Thesis presented September 22, 2015

Abstract:
The cytoskeleton plays a crucial role in cellular processes, including cell division, adhesion, migration and morphogenesis. One of its main compenent, the actin filaments, a polarised semi-flexible polymer, contributes to these processes by forming specific collective architectures, whose structural organisations are essential to perform their functions. A major challenge in cell biology is to understand how the cell can form such a variety of organisations by using the same basic entity, the actin monomers. Recently we discovered that limiting actin nucleation to specific regions was sufficient to obtain actin networks with different organization (Reymann et al., 2010). However, our understanding of the general parameters involved in geometrically-driven actin assembly was limited. To understand mechanistically how spatially constraining actin nucleation determines the emergent actin organization, I performed detailed simulations of the actin filament system using Cytosim, a simulation tool dedicated to cytoskeleton system. I found that geometry, actin filaments local interactions, bundle rigidity, and nucleation efficiency are the key parameters controlling the emergent actin architecture. This study sets the foundation for our understanding of actin cellular organization by identifying a reduced set of components that were sufficient to realistically reproduce in silico the emergence of the different types of actin organization (branched actin network, parallel or anti parallel actin bundles). We can now predict for any given nucleation geometry which structures will form.
Being able to control the formation of specific structures in vitro and in silico, we used the combination of both methods to study how the interplay between actin network architecture and its biochemical composition affects its contractile response. We highlighted the importance of the connectivity between filaments in the structures. Indeed, a loosely connected network cannot have a global behavior, but undergoes only local deformations. A highly connected network will be too rigid to be efficiently deformed by molecular motors. Only for an intermediate range of network connectivity the structures will contract, with an amplitude that depends notably on actin filaments organisation. This work explains how architecture and connectivity govern actin network contractility.
Finally, the microtubules are also essential actors of cellular processes. Being long and rigid, they serve as sensors of the cellular shape and can organize the position of organelles in the cytoplasm. Their spatial distribution in the cell is thus a crucial cellular feature. this distribution is determined in a vast number of cell types by the position of the centrosome, an organelle that nucleates the majority of microtubules. Quite strinkingly, the centrosome is able to find the center of the cell in a lot of different physiological conditions, but can nonetheless adopt a decentered position in specific cellular processes. How this positioning is controled is not yet fully understood, but a few potential mechanims have been proposed (Manneville et al., 2006; Zhu et al., 2010). I used the simulations to explore different mechanisms taht can explain the position of the centrosome under different conditions. These results offer theorical considerations as a basis to assess which mechanism might prevail in a specific experimental system and may help to design new experimental setups.
The simulations that I developed helped to study some specific behavior, by giving new insights into cytoskeleton collective organisations. These simulations can be further used as predictive tool or adapted to other experimental systems.

Keywords:
Numerical simulation, Cytoskeleton, Actin filament, Microtubule, Cytosim, Organisation

On-line thesis.