IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-40320-y.html
   My bibliography  Save this article

Partition complex structure can arise from sliding and bridging of ParB dimers

Author

Listed:
  • Lara Connolley

    (Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology)

  • Lucas Schnabel

    (University of Marburg)

  • Martin Thanbichler

    (Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology
    University of Marburg)

  • Seán M. Murray

    (Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology)

Abstract

In many bacteria, chromosome segregation requires the association of ParB to the parS-containing centromeric region to form the partition complex. However, the structure and formation of this complex have been unclear. Recently, studies have revealed that CTP binding enables ParB dimers to slide along DNA and condense the centromeric region through the formation of DNA bridges. Using semi-flexible polymer simulations, we demonstrate that these properties can explain partition complex formation. Transient ParB bridges organize DNA into globular states or hairpins and helical structures, depending on bridge lifetime, while separate simulations show that ParB sliding reproduces the multi-peaked binding profile observed in Caulobacter crescentus. Combining sliding and bridging into a unified model, we find that short-lived ParB bridges do not impede sliding and can reproduce both the binding profile and condensation of the nucleoprotein complex. Overall, our model elucidates the mechanism of partition complex formation and predicts its fine structure.

Suggested Citation

  • Lara Connolley & Lucas Schnabel & Martin Thanbichler & Seán M. Murray, 2023. "Partition complex structure can arise from sliding and bridging of ParB dimers," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40320-y
    DOI: 10.1038/s41467-023-40320-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-40320-y
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-40320-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Maria A. Schumacher & Barbara E. Funnell, 2005. "Structures of ParB bound to DNA reveal mechanism of partition complex formation," Nature, Nature, vol. 438(7067), pages 516-519, November.
    2. Lepage, Thibaut & Junier, Ivan, 2019. "A polymer model of bacterial supercoiled DNA including structural transitions of the double helix," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 527(C).
    3. Yan Zhang & Lin An & Jie Xu & Bo Zhang & W. Jim Zheng & Ming Hu & Jijun Tang & Feng Yue, 2018. "Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
    4. Manfred Bohn & Dieter W Heermann, 2010. "Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization," PLOS ONE, Public Library of Science, vol. 5(8), pages 1-14, August.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Sara Jakob & Wieland Steinchen & Juri Hanßmann & Julia Rosum & Katja Langenfeld & Manuel Osorio-Valeriano & Niklas Steube & Pietro I. Giammarinaro & Georg K. A. Hochberg & Timo Glatter & Gert Bange & , 2024. "The virulence regulator VirB from Shigella flexneri uses a CTP-dependent switch mechanism to activate gene expression," Nature Communications, Nature, vol. 15(1), pages 1-18, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Mochen Liao & Kai Lan & Yuan Yao, 2022. "Sustainability implications of artificial intelligence in the chemical industry: A conceptual framework," Journal of Industrial Ecology, Yale University, vol. 26(1), pages 164-182, February.
    2. Yufan Zhou & Tian Li & Lavanya Choppavarapu & Kun Fang & Shili Lin & Victor X. Jin, 2024. "Integration of scHi-C and scRNA-seq data defines distinct 3D-regulated and biological-context dependent cell subpopulations," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Jingxuan Xu & Xiang Xu & Dandan Huang & Yawen Luo & Lin Lin & Xuemei Bai & Yang Zheng & Qian Yang & Yu Cheng & An Huang & Jingyi Shi & Xiaochen Bo & Jin Gu & Hebing Chen, 2024. "A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    4. Ana Stanojevic & Stanisław Woźniak & Guillaume Bellec & Giovanni Cherubini & Angeliki Pantazi & Wulfram Gerstner, 2024. "High-performance deep spiking neural networks with 0.3 spikes per neuron," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    5. Hao Wang & Jiaxin Yang & Yu Zhang & Jianliang Qian & Jianrong Wang, 2022. "Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    6. Yanlin Zhang & Mathieu Blanchette, 2022. "Reference panel guided topological structure annotation of Hi-C data," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    7. Shaofu Xu & Jing Wang & Sicheng Yi & Weiwen Zou, 2022. "High-order tensor flow processing using integrated photonic circuits," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    8. Manfred Bohn & Dieter W Heermann, 2011. "Repulsive Forces Between Looping Chromosomes Induce Entropy-Driven Segregation," PLOS ONE, Public Library of Science, vol. 6(1), pages 1-8, January.
    9. Kevin B. Dsouza & Alexandra Maslova & Ediem Al-Jibury & Matthias Merkenschlager & Vijay K. Bhargava & Maxwell W. Libbrecht, 2022. "Learning representations of chromatin contacts using a recurrent neural network identifies genomic drivers of conformation," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    10. Vianne R. Gao & Rui Yang & Arnav Das & Renhe Luo & Hanzhi Luo & Dylan R. McNally & Ioannis Karagiannidis & Martin A. Rivas & Zhong-Min Wang & Darko Barisic & Alireza Karbalayghareh & Wilfred Wong & Yi, 2024. "ChromaFold predicts the 3D contact map from single-cell chromatin accessibility," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    11. Mattia Conte & Ehsan Irani & Andrea M. Chiariello & Alex Abraham & Simona Bianco & Andrea Esposito & Mario Nicodemi, 2022. "Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    12. Ofir Shukron & David Holcman, 2017. "Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data," PLOS Computational Biology, Public Library of Science, vol. 13(4), pages 1-20, April.
    13. Fan Feng & Yuan Yao & Xue Qing David Wang & Xiaotian Zhang & Jie Liu, 2022. "Connecting high-resolution 3D chromatin organization with epigenomics," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40320-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.