Liquid phase condensation in cell physiology and disease

Liquid-liquid phase separation in cell physiology and cancer biology: recent advances and therapeutic implications

Liquid-liquid phase separation (LLPS) is a pivotal biophysical phenomenon that plays a critical role in cellular organization and has garnered significant attention in the fields of molecular mechanism and pathophysiology of cancer. This dynamic process involves the spontaneous segregation of biomolecules, primarily proteins and nucleic acids, into condensed, liquid-like droplets under specific conditions. LLPS drives the formation of biomolecular condensates, which are crucial for various cellular functions. Increasing evidences link alterations in LLPS to the onset and progression of various diseases, particularly cancer. This review explores the diverse roles of LLPS in cancer, highlighting its underlying molecular mechanisms and far-reaching implications. We examine how dysregulated LLPS contributes to cancer development by influencing key processes such as genomic instability, metabolism, and immune evasion. Furthermore, we discuss emerging therapeutic strategies aimed at modulating LLPS, underscoring their potential to revolutionize cancer treatment.

On subcellular distribution of the zinc finger 469 protein (ZNF469) and observed discrepancy in the localization of endogenous and overexpressed ZNF469

The zinc finger 469 gene (ZNF469) is a single-exon gene predicted to encode a protein of 3953 amino acids. Despite pathogenic ZNF469 variants being associated with Brittle Cornea Syndrome (BCS), relatively little is known about ZNF469 beyond its participation in regulating the expression of genes encoding extracellular matrix proteins. In this study, we examined the expression and intracellular localization of ZNF469 in different cell lines. The level of ZNF469 mRNA varied from low levels in HEK293 cells to high levels in HeLa cells and primary fibroblasts. Antibodies against ZNF469 reacted among others with a protein of approximately 400 kDa in immunoblot analysis, which was mainly present in the insoluble fraction of the cytoplasm. Immunofluorescence analysis of interphase cells showed small cytoplasmic puncta and weak nuclear staining. In dividing HeLa cells, the antibodies recognized foci that also stained for proteasomes. In transfected cells, ZNF469 was observed mainly in foci resembling nuclear speckles in interphase and at the midbody during mitosis. The nuclear foci showed overlapping staining with proteasomes. In live cell imaging, liquid-like properties of the nuclear foci were recorded as they changed shape and position and occasionally fused with each other. During stress granule formation, cytoplasmic foci showed overlapping staining with G3BP1. Finally, in silico analysis revealed large intrinsically disordered regions with multiple low complexity domains in ZNF469. Our data indicate that ZNF469 forms aggregates possibly as biomolecular condensates when overexpressed. However, care must be taken when analyzing the intracellular distribution of ZNF469 due to the discrepancy in the localization of endogenous ZNF469 and overexpressed ZNF469 in transfected cells.

Genetically-Encoded Phase Separation Sensors Enable High-Fidelity Live-Cell Probing of Biomolecular Condensates

Biomolecular condensates are membraneless compartments with enigmatic roles across intracellular phenomena. Intrinsically disordered proteins (IDPs) often function as condensate scaffolds, fueled by liquid-liquid phase separation (LLPS) dynamics. Intracellular probing of condensates relies on live-cell imaging of IDP-scaffolds tagged with fluorescent proteins. Conformational heterogeneity in IDPs, however, renders them uniquely susceptible to artifacts from tagging. Probing epidermal condensates in skin, we recently introduced genetically-encoded LLPS-sensors that circumvent the need for molecular-level tagging of skin IDPs. Departing from subcellular tracking of IDP-scaffolds, LLPS-sensors report on the assembly and liquid-like dynamics of their condensates. Here, we demonstrate biomolecular approaches for the evolution and tunability of epidermal LLPS-sensors and assess their impact in the early and late stages of intracellular phase separation. Benchmarking against scaffold-bound fluorescent reporters, we discovered that tunable ultraweak scaffold-sensor interactions uniquely enable the sensitive and innocuous probing of nascent and established biomolecular condensates. Our LLPS-sensitive tools pave the way for the high-fidelity intracellular probing of IDP-governed biomolecular condensates across biological systems.

Interaction networks within biomolecular condensates feature topological cliques near the interface

Biomolecular condensates are typically maintained by networks of molecular interactions, with canonical examples including those formed by prion-like low complexity domains (LCDs) of proteins. Single-component LCD condensates have been predicted to exhibit small-world network topologies and spatial inhomogeneities in protein compaction. Here, we systematically characterize molecular networks underlying condensates and investigate the relationship between single molecule properties and network topologies. We employ a chemically specific coarse-grained model to probe LCD condensates and generalize our findings by varying sequence hydrophobicity via a generic model that describes "hydrophobic-polar" (HP) polymers. For both model systems, we find that condensates are sustained by small-world network topologies featuring molecular "hubs" and "cliques". Molecular hubs with high network betweenness centrality localize near the centers of condensates and adopt more elongated conformations. In contrast, network cliques-densely interacting molecules that form locally fully connected subgraphs-are bridged by hubs and tend to localize near the condensate interface. Interestingly, we find power-law relationships between the structure and dynamics of individual molecules and network betweenness centrality, which describes molecular connectivity. Thus, our work demonstrates that inhomogeneities in condensate network connectivity can be predicted from single-molecule properties. Furthermore, we find that network cliques have longer lifetimes and that their constituent molecules remain spatially constrained, suggesting a role in shaping interface material properties.

Metabolite-Responsive Control of Transcription by Phase Separation-Based Synthetic Organelles

Living natural materials have remarkable sensing abilities that translate external cues into functional changes of the material. The reconstruction of such sensing materials in bottom-up synthetic biology provides the opportunity to develop synthetic materials with life-like sensing and adaptation ability. Key to such functions are material modules that translate specific input signals into a biomolecular response. Here, we engineer a synthetic organelle based on liquid-liquid phase separation that translates a metabolic signal into the regulation of gene transcription. To this aim, we engineer the pyruvate-dependent repressor PdhR to undergo liquid-liquid phase separation in vitro by fusion to intrinsically disordered regions. We demonstrate that the resulting coacervates bind DNA harboring PdhR-responsive operator sites in a pyruvate dose-dependent and reversible manner. We observed that the activity of transcription units on the DNA was strongly attenuated following recruitment to the coacervates. However, the addition of pyruvate resulted in a reversible and dose-dependent reconstitution of transcriptional activity. The coacervate-based synthetic organelles linking metabolic cues to transcriptional signals represent a materials approach to confer stimulus responsiveness to minimal bottom-up synthetic biological systems and open opportunities in materials for sensor applications.

Lipid packing and cholesterol content regulate membrane wetting and remodeling by biomolecular condensates

Biomolecular condensates play a central role in cellular processes by interacting with membranes driving wetting transitions and inducing mutual remodeling. While condensates are known to locally alter membrane properties such as lipid packing and hydration, it remains unclear how membrane composition and phase state in turn affect condensate affinity. Here, we show that it is not only the membrane phase itself, but rather the degree of lipid packing that determines the condensate affinity for membranes. Increasing lipid chain length, saturation, or cholesterol content, enhances lipid packing, thereby decreasing condensate interaction. This regulatory mechanism is consistent across various condensate-membrane systems, highlighting the critical role of the membrane interface. In addition, protein adsorption promotes extensive membrane remodeling, including the formation of tubes and double-membrane sheets. Our findings reveal a mechanism by which membrane composition fine-tunes condensate wetting, highlighting its potential impact on cellular functions and organelle interactions.

Effects of Sup35 overexpression on the formation, morphology, and physiological functions of intracellular Sup35 assemblies

The yeast prion protein Sup35 is aggregation-prone at high concentrations. De novo Sup35 prion formation occurs at a significantly increased rate after transient overexpression of Sup35 in the presence of another prion, [PIN+], but it is still a rare event. Recent studies uncovered an additional and seemingly more prevalent role of Sup35: at its physiological level, it undergoes phase separation to form reversible condensates in response to transient stress. Stress-induced reversible Sup35 condensation in the [psi-] strain enhances cellular fitness after stress ceases, whereas irreversible Sup35 aggregates in the [PSI+] strain do not confer this advantage. However, how Sup35 overexpression, which could potentially lead to irreversible aggregation, affects its condensation under stress conditions remains unclear. In this study, we used a combinatorial method to examine how different levels of Sup35 overproduction and cellular conditions affect the nature, formation, and physical properties of Sup35 assemblies in yeast cells, as well as their impacts on cellular growth. We observed notable morphological distinctions between irreversible Sup35 aggregates and reversible Sup35 condensates, possibly indicating different formation mechanisms. In addition, Sup35 aggregation caused by a very high overexpression level can strongly inhibit cell growth, diminish the formation of stress-induced condensates when Sup35 is completely aggregated, and impair cellular recovery from stress. Together, this study advances our fundamental understanding of the physical properties and formation mechanism of different Sup35 assemblies and their impacts on cellular growth. We conclude that in vivo studies are sensitive to overexpression and can lead to assembly routes that strongly affect functions.

IMPORTANCE

The role of condensates in living cells is often studied by overexpression. For understanding their physiological role, this can be problematic. Overexpression can shift cellular functions, thereby changing the system under study, and overexpression can also affect the phase behavior of condensates by shifting the position of the system in the underlying phase diagram. Our detailed study of overexpression of Sup35 in S. cerevisiae shows the interplay between these factors and highlights basic features of intracellular condensation such as the balance between condensation and aggregation as well as how cellular localization and responsiveness depend on protein levels. We also apply super-resolution microscopy to highlight details within the cells.

Multiphasic condensates formed with mono-component of tetrapeptides via phase separation

Biomolecular condensates, formed by liquid-liquid phase separation of biomacromolecules, play crucial roles in regulating physiological events in biological systems. While multiphasic condensates have been extensively studied, those derived from a single component of short peptides have not yet been reported. Here, we report the symmetrical core-shell structural biomolecular condensates formed with a programmable tetrapeptide library via phase separation. Our findings reveal that tryptophan is essential for core-shell structure formation due to its strongest homotypical π-π interaction, enabling us to modulate the structure of condensates from core-shell to homogeneous by altering the amino acid composition. Molecular dynamics simulation combined with cryogenic focused ion beam scanning electron microscopy and cryogenic electron microscopy show that the inner core of multiphasic tetrapeptide condensates is solid-like, consisting of ordered structures. The core is enveloped by a liquid-like shell, stabilizing the core structure. Furthermore, we demonstrate control over multiphasic condensate formation through intrinsic redox reactions or post-translational modifications, facilitating the rational design of synthetic multiphasic condensates for various applications on demand.

Phase Separation Clustering of Poly Ubiquitin Cargos on Ternary Mixture Lipid Membranes by Synthetically Cross-Linked Ubiquitin Binder Peptides

Ubiquitylation is involved in various physiological processes, such as signaling and vesicle trafficking, whereas ubiquitin (UB) is considered an important clinical target. The polymeric addition of UB enables cargo molecules to be recognized specifically by multivalent binding interactions with UB-binding proteins, which results in various downstream processes. Recently, protein condensate formation by ubiquitylated proteins has been reported in many independent UB processes, suggesting its potential role in governing the spatial organization of ubiquitylated cargo proteins. We created modular polymeric UB binding motifs and polymeric UB cargos by synthetic bioconjugation and protein purification. Giant unilamellar vesicles with lipid raft composition were prepared to reconstitute the polymeric UB cargo organization on the membranes. Fluorescence imaging was used to observe the outcome. The polymeric UB cargos clustered on the membranes by forming a phase separation codomain during the interaction with the multivalent UB-binding conjugate. This phase separation was valence-dependent and strongly correlated with its potent ability to form protein condensate droplets in solution. Multivalent UB binding interactions exhibited a general trend toward the formation of phase-separated condensates and the resulting condensates were either in a liquid-like or solid-like state depending on the conditions and interactions. This suggests that the polymeric UB cargos on the plasma and endosomal membranes may use codomain phase separation to assist in the clustering of UB cargos on the membranes for cargo sorting. Our findings also indicate that such phase behavior model systems can be created by a modular synthetic approach that can potentially be used to further engineer biomimetic interactions in vitro.

An Overview of Liquid-Liquid Phase Separation and Its Mechanisms in Sepsis

Sepsis is a systemic inflammatory response syndrome triggered by the invasion of bacteria or pathogenic microorganisms into the human body, which may lead to a variety of serious complications and pose a serious threat to the patient's life and health. Liquid-liquid phase separation (LLPS) is a biomolecular process in which different biomolecules, such as proteins and nucleic acids, form liquid condensates through interactions, and these condensates play key roles in cellular physiological processes. LLPS may affect the development of sepsis through several pathways, such as modulation of inflammatory factors, immune responses, and cell death, by altering the function or activity of biomolecules, which, in turn, affect the cellular response to infection and inflammation. In this paper, we first discuss the mechanism of phase separation, then summarize the studies of LLPS in sepsis, and finally propose the potential application of LLPS in sepsis treatment strategies, while pointing out the limitations of the existing studies and the directions for future research.

Nuclear and genome dynamics underlying DNA double-strand break repair

Changes in nuclear shape and in the spatial organization of chromosomes in the nucleus commonly occur in cancer, ageing and other clinical contexts that are characterized by increased DNA damage. However, the relationship between nuclear architecture, genome organization, chromosome stability and health remains poorly defined. Studies exploring the connections between the positioning and mobility of damaged DNA relative to various nuclear structures and genomic loci have revealed nuclear and cytoplasmic processes that affect chromosome stability. In this Review, we discuss the dynamic mechanisms that regulate nuclear and genome organization to promote DNA double-strand break (DSB) repair, genome stability and cell survival. Genome dynamics that support DSB repair rely on chromatin states, repair-protein condensates, nuclear or cytoplasmic microtubules and actin filaments, kinesin or myosin motor proteins, the nuclear envelope, various nuclear compartments, chromosome topology, chromatin loop extrusion and diverse signalling cues. These processes are commonly altered in cancer and during natural or premature ageing. Indeed, the reshaping of the genome in nuclear space during DSB repair points to new avenues for therapeutic interventions that may take advantage of new cancer cell vulnerabilities or aim to reverse age-associated defects.

A nuclear pore-anchored condensate enables germ granule organization and transgenerational epigenetic inheritance

Biomolecular condensates, such as stress and germ granules, often contain subcompartments. For instance, the Caenorhabditis elegans germ granule, which localizes near the outer nuclear membrane of germ cell nuclei, is composed of at least four ordered compartments, each housing distinct sets of proteins and RNAs. How these compartments form and why they are spatially ordered remains poorly understood. Here, we show that the conserved DEAD-box RNA helicase DDX-19 defines another compartment of the larger C. elegans germ granule, which we term the D compartment. The D compartment exhibits properties of a liquid condensate and forms between the outer nuclear pore filament and other compartments of the germ granule. Two nuclear pore proteins, NPP-14 and GLEL-1, are required for its formation, suggesting that the D compartment localizes adjacent to the outer nuclear membrane through interactions with the nuclear pore. The loss of DDX-19, NPP-14 or GLEL-1 leads to functional defects, including aberrant formation of the other four germ granule compartments, a loss of germline immortality and dysregulation of small RNA-based transgenerational epigenetic inheritance programs. Hence, we propose that a function of the D compartment is to anchor larger germ granules to nuclear pores, enabling germ granule compartmentalization and promoting transgenerational RNA surveillance.

Transition-State-Dependent Spontaneous Generation of Reactive Oxygen Species by Aβ Assemblies Encodes a Self-Regulated Positive Feedback Loop for Aggregate Formation

Amyloid-β (Aβ) peptides exhibit distinct biological activities across multiple physical length scales, including monomers, oligomers, and fibrils. The transition from Aβ monomers to pathological aggregates correlates with the emergence of chemical toxicity, which plays a critical role in the progression of neurodegenerative disorders. However, the relationship between the physical state of Aβ assemblies and their chemical toxicity remains poorly understood. Here, we show that Aβ assemblies can spontaneously generate reactive oxygen species (ROS) through transition-state-specific inherent nonenzymatic redox activity. During the transition from initial monomers to intermediate oligomers or condensates to final fibrils, interfacial electrochemical environments emerge and vary at the liquid-liquid and liquid-solid interfaces. Determined by the vibrational Stark effect using electronic pre-resonance stimulated Raman scattering microscopy, the interfacial field of such assemblies is on the order of 10 MV/cm. Interfacial activity, which depends on the Aβ transition state, can modulate the spontaneous oxidation of hydroxide anions, which leads to the formation of hydroxyl radicals. Interestingly, this redox activity modifies the chemical composition of Aβ and establishes a self-regulated positive feedback loop that accelerates aggregation and promotes fibril formation, which represents a new functioning mechanism of Aβ aggregation beyond physical cross-linking. Leveraging this mechanistic insight, we identified small molecules capable of disrupting the feedback loop by scavenging hydroxyl radicals or perturbing the interface, thereby inhibiting fibril formation. Our findings provide a nonenzymatic model of neurotoxicity and reveal the critical role of physical interfaces in modulating the chemical dynamics of biomolecular assemblies. These results offer a novel framework for therapeutic intervention in Alzheimer's disease and related neurodegenerative disorders.

Coarse-Grained Model of Disordered RNA for Simulations of Biomolecular Condensates

Protein-RNA condensates are involved in a range of cellular activities. Coarse-grained molecular models of intrinsically disordered proteins have been developed to shed light on and predict single-chain properties and phase separation. An RNA model compatible with such models for disordered proteins would enable the study of complex biomolecular mixtures involving RNA. Here, we present a sequence-independent coarse-grained, two-beads-per-nucleotide model of disordered, flexible RNA based on a hydropathy scale. We parametrize the model, which we term CALVADOS-RNA, using a combination of bottom-up and top-down approaches to reproduce local RNA geometry and intramolecular interactions based on atomistic simulations and in vitro experiments. The model semiquantitatively captures several aspects of RNA-RNA and RNA-protein interactions. We examined RNA-RNA interactions by comparing calculated and experimental virial coefficients and nonspecific RNA-protein interaction by studying the reentrant phase behavior of protein-RNA mixtures. We demonstrate the utility of the model by simulating the formation of mixed condensates consisting of the disordered region of MED1 and RNA chains and the selective partitioning of disordered regions from transcription factors into these and compare the results to experiments. Despite the simplicity of our model, we show that it captures several key aspects of protein-RNA interactions and may therefore be used as a baseline model to study several aspects of the biophysics and biology of protein-RNA condensates.

Protein codes promote selective subcellular compartmentalization

Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. In this study, we demonstrate that proteins with shared functions share amino acid sequence codes that guide them to compartment destinations. We developed a protein language model, ProtGPS, that predicts with high performance the compartment localization of human proteins excluded from the training set. ProtGPS successfully guided generation of novel protein sequences that selectively assemble in the nucleolus. ProtGPS identified pathological mutations that change this code and lead to altered subcellular localization of proteins. Our results indicate that protein sequences contain not only a folding code but also a previously unrecognized code governing their distribution to diverse subcellular compartments.

Prediction of small-molecule partitioning into biomolecular condensates from simulation

Predicting small-molecule partitioning into biomolecular condensates is key to developing drugs that selectively target aberrant condensates. However, the molecular mechanisms underlying small-molecule partitioning remain largely unknown. Here, we first exploit atomistic molecular dynamics simulations of model condensates to elucidate physicochemical rules governing small-molecule partitioning. We find that while hydrophobicity is a major determinant, solubility becomes a stronger regulator of partitioning in more polar condensates. Additionally, more polar condensates exhibit selectivity toward certain compounds, suggesting that condensate-specific therapeutics can be engineered. Building on these insights, we develop minimal models (MAPPS) for efficient prediction of small-molecule partitioning into biologically relevant condensates. We demonstrate that this approach reproduces atomistic partition coefficients in both model systems and condensates composed of the low complexity domain (LCD) of FUS. Applying MAPPS to various LCD-based condensates shows that protein sequence can exert a selective pressure, thereby influencing small-molecule partitioning. Collectively, our findings reveal that partitioning is driven by both small-molecule-protein affinity and the complex interplay between the compounds and the condensate chemical environment.

Accurate prediction of thermoresponsive phase behavior of disordered proteins

Protein responses to environmental stress, particularly temperature fluctuations, have long been a subject of investigation, with a focus on how proteins maintain homeostasis and exhibit thermoresponsive properties. While UCST-type (upper critical solution temperature) phase behavior has been studied extensively and can now be predicted reliably using computational models, LCST-type (lower critical solution temperature) phase transitions remain less explored, with a lack of computational models capable of accurate prediction. This gap limits our ability to probe fully how proteins undergo phase transitions in response to temperature changes. Here, we introduce Mpipi-T, a residue-level coarse-grained model designed to predict LCST-type phase behavior of proteins. Parametrized using both atomistic simulations and experimental data, Mpipi-T accounts for entropically driven protein phase separation that occurs upon heating. Accordingly, Mpipi-T predicts temperature-driven protein behavior quantitatively in both single- and multi-chain systems. Beyond its predictive capabilities, we demonstrate that Mpipi-T provides a framework for uncovering the molecular mechanisms underlying heat stress responses, offering new insights into how proteins sense and adapt to thermal changes in biological systems.

Peptide-mediated liquid-liquid phase separation and biomolecular condensates

Liquid-liquid phase separation (LLPS) is a cornerstone of cellular organization, driving the formation of biomolecular condensates that regulate diverse biological processes and inspire innovative applications. This review explores the molecular mechanisms underlying peptide-mediated LLPS, emphasizing the roles of intermolecular interactions such as hydrophobic effects, electrostatic interactions, and π-π stacking in phase separation. The influence of environmental factors, such as pH, temperature, ionic strength, and molecular crowding on the stability and dynamics of peptide coacervates is examined, highlighting their tunable properties. Additionally, the unique physicochemical properties of peptide coacervates, including their viscoelastic behavior, interfacial dynamics, and stimuli-responsiveness, are discussed in the context of their biological relevance and engineering potential. Peptide coacervates are emerging as versatile platforms in biotechnology and medicine, particularly in drug delivery, tissue engineering, and synthetic biology. By integrating fundamental insights with practical applications, this review underscores the potential of peptide-mediated LLPS as a transformative tool for advancing science and healthcare.

Electrostatics of salt-dependent reentrant phase behaviors highlights diverse roles of ATP in biomolecular condensates

Liquid-liquid phase separation (LLPS) involving intrinsically disordered protein regions (IDRs) is a major physical mechanism for biological membraneless compartmentalization. The multifaceted electrostatic effects in these biomolecular condensates are exemplified here by experimental and theoretical investigations of the different salt- and ATP-dependent LLPSs of an IDR of messenger RNA-regulating protein Caprin1 and its phosphorylated variant pY-Caprin1, exhibiting, for example, reentrant behaviors in some instances but not others. Experimental data are rationalized by physical modeling using analytical theory, molecular dynamics, and polymer field-theoretic simulations, indicating that interchain ion bridges enhance LLPS of polyelectrolytes such as Caprin1 and the high valency of ATP-magnesium is a significant factor for its colocalization with the condensed phases, as similar trends are observed for other IDRs. The electrostatic nature of these features complements ATP's involvement in π-related interactions and as an amphiphilic hydrotrope, underscoring a general role of biomolecular condensates in modulating ion concentrations and its functional ramifications.

The Hippo pathway: Organ size control and beyond

The Hippo signaling pathway is a highly conserved signaling network for controlling organ size, tissue homeostasis, and regeneration. It integrates a wide range of intracellular and extracellular signals, such as cellular energy status, cell density, hormonal signals, and mechanical cues, to modulate the activity of YAP/TAZ transcriptional coactivators. A key aspect of Hippo pathway regulation involves its spatial organization at the plasma membrane, where upstream regulators localize to specific membrane subdomains to regulate the assembly and activation of the pathway components. This spatial organization is critical for the precise control of Hippo signaling, as it dictates the dynamic interactions between pathway components and their regulators. Recent studies have also uncovered the role of biomolecular condensation in regulating Hippo signaling, adding complexity to its control mechanisms. Dysregulation of the Hippo pathway is implicated in various pathological conditions, particularly cancer, where alterations in YAP/TAZ activity contribute to tumorigenesis and drug resistance. Therapeutic strategies targeting the Hippo pathway have shown promise in both cancer treatment, by inhibiting YAP/TAZ signaling, and regenerative medicine, by enhancing YAP/TAZ activity to promote tissue repair. The development of small molecule inhibitors targeting the YAP-TEAD interaction and other upstream regulators offers new avenues for therapeutic intervention. SIGNIFICANCE STATEMENT: The Hippo signaling pathway is a key regulator of organ size, tissue homeostasis, and regeneration, with its dysregulation linked to diseases such as cancer. Understanding this pathway opens new possibilities for therapeutic approaches in regenerative medicine and oncology, with the potential to translate basic research into improved clinical outcomes.

Nucleolar origins: challenging perspectives on evolution and function

The nucleolus, once considered a mere 'ribosome factory', is now recognized as a dynamic hub influencing nearly every aspect of cellular life, from genome organization to stress response and ageing. Despite being a hallmark of eukaryotic cells, recent discoveries reveal that even prokaryotes exhibit nucleolus-like structures, hinting at ancient origins for nucleolar functions. This review explores the evolutionary journey of the nucleolus, tracing its roots back to early life and examining its structural and functional diversity across domains. We highlight key nucleolar proteins that play vital roles not only in ribosome production but also in regulating cell cycle, DNA repair and cellular stress, linking nucleolar activity directly to health and disease. Dysfunctions in nucleolar processes are implicated in cancer, ribosomopathies and neurodegenerative disorders, positioning the nucleolus as a critical target for innovative therapeutic strategies. As advanced imaging and molecular techniques unlock deeper insights into both canonical and mysterious non-canonical roles, the nucleolus stands as a model for how cellular microenvironments can evolve to meet complex biological demands. By addressing open questions surrounding the evolution of the nucleolus, its organization and diverse functions, the ideas presented here aim to contribute to the ongoing discussion, challenging traditional paradigms and suggesting new avenues for uncovering the fundamental principles that drive cellular life.

Role of Assemblysomes in Cellular Stress Responses

Assemblysomes are recently discovered intracellular RNA-protein complexes that play important roles in cellular stress response, regulation of gene expression, and also in co-translational protein assembly. In this review, a wide spectrum overview of assemblysomes is provided, including their discovery, mechanism of action, characteristics, and potential applications in several fields. Assemblysomes are distinct liquid-liquid phase-separated condensates; they have certain unique properties differentiating them from other cellular granules. They are composed of ribosome-nascent protein chain complexes and are resistant to cycloheximide and EDTA. The discovery and observation of intracellular condensates, like assemblysomes, have further expanded our knowledge of cellular stress response mechanisms, particularly in DNA repair processes and defense against proteotoxicity. Ribosome profiling experiments and next-generation sequencing of cDNA libraries extracted from EDTA-resistant pellets-of ultracentrifuged cell lysates-have shed light on the composition and dynamics of assemblysomes, revealing their role as repositories for pre-made stress-responsive ribosome-nascent chain complexes. This review gives an exploration of assemblysomes' potential clinical applications from multiple aspects, including their usefulness as diagnostic biomarkers for chemotherapy resistance and their implications in cancer therapy. In addition, in this overview, we raise some theoretical ideas of industrial and agricultural applications connected to these membraneless organelles. However, we see several challenges. On one hand, we need to understand the complexity of assemblysomes' multiple functions and regulations; on the other hand, it is essential to bridge the gap between fundamental research and practical applications. Overall, assemblysome research can be perceived as a promising upcomer in the improvement of biomedical settings as well as those connected to agricultural and industrial aspects.

Bioinspired hierarchical porous tough adhesive to promote sealing of high-pressure bleeding

Timely and stable sealing of uncontrolled high-pressure hemorrhage in emergency situations outside surgical units remains a major clinical challenge, contributing to the high mortality rate associated with trauma. The currently widely used hemostatic bioadhesives are ineffective for hemorrhage from major arteries and the heart due to the absence of biologically compatible flexible structures capable of simultaneously ensuring conformal tough adhesion and biomechanical support. Here, inspired by the principle of chromatin assembly, we present a tissue-conformable tough matrix for robust sealing of severe bleeding. This hierarchical matrix is fabricated through a phase separation process, which involves the in-situ formation of nanoporous aggregates within a microporous double-network (DN) matrix. The dispersed aggregates disrupt the rigid physical crosslinking of the original DN matrix and function as a dissipative component, enabling the aggregate-based DN (aggDN) matrix to efficiently dissipate energy during stress and achieve improved conformal attachment to soft tissues. Subsequently, pre-activated bridging polymers facilitate rapid interfacial bonding between the matrix and tissue surfaces. They synergistically withstand considerable hydraulic pressure of approximately 700 mmHg and demonstrate exceptional tissue adhesion and sealing in rat cardiac and canine aortic hemorrhages, outperforming the commercially available bioadhesives. Our findings present a promising biomimetic strategy for engineering biomechanically compatible and tough adhesive hydrogels, facilitating prompt and effective treatment of hemorrhagic wounds.

Decoding the multifaceted roles of galectins in self-defense

In this review, we aim to explore the multifaceted roles of galectins in host defense from a broader perspective, particularly regarding their functions when host integrity is compromised. Numerous comprehensive reviews on galectin functions in immunity have already been published. For researchers new to the field, this wealth of information may create an impression of galectins as proteins involved in a wide array of biological processes. Furthermore, due to the heterogeneity of galectin ligands, glycans, there is a risk of perceiving galectin-specific functions as ambiguous, potentially obscuring their core biological significance. To address this, we revisit foundational aspects, focusing on the significance of the recognition of galactose, a "late-comer" monosaccharide in evolutionary terms, provide an overview of galectin glycan binding specificity, with emphasis on the potential biological importance of each carbohydrate-recognition domain. We also discuss the biological implications of the galectin location paradox wherein these cytosolic lectins function in host defense despite their glycan ligands being synthesized in the secretory pathway. Additionally, we examine the role of galectins in liquid-liquid phase separation on membranes, which may facilitate their diverse functions in cellular responses. Through this approach, we aim to re-evaluate the complex and diverse biological roles of galectins in host defense.

Synthetic biomolecular condensates enhance translation from a target mRNA in living cells

Biomolecular condensates composed of proteins and RNA are one approach by which cells regulate post-transcriptional gene expression. Their formation typically involves the phase separation of intrinsically disordered proteins with a target mRNA, sequestering the mRNA into a liquid condensate. This sequestration regulates gene expression by modulating translation or facilitating RNA processing. Here we engineer synthetic condensates using a fusion of an RNA-binding protein, the human Pumilio2 homology domain (Pum2), and a synthetic intrinsically disordered protein, an elastin-like polypeptide (ELP), that can bind and sequester a target mRNA transcript. In protocells, sequestration of a target mRNA largely limits its translation. Conversely, in Escherichia coli, sequestration of the same target mRNA increases its translation. We characterize the Pum2-ELP condensate system using microscopy, biophysical and biochemical assays, and RNA sequencing. This approach enables the modulation of cell function via the formation of synthetic biomolecular condensates that regulate the expression of a target protein.

Mesoscopic p53-rich clusters represent a new class of protein condensates

The protein p53 is an important tumor suppressor, which transforms, after mutation, into a potent cancer promotor. Both mutant and wild-type p53 form amyloid fibrils, and fibrillization is considered one of the pathways of the mutants' oncogenicity. p53 incorporates structured domains, essential to its function, and extensive disordered regions. Here, we address the roles of the ordered (where the vast majority of oncogenic mutations localize) and disordered (implicated in aggregation and condensation of numerous other proteins) domains in p53 aggregation. We show that in the cytosol of model breast cancer cells, the mutant p53 R248Q reproducibly forms fluid aggregates with narrow size distribution centered at approximately 40 nm. Similar aggregates were observed in experiments with purified p53 R248Q, which identified the aggregates as mesoscopic protein-rich clusters, a unique protein condensate. Direct TEM imaging demonstrates that the mesoscopic clusters host and facilitate the nucleation of amyloid fibrils. We show that in solutions of stand-alone ordered domain of WT p53 clusters form and support fibril nucleation, whereas the disordered N-terminus domain forms common dense liquid and no fibrils. These results highlight two unique features of the mesoscopic protein-rich clusters: their role in amyloid fibrillization that may have implications for the oncogenicity of p53 mutants and the defining role of the ordered protein domains in their formation. In a broader context, these findings demonstrate that mutations in the DBD domain, which underlie the loss of cancer-protective transcription function, are also responsible for fibrillization and, thus, the gain of oncogenic function of p53 mutants.

Transformable peptide blocks NF-κB/IκBα pathway through targeted coating IκBα against rheumatoid arthritis

Rheumatoid arthritis (RA) is an autoimmune disease characterized by destructive effects. Although current therapies utilizing antibodies against inflammatory cytokines have shown some success, the inhibition of a single inflammatory molecule may not suffice to impede the progression of RA due to the intricate pathogenesis involving multiple molecules. In this study, we have developed an intelligent transformable peptide, namely BP-FFVLK-DSGLDSM (BFD). BFD has the ability to self-assemble into spherical nanoparticles in water or in the blood circulation to facilitate their delivery and distribution. When endocytosed into immune cells, BFD can identify and attach to phosphorylation sites on IκBα and in situ transform into a nanofibrous network coating NF-κB/IκBα complexes, blocking the phosphorylation and degradation of IκBα. As a result, BFD enables decreasing expression of proinflammatory mediators. In the present study, we demonstrate that BFD exhibits notable efficacy in alleviating arthritis-related manifestations, such as joints and tissues swelling, as well as bone and cartilage destruction on the collagen-induced arthritis (CIA) rat model. The investigation of intracellular biodistribution, phosphorylation of IκBα, and cytokine detection in culture medium supernatant, joint tissue, and serum exhibits strong associations with therapeutic outcomes. The utilization of transformable peptide presents a novel approach for the management of inflammatory diseases.

Regulation of alternative splicing by CBF-mediated protein condensation in plant response to cold stress

Cold acclimation is critical for the survival of plants in temperate regions under low temperatures, and C-REPEAT BINDING FACTORs (CBFs) are well established as key transcriptional factors that regulate this adaptive process by controlling the expression of cold-responsive genes. Here we demonstrate that CBFs are involved in modulating alternative splicing during cold acclimation through their interaction with subunits of the spliceosome complex. Under cold stress, CBF proteins accumulate and directly interact with SKI-INTERACTING PROTEIN (SKIP), a key component of the spliceosome, which positively regulates acquired freezing tolerance. This interaction facilitates the formation of SKIP nuclear condensates, which enhances the association between SKIP and specific cold-responsive transcripts, thereby increasing their splicing efficiency. Our findings uncover a regulatory role of CBFs in alternative splicing and highlight their pivotal involvement in the full development of cold acclimation, bridging transcriptional and post-transcriptional regulatory mechanisms.

The dark side of fluorescent protein tagging-the impact of protein tags on biomolecular condensation

Biomolecular condensation has emerged as an important mechanism to control various cellular processes through the formation of membraneless organelles. Fluorescent protein tags have been extensively used to study the formation and the properties of condensates in vitro and in vivo, but there is evidence that tags may perturb the condensation properties of proteins. In this study, we carefully assess the effects of protein tags on the yeast DEAD-box ATPase Dhh1, a central regulator of processing bodies (P-bodies), which are biomolecular condensates involved in mRNA metabolism. We show that fluorescent tags as well as a polyhistidine tag greatly affect Dhh1 condensation in vitro and lead to condensates with different dynamic properties. Tagging of Dhh1 with various fluorescent proteins in vivo alters the number of P-bodies upon glucose starvation and some tags even show constitutive P-bodies in nonstressed cells. These data raise concerns about the accuracy of tagged protein condensation experiments, highlighting the need for caution when interpreting the results.

Structured protein domains enter the spotlight: modulators of biomolecular condensate form and function

Biomolecular condensates are membraneless organelles that concentrate proteins and nucleic acids. One of the primary components of condensates is multidomain proteins, whose domains can be broadly classified as structured and disordered. While structured protein domains are ubiquitous within biomolecular condensates, the physical ramifications of their unique properties have been relatively underexplored. Therefore, this review synthesizes current literature pertaining to structured protein domains within the context of condensates. We examine how the propensity of structured domains for high interaction specificity and low conformational heterogeneity contributes to the formation, material properties, and functions of biomolecular condensates. Finally, we propose unanswered questions on the behavior of structured protein domains within condensates, the answers of which will contribute to a more complete understanding of condensate biophysics.

PARPs and ADP-ribosylation-mediated biomolecular condensates: determinants, dynamics, and disease implications

Biomolecular condensates are cellular compartments that selectively enrich proteins and other macromolecules despite lacking enveloping membranes. These compartments often form through phase separation triggered by multivalent nucleic acids. Emerging data have revealed that poly(ADP-ribose) (PAR), a nucleic acid-based protein modification catalyzed by ADP-ribosyltransferases (commonly known as PARPs), plays a crucial role in this process. This review focuses on the role of PARPs and ADP-ribosylation, and explores the principles and mechanisms by which PAR regulates condensate formation, dissolution, and dynamics. Future studies with advanced tools to examine PAR binding sites, substrate interactions, PAR length and structure, and transitions from condensates to aggregates will be key to unraveling the complexity of ADP-ribosylation in health and disease, including cancer, viral infection, and neurodegeneration.

Comparative evaluation of cell-based assay technologies for scoring drug-induced condensation of SARS-CoV-2 nucleocapsid protein

Protein-nucleic acid phase separation has been implicated in many diseases such as viral infections, neurodegeneration, and cancer. There is great interest in identifying condensate modulators (CMODs), which are small molecules that alter the dynamics and functions of phase-separated condensates, as a potential therapeutic modality. Most CMODs were identified in cellular high-content screens (HCS) where micron-scale condensates were characterized by fluorescence microscopy. These approaches lack information on protein dynamics, are limited by microscope resolution, and are insensitive to subtle condensation phenotypes missed by overfit analysis pipelines. Here, we evaluate two alternative cell-based assays: high-throughput single molecule tracking (htSMT) and proximity-based condensate biosensors using NanoBIT (split luciferase) and NanoBRET (bioluminescence resonance energy transfer) technologies. We applied these methods to evaluate condensation of the SARS-CoV-2 nucleocapsid (N) protein under GSK3 inhibitor treatment, which we had previously identified in our HCS campaign to induce condensation with well-defined structure-activity relationships (SAR). Using htSMT, we observed robust changes in N protein diffusion as early as 3 h post GSK3 inhibition. Proximity-based N biosensors also reliably reported on condensation, enabling the rapid assaying of large compound libraries with a readout independent of imaging. Both htSMT and proximity-based biosensors performed well in a screening format and provided information on CMOD activity that was complementary to HCS. We expect that this expanded toolkit for interrogating phase-separated proteins will accelerate the identification of CMODs for important therapeutic targets.

Scale-free Spatio-temporal Correlations in Conformational Fluctuations of Intrinsically Disordered Proteins

The self-assembly of intrinsically disordered proteins (IDPs) into condensed phases and the formation of membrane-less organelles (MLOs) can be considered as the phenomenon of collective behavior. The conformational dynamics of IDPs are essential for their interactions and the formation of a condensed phase. From a physical perspective, collective behavior and the emergence of phase are associated with long-range correlations. Here the conformational dynamics of IDPs and the correlations therein are analyzed, using µs-scale atomistic molecular dynamics (MD) simulations and single-molecule Förster resonance energy transfer (smFRET) experiments. The existence of typical scale-free spatio-temporal correlations in IDP conformational fluctuations is demonstrated. Their conformational evolutions exhibit "1/f noise" power spectra and are accompanied by the appearance of residue domains following a power-law size distribution. Additionally, the motions of residues present scale-free behavioral correlation. These scale-free correlations resemble those in physical systems near critical points, suggesting that IDPs are poised at a critical state. Therefore, IDPs can effectively respond to finite differences in sequence compositions and engender considerable structural heterogeneity which is beneficial for IDP interactions and phase formation.

Charge screening and hydrophobicity drive progressive assembly and liquid-liquid phase separation of reflectin protein

The intrinsically disordered reflectin proteins drive tunable reflectivity for dynamic camouflage and communication in the recently evolved Loliginidae family of squid. Previous work revealed that reflectin A1 forms discrete assemblies whose size is precisely predicted by protein net charge density and charge screening by the local anion concentration. Using dynamic light scattering, FRET, and confocal microscopy, we show that these assemblies, of which 95 to 99% of bulk protein in solution is partitioned into, are dynamic intermediates to liquid protein-dense condensates formed by liquid-liquid phase separation (LLPS). Increasing salt concentration drives this progression by anionic screening of the cationic protein's Coulombic repulsion, and by increasing the contribution of the hydrophobic effect which tips the balance between short-range attraction and long-range repulsion to drive protein assembly and ultimately LLPS. Measuring fluorescence recovery after photobleaching and droplet fusion dynamics, we demonstrate that reflectin diffusivity in condensates is tuned by protein net charge density. These results illuminate the physical processes governing reflectin A1 assembly and LLPS and demonstrate the potential for reflectin A1 condensate-based tunable biomaterials. They also compliment previous observations of liquid phase separation in the Bragg lamellae of activated iridocytes and suggest that LLPS behavior may serve a critical role in governing the tunable and reversible dehydration of the membrane-bounded Bragg lamellae and vesicles containing reflectin in biophotonically active cells.

Transcription regulation by biomolecular condensates

Biomolecular condensates regulate transcription by dynamically compartmentalizing the transcription machinery. Classic models of transcription regulation focus on the recruitment and regulation of RNA polymerase II by the formation of complexes at the 1-10 nm length scale, which are driven by structured and stoichiometric interactions. These complexes are further organized into condensates at the 100-1,000 nm length scale, which are driven by dynamic multivalent interactions often involving domain-ligand pairs or intrinsically disordered regions. Regulation through condensate-mediated organization does not supersede the processes occurring at the 1-10 nm scale, but it provides regulatory mechanisms for promoting or preventing these processes in the crowded nuclear environment. Regulation of transcription by transcriptional condensates is involved in cell state transitions during animal and plant development, cell signalling and cellular responses to the environment. These condensate-mediated processes are dysregulated in developmental disorders, cancer and neurodegeneration. In this Review, we discuss the principles underlying the regulation of transcriptional condensates, their roles in physiology and their dysregulation in human diseases.

Evolution Driven Microscale Combinatorial Chemistry in Intracellular Mimicking Droplets to Engineer Thermostable RNA for Cellular Imaging

Fluorescent light-up aptamer/fluorogen pairs are powerful tools for tracking RNA in the cell, however limitations in thermostability and fluorescence intensity exist. Current in vitro selection techniques struggle to mimic complex intracellular environments, limiting in vivo biomolecule functionality. Taking inspiration from microenvironment-dependent RNA folding observed in cells and organelle-mimicking droplets, an efficient system is created that uses microscale heated water droplets to simulate intracellular conditions, effectively replicating the intracellular RNA folding landscape. This system is integrated with microfluidic droplet sorting to evolve RNA aptamers. Through this approach, an RNA aptamer is engineered with improved fluorescence activity by exploring the chemical fitness landscape under biomimetic conditions. The enhanced RNA aptamer named eBroccoli has increased fluorescence intensity and thermal stability, both in vitro and in vivo in bacterial and mammalian cells. In mammalian cell culture conditions, a fluorescence improvement of 3.9-times is observed and biological thermal stability up to 45 °C is observed in bacterial systems. eBroccoli enable real-time visualization of nanoscale stress granule formation in mammalian cells during heat shock at 42 °C. By introducing the concept of "biomimetic equivalence" based on RNA folding, the platform offers a simple yet effective strategy to mimic intracellular complexity in evolution-based engineering.

Metastable phase-separated droplet generation and long-time DNA enrichment by laser-induced Soret effect

Spatiotemporally controlled laser-induced phase separation (LIPS) offers unique research avenues and has potential for biological and biomedical applications. However, LIPS conditions often have drawbacks for practical use, which limit their applications. For instance, LIPS droplets are unstable and diminish after the laser is terminated. Here, we developed a novel LIPS method using laser-induced Soret effect with a simple setup to solve these problems. We generate liquid-liquid phase-separated (LLPS) droplets using LIPS in an aqueous two-phase system (ATPS) of dextran (DEX) and polyethylene glycol (PEG). When DEX-rich droplets were generated in the DEX/PEG mix on the phase boundary, the droplets showed unprecedently high longevity; the DEX droplets were retained over 48 h. This counterintuitive behaviour suggests that the droplet is in an unknown metastable state. By exploiting the capability of DEX-rich droplets to enrich nucleic acid polymers, we achieved stable DNA enrichment in LIPS DEX droplets with a high enrichment factor of 1400 ± 400. Further, we patterned DNA-carrying DEX-rich droplets into a designed structure to demonstrate the stability and spatiotemporal controllability of DEX-rich droplet formation. This is the first report for LIPS droplet generation in a DEX/PEG system, opening new avenues for biological and medical applications of LIPS.

Rational design of phytovirucide inhibiting nucleocapsid protein aggregation in tomato spotted wilt virus

Ineffectiveness of managing plant viruses by chemicals has posed serious challenges in crop production. Recently, phase separation has shown to play a key role in viral lifecycle. Using inhibitors that can disturb biomolecular condensates formed by phase separation for virus control has been reported in medical field. However, the applicability of this promising antiviral tactic for plant protection has not been explored. Here, we report an inhibitor, Z9, that targets the tomato spotted wilt virus (TSWV) N protein. Z9 is capable of interacting with the amino acids in the nucleic acid binding region of TSWV N, disrupting the assembly of N and RNA into phase-separated condensates, the reduction of which is detrimental to the stability of the N protein. This study provides a strategy for phase separation-based plant virus control.

Emergent 3D genome reorganization from the stepwise assembly of transcriptional condensates

Transcriptional condensates are clusters of transcription factors, coactivators, and RNA Pol II associated with high-level gene expression, yet how they assemble and function within the cell remains unclear. Here we show that transcriptional condensates form in a stepwise manner to enable both graded and three-dimensional (3D) gene control in the yeast heat shock response. Molecular dissection revealed a condensate cascade. First, the transcription factor Hsf1 clusters upon partial dissociation from the chaperone Hsp70. Next, the coactivator Mediator partitions following further Hsp70 dissociation and Hsf1 phosphorylation. Finally, Pol II condenses, driving the emergent coalescence of HSR genes. Molecular analysis of a series of Hsf1 mutants revealed graded, rather than switch-like, transcriptional activity. Separation-of-function mutants showed that condensate formation can be decoupled from gene activation. Instead, fully assembled HSR condensates promote adaptive 3D genome reconfiguration, suggesting a role of transcriptional condensates beyond gene activation.

Mug20-Rec25-Rec27 binds DNA and enhances meiotic DNA break formation via phase-separated condensates

During meiosis, programmed DNA double-strand breaks (DSBs) are formed at hotspots to initiate homologous recombination, which is vital for reassorting genetic material. In fission yeast, the linear element (LinE) proteins Mug20, Rec25, and Rec27 interdependently bind chromosomal hotspots with high specificity and are necessary for high-level DSB formation. However, their mechanistic role in regulating the meiotic DSB machinery remains unknown. Here, using purified Mug20-Rec25-Rec27 (MRR) complex and functional intracellular analyses, we reveal that the MRR-DNA nucleoprotein complex assembles phase-separated condensates that compact the DNA. Notably, MRR complex formation is a prerequisite for DNA binding and condensate assembly, with Rec27 playing a pivotal role in directly binding DNA. Consistent with this finding, failure to form MRR-DNA condensates results in defective intracellular meiotic DSB formation and recombination. Our results provide mechanistic insights into how LinEs enhance meiotic DSB formation and provide a paradigm for studies in other species.

Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates

Biomolecular condensates composed of highly charged biomolecules, such as DNA, RNA, chromatin, and nucleic-acid binding proteins, are ubiquitous in the cell nucleus. The biophysical properties of these charge-rich condensates are largely regulated by electrostatic interactions. Residue-resolution coarse-grained models that describe solvent and ions implicitly are widely used to gain mechanistic insights into the biophysical properties of condensates, offering transferability, computational efficiency, and accurate predictions for multiple systems. However, their predictive accuracy diminishes for charge-rich condensates due to the implicit treatment of solvent and ions. Here, we present Mpipi-Recharged, a residue-resolution coarse-grained model that improves the description of charge effects in biomolecular condensates containing disordered proteins, multidomain proteins, and/or disordered single-stranded RNAs. Mpipi-Recharged introduces a pair-specific asymmetric Yukawa electrostatic potential, informed by atomistic simulations. We show that this asymmetric coarse-graining of electrostatic forces captures intricate effects, such as charge blockiness, stoichiometry variations in complex coacervates, and modulation of salt concentration, without requiring explicit solvation. Mpipi-Recharged provides excellent agreement with experiments in predicting the phase behavior of highly charged condensates. Overall, Mpipi-Recharged improves the computational tools available to investigate the physicochemical mechanisms regulating biomolecular condensates, enhancing the scope of computer simulations in this field.

COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

Cu(I)-Induced G-Quartets: Robust Supramolecular Polymers Exhibiting Heating-Induced Aqueous Phase Transitions Into Gel or Precipitate

Certain proteins and synthetic covalent polymers experience aqueous phase transitions, driving functional self-assembly. Herein, we unveil the ability of supramolecular polymers (SPs) formed by G4.Cu+ to undergo heating-induced unexpected aqueous phase transitions. For the first time, guided by Cu+, guanosine (G) formed a highly stable G-quartet (G4.Cu+)/G-quadruplex as a non-canonical DNA secondary structure with temperature tolerance, distinct from the well-known G4.K+. The G4.Cu+ self-assembled in water through π-π stacking, metallophilic and hydrophobic interactions, forming thermally robust SPs. This enhanced stability is attributed to the stronger coordination of Cu+ to four carbonyl oxygens of G-quartet and the presence of Cu+- - -Cu+ attractive metallophilic interactions in Cu+-induced G-quadruplex, exhibiting a significantly higher interaction energy than K+ as determined computationally. Remarkably, the aqueous SP solution exhibited heating-induced phase transitions-forming a hydrogel through dehydration-driven crosslinking of SPs below cloud temperature (Tcp) and a hydrophobic collapse-induced solid precipitate above Tcp, showcasing a lower critical solution temperature (LCST) behavior. Notably, this LCST behavior of G4.Cu+ SP originates from biomolecular functionality rather than commonly exploited thermo-responsive oligoethylene glycols with supramolecular assemblies. Furthermore, exploiting the redox reversibility of Cu+/Cu2+, we demonstrated control over the assembly and disassembly of G-quartets/G-quadruplex and gelation reversibly.

Direct ionic stress sensing and mitigation by the transcription factor NFAT5

Rising temperatures and water scarcity caused by climate change are increasingly exposing our cells and tissues to ionic stress, a consequence of elevated cytoplasmic ionic strength that can disrupt protein, organelle, and genome function. Here, we unveil a single-protein mechanism for ionic strength sensing and mitigation in animal cells, one that is notably different from the analogous high osmolarity glycerol kinase cascade in yeast. The Rel family transcription factor NFAT5 directly senses intracellular ionic strength using a C-terminal prion-like domain (PLD). In response to elevated intracellular ionic strength, this PLD is necessary and sufficient to coordinate an adaptive gene expression program by recruiting the transcriptional coactivator BRD4. The purified NFAT5 PLD forms condensates in response to elevated solution ionic strength in vitro, and human NFAT5 alone is sufficient to reconstitute a mammalian transcriptional response to ionic stress in yeast. We propose that ion-sensitive conformational changes in a PLD directly regulate transcription to maintain ionic strength homeostasis in animal cells.

A biophysical basis for the spreading behavior and limited diffusion of Xist

Xist RNA initiates X inactivation as it spreads in cis across the chromosome. Here, we reveal a biophysical basis for its cis-limited diffusion. Xist RNA and HNRNPK together drive a liquid-liquid phase separation (LLPS) that encapsulates the chromosome. HNRNPK droplets pull on Xist and internalize the RNA. Once internalized, Xist induces a further phase transition and "softens" the HNRNPK droplet. Xist alters the condensate's deformability, adhesiveness, and wetting properties in vitro. Other Xist-interacting proteins are internalized and entrapped within the droplet, resulting in a concentration of Xist and protein partners within the condensate. We attribute LLPS to HNRNPK's RGG and Xist's repeat B (RepB) motifs. Mutating these motifs causes Xist diffusion, disrupts polycomb recruitment, and precludes the required mixing of chromosomal compartments for Xist's migration. Thus, we hypothesize that phase transitions in HNRNPK condensates allow Xist to locally concentrate silencing factors and to spread through internal channels of the HNRNPK-encapsulated chromosome.

The phenylalanine-and-glycine repeats of NUP98 oncofusions form condensates that selectively partition transcriptional coactivators

Recurrent cancer-causing fusions of NUP98 produce higher-order assemblies known as condensates. How NUP98 oncofusion-driven condensates activate oncogenes remains poorly understood. Here, we investigate NUP98-PHF23, a leukemogenic chimera of the disordered phenylalanine-and-glycine (FG)-repeat-rich region of NUP98 and the H3K4me3/2-binding plant homeodomain (PHD) finger domain of PHF23. Our integrated analyses using mutagenesis, proteomics, genomics, and condensate reconstitution demonstrate that the PHD domain targets condensate to the H3K4me3/2-demarcated developmental genes, while FG repeats determine the condensate composition and gene activation. FG repeats are necessary to form condensates that partition a specific set of transcriptional regulators, notably the KMT2/MLL H3K4 methyltransferases, histone acetyltransferases, and BRD4. FG repeats are sufficient to partition transcriptional regulators and activate a reporter when tethered to a genomic locus. NUP98-PHF23 assembles the chromatin-bound condensates that partition multiple positive regulators, initiating a feedforward loop of reading-and-writing the active histone modifications. This network of interactions enforces an open chromatin landscape at proto-oncogenes, thereby driving cancerous transcriptional programs.

Chemically Specific Coherent Raman Imaging of Liquid-Liquid Phase Separation and Its Sequelae

Liquid-liquid phase separation (LLPS) plays a pivotal role in processes ranging from cellular structure reorganization to the formation of crystalline structures in materials science. In the pharmaceutical field, it has been demonstrated to impact drug crystallization and delivery. To date, characterization of LLPS has been limited to nonspatially resolved or nonchemically resolved analyses. In this study, we employed chemically specific stimulated Raman scattering (SRS), combined with second harmonic generation (SHG), for the first time to image crystallization in the presence of LLPS. Using the model compound ibuprofen, we examined the interplay between LLPS and crystallization, and explored the influence of both dissolution medium and enantiomeric form on this behavior. In doing so, we also discovered and partially characterized a new polymorph of (S)-ibuprofen. Our results demonstrate the potential of correlative SRS and SHG for monitoring phase separation and crystallization in real time, giving mechanistic insights into the spatial distribution, chemical composition and structure of phase-separated domains and newly formed crystals. Such insights could benefit not only pharmaceutical development, but also the biomedical, food and chemical sectors.

Synthetic Biomolecular Condensates: Phase-Separation Control, Cytomimetic Modelling and Emerging Biomedical Potential

Liquid-liquid phase separation towards the formation of synthetic coacervate droplets represents a rapidly advancing frontier in the fields of synthetic biology, material science, and biomedicine. These artificial constructures mimic the biophysical principles and dynamic features of natural biomolecular condensates that are pivotal for cellular regulation and organization. Via adapting biological concepts, synthetic condensates with dynamic phase-separation control provide crucial insights into the fundamental cell processes and regulation of complex biological pathways. They are increasingly designed with the ability to display more complex and ambitious cell-like features and behaviors, which offer innovative solutions for cytomimetic modeling and engineering active materials with sophisticated functions. In this minireview, we highlight recent advancements in the design and construction of synthetic coacervate droplets; including their biomimicry structure and organization to replicate life-like properties and behaviors, and the dynamic control towards engineering active coacervates. Moreover, we highlight the unique applications of synthetic coacervates as catalytic centers and promising delivery vehicles, so that these biomimicry assemblies can be translated into practical applications.

Phase-Separated Spiropyran Coacervates as Dual-Wavelength-Switchable Reactive Oxygen Generators

Low-molecular-weight compounds of certain structural features may form coacervates through liquid-liquid phase separation (LLPS). These coacervates can enter mammalian cells and affect cellular physiology. Controlling the properties of the coacervates inside cells, however, is a challenge. Here, we report photochemical reactions of spiropyran (SP)-based coacervates with two wavelengths of light, in vitro, in the cell, and in animals, generating reactive oxygen species (ROS) for photo-controlled cell killing. We identify an SP-containing compound, SP-PEG8-SP, that forms coacervates (SP-C) in the aqueous solution. Photo illumination by a UV light triggers the isomerization of SP to merocyanine (MC), switching SP-C to the fluorescent coacervates MC-C. A visible light converts MC-C back to SP-C and induces ROS generation. Notably, coacervate formation increases the compound's ROS generation efficiency. The SP-C/MC-C coacervate system (collectively called spiropyran coacervates) can spontaneously enter cells, and a dual-wavelength-controlled reversible on/off switch and spatiotemporal-resolved ROS production is realized within the cytoplasm. Light-induced ROS generation leads to cytotoxicity to cancer cells, tumor organoids, and tumors in vivo, supporting spiropyran coacervates' potential use as coacervate photosensitizers in photodynamic therapies.