Biology subjects

Vavylonis, D.

Publications and source records attributed to Vavylonis, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Analysis of gene expression changes after Latrunculin B-induced actin depolymerization

Links between the cytoskeleton and gene expression are increasingly appreciated. The cytoskeleton dynamically regulates its own expression and organization through transcriptional feedback loops that sense cellular concentrations and mechanical forces. Disruption of cytoskeletal dynamics can also influence cell fate. However, the breadth, temporal dynamics, and mechanistic basis of the cytoskeleton-transcription coupling have yet to be fully resolved. To characterize this response more broadly, we re-analyzed time-resolved bulk RNA-seq data that were previously used to demonstrate that treatment with actin depolymerization drug Latrunculin B (LatB) drives differentiation of human pancreatic progenitor cells in culture. Beyond the previously identified induction of cell differentiation, we find that LatB produced extensive transcriptional changes within the actin cytoskeleton, including downregulation of actin, myosin II heavy chains, myosin I, tropomyosins, -actinins, filamins, talin, vinculin and plastin. The changes were not restricted to the actin system, but extended to microtubule and intermediate filament systems, with noticeable changes in the expression of KIF19, MAP1A, MAP1B, Type I and II keratins and Type IV neurofilaments. More broadly, the response extended to genes involved in transcription, vesicle trafficking, metabolism, translation, ion transport, protein homeostasis, and cell signaling. The breadth of this response suggested engagement of multiple transcriptional regulatory programs. Transcription factor activity inference using decoupleR identified MRTF/SRF as the most inactivated TF network, consistent with its known role in actin homeostasis, in addition to Hippo/YAP-TEAD, MYC, stress-response and other pathways. These results provide the broader landscape of cellular response to actin depolymerization, serving as a foundation for future studies to distinguish general mechanisms of cytoskeletal homeostasis from differentiation-associated responses, and to narrow the underlying regulatory mechanisms linking cytoskeletal state to gene expression.

cell biology↗

bioRxiv2025

Immune Cell Migration Models Synergize Nuclear Piston, Uropod, and Microenvironment into Hydraulic Cell Engine

The nucleus and uropod are the largest and most mechanically distinct structures in migrating amoeboid lymphocytes, including NK, B, and T cells. The biophysical properties of these structures may shape the ability of immune cells to navigate dense tissue microenvironments during immune surveillance. Using bead-spring and agent-based cell models, we explore the biomechanical contributions of the nucleus, uropod, septin-templated cortical rings, actomyosin cytoskeleton, and extracellular matrix obstacles to lymphocyte migration. Our results support a migration model in which, following cell-matrix collisions, septins mediate the formation of cortical rings that hydraulically seal cytoplasmic compartments on each side of the passing nucleus, generating a pressure difference that propels the nucleus forward. This hydraulically driven nuclear piston actively enhances migration through confined spaces. Concurrently, the uropod emerging from the peristaltic collapse of rear compartments stabilizes directional persistence and prevents T cell repolarization. We show that such polarity stabilization boosts immune surveillance efficiency. Together, these models redefine the nucleus as an active component of the migratory engine and the uropod as a locomotion stabilizer. Furthermore, the models offer a predictive framework towards engineering of immune cell motility in complex tissue microenvironments with broad implications for cancer immunotherapy, aging, and regenerative medicine.

biophysics↗

bioRxiv2025

3D printing cytoskeletal networks: ROS-induced filament severing leads to surge in actin polymerization

The cytoskeletal protein actin forms a spatially organized biopolymer network that plays a central role in many cellular processes. Actin filaments continuously assemble and disassemble, enabling cells to rapidly reorganize their cytoskeleton. Filament severing accelerates actin turnover, as both polymerization and depolymerization rates depend on the number of free filament ends. Here, we use light to control actin severing in vitro by locally generating reactive oxygen species (ROS) with photosensitive molecules such as fluorophores. We see that ROS sever actin filaments, which increases actin polymerization in our experiments. However, beyond a certain threshold, excessive severing leads to the disassembly of actin networks, allowing us to selectively remove actin structures. Our experimental data is supported by simulations using a kinetic model of actin polymerization, which helps us understand the underlying dynamics. In cells, ROS are known to regulate the actin cytoskeleton, but the molecular mechanisms are poorly understood. Here we show that, in vitro, ROS directly affect actin reorganization.

biophysics↗

bioRxiv2024

Ca2+-dependent vesicular and non-vesicular lipid transfer controls hypoosmotic plasma membrane expansion

Robust coordination of surface and volume changes is critical for cell integrity. Few studies have elucidated the plasma membrane (PM) remodeling events during cell surface and volume alteration, especially regarding PM sensing and its subsequent rearrangements. Here, using fission yeast protoplasts, we reveal a Ca2+-dependent mechanism for membrane addition that ensures PM integrity and allows its expansion during acute hypoosmotic cell swelling. We show that MscS-like mechanosensitive channels activated by PM tension control extracellular Ca2+ influx, which triggers direct lipid transfer at endoplasmic reticulum (ER)-PM contact sites by conserved extended-synaptotagmins and accelerates exocytosis, enabling PM expansion necessary for osmotic equilibrium. Defects in any of these key events result in rapid protoplast rupture upon severe hypotonic shock. Our numerical simulations of hypoosmotic expansion further propose a cellular strategy that combines instantaneous non-vesicular lipid transfer with bulk exocytic membrane delivery to maintain PM integrity for dramatic cell surface/volume adaptation.

cell biology↗

bioRxiv2024

Myosin-I Synergizes with Arp2/3 Complex to Enhance Pushing Forces of Branched Actin Networks

Myosin-Is colocalize with Arp2/3 complex-nucleated actin networks at sites of membrane protrusion and invagination, but the mechanisms by which myosin-I motor activity coordinates with branched actin assembly to generate force are unknown. We mimicked the interplay of these proteins using the "comet tail" bead motility assay, where branched actin networks are nucleated by Arp2/3 complex on the surface of beads coated with myosin-I and the WCA domain of N-WASP. We observed that myosin-I increased bead movement efficiency by thinning actin networks without affecting growth rates. Remarkably, myosin-I triggered symmetry breaking and comet-tail formation in dense networks resistant to spontaneous fracturing. Even with arrested actin assembly, myosin-I alone could break the network. Computational modeling recapitulated these observations suggesting myosin-I acts as a repulsive force shaping the networks architecture and boosting its force-generating capacity. We propose that myosin-I leverages its power stroke to amplify the forces generated by Arp2/3 complex-nucleated actin networks.

biophysics↗

bioRxiv2023

Cdc42 mobility and membrane flows regulate fission yeast cell shape and survival

Local Cdc42 GTPase activation promotes polarized exocytosis, resulting in membrane flows that deplete low-mobility membrane-associated proteins from the growth region. To investigate the self-organizing properties of the Cdc42 secretion-polarization system under membrane flow, we developed a reaction-diffusion particle model. The model includes positive feedback activation of Cdc42, hydrolysis by GTPase-activating proteins (GAPs), and flow-induced displacement by exo/endocytosis. Simulations show how polarization relies on flow-induced depletion of low mobility GAPs. To probe the role of Cdc42 mobility in the fission yeast Schizosaccharomyces pombe, we changed its membrane binding properties by replacing its prenylation site with 1, 2 or 3 repeats of the Rit1 C terminal membrane binding domain (ritC), yielding alleles with progressively lower unbinding and diffusion rates. Concordant modelling predictions and experimental observations show that lower Cdc42 mobility results in lower Cdc42 activation level and wider patches. Indeed, while Cdc42-1ritC cells are viable and polarized, Cdc42-2ritC polarize poorly and Cdc42-3ritC is inviable. The model further predicts that GAP depletion increases Cdc42 activity at the expense of loss of polarization. Experiments confirm this prediction, as deletion of Cdc42 GAPs restores viability to Cdc42-3ritC cells. Our combined experimental and modelling studies demonstrate how membrane flows are an integral part of Cdc42-driven pattern formation. Significance StatementThe delivery of new membrane from internal pools at zones of polarized secretion induces in-plane plasma membrane flows that displace slowly mobile membrane-associated proteins from the zone of secretion. However, zones of polarized secretion are themselves specified by the activity of membrane-associated polarity factors, such as the small GTPase Cdc42. Through combined modelling and experimental approaches, this work demonstrates that the fast mobility of the Cdc42 GTPase is critical to allow the establishment and maintenance of a polarity patch, which is reinforced by flow-mediated displacement of a negative regulator.

cell biology↗

bioRxiv2023

Design principles of Cdr2 node patterns in fission yeast cells

Pattern forming networks have diverse roles in cell biology. Rod-shaped fission yeast cells use pattern formation to control the localization of mitotic signaling proteins and the cytokinetic ring. During interphase, the kinase Cdr2 forms membrane-bound multiprotein complexes termed nodes, which are positioned in the cell middle due in part to the node inhibitor Pom1 enriched at cell tips. Node positioning is important for timely cell cycle progression and positioning of the cytokinetic ring. Here, we combined experimental and modeling approaches to investigate pattern formation by the Pom1-Cdr2 system. We found that Cdr2 nodes accumulate near the nucleus, and Cdr2 undergoes nucleocytoplasmic shuttling when cortical anchoring is reduced. We generated particle-based simulations based on tip inhibition, nuclear positioning, and cortical anchoring. We tested model predictions by investigating Pom1-Cdr2 localization patterns after perturbing each positioning mechanism, including in both anucleate and multinucleated cells. Experiments show that tip inhibition and cortical anchoring alone are sufficient for the assembly and positioning of nodes in the absence of the nucleus, but that the nucleus and Pom1 facilitate the formation of unexpected node patterns in multinucleated cells. These findings have implications for spatial control of cytokinesis by nodes and for spatial patterning in other biological systems.

cell biology↗

bioRxiv2023

Anillin Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study

The organization of the cytokinetic ring at the cell equator of dividing animal and fungi cells depends crucially on the anillin scaffold proteins. In fission yeast, anillin related Mid1 binds to the plasma membrane and helps anchor and organize a medial broad band of cytokinetic nodes, which are the precursors of the contractile ring. Similar to other anillins, Mid1 contains a C terminal globular domain with two potential regions for membrane binding, the Pleckstrin Homology (PH) and C2 domains, and an N terminal intrinsically disordered region that is strongly regulated by phosphorylation. Previous studies have shown that both PH and C2 domains can associate with the membrane, preferring phosphatidylinositol-(4,5)-bisphosphate (PIP2) lipids. However, it is unclear if they can simultaneously bind to the membrane in a way that allows dimerization or oligomerization of Mid1, and if one domain plays a dominant role. To elucidate Mid1s membrane binding mechanism, we used the available structural information of the C terminal region of Mid1 in all-atom molecular dynamics (MD) near a membrane with a lipid composition based on experimental measurements (including PIP2 lipids). The disordered L3 loop of C2, as well as the PH domain, separately bind the membrane through charged lipid contacts. In simulations with the full C terminal region started away from the membrane, Mid1 binds through the L3 loop and is stabilized in a vertical orientation with the PH domain away from the membrane. However, a configuration with both C2 and PH initially bound to the membrane remains associated with the membrane. These multiple modes of binding may reflect Mid1s multiple interactions with membranes and other node proteins, and ability to sustain mechanical forces.

biophysics↗

bioRxiv2022

Multiple polarity kinases inhibit phase separation of F-BAR protein Cdc15 and antagonize cytokinetic ring assembly in fission yeast

The F-BAR protein Cdc15 is essential for cytokinesis in Schizosaccharomyces pombe and it plays a key role in attaching the cytokinetic ring (CR) to the plasma membrane. Cdc15s abilities to bind to the membrane and oligomerize via its F-BAR domain are inhibited by phosphorylation of its intrinsically disordered region (IDR). Multiple cell polarity kinases regulate Cdc15 IDR phosphostate, and of these the DYRK kinase Pom1 phosphorylation sites on Cdc15 have been shown in vivo to prevent CR formation at cell tips. Here, we compared the ability of Pom1 to control of Cdc15 phosphostate and cortical localization to that of other Cdc15 kinases: Kin1, Pck1, and Shk1. We identified distinct but overlapping cohorts of Cdc15 phosphorylation sites targeted by each kinase, and the number of sites correlated with each kinases abilities to influence Cdc15 PM localization. Coarse-grained simulations predicted that cumulative IDR phosphorylation moves the IDRs of a dimer apart and toward the F-BAR tips. Further, simulations indicated that the overall negative charge of phosphorylation masks positively charged amino acids necessary for F-BAR oligomerization and membrane interaction. Finally, simulations suggested that dephosphorylated Cdc15 undergoes phase separation driven by IDR interactions. Indeed, dephosphorylated but not phosphorylated Cdc15 undergoes liquid-liquid phase separation to form droplets in vitro that recruit Cdc15 binding partners. In cells, Cdc15 phosphomutants also formed PM-bound condensates that recruit other CR components. Together, we propose that a threshold of Cdc15 phosphorylation by assorted kinases prevents Cdc15 condensation on the PM and antagonizes CR assembly.

cell biology↗

bioRxiv2022

Compressive forces stabilise microtubules in living cells

Cell mechano-sensation and adaptation are supported by the actin network. The microtubule network is not considered to be directly sensitive to mechanical forces acting on a cell. However, recent studies on isolated microtubules in vitro have shown that bending forces have an impact on their structure, composition and lifespan, suggesting that, in a cellular context, microtubules may react to mechanical forces. We tested this hypothesis in living cells by subjecting them to cycles of compressive forces and found that microtubules became distorted, less dynamic and more stable. This mechano-stabilisation depends on CLASP2, which relocates from the end to the deformed shaft of microtubules. These results demonstrate that microtubules in living cells have mechano-responsive properties that allow them to resist and even counteract the forces to which they are subjected.

cell biology↗

bioRxiv2021

Discrete mechanical model of lamellipodial actin network implements molecular clutch mechanism and generates arcs and microspikes

Mechanical forces, actin filament turnover, and adhesion to the extracellular environment regulate lamellipodial protrusions. Computational and mathematical models at the continuum level have been used to investigate the molecular clutch mechanism, calculating the stress profile through the lamellipodium and around focal adhesions. However, the forces and deformations of individual actin filaments have not been considered while interactions between actin networks and actin bundles is not easily accounted with such methods. We develop a filament-level model of a lamellipodial actin network undergoing retrograde flow using 3D Brownian dynamics. Retrograde flow is promoted in simulations by pushing forces from the leading edge (due to actin polymerization), pulling forces (due to molecular motors), and opposed by viscous drag in cytoplasm and focal adhesions. Simulated networks have densities similar to measurements in prior electron micrographs. Connectivity between individual actin segments is maintained by permanent and dynamic crosslinkers. Remodeling of the network occurs via the addition of single actin filaments near the leading edge and via filament bond severing. We investigated how several parameters affect the stress distribution, network deformation and retrograde flow speed. The model captures the decrease in retrograde flow upon increase of focal adhesion strength. The stress profile changes from compression to extension across the leading edge, with regions of filament bending around focal adhesions. The model reproduces the observed reduction in retrograde flow speed upon exposure to cytochalasin D, which halts actin polymerization. Changes in crosslinker concentration and dynamics, as well as in the orientation pattern of newly added filaments demonstrate the models ability to generate bundles of filaments perpendicular (actin arcs) or parallel (microspikes) to the protruding direction.

biophysics↗

bioRxiv2021

A mechanism with severing near barbed ends and annealing explains structure and dynamics of dendritic actin networks

Single molecule imaging has shown that part of actin disassembles within a few seconds after incorporation into the dendritic filament network in lamellipodia, suggestive of frequent destabilization near barbed ends. To investigate the mechanisms behind network remodeling, we created a stochastic model with polymerization, depolymerization, branching, capping, uncapping, severing, oligomer diffusion, annealing, and debranching. We find that filament severing, enhanced near barbed ends, can explain the single molecule actin lifetime distribution, if oligomer fragments reanneal to free ends with rate constants comparable to in vitro measurements. The same mechanism leads to actin networks consistent with measured filament, end, and branch concentrations. These networks undergo structural remodeling, leading to longer filaments away from the leading edge, at the +/- 35{degrees} orientation pattern. Imaging of actin speckle lifetimes at sub-second resolution verifies frequent disassembly of newly-assembled actin. We thus propose a unified mechanism that fits a diverse set of basic lamellipodia phenomenology.

cell biology↗

bioRxiv2020

Cell patterning by secretion-induced plasma membrane flows

Cells self-organize using reaction-diffusion and fluid-flow principles. Whether bulk membrane flows contribute to cell patterning has not been established. Here, using mathematical modelling, optogenetics and synthetic probes, we show that polarized exocytosis causes lateral membrane flows away from regions of membrane insertion. Plasma membrane-associated proteins with sufficiently low diffusion and/or detachment rates couple to the flows and deplete from areas of exocytosis. In rod-shaped fission yeast cells, zones of Cdc42 GTPase activity driving polarized exocytosis are limited by GTPase activating proteins (GAPs). We show that membrane flows pattern the GAP Rga4 distribution and coupling of a synthetic GAP to membrane flows is sufficient to establish the rod shape. Thus, membrane flows induced by Cdc42-dependent exocytosis form a negative feedback restricting the zone of Cdc42 activity. One Sentence SummaryExocytosis causes bulk membrane flows that drag associated proteins and form a negative feedback restricting the exocytic site.

cell biology↗

bioRxiv2020

Reconstitution of contractile actomyosin rings in vesicles

One of the grand challenges of bottom-up synthetic biology is the development of minimal machineries for cell division. The mechanical transformation of large-scale compartments, such as Giant Unilamellar Vesicles (GUVs), requires the geometry-specific coordination of active elements, several orders of magnitude larger than the molecular scale. Of all cytoskeletal structures, large-scale actomyosin rings appear to be the most promising cellular elements to accomplish this task. Here, we have adopted advanced encapsulation methods to study bundled actin filaments in GUVs and compare our results with theoretical modeling. By changing few key parameters, actin polymerization can be differentiated to resemble various types of networks in living cells. Importantly, we find membrane binding to be crucial for the robust condensation into a single actin ring in spherical vesicles, as predicted by theoretical considerations. Upon force generation by ATP-driven myosin motors, these ring-like actin structures contract and locally constrict the vesicle, forming furrow-like deformations. On the other hand, cortex-like actin networks are shown to induce and stabilize deformations from spherical shapes.

synthetic biology↗

bioRxiv2020

Cdc42 GTPase Activating Proteins (GAPs) Maintain Generational Inheritance of Cell Polarity and Cell Shape in Fission Yeast

The highly conserved small GTPase Cdc42 regulates polarized cell growth and morphogenesis from yeast to humans. We previously reported that Cdc42 activation exhibits oscillatory dynamics in Schizosaccharomyces pombe cells. Mathematical modeling suggests that this dynamic behavior enables a variety of symmetric and asymmetric Cdc42 distributions to coexist in cell populations. For individual wild type cells, however, growth follows a stereotypical pattern where Cdc42 distribution is initially asymmetrical in young daughter cells and becomes more symmetrical as cell volume increases, enabling bipolar growth activation. To explore whether different states of Cdc42 activation are possible in a biological context, we examined S. pombe rga4{Delta} mutant cells, lacking the Cdc42 GTPase activating protein (GAP) Rga4. We found that monopolar rga4{Delta} mother cells divide asymmetrically leading to the emergence of both symmetric and asymmetric Cdc42 distributions in rga4{Delta} daughter cells. Using genetic screening approaches to identify mutants that alter the rga4{Delta} phenotype, we tested the predictions of different computational models that reproduce the unequal fate of daughter cells. We found experimentally that the unequal distribution of active Cdc42 GTPase in daughter cells is consistent with an unequal inheritance of another Cdc42 GAP, Rga6, in the two daughter cells. Our findings highlight the crucial role of Cdc42 GAP protein localization in determining the morphological fate of cell progeny and ensuring consistent Cdc42 activation and growth patterns across generations.

cell biology↗

bioRxiv2019

Insights into actin polymerization and nucleation using a coarse grained model

We studied actin filament polymerization and nucleation with molecular dynamics simulations and a previously established coarse-grained model having each residue represented by a single interaction site located at the C atom. We approximate each actin protein as a fully or partially rigid unit to identify the equilibrium structural ensemble of interprotein complexes. Monomers in the F-actin configuration bound to both barbed and pointed ends of a short F-actin filament at the anticipated locations for polymerization. Binding at both ends occurred with similar affinity. Contacts between residues of the incoming subunit and the short filament were consistent with expectation from models based on crystallography, X-ray diffraction and cryo-electron microscopy. Binding at the barbed and pointed end also occurred at an angle with respect to the polymerizable bound structure, and the angle range depended on the flexibility of the D-loop. Additional barbed end bound states were seen when the incoming subunit was in the G-actin form. Consistent with an activation barrier for pointed end polymerization, G-actin did not bind at an F-actin pointed end. In all cases, binding at the barbed end also occurred in a configuration similar to the antiparallel (lower) dimer. Individual monomers bound each other in a short-pitch helix complex in addition to other configurations, with several of them apparently non-productive for polymerization. Simulations with multiple monomers in the F-actin form show assembly into filaments as well as transient aggregates at the barbed end. We discuss the implications of these observations on the kinetic pathway of actin filament nucleation and polymerization and possibilities for future improvements of the coarse-grained model. SIGNIFICANCEControl of actin filament nucleation and elongation has crucial importance to cellular life. We show that coarse-grained molecular dynamics simulations are a powerful tool which can gauge involved mechanisms at reasonable computational cost, while retaining essential features of the fully atomic, yet less computationally tractable, system. Using a knowledge-based potential demonstrates the power of these methods for explaining and reproducing polymerization. Intermediate actin complexes identified in the simulations may play critical roles in the kinetic pathways of actin polymerization which may have been difficult to observe in prior experiments. These methods have been sparsely applied to the actin system, yet have potential to answer many important questions in the field.

biophysics↗

bioRxiv2019

Organization of Associating or Crosslinked Actin Filaments in Confinement

A key factor of actin cytoskeleton organization in cells is the interplay between the dynamical properties of actin filaments and cell geometry, which restricts, confines and directs their orientation. Crosslinking interactions among actin filaments, together with geometrical cues and regulatory proteins can give rise to contractile rings in dividing cells and actin rings in neurons. Motivated by recent in vitro experiments, in this work we performed computer simulations to study basic aspects of the interplay between confinement and attractive interactions between actin filaments. We used a spring-bead model and Brownian dynamics to simulate semiflexible actin filaments that polymerize in a confining sphere with a rate proportional to the monomer concentration. We model crosslinking, or attraction through the depletion interaction, implicitly as an attractive short-range potential between filament beads. In confining geometries smaller than the persistence length of actin filaments, we show rings can form by curving of filaments of length comparable to, or longer than the confinement diameter. Rings form for optimal ranges of attractive interactions that exist in between open bundles, irregular loops, aggregated and unbundled morphologies. The probability of ring formation is promoted by attraction to the confining sphere boundary and decreases for large radii and initial monomer concentrations, in agreement with prior experimental data. The model reproduces ring formation along the flat axis of oblate ellipsoids.

biophysics↗

bioRxiv2018

Automated Tracking of Biopolymer Growth and Network Deformation with TSOAX

Studies of how individual semi-flexible biopolymers and their network assemblies change over time reveal dynamical and mechanical properties important to the understanding of their function in tissues and living cells. Automatic tracking of biopolymer networks from fluorescence microscopy time-lapse sequences facilitates such quantitative studies. We present an open source software tool that combines a global and local correspondence algorithm to track biopolymer networks in 2D and 3D, using stretching open active contours. We demonstrate its application in fully automated tracking of elongating and intersecting actin filaments, detection of loop formation and constriction of tilted contractile rings in live cells, and tracking of network deformation under shear deformation.

cell biology↗