Biology subjects

Spruijt, E.

Publications and source records attributed to Spruijt, E..

8 recordsLinked to original sources

bioRxiv2025

Amino acids bind to phase-separating proteins and modulate biomolecular condensate stability and dynamics

AbstractBiomolecular condensates (BCs) are versatile intracellular compartments that help organize intracellular space and perform diverse biological functions. In living cells, BCs are surrounded by a complex environment, of which amino acids (AAs) are prominent components. However, it is unclear how AAs interact with condensate components and influence the formation and material properties of condensates. Here, we show that phase separation is suppressed with increasing glycine concentration by using model heterotypic condensates made of nucleophosmin 1 (NPM1) and ribosomal ribonucleic acid (RNA): the condensate density is decreased and the dynamics inside the condensate are increased. We find that glycine weakly binds to amide groups in the protein backbone and aromatic groups in the side chains with a 1[~]2 M affinity, weakening the backbone-backbone interactions between neutral and charged disordered proteins while strengthening the interactions between aromatic stickers. This leads to different modulations of the phase behaviour in condensates formed by cation/{pi}-{pi} interactions and condensates formed by charge complexation. We further show that a similar modulation effect on BCs is observed for other proteinogenic AAs and can be transferred to short peptides. These insights offer a better understanding of BC stability, with implications for new strategies to modulate the dynamic properties of BCs in vivo.

biophysics↗

bioRxiv2025

Patching up the nucleus: a novel role for PMLII in nuclear envelope rupture repair

The nuclear envelope (NE) is important for cellular health as it protects and organizes the genome. NE dynamics is important for various cellular processes including cell growth, migration and removal of defective NE components. In extreme cases, the NE can rupture leading to exchange of material between the nuclear interior and the cytoplasm. Rapid repair of the NE is initiated to minimize the effect on the genome. While our understanding of the machinery involved in this repair process is increasing, a lot is still unknown about this process including events leading up to NE rupture. Interestingly, biomolecular condensates have recently been found to play important roles in membrane repair and remodelling in cells. Here, we found that promyelocytic leukemia protein isoform II (PMLII), a protein involved in nuclear PML body formation, forms condensates at the NE. These condensates specifically form at sites where the lamina is disrupted. We show that NE rupture often occurs at these sites and that PMLII stays present until rupture repair is initiated suggesting a role in stabilization of the site for effective repair.

cell biology↗

bioRxiv2024

Selective ion binding and uptake shape the microenvironment of biomolecular condensates

Biomolecular condensates modulate various ion-dependent cellular processes and can regulate subcellular ion distributions by selective uptake of ions. However, the molecular grammar governing condensate-ion interactions is poorly understood. Here, we use NMR spectroscopy of ions and model condensate components to quantify and spatially resolve selective ion binding to condensates and show that these interactions follow the law of matching water affinities, resulting in strong binding between proteins and chaotropic anions, and between nucleic acids and kosmotropic cations. Ion uptake into condensates directly follows binding affinities, resulting in selective uptake of strong-binding ions, but exclusion of weak-binding ions. Ion binding further shapes the condensate microenvironment by altering the composition, viscosity and interface potential. Such changes can have profound effects on biochemical processes taking place inside condensates, as we show for RNA duplex formation. Our findings provide a new perspective on the role of condensate-ion interactions in cellular bio- and electrochemistry and may aid design of condensate-targeting therapeutics.

biophysics↗

bioRxiv2024

Controlling interfacial protein adsorption, desorption and aggregation in biomolecular condensates

The aggregation of amyloidogenic proteins is linked to age-related diseases. The presence of interfaces can affect their aggregation mechanism, often speeding up aggregation. -Synuclein (Syn) can adsorb to biomolecular condensates, leading to heterogenous nucleation and faster aggregation. Understanding the mechanism underlying localization of amyloidogenic proteins at condensate interfaces is crucial for developing strategies to prevent or reverse their binding. We show that Syn localization to the surface of peptide-based heterotypic condensates is an adsorption process governed by the proteins condensate-amphiphilic nature. Adsorption occurs in multiple layers and levels off at micromolar concentrations. Based on these findings, we design three strategies to modulate Syn accumulation: (i) addition of biomolecules that decrease the condensate {zeta}-potential, such as NTPs and RNA, (ii) competitive adsorption of proteins targeting the condensate interface, such as G3BP1, DDX4-YFP, EGFP-NPM1, Hsp70, Hsc70, and (iii) preferential adsorption of Syn to membranes. Removing Syn from the condensate interface slows aggregation, highlighting potential cellular control over protein adsorption and implications for therapeutic strategies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/619145v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@159b012org.highwire.dtl.DTLVardef@1369671org.highwire.dtl.DTLVardef@ced970org.highwire.dtl.DTLVardef@2578b0_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

Dynamics and composition of small heat shock protein condensates and aggregates

Small heat shock proteins (sHSPs) are essential ATP-independent chaperones that protect the cellular proteome during stress. These proteins assemble into polydisperse oligomeric structures, the composition of which dramatically affects their chaperone activity. The biomolecular consequences of variations in sHSP ratios, especially inside living cells, remain elusive. Here, we study the consequences of altering the relative expression levels of HspB2 and HspB3. These chaperones are partners in a hetero-oligomeric complex, and genetic mutations that abolish their mutual interaction are associated with myopathic disorders. HspB2 displays three distinct phenotypes when co-expressed with HspB3 at varying ratios. Expression of HspB2 alone lead to formation of liquid nuclear condensates, while shifting the stoichiometry towards HspB3 resulted in the formation of large solid-like aggregates. Only cells co-expressing HspB2 with a limited amount of HspB3 showed a homogeneous nuclear distribution of HspB2. Strikingly, both condensates and aggregates were reversible, as shifting the HspB2:HspB3 balance in situ resulted in dissolution of these structures. To uncover the molecular composition of HspB2 condensates and aggregates, we used APEX-mediated proximity labelling. Most proteins interact transiently with the condensates and were neither enriched nor depleted. In contrast, we found that HspB2:HspB3 aggregates sequestered several disordered proteins among which autophagy factors, suggesting that the cell is actively attempting to clear these aggregates. This study presents a striking example of how changes in the relative expression levels of interacting proteins affects their phase behavior. Our approach can be a useful tool to study the role of protein stoichiometry in other biomolecular condensates. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/519563v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@bf5787org.highwire.dtl.DTLVardef@b7a18org.highwire.dtl.DTLVardef@17cd64corg.highwire.dtl.DTLVardef@d9392a_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- Small heat shock protein hetero-oligomerization affects their chaperone function - The HspB2:HspB3 expression ratio determines phase separation and aggregation - HspB2 condensates and HspB2:HspB3 aggregates are fully reversible - Proximity labelling unveils autophagy factor recruitment to HspB2:HspB3 aggregates - Stoichiometry-dependant regulation of phase behaviour may be widespread in biology

molecular biology↗

bioRxiv2022

Crowding-induced phase separation and solidification by co-condensation of PEG in NPM1-rRNA condensates

The crowdedness of the cell calls for adequate intracellular organization. Biomolecular condensates, formed by liquid-liquid phase separation of intrinsically disordered proteins and nucleic acids, are important organizers of cellular fluids. To underpin the molecular mechanisms of protein condensation, cell-free studies are often used where the role of crowding is not investigated in detail. Here, we investigate the effects of macromolecular crowding on the formation and material properties of a model heterotypic biomolecular condensate, consisting of nucleophosmin (NPM1) and ribosomal RNA (rRNA). We studied the effect of the macromolecular crowding agent PEG, which is often considered an inert crowding agent. We observed that PEG could induce both homotypic and heterotypic phase separation of NPM1 and NPM1-rRNA, respectively. Crowding increases the condensed concentration of NPM1 and decreases its equilibrium dilute phase concentration, while no significant change in the concentration of rRNA in the dilute phase was observed. Interestingly, the crowder itself is concentrated in the condensates, suggesting that co-condensation rather than excluded volume interactions underlie the enhanced phase separation by PEG. Fluorescence recovery after photobleaching (FRAP) measurements indicated that both NPM1 and rRNA become immobile at high PEG concentrations, indicative of a liquid-to-gel transition. Together, these results shed new light onto the role of synthetic crowding agents in phase separation, and demonstrate that condensate properties determined in vitro depend strongly on the addition of crowding agents. STATEMENT OF SIGNIFICANCELiquid-liquid phase separation of proteins and nucleic acids leads to the formation of biomolecular condensates. To mimic biomolecular condensates in vitro, polymeric crowding agents, such as PEG, are often added. Such crowding agents are considered to make in vitro solutions more physiologically relevant, by mimicking the high cellular macromolecule concentrations. However, these crowding agents are commonly selected for their commercial availability and solubility in water, and their influence on phase separation and the physicochemical properties of condensates are seldom studied. Here we use biophysical methods to show that PEG induces phase separation of a model condensate through co-condensation rather than volume exclusion. As a consequence, crowding changes the partitioning, concentrations and viscoelastic properties of the condensates significantly, which sheds new light onto studies aimed at quantifying the material properties of biomolecular condensates.

biophysics↗

bioRxiv2022

Biomolecular condensates can both accelerate and suppress aggregation of α-synuclein

Biomolecular condensates present in cells can fundamentally affect the aggregation of amyloidogenic proteins and play a role in the regulation of this process. While liquid-liquid phase separation of amyloidogenic proteins by themselves can act as an alternative nucleation pathway, interaction of partly disordered aggregation-prone proteins with pre-existing condensates that act as localization centers could be a far more general mechanism of altering their aggregation behavior. Here, we show that so-called host biomolecular condensates can both accelerate and slow down amyloid formation. We study the amyloidogenic protein -synuclein and two truncated -synuclein variants in the presence of three types of condensates composed of non-aggregating peptides, RNA or ATP. Our results demonstrate that condensates can dramatically speed up amyloid formation when proteins localize to their interface. However, condensates can also significantly suppress aggregation by sequestering and stabilizing amyloidogenic proteins, thereby providing living cells with a possible protection mechanism against amyloid formation.

biophysics↗

bioRxiv2021

ATP:Mg2+ shapes condensate properties of rRNA-NPM1 in vitro nucleolus model and its partitioning of ribosomes

Nucleoli have viscoelastic gel-like condensate dynamics that are not well represented in vitro. Nucleoli models, such as those formed by nucleophosmin 1 (NPM1) and ribosomal RNA (rRNA), exhibit condensate dynamics orders of magnitude faster than in vivo nucleoli. Here we show that an interplay between magnesium ions (Mg2+) and ATP governs rRNA dynamics, and this ultimately shapes the physical state of these condensates. Using quantitative fluorescence microscopy, we demonstrate that increased RNA compaction occurs in the condensates at high Mg2+ concentrations, contributing to the slowed RNA dynamics. At Mg2+ concentrations above 7 mM, rRNA is fully arrested and the condensates are gels. Below the critical gel point, NPM1-rRNA droplets age in a temperature-dependent manner, suggesting that condensates are viscoelastic materials, undergoing maturation driven by weak multivalent interactions. ATP addition reverses the dynamic arrest of rRNA, resulting in liquefaction of these gel-like structures. Surprisingly, ATP and Mg2+ both act to increase partitioning of NPM1-proteins as well as rRNA, which influences the partitioning of small client molecules. By contrast, larger ribosomes form a halo around NPM1-rRNA coacervates when Mg2+ concentrations are higher than ATP concentrations. Within cells, ATP levels fluctuate due to biomolecular reactions, and we demonstrate that a dissipative enzymatic reaction can control the biophysical properties of in vitro condensates through depletion of ATP. This enzymatic ATP depletion also reverses the formation of the ribosome halos. Our results illustrate how cells, by changing local ATP concentrations, may regulate the state and client partitioning of RNA-containing condensates such as the nucleolus. Significance StatementO_LIThere is a significant discrepancy between the dynamics of in vitro nucleolus models and in vivo nucleoli - with the latter more gel-like. C_LIO_LIThe interplay between Mg2+ ions, ATP and the nucleolus components - specifically RNA - governs the dynamics, and ultimately the physical state, of nucleolus-like condensates. C_LIO_LIWe show that the nucleolus are dynamically adapting condensates, responding to local ATP concentrations through Mg2+-induced compaction of the RNA, and reversible relaxation when ATP binds Mg2+ again. Other condensates containing RNA probably respond in similar ways to Mg2+ and ATP. C_LI

biophysics↗