1
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Takamori S, Mimura H, Osaki T, Kondo T, Shintomi M, Shintomi K, Ohsugi M, Takeuchi S. Nuclear Assembly in Giant Unilamellar Vesicles Encapsulating Xenopus Egg Extract. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2025:e2412126. [PMID: 40390663 DOI: 10.1002/smll.202412126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2024] [Revised: 03/17/2025] [Indexed: 05/21/2025]
Abstract
The reconstitution of a cell nucleus in a lipid bilayer-enclosed synthetic cell makes great strides in bottom-up synthetic biology. In this study, a method for assembling a nucleus in giant unilamellar vesicles (GUVs) is proposed. To induce reconstitution of the nucleus, the interphase egg extract of African clawed frogs Xenopus laevis is utilized, known as a biochemically controllable cell-free system capable of transforming an added sperm chromatin into a nucleus in vitro. The GUV formation efficiency is enhanced by the inverted emulsion method through incorporating prolonged waiting time and adding chloroform into lipid-dispersed oil, facilitating subsequent nuclear assembly reactions in the GUVs. Characterization of nucleus-like structures formed in the GUVs revealed the presence of dense DNA and accumulated GFP-NLS in the structure, indicative of functional nuclear import. Immunostaining further validated the presence of nuclear pore complexes on the surfaces of these nucleus-like structures. The approach offers a versatile platform for constructing artificial cellular systems that closely mimic eukaryotic cells.
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Affiliation(s)
- Sho Takamori
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Hisatoshi Mimura
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Toshihisa Osaki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Tomo Kondo
- Department of Life Science, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, 153-8902, Japan
| | - Miyuki Shintomi
- Life Science Network, The University of Tokyo, Meguro-ku, Tokyo, 153-8902, Japan
| | - Keishi Shintomi
- Chromosome Dynamics Laboratory, RIKEN, Wako, Saitama, 351-0198, Japan
| | - Miho Ohsugi
- Department of Life Science, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, 153-8902, Japan
| | - Shoji Takeuchi
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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2
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Kashiwabara T, Fukuyama T, Maeda YT. Density-dependent flow generation in active cytoskeletal fluids. Sci Rep 2024; 14:31339. [PMID: 39732914 PMCID: PMC11682274 DOI: 10.1038/s41598-024-82864-z] [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: 08/16/2024] [Accepted: 12/09/2024] [Indexed: 12/30/2024] Open
Abstract
The actomyosin cytoskeleton, a protein assembly comprising actin fibers and the myosin molecular motor, drives various cellular dynamics through contractile force generation at high densities. However, the relationship between the density dependence of the actomyosin cytoskeleton and force-controlled ordered structure remains poorly understood. In this study, we measured contraction-driven flow generation by varying the concentration of cell extracts containing the actomyosin cytoskeleton and associated nucleation factors. We observed continuous actin flow toward the center at a critical actomyosin density in cell-sized droplets. The actin flow exhibited an emergent oscillation in which the tracer advection in the bulk solution periodically changed in a stop-and-go fashion. In the vicinity of the actomyosin density where oscillatory dynamics occur, the velocity of tracer particle motion decreases with actomyosin density but exhibits superdiffusive motion. Furthermore, the increase or decrease in myosin activity causes the oscillatory flow generation to become irregular, indicating that the density-dependent flow generation of actomyosin is driven by an interplay between actin density and myosin force generation.
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Grants
- 24KJ1796 Japan Society for the Promotion of Science
- JPJSCCA20230002 Ministry of Education, Culture, Sports, Science and Technology
- 23H01144 Ministry of Education, Culture, Sports, Science and Technology
- 24K21534 Ministry of Education, Culture, Sports, Science and Technology
- 23H04711 Ministry of Education, Culture, Sports, Science and Technology
- 23H04599 Ministry of Education, Culture, Sports, Science and Technology
- 22K14014 Ministry of Education, Culture, Sports, Science and Technology
- JPMJFR2239 Japan Science and Technology Agency
- 23EXC205 Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences
- 24EXC206 Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences
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Affiliation(s)
- Tomoka Kashiwabara
- Department of Chemical Engineering, Kyoto University, Nishi-kyoku, Kyoto, 615-8510, Japan
| | - Tatsuya Fukuyama
- Department of Chemical Engineering, Kyoto University, Nishi-kyoku, Kyoto, 615-8510, Japan
| | - Yusuke T Maeda
- Department of Chemical Engineering, Kyoto University, Nishi-kyoku, Kyoto, 615-8510, Japan.
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3
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Takada S, Fujiwara K. Artificial cell system as a tool for investigating pattern formation mechanisms of intracellular reaction-diffusion waves. Biophys Physicobiol 2024; 21:e210022. [PMID: 39963599 PMCID: PMC11830476 DOI: 10.2142/biophysico.bppb-v21.0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 10/08/2024] [Indexed: 02/20/2025] Open
Abstract
Intracellular positional information is crucial for the precise control of biological phenomena, including cell division, polarity, and motility. Intracellular reaction-diffusion (iRD) waves are responsible for regulating positional information within cells as morphogens in multicellular tissues. However, iRD waves are explained by the coupling of biochemical reactions and molecular diffusion which indicates nonlinear systems under far from equilibrium conditions. Because of this complexity, experiments using defined elements rather than living cells containing endogenous factors are necessary to elucidate their pattern formation mechanisms. In this review, we summarize the effectiveness of artificial cell systems for investigating iRD waves derived from their high controllability and ability to emulate cell-size space effects. We describe how artificial cell systems reveal the characteristics of iRD waves, including the mechanisms of wave generation, mode selection, and period regulation. Furthermore, we introduce remaining open questions and discuss future challenges even in Min waves and in applying artificial cell systems to various iRD waves.
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Affiliation(s)
- Sakura Takada
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
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4
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Davutoglu MG, Geyer VF, Niese L, Soltwedel JR, Zoccoler ML, Sabatino V, Haase R, Kröger N, Diez S, Poulsen N. Gliding motility of the diatom Craspedostauros australis coincides with the intracellular movement of raphid-specific myosins. Commun Biol 2024; 7:1187. [PMID: 39313522 PMCID: PMC11420354 DOI: 10.1038/s42003-024-06889-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 09/12/2024] [Indexed: 09/25/2024] Open
Abstract
Raphid diatoms are one of the few eukaryotes capable of gliding motility, which is remarkably fast and allows for quasi-instantaneous directional reversals. Besides other mechanistic models, it has been suggested that an actomyosin system provides the force for diatom gliding. However, in vivo data on the dynamics of actin and myosin in diatoms are lacking. In this study, we demonstrate that the raphe-associated actin bundles required for diatom movement do not exhibit a directional turnover of subunits and thus their dynamics do not contribute directly to force generation. By phylogenomic analysis, we identified four raphid diatom-specific myosins in Craspedostauros australis (CaMyo51A-D) and investigated their in vivo localization and dynamics through GFP-tagging. Only CaMyo51B-D but not CaMyo51A exhibited coordinated movement during gliding, consistent with a role in force generation. The characterization of raphid diatom-specific myosins lays the foundation for unraveling the molecular mechanisms that underlie the gliding motility of diatoms.
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Affiliation(s)
- Metin G Davutoglu
- B CUBE - Center for Molecular Bioengineering, TUD Dresden University of Technology, Dresden, Germany
| | - Veikko F Geyer
- B CUBE - Center for Molecular Bioengineering, TUD Dresden University of Technology, Dresden, Germany
| | - Lukas Niese
- B CUBE - Center for Molecular Bioengineering, TUD Dresden University of Technology, Dresden, Germany
| | - Johannes R Soltwedel
- Cluster of Excellence Physics of Life, TUD Dresden University of Technology, Dresden, Germany
| | - Marcelo L Zoccoler
- Cluster of Excellence Physics of Life, TUD Dresden University of Technology, Dresden, Germany
| | - Valeria Sabatino
- B CUBE - Center for Molecular Bioengineering, TUD Dresden University of Technology, Dresden, Germany
| | - Robert Haase
- Cluster of Excellence Physics of Life, TUD Dresden University of Technology, Dresden, Germany
- Center for Scalable Data Analytics and Artificial Intelligence, Faculty of Mathematics and Computer Science, Leipzig University, Leipzig, Germany
| | - Nils Kröger
- B CUBE - Center for Molecular Bioengineering, TUD Dresden University of Technology, Dresden, Germany
- Cluster of Excellence Physics of Life, TUD Dresden University of Technology, Dresden, Germany
- Faculty of Chemistry and Food Chemistry, TUD Dresden University of Technology, Dresden, Germany
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, TUD Dresden University of Technology, Dresden, Germany.
- Cluster of Excellence Physics of Life, TUD Dresden University of Technology, Dresden, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Nicole Poulsen
- B CUBE - Center for Molecular Bioengineering, TUD Dresden University of Technology, Dresden, Germany.
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5
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Chakrabarti B, Rachh M, Shvartsman SY, Shelley MJ. Cytoplasmic stirring by active carpets. Proc Natl Acad Sci U S A 2024; 121:e2405114121. [PMID: 39012825 PMCID: PMC11287282 DOI: 10.1073/pnas.2405114121] [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: 03/13/2024] [Accepted: 06/13/2024] [Indexed: 07/18/2024] Open
Abstract
Large cells often rely on cytoplasmic flows for intracellular transport, maintaining homeostasis, and positioning cellular components. Understanding the mechanisms of these flows is essential for gaining insights into cell function, developmental processes, and evolutionary adaptability. Here, we focus on a class of self-organized cytoplasmic stirring mechanisms that result from fluid-structure interactions between cytoskeletal elements at the cell cortex. Drawing inspiration from streaming flows in late-stage fruit fly oocytes, we propose an analytically tractable active carpet theory. This model deciphers the origins and three-dimensional spatiotemporal organization of such flows. Through a combination of simulations and weakly nonlinear theory, we establish the pathway of the streaming flow to its global attractor: a cell-spanning vortical twister. Our study reveals the inherent symmetries of this emergent flow, its low-dimensional structure, and illustrates how complex fluid-structure interaction aligns with classical solutions in Stokes flow. This framework can be easily adapted to elucidate a broad spectrum of self-organized, cortex-driven intracellular flows.
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Affiliation(s)
- Brato Chakrabarti
- Center for Computational Biology, Flatiron Institute, New York, NY10010
- International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bengaluru560089, India
| | - Manas Rachh
- Center for Computational Mathematics, Flatiron Institute, New York, NY10010
| | - Stanislav Y. Shvartsman
- Center for Computational Biology, Flatiron Institute, New York, NY10010
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Michael J. Shelley
- Center for Computational Biology, Flatiron Institute, New York, NY10010
- The Courant Institute of Mathematical Sciences, New York University, New York, NY10012
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6
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Sakamoto R, Murrell MP. Composite branched and linear F-actin maximize myosin-induced membrane shape changes in a biomimetic cell model. Commun Biol 2024; 7:840. [PMID: 38987288 PMCID: PMC11236970 DOI: 10.1038/s42003-024-06528-4] [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: 03/04/2024] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
The architecture of the actin cortex determines the generation and transmission of stresses, during key events from cell division to migration. However, its impact on myosin-induced cell shape changes remains unclear. Here, we reconstitute a minimal model of the actomyosin cortex with branched or linear F-actin architecture within giant unilamellar vesicles (GUVs, liposomes). Upon light activation of myosin, neither the branched nor linear F-actin architecture alone induces significant liposome shape changes. The branched F-actin network forms an integrated, membrane-bound "no-slip boundary" -like cortex that attenuates actomyosin contractility. By contrast, the linear F-actin network forms an unintegrated "slip boundary" -like cortex, where actin asters form without inducing membrane deformations. Notably, liposomes undergo significant deformations at an optimized balance of branched and linear F-actin networks. Our findings highlight the pivotal roles of branched F-actin in force transmission and linear F-actin in force generation to yield membrane shape changes.
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Affiliation(s)
- Ryota Sakamoto
- Department of Biomedical Engineering, Yale University, 10 Hillhouse Avenue, New Haven, CT, USA
- Systems Biology Institute, 850 West Campus Drive, West Haven, CT, USA
| | - Michael P Murrell
- Department of Biomedical Engineering, Yale University, 10 Hillhouse Avenue, New Haven, CT, USA.
- Systems Biology Institute, 850 West Campus Drive, West Haven, CT, USA.
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT, USA.
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7
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Razavi S, Wong F, Abubaker-Sharif B, Matsubayashi HT, Nakamura H, Nguyen NTH, Robinson DN, Chen B, Iglesias PA, Inoue T. Synthetic control of actin polymerization and symmetry breaking in active protocells. SCIENCE ADVANCES 2024; 10:eadk9731. [PMID: 38865458 PMCID: PMC11168455 DOI: 10.1126/sciadv.adk9731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 05/08/2024] [Indexed: 06/14/2024]
Abstract
Nonlinear biomolecular interactions on membranes drive membrane remodeling crucial for biological processes including chemotaxis, cytokinesis, and endocytosis. The complexity of biomolecular interactions, their redundancy, and the importance of spatiotemporal context in membrane organization impede understanding of the physical principles governing membrane mechanics. Developing a minimal in vitro system that mimics molecular signaling and membrane remodeling while maintaining physiological fidelity poses a major challenge. Inspired by chemotaxis, we reconstructed chemically regulated actin polymerization inside vesicles, guiding membrane self-organization. An external, undirected chemical input induced directed actin polymerization and membrane deformation uncorrelated with upstream biochemical cues, suggesting symmetry breaking. A biophysical model incorporating actin dynamics and membrane mechanics proposes that uneven actin distributions cause nonlinear membrane deformations, consistent with experimental findings. This protocellular system illuminates the interplay between actin dynamics and membrane shape during symmetry breaking, offering insights into chemotaxis and other cell biological processes.
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Affiliation(s)
- Shiva Razavi
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Felix Wong
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Bedri Abubaker-Sharif
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hideaki T. Matsubayashi
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hideki Nakamura
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nhung Thi Hong Nguyen
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Douglas N. Robinson
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Pablo A. Iglesias
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Takanari Inoue
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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8
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Sakamoto R, Murrell MP. F-actin architecture determines the conversion of chemical energy into mechanical work. Nat Commun 2024; 15:3444. [PMID: 38658549 PMCID: PMC11043346 DOI: 10.1038/s41467-024-47593-x] [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: 10/13/2023] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
Mechanical work serves as the foundation for dynamic cellular processes, ranging from cell division to migration. A fundamental driver of cellular mechanical work is the actin cytoskeleton, composed of filamentous actin (F-actin) and myosin motors, where force generation relies on adenosine triphosphate (ATP) hydrolysis. F-actin architectures, whether bundled by crosslinkers or branched via nucleators, have emerged as pivotal regulators of myosin II force generation. However, it remains unclear how distinct F-actin architectures impact the conversion of chemical energy to mechanical work. Here, we employ in vitro reconstitution of distinct F-actin architectures with purified components to investigate their influence on myosin ATP hydrolysis (consumption). We find that F-actin bundles composed of mixed polarity F-actin hinder network contraction compared to non-crosslinked network and dramatically decelerate ATP consumption rates. Conversely, linear-nucleated networks allow network contraction despite reducing ATP consumption rates. Surprisingly, branched-nucleated networks facilitate high ATP consumption without significant network contraction, suggesting that the branched network dissipates energy without performing work. This study establishes a link between F-actin architecture and myosin energy consumption, elucidating the energetic principles underlying F-actin structure formation and the performance of mechanical work.
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Affiliation(s)
- Ryota Sakamoto
- Department of Biomedical Engineering, Yale University, 10 Hillhouse Avenue, New Haven, CT, USA
- Systems Biology Institute, 850 West Campus Drive, West Haven, CT, USA
| | - Michael P Murrell
- Department of Biomedical Engineering, Yale University, 10 Hillhouse Avenue, New Haven, CT, USA.
- Systems Biology Institute, 850 West Campus Drive, West Haven, CT, USA.
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT, USA.
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9
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Nishikawa S, Sato G, Takada S, Kohyama S, Honda G, Yanagisawa M, Hori Y, Doi N, Yoshinaga N, Fujiwara K. Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell-Size Space. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308030. [PMID: 38054641 PMCID: PMC10853730 DOI: 10.1002/advs.202308030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/22/2023] [Indexed: 12/07/2023]
Abstract
Cells are small, closed spaces filled with various types of macromolecules. Although it is shown that the characteristics of biochemical reactions in vitro are quite different from those in living cells, the role of the co-existence of various macromolecules in cell-size space remains still elusive. Here, using a constructive approach, it is demonstrated that the co-existence of various macromolecules themselves has the ability to tune protein localization for spatiotemporal regulation and a biochemical reaction system in a cell-size space. Both experimental and theoretical analyses reveal that enhancement of interfacial effects by a large surface-area-to-volume ratio facilitates membrane localization of molecules in the cell-size space, and the interfacial effects are alleviated by competitive binding to lipid membranes among multiple proteins even if their membrane affinities are weak. These results indicate that competition for membrane binding among various macromolecules in the cell-size space plays a role in regulating the spatiotemporal molecular organization and biochemical reaction networks. These findings shed light on the importance of surrounding molecules for biochemical reactions using purified elements in small spaces.
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Affiliation(s)
- Saki Nishikawa
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Gaku Sato
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Sakura Takada
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Shunshi Kohyama
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
- Present address:
Department for Cellular and Molecular BiophysicsMax Planck Institute for BiochemistryAm Klopferspitz 18D‐82152MartinsriedGermany
| | - Gen Honda
- Komaba Institute for ScienceGraduate School of Arts and SciencesThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
| | - Miho Yanagisawa
- Komaba Institute for ScienceGraduate School of Arts and SciencesThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
- Graduate School of ScienceThe University of TokyoHongo 7‐3‐1BunkyoTokyo113‐0033Japan
- Center for Complex Systems BiologyUniversal Biology InstituteThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
| | - Yutaka Hori
- Department of Applied Physics and Physico‐informaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Nobuhide Doi
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Natsuhiko Yoshinaga
- WPI Advanced Institute for Materials Research (WPI‐AIMR)Tohoku UniversityKatahira 2‐1‐1, Aoba‐KuSendai980‐8577Japan
- MathAM‐OILAISTSendai980‐8577Japan
| | - Kei Fujiwara
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
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10
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Razavi S, Wong F, Abubaker-Sharif B, Matsubayashi HT, Nakamura H, Sandoval E, Robinson DN, Chen B, Liu J, Iglesias PA, Inoue T. Synthetic control of actin polymerization and symmetry breaking in active protocells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559060. [PMID: 37790449 PMCID: PMC10542490 DOI: 10.1101/2023.09.22.559060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Non-linear biomolecular interactions on the membranes drive membrane remodeling that underlies fundamental biological processes including chemotaxis, cytokinesis, and endocytosis. The multitude of biomolecules, the redundancy in their interactions, and the importance of spatiotemporal context in membrane organization hampers understanding the physical principles governing membrane mechanics. A minimal, in vitro system that models the functional interactions between molecular signaling and membrane remodeling, while remaining faithful to cellular physiology and geometry is powerful yet remains unachieved. Here, inspired by the biophysical processes underpinning chemotaxis, we reconstituted externally-controlled actin polymerization inside giant unilamellar vesicles, guiding self-organization on the membrane. We show that applying undirected external chemical inputs to this system results in directed actin polymerization and membrane deformation that are uncorrelated with upstream biochemical cues, indicating symmetry breaking. A biophysical model of the dynamics and mechanics of both actin polymerization and membrane shape suggests that inhomogeneous distributions of actin generate membrane shape deformations in a non-linear fashion, a prediction consistent with experimental measurements and subsequent local perturbations. The active protocellular system demonstrates the interplay between actin dynamics and membrane shape in a symmetry breaking context that is relevant to chemotaxis and a suite of other biological processes.
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Affiliation(s)
- Shiva Razavi
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Felix Wong
- Institute for Medical Engineering & Science, Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Bedri Abubaker-Sharif
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hideaki T. Matsubayashi
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hideki Nakamura
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eduardo Sandoval
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Douglas N. Robinson
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Jian Liu
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pablo A. Iglesias
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Takanari Inoue
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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11
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Sakamoto R, Maeda YT. Unveiling the physics underlying symmetry breaking of the actin cytoskeleton: An artificial cell-based approach. Biophys Physicobiol 2023; 20:e200032. [PMID: 38124798 PMCID: PMC10728624 DOI: 10.2142/biophysico.bppb-v20.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/18/2023] [Indexed: 12/23/2023] Open
Abstract
Single-cell behaviors cover many biological functions, such as cell division during morphogenesis and tissue metastasis, and cell migration during cancer cell invasion and immune cell responses. Symmetry breaking of the positioning of organelles and the cell shape are often associated with these biological functions. One of the main players in symmetry breaking at the cellular scale is the actin cytoskeleton, comprising actin filaments and myosin motors that generate contractile forces. However, because the self-organization of the actomyosin network is regulated by the biochemical signaling in cells, how the mechanical contraction of the actin cytoskeleton induces diverse self-organized behaviors and drives the cell-scale symmetry breaking remains unclear. In recent times, to understand the physical underpinnings of the symmetry breaking exhibited in the actin cytoskeleton, artificial cell models encapsulating the cytoplasmic actomyosin networks covered with lipid monolayers have been developed. By decoupling the actomyosin mechanics from the complex biochemical signaling within living cells, this system allows one to study the self-organization of actomyosin networks confined in cell-sized spaces. We review the recent developments in the physics of confined actomyosin networks and provide future perspectives on the artificial cell-based approach. This review article is an extended version of the Japanese article, The Physical Principle of Cell Migration Under Confinement: Artificial Cell-based Bottom-up Approach, published in SEIBUTSU BUTSURI Vol. 63, p. 163-164 (2023).
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Affiliation(s)
- Ryota Sakamoto
- Department of Physics, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
- Department of Biomedical Engineering, Yale University, Connecticut 06520, USA
- Systems Biology Institute, Yale University, Connecticut 06516, USA
| | - Yusuke T. Maeda
- Department of Physics, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
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12
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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: 1] [Impact Index Per Article: 0.5] [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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13
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Ye Y, Homer HA. Two-step nuclear centring by competing microtubule- and actin-based mechanisms in 2-cell mouse embryos. EMBO Rep 2022; 23:e55251. [PMID: 36214648 PMCID: PMC9638869 DOI: 10.15252/embr.202255251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2024] Open
Abstract
Microtubules typically promote nuclear centring during early embryonic divisions in centrosome-containing vertebrates. In acentrosomal mouse zygotes, microtubules also centre male and female pronuclei prior to the first mitosis, this time in concert with actin. How nuclear centring is brought about in subsequent acentrosomal embryonic divisions has not been studied. Here, using time-lapse imaging in mouse embryos, we find that although nuclei are delivered to the cell centre upon completion of the first mitotic anaphase, the majority do not remain stationary and instead travel all the way to the cortex in a microtubule-dependent manner. High cytoplasmic viscosity in 2-cell embryos is associated with non-diffusive mechanisms involving actin for subsequent nuclear centring when microtubules again exert a negative influence. Thus, following the first mitotic division, pro-centring actin-dependent mechanisms work against microtubule-dependent de-centring forces. Disrupting the equilibrium of this tug-of-war compromises nuclear centring and symmetry of the subsequent division potentially risking embryonic development. This circuitous centring process exposes an embryonic vulnerability imposed by microtubule-dependent de-centring forces.
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Affiliation(s)
- Yunan Ye
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical ResearchThe University of QueenslandHerstonQLDAustralia
| | - Hayden A Homer
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical ResearchThe University of QueenslandHerstonQLDAustralia
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14
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Yanagisawa M, Watanabe C, Yoshinaga N, Fujiwara K. Cell-Size Space Regulates the Behavior of Confined Polymers: From Nano- and Micromaterials Science to Biology. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11811-11827. [PMID: 36125172 DOI: 10.1021/acs.langmuir.2c01397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polymer micromaterials in a liquid or gel phase covered with a surfactant membrane are widely used materials in pharmaceuticals, cosmetics, and foods. In particular, cell-sized micromaterials of biopolymer solutions covered with a lipid membrane have been studied as artificial cells to understand cells from a physicochemical perspective. The characteristics and phase transitions of polymers confined to a microscopic space often differ from those in bulk systems. The effect that causes this difference is referred to as the cell-size space effect (CSE), but the specific physicochemical factors remain unclear. This study introduces the analysis of CSE on molecular diffusion, nanostructure transition, and phase separation and presents their main factors, i.e., short- and long-range interactions with the membrane surface and small volume (finite element nature). This serves as a guide for determining the dominant factors of CSE. Furthermore, we also introduce other factors of CSE such as spatial closure and the relationships among space size, the characteristic length of periodicity, the structure size, and many others produced by biomolecular assemblies through the analysis of protein reaction-diffusion systems and biochemical reactions.
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Affiliation(s)
- Miho Yanagisawa
- Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo 113-0033, Japan
| | - Chiho Watanabe
- School of Integrated Arts and Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima 739-8521, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai 9808577, Japan
- MathAM-OIL, National Institute of Advanced Industrial Science and Technology, Sendai 980-8577, Japan
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, Yokohama 223-8522, Japan
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15
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Vasudevan J, Zheng C, Wan JG, Cham TJ, Teck LC, Fernandez JG. From qualitative data to correlation using deep generative networks: Demonstrating the relation of nuclear position with the arrangement of actin filaments. PLoS One 2022; 17:e0271056. [PMID: 35905093 PMCID: PMC9337686 DOI: 10.1371/journal.pone.0271056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/22/2022] [Indexed: 11/18/2022] Open
Abstract
The cell nucleus is a dynamic structure that changes locales during cellular processes such as proliferation, differentiation, or migration, and its mispositioning is a hallmark of several disorders. As with most mechanobiological activities of adherent cells, the repositioning and anchoring of the nucleus are presumed to be associated with the organization of the cytoskeleton, the network of protein filaments providing structural integrity to the cells. However, demonstrating this correlation between cytoskeleton organization and nuclear position requires the parameterization of the extraordinarily intricate cytoskeletal fiber arrangements. Here, we show that this parameterization and demonstration can be achieved outside the limits of human conceptualization, using generative network and raw microscope images, relying on machine-driven interpretation and selection of parameterizable features. The developed transformer-based architecture was able to generate high-quality, completed images of more than 8,000 cells, using only information on actin filaments, predicting the presence of a nucleus and its exact localization in more than 70 per cent of instances. Our results demonstrate one of the most basic principles of mechanobiology with a remarkable level of significance. They also highlight the role of deep learning as a powerful tool in biology beyond data augmentation and analysis, capable of interpreting—unconstrained by the principles of human reasoning—complex biological systems from qualitative data.
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Affiliation(s)
- Jyothsna Vasudevan
- Engineering and Product Development, Singapore University of Technology and Design, Singapore, Singapore
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Chuanxia Zheng
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - James G. Wan
- Engineering Systems and Design, Singapore University of Technology and Design, Singapore, Singapore
| | - Tat-Jen Cham
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Lim Chwee Teck
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Javier G. Fernandez
- Engineering and Product Development, Singapore University of Technology and Design, Singapore, Singapore
- * E-mail:
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16
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Geometric trade-off between contractile force and viscous drag determines the actomyosin-based motility of a cell-sized droplet. Proc Natl Acad Sci U S A 2022; 119:e2121147119. [PMID: 35857875 PMCID: PMC9335187 DOI: 10.1073/pnas.2121147119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Cell migration in confined environments is fundamental for diverse biological processes from cancer invasion to leukocyte trafficking. The cell body is propelled by the contractile force of actomyosin networks transmitted from the cell membrane to the external substrates. However, physical determinants of actomyosin-based migration capacity in confined environments are not fully understood. Here, we develop an in vitro migratory cell model, where cytoplasmic actomyosin networks are encapsulated into droplets surrounded by a lipid monolayer membrane. We find that the droplet can move when the actomyosin networks are bound to the membrane, in which the physical interaction between the contracting actomyosin networks and the membrane generates a propulsive force. The droplet moves faster when it has a larger contact area with the substrates, while narrower confinement reduces the migration speed. By combining experimental observations and active gel theory, we propose a mechanism where the balance between sliding friction force, which is a reaction force of the contractile force, and viscous drag determines the migration speed, providing a physical basis of actomyosin-based motility in confined environments.
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17
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Logan G, Chou WC, McCartney BM. A Diaphanous and Enabled-dependent asymmetric actin cable array repositions nuclei during Drosophila oogenesis. Development 2022; 149:275657. [DOI: 10.1242/dev.197442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/24/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Cells reposition their nuclei for diverse specialized functions through a wide variety of cytoskeletal mechanisms. During Drosophila oogenesis, 15 nurse cells connected by ring canals to each other and the oocyte contract, ‘dumping’ their cytoplasm into the oocyte. Prior to dumping, actin cables initiate from the nurse cell cortex and elongate toward their nuclei, pushing them away from ring canals to prevent obstruction. How the cable arrays reposition nuclei is unknown. We found that these arrays are asymmetric, with regional differences in actin cable growth rate dependent on the differential localization of the actin assembly factors Enabled and Diaphanous. Enabled mislocalization produces a uniform growth rate. In oocyte-contacting nurse cells with asymmetric cable arrays, nuclei move away from ring canals. With uniform arrays, these nuclei move toward the adjacent ring canal instead. This correlated with ring canal nuclear blockage and incomplete dumping. Our data suggest that nuclear repositioning relies on the regulated cortical localization of Diaphanous and Enabled to produce actin cable arrays with asymmetric growth that push nuclei away from ring canals, enabling successful oogenesis.
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Affiliation(s)
- Gregory Logan
- Carnegie Mellon University Department of Biological Sciences , , 4400 Fifth Avenue, Pittsburgh, PA 15213 , USA
| | - Wei-Chien Chou
- Carnegie Mellon University Department of Biological Sciences , , 4400 Fifth Avenue, Pittsburgh, PA 15213 , USA
| | - Brooke M. McCartney
- Carnegie Mellon University Department of Biological Sciences , , 4400 Fifth Avenue, Pittsburgh, PA 15213 , USA
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18
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Bashirzadeh Y, Moghimianavval H, Liu AP. Encapsulated actomyosin patterns drive cell-like membrane shape changes. iScience 2022; 25:104236. [PMID: 35521522 PMCID: PMC9061794 DOI: 10.1016/j.isci.2022.104236] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/26/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Cell shape changes from locomotion to cytokinesis are, to a large extent, driven by myosin-driven remodeling of cortical actin patterns. Passive crosslinkers such as α-actinin and fascin as well as actin nucleator Arp2/3 complex largely determine actin network architecture and, consequently, membrane shape changes. Here we reconstitute actomyosin networks inside cell-sized lipid bilayer vesicles and show that depending on vesicle size and concentrations of α-actinin and fascin actomyosin networks assemble into ring and aster-like patterns. Anchoring actin to the membrane does not change actin network architecture yet exerts forces and deforms the membrane when assembled in the form of a contractile ring. In the presence of α-actinin and fascin, an Arp2/3 complex-mediated actomyosin cortex is shown to assemble a ring-like pattern at the equatorial cortex followed by myosin-driven clustering and consequently blebbing. An active gel theory unifies a model for the observed membrane shape changes induced by the contractile cortex.
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Affiliation(s)
- Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
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19
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M’Bana V, Lahree A, Marques S, Slavic K, Mota MM. Plasmodium parasitophorous vacuole membrane-resident protein UIS4 manipulates host cell actin to avoid parasite elimination. iScience 2022; 25:104281. [PMID: 35573190 PMCID: PMC9095750 DOI: 10.1016/j.isci.2022.104281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/09/2022] [Accepted: 04/19/2022] [Indexed: 11/26/2022] Open
Abstract
Parasite-derived PVM-resident proteins are critical for complete parasite development inside hepatocytes, although the function of most of these proteins remains unknown. Here, we show that the upregulated in infectious sporozoites 4 (UIS4) protein, resident at the PVM, interacts with the host cell actin. By suppressing filamentous actin formation, UIS4 avoids parasite elimination. Host cell actin dynamics increases around UIS4-deficient parasites, which is associated with subsequent parasite elimination. Notably, parasite elimination is impaired significantly by the inhibition of host myosin-II, possibly through relieving the compression generated by actomyosin complexes at the host-parasite interface. Together, these data reveal that UIS4 has a critical role in the evasion of host defensive mechanisms, enabling hence EEF survival and development. Plasmodium PVM-resident protein UIS4 interacts with host cell actin Host actin dynamics is altered around exoerythocytic forms (EEFs) lacking UIS4 Actin activity around EEFs lacking UIS4 is associated with parasite elimination Parasite elimination depends on actomyosin complexes formed around the PVM
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20
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Araki S, Beppu K, Kabir AMR, Kakugo A, Maeda YT. Controlling Collective Motion of Kinesin-Driven Microtubules via Patterning of Topographic Landscapes. NANO LETTERS 2021; 21:10478-10485. [PMID: 34874725 DOI: 10.1021/acs.nanolett.1c03952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biomolecular motor proteins that generate forces by consuming chemical energy obtained from ATP hydrolysis play pivotal roles in organizing cytoskeletal structures in living cells. An ability to control cytoskeletal structures would benefit programmable protein patterning; however, our current knowledge is limited because of the underdevelopment of engineering approaches for controlling pattern formation. Here, we demonstrate the controlling of self-assembled patterns of microtubules (MTs) driven by kinesin motors by designing the boundary shape in fabricated microwells. By manipulating the collision angle of gliding MTs defined by the boundary shape, the self-assembly of MTs can be controlled to form protruding bundle and bridge patterns. Corroborated by the theory of self-propelled rods, we further show that the alignment of MTs determines the transition between the assembled patterns, providing a blueprint to reconstruct bridge structures in microchannels. Our findings introduce the tailoring of the self-organization of cytoskeletons and motor proteins for nanotechnological applications.
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Affiliation(s)
- Shunya Araki
- Department of Physics, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Kazusa Beppu
- Department of Physics, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Arif Md Rashedul Kabir
- Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Hokkaido Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Hokkaido Japan
| | - Yusuke T Maeda
- Department of Physics, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
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21
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Jia TZ, Kuruma Y. Increasing complexity of primitive compartments. Biophys Physicobiol 2021; 18:269-273. [PMID: 34909364 PMCID: PMC8639197 DOI: 10.2142/biophysico.bppb-v18.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/15/2021] [Indexed: 12/01/2022] Open
Affiliation(s)
- Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Blue Marble Space Institute of Science, Seattle, Washington 98154, USA
| | - Yutetsu Kuruma
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Extra-cutting-edge Science and Technology Avant-garde Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan.,Japan Science and Technology Agency, PRESTO, Kawaguchi, Saitama 332-0012, Japan
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22
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The Cytoskeleton and Its Roles in Self-Organization Phenomena: Insights from Xenopus Egg Extracts. Cells 2021; 10:cells10092197. [PMID: 34571847 PMCID: PMC8465277 DOI: 10.3390/cells10092197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 01/11/2023] Open
Abstract
Self-organization of and by the cytoskeleton is central to the biology of the cell. Since their introduction in the early 1980s, cytoplasmic extracts derived from the eggs of the African clawed-frog, Xenopus laevis, have flourished as a major experimental system to study the various facets of cytoskeleton-dependent self-organization. Over the years, the many investigations that have used these extracts uniquely benefited from their simplified cell cycle, large experimental volumes, biochemical tractability and cell-free nature. Here, we review the contributions of egg extracts to our understanding of the cytoplasmic aspects of self-organization by the microtubule and the actomyosin cytoskeletons as well as the importance of cytoskeletal filaments in organizing nuclear structure and function.
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23
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Waizumi T, Sakuta H, Hayashi M, Tsumoto K, Takiguchi K, Yoshikawa K. Polymerization/depolymerization of actin cooperates with the morphology and stability of cell-sized droplets generated in a polymer solution under a depletion effect. J Chem Phys 2021; 155:075101. [PMID: 34418942 DOI: 10.1063/5.0055460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Intercellular fluids in living organisms contain high concentrations of macromolecules such as nucleic acid and protein. Over the past few decades, several studies have examined membraneless organelles in terms of liquid-liquid phase separation. These studies have investigated aggregation/attraction among a rich variety of biomolecules. Here, we studied the association between the polymerization/depolymerization of actin, interconversion between monomeric (G-actin) and filamentous states (F-actin), and water/water phase separation in a binary polymer solution using polyethylene glycol (PEG) and dextran (DEX). We found that actin, which is a representative cytoskeleton, changes its distribution in a PEG/DEX binary solution depending on its polymerization state: monomeric G-actin is distributed homogeneously throughout the solution, whereas polymerized F-actin is localized only within the DEX-rich phase. We extended our study by using fragmin, which is a representative actin-severing and -depolymerizing factor. It took hours to restore a homogeneous actin distribution from localization within the DEX-rich phase, even with the addition of fragmin in an amount that causes complete depolymerization. In contrast, when actin that had been depolymerized by fragmin in advance was added to a solution with microphase-separation, F-actin was found in DEX-rich phase droplets. The micro-droplets tended to deform into a non-spherical morphology under conditions where they contained F-actin. These findings suggest that microphase-separation is associated with the dynamics of polymerization and localization of the actin cytoskeleton. We discuss our observations by taking into consideration the polymer depletion effect.
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Affiliation(s)
- Tatsuyuki Waizumi
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Hiroki Sakuta
- Faculty of Life and Medical Sciences, Doshisha University, Tatara, Kyotanabe, Kyoto 610-0394, Japan
| | - Masahito Hayashi
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Kanta Tsumoto
- Division of Chemistry for Materials, Graduate School of Engineering, Mie University, Kurimamachiya-cho 1577, Tsu, Mie 514-8507, Japan
| | - Kingo Takiguchi
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Tatara, Kyotanabe, Kyoto 610-0394, Japan
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24
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Ierushalmi N, Keren K. Cytoskeletal symmetry breaking in animal cells. Curr Opin Cell Biol 2021; 72:91-99. [PMID: 34375786 DOI: 10.1016/j.ceb.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/13/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
Abstract
Symmetry breaking is a crucial step in structure formation and function of all cells, necessary for cell movement, cell division, and polarity establishment. Although the mechanisms of symmetry breaking are diverse, they often share common characteristics. Here we review examples of nematic, polar, and chiral cytoskeletal symmetry breaking in animal cells, and analogous processes in simplified reconstituted systems. We discuss the origins of symmetry breaking, which can arise spontaneously, or involve amplification of a pre-existing external or internal bias to the whole cell level. The underlying mechanisms often involve both chemical and mechanical processes that cooperate to break symmetry in a robust manner, and typically depend on the shape, size, or properties of the cell's boundary.
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Affiliation(s)
- Niv Ierushalmi
- Department of Physics, Technion - Israel Institute of Technology, Haifa, Israel
| | - Kinneret Keren
- Department of Physics, Technion - Israel Institute of Technology, Haifa, Israel; Network Biology Research Laboratories and Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, Israel.
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25
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Feng P, Xie Q, Liu Z, Guo Z, Tang R, Yu Q. Study on the Reparative Effect of PEGylated Growth Hormone on Ovarian Parameters and Mitochondrial Function of Oocytes From Rats With Premature Ovarian Insufficiency. Front Cell Dev Biol 2021; 9:649005. [PMID: 33791307 PMCID: PMC8005617 DOI: 10.3389/fcell.2021.649005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 02/15/2021] [Indexed: 12/02/2022] Open
Abstract
Premature ovarian insufficiency (POI) is a heterogeneous disorder and lacks effective interventions in clinical applications. This research aimed to elucidate the potential effects of recombinant human PEGylated growth hormone (rhGH) on follicular development and mitochondrial function in oocytes as well as ovarian parameters in POI rats induced by the chemotherapeutic agent. The impacts of rhGH on ovarian function before superovulation on follicles, estrous cycle, and sex hormones were evaluated. Oocytes were retrieved to determine oocyte quality and oxidative stress parameters. Single-cell sequencing was applied to investigate the latent regulatory network. This study provides new evidence that a high dosage of rhGH increased the number of retrieved oocytes even though it did not completely restore the disturbed estrous cycle and sex hormones. rhGH attenuated the apoptosis of granulosa cells and oxidative stress response caused by reactive oxygen species (ROS) and mitochondrial superoxide. Additionally, rhGH modulated the energy metabolism of oocytes concerning the mitochondrial membrane potential and ATP content but not mtDNA copy numbers. Based on single-cell transcriptomic analysis, we found that rhGH directly or indirectly promoted the balance of oxidative stress and cellular oxidant detoxification. Four hub genes, Pxmp4, Ehbp1, Mt-cyb, and Enpp6, were identified to be closely related to the repair process in oocytes as potential targets for POI treatment.
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Affiliation(s)
- Penghui Feng
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Qiu Xie
- Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zhe Liu
- Laboratory of Clinical Genetics Medical Science Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zaixin Guo
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ruiyi Tang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Qi Yu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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Papalazarou V, Machesky LM. The cell pushes back: The Arp2/3 complex is a key orchestrator of cellular responses to environmental forces. Curr Opin Cell Biol 2021; 68:37-44. [PMID: 32977244 PMCID: PMC7938217 DOI: 10.1016/j.ceb.2020.08.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022]
Abstract
The Arp2/3 complex orchestrates the formation of branched actin networks at the interface between the cytoplasm and membranes. Although it is widely appreciated that these networks are useful for scaffolding, creating pushing forces and delineating zones at the membrane interface, it has only recently come to light that branched actin networks are mechanosensitive, giving them special properties. Here, we discuss recent advances in our understanding of how Arp2/3-generated actin networks respond to load forces and thus allow cells to create pushing forces in responsive and tuneable ways to effect cellular processes such as migration, invasion, phagocytosis, adhesion and even nuclear and DNA damage repair.
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Affiliation(s)
- Vassilis Papalazarou
- CRUK Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Laura M Machesky
- CRUK Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK; Institute of Cancer Sciences, Garscube Estate, University of Glasgow, Glasgow, G61 1BD, UK.
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Shamipour S, Caballero-Mancebo S, Heisenberg CP. Cytoplasm's Got Moves. Dev Cell 2021; 56:213-226. [PMID: 33321104 DOI: 10.1016/j.devcel.2020.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/22/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023]
Abstract
Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species.
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Affiliation(s)
- Shayan Shamipour
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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