Chemical-Reaction-Controlled Phase Separated Drops: Formation, Size Selection, and Coarsening

Wurtz, Jean David; Lee, Chiu Fan

doi:10.1103/physrevlett.120.078102

Cited by 91 publications

(124 citation statements)

References 24 publications

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“…Still, why do ArtiG mCh/PUM exhibit a limited size with respect to the protein-based ArtiG mCh ? Theoretical studies suggest that coarsening by Ostwald ripening could be counterbalanced if non-equilibrium chemical reactions are present in the droplets [61][62][63] . In X. laevis oocytes, nuclear actin network has been shown to stabilize nucleoli against coalescence 64 .…”

Section: Discussionmentioning

confidence: 99%

RNA is a critical element for the sizing and the composition of phase-separated RNA-protein condensates

Navarro

Kashida

Chouaib

et al. 2018

Preprint

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Liquid-liquid phase separation is thought to be a key organizing principle in eukaryotic cells to generate highly concentrated dynamic assemblies, such as the RNP granules. Numerous in vitro approaches have validated this model, yet a missing aspect is to take into consideration the complex molecular mixture and promiscuous interactions found in vivo. Here we report the versatile scaffold "ArtiG" to generate concentration-dependent RNA-protein condensates within living cells, as a bottom-up approach to study the impact of co-segregated endogenous components on phase separation. We demonstrate that endogenous RNA seeds the nucleation of the condensates, as it provides molecular cues to locally coordinate the formation of endogenous high order RNP assemblies. Interestingly, the co-segregation of intracellular components ultimately impacts the size of the phase-separated condensates. Thus, RNA arises as an architectural element that can influence the composition and the morphological outcome of the condensate phases in an intracellular context.implemented the PUM.HD domain of human Pumilio 1, a translational repressor that accumulates in P-bodies 24 , and we demonstrated that the resulting ArtiG PUM specifically recruit endogenous Pumilio 1 RNA-targets. Finally, this method enabled us to uncover the impact of intracellular RNA in different aspects of the condensate assembly: (i) ArtiG PUM form more efficiently than control ArtiG, underlining that the recruitment of endogenous RNA seeds and facilitates the condensate nucleation. (ii) The size and polydispersity of ArtiG PUM per cell is strikingly reduced, while their number is higher, compared to control ArtiG. This indicates that the incorporation of endogenous RNAs modulates the morphological outcome of phase-separated condensates. (iii) Micrometric bodies composed of P-body components localize at the periphery of ArtiG PUM , revealing that ArtiG PUM subsequently and specifically co-segregate the RBPs associated to the Pumilio-targeted RNAs. Interestingly, the ArtiG PUM interact with SG elements exclusively in response to stress. We suggest that the multivalent RNAs displayed on ArtiG PUM surface act as molecular cues that seed the recruitment of specific subsets of RBPs/RNAs and coordinate the coexistence of endogenous higher-structured assemblies, such as P-Body-like and SG-like assemblies. Furthermore, the docking of biochemically different phases, which is a conserved feature of numerous RNP granules, emerges as a parameter that can regulate the size of the condensates by limiting the growth by structural component addition or coalescence. observations support that RNA can act as key regulator of in vivo phase separation by seeding the process 18,21,22,39 .An open question is how the biochemical composition of RNP granules is determined and maintained 23 . Our results show that micrometric bodies of specific compositions are localized at the periphery of ArtiG PUM . The addition of a RNA binding domain to the protein-scaffold confers the capacity to communicate...

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Section: Discussionmentioning

confidence: 99%

RNA is a critical element for the sizing and the composition of phase-separated RNA-protein condensates

Navarro

Kashida

Chouaib

et al. 2018

Preprint

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“…Chemical reactions can also alter the physics of droplet size and number in ways that are likely important for cell function . In an equilibrium picture, a system containing several droplets will generally evolve by larger droplets growing at the expense of smaller ones, a process termed Ostwald ripening.…”

Section: Active Matter and Non‐equilibrium Effectsmentioning

confidence: 99%

“…Recent work has studied how chemical reactions can change these characteristics. The influence of Ostwald ripening can be opposed by chemical reactions that produce or deplete droplet material . In one example, a Flory–Huggins approach that included chemical reactions was used to model the dynamics of centrosomes, which are important in organizing networks of microtubules in cells .…”

Section: Active Matter and Non‐equilibrium Effectsmentioning

confidence: 99%

Physical Chemistry of Cellular Liquid‐Phase Separation

Bentley

Frey

Deniz

2019

Chemistry A European J

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Compartmentalization of biochemical processes is essential for cell function. Although membrane‐bound organelles are well studied in this context, recent work has shown that phase separation is a key contributor to cellular compartmentalization through the formation of liquid‐like membraneless organelles (MLOs). In this Minireview, the key mechanistic concepts that underlie MLO dynamics and function are first briefly discussed, including the relevant noncovalent interaction chemistry and polymer physical chemistry. Next, a few examples of MLOs and relevant proteins are given, along with their functions, which highlight the relevance of the above concepts. The developing area of active matter and non‐equilibrium systems, which can give rise to unexpected effects in fluctuating cellular conditions, are also discussed. Finally, our thoughts for emerging and future directions in the field are discussed, including in vitro and in vivo studies of MLO physical chemistry and function.

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“…Phase separation refers to the spontaneous partitioning of a system into compartments of distinct macroscopic properties, such as the condensation of water vapour into droplets when fog forms. Phase separation under equilibrium condition is a well-understood phenomenon [7], however the phase separation in the cytoplasm can be driven out of equilibrium by a number of effects that include activity of motor proteins shuttling along the cytoskeleton [8], and chemical reactions affecting the phase-separating behaviour of RNP granule constituents [9][10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

“…In this paper, we apply the theoretical formalism developed in [13] to investigate minimal models of SG regulation based on non-equilibrium, chemical reaction-controlled phase separation. SG are a particularly dynamic type of RNP granules as they form quickly, in the order of 10min, when the cell is under stress (e.g., heat shock, chemical stress, osmotic shock, etc), and also dissolve away rapidly when the stress is removed [14,15].…”

Section: Introductionmentioning

confidence: 99%

Stress granule formation via ATP depletion-triggered phase separation

Wurtz

Lee

2018

New J. Phys.

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Stress granules (SG) are droplets of proteins and RNA that form in the cell cytoplasm during stress conditions. We consider minimal models of stress granule formation based on the mechanism of phase separation regulated by ATP-driven chemical reactions. Motivated by experimental observations, we identify a minimal model of SG formation triggered by ATP depletion. Our analysis indicates that ATP is continuously hydrolysed to deter SG formation under normal conditions, and we provide specific predictions that can be tested experimentally. Experimental observationsExperimental studies have shown that SG assemble in response to multiple types of stress situations [21,22,23], and several pathways for SG formation have been identified. The most established is the ATP-dependent phosphorylation of the translation initiation factor eIF2α causing the arrest of RNA translation [16]. RNA is subsequently released from polysomes and aggregate with various proteins to form SG. There exist also other pathways that are independent of eIF2α phosphorylation [24], such as energy starvation [23]. Indeed, while various stress conditions causing SG assembly also cause a depletion of the cytoplasmic energy stores [21,25,26],

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Chemical-Reaction-Controlled Phase Separated Drops: Formation, Size Selection, and Coarsening

Cited by 91 publications

References 24 publications

RNA is a critical element for the sizing and the composition of phase-separated RNA-protein condensates

RNA is a critical element for the sizing and the composition of phase-separated RNA-protein condensates

Physical Chemistry of Cellular Liquid‐Phase Separation

Stress granule formation via ATP depletion-triggered phase separation

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