Search Results (134)

Liquid–liquid phase separation (LLPS) of RNA drives the formation of membraneless organelles, and its dysregulation is closely linked to major human diseases, including cancer, neurodegenerative disorders, and various rare genetic diseases. Current strategies for modulating LLPS often require the introduction of exogenous molecules or specific genetic modifications. Here, coarse-grained molecular dynamics (CGMD) simulations suggest that terahertz (THz) oscillatory fields may influence the condensation of pathogenic G4C2 RNA repeats under the simulated conditions. Oscillatory fields at 10 THz and 37.3 THz are shown to effectively counteract salt-induced condensate dissolution. At the molecular level, THz oscillatory fields are associated with reduced phosphate–sodium contacts at low ionic strengths and with faster water diffusion in the hydration layer at higher salt levels. These changes correlate with an increase in stable intermolecular contacts and a more compact RNA state, suggesting a field-driven shift in the balance of interactions. These findings provide a conceptual and mechanistic basis for understanding how oscillatory fields may influence biomolecular condensation, establishing a microscopic framework for using external variable fields to manipulate biomolecular assemblies. Full article

Autoantigens, targets of B cell antibodies, account for ~10% of the human proteome. It is not well understood why or how particular self-proteins become autoantigens. Prominent theories posit that failures of the immune system at various levels or exposure of aberrant proteins to the immune system are responsible for autoantigenicity. In contrast, we propose a completely unrelated mechanism of autoantigenicity that is based on normal cell functioning. We suggest that, when a protein associates with one of the ~100 types of biomolecular condensates, protein–protein interaction therein causes changes in protein structure or conformation that signal an untolerized state to the immune system. This proposal is derived from the fact that many macromolecules are more concentrated within condensates than in the extra-condensate environment. Thus, the propensity for macromolecular interaction may be greater in condensates compared with the non-condensate environment. In support of this proposal, we present examples of predicted conformational differences, with and without accompanying secondary structure differences, between proteins in known condensate heteromeric complexes and in their free monomer forms. In each case, the differences correlated with predicted B-cell binding, supporting our model. Further, from a compilation of ~1900 autoantigens, we estimate that autoantigens are twice as prevalent in condensates compared with the entire human proteome (Chi squared p < 0.0001), further suggesting that a property of condensates, e.g., protein conformational change, may contribute to autoantigenicity. Full article

Biomolecular condensates in the cytoplasm and nucleus contribute to carcinogenesis through aberrant signaling by assorted transcription factors and fusion oncoproteins. Oral cancer, which is highly prevalent worldwide, frequently occurs in a U-shaped “high-risk” zone (floor of mouth, side of tongue, and anterior fauces) which forms the path of liquid transit through the mouth. We previously reported that environmental stresses of saliva-like hypotonicity and beverage-like temperature changes triggered cycles of disassembly/reassembly of biomolecular condensates of GFP-tagged human myxovirus resistance protein (MxA; alias Mx1) in oral cancer cells. In the present study, we identified some of the constituents of GFP-MxA cytoplasmic condensates in oral cells. These condensates were isolated from interferon (IFN)-λ1-treated GFP-MxA expressing OECM1 human oral cancer cells using magnetic bead-based immunoisolation. Unbiased peptide identification confirmed the presence of MxA/Mx1 peptides; however, the strongest intensity was for the BACH1 transcription factor family. Immunofluorescence analyses confirmed the association of BACH1 and the family member Nrf2 with cytoplasmic human GFP-MxA condensates. Moreover, GFP-BACH1 and GFP-Nrf2 colocalized with cytoplasmic human HA-MxA condensates in transiently transfected OECM1 cells. Western blot assays confirmed the presence of BACH1 and Nrf2 proteins in complexes isolated using anti-MxA pAb. As much as BACH1 and Nrf2 regulate oxidative stress response genes, it was remarkable that immunofluorescence assays revealed the presence of heme oxygenase 1 (HO1)—a downstream redox regulator—in GFP-MxA condensates. However, these condensates were devoid of p62, KEAP1 and Cul3. In terms of aberrant function, in live cells, the Nrf2 transcription factor underwent rapid disassembly and reassembly cycles driven by saliva-like hypotonicity, and was also disassembled by sulforaphane. The data highlight the unexpected intersections in oral cells between MxA condensates and BACH1, Nrf2 and HO1—proteins well known to be involved in pathways regulating cellular responses to environmental and oxidative stresses, antiviral defense, oral epithelial dysplasia, and cancer progression and metastases. Full article

Plants frequently encounter overlapping, sequential, and recurrent stresses, but the cellular mechanisms that organize responses to these complex conditions remain incompletely understood. Biomolecular condensates are membrane-less assemblies formed through phase separation and multivalent molecular interactions, and they can regulate RNA metabolism, protein sequestration, signaling specificity, transcriptional control, and stress recovery. This review evaluates the hypothesis that plant condensates may contribute to the organization of combined and recurrent stress responses by modulating molecular accessibility, transcript fate, proteostasis, and regulatory crosstalk. We synthesize current knowledge on stress granules, processing bodies, nuclear condensates, plastid-associated condensate-like assemblies, and other stress-responsive compartments, with emphasis on their possible roles in signal filtering, RNA triage, and recovery-associated reprogramming. We also distinguish established evidence from emerging hypotheses, particularly regarding condensate-mediated signal prioritization and stress memory. Current data support condensates as rapid stress-responsive organizers, but direct evidence for their persistence after recovery or their causal roles under simultaneous multi-stress conditions remains limited. By integrating phase separation biology with plant multi-stress physiology, this review proposes a testable conceptual framework and identifies methodological priorities for future studies in plant stress resilience and crop improvement. Full article

The discovery of melatonin as a multifunctional free radical scavenger and its possible synthesis in the mitochondrial matrix of peripheral eukaryotic somatic cells highlights a critical new perspective on the importance of this indole. Experimental evidence supporting these findings is substantial, but there are still lingering questions whether melatonin is a direct radical scavenger in vivo and whether it is synthesized in the mitochondrial matrix. We systematically analyze the innovative experimental approaches that support melatonin’s radical scavenging actions and assess the compelling data supporting its production in mitochondria. Melatonin concentrations are reportedly higher in this organelle than in other cellular compartments. Proteins for the enzymes required to convert serotonin to melatonin are present in the mitochondrial matrix and purified mitochondria synthesize melatonin. In the mitochondrial matrix, melatonin is likely located within the “damage radius” of highly reactive oxygen species. We also summarize novel actions of melatonin associated with its regulation of membrane fluidity, determine the molecular composition of membrane lipid rafts, and modulate liquid–liquid phase separation and biomolecular condensates intracellularly. If the findings discussed herein continue to be validated, melatonin would be in an optimal position to function as an antioxidant and may be a key driver in the context of preserving mitochondrial redox homeostasis and disease mitigation. Full article

The cytoskeleton fulfills many essential roles that are necessary for cell function. Perhaps the most important of these roles is the formation of the mitotic spindle. The mitotic spindle is a complex and dynamic structure made up mainly of microtubules and numerous microtubule-associated proteins (MAPs), but the mechanisms behind its creation and regulation are not fully characterized. Recent research has focused on the link between liquid–liquid phase separation (LLPS) of MAPs and these microtubule organizations. Here, we focus on the protein regulator of cytokinesis 1 (PRC1), a spindle midzone-associated anti-parallel microtubule crosslinker. PRC1 is known to undergo LLPS to form condensed droplets without the need for additional crowders. Using confocal fluorescence microscopy and different constructs of PRC1, we investigate the ability of PRC1’s structural domains to form droplets and hierarchically organize microtubule tactoids. We find that the removal of PRC1’s unstructured C-terminal tail does not inhibit its ability to form droplets or microtubule tactoids in vitro. Removing part of PRC1’s N-terminal rod domain inhibits but does not completely suppress droplet formation. Full article

Ubiquitin-specific protease 7 (USP7/HAUSP) is one of the most studied deubiquitinating enzymes and plays a crucial role in regulating numerous cellular processes, making it a promising therapeutic target. In the nucleus, USP7 partially colocalizes with PML nuclear bodies (PML-NB)—multifunctional membraneless organelles involved in post-translational modifications and protein complexes assembly. The molecular basis and functional significance of this association remain uncharacterized. In this study, comparison of USP7 and PML interactomes revealed a significant overlap of 166 shared proteins. Functional enrichment analysis showed that USP7 and PML may operate within a common molecular context related to transcriptional regulation, chromatin remodeling, and DNA damage responses. Furthermore, these processes are also linked to cellular senescence and human aging (CellAge and GenAge databases). Focused analysis of overlaps between the USP7 interactome and core PML-NB proteins identified 61 proteins forming a dense “small-world” network. Most are prone to liquid–liquid phase separation, are intrinsically disordered, and serve as substrates for SUMOylation or ubiquitination. These findings not only expand our understanding of the molecular functions of USP7 but also highlight PML-NB as an important cellular context for investigating mechanisms associated with USP7 activity. Full article

Molecular engineering has traditionally followed a structure–function paradigm based on well-defined, folded architectures. However, intrinsically disordered proteins and regions (IDPs/IDRs) reveal that nature also exploits disorder as a functional design strategy. Here, we argue that intrinsic disorder can be understood as a biomimetic design principle for molecular and materials engineering. From a soft matter perspective, IDRs function through statistical ensembles, weak multivalent interactions, and collective behavior rather than fixed structure, with sequence features encoding a molecular grammar that governs phase behavior, viscoelasticity, and responsiveness. These principles closely parallel those found in associative polymers and colloidal systems. Recent advances in coarse-grained modeling, machine learning, and inverse design further enable disorder to be treated as a controllable engineering variable. By reframing intrinsic disorder as a programmable and bioinspired design strategy, this Perspective highlights its potential for the development of adaptive and responsive biomimetic materials. Full article

Neurodegenerative diseases arise when normally functional aggregation-prone proteins transition into stable cross-β amyloid fibrils. Although these fibrils share a conserved architecture, the pathways that lead to fibrillation vary across proteins and cellular environments. Liquid–liquid phase separation is now recognized as a central organizer of intracellular biochemistry that modulates protein aggregation. Physiological condensation can buffer aggregation by maintaining macromolecular solubility and providing partner interactions that compete against pathological protein–protein interactions. However, condensates can transform and age into gel-like states that can favor the emergence of β-rich oligomers and solid-state fibrils. Across six disease-linked proteins that include Tau, α-synuclein, amyloid-β, TDP-43, FUS, and hnRNPA1, we compare how sequence-encoded interaction motifs, cellular cofactors, and interfacial microenvironments shape the balance between physiological condensates and pathological amyloids. Here, we highlight the unifying drivers of aggregation and intervention points that preserve native function while limiting toxic amyloid formation. Full article

Neurodegenerative diseases feature diverse pathological protein aggregates, including Lewy bodies in Alzheimer’s disease (AD) and skein-like filaments in amyotrophic lateral sclerosis (ALS). The physical mechanisms underlying this morphological diversity remain unclear. Here, we demonstrate that aggregation of the prion-like domain of hnRNPA1 (A1PrD), implicated in AD and ALS, is driven by solution composition and phase transition dynamics. Utilizing 3D timelapse and fluorescence lifetime imaging microscopy, we show that solution conditions modulate phase separation, gelation, and fibrillation, resulting in distinct structures such as fibril, gel, and starburst morphologies. Homotypic and heterotypic interactions between A1PrD and RNA were observed to shift the balance between pathological and physiological condensates. Importantly, amyloid-rich starbursts displayed prion-like infection capabilities toward amyloid-poor condensates. Our findings highlight how the interplay between solution composition and kinetic balances of liquid-liquid phase separation, gelation, and fibrillation shapes the diverse pathological aggregate morphologies characteristic of neurodegenerative diseases. Full article

Low temperature and drought are among the most pervasive abiotic stresses limiting crop productivity worldwide, and their frequent co-occurrence or alternation imposes compounded constraints on agricultural sustainability. Increasing evidence supports cross-tolerance, whereby exposure to one stress enhances resistance to another, as an emergent property of shared signaling networks and integrative regulatory layers. In this review, we summarize recent advances in understanding cold–drought cross-talk, from early stress perception and secondary messengers to hormonal coordination via abscisic acid, transcriptional reprogramming centered on dehydration responsive element binding protein/C repeat binding factor (DREB/CBF) modules, and longer-term regulatory memory mediated by chromatin remodeling and biomolecular condensates. Importantly, we further discuss how these mechanistic insights can be translated into precision breeding strategies, including genome editing, allele mining, and backcross-assisted introgression, to accelerate the development of crop varieties with stable multi-stress tolerance. Finally, we highlight future directions for integrating multi-omics, high-throughput phenotyping, and data-driven approaches to enable efficient molecular design breeding for complex stress environments. Full article

The Keap1-Nrf2 signaling pathway is a central regulator of transcriptional responses to oxidative stress and is strongly linked to diverse pathologies, particularly cancer. In the cytoplasm, Keap1 (Kelch-like ECH-associated protein 1) promotes proteasomal degradation of Nrf2 (NF-E2–related factor 2). Oxidative stimuli disrupt the Keap1-Nrf2 interaction, facilitating Nrf2 nuclear accumulation and activation of antioxidant and detoxifying genes. Recent evidence suggests that Keap1 family proteins also enter the nucleus, bind chromatin, and regulate transcription, but the underlying mechanisms remain less understood. Here, we show that the Drosophila Keap1 ortholog, dKeap1, accumulates in the nucleus and gradually assembles stable nuclear foci in cells following oxidative treatment. FRAP analyses revealed reduced mobility of dKeap1 within these foci. Both the N-terminal (NTD) and C-terminal (CTD) domains of dKeap1 were required for foci formation. Two intrinsically disordered regions (IDRs) were identified within the CTD, and CTD-YFP fusion proteins readily formed condensates in vitro. Conversely, deletion of the Kelch domain resulted in robust cytoplasmic foci even under basal conditions, and in vitro assays also indicated that the Kelch domain suppresses dKeap1 condensate formation. Together, these findings reveal a novel molecular mechanism for the nuclear function of dKeap1, providing new insight into the broader roles of Keap1 factors in oxidative response, development, and disease. Full article

Chromosome dynamics, recombination, and nucleolar organization intersect during meiotic prophase I, yet how the recombination context influences nucleolar architecture remains unclear. We analyzed the nucleolar pool of Cdc14 in Saccharomyces cerevisiae under matched prophase I gating and a uniform, frame-based operational definition of transient two-focus episodes. In a prophase-arrest reference, Cdc14–mCherry formed a predominant single nucleolar focus with occasional, reversible two-focus episodes that Nop56–GFP placed within the nucleolar compartment (nucleolar splitting). Splitting rose sharply when interhomolog recombination was compromised and remained elevated when Spo11 catalytic activity was abolished, indicating that increased DSB formation is not required and pointing instead to the homolog engagement state as a key variable. Population checkpoint readouts did not map onto the phenotype: Hop1 phosphorylation differed strongly across genotypes, yet splitting remained high in recombination-defective and DSB-free contexts and low in the reference. Timing analyses showed that events concentrated early and declined in the reference, whereas recombination-defective and DSB-free backgrounds retained activity into later windows across thresholds. We propose that nucleolar splitting reflects a rheological response of the nucleolus to chromosome-scale forces that vary with homolog engagement, consistent with contributions from DSB-independent chromosome dynamics such as telomere clustering, telomere-led rapid prophase movements, and centromere coupling/pairing. Together, these data support the nucleolus as a mesoscale, mechanically sensitive readout of meiotic chromosome dynamics. Full article

Stress granules (SGs) are dynamic, membraneless organelles that form in response to stress and play pivotal roles in translational control, RNA metabolism, and cell survival. In cancer, SGs are increasingly recognized as central mediators of therapy resistance, enabling malignant cells to evade apoptosis, reprogram metabolism, and modulate immune responses. Understanding the mechanistic and clinical insights into SG kinetics in healthy versus cancer cells holds significant potential for targeting them in precision oncology. This review integrates current knowledge on how chemotherapeutic agents, oncogenic signaling pathways, and tumor microenvironmental stressors promote SG formation, as well as evidence of altered SG kinetics across tumor types. We further highlight how the upregulation of SG components within the tumor microenvironment shapes cancer cell behavior and adaptability, and how crosstalk between SGs and other biomolecular condensates could contribute to resistance. Finally, we discuss emerging therapeutic strategies targeting SGs, including kinase inhibitors and modulators of SG dynamics, and propose that SGs represent tractable vulnerabilities in precision oncology. By bridging mechanistic insights with clinical implications, this review positions SGs as a promising frontier in overcoming cancer therapy resistance. Full article

The recognition of liquid–liquid phase separation (LLPS) as a widespread organizing principle has revolutionized our view of cellular biochemistry. By forming biomolecular condensates, cells spatially orchestrate reactions without membranes. However, the dysregulation of this precise physical organization is emerging as a driver of diverse pathologies, collectively termed “Condensatopathies.” Unlike traditional proteinopathies defined by static aggregates, these disorders span a dynamic spectrum of material state dysfunctions, from the failure to assemble essential compartments to the formation of aberrant, toxic phases. While research has largely focused on neurodegeneration and cancer, the impact of condensate dysfunction likely extends across broad physiological landscapes. A central unresolved challenge lies in deciphering the “molecular grammar” that governs the transition from functional fluids to pathological solids and, critically, visualizing these transitions in situ. This “material science” perspective presents a profound conundrum for drug discovery: how to target the collective physical state of a protein ensemble rather than a fixed active site. This review navigates the evolving therapeutic horizon, examining the limitations of current pharmacological approaches in addressing the complex “condensatome.” Moving beyond inhibition, we propose that the future of intervention lies in “reverse-engineering” the biophysical codes of phase separation. We discuss how deciphering these principles enables the creation of programmable molecular tools—such as synthetic peptides and state-specific degraders—designed to precisely modulate or dismantle pathological condensates, paving the way for a new era of precision medicine governed by soft matter physics. Full article