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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
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    References listed on IDEAS

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    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.
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    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.

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