Biology subjects

Fuxreiter, M.

Publications and source records attributed to Fuxreiter, M..

8 recordsLinked to original sources

bioRxiv2026

The glycine-arginine-rich motif of 53BP1 modulates RNA interactions necessary for its liquid-liquid phase separation during DNA Damage Response

The DNA damage response relies on the rapid assembly of repair factors into foci with properties of liquid-liquid phase separation, driven by de novo transcription of damage-induced RNAs. 53BP1 is a key component of these condensates, yet the molecular determinants driving this process remain unknown. Here, through computational, structural and in vitro approaches, we identify the oligomerization domain of 53BP1 and its glycine-arginine-rich (GAR) motif as crucial for RNA interactions and phase separation. Biophysical characterization reveals that 53BP1-RNA condensates can progressively mature into a more stable state, and that GAR mutants display aberrant material properties. Using a cellular model of telomere fusion events, we demonstrate that the GAR motif is essential for 53BP1-mediated DNA repair, which depends on the combined contributions of RNA binding and appropriate condensate biophysical properties. Therefore, RNA-driven 53BP1 condensation is functionally required to maintain genome integrity.

biophysics↗

bioRxiv2024

Arc mediates intercellular tau transmission via extracellular vesicles

Intracellular neurofibrillary tangles that consist of misfolded tau protein1 cause neurodegeneration in Alzheimers disease (AD) and frontotemporal dementia (FTD). Tau pathology spreads cell-to-cell2 but the exact mechanisms of tau release and intercellular transmission remain poorly defined. Tau is released from neurons as free protein or in extracellular vesicles (EVs)3-5 but the role of these different release mechanisms in intercellular tau transmission is unclear. Here, we show that the neuronal gene Arc is critical for packaging tau into EVs. Brain EVs purified from human tau (hTau) transgenic rTg4510 mice (rTgWT) contain high levels of hTau that are capable of seeding tau pathology. In contrast, EVs purified from rTgWT crossed with Arc knock-out mice (rTgArc KO) have significantly less hTau and cannot seed tau aggregation. Arc facilitates the release of hTau in EVs produced via the I-BAR protein IRSp53, but not free tau. Arc protein directly binds hTau to form a fuzzy complex that we identified in both mouse and human brain tissue. We find that pathological intracellular hTau accumulates in neurons in rTgArc KO mice, which correlates with accelerated neuron loss in the hippocampus. Finally, we find that intercellular tau transmission is significantly abrogated in Arc KO mice. We conclude that Arc-dependent release of tau in EVs plays a significant role in intracellular tau elimination and intercellular tau transmission.

neuroscience↗

bioRxiv2024

Towards universal models for collective interactions in biomolecular condensates

A wide-range of higher-order structures, including dense, liquid-like assemblies, serve as key components of cellular matter. The molecular language of how protein sequences encode the formation and biophysical properties of biomolecular condensates, however, is not completely understood. Recent notion on the scale invariance of the cluster sizes below the critical concentration for phase separation suggests a universal mechanism, which can operate from oligomers to non-stoichiometric assemblies. Here we propose a model for collective interactions in condensates, based on context-dependent, variable interactions. We provide the mathematical formalism, which is capable describing growing dynamic clusters as well as changes in their material properties. Furthermore, we discuss the consequences of the model to maximise sensitivity to the environmental signals and to increase correlation lengths.

systems biology↗

bioRxiv2023

A scale-invariant log-normal droplet size distribution below the critical concentration for protein phase separation

Many proteins have been recently shown to undergo a process of phase separation that leads to the formation of biomolecular condensates. Intriguingly, it has been observed that some of these proteins form dense droplets of sizeable dimensions already below the critical concentration, which is the concentration at which phase separation occurs. To understand this phenomenon, which is not readily compatible with classical nucleation theory, we investigated the properties of the droplet size distributions as a function of protein concentration. We found that these distributions can be described by a scale-invariant log-normal function with an average that increases progressively as the concentration approaches the critical concentration from below. The results of this scaling analysis suggest the existence of a universal behaviour independent of the sequences and structures of the proteins undergoing phase separation. While we refrain from proposing a theoretical model here, we suggest that any model of protein phase separation should predict the scaling exponents that we reported here from the fitting of experimental measurements of droplet size distributions. Furthermore, based on these observations, we show that it is possible to use the scale invariance to estimate the critical concentration for protein phase separation.

biophysics↗

bioRxiv2021

Proteome-wide landscape of solubility limits in a bacterial cell

Proteins are prone to aggregate when they are expressed above their solubility limits, a phenomenon termed supersaturation. Aggregation may occur as proteins emerge from the ribosome or after they fold and accumulate in the cell, but the relative importance of these two routes remain poorly known. Here, we systematically probed the solubility limits of each Escherichia coli protein upon overexpression using an image-based screen coupled with machine learning. The analysis suggests that competition between folding and aggregation from the unfolded state governs the two aggregation routes. Remarkably, the majority (70%) of insoluble proteins have low supersaturation risks in their unfolded states and rather aggregate after folding. Furthermore, a substantial fraction ([~]35%) of the proteome remain soluble at concentrations much higher than those found naturally, indicating a large margin of safety to tolerate gene expression changes. We show that high disorder content and low surface stickiness are major determinants of high solubility and are favored in abundant bacterial proteins. Overall, our proteome-wide study provides empirical insights into the molecular determinants of protein aggregation routes in a bacterial cell.

molecular biology↗

bioRxiv2020

Frustration in protein complexes leads to interaction versatility

Disordered proteins can fold into a well-defined structure upon binding but these complexes are often fuzzy: the originally disordered partner adopts different binding modes when bound to different partners. Here we perform a systematic analysis of 160 proteins that form fuzzy complexes and demonstrate that the disordered partner displays a high degree of frustration in both the free and bound states. Although the folding of disordered regions upon binding reduces frustration relative to that of the unbound state, the interactions at the binding interface do not become fully optimized. In addition, we show that sub-optimal interactions lead to alternative frustration patterns in the complexes with different partners. These results demonstrate that disordered proteins do not always achieve fully optimal interactions in their complexes and their residual frustration leads to interaction versatility with different partners.

bioinformatics↗

bioRxiv2020

Observation of an α-synuclein liquid droplet state and its maturation into Lewy body-like assemblies

Misfolded -synuclein is a major component of Lewy bodies, which are a hallmark of Parkinsons disease. A large body of evidence shows that -synuclein can self-assemble into amyloid fibrils, but the relationship between amyloid formation and Lewy body formation still remains unclear. Here we show, both in vitro and in a C. elegans model of Parkinsons disease, that -synuclein undergoes liquid-liquid phase separation by forming a liquid droplet state, which converts into an amyloid-rich hydrogel. This maturation process towards the amyloid state is delayed in the presence of model synaptic vesicles in vitro. Taken together, these results suggest that the formation of Lewy bodies is linked to the arrested maturation of -synuclein condensates in the presence of lipids and other cellular components.

molecular biology↗

bioRxiv2019

Altered dynamics may drift pathological fibrillization in membraneless organelles

Protein phase transition can generate non-membrane bound cellular compartments, which can convert from liquid-like to solid-like states. While the molecular driving forces of phase separation have been largely understood, much less is known about the mechanisms of material-state conversion. We apply a recently developed algorithm to describe the weak interaction network of multivalent motifs, and simulate the effect of pathological mutations. We demonstrate that linker dynamics is critical to the material-state of biomolecular condensates. We show that linker flexibility/mobility is a major regulator of the weak, heterogeneous meshwork of multivalent motifs, which promotes phase transition and maintains a liquid-like state. Decreasing linker dynamics increases the propensity of amyloid-like fragments via hampering the motif-exchange and reorganization of the weak interaction network. In contrast, increasing linker mobility may compensate rigidifying mutations, suggesting that the meshwork of weak, variable interactions may provide a rescue mechanism from aggregation. Motif affinity, on the other hand, has a moderate impact on fibrillization. Here we demonstrate that the fuzzy framework provides an efficient approach to handle the intricate organization of membraneless organelles, and could also be applicable to screen for pathological effects of mutations.

bioinformatics↗