Liquid phase condensation in cell physiology and disease

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.

Deciphering the role of liquid-liquid phase separation in sarcoma: Implications for pathogenesis and treatment

Liquid-liquid phase separation (LLPS) is a significant reversible and dynamic process in organisms. Cells form droplets that are distinct from membrane-bound cell organelles by phase separation to keep biochemical processes in order. Nevertheless, the pathological state of LLPS contributes to the progression of a variety of tumor-related pathogenic issues. Sarcoma is one kind of highly malignant tumor characterized by aggressive metastatic potential and resistance to conventional therapeutic agents. Despite the significant clinical relevance, research on phase separation in sarcomas currently faces several major challenges. These include the limited availability of sarcoma samples, insufficient attention from the research community, and the complex genetic heterogeneity of sarcomas. Recently, emerging evidence have elaborated the specific effects and pathways of phase separation on different sarcoma subtypes, including the effect of sarcoma fusion proteins and other physicochemical factors on phase separation. This review aims to summarize the multiple roles of phase separation in sarcoma and novel molecular inhibitors that target phase separation. These insights will broaden the understanding of the mechanisms concerning sarcoma and offer new perspectives for future therapeutic strategies.

Intrinsic disorder in protein interaction networks linking cancer with metabolic diseases

Complex diseases are usually driven by numerous proteins that operate as intricate network systems. Deciphering of their signals is required for more advanced level understanding of the cellular processes driven by protein interactions. Therefore, placing diseases into a framework, where they can be viewed together, represents an important and fruitful approach. The goal of this study was to assess the intrinsic disorder present in the proteins forming PPI networks linking cancer with different human diseases. To this end, we used a set of bioinformatics tools to explore intrinsic disorder and liquid-liquid phase separation predispositions of 340 proteins reported earlier by Hirsch et al. (Cancer Cell (2010) 17(4), 348-361; doi: 10.1016/j.ccr.2010.01.022) as differently expressed in common chronic diseases, such as cancer, obesity, diabetes, and cardiovascular diseases. We further examined selected proteins from this set for their interactability and intrinsic disorder-based functionality. Our analyses demonstrated that intrinsically disordered proteins and proteins with intrinsically disordered regions may act as active network promoters and operate as highly connected hubs, which further enables them to play key roles in the disease pathways. The study also indicated that differently expressed proteins involved in disease progression could be characterized by diverse degrees of intrinsic disorder and LLPS propensity. We hope that our findings in combination with the outputs of the proteomic and functional genomic analyses contain essential clues that can be used in further medical research leading to the design of better therapies.

LncRNA-MEG3 Regulates Muscle Mass and Metabolic Homeostasis by Facilitating SUZ12 Liquid-Liquid Phase Separation

Skeletal muscle plays a crucial role in maintaining motor function and metabolic homeostasis, with its loss or atrophy leading to significant health consequences. Long non-coding RNAs (lncRNAs) have emerged as key regulators in muscle biology; however, their precise roles in muscle function and pathology remain to be fully elucidated. This study demonstrates that lncRNA maternally expressed gene 3 (MEG3) is preferentially expressed in slow-twitch muscle fibers and dynamically regulated during muscle development, aging, and in the context of Duchenne muscular dystrophy (DMD). Using both loss- and gain-of-function mice models, this study shows that lncRNA-MEG3 is critical for preserving muscle mass and function. Its depletion leads to muscle atrophy, mitochondrial dysfunction, and impaired regenerative capacity, while overexpression enhances muscle mass, increases oxidative muscle fiber content, and improves endurance. Notably, lncRNA-MEG3 overexpression in MDX mice significantly alleviates muscle wasting and adipose tissue infiltration. Mechanistically, this study uncovers a novel interaction between lncRNA-MEG3 and the polycomb repressive complex 2 (PRC2), where lncRNA-MEG3 binds to SUZ12 polycomb repressive complex 2 subunit (Suz12), stabilizes PRC2, facilitates SUZ12 liquid-liquid phase separation (LLPS), and regulates the epigenetic modulation of four and a half lim domains 3 (Fhl3) and ring finger protein 128 (Rnf128). These findings not only highlight the crucial role of lncRNA-MEG3 in muscle homeostasis but also provide new insights into lncRNA-based therapeutic strategies for muscle-related diseases.

Protecting centrosomes from fracturing enables efficient cell navigation

The centrosome is a microtubule orchestrator, nucleating and anchoring microtubules that grow radially and exert forces on cargos. At the same time, mechanical stresses from the microenvironment and cellular shape changes compress and bend microtubules. Yet, centrosomes are membraneless organelles, raising the question of how centrosomes withstand mechanical forces. Here, we discover that centrosomes can deform and even fracture. We reveal that centrosomes experience deformations during navigational pathfinding within motile cells. Coherence of the centrosome is maintained by Dyrk3 and cNAP1, preventing fracturing by forces. While cells can compensate for the depletion of centriolar-based centrosomes, the fracturing of centrosomes impedes cellular function by generating coexisting microtubule organizing centers that compete during path navigation and thereby cause cellular entanglement in the microenvironment. Our findings show that cells actively maintain the integrity of the centrosome to withstand mechanical forces. These results suggest that centrosome stability preservation is fundamental, given that almost all cells in multicellular organisms experience forces.

Phase separation as a key mechanism in plant development, environmental adaptation, and abiotic stress response

Liquid-liquid phase separation is a fundamental biophysical process in which biopolymers, such as proteins, nucleic acids, and their complexes, spontaneously demix into distinct coexisting phases. This phenomenon drives the formation of membraneless organelles-cellular subcompartments without a lipid bilayer that perform specialized functions. In plants, phase-separated biomolecular condensates play pivotal roles in regulating gene expression, from genome organization to transcriptional and post-transcriptional processes. In addition, phase separation governs plant-specific traits, such as flowering and photosynthesis. As sessile organisms, plants have evolved to leverage phase separation for rapid sensing and response to environmental fluctuations and stress conditions. Recent studies highlight the critical role of phase separation in plant adaptation, particularly in response to abiotic stress. This review compiles the latest research on biomolecular condensates in plant biology, providing examples of their diverse functions in development, environmental adaptation, and stress responses. We propose that phase separation represents a conserved and dynamic mechanism enabling plants to adapt efficiently to ever-changing environmental conditions. Deciphering the molecular mechanisms underlying phase separation in plant stress responses opens new avenues for biotechnological strategies aimed at engineering stress-resistant crops. These advancements have significant implications for agriculture, particularly in addressing crop productivity in the face of climate change.

Scaling Field-Theoretic Simulation for Multicomponent Mixtures with Neural Operators

Multicomponent polymer mixtures are ubiquitous in biological self-organization but are notoriously difficult to study computationally. Plagued by both slow single molecule relaxation times and slow equilibration within dense mixtures, molecular dynamics simulations are typically infeasible at the spatial scales required to study the stability of mesophase structure. Polymer field theories offer an attractive alternative, but analytical calculations are only tractable for mean-field theories and nearby perturbations, constraints that become especially problematic for fluctuation-induced effects such as coacervation. Here, we show that a recently developed technique for obtaining numerical solutions to partial differential equations based on operator learning, neural operators, lends itself to a highly scalable training strategy by parallelizing per-species operator maps. We illustrate the efficacy of our approach on six-component mixtures with randomly selected compositions and that it significantly outperforms the state-of-the-art pseudospectral integrators for field-theoretic simulations, especially as polymer lengths become long.

TFE3 fusion oncoprotein condensates drive transcriptional reprogramming and cancer progression in translocation renal cell carcinoma

Translocation renal cell carcinoma (tRCC) presents a significant clinical challenge due to its aggressiveness and limited treatment options. It is primarily driven by fusion oncoproteins (FOs), yet their role in oncogenesis is not fully understood. Here, we investigate TFE3 fusions in tRCC, focusing on NONO::TFE3 and SFPQ::TFE3. We demonstrate that TFE3 FOs form liquid-like condensates with increased transcriptional activity, localizing to TFE3 target genes and promoting cell proliferation and migration. The coiled-coil domains (CCDs) of NONO and SFPQ are essential for condensate formation, prolonging TFE3 FOs' chromatin binding time and enhancing transcription. Compared with wild-type TFE3, TFE3 FOs bind to new chromatin regions, alter chromatin accessibility, and form new enhancers and super-enhancers at pro-growth gene loci. Disruption of condensate formation via CCD modification abolishes these genome-wide changes. Altogether, our integrated analyses underscore the critical functions of TFE3 FO condensates in driving tumor cell growth, providing key insights for future therapeutic strategies.

Oligolysine Enhances and Inhibits DNA Condensate Formation

The formation of biomolecular condensates via phase separation relates to various cellular functions. Reconstituting these condensates with designed molecules facilitates the exploration of their mechanisms and potential applications. Sequence-designed DNA nanostructures enable the investigation of how structural design influences condensate formation and the construction of functional artificial condensates. Despite the high designability of DNA-based condensates, free nanostructures that do not assemble into condensates remain a challenge. Combining DNA nanostructures with other molecules, such as peptides, represents a promising approach to overcoming the limitations of DNA condensates and gaining a deeper understanding of molecular condensates. Herein, we report the effects of cationic oligolysines with several residues on DNA condensate formation assembled from Y-shaped DNA nanostructures. DNA condensate formation was enhanced by oligolysines at an appropriate L/P ratio, which refers to the ratio of positively charged amine groups in lysine (L) to negatively charged nucleic acid phosphate groups (P). Oligolysines with five residues enhanced condensate formation while maintaining the sequence-specific interaction of DNA. In contrast, oligolysines inhibited condensate formation depending on the L/P ratio and residue number. This was attributed to nanostructure deformation caused by oligolysines. These results suggest that the amount and length of cationic peptides significantly affect the self-assembly of branched DNA nanostructures. This study offers important insights into biomolecular condensates that can guide further development of DNA/peptide hybrid condensates to enhance the functions of artificial condensates for use in artificial cells and molecular robots.

Multiphasic protein condensation governed by shape and valency

Liquid-liquid phase separation (LLPS) of biological macromolecules leads to the formation of various membraneless organelles. The multilayered and multiphasic form of LLPS can mediate complex cellular functions; however, the determinants of its topological features are not fully understood. Herein, we focus on synaptic proteins consisting of Ca2+/calmodulin-dependent protein kinase II (CaMKII) and its interacting partners and present a computational model that reproduces forms of LLPS, including a form of two-phase condensates, phase-in-phase (PIP) organization. The model analyses reveal that the PIP formation requires competitive binding between the proteins. The PIP forms only when CaMKII has high valency and a short linker length. Such CaMKII exhibits low surface tension, a modular structure, and slow diffusion, enabling it to stay in small biochemical domains for a long time, which is necessary for synaptic plasticity. Thus, the computational modeling reveals new structure-function relationships for CaMKII as a synaptic memory unit.

Compartmentalized localization of perinuclear proteins within germ granules in C. elegans

Germ granules, or nuage, are RNA-rich condensates that are often docked on the cytoplasmic surface of germline nuclei. C. elegans perinuclear germ granules are composed of multiple subcompartments, including P granules, Mutator foci, Z granules, SIMR foci, P -bodies, and E granules. Although many perinuclear proteins have been identified, their precise localization within the subcompartments of the germ granule is still unclear. Here, we systematically labeled perinuclear proteins with fluorescent tags via CRISPR-Cas9 technology. Using this nematode strain library, we identified a series of proteins localized in Z or E granules and extended the characterization of the D granule. Finally, we found that the LOTUS domain protein MIP-1/EGGD-1 regulated the multiphase organization of the germ granule. Overall, our work identified the germ-granule architecture and redefined the compartmental localization of perinuclear proteins. Additionally, the library of genetically modified nematode strains will facilitate research on C. elegans germ granules.

Spatial analysis of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress

Protein- and RNA-rich bodies contribute to the spatial organization of gene expression in the cell and are also sites of quality control critical to cell fitness. In most eukaryotes, mitochondria harbor their own genome, and all steps of mitochondrial gene expression co-occur within a single compartment-the matrix. Here, we report that processed mitochondrial RNAs are consolidated into micrometer-scale translation hubs distal to mitochondrial DNA transcription and RNA processing sites in human cells. We find that, during stress, mitochondrial messenger and ribosomal RNA are sequestered in mesoscale bodies containing mitoribosome components, concurrent with suppression of active translation. Stress bodies are triggered by proteotoxic stress downstream of double-stranded RNA accumulation in cells lacking unwinding activity of the highly conserved helicase SUPV3L1/SUV3. We propose that the spatial organization of nascent polypeptide synthesis into discrete domains serves to throttle the flow of genetic information to support recovery of mitochondrial quality control.

Live-cell quantification reveals viscoelastic regulation of synapsin condensates by α-synuclein

Synapsin and α-synuclein represent a growing list of condensate-forming proteins where the material states of condensates are directly linked to cellular functions (e.g., neurotransmission) and pathology (e.g., neurodegeneration). However, quantifying condensate material properties in living systems has been a substantial challenge. Here, we develop micropipette aspiration and whole-cell patch-clamp (MAPAC), a platform that allows direct material quantification of condensates in live cells. We find 10,000-fold variations in the viscoelasticity of synapsin condensates, regulated by the partitioning of α-synuclein, a marker for synucleinopathies. Through in vitro reconstitutions, we identify multiple molecular factors that distinctly regulate the viscosity, interfacial tension, and maturation of synapsin condensates, confirming the cellular roles of α-synuclein. Overall, our study provides unprecedented quantitative insights into the material properties of neuronal condensates and reveals a crucial role of α-synuclein in regulating condensate viscoelasticity. Furthermore, we envision MAPAC applicable to study a broad range of condensates in vivo.

Hypoxia-induced phase separation of ZHX2 alters chromatin looping to drive cancer metastasis

Hypoxia and dysregulated phase separation can both activate oncogenic transcriptomic profiles. However, whether hypoxia regulates transcription-associated phase separation remains unknown. Here, we find that zinc fingers and homeoboxes 2 (ZHX2) undergoes phase separation in response to hypoxia, promoting their occupancy on chromatin and activating a cluster of oncogene transcription that is enriched by metastatic genes distinct from the targets of hypoxia-inducible factor (HIF) and pathologically relevant to breast cancer. Hypoxia induces ZHX2 phase separation via a proline-rich intrinsically disordered region (IDR), enhancing phosphorylation of ZHX2 at S625 and S628 that incorporates CCCTC-binding factor (CTCF) in condensates to alter chromatin looping, consequently driving metastatic gene transcription and cancer metastasis. Our findings provide significant insight into oncogene activation and suggest a phase-separation-based therapeutic strategy for cancer.

Optogenetic induction of TDP-43 aggregation impairs neuronal integrity and behavior in Caenorhabditis elegans

BACKGROUND

Cytoplasmic aggregation of TAR DNA binding protein 43 (TDP-43) in neurons is one of the hallmarks of TDP-43 proteinopathy. Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are closely associated with TDP-43 proteinopathy; however, it remains uncertain whether TDP-43 aggregation initiates the pathology or is a consequence of it.

METHODS

To demonstrate the pathology of TDP-43 aggregation, we applied the optoDroplet technique in Caenorhabditis elegans (C. elegans), which allows spatiotemporal modulation of TDP-43 phase separation and assembly.

RESULTS

We demonstrate that optogenetically induced TDP-43 aggregates exhibited insolubility similar to that observed in TDP-43 proteinopathy. These aggregates increased the severity of neurodegeneration, particularly in GABAergic motor neurons, and exacerbated sensorimotor dysfunction in C. elegans.

CONCLUSIONS

We present an optogenetic C. elegans model of TDP-43 proteinopathy that provides insight into the neuropathological mechanisms of TDP-43 aggregates. Our model serves as a promising tool for identifying therapeutic targets for TDP-43 proteinopathy.

Condensation of cellular prion protein promotes renal fibrosis through the TBK1-IRF3 signaling axis

Cellular prion protein (PrPC), known for its pathological isoform in prion diseases such as Creutzfeldt-Jakob disease, is primarily expressed in the nervous system but has also been detected in the blood and urine of individuals with renal dysfunction. However, the role of PrPC in the development of renal disease is unexplored. Here, we showed that PrPC was up-regulated in fibrotic renal lesions in biopsies from patients with chronic kidney disease (CKD), predominantly in proximal tubular epithelial cells (PTECs). Furthermore, renal expression of PrPC was positively correlated with the severity of renal failure and the decline in estimated glomerular filtration rate in patients with CKD. In mice, tubular-specific deletion of PrPC mitigated renal fibrosis induced by unilateral ureteral obstruction (UUO) or unilateral ischemia-reperfusion injury (UIRI). Mechanistically, PrPC was up-regulated by transforming growth factor-β1-suppressor of mothers against decapentaplegic 3 signaling. PrPC activated TANK binding kinase 1 (TBK1)-interferon regulatory factor 3 (IRF3) signaling through its capacity for liquid-liquid phase separation, which promoted a profibrotic response in PTECs and fibroblasts. Treating mice with amlexanox, a US Food and Drug Administration-approved inhibitor of TBK1, either before the onset of renal fibrosis (in UUO and UIRI models) or after its establishment (in adenine- and aristolochic acid-induced CKD models), mitigated worsening of renal fibrosis and renal function. Collectively, our findings uncovered a mechanism involving phase separation of PrPC underlying renal fibrosis and support further study of the PrPC-TBK1-IRF3 axis as a potential therapeutic target for CKD.

Design and Characterization of DNA-Driven Condensates: Regulating Topology, Mechanical Properties, and Immunorecognition

Cells maintain spatiotemporal control over biochemical processes through the formation and dissolution of biomolecular condensates, dynamic membraneless organelles formed via liquid-liquid phase separation. Composed primarily of proteins and nucleic acids, these condensates regulate key cellular functions, and their properties are influenced by the concentration and type of molecules involved. The structural versatility challenges the de novo design and assembly of condensates with predefined properties. Through feedback between computational and experimental approaches, we introduce a modular system for assembling condensates using nucleic acid nanotechnology. By utilizing programmable oligonucleotides and orthogonal synthesis methods, we control the structural parameters, responsive behavior, and immunorecognition of the products. Dissipative particle dynamics simulations predict some conditions to produce larger, well-defined condensates with compact, globular cores, while others result in smaller, more diffuse analogs. Fluorescence microscopy confirms these findings and microrheology demonstrates the viscoelastic adaptability of tested condensates. Nucleases trigger disruption of structures, and ethidium bromide intercalation protects condensates from digestion. Immunostimulatory assays suggest condensate-specific activation of the IRF pathway via cGAS-STING signaling. This study provides a framework for developing biomolecular condensates with customizable properties and immunorecognition for various biological applications.

NAL1 forms a molecular cage to regulate FZP phase separation

NARROW LEAF 1 (NAL1), originally identified for its role in shaping leaf morphology, plant architecture, and various agronomic traits in rice, has remained enigmatic in terms of the molecular mechanisms governing its multifaceted functions. In this study, we present a comprehensive structural analysis of NAL1 proteins, shedding light on how NAL1 regulates the phase separation of its physiological substrate, FRIZZY PANICLE (FZP), a transcription factor. We determined that NAL1 assembles as a hexamer and forms a molecular cage with a wide central channel and three narrower lateral channels, which could discriminate its different substrates into the catalytic sites. Most notably, our investigation unveils that FZP readily forms molecular condensates via phase separation both in vitro and in vivo. NAL1 fine-tunes FZP condensation, maintaining optimal concentrations to enhance transcriptional activity. While phase separation roles include sequestration and suppression of transcriptional or enzymatic activity, our study highlights its context-dependent contribution to transcriptional regulation. NAL1 assumes a pivotal role in regulating the states of these molecular condensates through its proteolytic activity, subsequently enhancing transcriptional cascades. Our findings offer insights into comprehending the molecular mechanisms underpinning NAL1's diverse functions, with far-reaching implications for the field of plant biology. Additionally, these insights provide valuable guidance for the development of rational breeding strategies aimed at enhancing crop productivity.

Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations

Biomolecular condensates are currently recognized to play a key role in organizing cellular space and in orchestrating biochemical processes. Despite an increasing interest in characterizing their internal organization at the molecular scale, not much is known about how the densely crowded environment within these condensates affects the structural properties of recruited macromolecules. Here, we adopted explicit-solvent all-atom simulations based on a combination of enhanced sampling approaches to investigate how the conformational ensemble of an RNA hairpin is reshaped in a highly concentrated peptide solution that mimics the interior of a biomolecular condensate. Our simulations indicate that RNA structure is greatly perturbed by this distinctive physico-chemical environment, which weakens RNA secondary structure and promotes extended nonnative conformations. The resulting high-resolution picture reveals that RNA unfolding is driven by the effective solvation of nucleobases through hydrogen bonding and stacking interactions with surrounding peptides. This solvent effect can be modulated by the amino acid composition of the model condensate as proven by the differential RNA behavior observed in the case of arginine-rich and lysine-rich peptides.

Super-Resolution Mapping and Quantification of Molecular Diffusion via Single-Molecule Displacement/Diffusivity Mapping (SMdM)

ConspectusDiffusion underlies vital physicochemical and biological processes and provides a valuable window into molecular states and interactions. However, it remains a challenge to map molecular diffusion at subcellular and submicrometer scales. Whereas single-particle tracking of fluorescent molecules provides a path to quantify motion at the nanoscale, its typical pursuit of long trajectories limits wide-field mapping to the slow diffusion of bound molecules.Single-molecule displacement/diffusivity mapping (SMdM) rises to the challenge. Rather than following each fluorescent molecule longitudinally as it randomly visits potentially heterogeneous environments, SMdM flips the question to ask, for every location (e.g., a 100 × 100 nm2 spatial bin) in a wide field, how different single molecules of identical nature move locally. This location-centered strategy is naturally effective for spatial mapping of diffusivity. Moreover, by focusing on local motion, each molecule only needs to be detected for its transient displacement within a fixed short time window to achieve local statistics. This task is fulfilled for fast-diffusing molecules using a tandem excitation scheme in which a pair of closely timed stroboscopic excitation pulses are applied across two tandem frames, so that wide-field single-molecule images are recorded at a pulse-defined ≲1 ms separation unlimited by the camera frame rate. With fitting models robust against mismatched molecules and diffusion anisotropy, SMdM thus successfully achieves super-resolution D mapping for fluorescently labeled molecules of contrasting sizes and properties in diverse cellular and in vitro systems.For intracellular protein diffusion, SMdM uncovers nanoscale diffusion heterogeneities in the mammalian cytoplasm and nucleus and further elucidates their origins from the macromolecular crowding effects of cytoskeletal and chromatin ultrastructures, respectively, through correlated single-molecule localization microscopy (SMLM). Across diverse compartments of the mammalian cell, including the cytoplasm, the nucleus, the endoplasmic reticulum (ER) lumen, and the mitochondrial matrix, SMdM further unveils a striking charge effect, in which the diffusion of positively charged proteins is biasedly impeded. For cellular membranes, the integration of SMdM with fluorogenic probes enables diffusivity fine-mapping, which, in combination with spectrally resolved SMLM (SR-SMLM), elucidates nanoscale diffusional heterogeneities of different origins. For biomolecular condensates, another synergy of SMdM and SR-SMLM uncovers the gradual formation of diffusion-suppressed, hydrophobic amyloid nanoaggregates at the surface of FUS (fused in sarcoma) protein condensates during aging. Beyond spatial mapping, the mass accumulation of single-molecule displacements in SMdM further affords a valuable means to quantify D with exceptional precision. This advantage is harnessed to show no enhanced diffusion of enzymes in reactions, to uncover ubiquitous net charge-driven protein-protein interactions in solution, and to show with strategically manipulated cytoplasmic extracts that molecular interaction in the crowded cell is defined by an overwhelmingly negatively charged macromolecular environment with dense meshworks, echoing our parallel results in the mammalian cell.Together, by uniquely enabling super-resolution mapping and high-precision quantification of molecular diffusion across diverse systems, SMdM opens a new door to reveal fascinating spatiotemporal heterogeneities in living cells and beyond.

Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates

Phase separation is a fundamental process that enables cellular organization by forming biomolecular condensates. These assemblies regulate diverse functions by creating distinct environments, influencing reaction kinetics, and facilitating processes such as genome organization, signal transduction, and RNA metabolism. Recent studies highlight the complexity of condensate properties, shaped by intrinsic molecular features and external factors such as temperature and pH. Molecular simulations serve as an effective approach to establishing a comprehensive framework for analyzing these influences, offering high-resolution insights into condensate stability, dynamics, and material properties. This review evaluates recent advancements in biomolecular condensate simulations, with a particular focus on coarse-grained 1-bead-per-amino-acid (1BPA) protein models, and emphasizes OpenABC, a tool designed to simplify and streamline condensate simulations. OpenABC supports the implementation of various coarse-grained force fields, enabling their performance evaluation. Our benchmarking identifies inconsistencies in phase behavior predictions across force fields, even though these models accurately capture single-chain statistics. This finding underscores the need for enhanced force field accuracy, achievable through enriched training data sets, many-body potentials, and advanced optimization techniques. Such refinements could significantly improve the predictive capacity of coarse-grained models, bridging molecular details with emergent condensate behaviors.

Accelerated Missense Mutation Identification in Intrinsically Disordered Proteins Using Deep Learning

We use a combination of Brownian dynamics (BD) simulation results and deep learning (DL) strategies for the rapid identification of large structural changes caused by missense mutations in intrinsically disordered proteins (IDPs). We used ∼6500 IDP sequences from MobiDB database of length 20-300 to obtain gyration radii from BD simulation on a coarse-grained single-bead amino acid model (HPS2 model) used by us and others [Dignon, G. L. PLoS Comput. Biol. 2018, 14, e1005941,Tesei, G. Proc. Natl. Acad. Sci. U.S.A. 2021, 118, e2111696118,Seth, S. J. Chem. Phys. 2024, 160, 014902] to generate the training sets for the DL algorithm. Using the gyration radii ⟨Rg⟩ of the simulated IDPs as the training set, we develop a multilayer perceptron neural net (NN) architecture that predicts the gyration radii of 33 IDPs previously studied by using BD simulation with 97% accuracy from the sequence and the corresponding parameters from the HPS model. We now utilize this NN to predict gyration radii of every permutation of missense mutations in IDPs. Our approach successfully identifies mutation-prone regions that induce significant alterations in the radius of gyration when compared to the wild-type IDP sequence. We further validate the prediction by running BD simulations on the subset of identified mutants. The neural network yields a (104-106)-fold faster computation in the search space for potentially harmful mutations. Our findings have substantial implications for rapid identification and understanding of diseases related to missense mutations in IDPs and for the development of potential therapeutic interventions. The method can be extended to accurate predictions of other mutation effects in disordered proteins.

Spontaneous Hollow Coacervate Transition of Silk Fibroin via Dilution and Its Transition to Microcapsules

Polymeric microcapsules are useful for drug delivery, microreactors, and cargo transport, but traditional fabrication methods require complex processes and harsh conditions. Coacervates, formed by liquid-liquid phase separation (LLPS), offer a promising alternative for microcapsule fabrication. Recent studies have shown that coacervates can spontaneously form hollow cavities under specific conditions. Here, we investigate the spontaneous hollow coacervate transition of silk fibroin (SF). SF coacervates, induced by mixing SF with dextran, calcium ions, and copper ions, transition to hollow coacervates upon dilution. Adding ethylenediaminetetraacetic acid (EDTA) further transforms them into vesicle-like capsule coacervates, which solidify into microcapsules. As a proof-of-concept, we successfully loaded a high-molecular-weight polymer cargo into the hollow cavity and bioactive enzyme cargo into the capsule layer by simply mixing the cargo with the coacervate solution. Our results demonstrate a facile, organic-solvent-free approach for fabricating SF-based microcapsules and provide insight into the mechanisms driving hollow coacervate formation.

Treacle's ability to form liquid-like phase condensates is essential for nucleolar fibrillar center assembly, efficient rRNA transcription and processing, and rRNA gene repair

We investigated the role of the nucleolar protein Treacle in organizing and regulating the nucleolus in human cells. Our results support Treacle's ability to form liquid-like phase condensates through electrostatic interactions among molecules. The formation of these biomolecular condensates is crucial for segregating nucleolar fibrillar centers from the dense fibrillar component and ensuring high levels of ribosomal RNA (rRNA) gene transcription and accurate rRNA processing. Both the central and C-terminal domains of Treacle are required to form liquid-like condensates. The initiation of phase separation is attributed to the C-terminal domain. The central domain is characterized by repeated stretches of alternatively charged amino acid residues and is vital for condensate stability. Overexpression of mutant forms of Treacle that cannot form liquid-like phase condensates compromises the assembly of fibrillar centers, suppressing rRNA gene transcription and disrupting rRNA processing. These mutant forms also fail to recruit DNA topoisomerase II binding protein 1 (TOPBP1), suppressing the DNA damage response in the nucleolus.

Applications of Liquid-Liquid Phase Separation in Biosensing

Phase separation, particularly liquid-liquid phase separation (LLPS), has emerged as a powerful tool in biological research, offering unique advantages for visualizing and analyzing biomolecular interactions. This review highlights recent advances in leveraging LLPS to develop experimental techniques for studying protein-protein interactions (PPIs), protein-RNA interactions, and enzyme activity. The integration of LLPS with advanced techniques has expanded its applications, offering new possibilities for unraveling the complexities of cellular function and disease mechanisms. Looking forward, the development of more versatile, sensitive, and targeted LLPS-based methods is poised to transform molecular biology, providing deeper insights into cellular dynamics and facilitating therapeutic advancements.

YTHDC1 phase separation drives the nuclear export of m6A-modified lncNONMMUT062668.2 through the transport complex SRSF3-ALYREF-XPO5 to aggravate pulmonary fibrosis

Fibroblast-to-myofibroblast differentiation is the main cytopathologic characteristic of pulmonary fibrosis. However, its underlying molecular mechanism remains poorly understood. This study elucidated that the nuclear export of lncNONMMUT062668.2 (lnc668) exacerbated pulmonary fibrosis by activating fibroblast-to-myofibroblast differentiation. Mechanistic research revealed that histone H3K9 lactylation in the promoter region of the N6-methyladenosine (m6A) writer METTL3 was enriched to enhance METTL3 transcription, leading to the lnc668 m6A modification. Meanwhile, the m6A reader YTHDC1 recognized m6A-modified lnc668 and elevated the METTL3-mediated lnc668 modification. Subsequently, phase-separating YTHDC1 promoted the nuclear export of m6A-modified lnc668. In this process, the phase-separating YTHDC1 formed a nuclear pore complex with serine/arginine-rich splicing factor 3, Aly/REF export factor, and exportin-5 to assist the translocation of m6A-modified lnc668 from nucleus to cytoplasm. After nuclear export, lnc668 facilitated the translation and stability of its host gene phosphatidylinositol-binding clathrin assembly protein to activate fibroblast-to-myofibroblast differentiation, leading to the aggravation of pulmonary fibrosis, which also depended on YTHDC1 phase separation. This study first clarified that YTHDC1 phase separation is crucial for the m6A modification, nuclear export, and profibrotic role of lnc668 in exacerbating pulmonary fibrosis. These findings provide new insights into the nuclear export of cytoplasmic lncRNAs and identified potential targets for pulmonary fibrosis therapy.

Differential interactions determine anisotropies at interfaces of RNA-based biomolecular condensates

Biomolecular condensates form via macromolecular phase separation. Here, we report results from our characterization of synthetic condensates formed by phase separation of mixtures comprising two types of RNA molecules and the biocompatible polymer polyethylene glycol. Purine-rich RNAs are scaffolds that drive phase separation via heterotypic interactions. Conversely, pyrimidine-rich RNA molecules are adsorbents defined by weaker heterotypic interactions. They adsorb onto and wet the interfaces of coexisting phases formed by scaffolds. Lattice-based simulations reproduce the phenomenology observed in experiments and these simulations predict that scaffolds and adsorbents have different non-random orientational preferences at interfaces. Dynamics at interfaces were probed using single-molecule tracking of fluorogenic probes bound to RNA molecules. These experiments revealed dynamical anisotropy at interfaces whereby motions of probe molecules parallel to the interface are faster than motions perpendicular to the interface. Taken together, our findings have broad implications for designing synthetic condensates with tunable interfacial properties.

Visual Monitoring of Biomolecular Self-Assembly Dynamics and Imaging of Protein Aggregates by Distinct Emission of a Unique Hydrophobic Carbon Dot

Here, we report a novel and unique application of a special hydrophobic carbon dot (HCD) to monitor biomolecular self-assembly, along with the detection of metastable intermediates and self-aggregates. We exploited the restricted rotation of the S-S bond of the HCD synthesized from dithiosalicylic acid and melamine to illuminate different emission behaviors during the self-assembly of amino acids and proteins. The HCD that exhibits blue emission in amino acid droplets or protein aggregates dynamically changes its emission from blue to red over the time course of the amino acid self-assembly process. This unique and distinct change in emission can be visualized by the naked eye under a UV lamp. The ability of HCD to distinguish the biomolecular self-aggregated structures and monitor the self-assembly dynamics can be utilized for the visual detection of uncontrolled aggregation of proteins and peptides related to neurodegenerative diseases like Alzheimer's disease and Parkinson's disease.

Universal membranization of synthetic coacervates and biomolecular condensates towards ultrastability and spontaneous emulsification

Membranization of membraneless coacervates and condensates is emerging as a promising strategy to resolve their inherent susceptibility to fusion, ripening and environmental variations. Yet current membranization agents by design are largely limited to a subclass or a specific kind of coacervate or condensate systems. Here we develop a library of condensate-amphiphilic block polymers that can efficiently form a polymeric layer on the droplet interface for a wide spectrum of synthetic coacervates and biomolecular condensates. Condensate-amphiphilic block polymers are designed with a condenophilic block firmly anchored to the condensed phase, a condenophobic block extended to the dilute phase and a self-association block to promote membrane formation. Critical to our design is the condenophilic block of phenylboronic acid and amidoamine that target the disparate chemistry of condensed droplets via multivalent affinities. The condensate-amphiphilic block polymer membranes render the droplets mechanically robust against fusion, regulate interfacial properties such as permeability and stiffness, and substantially improve droplet tolerance to challenging conditions of temperature, salinity, pH and organic solvents.

Activity-Induced Droplet Inversion in Multicomponent Liquid-Liquid Phase Separation

Liquid-liquid phase separation (LLPS) is a vital process in forming membrane-free organelles, crucial for cell physiology and recently gaining significant attention. However, the effects of nonequilibrium factors, which are common in real life, on the process of LLPS have not been fully explored. To address this issue, we developed a model for nonequilibrium phase separation involving three components (A, B, and C) by integrating a nonequilibrium term into the chemical potential for active component B. We find significant changes in the morphology and dynamics of nonequilibrium phase-separated droplets compared to their equilibrium counterparts. Remarkably, with a large enough activity, the B-A-C structure (B at the center, surrounded by A, then enveloped by C) under equilibrium conditions may change to a C-A-B structure. Further simulations give a global picture of the system under both active and passive conditions, revealing the shifts of the phase boundaries and unraveling the effect of activity on different droplet structures. We derived an effective free energy for the active LLPS system to provide a qualitative understanding of our observations. Our study presents a basic model for nonequilibrium phase separation processes, providing crucial insights into LLPS alongside intracellular nonequilibrium phenomena.

N6-methyladenosine in DNA promotes genome stability

DNA base lesions, such as incorporation of uracil into DNA or base mismatches, can be mutagenic and toxic to replicating cells. To discover factors in repair of genomic uracil, we performed a CRISPR knockout screen in the presence of floxuridine, a chemotherapeutic agent that incorporates uracil and fluorouracil into DNA. We identified known factors, such as uracil DNA N-glycosylase (UNG), and unknown factors, such as the N6-adenosine methyltransferase, METTL3, as required to overcome floxuridine-driven cytotoxicity. Visualized with immunofluorescence, the product of METTL3 activity, N6-methyladenosine, formed nuclear foci in cells treated with floxuridine. The observed N6-methyladenosine was embedded in DNA, called 6mA, and these results were confirmed using an orthogonal approach, liquid chromatography coupled to tandem mass spectrometry. METTL3 and 6mA were required for repair of lesions driven by additional base-damaging agents, including raltitrexed, gemcitabine, and hydroxyurea. Our results establish a role for METTL3 and 6mA in promoting genome stability in mammalian cells, especially in response to base damage.

β-Arrestin Condensates Regulate G Protein-Coupled Receptor Function

G protein-coupled receptors (GPCRs) are the largest class of receptors in the genome and control many signaling cascades essential for survival. GPCR signaling is regulated by β-arrestins, multifunctional adapter proteins that direct receptor desensitization, internalization, and signaling. While at many GPCRs, β-arrestins interact with a wide array of signaling effectors, it is unclear how β-arrestins promote such varied functions. Here we show that β-arrestins undergo liquid-liquid phase separation (LLPS) to form condensates that regulate GPCR function. We demonstrate that β-arrestin oligomerization occurs in proximity to the GPCR and regulates GPCR functions such as internalization and signaling. This model is supported by a cryoEM structure of the adhesion receptor ADGRE1 in a 2:2 complex with β-arrestin 1, with a β-arrestin orientation that can promote oligomerization. Our work provides a paradigm for β-arrestin condensates as regulators of GPCR function, with LLPS serving as an important promoter of signaling compartmentalization at GPCRs.

Novel subcellular regulatory mechanisms of protein homeostasis and its implications in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron degenerative disorder. Protein aggregates induce various forms of neuronal dysfunction and represent pathological hallmarks in ALS patients. Reducing protein aggregates could be a promising therapeutic strategy for ALS. While most studies have focused on cytoplasmic protein homeostasis, neurons adaptively reduce aggregates across subcellular compartments during stress through previously uncharacterized mechanisms. Here, we summarize novel compartment-specific proteostatic mechanisms: (1) the ERAD/RESET pathways, (2) HSPs-mediated nuclear sequestration, (3) mitochondrial aggregate import (MAGIC), (4) neurite-localized UPS/autophagosome and NMP, and (5) exopher-mediated extracellular disposal. These mechanisms collectively ensure cellular stress adaptation and provide novel therapeutic targets for ALS treatment.

Phase Separation in Biological Systems: Implications for Disease Pathogenesis

Phase separation is the phenomenon where distinct liquid phases, within solution, play a critical role in the organization and function of biomolecular condensates within cells. Dysregulation of phase separation has been implicated, which can be witnessed in various diseases including neurodegenerative disorders, metabolic syndromes, and cancer. This review provides a comprehensive analysis of the role of phase separation in disease pathogenesis, which focuses on single amino acids, carbohydrates, and nucleotides. Molecular mechanisms underlying phase separation are also discussed with specific examples of diseases associated with dysregulated phase separation. Furthermore, consideration of therapeutic strategies targeting phase separation for disease intervention is explored.

Three- and four-stranded nucleic acid structures and their ligands

Nucleic acids have the potential to form not only duplexes, but also various non-canonical secondary structures in living cells. Non-canonical structures play regulatory functions mainly in the central dogma. Therefore, nucleic acid targeting molecules are potential novel therapeutic drugs that can target 'undruggable' proteins in various diseases. One of the concerns of small molecules targeting nucleic acids is selectivity, because nucleic acids have only four different building blocks. Three- and four-stranded non-canonical structures, triplexes and quadruplexes, respectively, are promising targets of small molecules because their three-dimensional structures are significantly different from the canonical duplexes, which are the most abundant in cells. Here, we describe some basic properties of the triplexes and quadruplexes and small molecules targeting the triplexes and tetraplexes.

High temperature-responsive DEAR4 condensation confers thermotolerance through recruiting TOPLESS in Arabidopsis nucleus

Global warming is harmful to plants and threatens crop yields in the world. In contrast to other abiotic stresses, the molecular mechanisms for plant high temperature perception and signaling are still not fully understood. Here, we report that transcription factor DREB AND EAR MOTIF PROTEIN 4 (DEAR4) positively regulates heat tolerance in Arabidopsis thaliana. We further reveal that DEAR4 proteins undergo liquid-liquid phase separation (LLPS) and high temperature could induce DEAR4 condensate formation in the nucleus. Moreover, DEAR4 recruits the transcriptional co-repressor TOPLESS (TPL) into the nuclear speckles under high temperature. The high temperature triggered DEAR4-TPL co-condensates enhance their transcriptional repression activity through modulating histone deacetylation levels of GASA5, which is a reported negative regulator of HEAT SHOCK PROTEINs (HSPs). A genome-wide transcriptional landscape study confirms that DEAR4 induces the expression of multiple HSPs. Taken together, we illustrate a transcriptional repression mechanism mediated by DEAR4 through LLPS to confer plants thermotolerance and open a new avenue for translating this knowledge into crops for improving their heat resistance.

Signal-induced NLRP3 phase separation initiates inflammasome activation

NLRP3 inflammasome is activated by diverse stimuli including infections, intracellular and environmental irritants. How NLRP3 senses these unrelated stimuli and what activates NLRP3 remain unknown. Here we report that signal-dependent NLRP3 phase separation initiated its activation, in which the palmitoyltransferase ZDHHC7-mediated tonic NLRP3 palmitoylation and an IDR region in the FISNA domain of NLRP3 play important roles. Moreover, three conserved hydrophobic residues in the IDR critically mediate multivalent weak interactions. NLRP3-activating stimuli including K+ efflux and NLRP3-interacting molecules imiquimod, palmitate, and cardiolipin all cause NLRP3 conformational change and induce its phase separation and activation in cells and/or in vitro. Surprisingly, amphiphilic molecules like di-alcohols used to inhibit biomolecular phase separation and chemotherapeutic drugs doxorubicin and paclitaxel activate NLRP3 independently of ZDHHC7 by directly inducing NLRP3 phase separation. Mechanistically, amphiphilic molecules decrease the solubility of both palmitoylated and non-palmitoylated NLRP3 to directly induce its phase separation and activation while NLRP3 palmitoylation reduces its solubility to some extent without activation. Therefore, ZDHHC7-mediated NLRP3 palmitoylation in resting cells licenses its activation by lowering the threshold for NLRP3 phase separation in response to any of the diverse stimuli whereas NLRP3 solubility-reducing molecules like di-alcohols and chemotherapeutic drugs activate NLRP3 directly. The signal-induced NLRP3 phase separation likely provides the simplest and most direct mechanistic basis for NLRP3 activation.

Corelet™ platform: Precision high throughput screening for targeted drug discovery of biomolecular condensates

Biomolecular condensates (BMCs) are crucial for cellular organization and function, and their dysregulation is linked to neurological, oncologic and inflammatory diseases. This highlights the need for advanced investigative tools leading to targeted BMC therapeutics. To address this need, Nereid Therapeutics uses Corelet™ technology and an automated high-throughput screening (HTS) platform to precisely quantify phase separation events and identify BMC modulators for previously undruggable targets. Hundreds of thousands of small molecules have been screened utilizing Corelet technology, yielding small molecule BMC-modulating compounds which serve as the basis for the development of targeted therapies for diseases with high unmet need.

Angiopoietin-like protein 8 directs DNA damage responses towards apoptosis by stabilizing PARP1-DNA condensates

Upon genotoxic stresses, cells employ various DNA damage responses (DDRs), including DNA damage repair or apoptosis, to safeguard genome integrity. However, the determinants among different DDRs choices are largely unknown. Here, we report angiopoietin-like protein 8 (ANGPTL8), a secreted regulator of lipid metabolism, localizes to the nucleus and acts as a dynamic switch that directs DDRs towards apoptosis rather than DNA repair after genotoxin exposure. ANGPTL8 deficiency alleviates DNA damage and apoptosis in cells exposed to genotoxins, as well as in the liver or kidney of mice injured by hepatic ischemia/reperfusion or cisplatin treatment. Mechanistically, ANGPTL8 physically interacts with Poly (ADP-ribose) polymerase 1 (PARP1), in a PARylation-independent manner, and reduces the fluidity of PARP1-DNA condensates, thereby enhancing the pro-apoptotic accumulation of PARP1 and PAR chains on DNA lesions. However, the transcription of ANGPTL8 is gradually decreased following genotoxin treatment, partly due to downregulation of CCAAT enhancer binding protein alpha (CEBPA), presumably to avoid further cytotoxicity. Together, we provide new insights by which genotoxic stress induced DDRs are channeled to suicidal apoptosis to safeguard genome integrity.