Biology subjects

Jasnin, M.

Publications and source records attributed to Jasnin, M..

6 recordsLinked to original sources

bioRxiv2026

Layered helical order reveals assembly states in podosome actin networks

How stochastic molecular events are converted into ordered cellular machines that perform mechanical work remains a central question in biology. Cryo-electron tomography enables visualization of macromolecular assemblies inside cells at molecular resolution, but static tomograms are generally interpreted as structural snapshots, with limited access to assembly state and temporal progression. Here, we show that cellular tomograms retain interpretable information about the assembly of a force-generating actin network. Using human macrophage podosomes as a physiologically relevant system, we combine spatial mapping of actin filaments (F-actin) and Arp2/3-mediated branch junctions, orientation analysis of deep-learning-based filament segmentations and Markov-chain modeling to infer actin-network assembly in situ. We identify favored membrane-directed actin polymerization and Arp2/3-mediated branching, establishing a local growth axis for podosome network organization. At the network scale, podosomes display layered helical order: filament-orientation classes recur at intervals of approximately 33 nm along the membrane-normal axis, forming a three-class cycle that returns to an approximately equivalent non-polar orientation. Markov modeling identifies preferred mother-to-daughter filament-orientation transitions and yields a stationary composition of branch-orientation states that closely matches that observed in structurally more advanced network regions. Together, these results link local actin nucleation, network-scale architecture and structural assembly state in a native cellular machine. Our study advances cryo-electron tomography from structural description toward temporal inference and 4D in situ structural biology.

cell biology↗

bioRxiv2024

Self-organized spatial targeting of contractile actomyosin rings for synthetic cell division

One of the challenges of bottom-up synthetic biology is the engineering of a minimal module for self-division of synthetic cells. To produce the contractile forces required for the controlled excision of cell-like compartments such as giant unilamellar vesicles (GUVs), reconstituted cytokinetic rings made of actin are considered to be among the most promising structures of a potential synthetic division machinery. Although the targeting of actin rings to GUV membranes and their myosin-induced constriction have been previously demonstrated, large-scale vesicle deformation has been precluded due to the lacking spatial control of these contractile structures. Here, we show the combined in vitro reconstitution of actomyosin rings and the bacterial MinDE protein system, effective in targeting E.coli Z-rings to mid-cell, within GUVs. Incorporating this spatial positioning tool, which induces active transport of any diffusible molecule on membranes, yields self-organized assembly of actomyosin rings at the equatorial plane of vesicles. Remarkably, the synergistic effect of Min oscillations and the contractile nature of actomyosin bundles induces mid-vesicle membrane deformation and striking bleb-like protrusions, leading to shape remodeling and symmetry breaking. Our system showcases how functional machineries from various organisms may be synergistically combined in vitro, leading to the emergence of new functionality towards a synthetic division system.

synthetic biology↗

bioRxiv2023

Simulating the cellular context in synthetic datasets for cryo-electron tomography

Cryo-electron tomography (cryo-ET) allows to visualize the cellular context at macromolecular level. To date, the impossibility of obtaining a reliable ground truth is limiting the application of deep learning-based image processing algorithms in this field. As a consequence, there is a growing demand of realistic synthetic datasets for training deep learning algorithms. In addition, besides assisting the acquisition and interpretation of experimental data, synthetic tomograms are used as reference models for cellular organization analysis from cellular tomograms. Current simulators in cryo-ET focus on reproducing distortions from image acquisition and tomogram reconstruction, however, they can not generate many of the low order features present in cellular tomograms. Here we propose several geometric and organization models to simulate low order cellular structures imaged by cryo-ET. Specifically, clusters of any known cytosolic or membrane bound macromolecules, membranes with different geometries as well as different filamentous structures such as microtubules or actin-like networks. Moreover, we use parametrizable stochastic models to generate a high diversity of geometries and organizations to simulate representative and generalized datasets, including very crowded environments like those observed in native cells. These models have been implemented in a multiplatform open-source Python package, including scripts to generate cryo-tomograms with adjustable sizes and resolutions. In addition, these scripts provide also distortion-free density maps besides the ground truth in different file formats for efficient access and advanced visualization. We show that such a realistic synthetic dataset can be readily used to train generalizable deep learning algorithms.

bioinformatics↗

bioRxiv2023

Crosslinking by ZapD drives the assembly of short, discontinuous FtsZ filaments into ring-like structures in solution

Bacterial cell division relies on the Z ring, a cytoskeletal structure that acts as a scaffold for the assembly of the divisome. To date, the detailed mechanisms underlying the assembly and stabilization of the Z ring remain elusive. This study highlights the role of the FtsZ-associated protein (Zap) ZapD in the assembly and stabilization of Z-ring-like structures via filament crosslinking. Using cryo-electron tomography and biochemical analysis, we show that, at equimolar concentrations of ZapD and FtsZ, ZapD induces the formation of toroidal structures composed of short, curved FtsZ filaments that are crosslinked vertically, but also laterally and diagonally. At higher concentrations of ZapD, regularly spaced ZapD dimers crosslink FtsZ filaments from above, resulting in the formation of straight bundles. Despite the simplicity of this reconstituted system, these findings provide valuable insights into the structural organization and stabilization of the Z ring by Zap proteins in bacterial cells, revealing the key role of optimal crosslinking density and geometry in enabling filament curvature and ring formation.

biochemistry↗

bioRxiv2021

Elasticity of dense actin networks produces nanonewton protrusive forces

Actin filaments assemble into force-generating systems involved in diverse cellular functions, including cell motility, adhesion, contractility and division. It remains unclear how networks of actin filaments, which individually generate piconewton forces, can produce forces reaching tens of nanonewtons. Here we use in situ cryo-electron tomography to unveil how the nanoscale architecture of macrophage podosomes enables basal membrane protrusion. We show that the sum of the actin polymerization forces at the membrane is not sufficient to explain podosome protrusive forces. Quantitative analysis of podosome organization demonstrates that the core is composed of a dense network of bent actin filaments storing elastic energy. Theoretical modelling of the network as a spring-loaded elastic material reveals that it exerts forces of up to tens of nanonewtons, similar to those evaluated experimentally. Thus, taking into account not only the interface with the membrane but also the bulk of the network, is crucial to understand force generation by actin machineries. Our integrative approach sheds light on the elastic behavior of dense actin networks and opens new avenues to understand force production inside cells.

biophysics↗

bioRxiv2020

Molecular-scale visualization of sarcomere contraction within native cardiomyocytes

Sarcomeres, the basic contractile units of striated muscle, produce the forces driving muscular contraction through cross-bridge interactions between actin-containing thin filaments and myosin II-based thick filaments. Until now, direct visualization of the molecular architecture underlying sarcomere contractility has remained elusive. Here, we use in situ cryo-electron to-mography to unveil sarcomere contraction in frozen-hydrated neonatal rat cardiomyocytes. We show that the hexagonal lattice of the thick filaments is already established at the neonatal stage, with an excess of thin filaments outside the trigonal positions. Structural assessment of actin polarity by subtomogram averaging reveals that thin filaments in the fully activated state form overlapping arrays of opposite polarity in the center of the sarcomere. Our approach provides direct evidence for thin filament sliding during muscle contraction and may serve as a basis for structural understanding of thin filament activation and actomyosin interactions inside unperturbed cellular environments.

cell biology↗