1. Physics of Living Systems

Speed variations of bacterial replisomes

  1. Deepak Bhat
  2. Samuel Hauf
  3. Charles Plessy
  4. Yohei Yokobayashi
  5. Simone Pigolotti  Is a corresponding author
  1. Okinawa Institute of Science and Technology, Japan
https://doi.org/10.7554/eLife.75884
Share this article
Cite this article
  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
  2. Download BibTeX
  3. Download .RIS

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.

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.

Metrics

  • 1,986
    views
  • 467
    downloads
  • 13
    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. 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

Categories and tags

Research organism

Further reading

    1. Physics of Living Systems

    Modeling collective behavior in groups of mice housed under semi-naturalistic conditions

    Xiaowen Chen, Maciej Winiarksi ... Aleksandra M Walczak
    Research Article

    In social behavior research, the focus often remains on animal dyads, limiting the understanding of complex interactions. Recent trends favor naturalistic setups, offering unique insights into intricate social behaviors. Social behavior stems from chance, individual preferences, and group dynamics, necessitating high-resolution quantitative measurements and statistical modeling. This study leverages the Eco-HAB system, an automated experimental setup that employs radiofrequency identification tracking to observe naturally formed mouse cohorts in a controlled yet naturalistic setting, and uses statistical inference models to decipher rules governing the collective dynamics of groups of 10–15 individuals. Applying maximum entropy models on the coarse-grained co-localization patterns of mice unveils social rules in mouse hordes, quantifying sociability through pairwise interactions within groups, the impact of individual versus social preferences, and the effects of considering interaction structures among three animals instead of two. Reproducing co-localization patterns of individual mice reveals stability over time, with the statistics of the inferred interaction strength capturing social structure. By separating interactions from individual preferences, the study demonstrates that altering neuronal plasticity in the prelimbic cortex – the brain structure crucial for sociability – does not eliminate signatures of social interactions, but makes the transmission of social information between mice more challenging. The study demonstrates how the joint probability distribution of the mice positions can be used to quantify sociability.

    1. Physics of Living Systems

    Cell cycle and age-related modulations of mouse chromosome stiffness

    Ning Liu, Wenan Qiang ... Huanyu Qiao
    Research Article

    Chromosome structure is complex, and many aspects of chromosome organization are still not understood. Measuring the stiffness of chromosomes offers valuable insight into their structural properties. In this study, we analyzed the stiffness of chromosomes from metaphase I (MI) and metaphase II (MII) oocytes. Our results revealed a tenfold increase in stiffness (Young’s modulus) of MI chromosomes compared to somatic chromosomes. Furthermore, the stiffness of MII chromosomes was found to be lower than that of MI chromosomes. We examined the role of meiosis-specific cohesin complexes in regulating chromosome stiffness. Surprisingly, the stiffness of chromosomes from three meiosis-specific cohesin mutants did not significantly differ from that of wild-type chromosomes, indicating that these cohesins may not be primary determinants of chromosome stiffness. Additionally, our findings revealed an age-related increase of chromosome stiffness for MI oocytes. Since aging is associated with elevated levels of DNA damage, we investigated the impact of etoposide-induced DNA damage on chromosome stiffness and found that it led to a reduction in stiffness in MI oocytes. Overall, our study underscores the dynamic and cyclical nature of chromosome stiffness, modulated by both the cell cycle and age-related factors.