United States

Version history

  1. Received: May 7, 2014
  2. Accepted: August 8, 2014
  3. Accepted Manuscript published: August 12, 2014 (version 1)
  4. Version of Record published: September 2, 2014 (version 2)

Copyright

© 2014, Costa 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.

Metrics

  • 4,500
    views
  • 560
    downloads
  • 99
    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. Alessandro Costa
  2. Ludovic Renault
  3. Paolo Swuec
  4. Tatjana Petojevic
  5. Jim Pesavento
  6. Ivar Ilves
  7. Kirsty MacLellan-Gibson
  8. Roland A Fleck
  9. Michael R Botchan
  10. James M Berger
(2014)
DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome
eLife 3:e03273.
https://doi.org/10.7554/eLife.03273

Share this article

https://doi.org/10.7554/eLife.03273

Further reading

    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression
    Ramona Weber, Chung-Te Chang
    Research Article

    Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers the deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Amy H Andreotti, Volker Dötsch
    Editorial

    The articles in this special issue highlight how modern cellular, biochemical, biophysical and computational techniques are allowing deeper and more detailed studies of allosteric kinase regulation.