Physical modeling of a sliding clamp mechanism for the spreading of ParB at short genomic distance from bacterial centromere sites - Archive ouverte HAL Access content directly
Journal Articles iScience Year : 2020

Physical modeling of a sliding clamp mechanism for the spreading of ParB at short genomic distance from bacterial centromere sites

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Abstract

Bacterial ParB partitioning proteins involved in chromosomes and low-copy-number plasmid segregation are CTP-dependent molecular switches. CTP-binding converts ParB dimers to DNA clamps, allowing unidimensional diffusion along the DNA. This sliding property has been proposed to explain the ParB spreading over large distances from parS centromere sites where ParB is specifically loaded. We modeled such a ‘Clamping & sliding’ mechanism as a typical reaction-diffusion system, compared it to the F-plasmid ParB DNA binding pattern, and found that it can account neither for the long range of ParB binding to DNA, nor for the rapid assembly kinetics observed in vivo after parS duplication. Also, it predicts a strong effect on the F-plasmid ParB binding pattern from the presence of a roadblock that is not observed in ChIP-seq. We conclude that although ‘Clamping & sliding’ can occur at short distances from parS, another mechanism must apply for ParB recruitment at larger genomic distances.
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Dates and versions

hal-03052753 , version 1 (10-12-2020)

Licence

Attribution - CC BY 4.0

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Jean-Charles Walter, Jerome Rech, Nils-Ole Walliser, Jerome Dorignac, Frederic Geniet, et al.. Physical modeling of a sliding clamp mechanism for the spreading of ParB at short genomic distance from bacterial centromere sites. iScience, 2020, 23 (12), pp.101861. ⟨10.1016/j.isci.2020.101861⟩. ⟨hal-03052753⟩
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