Multiple Condensates Research Articles (Page 1)

Nuclear biomolecular condensates are essential sub-compartments within the cell nucleus and play key roles in transcription and RNA processing. Bottom-up construction of nuclear architectures in synthetic settings is non-trivial but vital for understanding the mechanisms of condensates in real cellular systems. Here, we present a facile and versatile synthetic DNA protonucleus (PN) platform that facilitates localized transcription of branched RNA motifs with kissing loops (KLs) for subsequent condensation into complex condensate architectures. We identify salinity, monomer feeding, and KL-PN interactions as key parameters to control co-transcriptional condensation of these KLs into diverse artificial nuclear patterns, including single and multiple condensates, interface condensates, and biphasic condensates. Over time, KL transcripts co-condense with the PN matrix, with the final architecture determined by their interactions, which can be precisely modulated using a short DNA invader strand that outcompetes these interactions. Our findings deepen the understanding of RNA condensation in nuclear environments and provide strategies for designing functional nucleus-mimetic systems with precise architectural control.

Phase-separated Condensates in Autophagosome Formation and Autophagy Regulation.

The synapse is polarized and highly compartmentalized on both its pre- and postsynaptic sides. The compartmentalization of synaptic vesicles, as well as vesicle releasing and recycling machineries, allows neurotransmitters to be released with precisely controlled timing, speed, and amplitude. The compartmentalized and clustered organization of neurotransmitter receptors and their downstream signaling enzymes allows neuronal signals to be properly received and amplified. Synaptic adhesion molecules also form clustered assemblies to align pre- and postsynaptic subcompartments for synaptic formation, stability, and transmission. Recent studies indicate that such synaptic and subsynaptic compartmentalized organizations are formed via phase separation. This review discusses how such condensed subsynaptic compartments may form and function in the context of synapse formation and plasticity. We discuss how phase separation allows for the formation of multiple distinct condensates on both sides of a synapse and how such condensates communicate with each other. We also highlight how proteins display unique properties in condensed phases compared to the same proteins in dilute solutions.

The Nambu-Goldstone modes on the exotic chiral condensed phase with chiral and tensor-type quark-antiquark condensates are investigated by using the two-point vertex functions. It is shown that one of the Nambu-Goldstone modes appears as a result of meson mixing. As is well known, another method to find the Nambu-Goldstone modes is given by the use of the algebraic commutation relations between broken generators and massless modes obtained through the spontaneous symmetry breaking. This method is adopted to the cases of the chiral symmetry breakings due to the tensor-type condensate and the inhomogeneous chiral condensate. The result obtained by the use of the meson two-point vertex functions is obviously reproduced in the case of the tensor-type condensate. Furthermore, we investigate the general rules for determining the broken symmetries and the Nambu-Goldstone modes algebraically. As examples, the symmetry breaking pattern and the Nambu-Goldstone modes due to the tensor-type condensate or the inhomogeneous chiral condensate are shown by adopting the general rules developed in this paper in the algebraic method. Published by the American Physical Society 2025

Several studies have attempted to replicate the complexhierarchyof eukaryotic cells for the bottom-up construction of artificial cells.Specifically, reconstruction of liquid–liquid phase separationsystems as membrane-less organelles is one of the key focuses of thisresearch field, with DNA condensates acting as versatile buildingblocks whose associative interactions can be precisely controlledvia sequence design. However, such control is only possible at thenanoscale as control over the size and morphology of the lipid vesiclesand liquid–liquid phase separation systems at the meso-to-microscaleis determined by the kinetic aspects of their formation processes.Microfluidics is well-suited for controlling dynamic molecular assembliesat the cellular scale. In this study, we report the controlled condensationof DNA nanostars in mass-produced monodisperse giant vesicles (GVs)generated using a microfluidic device by manipulating the concentrationsof DNA and salt associated with the GV volume changes. Our approachfacilitates the precise control of the dynamics of DNA condensateformation, final size of condensates, formation of multiple condensates,and reversible formation/dissociation of condensates in GVs servingas a chassis for an artificial cell. Furthermore, our approach eliminatesthe need for thermal annealing prior to DNA condensation, supportingthe coexistence of enzyme-containing biochemical reaction systems,such as gene expression systems.

Synapsin Condensation is Governed by Sequence-Encoded Molecular Grammars.

Phase separation in the multi-compartment organization of synapses.

Multiple biomolecular condensates coexist at the pre- and post- synapse to enable vesicle dynamics and controlled neurotransmitter release in the brain. In pre-synapses, intrinsically disordered regions (IDRs) of synaptic proteins are drivers of condensation that enable clustering of synaptic vesicles (SVs). Using computational analysis, we show that the IDRs of SV proteins feature evolutionarily conserved non-random compositional biases and sequence patterns. Synapsin-1 is essential for condensation of SVs, and its C-terminal IDR has been shown to be a key driver of condensation. Focusing on this IDR, we dissected the contributions of two conserved features namely the segregation of polar and proline residues along the linear sequence, and the compositional preference for arginine over lysine. Scrambling the blocks of polar and proline residues weakens the driving forces for forming micron-scale condensates. However, the extent of clustering in subsaturated solutions remains equivalent to that of the wild-type synapsin-1. In contrast, substituting arginine with lysine significantly weakens both the driving forces for condensation and the extent of clustering in subsaturated solutions. Co-expression of the scrambled variant of synapsin-1 with synaptophysin results in a gain-of-function phenotype in cells, whereas arginine to lysine substitutions eliminate condensation. We report an emergent consequence of synapsin-1 condensation, which is the generation of interphase pH gradients realized via differential partitioning of protons between coexisting phases. This pH gradient is likely to be directly relevant for vesicular ATPase functions and the loading of neurotransmitters. Our study highlights how conserved IDR grammars serve as drivers of synapsin-1 condensation.

Approximately one-third of global CO 2 assimilation is performed by the pyrenoid 1 , a liquid-like organelle found in most algae and some plants 2 . Specialized membranes are hypothesized to drive CO 2 assimilation in the pyrenoid by delivering concentrated CO 2 3,4 , but their biogenesis and function have not been experimentally characterized. Here, we show that homologous proteins SAGA1 and MITH1 mediate the biogenesis of the pyrenoid membrane tubules in the model alga Chlamydomonas reinhardtii and are sufficient to reconstitute pyrenoid-traversing membranes in a heterologous system, the plant Arabidopsis thaliana . SAGA1 localizes to the regions where thylakoid membranes transition into tubules and is necessary to initiate tubule formation. MITH1 localizes to the tubules and is necessary for their extension through the pyrenoid. Tubule-deficient mutants exhibit growth defects under CO 2 -limiting conditions, providing evidence for the function of membrane tubules in CO 2 delivery to the pyrenoid. Furthermore, these mutants form multiple aberrant condensates of pyrenoid matrix, indicating that a normal tubule network promotes the coalescence of a single pyrenoid. The reconstitution of pyrenoid-traversing membranes in a plant represents a key milestone toward engineering a functional pyrenoid into crops for improving crop yields. More broadly, our study demonstrates the functional importance of pyrenoid membranes, identifies key biogenesis factors, and paves the way for the molecular characterization of pyrenoid membranes across the tree of life.

The existence of multiple biomolecular condensates inside living cells is a peculiar phenomenon not compatible with the predictions of equilibrium statistical mechanics. In this work, we address the problem of multiple condensates state (MCS) from a functional perspective. We combine Langevin dynamics, reaction-diffusion simulation, and dynamical systems theory to demonstrate that MCS can indeed be a function optimization strategy. Using Arp2/3 mediated actin nucleation pathway as an example, we show that actin polymerization is maximum at an optimal number of condensates. For a fixed amount of Arp2/3, MCS produces a greater response compared to its single condensate counterpart. Our analysis reveals the functional significance of the condensate size distribution which can be mapped to the recent experimental findings. Given the spatial heterogeneity within condensates and non-linear nature of intracellular networks, we envision MCS to be a generic functional solution, so that structures of network motifs may have evolved to accommodate such configurations.

Reduced dynamicity and increased high-order protein assemblies in dense fibrillar component of the nucleolus under cellular senescence

Cells contain multiple condensates which spontaneously form due to the heterotypic interactions between their components. Although the proteins and disordered region sequences that are responsible for condensate formation have been extensively studied, the rule of interactions between the components that allow demixing, i.e., the coexistence of multiple condensates, is yet to be elucidated. Here, we construct an effective theory of the interaction between heteropolymers by fitting it to the molecular dynamics simulation results obtained for more than 200 sequences sampled from the disordered regions of human proteins. We find that the sum of amino acid pair interactions across two heteropolymers predicts the Boyle temperature qualitatively well, which can be quantitatively improved by the dimer pair approximation, where we incorporate the effect of neighboring amino acids in the sequences. The improved theory, combined with the finding of a metric that captures the effective interaction strength between distinct sequences, allowed the selection of up to three disordered region sequences that demix with each other in multicomponent simulations, as well as the generation of artificial sequences that demix with a given sequence. The theory points to a generic sequence design strategy to demix or hypermix thanks to the low-dimensional nature of the space of the interactions that we identify. As a consequence of the geometric arguments in the space of interactions, we find that the number of distinct sequences that can demix with each other is strongly constrained, irrespective of the choice of the coarse-grained model. Altogether, we construct a theoretical basis for methods to estimate the effective interaction between heteropolymers, which can be utilized in predicting phase separation properties as well as rules of assignment in the localization and functions of disordered proteins. Published by the American Physical Society 2024

Liquid–liquid phase separation plays a major role in the formation and maintenance of various membrane-less subcellular structures in the cytoplasm and nucleus of cells. Biological condensates contain enhanced concentrations of proteins and RNA, many of which can be continually exchanged with the surrounding medium. Coarsening is an important step in the kinetics of phase separation, whereby an emulsion of polydisperse condensates transitions to a single condensate in thermodynamic equilibrium with a surrounding dilute phase. A key feature of biological phase separation is the co-existence of multiple condensates over significant time scales, which is consistent with experimental observations showing a slowing of coarsening rates. It has recently been proposed that one rate limiting step could be the slow interfacial conversion of a molecular constituent between the dilute and dense phases. In this paper, we analyse conversion-limited phase separation within the framework of diffusion in singularly perturbed domains, which exploits the fact that biological condensates tend to be much smaller than the size of a cell. Using matched asymptotic analysis, we solve the quasi-static diffusion equation for the concentration in the dilute phase, and then derive kinetic equations for the slow growth/shrinkage of the condensates. This provides a systematic way of obtaining corrections to mean-field theory that take into account the geometry of the cell and the locations of all the condensates.

We undertake a systematic study of the 4-dimensional SU(N) 2-index chiral gauge theories and investigate their faithful global symmetries and dynamics. These are a finite set of theories with fermions in the 2-index symmetric and anti-symmetric representations, with no fundamentals, and they do not admit a large-N limit. We employ a combination of perturbative and nonperturbative methods, enabling us to constrain their infrared (IR) phases. Specifically, we leverage the ’t Hooft anomalies associated with continuous and discrete groups to eliminate a few scenarios. In some cases, the anomalies rule out the possibility of fermion composites. In other cases, the interplay between the continuous and discrete anomalies leads to multiple higher-order condensates, which inevitably form to match the anomalies. Further, we pinpoint the most probable symmetry-breaking patterns by searching for condensates that match the full set of anomalies resulting in the smallest number of IR degrees of freedom. Higher-loop β-function analysis suggests that a few theories may flow to a conformal fixed point.

DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites

Cellular proteins act as surfactants to control the interfacial behavior and function of biological condensates.

The Polycomb group (PcG) complex PRC1 localizes in the nucleus in condensed structures called Polycomb bodies. The PRC1 subunit Polyhomeotic (Ph) contains an oligomerizing sterile alpha motif (SAM) that is implicated in both PcG body formation and chromatin organization in Drosophila and mammalian cells. A truncated version of Ph containing the SAM (mini-Ph) forms phase-separated condensates with DNA or chromatin in vitro, suggesting that PcG bodies may form through SAM-driven phase separation. In cells, Ph forms multiple small condensates, while mini-Ph typically forms a single large nuclear condensate. We therefore hypothesized that sequences outside of mini-Ph, which are predicted to be intrinsically disordered, are required for proper condensate formation. We identified three distinct low-complexity regions in Ph based on sequence composition. We systematically tested the role of each of these sequences in Ph condensates using live imaging of transfected Drosophila S2 cells. Each sequence uniquely affected Ph SAM-dependent condensate size, number, and morphology, but the most dramatic effects occurred when the central, glutamine-rich intrinsically disordered region (IDR) was removed, which resulted in large Ph condensates. Like mini-Ph condensates, condensates lacking the glutamine-rich IDR excluded chromatin. Chromatin fractionation experiments indicated that the removal of the glutamine-rich IDR reduced chromatin binding and that the removal of either of the other IDRs increased chromatin binding. Our data suggest that all three IDRs, and functional interactions among them, regulate Ph condensate size and number. Our results can be explained by a model in which tight chromatin binding by Ph IDRs antagonizes Ph SAM-driven phase separation. Our observations highlight the complexity of regulation of biological condensates housed in single proteins.

The interference of multiple condensates coexisting in one system may lead to unconventional coherent behavior. This is expected when the spatial lengths of the condensates are essentially different. Traditionally, the characteristic spatial length of a superconducting condensate is associated with the gap function. However, the broader readership is more familiar with the concept of the Cooper-pair wave function. For conventional single-band superconductors, the gap function coincides with the center-of-mass Cooper-pair wave function up to the coupling constant, and the corresponding gap and wave function characteristic lengths are the same. Surprisingly, we find that in two-band superconductors, these lengths are the same only near the critical temperature. At lower temperatures, they can significantly deviate from each other, and the fundamental question of which of these lengths should be preferred when specifying the spatial scale of a band-dependent condensate in multiband superconducting materials arises.

We provide a framework to solve generic models describing the dissociation of multiple molecular Bose-Einstein condensates in a nonadiabatic regime. The competition between individual chemical reactions can lead to non-trivial dependence on critical components such as path interference and symmetries, thus, affecting the final distribution of atomic population. We find an analytical solution for an illustrative example model involving four atomic modes. When the system parameters satisfy $CPT$ symmetry, where $C$ is charge conjugation, $P$ is parity, and $T$ is time-reversal symmetry, our solution predicts a population imbalance between atomic modes that is exponentially sensitive to system parameters. However, a weakly broken symmetry alters the population in each atomic mode and can reverse the population imbalance. Our solution also demonstrates a strong quantum correlation between atomic modes that leads to the spontaneous production of atoms in a multi-mode squeezed state. Moreover, in our framework, a time-dependent non-Hermitian quantum mechanics naturally manifests which can alternatively be realized experimentally in photonic systems.

Illumination of light on matter normally causes heating and destroys the ordered ground states. Despite this common understanding, recent advances in ultrafast light sources have enabled the non-thermal control of quantum phases. Here, we report the light-induced enhancement of superconductivity in a thin film of an iron chalcogenide FeSe0.5Te0.5, which exhibits multiple quantum condensates associated with the multi-orbital character. Upon the photoexcitation, we observed a transient increase of the superfluid density as indicated by the optical conductivity in the frequency range of superconducting gaps. The light-induced enhancement of superconductivity is further corroborated by the photoinduced enhancement of terahertz third harmonic generation, which is accounted for by the Higgs mode response. The ultrafast dynamics of two superfluid components revealed by frequency- and time-resolved terahertz measurements indicate the interplay between the condensates through the interband Cooper pairings while suggesting the potential tunability of the pairing interaction by light in the ultrafast timescale.