Protein Phase Separation: A New Phase in Cell Biology

Germ granule-mediated mRNA storage and translational control

Germ cells depend on specialized post-transcriptional regulation for proper development and function, much of which is mediated by dynamic RNA granules. These membrane-less organelles form through the condensation of RNA and proteins, governed by multivalent biomolecular interactions. RNA granules compartmentalize cellular components, selectively enriching specific factors and modulating biochemical reactions. Over recent decades, various types of RNA granules have been identified in germ cells across species, with extensive studies uncovering their molecular roles and developmental significance. This review explores the mRNA regulatory mechanisms mediated by RNA granules in germ cells. We discuss the distinct spatial organization of specific granule components and the variations in material states of germ granules, which contribute to the regulation of mRNA storage and translation. Additionally, we highlight emerging research on how changes in these material states, during developmental stages, reflect the dynamic nature of germ granules and their critical role in development.

Natural product sennoside B disrupts liquid-liquid phase separation of SARS-CoV-2 nucleocapsid protein by inhibiting its RNA-binding activity

The nucleocapsid protein (NP) of SARS-CoV-2, an RNA-binding protein, is capable of undergoing liquid-liquid phase separation (LLPS) during viral infection, which plays a crucial role in virus assembly, replication, and immune regulation. In this study, we developed a homogeneous time-resolved fluorescence (HTRF) method for identifying inhibitors of the SARS-CoV-2 NP-RNA interaction. Using this HTRF-based approach, we identified two natural products, sennoside A and sennoside B, as effective blockers of this interaction. Bio-layer interferometry assays confirmed that both sennosides directly bind to the NP, with binding sites located within the C-terminal domain. Additionally, fluorescence recovery after photobleaching (FRAP) experiments revealed that sennoside B significantly inhibited RNA-induced LLPS of the NP, while sennoside A displayed comparatively weaker activity. Thus, the developed HTRF-based assay is a valuable tool for identifying novel compounds that disrupt the RNA-binding activity and LLPS of the SARS-CoV-2 NP. Our findings may facilitate the development of antiviral drugs targeting SARS-CoV-2 NP.

Liquid-to-gel transitions of phase-separated coacervate microdroplets enabled by endogenous enzymatic catalysis

Biomolecular condensates formed by liquid-liquid phase separation (LLPS) play a crucial role in organizing biochemical processes within living cells. The phase transition of these condensates from a functional liquid-like state to a pathological gel-like or solid-like state is believed to be linked to cellular dysfunction and various diseases. Here, we present a biomimetic model to demonstrate that endogenous enzyme-catalyzed crosslinking within condensate-mimicked coacervate microdroplets can promote a liquid-to-gel phase transition. We identify the transformation in physical characteristics of the densely packed microdroplets including reduced internal mobility, increased storage modulus, selective blocking of large nanoparticles, and enhanced salt resistance. The reversible dynamics of gel-like microdroplets mediated by ionic strength exhibited a limited release and recapture of sequestered positively charged guest molecules. Furthermore, we validate that the phase transition contributes to a restricted biochemical process through an enzymatic cascade. Overall, this work represents an adaptive in vitro platform for exploring the phase transitions associated with the physiological functions of biomolecular condensates and offers chemical insights and perspectives for investigating potential mechanisms involved in phase transitions.

A viral necrosome mediates direct RIPK3 activation to promote inflammatory necroptosis

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

Autophagy induced by mechanical stress sensitizes cells to ferroptosis by NCOA4-FTH1 axis

Ferroptosis is an iron-dependent regulated form of cell death implicated in various diseases, including cancers, with its progression influenced by iron-dependent peroxidation of phospholipids and dysregulation of the redox system. Whereas the extracellular matrix of tumors provides mechanical cues influencing tumor initiation and progression, its impact on ferroptosis and its mechanisms remains largely unexplored. In this study, we reveal that heightened mechanical tension sensitizes cells to ferroptosis, whereas decreased mechanics confers resistance. Mechanistically, reduced mechanical tension reduces intracellular free iron levels by enhancing FTH1 protein expression. Additionally, low mechanics significantly diminishes NCOA4, pivotal in mediating FTH1 phase separation-induced ferritinophagy. Targeting NCOA4 effectively rescues ferroptosis susceptibility under low mechanical tension through modulation of FTH1 phase separation-driven autophagy. In conclusion, our findings demonstrate that mechanics regulates iron metabolism via NCOA4-FTH1 phase separation-mediated autophagy, thereby influencing ferroptosis sensitivity and offering promising therapeutic avenues for future exploration.Abbreviations: ACO1: aconitase 1; ATG5: autophagy related 5; DMSO: dimethyl sulfoxide; EGFP: enhanced green fluorescent protein; FACS: fluorescence-activated cell sorting; FER-1: ferrostatin-1; FTH1: ferritin heavy chain 1; FTL: ferritin light chain; GPX4: glutathione peroxidase 4; IR: ionizing radiation; IREB2: iron responsive element binding protein 2; NCOA4: nuclear receptor coactivator 4; NFE2L2: NFE2 like bZIP transcription factor 2; NOPP: norepinephrine; PBS: phosphate-buffered saline; PI: propidium iodide; RSL3: (1S,3 R)-RSL3; TCGA: The Cancer Genome Atlas; WWTR1: WW domain containing transcription regulator 1; YAP1: Yes1 associated transcriptional regulator.

Coacervates meet the RNP-world: liquid-liquid phase separation and the emergence of biological compartmentalization

Understanding the emergence of biological compartmentalization in the context of the primordial soup is essential for unraveling the origin of life on Earth. This study revisits the classical coacervate theory, examining its historical development, supporting evidence, and major criticisms. Building upon Alexandr Oparin's foundational ideas, we propose an updated perspective in which the first biological compartments emerged through the formation of ribonucleoprotein (RNP) condensates-complexes of intrinsically disordered peptides and RNAs-via liquid-liquid phase separation (LLPS). Drawing on contemporary insights into how LLPS mediates intracellular organization, we argue that such membraneless RNP-based aggregates could have facilitated biochemical reactions in the aqueous environments of early Earth. By reinterpreting Oparin's coacervates through the lens of modern molecular biology, this study offers a renewed framework for understanding the origin of biological compartmentalization within the RNP-world hypothesis.

Ponceau S as a Targeted Modulator for Protein Liquid-Liquid Phase Separation

Liquid-liquid phase separation (LLPS) in proteins is essential for cellular organization and biomolecular condensation. However, current methods to induce phase separation often lack precise spatiotemporal control. This study introduces Ponceau S as a selective modulator and monitors phase separation in bovine serum albumin and lysozyme. We demonstrate that Ponceau S effectively promotes the protein complex into liquid droplets by binding to hydrophobic regions and driving intermolecular interactions. Notably, Ponceau S fluorescence increases within protein-rich phases, reflecting the restricted molecular motion in these environments. Furthermore, the phase separation induced by Ponceau S is finely tunable through salt and 1,6-hexanediol adjustments, which influence droplet fusion and dissolution dynamics. This work highlights the potential of small molecules like Ponceau S to precisely regulate and monitor protein phase separation, providing a new dimension of control for applications in biomolecular engineering, drug delivery, and synthetic biology.

Unraveling the Impact of Competing Interactions on Nonequilibrium Colloidal Gelation

Competing interactions stabilize exotic mesoscopic structures, yet the microscopic mechanisms by which they influence nonequilibrium processes leading to disordered states remain largely unexplored, despite their critical role in self-assembly across a range of nanomaterials and biological systems. Here, we numerically investigate the structural evolution in charged colloidal model systems, where short-range attractions and long-range repulsions compete. We reveal that these two interaction scales drive sequential ordering within clusters, from tetrahedra motifs to linear aggregates with chiral order. This process disrupts early stage percolated networks, resulting in reentrant behavior─a dynamic transition from disordered clusters to network to chiral rigid clusters. On the other hand, the cluster-elastic network boundary in the final state is governed by isostatic percolation, which slows structural rearrangements, preserves branching points, and sustains a long-lived network. The resulting structure consists of rigid Bernal spiral-like branches connected through flexible branching points lacking order. These insights advance our microscopic understanding of out-of-equilibrium ordering driven by competing interactions, especially phenomena such as temporally delayed frustration reflecting different length scales of competing interactions. The mechanisms identified here may play a crucial role in mesoscale self-organization across soft materials, from nanoparticle assemblies to biological gels and cytoskeletal networks. Understanding how competing interactions regulate structure and dynamics could guide the design of adaptive materials with tunable mechanical properties and offer valuable insights into biological processes such as cytoplasmic organization and cellular scaffolding.

Formation of Polyphasic RNP Granules by Intrinsically Disordered Qβ Coat Proteins and Hairpin-Containing RNA

RNA-protein (RNP) granules are fundamental components in cells, where they perform multiple crucial functions. Many RNP granules form via phase separation driven by protein-protein, protein-RNA, and RNA-RNA interactions. Notably, associated proteins frequently contain intrinsically disordered regions (IDRs) that can associate with multiple partners. Previously, we showed that synthetic RNA molecules containing multiple hairpin coat-protein binding sites can phase-separate, forming granules capable of selectively incorporating proteins inside. Here, we expand this platform by introducing a phage coat protein with a known IDR that facilitates protein-protein interactions. We show that the coat protein phase-separates on its own in vivo and that introduction of hairpin-containing RNA molecules can lead to dissolvement of the protein granules. We further demonstrate via multiple assays that RNA valency, determined by the number of hairpins present on the RNA, leads to distinctly different phase behaviors, effectively forming a polyphasic, programmable RNP granule. Moreover, by incorporating the gene for a blue fluorescent protein into the RNA, we demonstrate a phase-dependent boost of protein titer. These insights not only shed light on the behavior of natural granules but also hold profound implications for the biotechnology field, offering a blueprint for engineering cellular compartments with tailored functionalities.

TDP-43 seeding induces cytoplasmic aggregation heterogeneity and nuclear loss of function of TDP-43

Cytoplasmic aggregation and nuclear depletion of TAR DNA-binding protein 43 (TDP-43) are hallmarks of several neurodegenerative disorders. Yet, recapitulating both features in cellular systems has been challenging. Here, we produced amyloid-like fibrils from recombinant TDP-43 low-complexity domain and demonstrate that sonicated fibrils trigger TDP-43 pathology in human cells, including induced pluripotent stem cell (iPSC)-derived neurons. Fibril-induced cytoplasmic TDP-43 inclusions acquire distinct biophysical properties, recapitulate pathological hallmarks such as phosphorylation, ubiquitin, and p62 accumulation, and recruit nuclear endogenous TDP-43, leading to its loss of function. A transcriptomic signature linked to both aggregation and nuclear loss of TDP-43, including disease-specific cryptic splicing, is identified. Cytoplasmic TDP-43 aggregates exhibit time-dependent heterogeneous morphologies as observed in patients-including compacted, filamentous, or fragmented-which involve upregulation/recruitment of protein clearance pathways. Ultimately, cell-specific progressive toxicity is provoked by seeded TDP-43 pathology in human neurons. These findings identify TDP-43-templated aggregation as a key mechanism driving both cytoplasmic gain of function and nuclear loss of function, offering a valuable approach to identify modifiers of sporadic TDP-43 proteinopathies.

Phase separation of the oncogenic fusion protein EWS::FLI1 is modulated by its DNA-binding domain

Ewing sarcoma (EwS) is an aggressive cancer of bone and soft tissue that predominantly affects children and young adults. A chromosomal translocation joins the low-complexity domain (LCD) of the RNA-binding protein EWS (EWSLCD) with the DNA-binding domain of Friend leukemia integration 1 (FLI1DBD), creating EWS::FLI1, a potent fusion oncoprotein essential for EwS development and responsible for over 85% of EwS tumors. EWS::FLI1 forms biomolecular condensates in vivo and promotes tumorigenesis through mediation of aberrant transcriptional changes and by interfering with the normal functions of nucleic acid-binding proteins like EWS through a dominant-negative mechanism. In particular, the expression of EWS::FLI1 in EwS directly interferes with the biological functions of EWS leading to alternate splicing events and defects in DNA-damage repair pathways. Though the EWSLCD is capable of phase separation, here we report a direct interaction between FLI1DBD and EWSLCD that enhances condensate formation and alters the physical properties of the condensate. This effect was conserved for three related E-twenty-six transformation-specific (ETS) DNA-binding domains (DBDs) while DNA binding blocked the interaction with EWSLCD and inhibited EWS::FLI1 condensate formation. NMR spectroscopy and mutagenesis studies confirmed that ETS DBDs transiently interact with EWSLCD via the ETS DBDs "wings." Together these results revealed that ETS DBDs, particularly FLI1DBD, enhance EWSLCD condensate formation and rigidity, supporting a model in which electrostatic and structural interactions drive condensate dynamics with implications for EWS::FLI1-mediated transcriptional regulation in EwS.

Enhancement of CEP215 dynamics for spindle pole assembly during mitosis

The microtubule-organizing activity of centrosomes fluctuates during the cell cycle, reaching the highest levels at M phase. CEP215 (also known as CDK5RAP2) is a key pericentriolar material (PCM) protein for microtubule organization of the human centrosome. Here, we provide evidence that CEP215 exhibits a dynamically suppressed, solid-like state in interphase centrosomes, and becomes a more dynamic state in mitotic centrosomes. Specific interaction with PCNT, another centrosome protein, is crucial for diffusible molecular dynamicity of the CEP215 protein. We also found that the cluster formation activity of CEP215 is impaired in a light-inducible system when its coiled-coil domains (CCDs) are truncated. Defects in spindle pole assembly and spindle formation were accompanied in the cells whose CEP215 is replaced with the CCD-truncated mutants. Our results support the notion that the diffusible mobility of CEP215 is enhanced by both homotypic and heterotypic interactions among CCDs, especially at mitotic spindle poles. This work highlights that biophysical properties of the PCM proteins at the centrosomes fluctuate during the cell cycle.

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

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

Determining the Role of Electrostatics in the Making and Breaking of the Caprin1-ATP Nanocondensate

We employ a multiscale computational approach to investigate the condensation process of the C-terminal low-complexity region of the Caprin1 protein as a function of increasing ATP concentration for three states: the initial mixed state, nanocondensate formation, and dissolution of the droplet as it reenters the mixed state. We show that upon condensation, ATP assembles via pi-pi interactions, resulting in the formation of a large cluster of stacked ATP molecules stabilized by sodium counterions. The surface of the ATP assembly interacts with the arginine-rich regions of the Caprin1 protein, particularly with its N-terminus, to promote the complete phase-separated droplet on a length scale of tens of nanometers. In order to understand droplet stability, we analyzed the near-surface electrostatic potential (NS-ESP) of Caprin1 and estimated the zeta potential of the Caprin1-ATP assemblies. We predict a positive NS-ESP at the Caprin1 surface for low ATP concentrations that defines the early mixed state, in excellent agreement with the NS-ESP obtained from NMR experiments using paramagnetic resonance enhancement. By contrast, the NS-ESP of Caprin1 at the surface of the nanocondensate at moderate levels of ATP is highly negative compared to that at the mixed state, and estimates of a large zeta potential outside the highly dense region of charge further explain the remarkable stability of this phase-separated droplet assembly. As ATP concentrations rise further, the strong electrostatic forces needed for nanocondensate stability are replaced by weaker Caprin1-ATP interactions that drive the re-entry into the mixed state that exhibits a much lower zeta potential.

Coilin-containing nuclear biomolecular condensates in zebra finch Taeniopygia guttata growing oocytes

In most animals, oocyte growth is accompanied by genome activation, an increase in nuclear volume, and the formation of various biomolecular condensates (BioMCs) through multivalent interactions involving intrinsically disordered protein regions (IDRs) and phase separation. In this study, we characterize specific nuclear biomolecular condensates (NBioMCs) detectable by light microscopy in the oocytes of the zebra finch (Taeniopygia guttata, Passeriformes, Aves), a model species in genomics and neurobiology. We identified a nucleolus in oocytes at the early diplotene stage and observed numerous NBioMCs that tested positive for coilin in oocytes at the lampbrush stage, a period of active transcription. The coilin-positive NBioMCs may be freely distributed within the nucleus or associated with chromosome centromeres. They share characteristics with several known nuclear structures, including nucleoli (due to the presence of fibrillarin and nucleolin), Cajal bodies (marked by coilin and scaRNA2), interchromatin granule clusters (containing SRSF2), and centromeric protein bodies (CPBs) described in other avian species (exhibiting centromeric localization when chromosome-associated and containing STAG2 and SMC5). However, their specific function in zebra finch oocytes remains unclear and requires further investigation.

Phase Separation: Orchestrating Biological Adaptations to Environmental Fluctuations

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

Peptide nanoarchitectonics beyond long-range ordering

Long-range disordered structures are ubiquitous in biological organisms and hold crucial significance for their unique structure and function. Inspired by these natural architectures, much attention has been devoted to constructing long-range disordered materials based on biomolecules in vitro. Peptides, especially short peptides consisting of several to dozens of amino acids, have emerged as ideal building blocks due to their versatile structural and functional diversity, along with their notable biocompatibility and biodegradability. As a result, significant efforts have been made to develop short peptide nanoarchitectonics with long-range disorder (SPNLRD). Understanding the fundamental mechanisms underlying the formation of SPNLRD is crucial for the precise design and construction of these architectures with specific functionalities. This review summarizes the latest advancements in the construction and application of SPNLRD. We place particular emphasis on the design principles for SPNLRD construction and stabilization, based on a comprehensive discussion from the perspectives of thermodynamics, kinetics and intermolecular interactions. Finally, we assess the critical challenges currently facing SPNLRD and highlight the future directions in the field, proposing research strategies aimed at enhancing the stability and improving the precision of control over these materials.

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

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

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

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

Biomolecular Condensate-Based Artificial Organelle for Driving Compartmentalized Flux Control

Microbial cell factories have emerged as versatile bioreactors capable of orchestrating complex metabolic networks to convert renewable feedstocks into high-value biochemicals. Nevertheless, the diffusion-mediated dispersion of metabolic intermediates often compromises biosynthesis efficiency, primarily attributable to the absence of artificial subcellular compartments for spatiotemporal organization of catalytic enzymes. Herein, we established a synthetic biology platform leveraging engineered biomolecular condensates to achieve precise flux control via a modular pathway compartmentalization. First, the fused sarcoma low complexity domain (FUSLCD) was designed to combine the GCN4 to rationally integrate with GCN4 scaffold proteins to create programmable artificial organelles. Second, the protein recruitment and assembly functions of artificial organelles were identified by a short peptide pair or directly fusing with the FUSLCD protein in a spatial organization way. Third, using the 2'-fucosyllactose (2'-FL) de novo biosynthesis pathway as a model system, we demonstrated enhanced pathway efficiency by colocalizing critical enzymes within artificial organelles in engineered E. coli, yielding a significant improvement in 2'-FL titer through flux compartmentalization. This study not only overcome diffusion-limited reactions via engineered spatial organization but also offer a versatile toolkit for optimizing compartmentalized biosynthesis pathways.

Molecular mechanisms and consequences of TDP-43 phosphorylation in neurodegeneration

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

Current perspectives in drug targeting intrinsically disordered proteins and biomolecular condensates

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

Artificial Cells Capable of NO Generation with Light Controllable Membraneless Organelles for Melanoma Therapy

Membraneless organelles (MLOs) formed by liquid-liquid phase separation exhibit diverse important biofunctions in cells. The construction of artificial cells containing MLOs with enhanced complexity and functions is still challenging. Here a light-responsive protein, Cry2olig-IDRs, is designed and purified to form MLOs upon light (488 nm) irradiation. They are capable of rapidly recruiting positively charged inducible nitric oxide synthase (iNOS+) from surroundings to regulate its activity for NO production. NO-artificial cells are constructed by encapsulating Cry2olig-IDRs and iNOS+ into giant unilamellar vesicles, which are capable of rapid production of NO with high concentration due to the formation of MLOs upon light irradiation. NO-artificial cells are confirmed to possess the ability for melanoma tumor therapy in mice. These findings provide an efficient method for remotely regulating enzyme activity inside artificial cells, paving the path to build more sophisticated artificial cells for their biomedical applications.

Artificial metalloenzyme assembly in cellular compartments for enhanced catalysis

Artificial metalloenzymes (ArMs) integrated within whole cells have emerged as promising catalysts; however, their sensitivity to metal centers remains a systematic challenge, resulting in diminished activity and turnover. Here we address this issue by inducing in cellulo liquid-liquid phase separation through a self-labeling fusion protein, HaloTag-SNAPTag. This strategy creates membraneless, isolated liquid condensates within Escherichia coli as protective compartments for the assembly of ArMs using the same fusion protein. The approach allows for high ArM loading and stabilization by localizing the ArMs within the phase-separated regions. Consequently, the performance of ArM-based whole-cell catalysts is improved, with a demonstrated turnover per cell of up to 7.1 × 109 for the olefin metathesis reaction. Furthermore, we apply this to an engineered E. coli system in live mice, where host bacterial cells confine the metal catalytic species, and in a mouse colorectal cancer model, where ArM-containing whole-cell catalysts mediate concurrent reactions to activate prodrugs.

Downregulation of SENP1 impairs nuclear condensation of MEF2C and deteriorates ischemic cardiomyopathy

Ischemic cardiomyopathy (ICM) is characterised by the insufficient capacity of the heart to effectively pump blood, which ultimately contributes to heart failure (HF). In this study, the down regulation of SENP1 is identified in the cardiomyocyte of ICM mouse models and in patients. The depletion of SENP1 exacerbates hypoxia-induced apoptosis of cardiomyocytes in vitro and deteriorated cardiomyocyte injury of ICM mice in vivo. Mechanistically, SENP1 deSUMOylates the SUMO2-mediated modification of MEF2C at lysine 401 for stabilising protein stability. Moreover, the interaction with SENP1 controls the nuclear condensation of MEF2C to promote the expression of genes critical for cardiomyocyte function. When rescuing SENP1 expression using adeno-associated virus serotype 9, the attenuation of cardiomyocyte injury is discerned in the mouse model of ICM. Therefore, these finding elicits a previously unrecognised role and mechanism of SENP1 in safeguarding cardiomyocyte in ICM progression while establishing a basis for the development of SENP1 as a potential marker for ICM diagnosis and treatment. KEY POINTS: SNEP1 is downregulated in the cardiomyocyte of ICM mouse models and in patients. SENP1 deSUMOylates the SUMO2-mediated modification of MEF2C at lysine 401 for protein stability. The interaction with SENP1 controls the nuclear condensation of MEF2C to promote cardiomyocyte function. Cardiac rescue of SENP1 alleviates ischemic heart injury in ICM mouse models by AAV9.

Targeting a key disulfide linkage to regulate RIG-I condensation and cytosolic RNA-sensing

Maintaining innate immune homeostasis is critical for preventing infections and autoimmune diseases but effective interventions are lacking. Here we identified C864-C869-mediated intermolecular disulfide-linkage formation as a critical step for human RIG-I activation that can be bidirectionally regulated to control innate immune homeostasis. The viral-stimulated C864-C869 disulfide linkage mediates conjugation of an SDS-resistant RIG-I oligomer, which prevents RIG-I degradation by E3 ubiquitin-ligase MIB2 and is necessary for RIG-I to perform liquid-liquid phase separation to compartmentalize downstream signalsome, thereby stimulating type I interferon signalling. The corresponding C865S 'knock-in' caused an oligomerization defect and liquid-liquid phase separation in mouse RIG-I, which inhibited innate immunity, resulting in increased viral load and mortality in mice. Using unnatural amino acids to generate covalent C864-C869 linkage and the development of an interfering peptide to block C864-C869 residues, we bidirectionally regulated RIG-I activities in human diseases. These findings provide in-depth insights on mechanism of RIG-I activation, allowing for the development of methodologies that hold promising implications in clinics.

Enhancing specimen preparation for transmission electron microscopy: Trypan Blue staining and low-melting-point agar embedding for ultra-thin cell sections

The observation of ultrathin sections of cells and other specimens using transmission electron microscopy (TEM) is a standard technique in many biological research laboratories. Cells are typically collected, dehydrated through an ascending series of alcohols, and embedded in resin blocks before being sectioned with an ultramicrotome. This multi-step process can be time consuming and error prone. To address these challenges, we introduced modifications to improve sample visualization while avoiding hazardous substances like osmium tetroxide and epoxy resins (e.g., Araldite), which are increasingly regulated internationally. Specifically, we stained cells with Trypan Blue and used low melting point agar, facilitating visual identification of target areas and enabling precise embedding. As a result, visual tracking of samples prior to embedding for TEM was improved, preventing the cutting of empty blocks and ensuring efficient preparation of ultrathin sections.

Emerging Technologies for Multiphoton Writing and Reading of Polymeric Architectures for Biomedical Applications

The rise in popularity of two-photon polymerization (TPP) as an additive manufacturing technique has impacted many areas of science and engineering, particularly those related to biomedical applications. Compared with other fabrication methods used for biomedical applications, TPP offers 3D, nanometer-scale fabrication dexterity (free-form). Moreover, the existence of turnkey commercial systems has increased accessibility. In this review, we discuss the diversity of biomedical applications that have benefited from the unique features of TPP. We also present the state of the art in approaches for patterning and reading 3D TPP-fabricated structures. The reading process influences the fidelity for both in situ and ex situ characterization methods. We also review efforts to leverage machine learning to facilitate process control for TPP. Finally, we conclude with a discussion of both the current challenges and exciting opportunities for biomedical applications that lie ahead for this intriguing and emerging technology.

Protocol for identifying components of subcellular compartments by antibody-based in situ biotinylation

Recent studies revealed that membrane-less subcellular organelles play important roles in cellular functions. Here, we present a protocol for identifying subcellular compartment components by antibody-based in situ biotinylation. We describe steps for in situ biotinylation labeling using a horseradish peroxidase (HRP)-conjugated antibody, purification of the biotinylated components, and sample preparation for high-throughput analysis. This protocol has potential for application in the comprehensive analysis of dynamic subcellular organelles. For complete details on the use and execution of this protocol, please refer to Noguchi et al.1.

Decoupling Phase Separation and Fibrillization Preserves Activity of Biomolecular Condensates

Age-dependent transition of metastable, liquid-like protein condensates to amyloid fibrils is an emergent phenomenon of numerous neurodegeneration-linked protein systems. A key question is whether the thermodynamic forces underlying reversible phase separation and maturation to irreversible amyloids are distinct and separable. Here, we address this question using an engineered version of the microtubule-associated protein Tau, which forms biochemically active condensates. Liquid-like Tau condensates exhibit rapid aging to amyloid fibrils under quiescent, cofactor-free conditions. Tau condensate interface promotes fibril nucleation, impairing their activity to recruit tubulin and catalyze microtubule assembly. Remarkably, a small molecule metabolite, L-arginine, selectively impedes condensate-to-fibril transition without perturbing phase separation in a valence and chemistry-specific manner. By heightening the fibril nucleation barrier, L-arginine counteracts age-dependent decline in the biochemical activity of Tau condensates. These results provide a proof-of-principle demonstration that small molecule metabolites can enhance the metastability of protein condensates against a liquid-to-amyloid transition, thereby preserving condensate function.

Surface Localized Coacervation Controlled by Bioactive Nanoarchitectonic Polyelectrolyte Multilayers

Liquid-liquid phase separation (LLPS) of biomolecules is increasingly studied in bulk conditions mainly because of its expected implication in the emergence of life. However, in living systems, the LLPS occurs also at interfaces through a precise spatiotemporal localization-induction way. Based on enzymatically active nanoarchitectured polyelectrolyte multilayer (PEM) films, a tunable stimuli-responsive surface controlling coacervation processes specifically at the solid-liquid interface is developed. Urease, embedded in multilayers, is used as a trigger to increase locally the pH near the surface in the presence of urea. The deprotonation of a short peptide synthon FFssFF occurs in close vicinity of the surface and induces the formation of FFssFF coacervate droplets at, and in, the vicinity of the surface. The variation of i) the number of enzyme layers in the PEM film, the concentration of ii) urea, or iii) coacervator impacts the kinetic, the size, and the surface density of the droplets which can result in a quasi-full covering of the surface. Based on optical and fluorescence microscopy images using a fluorescently labelled FFssFFK-Bodipy coacervator, a mechanism of the droplet's formation is established explaining the spatial localization and the control of the coacervation process.

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.

Transcription-coupled repair: tangled up in convoluted repair

Significant progress has been made in understanding the mechanism of transcription-coupled nucleotide excision repair (TC-NER); however, numerous aspects remain elusive, including TC-NER regulation, lesion-specific and cell type-specific complex composition, structural insights, and lesion removal dynamics in living cells. This review summarizes and discusses recent advancements in TC-NER, focusing on newly identified interactors, mechanistic insights from cryo-electron microscopy (Cryo-EM) studies and live cell imaging, and the contribution of post-translational modifications (PTMs), such as ubiquitin, in regulating TC-NER. Furthermore, we elaborate on the consequences of TC-NER deficiencies and address the role of accumulated damage and persistent lesion-stalled RNA polymerase II (Pol II) as major drivers of the disease phenotype of Cockayne syndrome (CS) and its related disorders. In this context, we also discuss the severe effects of transcription-blocking lesions (TBLs) on neurons, highlighting their susceptibility to damage. Lastly, we explore the potential of investigating three-dimensional (3D) chromatin structure and phase separation to uncover further insights into this essential DNA repair pathway.

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.

X-Ray Photon Correlation Spectroscopy, Microscopy, and Fluorescence Recovery After Photobleaching to Study Phase Separation and Liquid-to-Solid Transition of Prion Protein Condensates

Biomolecular condensates are macromolecular assemblies constituted of proteins that possess intrinsically disordered regions and RNA-binding ability together with nucleic acids. These compartments formed via liquid-liquid phase separation (LLPS) provide spatiotemporal control of crucial cellular processes such as RNA metabolism. The liquid-like state is dynamic and reversible, containing highly diffusible molecules, whereas gel, glass, and solid phases might not be reversible due to the strong intermolecular crosslinks. Neurodegeneration-associated proteins such as the prion protein (PrP) and Tau form liquid-like condensates that transition to gel- or solid-like structures upon genetic mutations and/or persistent cellular stress. Mounting evidence suggests that progression to a less dynamic state underlies the formation of neurotoxic aggregates. Understanding the dynamics of proteins and biomolecules in condensates by measuring their movement in different timescales is indispensable to characterize their material state and assess the kinetics of LLPS. Herein, we describe protein expression in E. coli and purification of full-length mouse recombinant PrP, our in vitro experimental system. Then, we describe a systematic method to analyze the dynamics of protein condensates by X-ray photon correlation spectroscopy (XPCS). We also present fluorescence recovery after photobleaching (FRAP)-optimized protocols to characterize condensates, including in cells. Next, we detail strategies for using fluorescence microscopy to give insights into the folding state of proteins in condensates. Phase-separated systems display non-equilibrium behavior with length scales ranging from nanometers to microns and timescales from microseconds to minutes. XPCS experiments provide unique insights into biomolecular dynamics and condensate fluidity. Using the combination of the three strategies detailed herein enables robust characterization of the biophysical properties and the nature of protein phase-separated states. Key features • For FRAP in cells, we recommend using a spinning disk confocal microscope coupled with temperature and CO2 incubator. • For fluorescence microscopy, we recommend simultaneously imaging differential interference contrast (DIC) (or phase contrast) and fluorescence channels to obtain morphological details of phase-separated structures. • For XPCS, coherent X-ray beams, fast X-ray detectors in fourth and third synchrotron light sources, and X-ray free-electron lasers are required.

Aggregation of α-synuclein splice isoforms through a phase separation pathway

The aggregation of α-synuclein (αSyn) is associated with Parkinson's disease and other related synucleinopathies. Considerable efforts have thus been directed at understanding this process. However, the recently discovered condensation pathway, which involves the formation of phase-separated liquid intermediate states, has added further complexity. In parallel, it has been reported that different αSyn splice isoforms may be implicated in aggregate formation in disease. In this study, we compare the phase behavior of four αSyn isoforms (αSyn-140, αSyn-126, αSyn-112, and αSyn-98). Using different biophysical tools including confocal microscopy, kinetic assays and microfluidic-based approaches, we find stark differences between the four systems in their propensities to undergo phase separation and aggregation. Furthermore, we show that even small amounts of αSyn-112, one of the predominant isoforms after αSyn-140, can affect the phase separation of αSyn-140. These results highlight the importance of conducting further investigations to elucidate the role of alternative splicing in synucleinopathies.

Polyelectrolyte complex-based materials for separations: progress, challenges and opportunities

Polyelectrolyte complex (PEC) based materials could provide a sustainable alternative to conventional materials, especially for separation applications. However, reproducible production remains a challenge due to the many parameters influencing the polyelectrolyte complexation process, eventually affecting the properties and performance of the final material. Here, we provide an overview of how different parameters affect polyelectrolyte complexation and discuss promising PEC-based materials for separation applications, i.e., porous membranes, functional and barrier coatings, adhesives, saloplastics, and extraction media. Additionally, we highlight the challenges and opportunities and discuss what is needed to get to the next level. We envision that collaboration between experimentalists and theoreticians can leverage experimental datasets with accurate descriptions of all the parameters for multiscale modelling, machine learning and artificial intelligence approaches that can be used to design PEC materials and predict their properties.

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.

The impact of colloid-solvent dynamic coupling on the coarsening rate of colloidal phase separation

Phase separation, a fundamental phenomenon in both natural and industrial settings, involves the coarsening of domains over time t to reduce interfacial energy. While well-understood for simple viscous liquid mixtures, the physical laws governing coarsening dynamics in complex fluids, such as colloidal suspensions, remain unclear. Here, we investigate colloidal phase separation through particle-based simulations with and without hydrodynamic interactions (HIs). The former incorporates many-body HIs through momentum conservation, while the latter simplifies their effects into a constant friction coefficient on a particle. In cluster-forming phase separation with HIs, the domain size ℓ grows as ℓ∝t1/3, aligning with the Brownian-coagulation mechanism. Without HIs, ℓ∝t1/5, attributed to an improper calculation of cluster thermal diffusion. For network-forming phase separation, ℓ∝t1/2 with HIs, while ℓ∝t1/3 without HIs. In both cases, network coarsening is governed by the mechanical stress relaxation of the colloid-rich phase, yet with distinct mechanisms: slow solvent permeation through densely packed colloids for the former and free draining for the latter. Our results provide a clear and concise physical picture of colloid-solvent dynamic coupling via momentum conservation, offering valuable insights into the self-organization dynamics of particles like colloids, emulsions, and globular proteins suspended in a fluid.

CTPS cytoophidia in Drosophila: distribution, regulation, and physiological roles

Intracellular compartmentalization plays a critical role in maintaining cellular homeostasis and regulating metabolic processes. A growing body of evidence suggests that various metabolic enzymes, including CTP synthase (CTPS), can dynamically assemble into membraneless filamentous structures. The formation of these membraneless organelles is precisely regulated by the cellular metabolic state. CTPS, a rate-limiting enzyme in the de novo biosynthesis of CTP, has been shown to assemble into filamentous structures known as cytoophidium. First identified in 2010 by three independent research groups, cytoophidia are evolutionarily conserved across diverse organisms, including bacteria, archaea, yeast, mammals, and plants, suggesting a fundamental biological function. Given the well-established advantages of Drosophila melanogaster as a genetic model, this organism provides a powerful system for investigating the physiological roles of cytoophidia. This review synthesizes current findings on CTPS cytoophidia in Drosophila, with a particular focus on their spatiotemporal distribution in tissues and their regulatory roles in three key biological processes: intestinal homeostasis, lipid metabolism, and reproductive physiology. Furthermore, we discuss the challenges and future directions in cytoophidia research, offering insights into their broader implications in cellular metabolism and physiology.

Aggregation-induced emission-based fluorescent probes for cellular microenvironment detection

The cellular microenvironment exerts a pivotal regulatory influence on cell survival, function, and behavior. Dynamic analysis and detection of the cellular microenvironment can promptly elucidate changes in cellular microenvironmental information, uncover the pathogenesis of diseases associated with aberrant microenvironments, and aid in predicting disease risk and monitoring disease progression. Aggregation-induced emission (AIE) fluorescent molecules possess unique AIE characteristics and offer significant advantages in imaging and sensing cellular microenvironments. In this review, we present a profile of the remarkable progress achieved in utilizing AIE fluorescent molecules for detecting cellular microenvironments in recent years. We particularly focus on AIE fluorescent probes applied in imaging key parameters of the cellular microenvironment, including pH, viscosity, polarity, and temperature, as well as in analyzing critical biological components of the microenvironment, such as gas signal molecules, metal ions, redox state, and proteins. We underscore the design principles, detection mechanisms, sensing performance, and biological applications of these fluorescent probes. Furthermore, we address the current challenges confronting this field and provide prospects for the future development of AIE probes used for microenvironment detection. We trust that this review will inspire researchers to develop more precise and sensitive AIE fluorescent probes for the detection of cellular microenvironments.

Aqueous Two-Phase Submicron Droplets Catalyze DNA Nanostructure Assembly for Confined Fluorescent Biosensing

Membraneless organelles (MLOs) are fundamental to cellular organization, enabling biochemical processes by concentrating biomolecules and regulating reactions within confined environments. While micrometer-scale synthetic droplets are extensively studied as models of MLOs, submicron droplets remain largely unexplored despite their potential to uniquely regulate biomolecular processes. Here, submicron droplets are generated by a polyethylene glycol (PEG)/dextran aqueous two-phase system (ATPS) as a model to investigate their effect on DNA assembly in crowded environments. The findings reveal that submicron droplets exhibit distinct advantages over microdroplets by acting as submicron catalytic centers that concentrate DNA and accelerate assembly kinetics. This enhancement is driven by a cooperative mechanism wherein global crowding from PEG induces an excluded volume effect, while local crowding from dextran provides weak but nonspecific interactions with DNA. By exploiting both the confinement and phase properties of submicron droplets, a rapid and sensitive assay is developed for miRNA detection using confined fluorescent readouts. These findings highlight the unique ability of submicron droplets to amplify biomolecular assembly processes, provide new insights into the interplay between global and local crowding effects in cellular-like environments, and present a platform for biomarker detection and visualization.

Characterization and Expression Analysis of the ALOG Gene Family in Rice (Oryza sativa L.)

ALOG (Arabidopsis LSH1 and Oryza G1) proteins constitute a plant-specific family of transcription factors that play crucial roles in lateral organ development across land plants. Initially identified through forward genetic studies of Arabidopsis LSH1 and rice G1 proteins, ALOG family members have since been functionally characterized in various plant species. However, research focusing on the characteristics and expression patterns of all ALOG family members in rice remains relatively limited. In this study, we systematically characterized OsALOG family genes in rice. Compared to other genes in rice and Arabidopsis, the ALOG family genes have a relatively simple structure. The alignment of OsALOG amino acid sequences and analysis of disorder predictions reveal that all members possess conserved ALOG domains, while the conservation of intrinsically disordered regions (IDRs) is relatively low. Four amino acids-alanine, glycine, proline, and serine-are significantly enriched in the IDRs of each ALOG protein. Synteny analysis indicates that most OsALOG genes have undergone considerable divergence compared to their counterparts in Arabidopsis. Bioinformatic analysis of cis-regulatory elements predicts that OsALOG family genes contain elements responsive to ABA, light, and methyl jasmonate, although the abundance and composition of these elements vary among different members. The expression patterns associated with the rice floral development of OsALOG genes can be broadly categorized into two types; however, even within the same type, differences in expression levels, as well as the initiation time and duration of expression, were observed. These results provide a comprehensive understanding of the structural characteristics and expression patterns of OsALOG members in rice.

Polyphosphate: a cellular Swiss army knife

Inorganic polyphosphate (polyP) is a ubiquitous biopolymer whose functional repertoire has rapidly expanded over the past few years. How polyP controls these seemingly unrelated functions, which range from stress resistance, motility, and DNA damage control in bacteria to blood clotting, cancer and neurodegeneration in mammals, remains largely unknown. Here, we review what is known about its synthesis and degradation pathways in mammalian cells, provide an overview over the cell compartment-specific roles of polyP, and focus on recent studies, which showed that many of polyP's activities appear to be mediated by its ability to either solubilize, scaffold, or phase separate proteins. Future studies will show how polyP achieves these vastly different effects on proteins and hence controls its many functions.

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.

Insulin amyloid morphology is encoded in H-bonds and electrostatics interactions ruling protein phase separation

Ion-protein interactions regulate biological processes and are the basis of key strategies of modulating protein phase diagrams and stability in drug development. Here, we report the mechanisms by which H-bonds and electrostatic interactions in ion-protein systems determine phase separation and amyloid formation. Using microscopy, small-angle X-ray scattering, circular dichroism and atomistic molecular dynamics (MD) simulations, we found that anions specifically interacting with insulin induced phase separation by neutralising the protein charge and forming H-bond bridges between insulin molecules. The same interaction was responsible for an enhanced insulin conformational stability and resistance to oligomerisation. Under aggregation conditions, the anion-protein interaction translated into the activation of a coalescence process, leading to amyloid-like microparticles. This reaction is alternative to conformationally-driven pathways, giving rise to elongated amyloid-like fibrils and occurs in the absence of preferential ion-protein binding. Our findings depict a unifying scenario in which common interactions dictated both phase separation at low temperatures and the occurrence of pronounced heterogeneity in the amyloid morphology at high temperatures, similar to what has previously been reported for protein crystal growth.

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.

Assembly and Functionality of 2D Protein Arrays

Among the unique classes of 2D nanomaterials, 2D protein arrays garner increasing attention due to their remarkable structural stability, exceptional physiochemical properties, and tunable electronic and mechanical attributes. The interest in mimicking and surpassing the precise architecture and advanced functionality of natural protein systems drives the field of 2D protein assembly toward the development of sophisticated functional materials. Recent advancements deepen the understanding of the fundamental principles governing 2D protein self-assembly, accelerating the creation of novel functional biomaterials. These developments encompass biological, chemical, and templated strategies, facilitating the self-organization of proteins into highly ordered and intricate 2D patterns. Consequently, these 2D protein arrays create new opportunities for integrating diverse components, from small molecules to nanoparticles, thereby enhancing the performance and versatility of materials in various applications. This review comprehensively assesses the current state of 2D protein nanotechnology, highlighting the latest methodologies for directing protein assembly into precise 2D architectures. The transformative potential of 2D protein assemblies in designing next-generation biomaterials, particularly in areas such as biomedicine, catalysis, photosystems, and membrane filtration is also emphasized.

The potential mechanism maintaining transactive response DNA binding protein 43 kDa in the mouse stroke model

The disruption of transactive response DNA binding protein 43 kDa (TDP-43) shuttling leads to the depletion of nuclear localization and the cytoplasmic accumulation of TDP-43. We aimed to evaluate the mechanism underlying the behavior of TDP-43 in ischemic stroke. Adult male C57BL/6 J mice were subjected to 30 or 60 min of transient middle cerebral artery occlusion (tMCAO), and examined at 1, 6, and 24 h post reperfusion. Immunostaining was used to evaluate the expression of TDP-43, G3BP1, HDAC6, and RAD23B. The total and cytoplasmic number of TDP-43-positive cells increased compared with sham operation group and peaked at 6 h post reperfusion after tMCAO. The elevated expression of G3BP1 protein peaked at 6 h after reperfusion and decreased at 24 h after reperfusion in ischemic mice brains. We also observed an increase of expression level of HDAC6 and the number of RAD23B-positive cells increased after tMCAO. RAD23B was colocalized with TDP-43 24 h after tMCAO. We proposed that the formation of stress granules might be involved in the mislocalization of TDP-43, based on an evaluation of G3BP1 and HDAC6. Subsequently, RAD23B, may also contribute to the downstream degradation of mislocalized TDP-43 in mice tMCAO model.