Phase separation of polymer-bound particles induced by loop-mediated one dimensional effective long-range interactions

David, Gabriel; Walter, Jean‐Charles; Broedersz, Chase P.; Dorignac, Jérôme; Geniet, Frédéric; Parmeggiani, Andrea; Walliser, Nils-Ole; Palmeri, John

doi:10.1103/physrevresearch.2.033377

Cited by 5 publications

(6 citation statements)

References 51 publications

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“…In the dynamic simulations of the main text, we chose the value close to the estimated upper limit in order to be as close as possible to the .5 J = 4 experimental value of 90% of ParB inside the droplets ( (Sanchez et al 2015) , and here). This value is in semi-quantitative agreement with other simulation works on ParB-ParB (Broedersz et al 2014;David et al 2018) . At the gas density on the thermodynamic coexistence curve is very low (see Fig.…”

Section: Data Availability Statementsupporting

confidence: 92%

“…For 1d, 2d square, and 3d simple cubic lattices, the LG coordination number is q = 2d . Recent work (David et al 2018) shows that a 1D LG model on a fluctuating polymer like DNA can undergo phase separation and that such a model can, after averaging over the polymer conformational fluctuations, be assimilated approximately to a LG with short range (nearest-neighbor) interactions on a lattice with an effective, perhaps fractal, coordination number between 2 and 6 (G. David, PhD Thesis, in preparation). The increase in coordination number from the value of 2 expected for a linear polymer is due to the combined effects of nearest-neighbor (spreading) interactions along the polymer and bridging interactions between proteins widely separated on the polymer, but close in space.…”

Section: Figure S3mentioning

confidence: 99%

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ATP-driven separation of liquid phase condensates in bacteria

Guilhas

Walter

Rech

et al. 2019

Preprint

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Liquid-liquid phase separated (LLPS) states are key to compartmentalise components in the absence of membranes, however it is unclear whether LLPS condensates are actively and specifically organized in the sub-cellular space and by which mechanisms. Here, we address this question by focusing on the ParAB S DNA segregation system, composed of a centromeric-like sequence ( parS ), a DNA-binding protein (ParB) and a motor (ParA). We show that parS -ParB associate to form nanometer-sized, spherical droplets. ParB molecules diffuse rapidly within the nucleoid volume, but display confined motions when trapped inside ParB droplets. Single ParB molecules are able to rapidly diffuse between different droplets, and droplet nucleation is strongly favoured by parS . Notably, the ParA motor is required to prevent the fusion of ParB droplets. These results describe a novel active mechanism that splits, segregates and localises LLPS condensates in the sub-cellular space. 80 85 90 95 100 et al., 2005) , localizes to a large extent (~90% of ParB molecules) to regions containing parS (Sanchez et al., 2015) to form a tight nucleoprotein complex (partition complex). Formation of the partition complex requires weak ParB-ParB dimer interactions mediated by its disordered, low-complexity region. Here, we used super-resolution microscopy and single-particle analysis to investigate the physical mechanisms involved in the formation of partition complexes. We show that partition complexes are small (<50nm), spherical objects.Single, isolated ParB molecules diffuse rapidly within the nucleoid volume, but display confined motions when trapped inside partition complexes. These results suggest a partition of ParB into two phases: a gas-like phase, and a dense, liquid-like condensate phase that shows nanometer-sized, spherical droplets. Next, we show that the nucleation of ParB condensates is strongly favoured by the presence of the centromeric sequence parS .Separation and proper sub-cellular localization of ParB condensates require the ParA motor.Critically, different ParB condensates collapse into a single droplet upon the degradation of ParA. These results describe a novel active mechanism that splits, segregates and localises LLPS condensates in the sub-cellular space. Results ParB assembles into spherical nano-condensatesPrevious studies have revealed that the partition complex is made of ~300 dimers of ParB (Adachi et al., 2006;Bouet et al., 2005) and ~10kb of parS -proximal DNA (Rodionov et al., 1999) . This complex is held together by specific, high-affinity interactions between ParB and parS , and by low-affinity interactions between ParB dimers that are essential for the power-law distribution of ParB around parS sites ( Figure 1A) (Debaugny et al., 2018; Sanchez 455 460 465 470 475 480 485 https://docs.google.com/document/d/1xM7w7WU8bbag5sVCGg1xatPdYe5i1xia3PzXthmzPW8/edit# 24/45 530 535 540 545 550 555 560 https://docs.google.com/document/d/1xM7w7WU8bbag5sVCGg1xatPdYe5i1xia3PzXthmzPW8/edit# 25/45 565 570 575 580 585 590 595 https:/...

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Section: Data Availability Statementsupporting

confidence: 92%

Section: Figure S3mentioning

confidence: 99%

ATP-driven separation of liquid phase condensates in bacteria

Guilhas

Walter

Rech

et al. 2019

Preprint

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“…Super-resolution microscopic measurements suggest that these clusters result from a phase transition-like mechanism [14]. Theoretical models further suggest that this phase transition is unconventional as it may imply a framework of a lattice gas on a fluctuating polymer [30]. From a biological perspective, the mechanisms underlying the formation of a cluster should reflect the non-trivial cellular organization of genetic information and proteins [31].…”

Section: Leaky Vs Quenched Clustermentioning

confidence: 99%

Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex

et al. 2021

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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.

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“…Recent work has investigated the role of polymer ‘scaffolds’ on the phase-separation of 3D proteins [10, 36, 37], and how 3D proteins mediate communication between distal genomic regions [38, 39]. This work has emphasized that polymers can widen regimes in which a bulk fluid undergoes a phase-transition.…”

Section: Discussionmentioning

confidence: 99%

Polymer Collapse & Liquid-Liquid Phase-Separation are Coupled in a Generalized Prewetting Transition

Rouches,

Machta

2024

Preprint

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The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with particular sequences of DNA. At unphysiological concentrations many of these nuclear proteins can phase-separate in the absence of DNA, and it has been hypothesized that, in vivo, the thermodynamic forces driving these phases help determine chromosomal organization. However it is unclear how DNA, itself a long polymer subject to configurational transitions, interacts with three-dimensional protein phases. Here we show that a long compressible polymer can be coupled to interacting protein mixtures, leading to a generalized prewetting transition where polymer collapse is coincident with a locally stabilized liquid droplet. We use lattice Monte-Carlo simulations and a mean-field theory to show that these phases can be stable even in regimes where both polymer collapse and coexisting liquid phases are unstable in isolation, and that these new transitions can be either abrupt or continuous. For polymers with internal linear structure we further show that changes in the concentration of bulk components can lead to changes in three-dimensional polymer structure. In the nucleus there are many distinct proteins that interact with many different regions of chromatin, potentially giving rise to many different Prewet phases. The simple systems we consider here highlight chromatin's role as a lower-dimensional surface whose interactions with proteins are required for these novel phases.

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Phase separation of polymer-bound particles induced by loop-mediated one dimensional effective long-range interactions

Cited by 5 publications

References 51 publications

ATP-driven separation of liquid phase condensates in bacteria

ATP-driven separation of liquid phase condensates in bacteria

Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex

Polymer Collapse & Liquid-Liquid Phase-Separation are Coupled in a Generalized Prewetting Transition

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