1
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Lemma B, Lemma LM, Ems-McClung SC, Walczak CE, Dogic Z, Needleman DJ. Structure and dynamics of motor-driven microtubule bundles. SOFT MATTER 2024; 20:5715-5723. [PMID: 38872426 PMCID: PMC11268426 DOI: 10.1039/d3sm01336g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
Connecting the large-scale emergent behaviors of active cytoskeletal materials to the microscopic properties of their constituents is a challenge due to a lack of data on the multiscale dynamics and structure of such systems. We approach this problem by studying the impact of depletion attraction on bundles of microtubules and kinesin-14 molecular motors. For all depletant concentrations, kinesin-14 bundles generate comparable extensile dynamics. However, this invariable mesoscopic behavior masks the transition in the microscopic motion of microtubules. Specifically, with increasing attraction, we observe a transition from bi-directional sliding with extension to pure extension with no sliding. Small-angle X-ray scattering shows that the transition in microtubule dynamics is concurrent with a structural rearrangement of microtubules from an open hexagonal to a compressed rectangular lattice. These results demonstrate that bundles of microtubules and molecular motors can display the same mesoscopic extensile behaviors despite having different internal structures and microscopic dynamics. They provide essential information for developing multiscale models of active matter.
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Affiliation(s)
- Bezia Lemma
- Physics Department, Harvard University, Cambridge, MA 02138, USA
- Physics Department, Brandeis University, Waltham, MA 02453, USA.
- Physics Department, University of California, Santa Barbara, CA 93106, USA
| | - Linnea M Lemma
- Physics Department, Brandeis University, Waltham, MA 02453, USA.
- Physics Department, University of California, Santa Barbara, CA 93106, USA
| | | | - Claire E Walczak
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Zvonimir Dogic
- Physics Department, Brandeis University, Waltham, MA 02453, USA.
- Physics Department, University of California, Santa Barbara, CA 93106, USA
- Biomolecular Science & Engineering Department, University of California, Santa Barbara, CA 93106, USA
| | - Daniel J Needleman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Molecular & Cellular Biology Department, Harvard University, Cambridge, MA 02138, USA
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
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2
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Redford SA, Colen J, Shivers JL, Zemsky S, Molaei M, Floyd C, Ruijgrok PV, Vitelli V, Bryant Z, Dinner AR, Gardel ML. Motor crosslinking augments elasticity in active nematics. SOFT MATTER 2024; 20:2480-2490. [PMID: 38385209 PMCID: PMC10933839 DOI: 10.1039/d3sm01176c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024]
Abstract
In active materials, uncoordinated internal stresses lead to emergent long-range flows. An understanding of how the behavior of active materials depends on mesoscopic (hydrodynamic) parameters is developing, but there remains a gap in knowledge concerning how hydrodynamic parameters depend on the properties of microscopic elements. In this work, we combine experiments and multiscale modeling to relate the structure and dynamics of active nematics composed of biopolymer filaments and molecular motors to their microscopic properties, in particular motor processivity, speed, and valency. We show that crosslinking of filaments by both motors and passive crosslinkers not only augments the contributions to nematic elasticity from excluded volume effects but dominates them. By altering motor kinetics we show that a competition between motor speed and crosslinking results in a nonmonotonic dependence of nematic flow on motor speed. By modulating passive filament crosslinking we show that energy transfer into nematic flow is in large part dictated by crosslinking. Thus motor proteins both generate activity and contribute to nematic elasticity. Our results provide new insights for rationally engineering active materials.
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Affiliation(s)
- Steven A Redford
- The Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.
| | - Jonathan Colen
- Department of Physics, University of Chicago, Chicago, IL 60637, USA
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Jordan L Shivers
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Sasha Zemsky
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Program in Biophysics, Stanford University, Stanford, CA 94305, USA
| | - Mehdi Molaei
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Carlos Floyd
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Paul V Ruijgrok
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Vincenzo Vitelli
- Department of Physics, University of Chicago, Chicago, IL 60637, USA
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aaron R Dinner
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Margaret L Gardel
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.
- Department of Physics, University of Chicago, Chicago, IL 60637, USA
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
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3
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Najma B, Wei WS, Baskaran A, Foster PJ, Duclos G. Microscopic interactions control a structural transition in active mixtures of microtubules and molecular motors. Proc Natl Acad Sci U S A 2024; 121:e2300174121. [PMID: 38175870 PMCID: PMC10786313 DOI: 10.1073/pnas.2300174121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 10/07/2023] [Indexed: 01/06/2024] Open
Abstract
Microtubules and molecular motors are essential components of the cellular cytoskeleton, driving fundamental processes in vivo, including chromosome segregation and cargo transport. When reconstituted in vitro, these cytoskeletal proteins serve as energy-consuming building blocks to study the self-organization of active matter. Cytoskeletal active gels display rich emergent dynamics, including extensile flows, locally contractile asters, and bulk contraction. However, it is unclear how the protein-protein interaction kinetics set their contractile or extensile nature. Here, we explore the origin of the transition from extensile bundles to contractile asters in a minimal reconstituted system composed of stabilized microtubules, depletant, adenosine 5'-triphosphate (ATP), and clusters of kinesin-1 motors. We show that the microtubule-binding and unbinding kinetics of highly processive motor clusters set their ability to end-accumulate, which can drive polarity sorting of the microtubules and aster formation. We further demonstrate that the microscopic time scale of end-accumulation sets the emergent time scale of aster formation. Finally, we show that biochemical regulation is insufficient to fully explain the transition as generic aligning interactions through depletion, cross-linking, or excluded volume interactions can drive bundle formation despite end-accumulating motors. The extensile-to-contractile transition is well captured by a simple self-assembly model where nematic and polar aligning interactions compete to form either bundles or asters. Starting from a five-dimensional organization phase space, we identify a single control parameter given by the ratio of the different component concentrations that dictates the material-scale organization. Overall, this work shows that the interplay of biochemical and mechanical tuning at the microscopic level controls the robust self-organization of active cytoskeletal materials.
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Affiliation(s)
- Bibi Najma
- Department of Physics, Brandeis University, Waltham, MA02453
| | - Wei-Shao Wei
- Department of Physics, Brandeis University, Waltham, MA02453
| | - Aparna Baskaran
- Department of Physics, Brandeis University, Waltham, MA02453
| | - Peter J. Foster
- Department of Physics, Brandeis University, Waltham, MA02453
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4
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McGorty RJ, Currie CJ, Michel J, Sasanpour M, Gunter C, Lindsay KA, Rust MJ, Katira P, Das M, Ross JL, Robertson-Anderson RM. Kinesin and myosin motors compete to drive rich multiphase dynamics in programmable cytoskeletal composites. PNAS NEXUS 2023; 2:pgad245. [PMID: 37575673 PMCID: PMC10416814 DOI: 10.1093/pnasnexus/pgad245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023]
Abstract
The cellular cytoskeleton relies on diverse populations of motors, filaments, and binding proteins acting in concert to enable nonequilibrium processes ranging from mitosis to chemotaxis. The cytoskeleton's versatile reconfigurability, programmed by interactions between its constituents, makes it a foundational active matter platform. However, current active matter endeavors are limited largely to single force-generating components acting on a single substrate-far from the composite cytoskeleton in cells. Here, we engineer actin-microtubule (MT) composites, driven by kinesin and myosin motors and tuned by crosslinkers, to ballistically restructure and flow with speeds that span three orders of magnitude depending on the composite formulation and time relative to the onset of motor activity. Differential dynamic microscopy analyses reveal that kinesin and myosin compete to delay the onset of acceleration and suppress discrete restructuring events, while passive crosslinking of either actin or MTs has an opposite effect. Our minimal advection-diffusion model and spatial correlation analyses correlate these dynamics to structure, with motor antagonism suppressing reconfiguration and demixing, while crosslinking enhances clustering. Despite the rich formulation space and emergent formulation-dependent structures, the nonequilibrium dynamics across all composites and timescales can be organized into three classes-slow isotropic reorientation, fast directional flow, and multimode restructuring. Moreover, our mathematical model demonstrates that diverse structural motifs can arise simply from the interplay between motor-driven advection and frictional drag. These general features of our platform facilitate applicability to other active matter systems and shed light on diverse ways that cytoskeletal components can cooperate or compete to enable wide-ranging cellular processes.
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Affiliation(s)
- Ryan J McGorty
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA
| | - Christopher J Currie
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA
| | - Jonathan Michel
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Mehrzad Sasanpour
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA
| | - Christopher Gunter
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA
| | - K Alice Lindsay
- Department of Physics, Syracuse University, Syracuse, NY 13244, USA
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Parag Katira
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA
| | - Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Jennifer L Ross
- Department of Physics, Syracuse University, Syracuse, NY 13244, USA
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5
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Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg CP. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biol 2023; 21:e3002146. [PMID: 37289834 DOI: 10.1371/journal.pbio.3002146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/03/2023] [Indexed: 06/10/2023] Open
Abstract
Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation.
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Affiliation(s)
- Shayan Shamipour
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Laura Hofmann
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Irene Steccari
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Roland Kardos
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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6
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Lemma LM, Varghese M, Ross TD, Thomson M, Baskaran A, Dogic Z. Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids. PNAS NEXUS 2023; 2:pgad130. [PMID: 37168671 PMCID: PMC10165807 DOI: 10.1093/pnasnexus/pgad130] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 02/27/2023] [Accepted: 04/03/2023] [Indexed: 05/13/2023]
Abstract
Microtubule-based active fluids exhibit turbulent-like autonomous flows, which are driven by the molecular motor powered motion of filamentous constituents. Controlling active stresses in space and time is an essential prerequisite for controlling the intrinsically chaotic dynamics of extensile active fluids. We design single-headed kinesin molecular motors that exhibit optically enhanced clustering and thus enable precise and repeatable spatial and temporal control of extensile active stresses. Such motors enable rapid, reversible switching between flowing and quiescent states. In turn, spatio-temporal patterning of the active stress controls the evolution of the ubiquitous bend instability of extensile active fluids and determines its critical length dependence. Combining optically controlled clusters with conventional kinesin motors enables one-time switching from contractile to extensile active stresses. These results open a path towards real-time control of the autonomous flows generated by active fluids.
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Affiliation(s)
- Linnea M Lemma
- Department of Physics, Brandeis University, 415 South St., Waltham, 02453 MA, USA
- Department of Physics, University of California, Santa Barbara, 93106 CA, USA
| | - Minu Varghese
- Department of Physics, Brandeis University, 415 South St., Waltham, 02453 MA, USA
| | - Tyler D Ross
- Department of Computing and Mathematical Sciences, California Institute of Technology, 1200 E California Blvd. Pasadena, 91125 CA, USA
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, 91125 CA, USA
| | - Aparna Baskaran
- Department of Physics, Brandeis University, 415 South St., Waltham, 02453 MA, USA
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7
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Foster PJ, Bae J, Lemma B, Zheng J, Ireland W, Chandrakar P, Boros R, Dogic Z, Needleman DJ, Vlassak JJ. Dissipation and energy propagation across scales in an active cytoskeletal material. Proc Natl Acad Sci U S A 2023; 120:e2207662120. [PMID: 37000847 PMCID: PMC10083585 DOI: 10.1073/pnas.2207662120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 02/22/2023] [Indexed: 04/03/2023] Open
Abstract
Living systems are intrinsically nonequilibrium: They use metabolically derived chemical energy to power their emergent dynamics and self-organization. A crucial driver of these dynamics is the cellular cytoskeleton, a defining example of an active material where the energy injected by molecular motors cascades across length scales, allowing the material to break the constraints of thermodynamic equilibrium and display emergent nonequilibrium dynamics only possible due to the constant influx of energy. Notwithstanding recent experimental advances in the use of local probes to quantify entropy production and the breaking of detailed balance, little is known about the energetics of active materials or how energy propagates from the molecular to emergent length scales. Here, we use a recently developed picowatt calorimeter to experimentally measure the energetics of an active microtubule gel that displays emergent large-scale flows. We find that only approximately one-billionth of the system's total energy consumption contributes to these emergent flows. We develop a chemical kinetics model that quantitatively captures how the system's total thermal dissipation varies with ATP and microtubule concentrations but that breaks down at high motor concentration, signaling an interference between motors. Finally, we estimate how energy losses accumulate across scales. Taken together, these results highlight energetic efficiency as a key consideration for the engineering of active materials and are a powerful step toward developing a nonequilibrium thermodynamics of living systems.
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Affiliation(s)
- Peter J. Foster
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Physics, Brandeis University, Waltham, MA02454
| | - Jinhye Bae
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
- Department of NanoEngineering, University of California San Diego, La Jolla, CA92093
| | - Bezia Lemma
- Department of Physics, Brandeis University, Waltham, MA02454
- Department of Physics, Harvard University, Cambridge, MA02138
- Department of Physics, University of California, Santa Barbara, CA93106
| | - Juanjuan Zheng
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - William Ireland
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Pooja Chandrakar
- Department of Physics, Brandeis University, Waltham, MA02454
- Department of Physics, University of California, Santa Barbara, CA93106
| | - Rémi Boros
- Department of Physics, University of California, Santa Barbara, CA93106
| | - Zvonimir Dogic
- Department of Physics, Brandeis University, Waltham, MA02454
- Department of Physics, University of California, Santa Barbara, CA93106
| | - Daniel J. Needleman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
- Center for Computational Biology, Flatiron Institute, New York, NY10010
| | - Joost J. Vlassak
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
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8
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Chew WX, Henkin G, Nédélec F, Surrey T. Effects of microtubule length and crowding on active microtubule network organization. iScience 2023; 26:106063. [PMID: 36852161 PMCID: PMC9958361 DOI: 10.1016/j.isci.2023.106063] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/12/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Active filament networks can organize into various dynamic architectures driven by cross-linking motors. Densities and kinetic properties of motors and microtubules have been shown previously to determine active microtubule network self-organization, but the effects of other control parameters are less understood. Using computer simulations, we study here how microtubule lengths and crowding effects determine active network architecture and dynamics. We find that attractive interactions mimicking crowding effects or long microtubules both promote the formation of extensile nematic networks instead of asters. When microtubules are very long and the network is highly connected, a new isotropically motile network state resembling a "gliding mesh" is predicted. Using in vitro reconstitutions, we confirm the existence of this gliding mesh experimentally. These results provide a better understanding of how active microtubule network organization can be controlled, with implications for cell biology and active materials in general.
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Affiliation(s)
- Wei-Xiang Chew
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Gil Henkin
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
| | - François Nédélec
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK,Corresponding author
| | - Thomas Surrey
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain,ICREA, Passeig de Lluis Companys 23, 08010 Barcelona, Spain,Corresponding author
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9
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Striebel M, Brauns F, Frey E. Length Regulation Drives Self-Organization in Filament-Motor Mixtures. PHYSICAL REVIEW LETTERS 2022; 129:238102. [PMID: 36563230 DOI: 10.1103/physrevlett.129.238102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/10/2022] [Indexed: 06/17/2023]
Abstract
Cytoskeletal networks form complex intracellular structures. Here we investigate a minimal model for filament-motor mixtures in which motors act as depolymerases and thereby regulate filament length. Combining agent-based simulations and hydrodynamic equations, we show that resource-limited length regulation drives the formation of filament clusters despite the absence of mechanical interactions between filaments. Even though the orientation of individual remains fixed, collective filament orientation emerges in the clusters, aligned orthogonal to their interfaces.
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Affiliation(s)
- Moritz Striebel
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, D-80333 Munich, Germany
| | - Fridtjof Brauns
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, D-80333 Munich, Germany
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, D-80333 Munich, Germany
- Max Planck School Matter to Life, Hofgartenstraße 8, D-80539 Munich, Germany
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10
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Sheung JY, Garamella J, Kahl SK, Lee BY, McGorty RJ, Robertson-Anderson RM. Motor-driven advection competes with crowding to drive spatiotemporally heterogeneous transport in cytoskeleton composites. FRONTIERS IN PHYSICS 2022; 10:1055441. [PMID: 37547053 PMCID: PMC10403238 DOI: 10.3389/fphy.2022.1055441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The cytoskeleton-a composite network of biopolymers, molecular motors, and associated binding proteins-is a paradigmatic example of active matter. Particle transport through the cytoskeleton can range from anomalous and heterogeneous subdiffusion to superdiffusion and advection. Yet, recapitulating and understanding these properties-ubiquitous to the cytoskeleton and other out-of-equilibrium soft matter systems-remains challenging. Here, we combine light sheet microscopy with differential dynamic microscopy and single-particle tracking to elucidate anomalous and advective transport in actomyosin-microtubule composites. We show that particles exhibit multi-mode transport that transitions from pronounced subdiffusion to superdiffusion at tunable crossover timescales. Surprisingly, while higher actomyosin content increases the range of timescales over which transport is superdiffusive, it also markedly increases the degree of subdiffusion at short timescales and generally slows transport. Corresponding displacement distributions display unique combinations of non-Gaussianity, asymmetry, and non-zero modes, indicative of directed advection coupled with caged diffusion and hopping. At larger spatiotemporal scales, particles in active composites exhibit superdiffusive dynamics with scaling exponents that are robust to changing actomyosin fractions, in contrast to normal, yet faster, diffusion in networks without actomyosin. Our specific results shed important new light on the interplay between non-equilibrium processes, crowding and heterogeneity in active cytoskeletal systems. More generally, our approach is broadly applicable to active matter systems to elucidate transport and dynamics across scales.
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Affiliation(s)
- Janet Y. Sheung
- W. M. Keck Science Department, Scripps College, Claremont, CA, United States
- W. M. Keck Science Department, Pitzer College, Claremont, CA, United States
| | - Jonathan Garamella
- Physics and Biophysics Department, University of San Diego, San Diego, CA, United States
| | - Stella K. Kahl
- W. M. Keck Science Department, Scripps College, Claremont, CA, United States
| | - Brian Y. Lee
- W. M. Keck Science Department, Pitzer College, Claremont, CA, United States
| | - Ryan J. McGorty
- Physics and Biophysics Department, University of San Diego, San Diego, CA, United States
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11
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Najma B, Varghese M, Tsidilkovski L, Lemma L, Baskaran A, Duclos G. Competing instabilities reveal how to rationally design and control active crosslinked gels. Nat Commun 2022; 13:6465. [PMID: 36309493 PMCID: PMC9617906 DOI: 10.1038/s41467-022-34089-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/13/2022] [Indexed: 12/25/2022] Open
Abstract
How active stresses generated by molecular motors set the large-scale mechanics of the cell cytoskeleton remains poorly understood. Here, we combine experiments and theory to demonstrate how the emergent properties of a biomimetic active crosslinked gel depend on the properties of its microscopic constituents. We show that an extensile nematic elastomer exhibits two distinct activity-driven instabilities, spontaneously bending in-plane or buckling out-of-plane depending on its composition. Molecular motors play a dual antagonistic role, fluidizing or stiffening the gel depending on the ATP concentration. We demonstrate how active and elastic stresses are set by each component, providing estimates for the active gel theory parameters. Finally, activity and elasticity were manipulated in situ with light-activable motor proteins, controlling the direction of the instability optically. These results highlight how cytoskeletal stresses regulate the self-organization of living matter and set the foundations for the rational design and optogenetic control of active materials.
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Affiliation(s)
- Bibi Najma
- grid.253264.40000 0004 1936 9473Department of Physics, Brandeis University, Waltham, MA 02453 USA
| | - Minu Varghese
- grid.253264.40000 0004 1936 9473Department of Physics, Brandeis University, Waltham, MA 02453 USA ,grid.214458.e0000000086837370Department of Physics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Lev Tsidilkovski
- grid.253264.40000 0004 1936 9473Department of Physics, Brandeis University, Waltham, MA 02453 USA
| | - Linnea Lemma
- grid.253264.40000 0004 1936 9473Department of Physics, Brandeis University, Waltham, MA 02453 USA ,grid.133342.40000 0004 1936 9676Department of Physics, University of California at Santa Barbara, Santa Barbara, CA 93106 USA ,grid.16750.350000 0001 2097 5006Present Address: Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544 USA
| | - Aparna Baskaran
- grid.253264.40000 0004 1936 9473Department of Physics, Brandeis University, Waltham, MA 02453 USA
| | - Guillaume Duclos
- grid.253264.40000 0004 1936 9473Department of Physics, Brandeis University, Waltham, MA 02453 USA
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12
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Lorenz C, Köster S. Multiscale architecture: Mechanics of composite cytoskeletal networks. BIOPHYSICS REVIEWS 2022; 3:031304. [PMID: 38505277 PMCID: PMC10903411 DOI: 10.1063/5.0099405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/27/2022] [Indexed: 03/21/2024]
Abstract
Different types of biological cells respond differently to mechanical stresses, and these responses are mainly governed by the cytoskeleton. The main components of this biopolymer network are actin filaments, microtubules, and intermediate filaments, whose mechanical and dynamic properties are highly distinct, thus opening up a large mechanical parameter space. Aside from experiments on whole, living cells, "bottom-up" approaches, utilizing purified, reconstituted protein systems, tremendously help to shed light on the complex mechanics of cytoskeletal networks. Such experiments are relevant in at least three aspects: (i) from a fundamental point of view, cytoskeletal networks provide a perfect model system for polymer physics; (ii) in materials science and "synthetic cell" approaches, one goal is to fully understand properties of cellular materials and reconstitute them in synthetic systems; (iii) many diseases are associated with cell mechanics, so a thorough understanding of the underlying phenomena may help solving pressing biomedical questions. In this review, we discuss the work on networks consisting of one, two, or all three types of filaments, entangled or cross-linked, and consider active elements such as molecular motors and dynamically growing filaments. Interestingly, tuning the interactions among the different filament types results in emergent network properties. We discuss current experimental challenges, such as the comparability of different studies, and recent methodological advances concerning the quantification of attractive forces between filaments and their influence on network mechanics.
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Affiliation(s)
- C. Lorenz
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - S. Köster
- Author to whom correspondence should be addressed:
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13
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Sasanpour M, Achiriloaie DH, Lee G, Leech G, Hendija M, Lindsay KA, Ross JL, McGorty RJ, Robertson-Anderson RM. Reconstituting and Characterizing Actin-Microtubule Composites with Tunable Motor-Driven Dynamics and Mechanics. J Vis Exp 2022:10.3791/64228. [PMID: 36094259 PMCID: PMC10290881 DOI: 10.3791/64228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023] Open
Abstract
The composite cytoskeleton, comprising interacting networks of semiflexible actin filaments and rigid microtubules, restructures and generates forces using motor proteins such as myosin II and kinesin to drive key processes such as migration, cytokinesis, adhesion, and mechanosensing. While actin-microtubule interactions are key to the cytoskeleton's versatility and adaptability, an understanding of their interplay with myosin and kinesin activity is still nascent. This work describes how to engineer tunable three-dimensional composite networks of co-entangled actin filaments and microtubules that undergo active restructuring and ballistic motion, driven by myosin II and kinesin motors, and are tuned by the relative concentrations of actin, microtubules, motor proteins, and passive crosslinkers. Protocols for fluorescence labeling of the microtubules and actin filaments to most effectively visualize composite restructuring and motion using multi-spectral confocal imaging are also detailed. Finally, the results of data analysis methods that can be used to quantitatively characterize non-equilibrium structure, dynamics, and mechanics are presented. Recreating and investigating this tunable biomimetic platform provides valuable insight into how coupled motor activity, composite mechanics, and filament dynamics can lead to myriad cellular processes from mitosis to polarization to mechano-sensation.
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Affiliation(s)
| | - Daisy H Achiriloaie
- Department of Physics and Biophysics, University of San Diego; W. M. Keck Science Department, Scripps College, Pitzer College, and Claremont McKenna College
| | - Gloria Lee
- Department of Physics and Biophysics, University of San Diego
| | - Gregor Leech
- Department of Physics and Biophysics, University of San Diego
| | - Maya Hendija
- Department of Physics and Biophysics, University of San Diego
| | | | | | - Ryan J McGorty
- Department of Physics and Biophysics, University of San Diego
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14
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Cross-linker design determines microtubule network organization by opposing motors. Proc Natl Acad Sci U S A 2022; 119:e2206398119. [PMID: 35960844 PMCID: PMC9388136 DOI: 10.1073/pnas.2206398119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Inheritance of genetic material following chromosome duplication in eukaryotic cell division is coordinated by the spindle apparatus. The spindle is a highly interconnected network of microtubule filaments that are cross-linked by different types of molecular motors. How the different motors cooperate to organize the spindle network is not understood. Here, we show that an asymmetric cross-linker design can confer bifunctionality to a mitotic motor in the presence of other motors. The asymmetric motor supports both extensile and contractile microtubule network behaviors as observed in different parts of the spindle. These findings define rules controlling the generation of active microtubule networks and allow us to better understand how motors cooperate to organize the correct spindle architecture when a cell divides. During cell division, cross-linking motors determine the architecture of the spindle, a dynamic microtubule network that segregates the chromosomes in eukaryotes. It is unclear how motors with opposite directionality coordinate to drive both contractile and extensile behaviors in the spindle. Particularly, the impact of different cross-linker designs on network self-organization is not understood, limiting our understanding of self-organizing structures in cells but also our ability to engineer new active materials. Here, we use experiment and theory to examine active microtubule networks driven by mixtures of motors with opposite directionality and different cross-linker design. We find that although the kinesin-14 HSET causes network contraction when dominant, it can also assist the opposing kinesin-5 KIF11 to generate extensile networks. This bifunctionality results from HSET’s asymmetric design, distinct from symmetric KIF11. These findings expand the set of rules underlying patterning of active microtubule assemblies and allow a better understanding of motor cooperation in the spindle.
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15
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Lemma B, Mitchell NP, Subramanian R, Needleman DJ, Dogic Z. Active Microphase Separation in Mixtures of Microtubules and Tip-Accumulating Molecular Motors. PHYSICAL REVIEW. X 2022; 12:031006. [PMID: 36643940 PMCID: PMC9835929 DOI: 10.1103/physrevx.12.031006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Mixtures of filaments and molecular motors form active materials with diverse dynamical behaviors that vary based on their constituents' molecular properties. To develop a multiscale of these materials, we map the nonequilibrium phase diagram of microtubules and tip-accumulating kinesin-4 molecular motors. We find that kinesin-4 can drive either global contractions or turbulentlike extensile dynamics, depending on the concentrations of both microtubules and a bundling agent. We also observe a range of spatially heterogeneous nonequilibrium phases, including finite-sized radial asters, 1D wormlike chains, extended 2D bilayers, and system-spanning 3D active foams. Finally, we describe intricate kinetic pathways that yield microphase separated structures and arise from the inherent frustration between the orientational order of filamentous microtubules and the positional order of tip-accumulating molecular motors. Our work reveals a range of novel active states. It also shows that the form of active stresses is not solely dictated by the properties of individual motors and filaments, but is also contingent on the constituent concentrations and spatial arrangement of motors on the filaments.
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Affiliation(s)
- Bezia Lemma
- Physics Department, Harvard University, Cambridge, Massachusetts 02138, USA
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
- Physics Department, University of California, Santa Barbara, California 93106, USA
| | - Noah P. Mitchell
- Physics Department, University of California, Santa Barbara, California 93106, USA
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
| | - Radhika Subramanian
- Molecular Biology Department, Massachusetts General Hospital Boston, Massachusetts 02114, USA
- Genetics Department, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Daniel J. Needleman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
- Molecular and Cellular Biology Department, Harvard University, Cambridge, Massachusetts 02138, USA
- Center for Computational Biology, Flatiron Institute, New York, New York 10010, USA
| | - Zvonimir Dogic
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
- Physics Department, University of California, Santa Barbara, California 93106, USA
- Biomolecular Science and Engineering Department, University of California, Santa Barbara, California 93106, USA
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16
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Ansari S, Yan W, Lamson A, Shelley MJ, Glaser MA, Betterton MD. Active condensation of filaments under spatial confinement. FRONTIERS IN PHYSICS 2022; 10:897255. [PMID: 38116396 PMCID: PMC10730113 DOI: 10.3389/fphy.2022.897255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Living systems exhibit self-organization, a phenomenon that enables organisms to perform functions essential for life. The interior of living cells is a crowded environment in which the self-assembly of cytoskeletal networks is spatially constrained by membranes and organelles. Cytoskeletal filaments undergo active condensation in the presence of crosslinking motor proteins. In past studies, confinement has been shown to alter the morphology of active condensates. Here, we perform simulations to explore systems of filaments and crosslinking motors in a variety of confining geometries. We simulate spatial confinement imposed by hard spherical, cylindrical, and planar boundaries. These systems exhibit non-equilibrium condensation behavior where crosslinking motors condense a fraction of the overall filament population, leading to coexistence of vapor and condensed states. We find that the confinement lengthscale modifies the dynamics and condensate morphology. With end-pausing crosslinking motors, filaments self-organize into half asters and fully-symmetric asters under spherical confinement, polarity-sorted bilayers and bottle-brush-like states under cylindrical confinement, and flattened asters under planar confinement. The number of crosslinking motors controls the size and shape of condensates, with flattened asters becoming hollow and ring-like for larger motor number. End pausing plays a key role affecting condensate morphology: systems with end-pausing motors evolve into aster-like condensates while those with non-end-pausing crosslinking motor proteins evolve into disordered clusters and polarity-sorted bundles.
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Affiliation(s)
- Saad Ansari
- Department of Physics, University of Colorado Boulder, Colorado, USA
| | - Wen Yan
- Center for Computational Biology, Flatiron Institute, New York, USA
| | - Adam Lamson
- Center for Computational Biology, Flatiron Institute, New York, USA
| | - Michael J. Shelley
- Center for Computational Biology, Flatiron Institute, New York, USA
- Courant Institute, New York University, New York, USA
| | - Matthew A. Glaser
- Department of Physics, University of Colorado Boulder, Colorado, USA
- Center for Computational Biology, Flatiron Institute, New York, USA
| | - Meredith D. Betterton
- Department of Physics, University of Colorado Boulder, Colorado, USA
- Center for Computational Biology, Flatiron Institute, New York, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Colorado, USA
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17
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Sarfati G, Maitra A, Voituriez R, Galas JC, Estevez-Torres A. Crosslinking and depletion determine spatial instabilities in cytoskeletal active matter. SOFT MATTER 2022; 18:3793-3800. [PMID: 35521993 DOI: 10.1039/d2sm00130f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Active gels made of cytoskeletal proteins are valuable materials with attractive non-equilibrium properties such as spatial self-organization and self-propulsion. At least four typical routes to spatial patterning have been reported to date in different types of cytoskeletal active gels: bending and buckling instabilities in extensile systems, and global and local contraction instabilities in contractile gels. Here we report the observation of these four instabilities in a single type of active gel and we show that they are controlled by two parameters: the concentrations of ATP and depletion agent. We demonstrate that as the ATP concentration decreases, the concentration of passive motors increases until the gel undergoes a gelation transition. At this point, buckling is selected against bending, while global contraction is favored over local ones. Our observations are coherent with a hydrodynamic model of a viscoelastic active gel where the filaments are crosslinked with a characteristic time that diverges as the ATP concentration decreases. Our work thus provides a unified view of spatial instabilities in cytoskeletal active matter.
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Affiliation(s)
- Guillaume Sarfati
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin, (LJP), F-75005 Paris, France.
| | - Ananyo Maitra
- Laboratoire de Physique Théorique et Modélisation, CNRS UMR 8089, CY Cergy Paris, Université, F-95302 Cergy-Pontoise Cedex, France
| | - Raphael Voituriez
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin, (LJP), F-75005 Paris, France.
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, (LPTMC), F-75005 Paris, France
| | - Jean-Christophe Galas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin, (LJP), F-75005 Paris, France.
| | - André Estevez-Torres
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin, (LJP), F-75005 Paris, France.
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18
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Chandrakar P, Berezney J, Lemma B, Hishamunda B, Berry A, Wu KT, Subramanian R, Chung J, Needleman D, Gelles J, Dogic Z. Engineering stability, longevity, and miscibility of microtubule-based active fluids. SOFT MATTER 2022; 18:1825-1835. [PMID: 35167642 DOI: 10.1039/d1sm01289d] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Microtubule-based active matter provides insight into the self-organization of motile interacting constituents. We describe several formulations of microtubule-based 3D active isotropic fluids. Dynamics of these fluids is powered by three types of kinesin motors: a processive motor, a non-processive motor, and a motor which is permanently linked to a microtubule backbone. Another modification uses a specific microtubule crosslinker to induce bundle formation instead of a non-specific polymer depletant. In comparison to the already established system, each formulation exhibits distinct properties. These developments reveal the temporal stability of microtubule-based active fluids while extending their reach and the applicability.
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Affiliation(s)
- Pooja Chandrakar
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
- Department of Physics, University of California, Santa Barbara, California 93106, USA.
| | - John Berezney
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Bezia Lemma
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
- Department of Physics, University of California, Santa Barbara, California 93106, USA.
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Bernard Hishamunda
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Angela Berry
- Hampton University School of Pharmacy, 121 William R. Harvey Way, Hampton, VA 23668, USA
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Kun-Ta Wu
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
- Department of Physics, Worcester Polytechnic Institute, 100 Institute Road, Worcester, Massachusetts 01609, USA
| | - Radhika Subramanian
- Department of Genetics, HMS and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Johnson Chung
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Daniel Needleman
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Zvonimir Dogic
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA
- Department of Physics, University of California, Santa Barbara, California 93106, USA.
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19
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Extensile to contractile transition in active microtubule-actin composites generates layered asters with programmable lifetimes. Proc Natl Acad Sci U S A 2022; 119:2115895119. [PMID: 35086931 PMCID: PMC8812548 DOI: 10.1073/pnas.2115895119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
We study a reconstituted composite system consisting of an active microtubule network interdigitated with a passive network of entangled F-actin filaments. Increasing the concentration of filamentous actin controls the emergent dynamics, inducing a transition from turbulent-like flows to bulk contractions. At intermediate concentrations, where the active stresses change their symmetry from anisotropic extensile to isotropic contracting, the composite separates into layered asters that coexist with the background turbulent fluid. Contracted onion-like asters have a radially extending microtubule-rich cortex that envelops alternating layers of microtubules and F-actin. These self-regulating structures undergo internal reorganization, which appears to minimize the surface area and maintain the ordered layering, even when undergoing aster merging events. Finally, the layered asters are metastable structures. Their lifetime, which ranges from minutes to hours, is encoded in the material properties of the composite. These results challenge the current models of active matter. They demonstrate self-organized dynamical states and patterns evocative of those observed in the cytoskeleton do not require precise biochemical regulation, but can arise from purely mechanical interactions of actively driven filamentous materials.
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20
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Schildknecht D, Popova AN, Stellwagen J, Thomson M. Reinforcement learning reveals fundamental limits on the mixing of active particles. SOFT MATTER 2022; 18:617-625. [PMID: 34929723 DOI: 10.1039/d1sm01400e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The control of far-from-equilibrium physical systems, including active materials, requires advanced control strategies due to the non-linear dynamics and long-range interactions between particles, preventing explicit solutions to optimal control problems. In such situations, Reinforcement Learning (RL) has emerged as an approach to derive suitable control strategies. However, for active matter systems, it is an important open question how the mathematical structure and the physical properties determine the tractability of RL. In this paper, we demonstrate that RL can only find good mixing strategies for active matter systems that combine attractive and repulsive interactions. Using analytic results from dynamical systems theory, we show that combining both interaction types is indeed necessary for the existence of mixing-inducing hyperbolic dynamics and therefore the ability of RL to find homogeneous mixing strategies. In particular, we show that for drag-dominated translational-invariant particle systems, mixing relies on combined attractive and repulsive interactions. Therefore, our work demonstrates which experimental developments need to be made to make protein-based active matter applicable, and it provides some classification of microscopic interactions based on macroscopic behavior.
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Affiliation(s)
- Dominik Schildknecht
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Anastasia N Popova
- Applied and Computational Mathematics, California Institute of Technology, Pasadena CA, USA
| | - Jack Stellwagen
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Matt Thomson
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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21
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Yan W, Ansari S, Lamson A, Glaser MA, Blackwell R, Betterton MD, Shelley M. Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies. eLife 2022; 11:74160. [PMID: 35617115 PMCID: PMC9135453 DOI: 10.7554/elife.74160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 04/24/2022] [Indexed: 11/17/2022] Open
Abstract
The cytoskeleton - a collection of polymeric filaments, molecular motors, and crosslinkers - is a foundational example of active matter, and in the cell assembles into organelles that guide basic biological functions. Simulation of cytoskeletal assemblies is an important tool for modeling cellular processes and understanding their surprising material properties. Here, we present aLENS (a Living Ensemble Simulator), a novel computational framework designed to surmount the limits of conventional simulation methods. We model molecular motors with crosslinking kinetics that adhere to a thermodynamic energy landscape, and integrate the system dynamics while efficiently and stably enforcing hard-body repulsion between filaments. Molecular potentials are entirely avoided in imposing steric constraints. Utilizing parallel computing, we simulate tens to hundreds of thousands of cytoskeletal filaments and crosslinking motors, recapitulating emergent phenomena such as bundle formation and buckling. This simulation framework can help elucidate how motor type, thermal fluctuations, internal stresses, and confinement determine the evolution of cytoskeletal active matter.
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Affiliation(s)
- Wen Yan
- Center for Computational Biology, Flatiron InstituteNew YorkUnited States
| | - Saad Ansari
- Department of Physics, University of Colorado BoulderBoulderUnited States
| | - Adam Lamson
- Center for Computational Biology, Flatiron InstituteNew YorkUnited States,Department of Physics, University of Colorado BoulderBoulderUnited States
| | - Matthew A Glaser
- Department of Physics, University of Colorado BoulderBoulderUnited States
| | - Robert Blackwell
- Center for Computational Biology, Flatiron InstituteNew YorkUnited States
| | - Meredith D Betterton
- Center for Computational Biology, Flatiron InstituteNew YorkUnited States,Department of Physics, University of Colorado BoulderBoulderUnited States,Department of Molecular, Cellular, and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | - Michael Shelley
- Center for Computational Biology, Flatiron InstituteNew YorkUnited States,Courant Institute, New York UniversityNew YorkUnited States
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22
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Del Junco C, Estevez-Torres A, Maitra A. Front speed and pattern selection of a propagating chemical front in an active fluid. Phys Rev E 2022; 105:014602. [PMID: 35193207 DOI: 10.1103/physreve.105.014602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 11/24/2021] [Indexed: 01/18/2023]
Abstract
Spontaneous pattern formation in living systems is driven by reaction-diffusion chemistry and active mechanics. The feedback between chemical and mechanical forces is often essential to robust pattern formation, yet it remains poorly understood in general. In this analytical and numerical paper, we study an experimentally motivated minimal model of coupling between reaction-diffusion and active matter: a propagating front of an autocatalytic and stress-generating species. In the absence of activity, the front is described by the well-studied Kolmogorov, Petrovsky, and Piskunov equation. We find that front propagation is maintained even in active systems, with crucial differences: an extensile stress increases the front speed beyond a critical magnitude of the stress, while a contractile stress has no effect on the front speed but can generate a periodic instability in the high-concentration region behind the front. We expect our results to be useful in interpreting pattern formation in active systems with mechanochemical coupling in vivo and in vitro.
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Affiliation(s)
- Clara Del Junco
- Department of Chemistry and Department of Sociology, University of Chicago, Chicago, Illinois 60637, USA and Wesleyan University Library, Middletown, Connecticut 06459, USA
| | - André Estevez-Torres
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), F-75005, Paris
| | - Ananyo Maitra
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), F-75005, Paris and Laboratoire de Physique Théorique et Modélisation, CNRS UMR 8089, CY Cergy Paris Université, F-95302 Cergy-Pontoise Cedex, France
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23
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Senoussi A, Galas JC, Estevez-Torres A. Programmed mechano-chemical coupling in reaction-diffusion active matter. SCIENCE ADVANCES 2021; 7:eabi9865. [PMID: 34919433 PMCID: PMC8682988 DOI: 10.1126/sciadv.abi9865] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Embryo morphogenesis involves a complex combination of self-organization mechanisms that generate a great diversity of patterns. However, classical in vitro patterning experiments explore only one self-organization mechanism at a time, thus missing coupling effects. Here, we conjugate two major out-of-equilibrium patterning mechanisms—reaction-diffusion and active matter—by integrating dissipative DNA/enzyme reaction networks within an active gel composed of cytoskeletal motors and filaments. We show that the strength of the flow generated by the active gel controls the mechano-chemical coupling between the two subsystems. This property was used to engineer a synthetic material where contractions trigger chemical reaction networks both in time and space, thus mimicking key aspects of the polarization mechanism observed in C. elegans oocytes. We anticipate that reaction-diffusion active matter will promote the investigation of mechano-chemical transduction and the design of new materials with life-like properties.
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24
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Zhovmer AS, Manning A, Smith C, Hayes JB, Burnette DT, Wang J, Cartagena-Rivera AX, Dokholyan NV, Singh RK, Tabdanov ED. Mechanical Counterbalance of Kinesin and Dynein Motors in a Microtubular Network Regulates Cell Mechanics, 3D Architecture, and Mechanosensing. ACS NANO 2021; 15:17528-17548. [PMID: 34677937 PMCID: PMC9291236 DOI: 10.1021/acsnano.1c04435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Microtubules (MTs) and MT motor proteins form active 3D networks made of unstretchable cables with rod-like bending mechanics that provide cells with a dynamically changing structural scaffold. In this study, we report an antagonistic mechanical balance within the dynein-kinesin microtubular motor system. Dynein activity drives the microtubular network inward compaction, while isolated activity of kinesins bundles and expands MTs into giant circular bands that deform the cell cortex into discoids. Furthermore, we show that dyneins recruit MTs to sites of cell adhesion, increasing the topographic contact guidance of cells, while kinesins antagonize it via retraction of MTs from sites of cell adhesion. Actin-to-microtubule translocation of septin-9 enhances kinesin-MT interactions, outbalances the activity of kinesins over that of dyneins, and induces the discoid architecture of cells. These orthogonal mechanisms of MT network reorganization highlight the existence of an intricate mechanical balance between motor activities of kinesins and dyneins that controls cell 3D architecture, mechanics, and cell-microenvironment interactions.
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Affiliation(s)
- Alexander S. Zhovmer
- Center
for Biologics Evaluation and Research, U.S.
Food and Drug Administration, Silver Spring, Maryland 20903, United States
- . Tel: 1-301-402-1606
| | - Alexis Manning
- Center
for Biologics Evaluation and Research, U.S.
Food and Drug Administration, Silver Spring, Maryland 20903, United States
| | - Chynna Smith
- Section
on Mechanobiology, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - James B. Hayes
- Department
of Cell and Developmental Biology, Vanderbilt Medical Center, University of Vanderbilt, Nashville, Tennessee 37232, United States
| | - Dylan T. Burnette
- Department
of Cell and Developmental Biology, Vanderbilt Medical Center, University of Vanderbilt, Nashville, Tennessee 37232, United States
| | - Jian Wang
- Department
of Pharmacology, Penn State College of Medicine, Pennsylvania State University, Hummelstown, Pennsylvania 17036, United States
| | - Alexander X. Cartagena-Rivera
- Section
on Mechanobiology, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
- . Tel: 1-301-503-4033
| | - Nikolay V. Dokholyan
- Department
of Pharmacology, Penn State College of Medicine, Pennsylvania State University, Hummelstown, Pennsylvania 17036, United States
- Department
of Biochemistry & Molecular Biology, Penn State College of Medicine, Pennsylvania State University, Hershey, Pennsylvania 17033, United States
- . Tel: 1-717-531-5177
| | - Rakesh K. Singh
- Department
of Obstetrics and Gynecology, University
of Rochester Medical Center, Rochester, New York 14620, United States
- . Tel: 1-585-276-6281
| | - Erdem D. Tabdanov
- Department
of Pharmacology, Penn State College of Medicine, Pennsylvania State University, Hummelstown, Pennsylvania 17036, United States
- . Tel: 1-717-531-0003 Ext: 4430
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25
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Neahring L, Cho NH, Dumont S. Opposing motors provide mechanical and functional robustness in the human spindle. Dev Cell 2021; 56:3006-3018.e5. [PMID: 34614397 DOI: 10.1016/j.devcel.2021.09.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/27/2021] [Accepted: 09/13/2021] [Indexed: 11/30/2022]
Abstract
At each cell division, the spindle self-organizes from microtubules and motors. In human spindles, the motors dynein and Eg5 generate contractile and extensile stress, respectively. Inhibiting dynein or its targeting factor NuMA leads to unfocused, turbulent spindles, and inhibiting Eg5 leads to monopoles; yet, bipolar spindles form when both are inhibited together. What, then, are the roles of these opposing motors? Here, we generate NuMA/dynein- and Eg5-doubly inhibited spindles that not only attain a typical metaphase shape and size but also undergo anaphase. However, these spindles have reduced microtubule dynamics and are mechanically fragile, fracturing under force. Furthermore, they exhibit lagging chromosomes and a dramatic left-handed twist at anaphase. Thus, although these opposing motors are not required for spindle shape, they are essential to its mechanical and functional robustness. This work suggests a design principle whereby opposing active stresses provide robustness to force-generating cellular structures.
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Affiliation(s)
- Lila Neahring
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA 94158, USA; Developmental & Stem Cell Biology Graduate Program, UCSF, San Francisco, CA 94143, USA.
| | - Nathan H Cho
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA 94158, USA; Tetrad Graduate Program, UCSF, San Francisco, CA 94158, USA
| | - Sophie Dumont
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA 94158, USA; Developmental & Stem Cell Biology Graduate Program, UCSF, San Francisco, CA 94143, USA; Tetrad Graduate Program, UCSF, San Francisco, CA 94158, USA; Department of Biochemistry & Biophysics, UCSF, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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26
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Lemma LM, Norton MM, Tayar AM, DeCamp SJ, Aghvami SA, Fraden S, Hagan MF, Dogic Z. Multiscale Microtubule Dynamics in Active Nematics. PHYSICAL REVIEW LETTERS 2021; 127:148001. [PMID: 34652175 DOI: 10.1103/physrevlett.127.148001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 06/14/2021] [Accepted: 08/12/2021] [Indexed: 05/12/2023]
Abstract
In microtubule-based active nematics, motor-driven extensile motion of microtubule bundles powers chaotic large-scale dynamics. We quantify the interfilament sliding motion both in isolated bundles and in a dense active nematic. The extension speed of an isolated microtubule pair is comparable to the molecular motor stepping speed. In contrast, the net extension in dense 2D active nematics is significantly slower; the interfilament sliding speeds are widely distributed about the average and the filaments exhibit both contractile and extensile relative motion. These measurements highlight the challenge of connecting the extension rate of isolated bundles to the multimotor and multifilament interactions present in a dense 2D active nematic. They also provide quantitative data that is essential for building multiscale models.
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Affiliation(s)
- Linnea M Lemma
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Michael M Norton
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Alexandra M Tayar
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Stephen J DeCamp
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - S Ali Aghvami
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Seth Fraden
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Zvonimir Dogic
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
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27
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Nitta T, Wang Y, Du Z, Morishima K, Hiratsuka Y. A printable active network actuator built from an engineered biomolecular motor. NATURE MATERIALS 2021; 20:1149-1155. [PMID: 33875849 DOI: 10.1038/s41563-021-00969-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Leveraging the motion and force of individual molecular motors in a controlled manner to perform macroscopic tasks can provide substantial benefits to many applications, including robotics. Nonetheless, although millimetre-scale movement has been demonstrated with synthetic and biological molecular motors, their efficient integration into engineered systems that perform macroscopic tasks remains challenging. Here, we describe an active network capable of macroscopic actuation that is hierarchically assembled from an engineered kinesin, a biomolecular motor, and microtubules, resembling the contractile units in muscles. These contracting materials can be formed in desired areas using patterned ultraviolet illumination, allowing their incorporation into mechanically engineered systems, being also compatible with printing technologies. Due to the designed filamentous assembly of kinesins, the generated forces reach the micronewton range, enabling actuation of millimetre-scale mechanical components. These properties may be useful for the fabrication of soft robotic systems with advanced functionalities.
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Affiliation(s)
- Takahiro Nitta
- Applied Physics Course, Faculty of Engineering, Gifu University, Gifu, Japan
| | - Yingzhe Wang
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Zhao Du
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), Ishikawa, Japan
| | - Keisuke Morishima
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Yuichi Hiratsuka
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), Ishikawa, Japan.
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28
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Nasirimarekani V, Strübing T, Vilfan A, Guido I. Tuning the Properties of Active Microtubule Networks by Depletion Forces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7919-7927. [PMID: 34132558 PMCID: PMC8264947 DOI: 10.1021/acs.langmuir.1c00426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/05/2021] [Indexed: 05/12/2023]
Abstract
Suspensions of microtubules and nonadsorbing particles form thick and long bundles due to depletion forces. Such interactions act at the nanometer scale and define the structural and dynamical properties of the resulting networks. In this study, we analyze the depletion forces exerted by two types of nonadsorbing particles, namely, the polymer, poly(ethylene glycol) (PEG), and the block copolymer, Pluronic. We characterize their effects both in passive and active networks by adding motor proteins to the suspensions. By exploiting its bundling effect via entropic forces, we observed that PEG generates a network with thick structures showing a nematic order and larger mesh size. On the other hand, Pluronic builds up a much denser gel-like network without a recognizable mesh structure. This difference is also reflected in the network activity. PEG networks show moderate contraction in lateral directions while Pluronic networks exhibit faster and isotropic contraction. Interestingly, by mixing the two nonadsorbing polymers in different ratios, we observed that the system showed a behavior that exhibited properties of both agents, leading to a robust and fast responsive structure compared to the single-depletant networks. In conclusion, we show how passive osmotic compression modifies the distribution of biopolymers. Its combination with active motors results in a new active material with potential for nanotechnological applications.
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Affiliation(s)
- Vahid Nasirimarekani
- University
of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
- Max
Planck Institute for Dynamics and Self-Organization, 37077 Göttingen, Germany
| | - Tobias Strübing
- Max
Planck Institute for Dynamics and Self-Organization, 37077 Göttingen, Germany
| | - Andrej Vilfan
- Max
Planck Institute for Dynamics and Self-Organization, 37077 Göttingen, Germany
- Jožef
Stefan Institute, 1000 Ljubljana, Slovenia
| | - Isabella Guido
- Max
Planck Institute for Dynamics and Self-Organization, 37077 Göttingen, Germany
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29
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Gai Y, Cook B, Setru S, Stone HA, Petry S. Confinement size determines the architecture of Ran-induced microtubule networks. SOFT MATTER 2021; 17:5921-5931. [PMID: 34041514 PMCID: PMC8958645 DOI: 10.1039/d1sm00045d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The organization of microtubules (MTs) is critical for cells during interphase and mitosis. During mitotic spindle assembly, MTs are made and organized around chromosomes in a process regulated by RanGTP. The role of RanGTP has been explored in Xenopus egg extracts, which are not limited by a cell membrane. Here, we investigated whether cell-sized confinements affect the assembly of RanGTP-induced MT networks in Xenopus egg extracts. We used microfluidics to encapsulate extracts within monodisperse extract-in-oil droplets. Importantly, we find that the architecture of Ran-induced MT networks depends on the droplet diameter and the Ran concentration, and differs from structures formed in bulk extracts. Our results highlight that both MT nucleation and physical confinement play critical roles in determining the spatial organization of the MT cytoskeleton.
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Affiliation(s)
- Ya Gai
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, USA.
| | - Brian Cook
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Sagar Setru
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, USA.
| | - Sabine Petry
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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30
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Dalton BA, Sbalzarini IF, Hanasaki I. Fundamentals of the logarithmic measure for revealing multimodal diffusion. Biophys J 2021; 120:829-843. [PMID: 33453269 PMCID: PMC8008240 DOI: 10.1016/j.bpj.2021.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/16/2020] [Accepted: 01/07/2021] [Indexed: 01/07/2023] Open
Abstract
We develop a theoretical foundation for a time-series analysis method suitable for revealing the spectrum of diffusion coefficients in mixed Brownian systems, for which no prior knowledge of particle distinction is required. This method is directly relevant for particle tracking in biological systems, in which diffusion processes are often nonuniform. We transform Brownian data onto the logarithmic domain, in which the coefficients for individual modes of diffusion appear as distinct spectral peaks in the probability density. We refer to the method as the logarithmic measure of diffusion, or simply as the logarithmic measure. We provide a general protocol for deriving analytical expressions for the probability densities on the logarithmic domain. The protocol is applicable for any number of spatial dimensions with any number of diffusive states. The analytical form can be fitted to data to reveal multiple diffusive modes. We validate the theoretical distributions and benchmark the accuracy and sensitivity of the method by extracting multimodal diffusion coefficients from two-dimensional Brownian simulations of polydisperse filament bundles. Bundling the filaments allows us to control the system nonuniformity and hence quantify the sensitivity of the method. By exploiting the anisotropy of the simulated filaments, we generalize the logarithmic measure to rotational diffusion. By fitting the analytical forms to simulation data, we confirm the method's theoretical foundation. An error analysis in the single-mode regime shows that the proposed method is comparable in accuracy to the standard mean-squared displacement approach for evaluating diffusion coefficients. For the case of multimodal diffusion, we compare the logarithmic measure against other, more sophisticated methods, showing that both model selectivity and extraction accuracy are comparable for small data sets. Therefore, we suggest that the logarithmic measure, as a method for multimodal diffusion coefficient extraction, is ideally suited for small data sets, a condition often confronted in the experimental context. Finally, we critically discuss the proposed benefits of the method and its information content.
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Affiliation(s)
- Benjamin A Dalton
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany; Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Ivo F Sbalzarini
- Technische Universität Dresden, Faculty of Computer Science, Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Itsuo Hanasaki
- Institute of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan.
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31
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Ricketts SN, Khanal P, Rust MJ, Das M, Ross JL, Robertson-Anderson RM. Triggering Cation-Induced Contraction of Cytoskeleton Networks via Microfluidics. FRONTIERS IN PHYSICS 2020; 8:596699. [PMID: 34368112 PMCID: PMC8341456 DOI: 10.3389/fphy.2020.596699] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The dynamic morphology and mechanics of the cytoskeleton is determined by interacting networks of semiflexible actin filaments and rigid microtubules. Active rearrangement of networks of actin and microtubules can not only be driven by motor proteins but by changes to ionic conditions. For example, high concentrations of multivalent ions can induce bundling and crosslinking of both filaments. Yet, how cytoskeleton networks respond in real-time to changing ion concentrations, and how actin-microtubule interactions impact network response to these changing conditions remains unknown. Here, we use microfluidic perfusion chambers and two-color confocal fluorescence microscopy to show that increasing magnesium ions trigger contraction of both actin and actin-microtubule networks. Specifically, we use microfluidics to vary the Mg2+ concentration between 2 and 20 mM while simultaneously visualizing the triggered changes to the overall network size. We find that as Mg2+ concentration increases both actin and actin-microtubule networks undergo bulk contraction, which we measure as the shrinking width of each network. However, surprisingly, lowering the Mg2+concentration back to 2 mM does not stop or reverse the contraction but rather causes both networks to contract further. Further, actin networks begin to contract at lower Mg2+ concentrations and shorter times than actin-microtubule networks. In fact, actin-microtubule networks only undergo substantial contraction once the Mg2+ concentration begins to lower from 20 mM back to 2 mM. Our intriguing findings shed new light on how varying environmental conditions can dynamically tune the morphology of cytoskeleton networks and trigger active contraction without the use of motor proteins.
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Affiliation(s)
- Shea N. Ricketts
- Department of Physics and Biophysics, University of San Diego, San Diego, CA, United States
| | - Pawan Khanal
- Department of Physics and Biophysics, University of San Diego, San Diego, CA, United States
| | - Michael J. Rust
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, United States
| | - Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY, United States
| | - Jennifer L. Ross
- Department of Physics, Syracuse University, Syracuse, NY, United States
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32
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Gagnon DA, Dessi C, Berezney JP, Boros R, Chen DTN, Dogic Z, Blair DL. Shear-Induced Gelation of Self-Yielding Active Networks. PHYSICAL REVIEW LETTERS 2020; 125:178003. [PMID: 33156652 DOI: 10.1103/physrevlett.125.178003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
An enticing feature of active materials is the possibility of controlling macroscale rheological properties through the activity of the microscopic constituents. Using a unique combination of microscopy and rheology we study three dimensional microtubule-based active materials whose autonomous flows are powered by a continually rearranging connected network. We quantify the relationship between the microscopic dynamics and the bulk mechanical properties of these nonequilibrium networks. Experiments reveal a surprising nonmonotonic viscosity that strongly depends on the relative magnitude of the rate of internally generated activity and the externally applied shear. A simple two-state mechanical model that accounts for both the solidlike and yielded fluidlike elements of the network accurately describes the rheological measurements.
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Affiliation(s)
- David A Gagnon
- Department of Physics and Institute for Soft Matter Synthesis & Metrology, Georgetown University, 3700 O Street NW, Washington, D.C. 20057, USA
| | - Claudia Dessi
- Department of Physics and Institute for Soft Matter Synthesis & Metrology, Georgetown University, 3700 O Street NW, Washington, D.C. 20057, USA
| | - John P Berezney
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Remi Boros
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Daniel T-N Chen
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Zvonimir Dogic
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Daniel L Blair
- Department of Physics and Institute for Soft Matter Synthesis & Metrology, Georgetown University, 3700 O Street NW, Washington, D.C. 20057, USA
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33
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Maryshev I, Morozov A, Goryachev AB, Marenduzzo D. Pattern formation in active model C with anchoring: bands, aster networks, and foams. SOFT MATTER 2020; 16:8775-8781. [PMID: 32857081 DOI: 10.1039/d0sm00927j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We study the dynamics of pattern formation in a minimal model for active mixtures made of microtubules and molecular motors. We monitor the evolution of the (conserved) microtubule density and of the (non-conserved) nematic order parameter, focusing on the effects of an "anchoring" term that provides a direct coupling between the preferred microtubule direction and their density gradient. The key control parameter is the ratio between activity and elasticity. When elasticity dominates, the interplay between activity and anchoring leads to formation of banded structures that can undergo additional bending, rotational or splaying instabilities. When activity dominates, the nature of anchoring instead gives rise to a range of active cellular solids, including aster-like networks, disordered foams and spindle-like patterns. We speculate that the introduced "active model C" with anchoring is a minimal model to describe pattern formation in a biomimetic analogue of the microtubule cytoskeleton.
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Affiliation(s)
- Ivan Maryshev
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK. and Centre for Synthetic and Systems Biology, The University of Edinburgh, Institute of Cell Biology, Max Born Crescent, Edinburgh, EH9 3BF, UK.
| | - Alexander Morozov
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Andrew B Goryachev
- Centre for Synthetic and Systems Biology, The University of Edinburgh, Institute of Cell Biology, Max Born Crescent, Edinburgh, EH9 3BF, UK.
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
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34
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Modeling a Microtubule Filaments Mesh Structure from Confocal Microscopy Imaging. MICROMACHINES 2020; 11:mi11090844. [PMID: 32927718 PMCID: PMC7570018 DOI: 10.3390/mi11090844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 02/04/2023]
Abstract
This study introduces a modeling method for a supermolecular structure of microtubules for the development of a force generation material using motor proteins. 3D imaging by confocal laser scanning microscopy (CLSM) was used to obtain 3D volume density data. The density data were then interpreted by a set of cylinders with the general-purpose 3D modeling software Blender, and a 3D network structure of microtubules was constructed. Although motor proteins were not visualized experimentally, they were introduced into the model to simulate pulling of the microtubules toward each other to yield shrinking of the network, resulting in contraction of the artificial muscle. From the successful force generation simulation of the obtained model structure of artificial muscle, the modeling method introduced here could be useful in various studies for potential improvements of this contractile molecular system.
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35
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Strübing T, Khosravanizadeh A, Vilfan A, Bodenschatz E, Golestanian R, Guido I. Wrinkling Instability in 3D Active Nematics. NANO LETTERS 2020; 20:6281-6288. [PMID: 32786934 PMCID: PMC7496740 DOI: 10.1021/acs.nanolett.0c01546] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/04/2020] [Indexed: 05/13/2023]
Abstract
In nature, interactions between biopolymers and motor proteins give rise to biologically essential emergent behaviors. Besides cytoskeleton mechanics, active nematics arise from such interactions. Here we present a study on 3D active nematics made of microtubules, kinesin motors, and depleting agent. It shows a rich behavior evolving from a nematically ordered space-filling distribution of microtubule bundles toward a flattened and contracted 2D ribbon that undergoes a wrinkling instability and subsequently transitions into a 3D active turbulent state. The wrinkle wavelength is independent of the ATP concentration and our theoretical model describes its relation with the appearance time. We compare the experimental results with a numerical simulation that confirms the key role of kinesin motors in cross-linking and sliding the microtubules. Our results on the active contraction of the network and the independence of wrinkle wavelength on ATP concentration are important steps forward for the understanding of these 3D systems.
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Affiliation(s)
- Tobias Strübing
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
| | - Amir Khosravanizadeh
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
- Department
of Physics, Institute for Advanced Studies
in Basic Sciences, Zanjan 45137-66731, Iran
| | - Andrej Vilfan
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
- Jožef
Stefan Institute, 1000 Ljubljana, Slovenia
| | - Eberhard Bodenschatz
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
- Institute
for Dynamics of Complex Systems, Georg-August-University
Göttingen, 37073 Göttingen, Germany
- Laboratory
of Atomic and Solid-State Physics, Cornell
University, Ithaca, New York 14853, United
States
| | - Ramin Golestanian
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
- Rudolf
Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Isabella Guido
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
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36
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Active forces shape the metaphase spindle through a mechanical instability. Proc Natl Acad Sci U S A 2020; 117:16154-16159. [PMID: 32601228 DOI: 10.1073/pnas.2002446117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The metaphase spindle is a dynamic structure orchestrating chromosome segregation during cell division. Recently, soft matter approaches have shown that the spindle behaves as an active liquid crystal. Still, it remains unclear how active force generation contributes to its characteristic spindle-like shape. Here we combine theory and experiments to show that molecular motor-driven forces shape the structure through a barreling-type instability. We test our physical model by titrating dynein activity in Xenopus egg extract spindles and quantifying the shape and microtubule orientation. We conclude that spindles are shaped by the interplay between surface tension, nematic elasticity, and motor-driven active forces. Our study reveals how motor proteins can mold liquid crystalline droplets and has implications for the design of active soft materials.
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37
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Lenz M. Reversal of contractility as a signature of self-organization in cytoskeletal bundles. eLife 2020; 9:51751. [PMID: 32149609 PMCID: PMC7082124 DOI: 10.7554/elife.51751] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 03/05/2020] [Indexed: 12/13/2022] Open
Abstract
Bundles of cytoskeletal filaments and molecular motors generate motion in living cells, and have internal structures ranging from very organized to apparently disordered. The mechanisms powering the disordered structures are debated, and existing models predominantly predict that they are contractile. We reexamine this prediction through a theoretical treatment of the interplay between three well-characterized internal dynamical processes in cytoskeletal bundles: filament assembly and disassembly, the attachement-detachment dynamics of motors and that of crosslinking proteins. The resulting self-organization is easily understood in terms of motor and crosslink localization, and allows for an extensive control of the active bundle mechanics, including reversals of the filaments’ apparent velocities and the possibility of generating extension instead of contraction. This reversal mirrors some recent experimental observations, and provides a robust criterion to experimentally elucidate the underpinnings of both actomyosin activity and the dynamics of microtubule/motor assemblies in vitro as well as in diverse intracellular structures ranging from contractile bundles to the mitotic spindle.
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Affiliation(s)
- Martin Lenz
- Université Paris-Saclay, CNRS, LPTMS, Orsay, France.,PMMH, CNRS, ESPCI Paris, PSL University, Sorbonne Université, Université de Paris, Paris, France
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38
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Xie J, Minc N. Cytoskeleton Force Exertion in Bulk Cytoplasm. Front Cell Dev Biol 2020; 8:69. [PMID: 32117991 PMCID: PMC7031414 DOI: 10.3389/fcell.2020.00069] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/27/2020] [Indexed: 01/20/2023] Open
Abstract
The microtubule and actin cytoskeletons generate forces essential to position centrosomes, nuclei, and spindles for division plane specification. While the largest body of work has documented force exertion at, or close to the cell surface, mounting evidence suggests that cytoskeletal polymers can also produce significant forces directly from within the cytoplasm. Molecular motors such as kinesin or dynein may for instance displace cargos and endomembranes in the viscous cytoplasm yielding friction forces that pull or push microtubules. Similarly, the dynamics of bulk actin assembly/disassembly or myosin-dependent contractions produce cytoplasmic forces which influence the spatial organization of cells in a variety of processes. We here review the molecular and physical mechanisms supporting bulk cytoplasmic force generation by the cytoskeleton, their limits and relevance to organelle positioning, with a particular focus on cell division.
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Affiliation(s)
- Jing Xie
- Institut Jacques Monod, Université de Paris, CNRS UMR 7592, Paris, France
| | - Nicolas Minc
- Institut Jacques Monod, Université de Paris, CNRS UMR 7592, Paris, France
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39
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Fürthauer S, Lemma B, Foster PJ, Ems-McClung SC, Yu CH, Walczak CE, Dogic Z, Needleman DJ, Shelley MJ. Self-straining of actively crosslinked microtubule networks. NATURE PHYSICS 2019; 15:1295-1300. [PMID: 32322291 PMCID: PMC7176317 DOI: 10.1038/s41567-019-0642-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 07/17/2019] [Indexed: 05/26/2023]
Abstract
Cytoskeletal networks are foundational examples of active matter and central to self-organized structures in the cell. In vivo, these networks are active and densely crosslinked. Relating their large-scale dynamics to the properties of their constituents remains an unsolved problem. Here, we study an in vitro active gel made from aligned microtubules and XCTK2 kinesin motors. Using photobleaching, we demonstrate that the gel's aligned microtubules, driven by motors, continually slide past each other at a speed independent of the local microtubule polarity and motor concentration. This phenomenon is also observed, and remains unexplained, in spindles. We derive a general framework for coarse graining microtubule gels crosslinked by molecular motors from microscopic considerations. Using microtubule-microtubule coupling through a force-velocity relationship for kinesin, this theory naturally explains the experimental results: motors generate an active strain rate in regions of changing polarity, which allows microtubules of opposite polarities to slide past each other without stressing the material.
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Affiliation(s)
| | - Bezia Lemma
- Department of Physics, Harvard University, Cambridge, MA, USA
- Department of Physics, Brandeis University, Waltham, MA, USA
- Department of Physics, University of California, Santa Barbara, CA, USA
| | - Peter J Foster
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Che-Hang Yu
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA, USA
| | | | - Zvonimir Dogic
- Department of Physics, Brandeis University, Waltham, MA, USA
- Department of Physics, University of California, Santa Barbara, CA, USA
| | - Daniel J Needleman
- Paulson School of Engineering & Applied Science and Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael J Shelley
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Courant Institute, New York University, New York, NY, USA
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40
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Senoussi A, Kashida S, Voituriez R, Galas JC, Maitra A, Estevez-Torres A. Tunable corrugated patterns in an active nematic sheet. Proc Natl Acad Sci U S A 2019; 116:22464-22470. [PMID: 31611385 PMCID: PMC6842637 DOI: 10.1073/pnas.1912223116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Active matter locally converts chemical energy into mechanical work and, for this reason, it provides new mechanisms of pattern formation. In particular, active nematic fluids made of protein motors and filaments are far-from-equilibrium systems that may exhibit spontaneous motion, leading to actively driven spatiotemporally chaotic states in 2 and 3 dimensions and coherent flows in 3 dimensions (3D). Although these dynamic flows reveal a characteristic length scale resulting from the interplay between active forcing and passive restoring forces, the observation of static and large-scale spatial patterns in active nematic fluids has remained elusive. In this work, we demonstrate that a 3D solution of kinesin motors and microtubule filaments spontaneously forms a 2D free-standing nematic active sheet that actively buckles out of plane into a centimeter-sized periodic corrugated sheet that is stable for several days at low activity. Importantly, the nematic orientational field does not display topological defects in the corrugated state and the wavelength and stability of the corrugations are controlled by the motor concentration, in agreement with a hydrodynamic theory. At higher activities these patterns are transient and chaotic flows are observed at longer times. Our results underline the importance of both passive and active forces in shaping active matter and demonstrate that a spontaneously flowing active fluid can be sculpted into a static material through an active mechanism.
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Affiliation(s)
- Anis Senoussi
- Laboratoire Jean Perrin, Sorbonne Université and CNRS, F-75005 Paris, France
| | - Shunnichi Kashida
- Laboratoire Jean Perrin, Sorbonne Université and CNRS, F-75005 Paris, France
| | - Raphael Voituriez
- Laboratoire Jean Perrin, Sorbonne Université and CNRS, F-75005 Paris, France
- Laboratoire de Physique Théorique de la Matière Condensée, Sorbonne Université and CNRS, F-75005 Paris, France
| | | | - Ananyo Maitra
- Laboratoire Jean Perrin, Sorbonne Université and CNRS, F-75005 Paris, France;
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Alvarado J, Cipelletti L, Koenderink GH. Uncovering the dynamic precursors to motor-driven contraction of active gels. SOFT MATTER 2019; 15:8552-8565. [PMID: 31637398 DOI: 10.1039/c9sm01172b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cells and tissues have the remarkable ability to actively generate the forces required to change their shape. This active mechanical behavior is largely mediated by the actin cytoskeleton, a crosslinked network of actin filaments that is contracted by myosin motors. Experiments and active gel theories have established that the length scale over which gel contraction occurs is governed by a balance between molecular motor activity and crosslink density. By contrast, the dynamics that govern the contractile activity of the cytoskeleton remain poorly understood. Here we investigate the microscopic dynamics of reconstituted actin-myosin networks using simultaneous real-space video microscopy and Fourier-space dynamic light scattering. Light scattering reveals different regimes of microscopic dynamics as a function of sample age. We uncover two dynamical precursors that precede macroscopic gel contraction. One is characterized by a progressive acceleration of stress-induced rearrangements, while the other consists of sudden, heterogeneous rearrangements. Intriguingly, our findings suggest a qualitative analogy between self-driven rupture and collapse of active gels and the delayed rupture of passive gels observed in earlier studies of colloidal gels under external loads.
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Affiliation(s)
- José Alvarado
- AMOLF, Living Matter Department, 1098 XG Amsterdam, The Netherlands.
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42
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Redemann S, Fürthauer S, Shelley M, Müller-Reichert T. Current approaches for the analysis of spindle organization. Curr Opin Struct Biol 2019; 58:269-277. [DOI: 10.1016/j.sbi.2019.05.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 01/06/2023]
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Maryshev I, Goryachev AB, Marenduzzo D, Morozov A. Dry active turbulence in a model for microtubule-motor mixtures. SOFT MATTER 2019; 15:6038-6043. [PMID: 31298679 DOI: 10.1039/c9sm00558g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We study the dynamics and phase behaviour of a dry suspension of microtubules and molecular motors. We obtain a set of continuum equations by rigorously coarse graining a microscopic model where motor-induced interactions lead to parallel or antiparallel ordering. Through numerical simulations, we show that this model generically creates either stable stripes, or a never-settling pattern where stripes periodically form, rotate and then split up. We derive a minimal model which displays the same instability as the full model, and clarifies the underlying physical mechanism. The necessary ingredients are an extensile flux arising from microtubule sliding and an interfacial torque favouring ordering along density gradients. We argue that our minimal model unifies various previous observations of chaotic behaviour in dry active matter into a general universality class.
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Affiliation(s)
- Ivan Maryshev
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK.
| | - Andrew B Goryachev
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK.
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Alexander Morozov
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
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Ross TD, Lee HJ, Qu Z, Banks RA, Phillips R, Thomson M. Controlling organization and forces in active matter through optically defined boundaries. Nature 2019; 572:224-229. [PMID: 31391558 PMCID: PMC6719720 DOI: 10.1038/s41586-019-1447-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/05/2019] [Indexed: 12/22/2022]
Abstract
Living systems are capable of locomotion, reconfiguration and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, 'active' molecules that create and manipulate non-equilibrium structures and force fields of up to millimetre length scales1-3. Experimental active-matter systems of biological or synthetic molecules are capable of spontaneously organizing into structures4,5 and generating global flows6-9. However, these experimental systems lack the spatiotemporal control found in cells, limiting their utility for studying non-equilibrium phenomena and bioinspired engineering. Here we uncover non-equilibrium phenomena and principles of boundary-mediated control by optically modulating structures and fluid flow in an engineered system of active biomolecules. Our system consists of purified microtubules and light-activatable motor proteins that crosslink and organize the microtubules into distinct structures upon illumination. We develop basic operations-defined as sets of light patterns-to create, move and merge the microtubule structures. By combining these operations, we create microtubule networks that span several hundred micrometres in length and contract at speeds up to an order of magnitude higher than the speed of an individual motor protein. We manipulate these contractile networks to generate and sculpt persistent fluid flows. The principles of boundary-mediated control that we uncover may be used to study emergent cellular structures and forces and to develop programmable active-matter devices.
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Affiliation(s)
- Tyler D Ross
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Heun Jin Lee
- Department of Applied Physics, California Institute of Technology, Pasadena, CA, USA
| | - Zijie Qu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rachel A Banks
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Applied Physics, California Institute of Technology, Pasadena, CA, USA
- Department of Physics, California Institute of Technology, Pasadena, CA, USA
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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Andorfer R, Alper JD. From isolated structures to continuous networks: A categorization of cytoskeleton-based motile engineered biological microstructures. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 11:e1553. [PMID: 30740918 PMCID: PMC6881777 DOI: 10.1002/wnan.1553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 11/06/2022]
Abstract
As technology at the small scale is advancing, motile engineered microstructures are becoming useful in drug delivery, biomedicine, and lab-on-a-chip devices. However, traditional engineering methods and materials can be inefficient or functionally inadequate for small-scale applications. Increasingly, researchers are turning to the biology of the cytoskeleton, including microtubules, actin filaments, kinesins, dyneins, myosins, and associated proteins, for both inspiration and solutions. They are engineering structures with components that range from being entirely biological to being entirely synthetic mimics of biology and on scales that range from isotropic continuous networks to single isolated structures. Motile biological microstructures trace their origins from the development of assays used to study the cytoskeleton to the array of structures currently available today. We define 12 types of motile biological microstructures, based on four categories: entirely biological, modular, hybrid, and synthetic, and three scales: networks, clusters, and isolated structures. We highlight some key examples, the unique functionalities, and the potential applications of each microstructure type, and we summarize the quantitative models that enable engineering them. By categorizing the diversity of motile biological microstructures in this way, we aim to establish a framework to classify these structures, define the gaps in current research, and spur ideas to fill those gaps. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Nanotechnology Approaches to Biology > Cells at the Nanoscale Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Rachel Andorfer
- Department of Bioengineering, Clemson University, Clemson, South Carolina
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Joshua D. Alper
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
- Department of Biological Sciences, Clemson University, Clemson, South Carolina
- Eukaryotic Pathogen Innovations Center, Clemson University, Clemson, South Carolina
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Matsuda K, Kabir AMR, Akamatsu N, Saito A, Ishikawa S, Matsuyama T, Ditzer O, Islam MS, Ohya Y, Sada K, Konagaya A, Kuzuya A, Kakugo A. Artificial Smooth Muscle Model Composed of Hierarchically Ordered Microtubule Asters Mediated by DNA Origami Nanostructures. NANO LETTERS 2019; 19:3933-3938. [PMID: 31037942 DOI: 10.1021/acs.nanolett.9b01201] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA has been well-known for its applications in programmable self-assembly of materials. Nonetheless, utility of DNA origami, which offers more opportunity to realize complicated operations, has been very limited. Here we report self-assembly of a biomolecular motor system, microtubule-kinesin mediated by DNA origami nanostructures. We demonstrate that a rodlike DNA origami motif facilitates self-assembly of microtubules into asters. A smooth-muscle like molecular contraction system has also been realized using the DNA origami in which self-assembled microtubules exhibited fast and dynamic contraction in the presence of kinesins through an energy dissipative process. This work provides potential nanotechnological applications of DNA and biomolecular motor proteins.
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Affiliation(s)
| | | | - Naohide Akamatsu
- Department of Chemistry and Materials Engineering , Kansai University , Osaka 564-8680 , Japan
| | | | - Shumpei Ishikawa
- Department of Chemistry and Materials Engineering , Kansai University , Osaka 564-8680 , Japan
| | - Tsuyoshi Matsuyama
- Department of Chemistry and Materials Engineering , Kansai University , Osaka 564-8680 , Japan
| | - Oliver Ditzer
- Faculty of Chemistry and Food Chemistry , Technische Universität Dresden , Prüfungsamt, 01062 Dresden , Germany
| | - Md Sirajul Islam
- Organization for Research and Development of Innovative Science and Technology , Kansai University , Osaka 564-8680 , Japan
| | - Yuichi Ohya
- Department of Chemistry and Materials Engineering , Kansai University , Osaka 564-8680 , Japan
- Organization for Research and Development of Innovative Science and Technology , Kansai University , Osaka 564-8680 , Japan
| | | | - Akihiko Konagaya
- Department of Computational Intelligence and Systems Science , Tokyo Institute of Technology , Kanagawa 226-8502 , Japan
| | - Akinori Kuzuya
- Department of Chemistry and Materials Engineering , Kansai University , Osaka 564-8680 , Japan
- Organization for Research and Development of Innovative Science and Technology , Kansai University , Osaka 564-8680 , Japan
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47
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Abstract
The assembly of the mitotic spindle and the subsequent segregation of sister chromatids are based on the self-organized action of microtubule filaments, motor proteins, and other microtubule-associated proteins, which constitute the fundamental force-generating elements in the system. Many of the components in the spindle have been identified, but until recently it remained unclear how their collective behaviors resulted in such a robust bipolar structure. Here, we review the current understanding of the physics of the metaphase spindle that is only now starting to emerge.
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Affiliation(s)
- David Oriola
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany; .,Max Planck Institute for the Physics of Complex Systems, 01187, Dresden, Germany.,Center for Systems Biology Dresden, 01307, Dresden, Germany
| | - Daniel J Needleman
- School of Engineering and Applied Sciences, Department of Molecular and Cellular Biology, and FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 021382, USA
| | - Jan Brugués
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany; .,Max Planck Institute for the Physics of Complex Systems, 01187, Dresden, Germany.,Center for Systems Biology Dresden, 01307, Dresden, Germany
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48
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Rickman J, Nédélec F, Surrey T. Effects of spatial dimensionality and steric interactions on microtubule-motor self-organization. Phys Biol 2019; 16:046004. [PMID: 31013252 PMCID: PMC7655122 DOI: 10.1088/1478-3975/ab0fb1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Active networks composed of filaments and motor proteins can self-organize into a
variety of architectures. Computer simulations in two or three spatial
dimensions and including or omitting steric interactions between filaments can
be used to model active networks. Here we examine how these modelling choices
affect the state space of network self-organization. We compare the networks
generated by different models of a system of dynamic microtubules and
microtubule-crosslinking motors. We find that a thin 3D model that includes
steric interactions between filaments is the most versatile, capturing a variety
of network states observed in recent experiments. In contrast, 2D models either
with or without steric interactions which prohibit microtubule crossings can
produce some, but not all, observed network states. Our results provide
guidelines for the most appropriate choice of model for the study of different
network types and elucidate mechanisms of active network organization.
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Affiliation(s)
- Jamie Rickman
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom. Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London WC1 6BT, United Kingdom
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49
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Miles CJ, Evans AA, Shelley MJ, Spagnolie SE. Active matter invasion of a viscous fluid: Unstable sheets and a no-flow theorem. PHYSICAL REVIEW LETTERS 2019; 122:098002. [PMID: 30932541 DOI: 10.1103/physrevlett.122.098002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 11/29/2018] [Indexed: 06/09/2023]
Abstract
We investigate the dynamics of a dilute suspension of hydrodynamically interacting motile or immotile stress-generating swimmers or particles as they invade a surrounding viscous fluid. Colonies of aligned pusher particles are shown to elongate in the direction of particle orientation and undergo a cascade of transverse concentration instabilities, governed at small times by an equation that also describes the Saffman-Taylor instability in a Hele-Shaw cell, or the Rayleigh-Taylor instability in a two-dimensional flow through a porous medium. Thin sheets of aligned pusher particles are always unstable, while sheets of aligned puller particles can either be stable (immotile particles), or unstable (motile particles) with a growth rate that is nonmonotonic in the force dipole strength. We also prove a surprising "no-flow theorem": a distribution initially isotropic in orientation loses isotropy immediately but in such a way that results in no fluid flow everywhere and for all time.
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Affiliation(s)
- Christopher J Miles
- Department of Physics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
| | - Arthur A Evans
- Department of Mathematics, University of Wisconsin-Madison, 480 Lincoln Dr., Madison, Wisconsin 53706, USA
| | - Michael J Shelley
- Flatiron Institute, Simons Foundation, New York, New York, USA; and Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
| | - Saverio E Spagnolie
- Department of Mathematics, University of Wisconsin-Madison, 480 Lincoln Dr., Madison, Wisconsin 53706, USA
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50
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Hueschen CL, Galstyan V, Amouzgar M, Phillips R, Dumont S. Microtubule End-Clustering Maintains a Steady-State Spindle Shape. Curr Biol 2019; 29:700-708.e5. [PMID: 30744975 DOI: 10.1016/j.cub.2019.01.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/26/2018] [Accepted: 01/08/2019] [Indexed: 01/01/2023]
Abstract
Each time a cell divides, the microtubule cytoskeleton self-organizes into the metaphase spindle: an ellipsoidal steady-state structure that holds its stereotyped geometry despite microtubule turnover and internal stresses [1-6]. Regulation of microtubule dynamics, motor proteins, microtubule crosslinking, and chromatid cohesion can modulate spindle size and shape, and yet modulated spindles reach and hold a new steady state [7-11]. Here, we ask what maintains any spindle steady-state geometry. We report that clustering of microtubule ends by dynein and NuMA is essential for mammalian spindles to hold a steady-state shape. After dynein or NuMA deletion, the mitotic microtubule network is "turbulent"; microtubule bundles extend and bend against the cell cortex, constantly remodeling network shape. We find that spindle turbulence is driven by the homotetrameric kinesin-5 Eg5, and that acute Eg5 inhibition in turbulent spindles recovers spindle geometry and stability. Inspired by in vitro work on active turbulent gels of microtubules and kinesin [12, 13], we explore the kinematics of this in vivo turbulent network. We find that turbulent spindles display decreased nematic order and that motile asters distort the nematic director field. Finally, we see that turbulent spindles can drive both flow of cytoplasmic organelles and whole-cell movement-analogous to the autonomous motility displayed by droplet-encapsulated turbulent gels [12]. Thus, end-clustering by dynein and NuMA is required for mammalian spindles to reach a steady-state geometry, and in their absence Eg5 powers a turbulent microtubule network inside mitotic cells.
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Affiliation(s)
- Christina L Hueschen
- Department of Cell and Tissue Biology, UCSF, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, UCSF, San Francisco, CA 94143, USA.
| | - Vahe Galstyan
- Biochemistry and Molecular Biophysics Option, California Institute of Technology, Pasadena, CA 91106, USA
| | - Meelad Amouzgar
- Department of Cell and Tissue Biology, UCSF, San Francisco, CA 94143, USA
| | - Rob Phillips
- Department of Physics, California Institute of Technology, Pasadena, CA 91106, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91106, USA
| | - Sophie Dumont
- Department of Cell and Tissue Biology, UCSF, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, UCSF, San Francisco, CA 94143, USA; Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA 94143, USA.
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