Biology subjects

Stelzl, L.

Publications and source records attributed to Stelzl, L..

6 recordsLinked to original sources

bioRxiv2026

A Phosphorylation-Induced Micellization switch in the low complexity domain of TDP-43

Abstract textPhase separation (PS) of the low-complexity domain (LCD) of TDP-43 is linked to pathogenic aggregates in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-TDP). Here, we show that extensive phosphorylation of the LCD C-terminus redirects its self-assembly. Coarse-grained Monte Carlo simulations predicted that 12 Ser phosphorylations partition the 148-residue LCD into a hydrophobic N-terminal and highly charged C-terminal block, favoring finite-sized micellization over macroscopic PS. In vitro, LCD phosphorylated by casein kinase 1 delta (CK1{delta}; mean of 12 phosphorylations by native mass spectrometry) and phosphomimetic 12D/12DD mutants formed spherical nanoparticles ({approx} 20-50 nm) above a low-micromolar critical micelle concentration, whereas the unphosphorylated LCD underwent reversible PS that matured into fibrils. Increasing ionic strength shifted the mutants toward anisotropic morphologies (worm-like 12D micelles and rigid 12DD nanocylinders). Turbidity assays and confocal imaging directly visualized the absence of PS in the phosphorylated form. Negative-stain and cryo-EM confirmed the spherical micellar architecture for the phosphorylated LCD and 12D/12DD mimics. Our data identify phosphorylation as a molecular switch tuning macrophase separation and fibril formation of TDP-43 LCD, providing a framework for an aggregation-protective role through microphase separation into size-limited micelles. Whether these assemblies are stable or kinetically trapped on pathological timescales remains unclear.

biophysics↗

bioRxiv2026

Phase separation behavior of TDP-43 governs its protein interactome and regulation of altern

TDP-43 is a nuclear RNA-binding protein that regulates RNA metabolism, including alternative splicing. Its aggregation is a major pathological hallmark of several neurodegenerative diseases. TDP-43 undergoes phase separation (PS) and this condensation behavior may be linked to aggregate formation. Whether and how PS governs TDP-43 RNA regulatory functions remains poorly understood. Here we utilized rationally designed mutations in the TDP-43 low complexity domain to tune TDP-43 PS, yielding a panel of TDP-43 variants with reduced propensity to form condensates (PS-deficient), and a panel forming irreversible, undynamic condensates (solid-like) in vitro and in cells. Two complementary interactomics approaches identified PS-dependent interactions between TDP-43 and key RNA regulatory factors, including splicing regulators and the RNA helicase UPF1, which show increased interactions with solid-like variants. Our results highlight that TDP-43 PS regulates RNA and protein homeostasis by modulating a subset of TDP-43-dependent alternative splicing events and by reshaping interactions with RNA regulatory factors.

biochemistry↗

bioRxiv2025

Proteolytic Control of an Auto-inhibitory Intrinsically Disordered Region Governs Small RNA Selectivity in Argonaute Proteins

Argonaute proteins are central to small RNA-mediated gene regulation, yet the mechanisms controlling their activity remain incompletely understood. We elucidate a novel regulatory mechanism governing small RNA loading into the C. elegans Argonaute proteins WAGO-1 and WAGO-3. We show that N-terminal intrinsically disordered regions (N-IDRs) of these proteins do not affect subcellular localization but play critical roles in small RNA loading. We demonstrate that the N-IDR-processing protease DPF-3 facilitates small RNA loading in a catalysis-independent manner. Catalysis by DPF-3 and a second protease APP-1 is required, however, for activity. Deletion of these N-IDRs results in loading of aberrant small RNA species that trigger erroneous gene silencing. Supported by atomistic molecular dynamics simulations, we propose a model in which N-IDRs can simultaneously act as tuneable gatekeepers that auto-inhibit small RNA loading and as regulators of Argonaute stability, representing a previously unrecognized layer of regulation in Argonaute activity in small RNA pathways.

molecular biology↗

bioRxiv2024

Entropy production constrains information throughput in gene regulation

Biochemical systems process signals through stochastic reaction dynamics that are inherently continuous in time and often exhibit memory, feedback, and nonequilibrium driving. At the same time, they are frequently modeled by effective reactions, e.g., multi-step processes such as transcription are treated as single events, while energetic bookkeeping is commonly omitted. Moreover, mesoscopic dissipation estimates are highly sensitive to whether coarse-graining and reservoir coupling are performed in a thermodynamically consistent way. Together, these features complicate the direct application of classical Shannon information theory and stochastic thermodynamics "as is" to biochemical reaction networks. This paper provides a self-contained route from first principles to a practically usable framework for studying information transmission through chemical reaction networks (CRNs) under energetic constraints. In particular, we discuss and extend the notions of classical information theory, methodically progressing to a level of generality that is necessary for the theme of causal communication through general CRNs. We then derive expressions for mutual information and directed information between bipartite CRN trajectories of disjoint sets of molecular species and show that the MI diverges without bipartiteness. These expressions account for cases in which different reactions are indistinguishable after projection to the respective subnetworks or where multiple driving mechanisms produce the same observable effect. We finally introduce a rigorous, operational Shannon-style continuous-time chemical communication model: messages are encoded by time-dependent chemostat protocols for a set of signaling molecules, the causal channel law is an immutable property of the reaction dynamics, and channel capacity is posed as an optimization over causal chemical encoders subject to thermodynamic costs of encoding and transmission. Trajectory information measures and the operational channel capacity are related by a Fano-type converse theorem. Complementary, we formulate the dual perspective of minimum-energy-per-bit necessary for reliable communication. A tractable promoter-switching example illustrates the practical application. Our work provides a formal and general framework to obtain universal energetic bounds for reliable communication in biochemical systems.

systems biology↗

bioRxiv2024

Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates

Understanding the condensation and aggregation of intrinsically disordered proteins in a non-equilibrium environment is crucial for unraveling many biological processes. Active enzymes catalyse many processes by consuming chemical fuels such as ATP. Enzymes called kinases phosphorylate disordered regions of proteins and thus profoundly affect their properties and interactions. Protein phosphorylation is implicated in neurodegenerative diseases and may modulate pathogenesis. However, how protein sequence and molecular recognition of a disordered protein by kinases determine phosphorylation patterns is not understood. In principle, molecular dynamics simulations hold the promise to resolve how phosphorylation affects disordered proteins and their assemblies. In practice, chemically-detailed simulations of enzymatic reactions and the dynamics of enzymes are highly challenging, in particular it is difficult to verify whether implementations of driven simulations are thermodynamically consistent. We can now address this problem with residue-level coarse-grained molecular dynamics simulations, integrating Metropolis Monte Carlo steps to model chemical reactions. Importantly, we show how to verify by Markov-state modeling that the realisation of a non-equilibrium steady state satisfies local-detailed balance. We investigate TDP-43 phosphorylation by the kinase CK1{delta} in simulations, examining patterns of phosphorylation and assessing its preventive role in chain aggregation, which may be a cytoprotective mechanism in neurodegenerative diseases. We find that the degree of residue phosphorylation is determined by sequence preference and charges, rather than by the position in the chain. The phosphorylation frequency is also affected by the phosphorylation patterns, since the interactions between CK1{delta} and TDP-43 actively change after each reaction. For TDP-43, our simulations show condensates dissolution through phosphorylation with kinases binding to the condensates and phosphorylating TDP-43 in the condensates.

biophysics↗

bioRxiv2023

An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis in Bombyx mori

Piwi-interacting RNAs (piRNAs) direct PIWI proteins to transposons to silence them, thereby preserving genome integrity and fertility. The piRNA population can be expanded in the ping-pong amplification loop. Within this process, piRNA-associated PIWI proteins (piRISC) enter the nuage to cleave target RNA, which is stimulated by Gtsf proteins. The resulting cleavage product gets loaded into an empty PIWI protein to form a new piRISC complex. However, for piRNA amplification to occur, it is required that new RNA substrates, Gtsf-piRISC and empty PIWI proteins are all in physical proximity. In this study we show that BmGtsf1L binds to piRNA-loaded BmAgo3 and co-localizes to BmAgo3-BmVreteno positive granules. Biochemical assays further revealed that conserved residues within the unstructured tail of BmGtsf1L directly interact with BmVreteno. Using a combination of AlphaFold modeling, atomistic molecular dynamics simulations and in vitro assays we identified a novel binding interface on a BmVreteno-eTudor domain, which is required for BmGtsf1L binding. Our study reveals that a single eTudor domain within BmVreteno provides two binding interfaces and thereby interconnects piRNA-loaded BmAgo3 and BmGtsf1L.

molecular biology↗