Liquid–liquid phase separation in cells

Biomolecular condensates are emerging as hubs of splicing regulation. This Review discusses the modulation of condensate functions through alternative splicing, regulation of (co-transcriptional) splicing at condensates and the involvement of these condensates in human diseases.

Biomolecular condensates help organize cell components under normal conditions but can also be involved in pathological protein aggregation when condensate proteins carry mutations or under stress conditions. This Review discusses the possible mechanisms behind such aggregation processes that potentially lead to neurodegenerative diseases.

High-throughput proteome-wide methods for identifying endogenous proteins that phase separate or partition into condensates during certain physiological events are needed but remain a challenge. Now, a high-throughput, unbiased and quantitative strategy can identify endogenous biomolecular condensates and screen proteins involved in phase separation on a proteome-wide scale.

Oncoprotein transcription factor MYC undergoes phase separation, forming transcriptionally active condensates. The chemogenetic tool SPARK-ON reveals that MYC phase separation selectively modulates the transcriptome and promotes cell proliferation.

Lu et al. investigate the involvement of liquid–liquid phase separation in the progression of triple-negative breast cancer and find that phosphorylated histone deacetylase 6 forms condensates that affect chromatin accessibility and oncogenic transcriptional programs.

Liquid–liquid phase separation (LLPS) has been revealed as a widespread mechanism underlying the spatiotemporal coordination of biological activities in cells. This Perspective discusses how LLPS shapes the biochemical landscape of cancer cells, providing insight into emerging findings of dysregulated LLPS promoting cancer pathology.

Biomolecular condensates are membraneless compartments that typically contain proteins and RNAs and broadly affect many cell types and organs. In the kidney in particular, rapid and reversible assembly of biomolecular condensates occurs through the process of hyperosmotic phase separation. This Review describes emerging evidence for, and the impact of, biomolecular condensates on kidney physiology and disease.

Fluid protein condensates are utilized as precursors in the production of high-performance biological fibres, adhesives and composites. This Review outlines the key role of condensates in the formation of several well-studied biological materials and highlights bioengineered materials with biomedical applications that draw inspiration from these archetypes.

Phase separation of biomolecular condensates provides a new framework to understand cellular organization and functions. In this Review, the authors discuss the applications and design considerations of synthetic biomolecular condensates to regulate cellular functions as a new paradigm for synthetic biology.

Frameshift mutations that create arginine-rich basic tails in transcription factors and other proteins can lead to altered phase separation in the nucleolus, which in turn leads to syndromes such as brachyphalangy, polydactyly and tibial aplasia.

Condensates have been proposed to create a distinct chemical solvating environment. In vitro condensate screens suggest that condensate chemical environments influence the intracellular distribution of small molecules.

In this work the authors describe antimicrobial peptides (AMPs)-driven phase transitions of intracellular nucleic acids, whereby AMPs induce compaction and phase separation of nucleic acids, resulting in their sequestration and eventual cell death.

This review discusses the principles of phase separation and highlights how it impacts diverse processes in fungi.

ALBATROSS is a deep-learning-based model for predicting ensemble properties of intrinsically disordered proteins and protein regions, such as radius of gyration, end-to-end distance, polymer-scaling exponent and ensemble asphericity, directly from sequences.

Cells spatially organize biochemical reactions within membrane-bound and membraneless compartments. The extent to which intrinsically disordered proteins themselves can form discrete compartments or condensed phases is poorly understood. Now a pair of model IDRs that display orthogonality in condensation and the chain features governing selective assembly have been identified.

Keber et al. use filtration chromatography and quantitative proteomics of Xenopus egg extracts and show that at least 18% of cytoplasmic proteins are organized in small ~100-nm biomolecular condensates.

Arabidopsis photoreceptor CRY2 controls chlorophyll homeostasis by blue light-induced liquid–liquid phase separation of the CRY2/SPA1/FIO1 complex, resulting in activation of the m⁶A writer FIO1, regulating mRNAs encoding chlorophyll homeostasis proteins.

The active zone primes synaptic vesicles and clusters voltage-gated Ca²⁺ channels fast neurotransmitter release. Here the authors dissect the underlying molecular architecture and show that distinct protein machineries execute these functions.

Experimental and theoretical results demonstrate that tight-junction formation depends on the growth of a condensed layer of ZO-1 proteins at the interface of the apical and lateral membrane, providing insight into self-assembly of complex mesoscale structures in cells.

The time-dependent viscoelastic moduli of biomolecular condensates are connected to the functions that the condensates influence in cells. Now sticker and spacer residues in proteins are shown to regulate condensate viscoelasticity and ageing dynamics.

This Review outlines our current understanding of the biogenesis and functions of lipid droplets in health and disease, highlighting a key role for lipid droplet biogenesis in alleviating cellular stress.

Liquid-liquid phase separation (LLPS) underlies the formation of intracellular membraneless compartments in biology and may have played a role in the formation of protocells that concentrate key chemicals during the origins of life. While LLPS of simple systems, such as oil and water, is well understood, many aspects of LLPS in complex, out-of-equilibrium molecular systems remain elusive. Here, the author discusses open questions and recent insights related to the formation, function and fate of such condensates both in cell biology and protocell research.

Biomolecular condensates compartmentalize molecules without membranes. Understanding condensate composition is important given that their function relies on the selective exclusion or enrichment of molecules. Now, investigating small-molecule partitioning reveals variations across compounds, yet correlations indicate physical similarities between disparate condensates. Machine learning accurately predicts partitioning on the basis of physicochemical features, demonstrating the role of a hydrophobic environment in driving enrichment and exclusion.

The molecular mechanisms underlying the formation of biomolecular condensates have not been fully elucidated. Here the authors show that the LLPS propensity, dynamics, and encapsulation efficiency of designed peptide condensates can be tuned by subtle changes to the peptide composition.

Aggregated forms of α-synuclein are characteristic of Parkinson’s disease. Here the authors show that the condensation-driven aggregation pathway of α-synuclein can be inhibited using small molecules: the aminosterol claramine stabilizes α-synuclein condensates and inhibits α-synuclein primary nucleation in the aggregation process.

Condensates with a shell can be formed by liquid-liquid phase separation and can burst like viscous bubbles by nucleation and growth of a hole in the shell surrounded by a rim. The authors develop a model to extract a broad range of rheological properties for spherical shells to understand the conditions for bursting.

Water/water phase separation in cells facilitates the spatial localization of biological components, but its influence on mechanical processes driven by protein motors has been largely overlooked. Here, the interface of water/water phase separation is shown to produce mechanical motion by spontaneously entrapping kinesins and microtubules and generating a micrometre-scale vortex flow inside cell-sized droplets.

Mechanistic studies on KDM2B interaction with BCOR/PCGF1 sheds light on the role of calcium and liquid-liquid phase separation in KDM2B recruiting BCOR-PRC1.1 on chromatin.

An investigation of tau’s phase separation propensity and interactions with DNA, nucleosome arrays, and heterochromatin proteins shows that these properties are dependent on tau’s phosphorylation state.