Biology subjects

Speck, T.

Publications and source records attributed to Speck, T..

7 recordsLinked to original sources

bioRxiv2026

Kinase-phosphatase cycles drive self-sustained oscillations of protein condensates

Phase-separated protein condensates organize biochemical processes in cells. ATP-driven enzymatic reactions can change the physical properties and even trigger the dissolution of such condensates. Here we use molecular simulations to show how ATP-driven kinase and phosphatase reactions modulate the organization of TDP-43 low complexity domain (LCD) condensates. TDP-43 phosphorylation is enhanced by condensation, as CK1{delta} preferentially binds to and acts in TDP-43 LCD condensates, whereas dephosphorylation by the phosphatase calcineurin occurs predominantly in the dilute phase. This differential recruitment of kinases and phosphatases, together with the slow redistribution of kinases into newly formed condensates, triggers oscillatory appearance and disappearance of TDP-43 LCD condensates. The oscillations are self-sustained, persisting at constant chemical driving, showing that an antagonistic kinase-phosphatase pair can endow a condensate with autonomous dynamics rather than only setting its structure.

biophysics↗

bioRxiv2026

BRD4, Mediator, and Pol II form heterogeneous condensates with distinct transcriptional and acetylation-dependent states

Transcriptional condensates at super-enhancers are thought to concentrate BRD4, Mediator, and RNA polymerase II (Pol II) to promote gene activation, yet their compositional organization and regulation remain poorly understood. We developed a high-throughput live-cell phenomics platform based on endogenous fluorescent tagging of BRD4, MED14 (Mediator), and POLR2A (Pol II) to systematically quantify transcriptional condensate states across >1,000 chemical perturbations. Contrary to prevailing models of largely co-occupied assemblies, we find compositionally heterogenous condensate populations. In particular, BRD4-only spots emerged as a prominent class that is depleted of Mediator and Pol II, enriched at chromatin, and resistant to transcription initiation inhibition. Mechanistically, compound screening coupled to mechanism-of-action analysis identifies histone acetylation as a dominant regulatory axis for BRD4-only spots: Bromodomain and Extra-Terminal motif (BET) and histone acetyltransferase inhibition selectively deplete BRD4-only condensates, while histone deacetylase inhibition expands them. Together, these findings support a model in which acetylation-dependent BRD4 condensates define a distinct chromatin-associated regulatory state that is separable from canonical transcriptionally engaged condensates. More broadly, our work establishes condensate composition as a quantitative phenotype and provides a scalable framework for systematically dissecting the regulation of condensates across perturbations, cell types, and disease contexts.

cell biology↗

bioRxiv2026

Active field theory approach to explain size control of transcriptional condensates

Transcription factors organize into liquid-like condensates to facilitate gene expression, yet the physical mechanisms governing their formation and properties remain poorly understood. We study the size statistics of transcriptional condensates in human HAP1 cells using widefield and super-resolution microscopy tagging the epigenetic reader BRD4. We find that hubs that appear monolithic in widefield resolve into clusters of smaller droplets that resist coarsening. We link this size control to Active Model B+, a non-equilibrium field theory that captures a regime of reverse Ostwald ripening out of thermal equilibrium. In this regime, chemically driven currents cause larger droplets to transfer mass back to smaller ones, stabilizing a state of microphase segregation. The observed exponential size distribution of BRD4 foci quantitatively matches our numerical simulations, suggesting a universal physical picture for the non-equilibrium self-limitation of cellular condensates.

biophysics↗

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

Force generation in the coiling tendrils of Passiflora caerulea

Tendrils of climbing plants coil along their length and thus form a striking helical spring and generate tensional forces. We have found that, for tendrils of the passion flower Passiflora caerulea, the generated force lies in the range of 6-140 mN, which is sufficient to lash the plant tightly to its substrate. Further, we revealed that the generated force strongly correlates with the water status of the plant. By combining force measurements with anatomical investigations and dehydration-rehydration experiments on both entire tendril segments and isolated lignified tissues, we are able to propose a two-phasic principle of spring formation: First, during the free coiling phase, the tendril coiling is based on the active contraction of a fiber ribbon in interaction with the surrounding parenchyma as resistance layer. Second, in a stabilization phase, the entire center of the coiled tendril lignifies, stiffening the spring and securing its function independent of hydration status.

plant biology↗

bioRxiv2021

Facing the green threat: A waterflea's defenses against a carnivorous plant

Water fleas of the family Daphniidae are keystone species in many lentic ecosystems and, as most abundant filter feeders, link the primary production to higher trophic levels. As a response to the high predatory pressures, water fleas have evolved a range of defenses, including inducible defenses against animal predators. Here we show in Ceriodaphnia dubia a first example of such defenses induced by the presence of a coexisting plant predator, i.e. the carnivorous southern bladderwort (Utricularia australis, Lentibulariaceae), which possesses ultrafast underwater suction traps. When the bladderwort is present, C. dubia shows changes in morphology, life-history and behavior. While the morphological and behavioral adaptations improve C. dubias survival rate in the presence of this predator, the life-history parameters likely reflect trade-offs for the defense. Our study demonstrates plant-induced animal defenses, implying their potential relevance in freshwater ecosystems and contributing to an overall yet underestimated biodiversity of inducible defenses. Open Research StatementData is not finally prepared for upload yet. Once most fitting file types are determined and metadata is created we aim to upload all raw data as supporting information.

ecology↗

bioRxiv2020

Spatiotemporal development of cuticular ridges on the leaf surfaces of Hevea brasiliensis alters insect attachment

Cuticular ridges on plant surfaces can control insect adhesion and wetting behaviour and might also offer stability to underlying cells during growth. The growth of the plant cuticle and its underlying cells possibly results in changes in the morphology of cuticular ridges and may also affect their function. We present spatial and temporal patterns in cuticular ridge development on the leaf surfaces of the model plant, Hevea brasiliensis. We have identified, by confocal laser scanning microscopy of polymer leaf replicas, an acropetally directed progression of ridges during the ontogeny of Hevea brasiliensis leaf surfaces. The use of Colorado potato beetles (Leptinotarsa decemlineata) as a model insect species has shown that the changing dimensions of cuticular ridges on plant leaves during ontogeny have a significant impact on insect traction forces and act as an effective indirect defence mechanism. The traction forces of walking insects are significantly lower on mature leaf surfaces compared with young leaf surfaces. The measured walking traction forces exhibit a strong negative correlation with the dimensions of the cuticular ridges.

ecology↗