Nucleation causes an actin network to fragment into multiple high-density domains

Published:August 03, 2022DOI:


      Actin networks rely on nucleation mechanisms to generate new filaments because spontaneous nucleation is kinetically disfavored. Branching nucleation of actin filaments by actin-related protein (Arp2/3), in particular, is critical for actin self-organization. In this study, we use the simulation platform for active matter MEDYAN to generate 2000 s long stochastic trajectories of actin networks, under varying Arp2/3 concentrations, in reaction volumes of biologically meaningful size (>20 μm3). We find that the dynamics of Arp2/3 increase the abundance of short filaments and increases network treadmilling rate. By analyzing the density fields of F-actin, we find that at low Arp2/3 concentrations, F-actin is organized into a single connected and contractile domain, while at elevated Arp2/3 levels (10 nM and above), such high-density actin domains fragment into smaller domains spanning a wide range of volumes. These fragmented domains are extremely dynamic, continuously merging and splitting, owing to the high treadmilling rate of the underlying actin network. Treating the domain dynamics as a drift-diffusion process, we find that the fragmented state is stochastically favored, and the network state slowly drifts toward the fragmented state with considerable diffusion (variability) in the number of domains. We suggest that tuning the Arp2/3 concentration enables cells to transition from a globally coherent cytoskeleton, whose response involves the entire cytoplasmic network, to a fragmented cytoskeleton, where domains can respond independently to locally varying signals.
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        • Alvarado J.
        • Sheinman M.
        • Koenderink G.H.
        • et al.
        Molecular motors robustly drive active gels to a critically connected state.
        Nat. Phys. 2013; 9: 591-597
        • Koenderink G.H.
        • Paluch E.K.
        Architecture shapes contractility in actomyosin networks.
        Curr. Opin. Cell Biol. 2018; 50: 79-85
        • Sonal K.A.
        • Ganzinger K.A.
        • Schwille P.
        • et al.
        Myosin-II activity generates a dynamic steady state with continuous actin turnover in a minimal actin cortex.
        J. Cell Sci. 2019; 132
        • Soares E Silva M.
        • Depken M.
        • Koenderink G.H.
        • et al.
        Active multistage coarsening of actin networks driven by myosin motors.
        Proc. Natl. Acad. Sci. USA. 2011; 108: 9408-9413
        • Hannezo E.
        • Dong B.
        • Hayashi S.
        • et al.
        Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes.
        Proc. Natl. Acad. Sci. USA. 2015; 112: 8620-8625
        • Firat-Karalar E.N.
        • Welch M.D.
        New mechanisms and functions of actin nucleation.
        Curr. Opin. Cell Biol. 2011; 23: 4-13
        • Bovellan M.
        • Romeo Y.
        • Charras G.
        • et al.
        Cellular control of cortical actin nucleation.
        Curr. Biol. 2014; 24: 1628-1635
        • Swaney K.F.
        • Li R.
        Function and regulation of the Arp2/3 complex during cell migration in diverse environments.
        Curr. Opin. Cell Biol. 2016; 42: 63-72
        • Mullins R.D.
        • Heuser J.A.
        • Pollard T.D.
        The interaction of Arp2/3 complex with actin: nucleation, high affinity pointed end capping, and formation of branching networks of filaments.
        Proc. Natl. Acad. Sci. USA. 1998; 95: 6181-6186
        • Pollard T.D.
        Regulation of actin filament assembly by Arp2/3 complex and formins.
        Annu. Rev. Biophys. Biomol. Struct. 2007; 36: 451-477
        • Goley E.D.
        • Welch M.D.
        The ARP2/3 complex: an actin nucleator comes of age.
        Nat. Rev. Mol. Cell Biol. 2006; 7: 713-726
        • Pollitt A.Y.
        • Insall R.H.
        WASP and SCAR/WAVE proteins: the drivers of actin assembly.
        J. Cell Sci. 2009; 122: 2575-2578
        • Molinie N.
        • Gautreau A.
        The Arp2/3 regulatory system and its deregulation in cancer.
        Physiol. Rev. 2018; 98: 215-238
        • Padrick S.B.
        • Rosen M.K.
        Physical mechanisms of signal integration by WASP family proteins.
        Annu. Rev. Biochem. 2010; 79: 707-735
        • Tyler J.J.
        • Allwood E.G.
        • Ayscough K.R.
        WASP family proteins, more than Arp2/3 activators.
        Biochem. Soc. Trans. 2016; 44: 1339-1345
        • Rotty J.D.
        • Wu C.
        • Bear J.E.
        New insights into the regulation and cellular functions of the ARP2/3 complex.
        Nat. Rev. Mol. Cell Biol. 2013; 14: 7-12
        • Papalazarou V.
        • Machesky L.M.
        The cell pushes back: the Arp2/3 complex is a key orchestrator of cellular responses to environmental forces.
        Curr. Opin. Cell Biol. 2021; 68: 37-44
        • Floyd C.
        • Papoian G.A.
        • Jarzynski C.
        Quantifying dissipation in actomyosin networks.
        Interface Focus. 2019; 9: 20180078-20180110
        • Alvarado J.
        • Sheinman M.
        • Koenderink G.H.
        • et al.
        Force percolation of contractile active gels.
        Soft Matter. 2017; 13: 5624-5644
        • Mulla Y.
        • Mackintosh F.C.
        • Koenderink G.H.
        Origin of slow stress relaxation in the cytoskeleton.
        Phys. Rev. Lett. 2019; 122: 218102
        • Lieleg O.
        • Kayser J.
        • Bausch A.R.
        • et al.
        Slow dynamics and internal stress relaxation in bundled cytoskeletal networks.
        Nat. Mater. 2011; 10: 236-242
        • Stricker J.
        • Falzone T.
        • Gardel M.L.
        Mechanics of the F-actin cytoskeleton.
        J. Biomech. 2010; 43: 9-14
        • Weirich K.L.
        • Banerjee S.
        • Gardel M.L.
        • et al.
        Liquid behavior of cross-linked actin bundles.
        Proc. Natl. Acad. Sci. USA. 2017; 114: 2131-2136
        • Weirich K.L.
        • Dasbiswas K.
        • Gardel M.L.
        • et al.
        Self-organizing motors divide active liquid droplets.
        Proc. Natl. Acad. Sci. USA. 2019; 116: 11125-11130
        • Bendix P.M.
        • Koenderink G.H.
        • Weitz D.A.
        • et al.
        A quantitative analysis of contractility in active cytoskeletal protein networks.
        Biophys. J. 2008; 94: 3126-3136
        • Haase K.
        • Pelling A.E.
        The role of the actin cortex in maintaining cell shape.
        Commun. Integr. Biol. 2013; 6: e26714
        • Ni Q.
        • Papoian G.A.
        Turnover versus treadmilling in actin network assembly and remodeling.
        Cytoskeleton. 2019; 76: 562-570
        • Liman J.
        • Bueno C.
        • Cheung M.S.
        • et al.
        The role of the Arp2/3 complex in shaping the dynamics and structures of branched actomyosin networks.
        Proc. Natl. Acad. Sci. USA. 2020; 117: 10825-10831
        • Clarke A.
        • McQueen P.G.
        • Giniger E.
        • et al.
        Abl signaling directs growth of a pioneer axon in Drosophila by shaping the intrinsic fluctuations of actin.
        Mol. Biol. Cell. 2020; 31: 466-477
        • Clarke A.
        • McQueen P.G.
        • Giniger E.
        • et al.
        Dynamic morphogenesis of a pioneer axon in Drosophila and its regulation by Abl tyrosine kinase.
        Mol. Biol. Cell. 2020; 31: 452-465
        • Popov K.
        • Komianos J.
        • Papoian G.A.
        Medyan : mechanochemical simulations of contraction and polarity alignment in actomyosin networks.
        PLoS Comput. Biol. 2016; 12 (e1004877)
        • Gibson M.A.
        • Bruck J.
        Efficient exact stochastic simulation of chemical systems with many species and many channels.
        J. Phys. Chem. A. 2000; 104: 1876-1889
        • Chandrasekaran A.
        • Upadhyaya A.
        • Papoian G.A.
        Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling.
        PLoS Comput. Biol. 2019; 15 (e1007156)
        • Li X.
        • Ni Q.
        • Jiang Y.
        • et al.
        Tensile force-induced cytoskeletal remodeling: mechanics before chemistry.
        PLoS Comput. Biol. 2020; 16 (e1007693)
        • Ni Q.
        • Wagh K.
        • Papoian G.A.
        • et al.
        A tug of war between filament treadmilling and myosin induced contractility generates actin cortex.
        bioRxiv. 2021; (Preprint at)
        • Komianos J.E.
        • Papoian G.A.
        Stochastic ratcheting on a funneled energy landscape is necessary for highly efficient contractility of actomyosin force dipoles.
        Phys. Rev. X. 2018; 8: 021006
        • Faust J.J.
        • Millis B.A.
        • Tyska M.J.
        Profilin-mediated actin allocation regulates the growth of epithelial microvilli.
        Curr. Biol. 2019; 29: 3457-3465.e3
        • Ott A.
        • Magnasco M.
        • Libchaber A.
        • et al.
        Measurement of the persistence length of polymerized actin using fluorescence microscopy.
        Phys. Rev. E. 1993; 48: R1642-R1645
        • Kojima H.
        • Ishijima A.
        • Yanagida T.
        Direct measurement of stiffness of single actin filaments with and without tropomyosin by in vitro nanomanipulation.
        Proc. Natl. Acad. Sci. USA. 1994; 91: 12962-12966
        • Han X.
        • Su Y.
        • Shroff H.
        • et al.
        A polymer index-matched to water enables diverse applications in fluorescence microscopy.
        Lab Chip. 2021; 21: 1549-1562
        • Svitkina T.M.
        • Borisy G.G.
        Arp2/3 complex and actin depolymerizing factor/cofilin in dendritic organization and treadmilling of actin filament array in lamellipodia.
        J. Cell Biol. 1999; 145: 1009-1026
        • Mahaffy R.E.
        • Pollard T.D.
        Kinetics of the formation and dissociation of actin filament branches mediated by Arp2/3 complex.
        Biophys. J. 2006; 91: 3519-3528
        • Chandrasekaran A.
        • Clarke A.
        • Giniger E.
        • et al.
        Computational simulations reveal that Abl activity controls cohesiveness of actin networks in growth cones.
        Mol. Biol. Cell. 2021; (33:mbcE21110535)
        • Fujiwara I.
        • Suetsugu S.
        • Ishiwata S.
        • et al.
        Visualization and force measurement of branching by Arp2/3 complex and N-WASP in actin filament.
        Biochem. Biophys. Res. Commun. 2002; 293: 1550-1555
        • Paciolla M.
        • Arismendi-Arrieta D.J.
        • Moreno A.J.
        Coarsening kinetics of complex macromolecular architectures in bad solvent.
        Polymers. 2020; 12: 5311-E620
        • Testard V.
        • Berthier L.
        • Kob W.
        Intermittent dynamics and logarithmic domain growth during the spinodal decomposition of a glass-forming liquid.
        J. Chem. Phys. 2014; 140: 164502
        • Hu S.
        • Dasbiswas K.
        • Bershadsky A.D.
        • et al.
        Long-range self-organization of cytoskeletal myosin II filament stacks.
        Nat. Cell Biol. 2017; 19: 133-141
        • Gardiner C.W.
        Stochastic Methods A Handbook for the Natural and Social Sciences.
        Springer-Verlag Berlin Heidelberg, 2009
        • Millius A.
        • Watanabe N.
        • Weiner O.D.
        Diffusion, capture and recycling of SCAR/WAVE and Arp2/3 complexes observed in cells by singlemolecule imaging.
        J. Cell Sci. 2012; 125: 1165-1176
        • Li C.
        • Liman J.
        • Cheung M.S.
        • et al.
        Forecasting avalanches in branched actomyosin networks with network science and Machine learning.
        J. Phys. Chem. B. 2021; 125: 11591-11605
        • Shi Y.
        • Porter C.L.
        • Reich D.H.
        • et al.
        Dissecting fat-tailed fluctuations in the cytoskeleton with active micropost arrays.
        Proc. Natl. Acad. Sci. USA. 2019; 116: 13839-13846
        • Alencar A.M.
        • Ferraz M.S.A.
        • Butler J.P.
        • et al.
        Non-equilibrium cytoquake dynamics in cytoskeletal remodeling and stabilization.
        Soft Matter. 2016; 12: 8506-8511
        • Floyd C.
        • Levine H.
        • Papoian G.A.
        • et al.
        Understanding cytoskeletal avalanches using mechanical stability analysis.
        Proc. Natl. Acad. Sci. USA. 2021; 118 (e2110239118)
        • Toyota T.
        • Head D.A.
        • Mizuno D.
        • et al.
        Non-Gaussian athermal fluctuations in active gels.
        Soft Matter. 2011; 7: 3234-3239
        • Letort G.
        • Politi A.
        • Blanchoin L.
        • et al.
        Geometrical and mechanical properties control actin filament organization.
        Biophys. J. 2014; 106: 568a-569a
        • Reymann A.C.
        • Martiel J.L.
        • Théry M.
        • et al.
        Nucleation geometry governs ordered actin networks structures.
        Nat. Mater. 2010; 9: 827-832
        • Kodera N.
        • Yamamoto D.
        • Ando T.
        • et al.
        Video imaging of walking myosin v by high-speed atomic force microscopy.
        Nature. 2010; 468: 72-76
        • Berg J.S.
        • Cheney R.E.
        Myosin-X is an unconventional myosin that undergoes intrafilopodial motility.
        Nat. Cell Biol. 2002; 4: 246-250
        • Moore A.S.
        • Wong Y.C.
        • Holzbaur E.L.F.
        • et al.
        Dynamic actin cycling through mitochondrial subpopulations locally regulates the fission-fusion balance within mitochondrial networks.
        Nat. Commun. 2016; 7: 12886
        • McCall P.M.
        • Srivastava S.
        • Tirrell M.V.
        • et al.
        Partitioning and enhanced self-assembly of actin in polypeptide coacervates.
        Biophys. J. 2018; 114: 1636-1645
        • Schaus T.E.
        • Taylor E.W.
        • Borisy G.G.
        Self-organization of actin filament orientation in the dendritic-nucleation/array-treadmilling model.
        Proc. Natl. Acad. Sci. USA. 2007; 104: 7086-7091
        • Wu C.
        • Asokan S.B.
        • Bear J.E.
        • et al.
        Arp2/3 is critical for lamellipodia and response to extracellular matrix cues but is dispensable for chemotaxis.
        Cell. 2012; 148: 973-987
        • Mueller J.
        • Szep G.
        • Sixt M.
        • et al.
        Load adaptation of lamellipodial actin networks.
        Cell. 2017; 171: 188-200.e16