Biology subjects

Jahnel, M.

Publications and source records attributed to Jahnel, M..

8 recordsLinked to original sources

bioRxiv2025

Droplet-assisted folding of long regulatory RNAs

Long regulatory RNA regions orchestrate complex cellular processes, including gene expression and epigenetic modifications. How these RNAs dynamically fold and refold in response to cellular signals remains poorly understood. Given that RNAs interact with ubiquitous RNA-binding proteins (RBPs) prone to form biomolecular condensates, we explore how protein droplets interacting along an RNA impact its folding process. Attached droplets prevent premature folding by competing with RNA:RNA interactions. When droplets dissolve due to cellular signals, capillary effects cause the RNA to collapse while refolding. We test this process of condensate-guided RNA folding by adapting established RNA secondary structure predictors to mimic various folding pathways and supplement this with coarse-grained simulations. We find that interactions with transient droplets robustly leads to the formation of long-range RNA contacts, which are otherwise hard to achieve. Our results compare favorably with available experimental data. We propose that this strategy, which we call droplet-assisted RNA folding, represents a previously unexplored mechanism for shaping RNA structures. Given the widespread propensity of RBPs to form condensates, this process could play a fundamental role in the structural organization, conditional reshaping, and functional regulation of long regulatory RNAs. SignificanceComplex non-coding RNA regions (e.g. lncRNAs, 3UTRs, etc.) perform several important functions in higher organisms. However, the longer an RNA, the more likely it is to misfold. How can such regulatory regions of more than 1000 nts be reliably folded, considering that premature co-transcriptional folding favors local interactions? We present a mechanism by which biomolecular condensates of RNA-binding proteins (RBPs) assist and control the folding of complex RNAs. Here, droplets of RBPs nucleate around RNA binding motifs, prevent premature misfolding through their RNA chaperone function, and allow robust folding of initially distant regions through coordinated droplet dissolution and detachment. This mechanism provides an alternative perspective on how long RNAs acquire their structures in a context that is functionally dynamic.

molecular biology↗

bioRxiv2022

GTPase-dependent cyclic flexibility transitions drive the two-component EEA1-Rab5 molecular motor

The recognition of vesicles by their correct target compartment depends on the pairing of small GTPases with effector proteins (1-3). Whereas ATPases can cyclically convert the free energy of ATP hydrolysis into mechanical work, the function of small GTPases is predominantly associated with signal transduction processes, and their role in mechano-transduction is less established (4-6). However, binding of the GTPase Rab5 to the long coiled-coil tethering protein EEA1 on an early endosome induces a rigidity transition resulting in a large conformational change in EEA1 from a rigid and extended to a flexible and collapsed state. This entropic collapse of EEA1 gives rise to an effective force that can pull tethered membranes closer (7). It currently remains unclear if EEA1 can return from the collapsed to the extended conformation without the aid of chaperones. Here, we use fluorescence correlation spectroscopy to reveal that EEA1 in bulk solution can undergo multiple flexibility transition cycles that are associated with the binding and release of Rab5(GTP) and Rab5(GDP). Using semi-flexible polymer theory we provide evidence that the cyclic transitioning of Rab5-EEA1 between extended and collapsed conformations is driven by the energetics of Rab5 binding/unbinding and GTP hydrolysis. Cyclic flexibility transitions represent a complete mechanical work cycle that is able to perform up to 20 kBT of mechanical work per cycle, against an opposing force. Hence, Rab5 and EEA1 constitute a two-component molecular motor driven by the chemical energy derived from GTP hydrolysis by Rab5. We conclude that coiled-coil tethering proteins and their small GTPase partners can have active mechanical roles in membrane trafficking.

biophysics↗

bioRxiv2021

HspB8 prevents aberrant phase transitions of FUS by chaperoning its folded RNA binding domain

Aberrant liquid-to-solid phase transitions of biomolecular condensates have been linked to various neurodegenerative diseases. However, the underlying molecular interactions that drive aging remain enigmatic. Here, we develop quantitative time-resolved crosslinking mass spectrometry to monitor protein interactions and dynamics inside condensates formed by the protein fused in sarcoma (FUS). We identify misfolding of the RNA recognition motif (RRM) of FUS as a key driver of condensate ageing. We demonstrate that the small heat shock protein HspB8 partitions into FUS condensates via its intrinsically disordered domain and prevents condensate hardening via condensate-specific interactions that are mediated by its -crystallin domain (CD). These CD-mediated interactions are altered in a disease-associated mutant of HspB8, which abrogates the ability of HspB8 to prevent condensate hardening. We propose that stabilizing aggregation-prone folded RNA-binding domains inside condensates by molecular chaperones may be a general mechanism to prevent aberrant phase transitions.

biochemistry↗

bioRxiv2021

The arrested state of processing bodies supports mRNA regulation in early development

Biomolecular condensates that form via liquid-liquid phase separation can exhibit diverse physical states. Despite considerable progress, the relevance of condensate physical states for in vivo biological function remains limited. Here, we investigated the physical properties of in vivo processing bodies (P bodies) and their impact on mRNA storage in mature Drosophila oocytes. We show that the conserved DEAD-box RNA helicase Me31B forms P body condensates which adopt a less dynamic, arrested physical state. We demonstrate that structurally distinct proteins and hydrophobic and electrostatic interactions, together with RNA and intrinsically disordered regions, regulate the physical properties of P bodies. Finally, using live imaging, we show that the arrested state of P bodies is required to prevent the premature release of bicoid (bcd) mRNA, a body axis determinant, and that P body dissolution leads to bcd release. Together, this work establishes a role for arrested states of biomolecular condensates in regulating cellular function in a developing organism.

cell biology↗

bioRxiv2020

Thermal fluctuations assist mechanical signal propagation in coiled-coil proteins

Recently it has been shown that the long coiled-coil membrane tether protein Early Endosome Antigen 1 (EEA1) switches from a rigid to a flexible conformation upon binding of a signaling protein to its free end. This flexibility switch represents a novel motor-like activity, allowing EEA1 to generate a force that moves vesicles closer to the membrane they will fuse with. To elucidate how binding of a single signaling protein can globally change the stiffness of a 200 nm long chain, we propose a simplified description of the coiled-coil as a one-dimensional Frenkel-Kontorova chain. Using numerical simulations, we find that an initial perturbation of the chain can propagate along its whole length in the presence of thermal fluctuations, changing the configuration of the entire molecule and thereby affecting its stiffness. Our work sheds light onto intramolecular communication and force generation in long coiled-coil proteins.

biophysics↗

bioRxiv2020

Single particle zeta-potential measurements reveal the role of electrostatics in protein condensate stability

Liquid-liquid phase separation underlies the formation of biological condensates. Physically, such systems are microemulsions which have a general propensity to fuse and coalesce; however, many condensates persist as independent droplets inside cells. This stability is crucial for their functioning, but the physicochemical mechanisms that control the emulsion stability of condensates remain poorly understood. Here, by combining single-condensate zeta potential measurements, optical microscopy, tweezer experiments, and multiscale molecular modelling, we investigate how the forces that sustain condensates impact their stability against fusion. By comparing PR25:PolyU and FUS condensates, we show that a higher condensate surface charge correlates with a lower fusion propensity, and that this behavior can be inferred from their zeta potentials. We reveal that overall stabilization against fusion stems from a combination of repulsive forces between condensates and the effects that surface electrostatics have on lowering surface tension, thus shedding light on the molecular determinants of condensate coalescence.

biophysics↗

bioRxiv2019

Small molecules for modulating protein driven liquid-liquid phase separation in treating neurodegenerative disease

Neurodegenerave diseases such as amyotrophic lateral sclerosis (ALS) are oten associated with mutaons in proteins that are associated with stress granules. Stress granules are condensates formed by liquid-liquid phase separaon which, when aberrant, can lead to altered condensaon behaviours and disease phenotypes. Here, we identified lipoamide, a small molecule which specifically prevents cytoplasmic condensaon of stress granule proteins. Thermal proteome profiling showed that lipoamide preferentially stabilises intrinsically disordered domain-containing proteins. These include SRSF1 and SFPQ, stress granule proteins necessary for lipoamide activity. The redox state of SFPQ correlates with its condensate-dissolving behaviour, in concordance with the importance of the dithiolane ring for lipoamide activity. In animals, lipoamide ameliorates aging-associated aggregaon of a stress granule reporter, improves neuronal morphology, and recovers motor defects caused by expression of ALS-associated FUS and TDP-43 mutants. In conclusion, lipoamide is a well-tolerated small molecule modulator of stress granule condensaon and dissection of its molecular mechanism identified a cellular pathway for redox regulaon of stress granule formaon.

cell biology↗

bioRxiv2017

Local Nucleation Of Microtubule Bundles Through Tubulin Concentration Into A Condensed Tau Phase

Non-centrosomal microtubule bundles play important roles in cellular organization and function. Although many diverse proteins are known that can bundle microtubules, biochemical mechanisms by which cells could locally control the nucleation and formation of microtubule bundles are understudied. Here, we demonstrate that concentration of tubulin into a condensed, liquid-like compartment composed of the unstructured neuronal protein tau is sufficient to nucleate microtubule bundles. We show that under conditions of macro-molecular crowding, tau forms liquid drops. Tubulin partitions into these drops, efficiently increasing tubulin concentration and driving the nucleation of microtubules. These growing microtubules form bundles enclosed in a liquid sheath of tau. Our data suggest that condensed compartments of microtubule bundling proteins could promote the local formation of microtubule bundles in neurons by acting as non-centrosomal microtubule nucleation centers, and that liquid-like tau encapsulation could provide both stability and plasticity to long axonal microtubule bundles.

cell biology↗