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Physical modeling of a sliding clamp mechanism for the spreading of ParB at short genomic distance from bacterial centromere sites
Auteur(s): Walter J.-C., Rech Jerome, Walliser N.-O., Dorignac J., Geniet F., Palmeri J., Parmeggiani A., Bouet Jean-Yves
(Article) Publié:
Iscience, vol. 23 p.101861 (2020)
Texte intégral en Openaccess :
Ref HAL: hal-03052753_v1
DOI: 10.1016/j.isci.2020.101861
Exporter : BibTex | endNote
Résumé: 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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Modeling supercoiled DNA interacting with an anchored cluster of proteins: towards a quantitative estimation of chromosomal DNA supercoiling
Auteur(s): Walter J.-C., Lepage Thibaut, Dorignac J., Geniet F., Parmeggiani A., Palmeri J., Bouet Jean-Yves, Junier Ivan
(Document sans référence bibliographique) 2020-04-07Texte intégral en Openaccess :
Ref HAL: hal-02990631_v1
Ref Arxiv: 2002.00111
Ref. & Cit.: NASA ADS
Exporter : BibTex | endNote
Résumé: We investigate the measurement of DNA supercoiling density ($\sigma$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB proteins around their centromere-like site, {\it parS}. Using this framework, we provide an upper bound for $\sigma$ in the {\it Escherichia coli} chromosome, consistent with plasmid values, and offer a proof of concept for a high accuracy measurement. To reach these conclusions, we revisit the problem of the formation of ParB clusters. We predict, in particular, that they result from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., they behave like liquid-like protein condensates with unconventional ``leaky'' boundaries.
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Modelling the effect of ribosome mobility on the rate of protein synthesis
Auteur(s): Dauloudet O., Neri I., Walter J.-C., Dorignac J., Geniet F., Parmeggiani A.
(Article) Publié:
European Physical Journal E, vol. p.19 (2021)
Texte intégral en Openaccess :
Ref HAL: hal-02989969_v1
Ref Arxiv: 2009.14533
DOI: 10.1140/epje/s10189-021-00019-8
Ref. & Cit.: NASA ADS
Exporter : BibTex | endNote
Résumé: Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally, while unbound ribosomes diffuse in the cytoplasm. It has been hypothesized that finite diffusion of ribosomes plays an important role in ribosome recycling and that mRNA circularization enhances the efficiency of translation. In order to estimate the effect of cytoplasmic diffusion on the rate of translation, we consider a Totally Asymmetric Simple Exclusion Process (TASEP) coupled to a finite diffusive reservoir, which we call the Ribosome Transport model with Diffusion (RTD). In this model, we derive an analytical expression for the rate of protein synthesis as a function of the diffusion constant of ribosomes, which is corroborated with results from continuous-time Monte Carlo simulations. Using a wide range of biological relevant parameters, we conclude that diffusion in biological cells is fast enough so that it does not play a role in controlling the rate of translation initiation.
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Phase separation of polymer-bound particles induced by loop-mediated one dimensional effective long-range interactions
Auteur(s): David G., Walter J.-C., Broedersz Chase P., Dorignac J., Geniet F., Parmeggiani A., Walliser N.-O., Palmeri J.
(Article) Publié:
Physical Review Research, vol. 2 p. (2020)
Texte intégral en Openaccess :
Ref HAL: hal-02950974_v1
DOI: 10.1103/PhysRevResearch.2.033377
Exporter : BibTex | endNote
Résumé: The cellular cytoplasm is organized into compartments. Phase separation is a simple manner to create membraneless compartments in order to confine and localize particles like proteins. In many cases, these particles are bound to fluctuating polymers like DNA or RNA. We propose a general theoretical framework for such polymer-bound particles and derive an effective 1D lattice gas model with both nearest-neighbor and emergent long-range interactions arising from looped configurations of the fluctuating polymer. We argue that 1D phase transitions exist in such systems for both Gaussian and self-avoiding polymers and, using a variational method that goes beyond mean-field theory, we obtain the complete mean occupation-temperature phase diagram. To illustrate this model, we apply it to the biologically relevant case of ParABS, a prevalent bacterial DNA segregation system.
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Physical modeling of a sliding clamp mechanism for the spreading of ParB at short genomic distance from bacterial centromere sites
Auteur(s): Walter J.-C., Rech Jerome, Walliser N.-O., Dorignac J., Geniet F., Palmeri J., Parmeggiani A., Bouet Jean-Yves
(Document sans référence bibliographique) 2020-07-24Texte intégral en Openaccess :
Ref HAL: hal-02990554_v1
Exporter : BibTex | endNote
Résumé: Bacterial ParB partitioning proteins involved in chromosomes and low-copy-number plasmid segregation have recently been shown to belong to a new class of CTP-dependent molecular switches. Strikingly, CTP binding and hydrolysis was shown to induce a conformational change enabling ParB dimers to switch between an open and a closed conformation. This latter conformation clamps ParB dimers on DNA molecules, allowing their diffusion in one dimension along the DNA. It has been proposed that this novel sliding property may explain the spreading capability of ParB over more than 10-Kb from parS centromere sites where ParB is specifically loaded. Here, we modeled such a mechanism as a typical reaction-diffusion system and compared this ‘Clamping & sliding’ model to the ParB DNA binding pattern from high-resolution ChIP-sequencing data. We found that this mechanism can not account for all the in vivo characteristics, especially the long range of ParB binding to DNA. In particular, it predicts a strong effect of the presence of a roadblock on the ParB binding pattern that is not observed in ChIP-seq. Moreover, the rapid assembly kinetics observed in vivo after the duplication of parS sites is not easily explained by this mechanism. We propose that ‘Clamping & sliding’ might explain the ParB spreading pattern at short distances from parS but that another mechanism must apply for ParB recruitment at larger genomic distances.
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Modeling the formation and positioning of intracellular macromolecular assemblies: Application to bacterial DNA segregation
Auteur(s): Walter J.-C.
(H.D.R.)
, 2020Texte intégral en Openaccess :
Ref HAL: tel-02893703_v1
Exporter : BibTex | endNote
Résumé: Biology offers new systems for Physics, namely proteins and molecular motors in interaction with biopolymers like DNA and messenger RNA. This field is at the interface between active matter, polymer physics, and physics of colloids. Interestingly, cells also need to increase locally concentrations of proteins in a phase transition-like mechanism to realize vital function like cell division, DNA repair, DNA segregation etc. During this HDR defense, I will offer a physical perspective of intracellular phase transition with the example of bacterial DNA segregation. I will also discuss the motion of ribosomes along messenger RNA, an example of unidimensional inhomogeneous transport giving rise to different dynamical regimes.
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Biophysical Modeling of Translation in Cancer Cells
Auteur(s): Walter J.-C.
Conference: Life of Cancer Cells (Montpellier, FR, 2019-12-12)
Ref HAL: hal-02409954_v1
Exporter : BibTex | endNote
Résumé: The translation apparatus has long been viewed as a mere factory until recent findings this last decade have unraveled its unexpected role in orchestrating real time gene regulation. Far from being a molecular monolith, the ribosome displays a remarkable heterogeneity along with a striking ability to orchestrate real-time control of gene expression. In the meantime, several reports connect alteration of the translation machinery with elevated cancer risk as well as in tumor initiation and progression. We aim to decipher the variety of translation mechanisms by modeling dedicated Ribo-sequencing experiments. We have designed a new set of Ribo-seq experiments with purified polysomes in order to understand the role of the ribosome density onto translation and to characterized biophysical parameters of translations (hopping rates of ribosomes, initiation rate, termination rate). Preliminary data will be modeled as a proof of concept to pave the way to a genome wide analysis with morefinely regulated genes in charge, e.g., for cell phenotype. After a presentation of the physical perspective of translation, I will discuss the usefulness of biophysical modeling approaches to estimate the codon-dependent hopping, initiation and termination rates of ribosomes from Ribo-seq data. I will discuss designed Ribo-seq experiments (purified polysomes) obtained at IGF suggesting that the ribosome dynamics depends on various conditions: modified dynamics of the first ribosome entering the newly transcripted mRNA, different paradigms for translation (cytoplasmic versus membrane translation), effect of inhomogeneous hopping rates on ribosome traffic etc. Finally, I will consider how these findings will help to understand the epithelial-mesenchymal transition: we have performed designed Ribo-seq experiments inducing a change of the ribosomes concentration level in vivo in tumor human cells and observed induced change of phenotype to mezenchymal cells.
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