Abstract

Replisomes are multi-protein complexes that replicate genomes with remarkable speed and accuracy. Despite their importance, their dynamics is poorly characterized, especially in vivo. In this paper, we present an approach to infer the replisome dynamics from the DNA abundance distribution measured in a growing bacterial population. Our method is sensitive enough to detect subtle variations of the replisome speed along the genome. As an application, we experimentally measured the DNA abundance distribution in Escherichia coli populations growing at different temperatures using deep sequencing. We find that the average replisome speed increases nearly five-fold between 17°C and 37°C. Further, we observe wave-like variations of the replisome speed along the genome. These variations correlate with previously observed variations of the mutation rate, suggesting a common dynamical origin. Our approach has the potential to elucidate replication dynamics in E. coli mutants and in other bacterial species.

Data availability

Sequence reads were deposited in the NCBI Sequence Read Archive with links to BioProject accession number PRJNA772106. Corresponding read frequencies along the genome were deposited in Zenodo (DOI:10.5281/zenodo.5577986).

The following data sets were generated

Article and author information

Author details

  1. Deepak Bhat

    Biological Complexity Unit, Okinawa Institute of Science and Technology, Onna, Japan
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9387-4951
  2. Samuel Hauf

    Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology, Onna, Japan
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3034-8441
  3. Charles Plessy

    Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Onna, Japan
    Competing interests
    The authors declare that no competing interests exist.
  4. Yohei Yokobayashi

    Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology, Onna, Japan
    Competing interests
    The authors declare that no competing interests exist.
  5. Simone Pigolotti

    Biological Complexity Unit, Okinawa Institute of Science and Technology, Onna, Japan
    For correspondence
    simone.pigolotti@oist.jp
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6157-6906

Funding

Japan Society for the Promotion of Science (JP18K03473)

  • Simone Pigolotti

Deutsche Forschungsgemeinschaft (Projektnummer 452628014,Geschätszeichen: HA9374/1-1)

  • Samuel Hauf

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

Reviewing Editor

  1. Armita Nourmohammad, University of Washington, United States

Version history

  1. Preprint posted: October 15, 2021 (view preprint)
  2. Received: November 26, 2021
  3. Accepted: July 13, 2022
  4. Accepted Manuscript published: July 25, 2022 (version 1)
  5. Version of Record published: August 17, 2022 (version 2)
  6. Version of Record updated: April 19, 2023 (version 3)

Copyright

© 2022, Bhat 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. Deepak Bhat
  2. Samuel Hauf
  3. Charles Plessy
  4. Yohei Yokobayashi
  5. Simone Pigolotti
(2022)
Speed variations of bacterial replisomes
eLife 11:e75884.
https://doi.org/10.7554/eLife.75884

Share this article

https://doi.org/10.7554/eLife.75884

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