CTP promotes efficient ParB-dependent DNA condensation by facilitating one-dimensional diffusion from parS

  1. Francisco de Asis Balaguer
  2. Clara Aicart-Ramos
  3. Gemma LM Fisher
  4. Sara de Bragança
  5. Eva M Martin-Cuevas
  6. Cesar L Pastrana
  7. Mark Simon Dillingham  Is a corresponding author
  8. Fernando Moreno-Herrero  Is a corresponding author
  1. Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Spain
  2. University of Bristol, United Kingdom

Abstract

Faithful segregation of bacterial chromosomes relies on the ParABS partitioning system and the SMC complex. In this work, we used single molecule techniques to investigate the role of cytidine triphosphate (CTP) binding and hydrolysis in the critical interaction between centromere-like parS DNA sequences and the ParB CTPase. Using a combined optical tweezers confocal microscope, we observe the specific interaction of ParB with parS directly. Binding around parS is enhanced by the presence of CTP or the non-hydrolysable analogue CTPgS. However, ParB proteins are also detected at a lower density in distal non-specific DNA. This requires the presence of a parS loading site and is prevented by protein roadblocks, consistent with one dimensional diffusion by a sliding clamp. ParB diffusion on non-specific DNA is corroborated by direct visualization and quantification of movement of individual quantum-dot labelled ParB. Magnetic tweezers experiments show that the spreading activity, which has an absolute requirement for CTP binding but not hydrolysis, results in the condensation of parS-containing DNA molecules at low nanomolar protein concentrations.

Data availability

All DNA sequences used are included in Supplementary Information.Data sets for Fig. 1E, 1F; Fig. 1-S1B, Fig.1-S1C; Fig.1-S4C, Fig1-S4D; Fig. 2C, 2G; Fig. 4C, 4D, 4E, 4F, 4G; Fig. 4-S1A, Fig. 4-S1B, Fig. 4-S1C; Fig. 5A, 5B; Fig. 6A, 6B, 6D, 6F, have been provided.

Article and author information

Author details

  1. Francisco de Asis Balaguer

    Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  2. Clara Aicart-Ramos

    Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  3. Gemma LM Fisher

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Sara de Bragança

    Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4039-1993
  5. Eva M Martin-Cuevas

    Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  6. Cesar L Pastrana

    Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  7. Mark Simon Dillingham

    School of Biochemistry, University of Bristol, Bristol, United Kingdom
    For correspondence
    mark.dillingham@bristol.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4612-7141
  8. Fernando Moreno-Herrero

    Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
    For correspondence
    fernando.moreno@cnb.csic.es
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4083-1709

Funding

European Research Council (681299)

  • Fernando Moreno-Herrero

Wellcome Trust (100401/Z/12/Z)

  • Mark Simon Dillingham

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. Preprint posted: February 11, 2021 (view preprint)
  2. Received: February 15, 2021
  3. Accepted: July 9, 2021
  4. Accepted Manuscript published: July 12, 2021 (version 1)
  5. Version of Record published: July 22, 2021 (version 2)

Copyright

© 2021, Balaguer 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. Francisco de Asis Balaguer
  2. Clara Aicart-Ramos
  3. Gemma LM Fisher
  4. Sara de Bragança
  5. Eva M Martin-Cuevas
  6. Cesar L Pastrana
  7. Mark Simon Dillingham
  8. Fernando Moreno-Herrero
(2021)
CTP promotes efficient ParB-dependent DNA condensation by facilitating one-dimensional diffusion from parS
eLife 10:e67554.
https://doi.org/10.7554/eLife.67554

Share this article

https://doi.org/10.7554/eLife.67554

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