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PubMed2026

From pan-life phase insights to PhaseHub: Analyzing protein condensate complexity.

Intracellular biomolecular condensation forms multicomponent signaling hubs that regulate development, stress responses, and environmental adaptation. While the molecular grammar encoded within scaffold proteins defines the basal associative features driving condensation, heterotypic condensates are intrinsically dynamic, multicomponent, and far-from-equilibrium systems. Consequently, how condensates organize component composition, stoichiometry, and functional specificity in space and time under physiological conditions remains poorly understood. Addressing this challenge requires integrative frameworks that combine predictive biophysical features with experimental information on protein abundance, interaction networks, subcellular localization, and evolutionary conservation. In this study, we first analyzed phase separation (PS) proteins across the tree of life in 1106 species, revealing a stark contrast in computationally predicted PS propensity between eukaryotes and prokaryotes, with genome size as a key determinant. Through a broad analysis of amino acid homorepeat-containing proteins (HRPs) across all species, we uncovered how PS evolves via a balance between functional condensation and avoidance of harmful, aggregation-prone sequences. We further identified potential signaling hubs and components across kingdoms by integrating PS-positive proteins with experimentally derived abundance and interactome data from four model eukaryotic species. Using Arabidopsis as a model, we dissected the relationships among PS propensity, condensation hub prediction, HRPs, subcellular localization, and structural conservation. Finally, we developed PhaseHub, a user-friendly interface for exploring scaffold-client dynamics, PS components, sequence signatures within each PS protein, and hubs. Collectively, our work provides an evolutionary framework for understanding multicomponent PS hubs by integrating molecular grammar with physiological context, thereby facilitating hypothesis generation and rational design.

Phase Separation↗

PubMed2025

Live-Cell Monitoring and Omics Analysis of Liquid-Solid Transitions of Biomolecular Condensates.

Biomolecular condensates, or so-called membraneless organelles, transition from liquid into more solid-like states over time, contributing to the development of pathological conditions. The present study proposes a simple method using photoactive yellow protein (PYP) and its specific fluorescent covalent ligands to distinguish between the liquid and solid states of protein condensates in live cells. The method, compatible with fluorescence-activated cell sorting (FACS), correlates the stiffness of specific protein condensates with their accessibility to PYP ligands, enabling quantitative multicolor monitoring of condensate solidification. We applied this technique to 12 phase-separating proteins and their mutants, finding that TDP-43, particularly its A315T mutant linked to familial amyotrophic lateral sclerosis, most readily forms solid aggregates. Furthermore, this FACS-compatible strategy enabled the isolation of distinct cell populations based on condensate states, allowing for subsequent proteomic and transcriptomic analyses. Our findings demonstrate that condensate solidification is accompanied by the upregulated expression of extracellular matrix proteins, suggesting a previously unrecognized link between solid aggregate formation and extracellular matrix hardening.

Humans↗

PubMed2026

High-throughput identification of endogenous biomolecular condensates and phase-separating proteins.

Biomolecular condensates formed through liquid-liquid phase separation regulate cellular processes, and their dysregulation causes disease. Current methods for identifying endogenous phase-separating proteins have low throughput and cannot capture dynamic responses to stimuli. Here we present a protocol combining osmotic compression or transforming growth factor-β (TGF-β) treatment to induce condensation with sucrose density gradient centrifugation and quantitative mass spectrometry to enable systematic, high-throughput identification of endogenous condensates and phase-separating proteins. The method exploits the density changes that occur when phase-separating proteins undergo oligomerization during condensate formation. In H1975 cells, we identified over 1,500 phase-separating proteins under osmotic compression or TGF-β treatment; 538 of these candidates were not present in PhaSepDB, a database that compiles in vivo, in vitro and omics-derived proteins. The approach detects constitutive condensates and proteins that dynamically phase-separate in response to osmotic stress or TGF-β signaling. This protocol provides proteome-wide analysis of fractions of proteins having different densities and enables temporal resolution of phase-separation events. The procedure takes ~9 d and requires expertise in cell culture, biochemistry and mass spectrometry. This method enables systematic study of biomolecular condensates and disease-associated phase-separation mechanisms.

Phase Separation↗

PubMed1976

Cyclic condensed metaphosphates and linear polyphosphates in brown and red algae.

The occurrence of linear condensed polyphosphates and cyclic condensed metaphosphates was studied by means of pulse-labeling with 32P-orthophosphate (3--5h) in a number of Phaeophyceae species: Pylaiella litoralis, Ilea fascia, Ectocarpus siliculosus and also Rhodophyceae species: Ceramiumdeslongchampsii, C. rubrum, Rhodomela confervoides, Porphyridium purpureum and P. aerugineum. Two-dimensional cellulose thin layer chromatography revealed that in all species studied 32P-radioactivity was generally present in all oligopolyphosphates containing 2 to 7 phosphate residues, in cyclic metaphosphates (tri-, tetra-, penta- and hexametaphosphates) and in high-molecular-weight condensed phosphates which remained at the starting point. Among the low-molecular-weight condensed inorganic phosphates the trimetaphosphate had a significantly higher specific activity than the other oligophosphates which were separated on the chromatography plates as measured by the direct scanning with a Geiger-Muller counter. The phosphate uptake strongly depends on the internal pool of reserve phosphates of the algae cells. The 32P-orthophosphate incorporation of the cells is low and sluggish when growning in a synthetic medium or in sea water. Accordingly 32P appeared preferentially in the low-molecular-weight fractions of condensed phosphates since the storage phosphates were not yet used. After previous incubation in a P-free culture medium of the algae the 32P was rather rapidly incorporated and was found mostly in the high-molecular-weight condensed phosphates. During MAK-chromatography the high-molecular-weight fractions were eluted together with the nucleic acids (tRNA and DNA) while most of the low-molecular-weight fractions left the column immediately on elution.

Eukaryota↗

PubMed1976

The possible role of solid surface area in condensation reactions during chemical evolution: reevaluation.

Published data on adsorption and condensation of amino acids, purine and pyrimidine bases, sugars, nucleosides, and nucleotides are analyzed in connection with Bernal's hypothesis that clays and other minerals may have provided the most likely surface for adsorption and condensation of these molecules in prebiotic times. Using surface concentration and reaction rate as the main criteria for the feasibility of condensation reactions, four types of prebiotic environments were analyzed: (1) an ocean-sediment system, (2) a dehydrated lagoon bed produced by evaporation, (3) the surface of a frozen sediment, and (4) a fluctuating system where hydration (rainstorms, tidal variations, flooding) and dehysration (evaporation) take place in a cyclic manner. With the possible exception of nucleotides, low adsorption of organomonomers on sediment surfaces of a prebiotic ocean (pH 8) is expected, and significant condensation is considered unlikely. In dehydrated and frozen systems, high surface concentrations are probable and condensation is more likely. In fluctuating environments, condensation rates will be enhanced and the size distribution of the oligomers formed during dehydration may be influenced by a "redistribution mechanism" in which adsorbed oligomers and monomers are desorbed and redistributed on the solid surface during the next hydration-dehydration cycle.

Adsorption↗

PubMed1977

Relation between chemical constituents of tobacco and mutagenic activity of cigarette smoke condensate.

Mutagenic activities of cigarette smoke condensate were assayed in the presence of S-9 Mix using Salmonella typhimurium TA 98. The results were examined in relation to chemical data of tobacco leaves. Among the nitrogenous constituents examined, the contents of total nitrogen and protein nitrogen and the soluble nitrogenous fraction were positively and significantly related to an increase in mutagenic activity of the smoke condensate, whereas nicotine and nitrate were not important in contributing to mutagenic potency of such condensates. The age of tobacco leaves influenced the mutagenic potency of the condensate, which was lowest in leaves from the lower stalk position and increased with ascending leaf position on the stalk. Smoke condensate from tobacco with higher sugar content resulted in lower mutagenic activity. The present results, together with the previous study on the mutagenicity of the amino acid pyrolyzates, suggest that potent mutagens in cigarette smoke condensate are nitrogen-containing compounds, which may be formed from proteins and amino acids during the burning of a cigarette.

Amino Acids↗

PubMed1977

Studies on the local and systemic carcinogenicity of topically applied smoke condensate from a substitute smoking material.

The topical carcinogenicity to mouse skin of smoke condensates obtained from a tobacco substitute (NSM), alone or in combination with tobacco, has been compared with condensate from tobacco and with acetone, the solvent used. Sixteen different types of cigarette were used to make the condensates, and the age-standardized results have been analysed according to the Weibull distribution model. The results show that NSM condensate has less than 25% of the potency of tobacco condensate (37% at 95% upper confidence limit), and that condensates from blends of NSM and tobacco are similarly reduced in activity. General pathology analysis failed to reveal abnormalities due to NSM.

Animals↗

PubMed2026

NAP1 switches from an activator to a limiter of interferon induction by trapping TBK1 in condensates.

TBK1 kinase is a central regulator of type I IFN production. Upon activation of the IFN-β induction pathway, TBK1-adaptor proteins (NAP1, SINTBAD, TANK) form liquid condensates. We show that NAP1 condensates concentrate TBK1. Using NAP1KO cell lines, we demonstrate that NAP1 exerts a dual effect on TBK1 activity. Initially, NAP1 binds TBK1 and increases its activity, promoting IFN pathway activation. Subsequently, TBK1-mediated phosphorylation of NAP1 induces the formation of condensates. These NAP1 condensates concentrate both TBK1 and the phosphatase PP2A, which dephosphorylates and consequently deactivates TBK1, thus limiting IFN induction. Additionally, in patients with lupus or interferonopathies, we identify NAP1 variants unable to form condensates upon danger signal exposure, which sustain TBK1 activation without limiting its activity. This study reveals a mode of regulating a signaling pathway through condensate formation and provides a potential molecular explanation for immune dysregulation associated with NAP1 variants in certain patients with interferonopathies.

Protein Serine-Threonine Kinases↗

PubMed1977

Preleptotene chromosome condensation in mouse oogenesis.

In the embryonic mouse ovary, studies of meiotic onset reveal the existence of a preleptotene stage of chromosome condensation. This stage begins with the appearance of very fine and irregular filaments, which gather around the chromocenters constituted by centromeric heterochromatin. At maximal condensation the nucleus contains 40 compact chromosomal masses. Decondensation engenders the reappearance of filaments more dense and regular than those seen at the onset of the condensation stage. The filaments elongate while progressively taking on the appearance of leptotene-stage chromosomes. The oocytes at different phases of condensation stage represent 41% of the germ cels in the 13-day-old mouse embryo. This proportion reaches 63% at 14 days and then declines to 3% at 17 days. Spectrophotometric studies of the condensation-stage nucleus, following staining by the Feulgen reaction, indicated that the nucleus contains 4C DNA. This observation, together with the morphologic characteristics of this stage, suggests that the oocyte is already engaged in prophase. Time studies indicate that the condensation stage occurs immediately prior to leptotene.

Animals↗

PubMed1976

Fine structure of the heterochromatin of the kangaroo rat Dipidomys ordii, and examination of the possible role of actin and myosin in heterochromatin condensation.

Biochemical studies have suggested that some actin and myosin may be present in the nucleus. This raises the possibility that heterochromatin condensation might be the result of an actin-myosin rigour type complex. Since ATP dissociates actin and myosin, this possibility could be examined by determining the effect of ATP on heterochromatin condensation. Thin-section electron microscopy showed large amounts of condensed constitutive heterochromatin in the kidney nuclei and somewhat less in the liver nuclei of the kangaroo rat, Dipidomys ordii. Surprisingly, there were some nuclei in the brain which contained no condensed heterochromatin despite the fact that this genome is composed of 50% satellite DNA. Although washing kidney nuclei with solutions of 10 mM Tris-ATP caused marked decondensation of the heterochromatin, when they were washed with Mg-ATP the heterochromatin was more condensed than in the controls. This suggests the decondensation by Tris-ATP is due to its ability to chelate divalent cations and provides no support for condensation of heterochromatin being the result of myosin-actin interaction. Despite being decondensed, the chromatin fibres of heterochromatin were distinct from those of euchromatin. The heterochromatin formed rod-like 19-5 nm fibres, the euchromatin formed random coils of 11-0-nm fibres.

Actins↗

PubMed1976

Circular dichroism studies on DNA condensed in NaCl cetyltrimethyl ammonium bromide solutions.

It is shown by means of circular dichroism studies of variously condensed forms of DNA that the specific supramolecular structure of DNA determines the type of CD spectra. DNA, condensed (crystallized) slowly in the presence of cetyltrimethyl ammonium bromide yields a spectrum very similar to that of DNA in solution in the B-form. The condensates appear in the phase-contrast microscope as spherulitic crystallites. Rapidly condensed DNA in the presence of cetyltrimethyl ammonium bromide shows a spectrum of the psi-type with large negative ellipticites. The influence of condensation velocity upon the supramolecular structure of DNA gives evidence that the various condensation forms of DNA are not thermodynamical equilibrium conformations.

Bromides↗

PubMed1975

Metabolism of cigarette smoke condensates by human and rat homogenates to form mutagens detectable by Salmonella typhimurium TA1538.

Nineteen fractions of whole condensate of smoke from the University of Kentucky Reference Cigarette IRI were tested for mutagenicity in vitro using a bacterial indicator system. As little as 25 mug of the active fractions were mutagenic toward histidine-requiring Salmonella typhimurium TA1538, if the condensates were incubated in the presence of rat or human liver homogenates of lung were relatively inactive. Homogenates from livers of rats that had been treated with 3-methylcholanthrene converted condensates to mutagens more efficiently than did liver homogenates from man or from normal or phenobarbital-treated rats. Use of homogenates from animals treated with 3-methylcholanthrene gave much more reproducible results in smoke fraction assays because larger numbers of revertants were obtained, and dose-response curves were linear over the range 25 to 250 mug condensate. The linear dose-response curves permitted quantitative comparison of the various fractions. The mutagenicity per mg of basic fractions of whole smoke condensate is very high and that of neutral polycyclic hydrocarbons is very low. Because of the exquisite preferential sensitivity of the TA1538 test system to polycyclic amines and insensitively to alkyl polycyclics, there is a poor quantitative correlation between mutagenicity and carcinogenicity, as measured by skin painting or in vitro cell transformation. There is substantial evidence that many carcinogens are mutagens but that most of these compounds require metabolism before they are biologically active. If further development improves the sensitivity of the bacterial testing system to mutagenic derivatives of alkyl polycyclic and heteropolycyclic hydrocarbons, it may provide a convenient, rapid, quantitative, and inexpensive bioassay for the detection of potentially carcinogenic substances in tobacco smoke condensates.

Animals↗

PubMed1978

[Secondary structure of condensed DNA. wide-angle, small-angle x-ray scattering and circular dichroism].

Ethanol precipitated DNA shows a CD spectrum of the +psi-type which is similar to that of DNA in the A-form. DNA condensed with cetyl-trimethylammonium-bromide shows, depending on the condensation velocity, a CD spectrum of the -psi-type, or a CD spectrum only slightly modified from that of DNA in solution. The first spectrum is similar to that of DNA in the C-form, and the second one, to that of DNA in the B-form. Using large-angle X-ray scattering of the three DNA condensates and comparing them with the scattering curves calculated from the atom coordinates for the A-, B-, and C-form of DNA it is shown that the secondary structure of the DNA belongs in all three cases to the B-family. It follows from this result that the secondary structure of DNA alone does not determine the type of CD spectrum. The CD spectrum of condensed DNA is essentially determined by the supramolecular structures of the partially crystalline DNA condensates. These supramolecular structures can be demonstrated by the small-angle X-ray diagrams. The condensation of DNA by ethanol and cetyl-trimethylammonium-bromide proceeds in the form of a partial crystallization of the DNA.

Animals↗

PubMed2026

Mediator at the Helm: Coordinating transcription and biomolecular condensates in hematopoiesis.

Hematopoiesis relies on precisely coordinated transcriptional programs that balance stem cell self-renewal, lineage commitment, and terminal differentiation. Central to this regulation is the Mediator complex, a large multi-subunit transcriptional co-regulator that integrates signals from transcription factors and chromatin regulators to control RNA polymerase Ⅱ (Pol Ⅱ) activity. The dynamic and modular composition of Mediator enables context-dependent transcriptional outputs, while individual subunits can exert specialized regulatory functions during hematopoietic lineage specification, thereby contributing to cell-fate-specific transcriptional outputs. Recent advances further reveal that transcriptional regulation is shaped by the spatial organization of regulatory machinery with biomolecular condensates formed through liquid-liquid phase separation (LLPS), particularly at super-enhancers. In this emerging framework, Mediator functions not only as a transcriptional integrator but also as a key coordinator of transcriptional machinery within condensates at cell-fate-related gene loci. In this chapter, we summarize how distinct Mediator subunits confer specific modes of transcriptional regulation and discuss how the interplay between Mediator and phase-separated condensates shapes transcriptional control during hematopoiesis. We highlight how specific subunits, including MED1 and MED26, participate in distinct regulatory modes in erythropoiesis, spanning super-enhancer-driven transcriptional activation, progenitor expansion, and condensate-associated mechanisms that influence Pol Ⅱ pausing and global transcription repression during terminal differentiation. Together, these findings support a model in which Mediator integrates transcriptional regulation with nuclear organization through condensate-mediated mechanisms, providing a conceptual framework for understanding hematopoietic cell fate decisions and transcriptional dysregulation in hematological diseases.

Hematopoiesis↗

PubMed2026

ATRX Condensates as Candidate Organizers of Enhancer-Centered Nuclear Microenvironments in Neural Progenitors: A Hypothesis for Enhancer-Associated ATRX Function in Neural Progenitors.

Neural progenitor cells (NPCs) must preserve lineage identity while remaining responsive to developmental cues. Here, we discuss the hypothesis that ATRX condensates help organize enhancer-centered nuclear microenvironments in NPCs. ATRX has long been studied in heterochromatin maintenance, histone variant deposition, and chromatin remodeling; earlier work has also shown that ATRX can occupy euchromatic and active regulatory regions and contribute to transcriptional regulation. Recent evidence in human NPCs indicates that ATRX forms nuclear puncta with condensate-like properties, associates with neurogenic enhancer-rich regions, and incorporates regulatory factors such as CHD7 and p300. Perturbation of ATRX condensate formation is associated with changes in enhancer-associated ATRX occupancy, neural gene-expression programs, and neuroepithelial organization, suggesting a regulatory mode that may complement canonical heterochromatin-associated functions. We propose a dual-mode model in which folded domains contribute to chromatin anchoring at repressive regions, whereas intrinsically disordered regions support condensate-associated organization at active developmental enhancers. We emphasize that whether ATRX condensates activate enhancers de novo, stabilize pre-existing enhancer states, buffer transcriptional variability, or primarily organize cofactor localization remains unresolved. We also discuss limitations of the current evidence and outline acute, locus-specific experiments needed to test the model.

X-linked Nuclear Protein↗

PubMed2026

Molecular origins of pH gradients in charge-regulated biomolecular condensates.

Biomolecular condensates exhibit spontaneous electrochemical microenvironments characterized by asymmetric ion distributions and pH gradients that emerge from protein-sequence-dependent charge regulation. Despite their biological importance, mechanistic understanding of these microenvironments has been constrained by the absence of computationally tractable frameworks capable of treating proton exchange, counterion partitioning, and buffer equilibria on consistent thermodynamic footing. Here, we introduce the buffered Charge-Regulation Monte Carlo (b-CR-MC) framework, which couples grand-canonical exchange of ions and buffer species with explicit charge regulation of titratable residues. By extending the CR-MC ion-merging strategy to multicomponent reservoirs and employing the restricted primitive model, b-CR-MC achieves computational efficiency while maintaining thermodynamic rigor, achievingquantitative agreement with the more expensive generalized grand-reaction Monte Carlo approach. Applied to full-length FUS (net positive) and PGL-3 (net negative) under physiological conditions, the framework reveals sequence-dependent pH gradients: the dense phase of FUS exhibits an alkaline shift, while that of PGL-3 exhibits an acidic shift, in both cases driving the condensate interior toward the protein's isoelectric point. Slab-geometry simulations further resolve the Donnan potential and continuous ion profiles across the condensate interface, confirming the direction of these electrochemical shifts. Additionally, we identify spatially resolved buffer depletion within dense phases, establishing that dynamic charge regulation is a primary determinant rather than a secondary correction to condensate electrochemistry. By establishing a sequence-resolved, thermodynamically consistent computational platform, b-CR-MC enables quantitative prediction of how mutations and post-translational modifications reprogram condensate microenvironments across biological and pathophysiological contexts.

Hydrogen-Ion Concentration↗

PubMed2026

Biomolecular Condensates Integrate Transcriptional and Epigenetic Responses to Hypoxia.

Hypoxia is a defining feature of physiological stress and the core of solid tumors, where aberrant vascularization limits oxygen delivery; cells respond through mechanisms that extend beyond the canonical stabilization of hypoxia-inducible factors (HIFs). Recent studies suggest that hypoxia can promote the formation of specific biomolecular conden-sates, membraneless compartments generated through liquid-liquid phase separation in which regulatory proteins and RNAs become locally enriched at genomic regions, while chromatin mainly serves as an organizational scaffold. Transcription factors, the coacti-vators p300/CBP, Mediator, and BRD4, chromatin-modifying enzymes, and architectural RNAs such as NEAT1 and MALAT1 partition into these compartments, and their con-densation can help reorganize local chromatin structure and enhancer-promoter interac-tions. Because molecular oxygen is a shared co-substrate for the Jumonji-C histone demethylases and the ten-eleven translocation (TET) DNA dioxygenases, hypoxia reshapes histone methylation and DNA methylation in parallel, and readers that bridge these marks, including UHRF1, may participate in condensate-associated chromatin regulation. Hypoxia-driven condensation of ZHX2 rewires enhancer-promoter contacts and higher-order genome architecture, influencing cell identity, stemness, and metastatic potential, and Polycomb condensates represent another candidate epigenetic compartment that may be influenced by hypoxic signaling. These processes may be particularly important in cancer, where chronic hypoxia provides a sustained stimulus for condensate formation and epigenetic remodeling. Together, these findings support a model in which phase separation and epigenetic reprogramming are not separate layers but one integrated response to low oxygen, offering opportunities to target maladaptive condensates in disease.

Epigenesis, Genetic↗

PubMed1975

Implications of the reorganizational behavior of condensed phosphates for mitochondrial phosphorylation.

The composition of phosphorus-32 labeled polyphosphoric acid (32PPA) prepared from, (i) H3(32)PO4 and (82 percent w/w) P2O5 and, (ii) by incorporation of radioactivity from H3(32)PO4 into unlabeled polyphosphoric acid (PPA) was examined and found to be the same. The identity of these condensed phosphorate mixtures, as established, argues strongly in favor of a rapid and complete equilibration and provides direct evidence in support of Van Wazer's reorganization theory of condensed phosphates. No evidence for metaphosphates or label exchange in an aqueous environment was found. 32PPA was found to exist in metastable equilibrium with 32PPA as a crystalline solid of different composition. Agreement of hydrolytic rate data from the mixtures of condensed phosphates with literature values for individual species suggests that the hydrolysis of the pyro- and tripoly-phosphate species proceeds independently in the presence of other homologs. The rate of hydrolysis of the condensed phosphates (at pH5.0 and 65 degrees C) was found to be proportional to chain length, increasing about four-fold between pyro- and hexapoly-phosphate. The same correlation is also manifest in the adenosine 5' polyphosphates. A slight enhancement in the rate of hydrolysis of adenosine diphosphate, increasingly more pronounced in the case of adenosine tri- and tetra-phosphate, was also noted. This effect is attributed to the presence of the adenosine moiety. The most interesting aspect of the rate data is to be found in the similarity of the rates of hydrolysis of the adenosine 5' polyphosphates, relative to their inorganic polyphosphate counterparts. The significance of these findings is discussed and the viewpoint is presented that the properties of condensed phosphates are compatible with the requisite characteristics that must be predicated of any in situ phosphoryl precursor in mitochondrial phosphorylation.

Diphosphates↗