a-typical-workflow-to-simulate-cytoskeletal-systems

A Typical Workflow to Simulate Cytoskeletal Systems

Many cytoskeletal systems are now sufficiently well known to permit their precise quantitative modeling. Microtubule and actin filaments are well ...

Cambridge University

In anaphase spindles, antiparallel microtubules associate to form tight midzone bundles, as required for functional spindle architecture and correct chromosome segregation. Several proteins selectively bind to these overlaps to control cytokinesis. How midzone bundles assemble is poorly understood. Here, using an in vitro reconstitution approach, we demonstrate that minimal midzone bundles can reliably self-organize in solution from dynamic microtubules, the microtubule crosslinker PRC1, and the motor protein KIF4A. The length of the central antiparallel overlaps in these microtubule bundles is similar to that observed in cells and is controlled by the PRC1/KIF4A ratio. Experiments and computer simulations demonstrate that minimal midzone bundle formation results from promoting antiparallel microtubule crosslinking, stopping microtubule plus-end dynamicity, and motor-driven midzone compaction and alignment. The robustness of this process suggests that a similar self-organization mechanism may contribute to the reorganization of the spindle architecture during the metaphase to anaphase transition in cells.

Self-Organization of Minimal Anaphase Spindle Midzone Bundles.

Antiparallel microtubule bundles are essential structural elements of many cytoskeletal structures, for instance, the mitotic spindle. Sliding of microtubules relative to each other can lead to an overall elongation of the bundle. However, such sliding must be accompanied by microtubule growth, to maintain the overlap, which is a landmark of anaphase. Diffusive crosslinkers of the Ase1/PRC1/MAP65 family are able to form stable overlaps in combination with kinesin-14 motors. This process is thought to arise through a balance of forces between motors and crosslinkers, the latter effectively producing an entropic pressure. We provide a continuous theory to explain the formation of stable overlaps, in which steric effects caused by the finite number of binding sites available on the microtubule lattice play a leading role. We confirmed the validity of this approach using discrete stochastic simulations performed with the Open Source simulation engine Cytosim. From the densities of motors and crosslinkers, their diffusion rates, and the velocities of motors, the theory predicts the sliding speed of microtubules and explains the force production and breaking effect of crosslinkers and motors containing diffusible microtubule-binding domains. Finally, we discuss a mechanism by which sliding and microtubule growth can be coordinated without the need for fine-tuning the parameters of the system, in line with the known robustness of mitosis.

Theory of antiparallel microtubule overlap stabilization by motors and diffusible crosslinkers.

Cell biologists generally consider that microtubules and actin play complementary roles in long- and short-distance transport in animal cells. On the contrary, using melanosomes of melanocytes as a model, we recently discovered that the motor protein myosin-Va works with dynamic actin tracks to drive long-range organelle dispersion in opposition to microtubules. This suggests that in animals, as in yeast and plants, myosin/actin can drive long-range transport. Here, we show that the SPIRE-type actin nucleators (predominantly SPIRE1) are Rab27a effectors that co-operate with formin-1 to generate actin tracks required for myosin-Va-dependent transport in melanocytes. Thus, in addition to melanophilin/myosin-Va, Rab27a can recruit SPIREs to melanosomes, thereby integrating motor and track assembly activity at the organelle membrane. Based on this, we suggest a model in which organelles and force generators (motors and track assemblers) are linked, forming an organelle-based, cell-wide network that allows their collective activity to rapidly disperse the population of organelles long-distance throughout the cytoplasm.

Rab27a co-ordinates actin-dependent transport by controlling organelle-associated motors and track assembly proteins.

Quantifying the influence of microscopic details on the dynamics of development of the overall structure of a filamentous network is important in a number of biologically relevant contexts, but it is not obvious what order parameters can be used to adequately describe this complex process. In this paper we investigated the role of multivalent actin-binding proteins (ABPs) in reorganizing actin filaments into higher-order complex networks via a computer model of semiflexible filaments. We characterize the importance of local connectivity among actin filaments, as well as the global features of actomyosin networks. We first map the networks into local graph representations and then, using principles from network-theory order parameters, combine properties from these representations to gain insight into the heterogeneous morphologies of actomyosin networks at a global level. We find that ABPs with a valency greater than 2 promote filament bundles and large filament clusters to a much greater extent than bivalent multilinkers. We also show that active myosinlike motor proteins promote the formation of dendritic branches from a stalk of actin bundles. Our work motivates future studies to embrace network theory as a tool to characterize complex morphologies of actomyosin detected by experiments, leading to a quantitative understanding of the role of ABPs in manipulating the self-assembly of actin filaments into unique architectures that underlie the structural scaffold of a cell relating to its mobility and shape.

Insights from graph theory on the morphologies of actomyosin networks with multilinkers.

During anaphase B, molecular motors slide interpolar microtubules to elongate the mitotic spindle, contributing to the separation of chromosomes. However, sliding of antiparallel microtubules reduces their overlap, which may lead to spindle breakage, unless microtubules grow to compensate sliding. How sliding and growth are coordinated is still poorly understood. In this study, we have used the fission yeast  to measure microtubule dynamics during anaphase B. We report that the coordination of microtubule growth and sliding relies on promoting rescues at the midzone edges. This makes microtubules stable from pole to midzone, while their distal parts including the plus ends alternate between assembly and disassembly. Consequently, the midzone keeps a constant length throughout anaphase, enabling sustained sliding without the need for a precise regulation of microtubule growth speed. Additionally, we found that in , which undergoes closed mitosis, microtubule growth speed decreases when the nuclear membrane wraps around the spindle midzone.

Article	Year
Self-Organization of Minimal Anaphase Spindle Midzone Bundles. Current biology : CB\| PubMed ID: 31231047	2019
Theory of antiparallel microtubule overlap stabilization by motors and diffusible crosslinkers. Cytoskeleton (Hoboken, N.J.)\| PubMed ID: 31658404	2019
Rab27a co-ordinates actin-dependent transport by controlling organelle-associated motors and track assembly proteins. Nature communications\| PubMed ID: 32661310	2020
Insights from graph theory on the morphologies of actomyosin networks with multilinkers. Physical review. E\| PubMed ID: 33466104	2020
Microtubule rescue at midzone edges promotes overlap stability and prevents spindle collapse during anaphase B. eLife\| PubMed ID: 35293864	2022

Francois Nedelec

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