Liquid phase condensation in cell physiology and disease

Micropore structure engineering of injectable granular hydrogels via controlled liquid-liquid phase separation facilitates regenerative wound healing in mice and pigs

Biomaterials can play a crucial role in facilitating tissue regeneration, but their application is often limited by that they induce scarring rather than complete tissue restoration. Hydrogels with microporous architectures, engineered via 3D printing techniques or particle packing (granular hydrogels), have shown promise in providing a conducive microenvironment for cellular infiltration and favorable immune response. Nonetheless, there is a notably lacking in studies that demonstrate scarless regeneration solely through pore structure engineering. In this study, we demonstrate that optimizing micropore structure of injectable granular hydrogels via controlled liquid-liquid phase separation facilitates scarless wound healing. The building block particles are fabricated by precisely controlling the separation kinetics of two immiscible aqueous phases (gelling and porogenic) and timely arresting phase separation, to generate bicontinuous, hollow or closed porous structure. Employing a murine model, we reveal that the optimized pore structure significantly facilitates mature vascular network boosts pro-regenerative macrophage polarization (M2/M1) and CD4+/Foxp3+ regulatory T cells, culminating in scarless skin regeneration enriched with hair follicles. Moreover, our hydrogels outperform the clinical gold-standard collagen/proteoglycan scaffolds in a porcine model, showcasing superior cell infiltration, epidermal integration, and dermal regeneration. Micropore structure engineering of biomaterials presents a promising and biologics free pathway for tissue regeneration.

Synthetic Forms Most Beautiful: Engineering Insights into Self-Organization

Reflecting on the diversity of the natural world, Darwin famously observed that "from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved." However, the examples that we are able to observe in nature are a consequence of chance, constrained by selection, drift, and epistasis. Here we explore how the efforts of synthetic biology to build new living systems can expand our understanding of the fundamental design principles that allow life to self-organize biological form, from cellular to organismal levels. We suggest that the ability to impose a length or timescale onto a biological activity is an essential strategy for self-organization in evolved systems and a key design target that is now being realized synthetically at all scales. By learning to integrate these strategies together, we are poised to expand on evolution's success and realize a space of synthetic forms not only beautiful but with diverse applications and transformative potential.

Micropipette aspiration reveals differential RNA-dependent viscoelasticity of nucleolar subcompartments

The nucleolus is a multiphasic biomolecular condensate that facilitates ribosome biogenesis, a complex process involving hundreds of proteins and RNAs. The proper execution of ribosome biogenesis likely depends on the material properties of the nucleolus. However, these material properties remain poorly understood due to the challenges of in vivo measurements. Here, we use micropipette aspiration (MPA) to directly characterize the viscoelasticity and interfacial tensions of nucleoli within transcriptionally active Xenopus laevis oocytes. We examine the major nucleolar subphases, the outer granular component (GC) and the inner dense fibrillar component (DFC), which itself contains a third small phase known as the fibrillar center (FC). We show that the behavior of the GC is more liquid-like, while the behavior of the DFC/FC is consistent with that of a partially viscoelastic solid. To determine the role of ribosomal RNA in nucleolar material properties, we degrade RNA using RNase A, which causes the DFC/FC to become more fluid-like and alters interfacial tension. Together, our findings suggest that RNA underlies the partially solid-like properties of the DFC/FC and provide insights into how material properties of nucleoli in a near-native environment are related to their RNA-dependent function.

A viral necrosome mediates direct RIPK3 activation to promote inflammatory necroptosis

Necroptosis is an inflammatory programmed cell death pathway triggered by RIPK3 activation through one of the upstream RHIM-domain-containing proteins including RIPK1, TRIF, and ZBP1. Whether necroptosis can be activated independent of the upstream signaling pathways leading to inflammatory pathogenesis remains ambiguous. Here, we revealed a mechanism in which a viral protein mediates direct RIPK3 activation resulting in severe inflammatory pathogenesis in patients. The nonstructural protein NSs of a pathogenic hemorrhagic virus, SFTSV, interacts with the RIPK3 kinase domain and forms biocondensate to promote RIPK3 autophosphorylation and necroptosis activation in an RHIM-independent manner. In parallel, sequestration of RIPK3 within the NSs-RIPK3 condensate inhibited RIPK3-mediated apoptosis and promoted viral replication. Infection with an SFTSV NSs mutant virus not forming NSs condensate triggered pronounced apoptosis resulting in reduced viral replication and decreased fatality in vivo. Blocking SFTSV-triggered necroptosis through depletion of MLKL or treatment with a RIPK3-kinase inhibitor reduced viral inflammatory pathogenesis and fatality in vivo. In contrast, blocking SFTSV-triggered apoptosis through depletion of RIPK3 resulted in enhanced viral replication and increased fatality in vivo. The virus-triggered necroptosis correlated with severe inflammatory pathogenesis and lethality in virus-infected patients. The NSs-RIPK3 condensate may represent a necroptosis activation mechanism that promotes viral pathogenesis.

Intrinsically disordered regions as facilitators of the transcription factor target search

Transcription factors (TFs) contribute to organismal development and function by regulating gene expression. Despite decades of research, the factors determining the specificity and speed at which eukaryotic TFs detect their target binding sites remain poorly understood. Recent studies have pointed to intrinsically disordered regions (IDRs) within TFs as key regulators of the process by which TFs find their target sites on DNA (the TF target search). However, IDRs are challenging to study because they can confer specificity despite low sequence complexity and can be functionally conserved despite rapid sequence divergence. Nevertheless, emerging computational and experimental approaches are beginning to elucidate the sequence-function relationship within the IDRs of TFs. Additional insights are informing potential mechanisms underlying the IDR-directed search for the DNA targets of TFs, including incorporation into biomolecular condensates, facilitating TF co-localization, and the hypothesis that IDRs recognize and directly interact with specific genomic regions.

Dynamic Plasma Membrane Topography Linked With Arp2/3 Actin Network Induction During Cell Shape Change

Recent studies show the importance of mesoscale changes to plasma membrane (PM) topography during cell shape change. Local folding and flattening of the cell surface is mechanosensitive, changing in response to both microenvironment structural elements and intracellular cytoskeletal activities. These topography changes elicit local mechanical signaling events that act in conjunction with molecular signal transduction pathways to remodel the cell cortex. Experimental manipulations of local PM curvature show its sufficiency for recruiting Arp2/3 actin network induction pathways. Additionally, studies of diverse cell shape changes-ranging from neutrophil migration to early Drosophila embryo cleavage to neural stem cell asymmetric division-show that local generation of PM folding is linked with local Arp2/3 actin network induction, which then remodels the PM topography during dynamic control of cell structure. These examples are reviewed in detail, together with known and potential causes of PM topography changes, downstream effects, and higher-order feedback.

The thermodynamic hypothesis of protein aggregation

Protein misfolding and aggregation drive some of the most prevalent and lethal disorders of our time, including Alzheimer's and Parkinson's diseases, now affecting tens of millions of people worldwide. The complexity of these diseases, which are often multifactorial and related to age and lifestyle, has made it challenging to identify the causes of the accumulation of aberrant protein deposits. An insight into the origins of these deposits comes from reports of a widespread presence of protein aggregates even under normal cellular conditions. This observation is best accounted for by the thermodynamic hypothesis of protein aggregation. According to this hypothesis, many proteins are expressed at levels close to their supersaturation limits, so that their native states are metastable against aggregation. Here we integrate the evidence behind this hypothesis and outline actionable therapeutic strategies that could halt protein aggregation at its source.

Protein-RNA condensation kinetics via filamentous nanoclusters

Protein-RNA phase separation is at the center of membraneless biomolecular condensates governing cell physiology and pathology. Using an archetypical viral protein-RNA condensation model, we determined the sequence of events that starts with sub-second formation of a protomer with two RNAs per protein dimer. Association of additional RNA molecules to weaker secondary binding sites in this protomer kickstarts crystallization-like assembly of a molecular condensate. Primary nucleation is faster than the sum of secondary nucleation and growth, which is a multistep process. Protein-RNA nuclei grow over hundreds of seconds into filaments and subsequently into nanoclusters with approximately 600 nm diameter. Cryoelectron microscopy reveals an internal structure formed by incoming layers of protein-RNA filaments made of ribonucleoprotein oligomers, reminiscent of genome packing of a nucleocapsid. These nanoclusters progress to liquid condensate droplets that undergo further partial coalescence to yield typical hydrogel-like protein-RNA coacervates that may represent the scaffold of large viral factory condensates in infected cells. Our integrated experimental kinetic investigation exposes rate-limiting steps and structures along a key biological multistep pathway present across life kingdoms.

Unveiling the dynamic drivers: phase separation's pivotal role in stem cell biology and therapeutic potential

Phase separation is fundamental for cellular organization and function, profoundly impacting a range of biological processes from gene expression to cellular signaling pathways, pivotal in stem cell biology. This review explores the primary types of phase separation and their mechanisms, emphasizing how phase separation is integral to maintaining cellular integrity and its significant implications for disease progression. It elaborates on current insights into how phase separation influences stem cell biology, discussing the challenges in translating these insights into practical applications. These challenges stem from the complex dynamics of phase separation, the need for advanced imaging techniques, and the necessity for real-time, in situ analysis within living systems. Addressing these challenges through innovative methodologies and gaining a deeper understanding of the molecular interactions that govern phase separation in stem cells are essential for developing precise, targeted therapies. Ultimately, advancing our understanding of phase separation could transform stem cell-based therapeutic approaches, opening up novel strategies for disease treatment and advancements in regenerative medicine.

JMJD1C forms condensate to facilitate a RUNX1-dependent gene expression program shared by multiple types of AML cells

JMJD1C (Jumonji Domain Containing 1C), a member of the lysine demethylase 3 (KDM3) family, is universally required for the survival of several types of acute myeloid leukemia (AML) cells with different genetic mutations, representing a therapeutic opportunity with broad application. Yet how JMJD1C regulates the leukemic programs of various AML cells is largely unexplored. Here we show that JMJD1C interacts with the master hematopoietic transcription factor RUNX1, which thereby recruits JMJD1C to the genome to facilitate a RUNX1-driven transcriptional program that supports leukemic cell survival. The underlying mechanism hinges on the long N-terminal disordered region of JMJD1C, which harbors two inseparable abilities: condensate formation and direct interaction with RUNX1. This dual capability of JMJD1C may influence enhancer-promoter contacts crucial for the expression of key leukemic genes regulated by RUNX1. Our findings demonstrate a previously unappreciated role for the non-catalytic function of JMJD1C in transcriptional regulation, underlying a mechanism shared by different types of leukemias.

A novel microscopic origin of co-nonsolvency

Co-nonsolvency presents a fundamental paradox in polymer physics where macromolecules undergo collapse or precipitation in mixed good solvents. Through investigations combining simulations of various binary good solvent systems of polymers, including single-chain and multi-chain of homopolymers and block copolymers, and ternary Flory-Huggins theoretical validation, we reveal that the competition between the enthalpy of the system and the mixing entropy of binary solvents results in the liquid-liquid phase separation (LLPS) of the better solvent (S-solvent) and the co-nonsolvency phenomenon. To reduce the enthalpy, the polymer and S-solvent tend to mix together to maximize their contact, which, however, is entropically unfavorable due to the localization of the S-solvent in the polymer domain. The LLPS of the S-solvent, where different chain segments share the localized S-solvent molecules, simultaneously lowers the enthalpy and reduces the loss of the mixing entropy. This sharing leads the chain in single-chain systems to be in a locally folding conformation with a size being much smaller than that of the ideal chain. In multi-chain systems, however, the sharing can be among segments from different chains, which causes chain condensation and hence an average chain size larger than its ideal value. Our study provides a novel mechanism for co-nonsolvency and may provide insights into the LLPS in other soft matter systems.

Large-scale purifications reveal yeast and human stress granule cores are heterogeneous particles with complex transcriptomes and proteomes

Stress granules are a conserved response of eukaryotic cells to environmental insults. These cytoplasmic ribonucleoprotein condensates have hitherto been primarily studied by microscopy, which showed previously that they comprise dense ∼200 nm cores embedded in a diffuse shell. We have developed large-scale purifications of budding yeast and mammalian (HEK293T cell) stress granule cores that do not rely on immunoprecipitation of candidate protein constituents. These unbiased preparations reveal that stress granule cores are discrete particles with variable size (average, 135 and 225 nm for yeast and human, respectively) and shape. Proteomics and transcriptomics demonstrate complex composition. The results of hybridization chain reaction fluorescence in situ hybridization (FISH) analyses in HEK293T cells are consistent with stress granule cores having heterogeneous composition, i.e., each stress granule core particle contains only a limited number of mRNA species. Biochemical purification now opens the way to mechanistic analysis of the heterogeneity and complexity of stress granules.

A compartmentalized model of multiphase chemical kinetics

There are significant challenges in predicting multiphase chemical kinetics due to the complex coupling of reaction and mass transport across a phase boundary (i.e., interface). Here, we describe a framework for predicting multiphase kinetics that embeds the elementary kinetic steps of reaction, solvation, and diffusion into a coarse grain spatial description of two phases. The model is constructed to bridge the short-timescale interfacial dynamics observed in molecular simulations with the longer timescales observed in kinetic experiments. A simple set of governing differential equations is derived, which, when solved numerically or analytically, yield accurate predictions of multiphase kinetics in microdroplets. Although the equations are formulated for gas-liquid reactions, the underlying conceptual framework is general and can be applied to transformations in other two-phase systems (solid-liquid, liquid-liquid, etc.).

Expansion Microscopy Provides Nanoscale Insight into Nucleolar Reorganization and Nuclear Foci Formation during Nucleolar Stress

The nucleolus, a membraneless organelle crucial for ribosome production, has a unique nanoscale structure whose organization is responsive to cell signals and disease progression. Here, we highlight the potential of Expansion Microscopy (ExM) for capturing intricate spatial and functional information about membraneless organelles such as the nucleolus and nuclear foci. We apply dual protein Expansion Microscopy (dual-proExM) in combination with click Expansion Microscopy (click-ExM) to capture images at the highest resolution reported for the nucleolus of ∼45 ± 2 nm. Inhibition of nucleolar processes triggers a nucleolar stress response, causing distinct structural rearrangements whose molecular basis is an area of active investigation. We investigate time-dependent changes in nucleolar structure and function under nucleolar stress induced by oxaliplatin, actinomycin D, and other platinum-based compounds. Our findings reveal new stages that occur prior to the complete sequestration of RNA Pol I into nucleolar caps, shedding light on the early mechanisms of the nucleolar stress response. RNA transcription is linked to nanoscale protein rearrangements using a combination of click-ExM and pro-ExM, revealing locations of active transcripts during the early stages of nucleolar stress reorganization. With prolonged stress, fibrillarin and NPM1 segregate from the nucleolus into nucleoplasmic foci that are for the first time imaged at nanometer resolution. In addition to revealing new morphological information about the nucleolus, this study demonstrates the potential of ExM for imaging membraneless organelles with nanometer-scale precision.

Net charge driven recruitment of supercharged GFP mutants into FUS droplets

Liquid droplets recruit their relevant proteins and function together. Previous studies for a series of guest proteins clarified several rules of the recruitment and translational dynamics in the droplets; however, the other guest parameters such as structures, sizes, and amino-acid compositions might mask the single parameter effect. Here, we characterized the properties of GFP mutants with different charged compositions, but the same structure and size, in fused in sarcoma (FUS) droplets using single-molecule fluorescence microscopy. The recruitment of GFP mutants depended on their absolute net charge, whereas the diffusion did not. In the recruitment vs. diffusion plots, GFP mutants with large net charges were distinct from other proteins, demonstrating the importance of long-range electrostatic interaction on the recruitment.

Mysteries of adenovirus packaging

It is conventionally held that most DNA viruses package their genomes by one of two fundamental mechanisms: described by the sequential or concurrent models of assembly and packaging. Sequential packaging involves the translocation of a viral genome into a pre-formed capsid, often referred to as the pro-capsid. In contrast, concurrent packaging does not require the assembly of a pro-capsid. Instead, the genome is condensed, and the capsid shell is formed around the genome. The accumulation of empty particles in adenovirus infected cells has led to the assumption that adenovirus packaging may be best described by the sequential model. However, existing models fail to adequately explain all experimental observations, leaving many mysteries of adenovirus genome packaging unresolved. In this review, we describe key findings in adenovirus assembly and packaging, and we discuss them in the context of the competing models of sequential versus concurrent packaging. We discuss recent findings that have redefined our understanding of adenovirus packaging, including the role of viral biomolecular condensates and visualization of viral assembly and packaging in situ. These advances have renewed interest in the concurrent model of packaging. We anticipate that lessons learned from adenovirus packaging will be highly valuable for the advancement of viral vectors and gene-delivery technologies. In reviewing this topic, we hope to stimulate discussion and facilitate future investigation that will ultimately resolve gaps in knowledge and expand our understanding of DNA virus genome packaging.

Noncovalent Lasso Entanglements are Common in Experimentally Derived Intrinsically Disordered Protein Ensembles and Strongly Influenced by Protein Length and Charge

Noncovalent lasso entanglements are conformations in which a protein backbone segment forms a loop closed by noncovalent interactions and that loop is threaded one or more times by either the N- or C-terminal segment of the backbone or both. While these entanglements are common in globular proteins, their presence in intrinsically disordered proteins or regions (IDPs/IDRs) remains largely unexplored. Here, we examine whether IDPs/IDRs in their monomeric form populate these conformations and how sequence length and charge composition influence entanglement prevalence. Using experimentally derived IDP/IDR ensembles from the Protein Ensemble Database, we find that 48% (199 of 416) of its entries contain subpopulations with entangled conformations, with 25% of entries having conformational ensembles in which 50% or more are entangled. This includes IDPs such as nuclear pore complex protein Nup153, nonstructural protein V of Hendra virus, and Eukaryotic initiation factor 4F subunit p150. Using molecular simulations, we find that (i) entanglements are most prevalent in weak polyampholytes and polyelectrolytes, and strong polyampholytes but rare in strong polyelectrolytes; (ii) entanglement populations increase with IDP length; (iii) entanglement probability positively correlates with chain compaction; and (iv) most IDPs/IDRs in the human proteome exhibit entangled conformations. A GO enrichment analysis reveals that the entanglement probability correlates with IDP/IDR function and subcellular localization. Thus, these findings indicate that noncovalent lasso entanglements are a widespread structural feature of IDPs/IDRs and have the potential to be biologically relevant.

Peptide Coacervates: Formation, Mechanism, and Biological Applications

Biomolecular coacervates, dynamic compartments formed via liquid-liquid phase separation (LLPS), are essential for orchestrating intracellular processes and have emerged as versatile tools in bioengineering. Peptides, with their modular amino acid sequences, exhibit unique potential in coacervate design due to their ability to undergo LLPS while offering precise control over molecular architecture and environmental responsiveness. Their simplicity, synthetic accessibility, and tunability make peptide-based coacervates particularly attractive for biomedical and materials applications. However, the formation and stability of these systems depend on a delicate balance of intrinsic factors (e.g., sequence charge, hydrophobicity, and chain length) and extrinsic conditions (e.g., pH, ionic strength, and temperature), necessitating a deeper understanding of their interplay. This review synthesizes recent advances in the molecular mechanisms driving peptide coacervation, emphasizing how sequence design and environmental cues govern phase behavior. We further highlight groundbreaking applications, from drug delivery platforms to protocell mimics, and discuss strategies to translate mechanistic insights into functional materials. By bridging fundamental principles with innovative applications, this work aims to accelerate the development of peptide coacervates as programmable, multifunctional systems, offering a roadmap for next-generation biochemical technologies.

Active phase separation: new phenomenology from non-equilibrium physics

In active systems, whose constituents have non-equilibrium dynamics at local level, fluid-fluid phase separation is widely observed. Examples include the formation of membraneless organelles within cells; the clustering of self-propelled colloidal particles in the absence of attractive forces, and some types of ecological segregation. A schematic understanding of such active phase separation was initially borrowed from what is known for the equilibrium case, in which detailed balance holds at microscopic level. However it has recently become clear that in active systems the absence of detailed balance, although it leave phase separation qualitatively unchanged in some regimes (for example domain growth driven by interfacial tension via Ostwald ripening), can in other regimes radically alter its phenomenology at mechanistic level. For example, microphase separation can be caused by reverse Ostwald ripening, a process that is hard to imagine from an equilibrium perspective. This and other new phenomena arise because, instead of having a single, positive interfacial tension like their equilibrium counterparts, the fluid-fluid interfaces created by active phase separation can have several distinct interfacial tensions governing different properties, some of which can be negative. These phenomena can be broadly understood by studying continuum field theories for a single conserved scalar order parameter (the fluid density), supplemented with a velocity field in cases where momentum conservation is also present. More complex regimes arise in systems described by multiple scalar order parameters (especially with nonreciprocal interactions between these); or when an order parameter undergoes both conserved and non-conserved dynamics (such that the combination breaks detailed balance); or in systems that support orientational long-range order in one or more of the coexisting phases. In this Review, we survey recent progress in understanding the specific role of activity in phase separation, drawing attention to many open questions. We focus primarily on continuum theories, especially those with a single scalar order parameter, reviewing both analytical and numerical work. We compare their predictions with particle-based models, which have mostly been studied numerically although a few have been explicitly coarse-grained to continuum level. We also compare, where possible, with experimental results. In the latter case, qualitative comparisons are broadly encouraging whereas quantitative ones are hindered by the dynamical complexity of most experimental systems relative that of simplified (particle-level or continuum) models of active matter.

Programmable Coacervate Droplets via Reaction-Coupled Liquid-Liquid Phase Separation (LLPS) and Competitive Inhibition

Membraneless biomolecular condensates formed by liquid-liquid phase separation (LLPS) are crucial for many spatiotemporal biological functions. Designing synthetic mimics to emulate and understand LLPS is an active area of research, which has led to the development of coacervate droplets through elegant bioinspired designs. However, recent interest in this field has shifted toward designing programmable coacervates to impart spatiotemporal control over these liquid phases. Herein, we demonstrate the programming of LLPS in synthetic systems by employing concepts of competitive binding and reaction-coupled assembly involving dynamic covalent bonds. Our results utilize small building blocks that follow a simple coacervation mechanism, distinguishing this approach from previously reported programmable complex coacervates, which often rely on reaction-controlled generation of one of the components. We introduce these concepts using dynamic covalent bonds (boronate esters) and small chromophoric building blocks appended with terminal boronic acid groups. Upon reaction with substrates (monosaccharides), these building blocks form molecular structures resembling "sticker-and-spacer" designs for coacervation, leading to a reaction-driven, temporally controlled LLPS process. The differential reactivity of various monosaccharides, combined with the reversibility of dynamic bonds, enables competitive binding-driven control over the growth, inhibition, and dissolution of the coacervation process, offering new strategies for programmable LLPS that are reminiscent of protein-induced inhibition in biomolecular condensates. Detailed spectroscopic probing and kinetic analyses provide mechanistic insights into the reaction-coupled and autocatalytic growth processes, revealing the glucose-selective nature of this coacervation system. Finally, coupling dynamic covalent reactions with temporal pH modulation results in transient coacervation, which can be visualized by using confocal microscopy. We anticipate that this approach will pave the way for designing coacervate droplets with novel biorelevant emergent properties.

Exploring Endoplasmic Reticulum Dysfunction on Protein Phase Separation Using Viscosity-Sensitive Fluorescent Lifetime Probe

Degenerative diseases are closely associated with protein phase transitions. Endoplasmic reticulum (ER), the primary site of protein synthesis, experiences homeostasis imbalance as the key trigger of the protein phase transition. Effective tools to monitor ER microenvironment changes are crucial for investigating protein phase behavior. In this work, we developed a set of viscosity-sensitive probes based on dicyanomethylene-4H-pyran (namely, VisDCM probes) with dual response of fluorescence intensity and fluorescence lifetime to local viscosity changes. Computational analysis demonstrated that fluorescence activation of VisDCM probes is due to the restricted accessible conical intersection mechanism under specific viscosity. Dual-color probes targeting the ER and protein of interest were designed. They revealed how ER stress regulates TDP-43 protein phase separation via Ca2+ signaling. In vitro experiments exhibited that TDP-43 phase separation is Ca2+-dependent. Increased Ca2+ promotes TDP-43 liquid-liquid phase separation and aggregation. Finally, fluorescence lifetime imaging was applied to map ERS-induced microenvironment changes. In summary, this work provides a novel toolbox to visualize protein phase transitions as well as highlights Ca2+ role in TDP-43 phase separation and aggregation, offering insights and potential therapies for degenerative diseases.

Quantitative spatial analysis of chromatin biomolecular condensates using cryoelectron tomography

Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at high resolution. Here, we analyzed the structure of biochemically reconstituted chromatin condensates through cryoelectron tomography. We found that traditional blotting methods of sample preparation were inadequate, and high-pressure freezing plus focused ion beam milling was essential to maintain condensate integrity. To identify densely packed molecules within the condensate, we integrated deep learning-based segmentation with context-aware template matching. Our approaches were developed on chromatin condensates and were also effective on condensed regions of in situ native chromatin. Using these methods, we determined the average structure of nucleosomes to 6.1 and 12 Å resolution in reconstituted and native systems, respectively, found that nucleosomes form heterogeneous interaction networks in both cases, and gained insight into the molecular origins of surface tension in chromatin condensates. Our methods should be applicable to biomolecular condensates containing large and distinctive components in both biochemical reconstitutions and certain cellular systems.

Phase Separation: Orchestrating Biological Adaptations to Environmental Fluctuations

Organisms have evolved various protective mechanisms to survive in complex and dynamic environments. Phase separation is a ubiquitous mechanism in plants, animals, and microorganisms. It facilitates the aggregation of biomolecules through weak interactions, forming membrane-less organelles that help organisms respond effectively to stress signals. These biomolecular condensates include DNA, RNA, and proteins. Proteins are categorized into scaffold and client proteins, whose coordinated actions ensure the compartmentalization of cellular signals, thereby regulating various biological processes. Studies indicate that, in response to stress, phase separation modulates gene expression, signal transduction, cytoskeleton dynamics, and protein homeostasis, ensuring the precise spatiotemporal control of cellular functions. These insights underscore the crucial role of phase separation in maintaining cellular integrity and adaptability.

The heat shock response in plants: new insights into modes of perception, signaling, and the contribution of hormones

Plants have evolved specific temperature preferences, and shifts above this range cause heat stress with detrimental effects such as physiological disruptions, metabolic imbalances, and growth arrest. To reduce damage, plants utilize the heat shock response (HSR), signaling cascades that activate heat shock factors (HSFs), transcription factors that control the heat stress-responsive transcriptome for activation of protective measures. While the core HSR is well studied, we still know relatively little about heat stress perception and signal integration or crosstalk with other pathways. In the last few years, however, significant progress has been made in this area, which is summarized here. It has emerged that the plant hormones brassinosteroids (BRs) and abscisic acid (ABA) contribute to heat stress tolerance by impacting the modes of activity of HSFs. Also, we began to understand that heat stress is sensed in different cellular compartments and that events in the nucleus, such as nuclear condensate formation via liquid-liquid phase separation, play a key role. In the future, it will be important to explore how these multilayered perception and signaling modes are utilized to understand how environmental context and developmental stage determine the outcome of heat stress effects on plant growth and development.

Terahertz calorimetry spotlights the role of water in biological processes

Terahertz (THz) calorimetry is a framework that allows for the deduction and quantification of changes in solvation entropy and enthalpy associated with biological processes in real-time. Fundamental biological processes are inherently non-equilibrium, and a small imbalance in free energy can trigger protein condensation or folding. Although biophysical techniques typically focus mainly on structural characterization, water is often ignored. Being a generic solvent, the intermolecular protein-water interactions act as a strong competitor for intramolecular protein-protein interactions, leading to a delicate balance between functional structure formation and complete solvation. Characteristics for biological processes are large, but competing enthalpic and entropic solvation contributions to the total Gibbs free energy lead to subtle energy differences of only a few kJ mol-1 that are capable of dictating biological functions. THz calorimetry spotlights these intermolecular coupled protein-water interactions. With experimental advances in THz technology, a new frequency window has opened, which is ideally suited to probe these low-frequency intermolecular interactions. The future impact of these studies is based on the belief that the observed changes in solvation entropy and enthalpy are not secondary effects but dictate biological function.

Condensation-dependent multivalent interactions of EB1 and CENP-R regulate chromosome oscillations in mitosis

Mitotic chromosomes oscillate between the spindle poles upon the establishment of bi-orientation, which is essential for chromosome alignment and subsequent synchronous segregation. However, the molecular mechanisms underlying the oscillatory movement remain unclear. Recent studies revealed that phase separation of the end-binding protein 1 (EB1) is essential for eukaryotic cell division. Here, we show that EB1 interacts with CENP-R and that the phase separation-defective EB1 mutant fails to power the chromosome oscillations. Biochemical analyses reveal a co-condensation of EB1 and CENP-R, a subunit of the constitutive centromere-associated network. Nuclear magnetic resonance assays reveal that the interaction and co-condensation are largely mediated by the structured end-binding homology domain of EB1 and the non-structured N-terminal intrinsic disorder region of CENP-R. Chromosome oscillation is perturbed in cells expressing the EB1-binding-defective CENP-R mutant. Thus, phase-separated EB1 binding to CENP-R forms a physical link between inner kinetochore and dynamic spindle microtubule plus-ends to guide accurate chromosome oscillations.

Emerging connections: Poly(ADP-ribose), FET proteins and RNA in the regulation of DNA damage condensates

Our genome is exposed to thousands of DNA lesions every day, posing a significant threat to cellular viability. To deal with these lesions, cells have evolved sophisticated repair mechanisms collectively known as the DNA damage response. DNA double-strand breaks (DSBs) are very cytotoxic damages, and their repair requires the precise and coordinated recruitment of multiple repair factors to form nuclear foci. Recent research highlighted that these repair structures behave as biomolecular condensates, i.e. membraneless compartments with liquid-like properties. The formation of condensates is driven by weak, multivalent interactions among proteins and nucleic acids, and recent studies highlighted the roles of poly(ADP-ribose) (PAR) and RNA in regulating DSBs-related condensates. Additionally, the FET family of RNA-binding proteins (including FUS, EWS and TAF15), has emerged as a critical player in the DNA damage response, with recent evidence suggesting that FET proteins support the formation and dynamics of repair condensates. Notably, phase separation of FET proteins is implicated also in their pathological functions in cancer biology, highlighting the pervasive role of condensation. This review will provide an overview of biomolecular condensates at DSBs, focusing on the interplay among PAR and RNA in the spatiotemporal regulation of FET proteins at repair complexes. We will also discuss the role of FET condensates in cancer biology and how they are targeted for therapeutic purposes. The study of biomolecular condensates holds great promise for advancing our understanding of key cellular processes and developing novel therapeutic strategies, but requires careful consideration of potential challenges.

Unraveling architectural RNAs: Structural and functional blueprints of membraneless organelles and strategies for genome-scale identification

Architectural RNAs (arcRNAs) are long noncoding RNAs that serve as structural scaffolds for membraneless organelles (MLOs), facilitating cellular organization and dynamic responses to stimuli. Acting as blueprints for MLO assembly, arcRNAs recruit specific proteins and nucleic acids to establish and maintain the internal structure of MLOs while coordinating their spatial relationships with other organelles. This organized framework enables precise spatiotemporal regulation, allowing for targeted control of transcription, RNA processing, and cellular responses to stress. Notably, arcRNAs exhibit the "semi-extractable" feature, a property derived from their stable binding to cellular structures, making them partially resistant to conventional RNA extraction methods. This unique feature serves as a useful criterion for identifying novel arcRNAs, providing an opportunity to accelerate research in long noncoding RNAs and deepen our understanding of their functional roles in cellular processes.

Molecular Mechanisms of Protein Aggregation in ALS-FTD: Focus on TDP-43 and Cellular Protective Responses

Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) are two neurodegenerative disorders that share common genes and pathomechanisms and are referred to as the ALS-FTD spectrum. A hallmark of ALS-FTD pathology is the abnormal aggregation of proteins, including Cu/Zn superoxide dismutase (SOD1), transactive response DNA-binding protein 43 (TDP-43), fused in sarcoma/translocated in liposarcoma (FUS/TLS), and dipeptide repeat proteins resulting from C9orf72 hexanucleotide expansions. Genetic mutations linked to ALS-FTD disrupt protein stability, phase separation, and interaction networks, promoting misfolding and insolubility. This review explores the molecular mechanisms underlying protein aggregation in ALS-FTD, with a particular focus on TDP-43, as it represents the main aggregated species inside pathological inclusions and can also aggregate in its wild-type form. Moreover, this review describes the protective mechanisms activated by the cells to prevent protein aggregation, including molecular chaperones and post-translational modifications (PTMs). Understanding these regulatory pathways could offer new insights into targeted interventions aimed at mitigating cell toxicity and restoring cellular function.

Molecular mechanisms and consequences of TDP-43 phosphorylation in neurodegeneration

Increased phosphorylation of TDP-43 is a pathological hallmark of several neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). However, the regulation and roles of TDP-43 phosphorylation remain incompletely understood. A variety of techniques have been utilized to understand TDP-43 phosphorylation, including kinase/phosphatase manipulation, phosphomimic variants, and genetic, physical, or chemical inducement in a variety of cell cultures and animal models, and via analyses of post-mortem human tissues. These studies have produced conflicting results: suggesting incongruously that TDP-43 phosphorylation may either drive disease progression or serve a neuroprotective role. In this review, we explore the roles of regulators of TDP-43 phosphorylation including the putative TDP-43 kinases c-Abl, CDC7, CK1, CK2, IKKβ, p38α/MAPK14, MEK1, TTBK1, and TTBK2, and TDP-43 phosphatases PP1, PP2A, and PP2B, in disease. Building on recent studies, we also examine the consequences of TDP-43 phosphorylation on TDP-43 pathology, especially related to TDP-43 mislocalisation, liquid-liquid phase separation, aggregation, and neurotoxicity. By comparing conflicting findings from various techniques and models, this review highlights both the discrepancies and unresolved aspects in the understanding of TDP-43 phosphorylation. We propose that the role of TDP-43 phosphorylation is site and context dependent, and includes regulation of liquid-liquid phase separation, subcellular mislocalisation, and degradation. We further suggest that greater consideration of the normal functions of the regulators of TDP-43 phosphorylation that may be perturbed in disease is warranted. This synthesis aims to build towards a comprehensive understanding of the complex role of TDP-43 phosphorylation in the pathogenesis of neurodegeneration.

Current perspectives in drug targeting intrinsically disordered proteins and biomolecular condensates

Intrinsically disordered proteins (IDPs) and biomolecular condensates are critical for cellular processes and physiological functions. Abnormal biomolecular condensates can cause diseases such as cancer and neurodegenerative disorders. IDPs, including intrinsically disordered regions (IDRs), were previously considered undruggable due to their lack of stable binding pockets. However, recent evidence indicates that targeting them can influence cellular processes. This review explores current strategies to target IDPs and biomolecular condensates, potential improvements, and the challenges and opportunities in this evolving field.

Predictability of environment-dependent formation of G-quadruplex DNAs in human mitochondria

Molecular crowding affects the stability of nucleic acids (DNA and RNA) and induces their non-canonical structures. As the level of molecular crowding varies spatio-temporally in cells, it would be beneficial to predict the behaviour of DNA and RNA structures depending on the local cellular environments. This has applications in human mitochondria, which possess an especially crowded condition. In this study, the predictability of guanine-quadruplex (G4) DNA formation in the environment specific to human mitochondria was investigated. In accordance with the stability of duplexes predicted by our nearest-neighbour parameters, the G-rich duplex stability was found to effectively decrease and G4 formation was induced in mitochondrion-like conditions compared to the nucleus-like conditions. Using a peptide-based mitochondrial targeting system, a G4 reporter assay performed in mitochondria indicated that G4 formation were more favoured in mitochondria more than in the nucleus. These findings provide insights useful for the prediction of the behaviour of nucleic acids in mitochondria.

Bioelectric and physicochemical foundations of bioelectronics in tissue regeneration

Understanding and exploiting bioelectric signaling pathways and physicochemical properties of materials that interface with living tissues is central to advancing tissue regeneration. In particular, the emerging field of bioelectronics leverages these principles to develop personalized, minimally invasive therapeutic strategies tailored to the dynamic demands of individual patients. By integrating sensing and actuation modules into flexible, biocompatible devices, clinicians can continuously monitor and modulate local electrical microenvironments, thereby guiding regenerative processes without extensive surgical interventions. This review provides a critical examination of how fundamental bioelectric cues and physicochemical considerations drive the design and engineering of next-generation bioelectronic platforms. These platforms not only promote the formation and maturation of new tissues across neural, cardiac, musculoskeletal, skin, and gastrointestinal systems but also precisely align therapies with the unique structural, functional, and electrophysiological characteristics of each tissue type. Collectively, these insights and innovations represent a convergence of biology, electronics, and materials science that holds tremendous promise for enhancing the efficacy, specificity, and long-term stability of regenerative treatments, ushering in a new era of advanced tissue engineering and patient-centered regenerative medicine.

piRNA gene density and SUMOylation organize piRNA transcriptional condensate formation

Piwi-interacting RNAs (piRNAs) are essential for maintaining genome integrity and fertility in various organisms. In flies and nematodes, piRNA genes are encoded in heterochromatinized genomic clusters. The molecular mechanisms of piRNA transcription remain intriguing. Through small RNA sequencing and chromatin editing, we discovered that spatial aggregation of piRNA genes enhances their transcription in nematodes. The facultative heterochromatinized piRNA genome recruits the piRNA upstream sequence transcription complex (USTC; including PRDE-1, SNPC4, TOFU-4 and TOFU-5) and the H3K27me3 reader UAD-2, which phase-separate into droplets to initiate piRNA transcription. We searched for factors that regulate piRNA transcription and isolated the SUMO E3 ligase GEI-17 as inhibiting and the SUMO protease TOFU-3 as promoting piRNA transcription foci formation, thereby regulating piRNA production. Our study revealed that spatial aggregation of piRNA genes, phase separation and deSUMOylation may benefit the organization of functional biomolecular condensates to direct piRNA transcription in the facultative heterochromatinized genome.

Compartmentation of multiple metabolic enzymes and their preparation in vitro and in cellulo

Compartmentalization of multiple enzymes in cellulo and in vitro is a means of controlling the cascade reaction of metabolic enzymes. The compartmentation of enzymes through liquid-liquid phase separation may facilitate the reversible control of biocatalytic cascade reactions, thereby reducing the transcriptional and translational burden. This has attracted attention as a potential application in bioproduction. Recent research has demonstrated the existence and regulatory mechanisms of various enzyme compartments within cells. Mounting evidence suggests that enzyme compartmentation allows in vitro and in vivo regulation of cellular metabolism. However, the comprehensive regulatory mechanisms of enzyme condensates in cells and ideal organization of cellular systems remain unknown. This review provides an overview of the recent progress in multiple enzyme compartmentation in cells and summarizes strategies to reconstruct multiple enzyme assemblies in vitro and in cellulo. By examining parallel examples, we have evaluated the consensus and future perspectives of enzyme condensation.

Drosophila Clu ribonucleoprotein particle dynamics rely on the availability of functional Clu and translating ribosomes

Drosophila Clu is a conserved multi-domain ribonucleoprotein essential for mitochondrial function that forms dynamic particles within the cytoplasm. Unlike stress granules and processing bodies (P-bodies), Clu particles disassemble under nutritional or oxidative stress. However, it is unclear how disrupting protein synthesis affects Clu particle dynamics, especially given that Clu binds mRNA and ribosomes. Here, we capitalize on ex vivo and in vivo imaging of Drosophila female germ cells to determine what domains of Clu are necessary for Clu particle assembly and how manipulating translation affects particle dynamics. Using domain deletion analysis, we identified three domains of Clu essential for particle assembly. We also demonstrated that overexpressing functional Clu led to disassembly of particles. In addition, we inhibited translation using cycloheximide and puromycin. In contrast to P-bodies, cycloheximide treatment did not disassemble Clu particles yet puromycin treatment did. Surprisingly, cycloheximide stabilized particles under oxidative and nutritional stress. These findings demonstrate that Clu particles display novel dynamics in response to altered ribosome activity and support a model where they function as translation hubs whose assembly heavily depends on the dynamic availability of translating ribosomes.

Biophysical Aspect of Assembly and Regulation of Nuclear Bodies Scaffolded by Architectural RNA

A growing body of evidence suggests that nuclear bodies, condensates of RNAs and proteins within the nucleus, are assembled through liquid-liquid phase separation. Some nuclear bodies, such as paraspeckles, are scaffolded by a class of RNAs known as architectural RNAs. From a materials science perspective, RNAs are categorized as polymers, which have been extensively studied in soft matter physics. While soft matter physics has the potential to provide significant insights, it is not directly applicable because transcription and other biochemical processes differentiate RNAs from other polymers studied in this field. Therefore, an interdisciplinary research fusing molecular biology and soft matter physics offers a powerful approach to studying nuclear bodies. This review introduces the biophysical insights provided by such interdisciplinary research in the assembly and regulation of nuclear bodies.

Interferon-induced PARP14-mediated ADP-ribosylation in p62 bodies requires the ubiquitin-proteasome system

Biomolecular condensates are cellular compartments without enveloping membranes, enabling them to dynamically adjust their composition in response to environmental changes through post-translational modifications. Recent work has revealed that interferon-induced ADP-ribosylation (ADPr), which can be reversed by a SARS-CoV-2-encoded hydrolase, is enriched within a condensate. However, the identity of the condensate and the responsible host ADP-ribosyltransferase remain elusive. Here, we demonstrate that interferon induces ADPr through transcriptional activation of PARP14, requiring both the physical presence and catalytic activity of PARP14 for condensate formation. Interferon-induced ADPr colocalizes with PARP14 and its associated E3 ligase, DTX3L. These PARP14/ADPr condensates contain key components of p62 bodies-including the selective autophagy receptor p62, its binding partner NBR1 and the associated protein TAX1BP1, along with K48-linked and K63-linked polyubiquitin chains-but lack the autophagosome marker LC3B. Knockdown of p62 disrupts the formation of these ADPr condensates. Importantly, these structures are unaffected by autophagy inhibition, but depend on ubiquitination and proteasome activity. Taken together, these findings demonstrate that interferon triggers PARP14-mediated ADP-ribosylation in p62 bodies, which requires an active ubiquitin-proteasome system.

DEAD/DEAH-box RNA helicases shape the risk of neurodevelopmental disorders

The DEAD/DEAH-box family of RNA helicases (RHs) is among the most abundant and conserved in eukaryotes. These proteins catalyze the remodeling of RNAs to regulate their splicing, stability, localization, and translation. Rare genetic variants in DEAD/DEAH-box proteins have recently emerged as being associated with neurodevelopmental disorders (NDDs). Analyses in cellular and animal models have uncovered fundamental roles for these proteins during brain development. We discuss the genetic and functional evidence that implicates DEAD/DEAH-box proteins in brain development and NDDs, with a focus on how structural insights from paralogous genes can be leveraged to advance our understanding of the pathogenic mechanisms at play.

Regulating Protein Immobilization During Cell-Free Protein Synthesis in Hyaluronan Microgels

Cell-like platforms are being studied intensively for their application in synthetic biology to mimic aspects of life in an artificial environment. Here, micrometer-sized, bifunctional microgels are used as an experimental platform to investigate the interplay of cell-free protein synthesis (CFPS) and in situ protein accumulation inside the microgel volume. In detail, microgels made of hyaluronic acid (HA) are first modified with different amounts of nitrilotriacetic acid (NTA) moieties to characterize the capability and maximum capacity of binding His-tag modified GFP. CFPS is optimized for the system used here, particularly when using a linear DNA template. Afterward, HA-microgels are functionalized with the linear DNA template and Ni2+-activated NTA moieties to bind in situ synthesized GFP-His. CFPS and parallel protein accumulation within the microgels are observed over time to determine the GFP-His binding to the microgel platform. With this approach, the study presents the first steps for a platform to study the temporal-spatial regulation of protein synthesis by tailored protein binding or release from the microgel matrix-based reaction environment.

Evidence for biomolecular condensates formed by the Escherichia coli MatP protein in spatiotemporal regulation of the bacterial cell division cycle

An increasing number of proteins involved in bacterial cell cycle events have been recently shown to form biomolecular condensates important for their functions that may play a role in development of antibiotic-tolerant persister cells. Here we report that the E. coli chromosomal Ter macrodomain organizer MatP, a division site selection protein coordinating chromosome segregation with cell division, formed biomolecular condensates in crowding cytomimetic systems preferentially localized at the membrane of microfluidics droplets. Condensates were antagonized and partially dislodged from the membrane by DNA sequences recognized by MatP (matS), which partitioned into them. FtsZ, a core component of the division machinery previously described to phase-separate, unexpectedly enhanced MatP condensation. Our biophysical analyses uncovered direct interaction between both proteins, disrupted by matS. This may have potential implications for midcell FtsZ ring positioning by the Ter-linkage, which comprises MatP and two other proteins bridging the canonical MatP-FtsZ interaction. FtsZ/MatP condensates interconverted with GTP-triggered bundles, suggesting that local fluctuations of GTP concentrations may regulate FtsZ/MatP phase separation. Consistent with discrete MatP foci previously reported in cells, phase separation might influence MatP-dependent chromosome organization, spatiotemporal coordination of cytokinesis and DNA segregation, which is potentially relevant for cell entry into dormant states that can resist antibiotic treatments.

Aging-dependent evolving electrochemical potentials of biomolecular condensates regulate their physicochemical activities

A passive consequence of macromolecular condensation is the establishment of an ion concentration gradient between the dilute and dense phases, which in turn governs distinct electrochemical properties of condensates. However, the mechanisms that regulate the electrochemical equilibrium of condensates and their impacts on emergent physicochemical functions remain unknown. Here we demonstrate that the electrochemical environments and the physical and chemical activities of biomolecular condensates, dependent on the electrochemical potential of condensates, are regulated by aging-associated intermolecular interactions and interfacial effects. Our findings reveal that enhanced dense-phase interactions during condensate maturation continuously modulate the ion distribution between the two phases. Moreover, modulating the interfacial regions of condensates can affect the apparent pH within the condensates. To directly probe the interphase and interfacial electric potentials of condensates, we have designed and implemented electrochemical potentiometry and second harmonic generation-based approaches. Our results suggest that the non-equilibrium nature of biomolecular condensates might play a crucial role in modulating the electrochemical activities of living systems.

Molecular insights into the effect of 1,6-hexanediol on FUS phase separation

The alkanediol 1,6-hexanediol has been widely used to dissolve liquid-liquid phase-separated condensates in cells and in vitro, but the details of how it perturbs the molecular interactions underlying liquid-liquid assembly remain unclear. In this study we use a combination of microscopy, nuclear magnetic resonance (NMR) spectroscopy, molecular simulation, and biochemical assays to probe how alkanediols suppress phase separation and why certain isomers are more effective. We show that alkanediols of different lengths and configurations are all capable of disrupting phase separation of the RNA-binding protein Fused in Sarcoma (FUS), although potency varies depending on both geometry and hydrophobicity, which we measure directly. Alkanediols induce a shared pattern of changes to the chemical environment of the protein, to different extents depending on the specific compound. Furthermore, we use lysozyme as a model globular protein to demonstrate that alkanediols decrease the proteins' thermal stability, which is consistent with the view that they disrupt phase separation driven by hydrophobic groups. Conversely, 1,6-hexanediol does not disrupt charge-mediated phase separation, such as FUS RGG-RNA and poly-lysine/poly-aspartic acid condensates. All-atom simulations show that hydroxyl groups in alkanediols mediate interactions with the protein backbone and polar amino acid side chains, while the aliphatic chain allows contact with hydrophobic and aromatic residues, providing a molecular picture of how amphiphilic interactions disrupt FUS phase separation.

Coacervates Composed of Low-Molecular-Weight Compounds- Molecular Design, Stimuli Responsiveness, Confined Reaction

The discovery of coacervation within living cells through liquid-liquid phase separation has inspired scientists to investigate its fundamental principles and significance. Indeed, coacervates composed of low-molecular-weight compounds based on supramolecular strategy can offer valuable models for biomolecular condensates and useful tools. This mini-review highlights recent findings and advances in coacervates (artificial condensates), primarily composed of low-molecular-weight compounds, with focuses on their molecular design, stimuli responsiveness, and controlled reactions within or leading to the coacervates.

Design and development of drug delivery nanocarriers based on liquid-liquid phase separation, improved stability, cell-penetration and anti-cancer effect

Liquid-liquid phase separation (LLPS) of nuclear pore complex (NPC) with nuclear transport proteins (NTPs) via intrinsically disordered regions (IDRs) plays a crucial role in the nucleocytoplasmic transport. The development of efficient targeted delivery systems based on LLPS has attracted widespread attention. Here, we developed nanocarriers of casein peptides, a natural intrinsically disordered proteins (IDPs), modified with fatty acids of different alkyl chains (C10-C18) and decorated by shellac for highly effective drug delivery and cancer therapy. The curcumin (Cur)-loading nanocarriers (CSLNCs) showed excellent stability and dispersity in the natural environment over 30 days, with Cur encapsulation efficiency and loading capacity of ~90 % and ~57 %. Electron microscope (EM) indicated an aggregated homogeneous elliptical shape of CSLNCs(C10) and the morphology of CSLNCs(C18) transited to a distributed cubic shape. CSLNCs(C10, C12, C14 and C18) exhibited cytotoxicity against human lung adenocarcinoma NCI-H1975 cells with an IC50 value of 17.5 μM, 17.3 μM, 10.2 μM and 19.3 μM after 24 h of incubation, respectively. CSLNCs were also found to inhibit the cell wound healing with a migration rate of 12.72 %, 10.93 %, 4.28 % and 13.62 %, respectively. CSLNCs especially increased the percentage of late apoptotic cells. As indications of confocal microscopy, the fluorescence intensities of NCI-H1975 cells were enhanced with a cytosolic distribution and noticeably florescence in the nucleus after 0.5 h of incubation CSLNCs. CSLNCs treated cells adopted a rounded morphology with a dramatic reduction in fluorescence intensity after 1 h of incubation. Among CSLNCs, CSLNCs(C14) improved considerably the cytotoxicity activity and intercellular localization in the nucleus. The cell-penetration ability was also confirmed by the binding of CSLNCs in a model bicelles membrane system composed of DMPC and DHPC investigated by 1H NMR. It was proposed that CSLNCs with cell-penetrating and nuclear targeting performance may regulate the LLPS of nuclear pore complex and thus improved its nuclear penetration and cytotoxic activity.

Phosphorylation-dependent charge blocks regulate the relaxation of nuclear speckle networks

Nuclear speckles (NSs) are viscoelastic network fluids formed via phase separation coupled to percolation (PSCP). Intermolecular crosslinks of SRRM2 lead to the emergence of system-spanning networks, although the physicochemical grammar governing SRRM2 PSCP remains poorly decoded. Here, we demonstrate that SRRM2 is extensively phosphorylated within the intrinsically disordered region (IDR), creating alternating charge blocks. We show that this specific charge pattern does not markedly alter the condensation threshold of SRRM2 in cells. Instead, SRRM2 charge blocks intensify intra-network molecular interactions to modulate the material properties of mesoscopic SRRM2 condensates. We further identify casein kinase 2 (CK2) as the upstream enzyme to catalyze SRRM2 phosphorylation. Phosphorylation of SRRM2 IDR by CK2 facilitates NS relaxation, which is associated with enhanced efficiency of mRNA splicing to safeguard genome stability during DNA damage. Our findings reveal important regulatory mechanisms of charge blocks in modulating the material properties and functions of biomolecular condensates in human cells.

LncRNA RMG controls liquid-liquid phase separation of MEIS2 to regulate myogenesis

Long non-coding RNAs (lncRNAs) regulate liquid-liquid phase separation (LLPS), driving the formation of biomolecular condensates essential for cellular function. However, this regulatory mechanism is yet to be reported in skeletal muscles. In this study, we comprehensively analyzed lncRNAs in skeletal muscle across multiple pig breeds, developmental stages, and tissues. Our analysis identified over 10,000 novel lncRNAs. We found that the lnc-regulator of muscle growth (lnc-RMG) regulates myogenesis by modulating the LLPS of Meis homeobox 2 (MEIS2). Lnc-RMG was specifically expressed in the skeletal muscle, with significantly higher expression in the fetal stage than in the embryonic stage. Notably, lnc-RMG was highly conserved between pigs and humans and exhibits similar biological functions in myogenesis. Furthermore, lnc-RMG knockdown promoted skeletal muscle regeneration. Mechanistically, lnc-RMG produces mature microRNA (miR)-133a-3p, which targets and inhibits MEIS2 expression, thereby inhibiting MEIS2 LLPS. This inhibition promoted the transcription of transforming growth factor-β receptor II (TGFβR2), ultimately regulating myogenesis. Overall, our findings revealed a novel lnc-RMG/miR-133a-3p/MEIS2/TGFβR2 axis that regulated myogenesis through LLPS and provided new insights into the molecular mechanisms that drive muscle development and regeneration. These findings highlight potential therapeutic targets for muscle-related diseases and novel strategies for livestock improvement.

Liquid-Liquid Phase Separation-Mediated Cellular-Scale Compartmentalization of Hydrogel Covalent Cross-Linking Promotes Microtubule-Based Mechanosensing

Controlled liquid-liquid phase separation (LLPS) plays an important role in the formation of a heterogeneously structured extracellular matrix (ECM) consisting of densely cross-linked stiff structures compartmentalized in a loosely cross-linked matrix. Moreover, the mechanical cues presented by the cellular-scale structural heterogeneity of the ECM facilitate the mechanotransduction of cells and subsequent cellular development. Therefore, developing ECM-mimetic hydrogels with compartmentalized structural heterogeneity as inductive cell carriers is highly desirable but challenging. Inspired by the ECM formation process, we capitalized on the temperature-assisted LLPS of a custom-designed temperature-responsive macromer (TRM) to concentrate and compartmentalize the TRM in the dense phase of the phase-separated precursor solution while keeping the gelatin comacromer complex in the dilute phase. The subsequent cross-linking produces the cellular (micron)-scale microdomains with dense covalent cross-linking interspersed in the loosely cross-linked cell-adaptable interdomain hydrogel matrix. The obtained ECM-mimetic heterogeneous hydrogel, which is solely cross-linked by covalent bonds, promotes extensive spreading, microtubule-based mechanotransduction, and autophagic flux of encapsulated human mesenchymal stem cells (hMSCs), thereby enhancing osteogenesis and bone regeneration. Our findings not only provide valuable guidance for the fabrication of ECM-mimetic biomaterials via LLPS-mediated assembly but also shed light on the mechanobiological mechanism underlying the regulation of cellular development by mechanical cues of the ECM.

Coalescence-Driven Local Crowding Promotes Liquid-to-Solid-Like Phase Transition in a Homogeneous and Heterogeneous Droplet Assembly: Regulatory Role of Ligands

Liquid-to-solid-like phase transition (LSPT) of disordered proteins via metastable liquid-like droplets is a well-documented phenomenon in biology and is linked to many pathological conditions including neurodegenerative diseases. However, very less is known about the early microscopic events and transient intermediates involved in the irreversible protein aggregation of functional globular proteins. Herein, using a range of microscopic and spectroscopic techniques, we show that the LSPT of a functional globular protein, human serum albumin (HSA), is exclusively driven by spontaneous coalescence of liquid-like droplets involving various transient intermediates in a temporal manner. We show that interdroplet communication via coalescence is essential for both initial aggregation and growth of amorphous aggregates within individual droplets, which subsequently transform to amyloid-like fibrils. Immobilized droplets neither show any nucleation nor any growth upon aging. Moreover, we found that the exchange of materials with the dilute dispersed phase has negligible influence on the LSPT of HSA. Our findings reveal that interfacial properties effectively modulate the feasibility and kinetics of LSPT of HSA via ligand binding, suggesting a possible regulatory mechanism that cells utilize to control the dynamics of LSPT. Furthermore, using a dynamic heterogeneous droplet assembly of two functional proteins, HSA and human serum transferrin (Tf), we show an intriguing phenomenon within the fused droplets where both liquid-like and solid-like phases coexist within the same droplet, which eventually transform to a mixed fibrillar assembly. These microscopic insights not only highlight the importance of interdroplet interactions behind the LSPT of biomolecules but also showcase its adverse effect on the structure and function of other functional proteins in a crowded and heterogeneous protein assembly.

Intrinsic Disorder and Phase Separation Coordinate Exocytosis, Motility, and Chromatin Remodeling in the Human Acrosomal Proteome

Intrinsic disorder refers to protein regions that lack a fixed three-dimensional structure under physiological conditions, enabling conformational plasticity. This flexibility allows for diverse functions, including transient interactions, signaling, and phase separation via disorder-to-order transitions upon binding. Our study focused on investigating the role of intrinsic disorder and liquid-liquid phase separation (LLPS) in the human acrosome, a sperm-specific organelle essential for fertilization. Using computational prediction models, network analysis, Structural Classification of Proteins (SCOP) functional assessments, and Gene Ontology, we analyzed 250 proteins within the acrosomal proteome. Our bioinformatic analysis yielded 97 proteins with high levels (>30%) of structural disorder. Further analysis of functional enrichment identified associations between disordered regions overlapping with SCOP domains and critical acrosomal processes, including vesicle trafficking, membrane fusion, and enzymatic activation. Examples of disordered SCOP domains include the PLC-like phosphodiesterase domain, the t-SNARE domain, and the P-domain of calnexin/calreticulin. Protein-protein interaction networks revealed acrosomal proteins as hubs in tightly interconnected systems, emphasizing their functional importance. LLPS propensity modeling determined that over 30% of these proteins are high-probability LLPS drivers (>60%), underscoring their role in dynamic compartmentalization. Proteins such as myristoylated alanine-rich C-kinase substrate and nuclear transition protein 2 exhibited both high LLPS propensities and high levels of structural disorder. A significant relationship (p < 0.0001, R² = 0.649) was observed between the level of intrinsic disorder and LLPS propensity, showing the role of disorder in facilitating phase separation. Overall, these findings provide insights into how intrinsic disorder and LLPS contribute to the structural adaptability and functional precision required for fertilization, with implications for understanding disorders associated with the human acrosome reaction.