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• Expert MSTP/AERES

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• Physique/Physique/Biophysique
  
• Science non linéaire/Automates cellulaires et gaz sur réseau [nlin.CG]
  
• Science non linéaire/Adaptation et Systèmes auto-organisés [nlin.AO]
  
• Sciences du Vivant/Cancer
  
• Sciences du Vivant/Biologie cellulaire/Organisation et fonctions cellulaires [q-bio.SC]
  
• Sciences du Vivant/Biochimie, Biologie Moléculaire/Réseaux moléculaires [q-bio.MN]
  
• Physique/Physique/Physique et Société
  

ParABS, the most widespread bacterial DNA segregation system, is composed of a centromeric sequence, parS, and two proteins, the ParA ATPase and the ParB DNA binding proteins. Hundreds of ParB proteins assemble dynamically to form nucleoprotein parS-anchored complexes that serve as substrates for ParA molecules to catalyze positioning and segregation events. The exact nature of this ParBS complex has remained elusive, what we address here by revisiting the Stochastic Binding model (SBM) introduced to explain the non-specific binding profile of ParB in the vicinity of parS. In the SBM, DNA loops stochastically bring loci inside a sharp cluster of ParB. However, previous SBM versions did not include the negative supercoiling of bacterial DNA, leading to use unphysically small DNA persistences to explain the ParB binding profiles. In addition, recent super-resolution microscopy experiments have revealed a ParB cluster that is significantly smaller than previous estimations and suggest that it results from a liquid-liquid like phase separation. Here, by simulating the folding of long (>30 kb) supercoiled DNA molecules calibrated with realistic DNA parameters and by considering different possibilities for the physics of the ParB cluster assembly, we show that the SBM can quantitatively explain the ChIP-seq ParB binding profiles without any fitting parameter, aside from the supercoiling density of DNA, which, remarkably, is in accord with independent measurements. We also predict that ParB assembly results from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., ParB clusters behave like liquid-like protein condensates with unconventional “leaky” boundaries.

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.

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.

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.

The cytoskeleton in eukaryotic cells plays several crucial roles. In terms of intracellular transport, motor proteins use the cytoskeletal filaments as a backbone along which they can actively transport biological cargos such as vesicles carrying biochemical reactants. Crossings between such filaments constitute a key element, as they may serve to alter the destination of such payload. Although motor proteins are known to display a rich behaviour at such crossings, the latter have so far only been modelled as simple branching points. Here we explore a model for a crossing between two microtubules which retains the individual tracks consisting of protofilaments, and we construct a schematic representation of the transport paths. We study collective transport exemplified by the Totally Asymmetric Simple Exclusion Process (TASEP), and provide a full analysis of the transport features and the associated phase diagram, by a generic mean-field approach which we confirm through particle-based stochastic simulations. In particular we show that transport through such a compound crossing cannot be approximated from a coarse-grained structure with a simple branching point. Instead, it gives rise to entirely new and counterintuitive features: the fundamental current-density relation for traffic flow is no longer a single-valued function, and it furthermore differs according to whether it is observed upstream or downstream from the crossing. We argue that these novel features may be directly relevant for interpreting experimental measurements.