1
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Daly ML, Nishi K, Klawa SJ, Hinton KY, Gao Y, Freeman R. Designer peptide-DNA cytoskeletons regulate the function of synthetic cells. Nat Chem 2024:10.1038/s41557-024-01509-w. [PMID: 38654104 DOI: 10.1038/s41557-024-01509-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/15/2024] [Indexed: 04/25/2024]
Abstract
The bottom-up engineering of artificial cells requires a reconfigurable cytoskeleton that can organize at distinct locations and dynamically modulate its structural and mechanical properties. Here, inspired by the vast array of actin-binding proteins and their ability to reversibly crosslink or bundle filaments, we have designed a library of peptide-DNA crosslinkers varying in length, valency and geometry. Peptide filaments conjoint through DNA hybridization give rise to tactoid-shaped bundles with tunable aspect ratios and mechanics. When confined in cell-sized water-in-oil droplets, the DNA crosslinker design guides the localization of cytoskeletal structures at the cortex or within the lumen of the synthetic cells. The tunable spatial arrangement regulates the passive diffusion of payloads within the droplets and complementary DNA handles allow for the reversible recruitment and release of payloads on and off the cytoskeleton. Heat-induced reconfiguration of peptide-DNA architectures triggers shape deformations of droplets, regulated by DNA melting temperatures. Altogether, the modular design of peptide-DNA architectures is a powerful strategy towards the bottom-up assembly of synthetic cells.
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Affiliation(s)
- Margaret L Daly
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kengo Nishi
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen J Klawa
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kameryn Y Hinton
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Yuan Gao
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA.
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2
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Waechtler BE, Jayasankar R, Morin EP, Robinson DN. Benefits and challenges of reconstituting the actin cortex. Cytoskeleton (Hoboken) 2024. [PMID: 38520148 DOI: 10.1002/cm.21855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/21/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024]
Abstract
The cell's ability to change shape is a central feature in many cellular processes, including cytokinesis, motility, migration, and tissue formation. The cell constructs a network of contractile proteins underneath the cell membrane to form the cortex, and the reorganization of these components directly contributes to cellular shape changes. The desire to mimic these cell shape changes to aid in the creation of a synthetic cell has been increasing. Therefore, membrane-based reconstitution experiments have flourished, furthering our understanding of the minimal components the cell uses throughout these processes. Although biochemical approaches increased our understanding of actin, myosin II, and actin-associated proteins, using membrane-based reconstituted systems has further expanded our understanding of actin structures and functions because membrane-cortex interactions can be analyzed. In this review, we highlight the recent developments in membrane-based reconstitution techniques. We examine the current findings on the minimal components needed to recapitulate distinct actin structures and functions and how they relate to the cortex's impact on cellular mechanical properties. We also explore how co-processing of computational models with wet-lab experiments enhances our understanding of these properties. Finally, we emphasize the benefits and challenges inherent to membrane-based, reconstitution assays, ranging from the advantage of precise control over the system to the difficulty of integrating these findings into the complex cellular environment.
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Affiliation(s)
- Brooke E Waechtler
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rajan Jayasankar
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Baltimore, Maryland, USA
| | - Emma P Morin
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Douglas N Robinson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Baltimore, Maryland, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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3
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Reboucas RB, Faizi HA, Miksis MJ, Vlahovska PM. Stationary shapes of axisymmetric vesicles beyond lowest-energy configurations. SOFT MATTER 2024; 20:2258-2271. [PMID: 38353299 DOI: 10.1039/d3sm01463k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
We conduct a systematic exploration of the energy landscape of vesicle morphologies within the framework of the Helfrich model. Vesicle shapes are determined by minimizing the elastic energy subject to constraints of constant area and volume. The results show that pressurized vesicles can adopt higher-energy spindle-like configurations that require the action of point forces at the poles. If the internal pressure is lower than the external one, multilobed shapes are predicted. We utilize our results to rationalize experimentally observed spindle shapes of giant vesicles in a uniform AC electric field.
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Affiliation(s)
- Rodrigo B Reboucas
- Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA.
| | - Hammad A Faizi
- Department of Mechanical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Michael J Miksis
- Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA.
| | - Petia M Vlahovska
- Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA.
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4
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Van de Cauter L, van Buren L, Koenderink GH, Ganzinger KA. Exploring Giant Unilamellar Vesicle Production for Artificial Cells - Current Challenges and Future Directions. SMALL METHODS 2023; 7:e2300416. [PMID: 37464561 DOI: 10.1002/smtd.202300416] [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: 03/30/2023] [Revised: 05/30/2023] [Indexed: 07/20/2023]
Abstract
Creating an artificial cell from the bottom up is a long-standing challenge and, while significant progress has been made, the full realization of this goal remains elusive. Arguably, one of the biggest hurdles that researchers are facing now is the assembly of different modules of cell function inside a single container. Giant unilamellar vesicles (GUVs) have emerged as a suitable container with many methods available for their production. Well-studied swelling-based methods offer a wide range of lipid compositions but at the expense of limited encapsulation efficiency. Emulsion-based methods, on the other hand, excel at encapsulation but are only effective with a limited set of membrane compositions and may entrap residual additives in the lipid bilayer. Since the ultimate artificial cell will need to comply with both specific membrane and encapsulation requirements, there is still no one-method-fits-all solution for GUV formation available today. This review discusses the state of the art in different GUV production methods and their compatibility with GUV requirements and operational requirements such as reproducibility and ease of use. It concludes by identifying the most pressing issues and proposes potential avenues for future research to bring us one step closer to turning artificial cells into a reality.
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Affiliation(s)
- Lori Van de Cauter
- Autonomous Matter Department, AMOLF, Amsterdam, 1098 XG, The Netherlands
| | - Lennard van Buren
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
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5
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Lopes Dos Santos R, Malo M, Campillo C. Spatial Control of Arp2/3-Induced Actin Polymerization on Phase-Separated Giant Unilamellar Vesicles. ACS Synth Biol 2023; 12:3267-3274. [PMID: 37909673 DOI: 10.1021/acssynbio.3c00268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Deciphering the physical mechanisms underlying cell shape changes, while avoiding the cellular interior's complexity, involves the development of controlled basic biomimetic systems that imitate cell functions. In particular, the reconstruction of cytoskeletal dynamics on cell-sized giant unilamellar vesicles (GUVs) has allowed for the reconstituting of some cell-like processes in vitro. In fact, such a bottom-up strategy could be the basis for forming protocells able to reorganize or even move autonomously. However, reconstituting the subtle and controlled dynamics of the cytoskeleton-membrane interface in vitro remains an experimental challenge. Taking advantage of the lipid-induced segregation of an actin polymerization activator, we present a system that targets actin polymerization in specific domains of phase-separated GUVs. We observe actin networks localized on Lo, Ld, or on both types of domains and the actin-induced deformation or reorganization of these domains. These results suggest that the system we have developed here could pave the way for future experiments further detailing the interplay between actin dynamics and membrane heterogeneities.
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Affiliation(s)
- Rogério Lopes Dos Santos
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry, Courcouronnes, France
| | - Michel Malo
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry, Courcouronnes, France
| | - Clément Campillo
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry, Courcouronnes, France
- Institut Universitaire de France (IUF), 75005 Paris, France
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6
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Nakazawa K, Chauvin B, Mangenot S, Bertin A. Reconstituted in vitro systems to reveal the roles and functions of septins. J Cell Sci 2023; 136:jcs259448. [PMID: 37815088 DOI: 10.1242/jcs.259448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023] Open
Abstract
Septins are essential cytoskeletal proteins involved in key cellular processes and have also been implicated in diseases from cancers to neurodegenerative pathologies. However, they have not been as thoroughly studied as other cytoskeletal proteins. In vivo, septins interact with other cytoskeletal proteins and with the inner plasma membrane. Hence, bottom-up in vitro cell-free assays are well suited to dissect the roles and behavior of septins in a controlled environment. Specifically, in vitro studies have been invaluable in describing the self-assembly of septins into a large diversity of ultrastructures. Given that septins interact specifically with membrane, the details of these septin-membrane interactions have been analyzed using reconstituted lipid systems. In particular, at a membrane, septins are often localized at curvatures of micrometer scale. In that context, in vitro assays have been performed with substrates of varying curvatures (spheres, cylinders or undulated substrates) to probe the sensitivity of septins to membrane curvature. This Review will first present the structural properties of septins in solution and describe the interplay of septins with cytoskeletal partners. We will then discuss how septins interact with biomimetic membranes and induce their reshaping. Finally, we will highlight the curvature sensitivity of septins and how they alter the mechanical properties of membranes.
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Affiliation(s)
- Koyomi Nakazawa
- Physico Chimie Curie , Institut Curie, CNRS UMR 168, Sorbonne Université, 11 Rue Pierre et Paris Curie, 75005 Paris, France
| | - Brieuc Chauvin
- Physico Chimie Curie , Institut Curie, CNRS UMR 168, Sorbonne Université, 11 Rue Pierre et Paris Curie, 75005 Paris, France
| | - Stéphanie Mangenot
- Laboratoire Matière et Systèmes Complexes , Université de Paris Cité, CNRS UMR 7057, 45 Rue des Saint Pères, 75006 Paris, France
| | - Aurélie Bertin
- Physico Chimie Curie , Institut Curie, CNRS UMR 168, Sorbonne Université, 11 Rue Pierre et Paris Curie, 75005 Paris, France
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7
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Chen X, Roeters SJ, Cavanna F, Alvarado J, Baiz CR. Crowding alters F-actin secondary structure and hydration. Commun Biol 2023; 6:900. [PMID: 37660224 PMCID: PMC10475093 DOI: 10.1038/s42003-023-05274-3] [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: 04/28/2023] [Accepted: 08/22/2023] [Indexed: 09/04/2023] Open
Abstract
Actin, an important component of eukaryotic cell cytoskeleton, regulates cell shape and transport. The morphology and biochemical properties of actin filaments are determined by their structure and protein-protein contacts. Crowded environments can organize filaments into bundles, but less is known about how they affect F-actin structure. This study used 2D IR spectroscopy and spectral calculations to examine how crowding and bundling impact the secondary structure and local environments in filaments and weakly or strongly bundled networks. The results reveal that bundling induces changes in actin's secondary structure, leading to a decrease in β-sheet and an increase in loop conformations. Strongly bundled networks exhibit a decrease in backbone solvent exposure, with less perturbed α-helices and nearly "locked" β-sheets. Similarly, the loops become less hydrated but maintain a dynamic environment. These findings highlight the role of loop structure in actin network morphology and stability under morphology control by PEG.
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Affiliation(s)
- Xiaobing Chen
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA
| | - Steven J Roeters
- Department of Chemistry, Aarhus University, Aarhus, Denmark
- Department of Anatomy and Neurosciences, Vrije Universiteit, Amsterdam UMC, Amsterdam, Netherlands
| | - Francis Cavanna
- Department of Physics, University of Texas at Austin, Center for Nonlinear Dynamics, Austin, TX, USA
| | - José Alvarado
- Department of Physics, University of Texas at Austin, Center for Nonlinear Dynamics, Austin, TX, USA
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA.
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8
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Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. Steering self-organisation through confinement. SOFT MATTER 2023; 19:1695-1704. [PMID: 36779972 PMCID: PMC9977364 DOI: 10.1039/d2sm01562e] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units' translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.
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Affiliation(s)
- Nuno A M Araújo
- Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Liesbeth M C Janssen
- Department of Applied Physics and Science Education, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Thomas Barois
- University of Bordeaux, CNRS, LOMA, UMR 5798, F-33400, Talence, France
| | - Guido Boffetta
- Department of Physics and INFN, University of Torino, via Pietro Giuria 1, 10125, Torino, Italy
| | - Itai Cohen
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York, USA
- Laboratory of Atomic and Solid-State Physics, Cornell University, Ithaca, New York, USA
| | - Alessandro Corbetta
- Department of Applied Physics and Science Education, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.
| | - Olivier Dauchot
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005, Paris, France
| | - Marjolein Dijkstra
- Soft condensed matter, Department of Physics, Debye institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC, Utrecht, The Netherlands
| | - William M Durham
- Department of Physics and Astronomy, University of Sheffield, Hounsfield Road, Sheffield, S3 7RH, UK
| | - Audrey Dussutour
- Research Centre on Animal Cognition (CRCA), Centre for Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, 31062, AD, France
| | - Simon Garnier
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Hanneke Gelderblom
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
- Department of Applied Physics and J. M. Burgers Center for Fluid Dynamics, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077, Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Lucio Isa
- Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, 8093, Zürich, Switzerland
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Ralf Metzler
- Institute of Physics & Astronomy, University of Potsdam, Karl-Liebknecht-Str 24/25, D-14476, Potsdam-Golm, Germany
| | - Marco Polin
- Mediterranean Institute for Advanced Studies, IMEDEA UIB-CSIC, C/Miquel Marqués 21, 07190, Esporles, Spain
- Department of Physics, University of Warwick, Gibbet Hill road, CV4 7AL, Coventry, UK
| | - C Patrick Royall
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005, Paris, France
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria
| | - Anupam Sengupta
- Physics of Living Matter, Department of Physics and Materials Science, University of Luxembourg, 162 A, Avenue de la Faïencerie, L-1511, Luxembourg
| | - Cécile Sykes
- Laboratoire de Physique de lÉcole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France
| | - Vito Trianni
- Institute of Cognitive Sciences and Technologies, CNR, Via San Martino della Battaglia 44, 00185, Rome, Italy
| | - Idan Tuval
- Mediterranean Institute for Advanced Studies, IMEDEA UIB-CSIC, C/Miquel Marqués 21, 07190, Esporles, Spain
| | - Nicolas Vogel
- Institute of Particle Technology, Friedrich-Alexander Universität Erlangen-Nürnberg, Cauerstrasse 4, 91058, Erlangen, Germany
| | - Julia M Yeomans
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Iker Zuriguel
- Departamento de Física y Matemática Aplicada, Facultad de Ciencias, Universidad de Navarra, Pamplona, Spain
| | - Alvaro Marin
- Physics of Fluids Group, Mesa+ Institute, Max Planck Center for Complex Fluid Dynamics and J. M. Burgers Center for Fluid Dynamics, University of Twente, 7500AE, Enschede, The Netherlands.
| | - Giorgio Volpe
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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9
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Baldauf L, Frey F, Arribas Perez M, Idema T, Koenderink GH. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophys J 2023:S0006-3495(23)00124-8. [PMID: 36806830 DOI: 10.1016/j.bpj.2023.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/16/2022] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks are inherently able to sense and generate membrane curvature, or whether they rely on their diverse binding partners to accomplish this. Here, we show that curvature sensing is an inherent capability of branched actin networks nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface of the GUV membrane. We show that actin forms a uniform and thin cortical layer when present at high concentration and distinct patches associated with negative membrane curvature at low concentration. Serendipitously, we find that the GUV production method also produces dumbbell-shaped GUVs, which we explain using mathematical modeling in terms of membrane hemifusion of nested GUVs. We find that branched actin networks preferentially assemble at the neck of the dumbbells, which possess a micrometer-range convex curvature comparable with the curvature of the actin patches found in spherical GUVs. Minimal branched actin networks can thus sense membrane curvature, which may help mammalian cells to robustly recruit actin to curved membranes to facilitate diverse cellular functions such as cytokinesis and migration.
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Affiliation(s)
- Lucia Baldauf
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Felix Frey
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Marcos Arribas Perez
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Timon Idema
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
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10
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Aufderhorst-Roberts A, Staykova M. Scratching beyond the surface - minimal actin assemblies as tools to elucidate mechanical reinforcement and shape change. Emerg Top Life Sci 2022; 6:ETLS20220052. [PMID: 36541184 PMCID: PMC9788373 DOI: 10.1042/etls20220052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
The interaction between the actin cytoskeleton and the plasma membrane in eukaryotic cells is integral to a large number of functions such as shape change, mechanical reinforcement and contraction. These phenomena are driven by the architectural regulation of a thin actin network, directly beneath the membrane through interactions with a variety of binding proteins, membrane anchoring proteins and molecular motors. An increasingly common approach to understanding the mechanisms that drive these processes is to build model systems from reconstituted lipids, actin filaments and associated actin-binding proteins. Here we review recent progress in this field, with a particular emphasis on how the actin cytoskeleton provides mechanical reinforcement, drives shape change and induces contraction. Finally, we discuss potential future developments in the field, which would allow the extension of these techniques to more complex cellular processes.
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Affiliation(s)
| | - Margarita Staykova
- Centre for Materials Physics, Department of Physics, Durham University, Durham DH1 3LE, U.K
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11
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Shimomura A, Ina S, Oki M, Tsuji G. Effects of Charged Lipids on Giant Unilamellar Vesicle Fusion and Inner Content Mixing via Freeze-Thawing. Chembiochem 2022; 23:e202200550. [PMID: 36321751 DOI: 10.1002/cbic.202200550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/01/2022] [Indexed: 11/21/2022]
Abstract
Fusion between giant unilamellar vesicles (GUVs) can incorporate and mix components of biochemical reactions. Recently, GUV fusion induced by freeze-thawing (F/T) was employed to construct artificial cells that can easily and repeatedly fuse GUVs with efficient content mixing. However, GUVs were ruptured during F/T, and the inner contents leaked. Herein, we investigated the effects of charged lipids on GUV fusion via F/T. The presence of 10 %-50 % (w/w%) negatively charged lipids in GUV membranes, mainly composed of the neutral charged lipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), improved resistance to GUV rupture and decreased inner content leakage. Furthermore, we found that the presence of positively charged lipids in GUV membranes elevated GUV rupture compared with F/T between GUVs containing POPC alone. Modified GUVs may better incorporate nutrients and lipid membranes with less damage following GUV fusion via F/T, providing an improved artificial model.
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Affiliation(s)
- Ayu Shimomura
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui-shi, Fukui, 910-8507, Japan
| | - Shiori Ina
- Department of Materials Science and Biotechnology, School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui-shi, Fukui, 910-8507, Japan
| | - Masaya Oki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui-shi, Fukui, 910-8507, Japan.,Department of Materials Science and Biotechnology, School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui-shi, Fukui, 910-8507, Japan.,Life Science Innovation Center, University of Fukui, 3-9-1 Bunkyo, Fukui-shi, Fukui, 910-8507, Japan
| | - Gakushi Tsuji
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui-shi, Fukui, 910-8507, Japan.,Department of Materials Science and Biotechnology, School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui-shi, Fukui, 910-8507, Japan.,Life Science Innovation Center, University of Fukui, 3-9-1 Bunkyo, Fukui-shi, Fukui, 910-8507, Japan
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12
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van Buren L, Koenderink GH, Martinez-Torres C. DisGUVery: A Versatile Open-Source Software for High-Throughput Image Analysis of Giant Unilamellar Vesicles. ACS Synth Biol 2022; 12:120-135. [PMID: 36508359 PMCID: PMC9872171 DOI: 10.1021/acssynbio.2c00407] [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] [Indexed: 12/14/2022]
Abstract
Giant unilamellar vesicles (GUVs) are cell-sized aqueous compartments enclosed by a phospholipid bilayer. Due to their cell-mimicking properties, GUVs have become a widespread experimental tool in synthetic biology to study membrane properties and cellular processes. In stark contrast to the experimental progress, quantitative analysis of GUV microscopy images has received much less attention. Currently, most analysis is performed either manually or with custom-made scripts, which makes analysis time-consuming and results difficult to compare across studies. To make quantitative GUV analysis accessible and fast, we present DisGUVery, an open-source, versatile software that encapsulates multiple algorithms for automated detection and analysis of GUVs in microscopy images. With a performance analysis, we demonstrate that DisGUVery's three vesicle detection modules successfully identify GUVs in images obtained with a wide range of imaging sources, in various typical GUV experiments. Multiple predefined analysis modules allow the user to extract properties such as membrane fluorescence, vesicle shape, and internal fluorescence from large populations. A new membrane segmentation algorithm facilitates spatial fluorescence analysis of nonspherical vesicles. Altogether, DisGUVery provides an accessible tool to enable high-throughput automated analysis of GUVs, and thereby to promote quantitative data analysis in synthetic cell research.
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Affiliation(s)
- Lennard van Buren
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Gijsje Hendrika Koenderink
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands,
| | - Cristina Martinez-Torres
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands,
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13
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Lopes dos Santos R, Campillo C. Studying actin-induced cell shape changes using Giant Unilamellar Vesicles and reconstituted actin networks. Biochem Soc Trans 2022; 50:1527-1539. [PMID: 36111807 PMCID: PMC9704537 DOI: 10.1042/bst20220900] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 10/05/2023]
Abstract
Cell shape changes that are fuelled by the dynamics of the actomyosin cytoskeleton control cellular processes such as motility and division. However, the mechanisms of interplay between cell membranes and actomyosin are complicated to decipher in the complex environment of the cytoplasm. Using biomimetic systems offers an alternative approach to studying cell shape changes in assays with controlled biochemical composition. Biomimetic systems allow quantitative experiments that can help to build physical models describing the processes of cell shape changes. This article reviews works in which actin networks are reconstructed inside or outside cell-sized Giant Unilamellar Vesicles (GUVs), which are models of cell membranes. We show how various actin networks affect the shape and mechanics of GUVs and how some cell shape changes can be reproduced in vitro using these minimal systems.
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Affiliation(s)
- Rogério Lopes dos Santos
- LAMBE, Université d'Evry Val d'Essonne, CNRS, CEA, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
| | - Clément Campillo
- LAMBE, Université d'Evry Val d'Essonne, CNRS, CEA, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
- Institut Universitaire de France (IUF), Paris, France
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14
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Abstract
One of the major challenges of bottom-up synthetic biology is rebuilding a minimal cell division machinery. From a reconstitution perspective, the animal cell division apparatus is mechanically the simplest and therefore attractive to rebuild. An actin-based ring produces contractile force to constrict the membrane. By contrast, microbes and plant cells have a cell wall, so division requires concerted membrane constriction and cell wall synthesis. Furthermore, reconstitution of the actin division machinery helps in understanding the physical and molecular mechanisms of cytokinesis in animal cells and thus our own cells. In this review, we describe the state-of-the-art research on reconstitution of minimal actin-mediated cytokinetic machineries. Based on the conceptual requirements that we obtained from the physics of the shape changes involved in cell division, we propose two major routes for building a minimal actin apparatus capable of division. Importantly, we acknowledge both the passive and active roles that the confining lipid membrane can play in synthetic cytokinesis. We conclude this review by identifying the most pressing challenges for future reconstitution work, thereby laying out a roadmap for building a synthetic cell equipped with a minimal actin division machinery.
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15
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Li C, Zhang X, Yang B, Wei F, Ren Y, Mu W, Han X. Reversible Deformation of Artificial Cell Colonies Triggered by Actin Polymerization for Muscle Behavior Mimicry. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2204039. [PMID: 35765153 DOI: 10.1002/adma.202204039] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The use of artificial cells to mimic living tissues is beneficial for understanding the mechanism of interaction among cells. Artificial cells hold immense potential in the field of tissue engineering. Self-powered artificial cells capable of reversible deformation are developed by encapsulating living mitochondria, actins, and methylcellulose. Upon addition of pyruvate molecules, the mitochondria produce adenosine triphosphate (ATP), which acts as an energy source to trigger actin polymerization. The reversible deformation of artificial cells occurs with a spindle shape resulting from the polymerization of actins to form filaments adjacent to the lipid bilayer that subsequently returns to a spherical shape resulting from the depolymerization of actin filaments upon laser irradiation. The linear colonies composed of these artificial cells exhibit collective contraction and relaxation to mimic muscle tissues. At maximum contraction, the long axis of each giant unilamellar vesicle (GUV) is parallel to each other. All the colonies are synchronized in the contraction phase. The deformation of each GUV in the colonies is influenced by its adjacent GUVs. The muscle-like artificial cell colonies described here pave the way to develop sustainably self-powered artificial tissues.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
| | - Xiangxiang Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
| | - Boyu Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
| | - Feng Wei
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
| | - Yongshuo Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
| | - Wei Mu
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China
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16
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Kajii K, Shimomura A, T Higashide M, Oki M, Tsuji G. Effects of Sugars on Giant Unilamellar Vesicle Preparation, Fusion, PCR in Liposomes, and Pore Formation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8871-8880. [PMID: 35836326 DOI: 10.1021/acs.langmuir.2c00989] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The water-in-oil emulsion transfer method was developed for preparing giant unilamellar vesicles (GUVs) and is useful for studying cellular functions under conditions that mimic cellular environments. A shortcoming of this method for encapsulating biochemical reactions is that it requires high sugar concentrations to enable the density effect to transverse the oil-water interface. In this study, we investigated the effects of sugars on GUV preparation and several biochemical reactions. We found that changing the sugar in the inner solution from sucrose to maltose or trehalose improved GUV formation. The fusion ratio of the freeze-thaw method was better in the traditional glucose-sucrose condition compared with the other examined conditions. For the inner biochemical reaction, we performed PCR in liposomes. The presence of maltose in the inner solution improved the stability of GUVs against damage caused by thermal cycles. Finally, fructose in the outer solution reduced leakage of the inner solution via pores on the membranes of GUVs. Our findings provide new insight for optimizing sugar conditions for preparing GUVs and inner GUV reactions. This could increase the utilization of GUVs as artificial cell compartment models.
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Affiliation(s)
- Kyoka Kajii
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui City 910-8507, Fukui, Japan
| | - Ayu Shimomura
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui City 910-8507, Fukui, Japan
| | - Mika T Higashide
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui City 910-8507, Fukui, Japan
| | - Masaya Oki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui City 910-8507, Fukui, Japan
- Life Science Innovation Center, University of Fukui, 3-9-1 Bunkyo, Fukui City 910-8507, Fukui, Japan
| | - Gakushi Tsuji
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui City 910-8507, Fukui, Japan
- Life Science Innovation Center, University of Fukui, 3-9-1 Bunkyo, Fukui City 910-8507, Fukui, Japan
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17
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Li C, Zhang X, Dong M, Han X. Progress on Crowding Effect in Cell-like Structures. MEMBRANES 2022; 12:membranes12060593. [PMID: 35736300 PMCID: PMC9228500 DOI: 10.3390/membranes12060593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/10/2022]
Abstract
Several biological macromolecules, such as proteins, nucleic acids, and polysaccharides, occupy about 30% of the space in cells, resulting in a crowded macromolecule environment. The crowding effect within cells exerts an impact on the functions of biological components, the assembly behavior of biomacromolecules, and the thermodynamics and kinetics of metabolic reactions. Cell-like structures provide confined and independent compartments for studying the working mechanisms of cells, which can be used to study the physiological functions arising from the crowding effect of macromolecules in cells. This article mainly summarizes the progress of research on the macromolecular crowding effects in cell-like structures. It includes the effects of this crowding on actin assembly behavior, tubulin aggregation behavior, and gene expression. The challenges and future trends in this field are presented at the end of the paper.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China; (C.L.); (X.Z.)
| | - Xiangxiang Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China; (C.L.); (X.Z.)
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
- Correspondence: (M.D.); (X.H.)
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China; (C.L.); (X.Z.)
- Correspondence: (M.D.); (X.H.)
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18
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Booth R, Insua I, Ahmed S, Rioboo A, Montenegro J. Supramolecular fibrillation of peptide amphiphiles induces environmental responses in aqueous droplets. Nat Commun 2021; 12:6421. [PMID: 34741043 PMCID: PMC8571317 DOI: 10.1038/s41467-021-26681-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/17/2021] [Indexed: 02/02/2023] Open
Abstract
One-dimensional (1D) supramolecular polymers are commonly found in natural and synthetic systems to prompt functional responses that capitalise on hierarchical molecular ordering. Despite amphiphilic self-assembly being significantly studied in the context of aqueous encapsulation and autopoiesis, very little is currently known about the physico-chemical consequences and functional role of 1D supramolecular polymerisation confined in aqueous compartments. Here, we describe the different phenomena that resulted from the chemically triggered supramolecular fibrillation of synthetic peptide amphiphiles inside water microdroplets. The confined connection of suitable dormant precursors triggered a physically autocatalysed chemical reaction that resulted in functional environmental responses such as molecular uptake, fusion and chemical exchange. These results demonstrate the potential of minimalistic 1D supramolecular polymerisation to modulate the behaviour of individual aqueous entities with their environment and within communities.
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Affiliation(s)
- Richard Booth
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Ignacio Insua
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Sahnawaz Ahmed
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Alicia Rioboo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain.
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19
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Kattan J, Doerr A, Dogterom M, Danelon C. Shaping Liposomes by Cell-Free Expressed Bacterial Microtubules. ACS Synth Biol 2021; 10:2447-2455. [PMID: 34585918 PMCID: PMC8524656 DOI: 10.1021/acssynbio.1c00278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Genetic control over
a cytoskeletal network inside lipid vesicles
offers a potential route to controlled shape changes and DNA segregation
in synthetic cell biology. Bacterial microtubules (bMTs) are protein
filaments found in bacteria of the genus Prosthecobacter. They are formed by the tubulins BtubA and BtubB, which polymerize
in the presence of GTP. Here, we show that the tubulins BtubA/B can
be functionally expressed from DNA templates in a reconstituted transcription-translation
system, thus providing a cytosol-like environment to study their biochemical
and biophysical properties. We found that bMTs spontaneously interact
with lipid membranes and display treadmilling. When compartmentalized
inside liposomes, de novo synthesized BtubA/B tubulins
self-organize into cytoskeletal structures of different morphologies.
Moreover, bMTs can exert a pushing force on the membrane and deform
liposomes, a phenomenon that can be reversed by a light-activated
disassembly of the filaments. Our work establishes bMTs as a new building
block in synthetic biology. In the context of creating a synthetic
cell, bMTs could help shape the lipid compartment, establish polarity
or directional transport, and assist the division machinery.
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Affiliation(s)
- Johannes Kattan
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Anne Doerr
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marileen Dogterom
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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20
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Ni H, Papoian GA. Membrane-MEDYAN: Simulating Deformable Vesicles Containing Complex Cytoskeletal Networks. J Phys Chem B 2021; 125:10710-10719. [PMID: 34461720 DOI: 10.1021/acs.jpcb.1c02336] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The plasma membrane defines the shape of the cell and plays an indispensable role in bridging intra- and extracellular environments. Mechanochemical interactions between plasma membrane and cytoskeleton are vital for cell biomechanics and mechanosensing. A computational model that comprehensively captures the complex, cell-scale cytoskeleton-membrane dynamics is still lacking. In this work, we introduce a triangulated membrane model that accounts for the membrane's elastic properties, as well as for membrane-filament steric interactions. The corresponding force-field was incorporated into the active biological matter simulation platform, MEDYAN ("mechanochemical dynamics of active networks"). Simulations using the new model shed light on how actin filament bundling affects generation of tubular membrane protrusions. In particular, we used membrane-MEDYAN simulations to investigate protrusion initiation and dynamics while varying geometries of filament bundles, membrane rigidities and local G-Actin concentrations. We found that the bundles' protrusion propensities sensitively depend on the synergy between bundle thickness and inclination angle at which the bundle approaches the membrane. The new model paves the way for simulations of biological systems involving intricate membrane-cytoskeleton interactions, such as those occurring at the leading edge and the cortex, eventually helping to uncover the fundamental principles underlying the active matter organization in the vicinity of the membrane.
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Affiliation(s)
- Haoran Ni
- Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
| | - Garegin A Papoian
- Biophysics Program, University of Maryland, College Park, Maryland 20742, United States.,Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States.,Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
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21
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Olivi L, Berger M, Creyghton RNP, De Franceschi N, Dekker C, Mulder BM, Claassens NJ, Ten Wolde PR, van der Oost J. Towards a synthetic cell cycle. Nat Commun 2021; 12:4531. [PMID: 34312383 PMCID: PMC8313558 DOI: 10.1038/s41467-021-24772-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/29/2021] [Indexed: 02/08/2023] Open
Abstract
Recent developments in synthetic biology may bring the bottom-up generation of a synthetic cell within reach. A key feature of a living synthetic cell is a functional cell cycle, in which DNA replication and segregation as well as cell growth and division are well integrated. Here, we describe different approaches to recreate these processes in a synthetic cell, based on natural systems and/or synthetic alternatives. Although some individual machineries have recently been established, their integration and control in a synthetic cell cycle remain to be addressed. In this Perspective, we discuss potential paths towards an integrated synthetic cell cycle.
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Affiliation(s)
- Lorenzo Olivi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | | | - Nicola De Franceschi
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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22
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Van de Cauter L, Fanalista F, van Buren L, De Franceschi N, Godino E, Bouw S, Danelon C, Dekker C, Koenderink GH, Ganzinger KA. Optimized cDICE for Efficient Reconstitution of Biological Systems in Giant Unilamellar Vesicles. ACS Synth Biol 2021. [PMID: 34185516 DOI: 10.1101/2021.02.24.432456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells, as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to encapsulate functional biomolecules in GUVs, there is no one-size-fits-all solution and reliable GUV fabrication still remains a major experimental hurdle in the field. Here, we show that defect-free GUVs containing complex biochemical systems can be generated by optimizing a double-emulsion method for GUV formation called continuous droplet interface crossing encapsulation (cDICE). By tightly controlling environmental conditions and tuning the lipid-in-oil dispersion, we show that it is possible to significantly improve the reproducibility of high-quality GUV formation as well as the encapsulation efficiency. We demonstrate efficient encapsulation for a range of biological systems including a minimal actin cytoskeleton, membrane-anchored DNA nanostructures, and a functional PURE (protein synthesis using recombinant elements) system. Our optimized cDICE method displays promising potential to become a standard method in biophysics and bottom-up synthetic biology.
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Affiliation(s)
| | - Federico Fanalista
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Lennard van Buren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nicola De Franceschi
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sharon Bouw
- Department of Living Matter, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
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23
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Van de Cauter L, Fanalista F, van Buren L, De Franceschi N, Godino E, Bouw S, Danelon C, Dekker C, Koenderink GH, Ganzinger KA. Optimized cDICE for Efficient Reconstitution of Biological Systems in Giant Unilamellar Vesicles. ACS Synth Biol 2021; 10:1690-1702. [PMID: 34185516 PMCID: PMC8291763 DOI: 10.1021/acssynbio.1c00068] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Indexed: 12/17/2022]
Abstract
Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells, as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to encapsulate functional biomolecules in GUVs, there is no one-size-fits-all solution and reliable GUV fabrication still remains a major experimental hurdle in the field. Here, we show that defect-free GUVs containing complex biochemical systems can be generated by optimizing a double-emulsion method for GUV formation called continuous droplet interface crossing encapsulation (cDICE). By tightly controlling environmental conditions and tuning the lipid-in-oil dispersion, we show that it is possible to significantly improve the reproducibility of high-quality GUV formation as well as the encapsulation efficiency. We demonstrate efficient encapsulation for a range of biological systems including a minimal actin cytoskeleton, membrane-anchored DNA nanostructures, and a functional PURE (protein synthesis using recombinant elements) system. Our optimized cDICE method displays promising potential to become a standard method in biophysics and bottom-up synthetic biology.
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Affiliation(s)
| | - Federico Fanalista
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Lennard van Buren
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nicola De Franceschi
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Elisa Godino
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sharon Bouw
- Department
of Living Matter, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Christophe Danelon
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Gijsje H. Koenderink
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
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24
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Wubshet NH, Bashirzadeh Y, Liu AP. Fascin-induced actin protrusions are suppressed by dendritic networks in giant unilamellar vesicles. Mol Biol Cell 2021; 32:1634-1640. [PMID: 34133215 PMCID: PMC8684724 DOI: 10.1091/mbc.e21-02-0080] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The interactions between actin networks and cell membrane are immensely important for eukaryotic cell functions including cell shape changes, motility, polarity establishment, and adhesion. Actin-binding proteins are known to compete and cooperate using a finite amount of actin monomers to form distinct actin networks. How actin-bundling protein fascin and actin-branching protein Arp2/3 complex compete to remodel membranes is not entirely clear. To investigate fascin- and Arp2/3-mediated actin network remodeling, we applied a reconstitution approach encapsulating bundled and dendritic actin networks inside giant unilamellar vesicles (GUVs). Independently reconstituted, membrane-bound Arp2/3 nucleation forms an actin cortex in GUVs, whereas fascin mediates formation of actin bundles that protrude out of GUVs. Coencapsulating both fascin and Arp2/3 complex leads to polarized dendritic aggregates and significantly reduces membrane protrusions, irrespective of whether the dendritic network is membrane bound or not. However, reducing Arp2/3 complex while increasing fascin restores membrane protrusion. Such changes in network assembly and the subsequent interplay with membrane can be attributed to competition between fascin and Arp2/3 complex to utilize a finite pool of actin.
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Affiliation(s)
- Nadab H Wubshet
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109
| | - Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109.,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109.,Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109
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25
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Agarwal S, Klocke MA, Pungchai PE, Franco E. Dynamic self-assembly of compartmentalized DNA nanotubes. Nat Commun 2021; 12:3557. [PMID: 34117248 PMCID: PMC8196065 DOI: 10.1038/s41467-021-23850-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 05/20/2021] [Indexed: 02/05/2023] Open
Abstract
Bottom-up synthetic biology aims to engineer artificial cells capable of responsive behaviors by using a minimal set of molecular components. An important challenge toward this goal is the development of programmable biomaterials that can provide active spatial organization in cell-sized compartments. Here, we demonstrate the dynamic self-assembly of nucleic acid (NA) nanotubes inside water-in-oil droplets. We develop methods to encapsulate and assemble different types of DNA nanotubes from programmable DNA monomers, and demonstrate temporal control of assembly via designed pathways of RNA production and degradation. We examine the dynamic response of encapsulated nanotube assembly and disassembly with the support of statistical analysis of droplet images. Our study provides a toolkit of methods and components to build increasingly complex and functional NA materials to mimic life-like functions in synthetic cells.
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Affiliation(s)
- Siddharth Agarwal
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Melissa A Klocke
- Department of Mechanical Engineering, University of California, Riverside, CA, USA
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA
| | - Passa E Pungchai
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Elisa Franco
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
- Department of Mechanical Engineering, University of California, Riverside, CA, USA.
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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26
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Litschel T, Kelley CF, Holz D, Adeli Koudehi M, Vogel SK, Burbaum L, Mizuno N, Vavylonis D, Schwille P. Reconstitution of contractile actomyosin rings in vesicles. Nat Commun 2021; 12:2254. [PMID: 33859190 PMCID: PMC8050101 DOI: 10.1038/s41467-021-22422-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
One of the grand challenges of bottom-up synthetic biology is the development of minimal machineries for cell division. The mechanical transformation of large-scale compartments, such as Giant Unilamellar Vesicles (GUVs), requires the geometry-specific coordination of active elements, several orders of magnitude larger than the molecular scale. Of all cytoskeletal structures, large-scale actomyosin rings appear to be the most promising cellular elements to accomplish this task. Here, we have adopted advanced encapsulation methods to study bundled actin filaments in GUVs and compare our results with theoretical modeling. By changing few key parameters, actin polymerization can be differentiated to resemble various types of networks in living cells. Importantly, we find membrane binding to be crucial for the robust condensation into a single actin ring in spherical vesicles, as predicted by theoretical considerations. Upon force generation by ATP-driven myosin motors, these ring-like actin structures contract and locally constrict the vesicle, forming furrow-like deformations. On the other hand, cortex-like actin networks are shown to induce and stabilize deformations from spherical shapes. Cytoskeletal networks support and direct cell shape and guide intercellular transport, but relatively little is understood about the self-organization of cytoskeletal components on the scale of an entire cell. Here, authors use an in vitro system and observe the assembly of different types of actin networks and the condensation of membrane-bound actin into single rings.
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Affiliation(s)
- Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Charlotte F Kelley
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Danielle Holz
- Department of Physics, Lehigh University, Bethlehem, PA, USA
| | | | - Sven K Vogel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Laura Burbaum
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Naoko Mizuno
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
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27
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Abstract
Giant unilamellar vesicles (GUVs) have gained great popularity as mimicries for cellular membranes. As their sizes are comfortably above the optical resolution limit, and their lipid composition is easily controlled, they are ideal for quantitative light microscopic investigation of dynamic processes in and on membranes. However, reconstitution of functional proteins into the lumen or the GUV membrane itself has proven technically challenging. In recent years, a selection of techniques has been introduced that tremendously improve GUV-assay development and enable the precise investigation of protein-membrane interactions under well-controlled conditions. Moreover, due to these methodological advances, GUVs are considered important candidates as protocells in bottom-up synthetic biology. In this review, we discuss the state of the art of the most important vesicle production and protein encapsulation methods and highlight some key protein systems whose functional reconstitution has advanced the field.
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Affiliation(s)
- Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; ,
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; ,
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28
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Mesarec L, Drab M, Penič S, Kralj-Iglič V, Iglič A. On the Role of Curved Membrane Nanodomains, and Passive and Active Skeleton Forces in the Determination of Cell Shape and Membrane Budding. Int J Mol Sci 2021; 22:2348. [PMID: 33652934 PMCID: PMC7956631 DOI: 10.3390/ijms22052348] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 02/03/2023] Open
Abstract
Biological membranes are composed of isotropic and anisotropic curved nanodomains. Anisotropic membrane components, such as Bin/Amphiphysin/Rvs (BAR) superfamily protein domains, could trigger/facilitate the growth of membrane tubular protrusions, while isotropic curved nanodomains may induce undulated (necklace-like) membrane protrusions. We review the role of isotropic and anisotropic membrane nanodomains in stability of tubular and undulated membrane structures generated or stabilized by cyto- or membrane-skeleton. We also describe the theory of spontaneous self-assembly of isotropic curved membrane nanodomains and derive the critical concentration above which the spontaneous necklace-like membrane protrusion growth is favorable. We show that the actin cytoskeleton growth inside the vesicle or cell can change its equilibrium shape, induce higher degree of segregation of membrane nanodomains or even alter the average orientation angle of anisotropic nanodomains such as BAR domains. These effects may indicate whether the actin cytoskeleton role is only to stabilize membrane protrusions or to generate them by stretching the vesicle membrane. Furthermore, we demonstrate that by taking into account the in-plane orientational ordering of anisotropic membrane nanodomains, direct interactions between them and the extrinsic (deviatoric) curvature elasticity, it is possible to explain the experimentally observed stability of oblate (discocyte) shapes of red blood cells in a broad interval of cell reduced volume. Finally, we present results of numerical calculations and Monte-Carlo simulations which indicate that the active forces of membrane skeleton and cytoskeleton applied to plasma membrane may considerably influence cell shape and membrane budding.
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Affiliation(s)
- Luka Mesarec
- Faculty of Electrical Engineering, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (L.M.); (M.D.); (S.P.)
| | - Mitja Drab
- Faculty of Electrical Engineering, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (L.M.); (M.D.); (S.P.)
| | - Samo Penič
- Faculty of Electrical Engineering, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (L.M.); (M.D.); (S.P.)
| | - Veronika Kralj-Iglič
- Faculty of Health Sciences, University of Ljubljana, SI-1000 Ljubljana, Slovenia;
- Institute of Biosciences and Bioresources, National Research Council, 80131 Napoli, Italy
| | - Aleš Iglič
- Faculty of Electrical Engineering, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (L.M.); (M.D.); (S.P.)
- Institute of Biosciences and Bioresources, National Research Council, 80131 Napoli, Italy
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29
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In Vitro Reconstitution of Dynamic Co-organization of Microtubules and Actin Filaments in Emulsion Droplets. Methods Mol Biol 2021. [PMID: 31879898 DOI: 10.1007/978-1-0716-0219-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In vitro (or cell-free) reconstitution is a powerful tool to study the physical basis of cytoskeletal organization in eukaryotic cells. Cytoskeletal reconstitution studies have mostly been done for individual cytoskeleton systems in unconfined 3D or quasi-2D geometries, which lack complexity relative to a cellular environment. To increase the level of complexity, we present a method to study co-organization of two cytoskeletal components, namely microtubules and actin filaments, confined in cell-sized water-in-oil emulsion droplets. We show that centrosome-nucleated dynamic microtubules can be made to interact with actin filaments through a tip-tracking complex consisting of microtubule end-binding proteins and an actin-microtubule cytolinker. In addition to the protocols themselves, we discuss the optimization steps required in order to build these more complex in vitro model systems of cytoskeletal interactions.
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30
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Bashirzadeh Y, Wubshet NH, Liu AP. Confinement Geometry Tunes Fascin-Actin Bundle Structures and Consequently the Shape of a Lipid Bilayer Vesicle. Front Mol Biosci 2020; 7:610277. [PMID: 33240934 PMCID: PMC7680900 DOI: 10.3389/fmolb.2020.610277] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 10/20/2020] [Indexed: 12/27/2022] Open
Abstract
Depending on the physical and biochemical properties of actin-binding proteins, actin networks form different types of membrane protrusions at the cell periphery. Actin crosslinkers, which facilitate the interaction of actin filaments with one another, are pivotal in determining the mechanical properties and protrusive behavior of actin networks. Short crosslinkers such as fascin bundle F-actin to form rigid spiky filopodial protrusions. By encapsulation of fascin and actin in giant unilamellar vesicles (GUVs), we show that fascin-actin bundles cause various GUV shape changes by forming bundle networks or straight single bundles depending on GUV size and fascin concentration. We also show that the presence of a long crosslinker, α-actinin, impacts fascin-induced GUV shape changes and significantly impairs the formation of filopodia-like protrusions. Actin bundle-induced GUV shape changes are confirmed by light-induced disassembly of actin bundles leading to the reversal of GUV shape. Our study contributes to advancing the design of shape-changing minimal cells for better characterization of the interaction between lipid bilayer membranes and actin cytoskeleton.
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Affiliation(s)
- Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Nadab H. Wubshet
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
- Department of Biophysics, University of Michigan, Ann Arbor, MI, United States
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, United States
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31
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Méndez‐Ardoy A, Bayón‐Fernández A, Yu Z, Abell C, Granja JR, Montenegro J. Spatially Controlled Supramolecular Polymerization of Peptide Nanotubes by Microfluidics. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000103] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Alejandro Méndez‐Ardoy
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Alfonso Bayón‐Fernández
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Ziyi Yu
- Department of ChemistryUniversity of Cambridge Cambridge CB2 1EW UK
| | - Chris Abell
- Department of ChemistryUniversity of Cambridge Cambridge CB2 1EW UK
| | - Juan R. Granja
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de Compostela 15782 Santiago de Compostela Spain
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32
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Schroer CFE, Baldauf L, van Buren L, Wassenaar TA, Melo MN, Koenderink GH, Marrink SJ. Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers. Proc Natl Acad Sci U S A 2020; 117:5861-5872. [PMID: 32123101 PMCID: PMC7084070 DOI: 10.1073/pnas.1914884117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The cytoskeletal protein actin polymerizes into filaments that are essential for the mechanical stability of mammalian cells. In vitro experiments showed that direct interactions between actin filaments and lipid bilayers are possible and that the net charge of the bilayer as well as the presence of divalent ions in the buffer play an important role. In vivo, colocalization of actin filaments and divalent ions are suppressed, and cells rely on linker proteins to connect the plasma membrane to the actin network. Little is known, however, about why this is the case and what microscopic interactions are important. A deeper understanding is highly beneficial, first, to obtain understanding in the biological design of cells and, second, as a possible basis for the building of artificial cortices for the stabilization of synthetic cells. Here, we report the results of coarse-grained molecular dynamics simulations of monomeric and filamentous actin in the vicinity of differently charged lipid bilayers. We observe that charges on the lipid head groups strongly determine the ability of actin to adsorb to the bilayer. The inclusion of divalent ions leads to a reversal of the binding affinity. Our in silico results are validated experimentally by reconstitution assays with actin on lipid bilayer membranes and provide a molecular-level understanding of the actin-membrane interaction.
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Affiliation(s)
- Carsten F E Schroer
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Lucia Baldauf
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Living Matter Department, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Lennard van Buren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Living Matter Department, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica, New University of Lisbon, 2780-157, Oeiras, Portugal
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands;
- Living Matter Department, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands;
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
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33
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Méndez‐Ardoy A, Bayón‐Fernández A, Yu Z, Abell C, Granja JR, Montenegro J. Spatially Controlled Supramolecular Polymerization of Peptide Nanotubes by Microfluidics. Angew Chem Int Ed Engl 2020; 59:6902-6908. [DOI: 10.1002/anie.202000103] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Alejandro Méndez‐Ardoy
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Alfonso Bayón‐Fernández
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Ziyi Yu
- Department of ChemistryUniversity of Cambridge Cambridge CB2 1EW UK
| | - Chris Abell
- Department of ChemistryUniversity of Cambridge Cambridge CB2 1EW UK
| | - Juan R. Granja
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química OrgánicaUniversidad de Santiago de Compostela 15782 Santiago de Compostela Spain
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34
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Adeli Koudehi M, Rutkowski DM, Vavylonis D. Organization of associating or crosslinked actin filaments in confinement. Cytoskeleton (Hoboken) 2019; 76:532-548. [PMID: 31525281 DOI: 10.1002/cm.21565] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 12/13/2022]
Abstract
A key factor of actin cytoskeleton organization in cells is the interplay between the dynamical properties of actin filaments and cell geometry, which restricts, confines and directs their orientation. Crosslinking interactions among actin filaments, together with geometrical cues and regulatory proteins can give rise to contractile rings in dividing cells and actin rings in neurons. Motivated by recent in vitro experiments, in this work we performed computer simulations to study basic aspects of the interplay between confinement and attractive interactions between actin filaments. We used a spring-bead model and Brownian dynamics to simulate semiflexible actin filaments that polymerize in a confining sphere with a rate proportional to the monomer concentration. We model crosslinking, or attraction through the depletion interaction, implicitly as an attractive short-range potential between filament beads. In confining geometries smaller than the persistence length of actin filaments, we show rings can form by curving of filaments of length comparable to, or longer than the confinement diameter. Rings form for optimal ranges of attractive interactions that exist in between open bundles, irregular loops, aggregated, and unbundled morphologies. The probability of ring formation is promoted by attraction to the confining sphere boundary and decreases for large radii and initial monomer concentrations, in agreement with prior experimental data. The model reproduces ring formation along the flat plane of oblate ellipsoids.
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35
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Bashirzadeh Y, Liu AP. Encapsulation of the cytoskeleton: towards mimicking the mechanics of a cell. SOFT MATTER 2019; 15:8425-8436. [PMID: 31621750 DOI: 10.1039/c9sm01669d] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The cytoskeleton of a cell controls all the aspects of cell shape changes and motility from its physiological functions for survival to reproduction to death. The structure and dynamics of the cytoskeletal components: actin, microtubules, intermediate filaments, and septins - recently regarded as the fourth member of the cytoskeleton family - are conserved during evolution. Such conserved and effective control over the mechanics of the cell makes the cytoskeletal components great candidates for in vitro reconstitution and bottom-up synthetic biology studies. Here, we review the recent efforts in reconstitution of the cytoskeleton in and on membrane-enclosed biomimetic systems and argue that co-reconstitution and synergistic interplay between cytoskeletal filaments might be indispensable for efficient mechanical functionality of active minimal cells. Further, mechanical equilibrium in adherent eukaryotic cells is achieved by the formation of integrin-based focal contacts with extracellular matrix (ECM) and the transmission of stresses generated by actomyosin contraction to ECM. Therefore, a minimal mimic of such balance of forces and quasi-static kinetics of the cell by bottom-up reconstitution requires a careful construction of contractile machineries and their link with adhesive contacts. In this review, in addition to cytoskeletal crosstalk, we provide a perspective on reconstruction of cell mechanical equilibrium by reconstitution of cortical actomyosin networks in lipid membrane vesicles adhered on compliant substrates and also discuss future perspectives of this active research area.
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Affiliation(s)
- Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, 2350 Hayward Street, Ann Arbor, Michigan, USA.
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36
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Moreno-Pescador G, Florentsen CD, Østbye H, Sønder SL, Boye TL, Veje EL, Sonne AK, Semsey S, Nylandsted J, Daniels R, Bendix PM. Curvature- and Phase-Induced Protein Sorting Quantified in Transfected Cell-Derived Giant Vesicles. ACS NANO 2019; 13:6689-6701. [PMID: 31199124 DOI: 10.1021/acsnano.9b01052] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Eukaryotic cells possess a dynamic network of membranes that vary in lipid composition. To perform numerous biological functions, cells modulate their shape and the lateral organization of proteins associated with membranes. The modulation is generally facilitated by physical cues that recruit proteins to specific regions of the membrane. Analyzing these cues is difficult due to the complexity of the membrane conformations that exist in cells. Here, we examine how different types of membrane proteins respond to changes in curvature and to lipid phases found in the plasma membrane. By using giant plasma membrane vesicles derived from transfected cells, the proteins were positioned in the correct orientation and the analysis was performed in plasma membranes with a biological composition. Nanoscale membrane curvatures were generated by extracting nanotubes from these vesicles with an optical trap. The viral membrane protein neuraminidase was not sensitive to curvature, but it did exhibit strong partitioning (coefficient of K = 0.16) disordered membrane regions. In contrast, the membrane repair protein annexin 5 showed a preference for nanotubes with a density up to 10-15 times higher than that on the more flat vesicle membrane. The investigation of nanoscale effects in isolated plasma membranes provides a quantitative platform for studying peripheral and integral membrane proteins in their natural environment.
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Affiliation(s)
| | | | - Henrik Østbye
- Department of Biochemistry and Biophysics , Stockholm University , 10691 Stockholm , Sweden
| | - Stine L Sønder
- Membrane Integrity Group, Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease , Danish Cancer Society Research Center , Strandboulevarden 49 , DK-2100 Copenhagen , Denmark
| | - Theresa L Boye
- Membrane Integrity Group, Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease , Danish Cancer Society Research Center , Strandboulevarden 49 , DK-2100 Copenhagen , Denmark
| | - Emilie L Veje
- Niels Bohr Institute , University of Copenhagen , DK-2100 Copenhagen , Denmark
| | - Alexander K Sonne
- Niels Bohr Institute , University of Copenhagen , DK-2100 Copenhagen , Denmark
| | - Szabolcs Semsey
- Niels Bohr Institute , University of Copenhagen , DK-2100 Copenhagen , Denmark
| | - Jesper Nylandsted
- Membrane Integrity Group, Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease , Danish Cancer Society Research Center , Strandboulevarden 49 , DK-2100 Copenhagen , Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences , University of Copenhagen , DK-2200 Copenhagen N , Denmark
| | - Robert Daniels
- Department of Biochemistry and Biophysics , Stockholm University , 10691 Stockholm , Sweden
| | - Poul Martin Bendix
- Niels Bohr Institute , University of Copenhagen , DK-2100 Copenhagen , Denmark
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37
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Wu Z, Yuan H, Zhang X, Yi X. Sidewall contact regulating the nanorod packing inside vesicles with relative volumes. SOFT MATTER 2019; 15:2552-2559. [PMID: 30839980 DOI: 10.1039/c8sm01656a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Intracellular packing of one-dimensional and rodlike materials plays an important role in many biological processes such as cell mimicking, microtubule protrusion, cell division, frustrated phagocytosis, and pathogenicity. To understand the mechanical interplay between cells/intracellular membranous organelles and encapsulated rodlike materials, we perform theoretical analyses to investigate how the morphologies and mechanical behaviors of lipid vesicles of given relative volumes are regulated by encapsulated rigid nanorods of finite diameters and selected geometries, including a cylindrical nanorod, a nanorod with one widened end, and a cone-shaped nanorod. The contact between the vesicle protrusion and the sidewall of the rod, neglected in most theoretical studies, is shown to play an important role in regulating vesicle tubulation, membrane tension, and axial contact force on the nanorod. As the nanorod length increases, the confining vesicle evolves from a prolate into different shapes, such as a lemon, a conga drum, a cherry, and a bowling pin, depending on the radical size of the nanorod and the relative vesicle volume. The corresponding morphological phase diagrams are determined. Moreover, phase diagrams of the buckling of the encapsulated nanorods are determined based on the classical Euler buckling theory. It is shown that there exists an optimal filament number at which the encapsulated weakly cross-linked filament bundle maintains the largest length in a mechanically stable state. Similarities and differences between the nanorod packing in vesicles at a given pressure difference and a relative volume are discussed. Our results provide valuable insight into the biophysics underlying cell interactions with one-dimensional and rodlike materials.
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Affiliation(s)
- Zeming Wu
- Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing 100871, China.
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38
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Ganzinger KA, Schwille P. More from less - bottom-up reconstitution of cell biology. J Cell Sci 2019; 132:132/4/jcs227488. [PMID: 30718262 DOI: 10.1242/jcs.227488] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ultimate goal of bottom-up synthetic biology is recreating life in its simplest form. However, in its quest to find the minimal functional units of life, this field contributes more than its main aim by also offering a range of tools for asking, and experimentally approaching, biological questions. This Review focusses on how bottom-up reconstitution has furthered our understanding of cell biology. Studying cell biological processes in vitro has a long tradition, but only recent technological advances have enabled researchers to reconstitute increasingly complex biomolecular systems by controlling their multi-component composition and their spatiotemporal arrangements. We illustrate this progress using the example of cytoskeletal processes. Our understanding of these has been greatly enhanced by reconstitution experiments, from the first in vitro experiments 70 years ago to recent work on minimal cytoskeleton systems (including this Special Issue of Journal of Cell Science). Importantly, reconstitution approaches are not limited to the cytoskeleton field. Thus, we also discuss progress in other areas, such as the shaping of biomembranes and cellular signalling, and prompt the reader to add their subfield of cell biology to this list in the future.
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Affiliation(s)
- Kristina A Ganzinger
- Physics of Cellular Interactions Group, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Petra Schwille
- Department Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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Yewdall NA, Mason AF, van Hest JCM. The hallmarks of living systems: towards creating artificial cells. Interface Focus 2018; 8:20180023. [PMID: 30443324 PMCID: PMC6227776 DOI: 10.1098/rsfs.2018.0023] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2018] [Indexed: 01/01/2023] Open
Abstract
Despite the astonishing diversity and complexity of living systems, they all share five common hallmarks: compartmentalization, growth and division, information processing, energy transduction and adaptability. In this review, we give not only examples of how cells satisfy these requirements for life and the ways in which it is possible to emulate these characteristics in engineered platforms, but also the gaps that remain to be bridged. The bottom-up synthesis of life-like systems continues to be driven forward by the advent of new technologies, by the discovery of biological phenomena through their transplantation to experimentally simpler constructs and by providing insights into one of the oldest questions posed by mankind, the origin of life on Earth.
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Affiliation(s)
| | | | - Jan C. M. van Hest
- Eindhoven University of Technology, PO Box 513 (STO 3.31), Eindhoven, MB, The Netherlands
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Tang VW. Cell-cell adhesion interface: orthogonal and parallel forces from contraction, protrusion, and retraction. F1000Res 2018; 7. [PMID: 30345009 PMCID: PMC6173117 DOI: 10.12688/f1000research.15860.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/19/2018] [Indexed: 01/22/2023] Open
Abstract
The epithelial lateral membrane plays a central role in the integration of intercellular signals and, by doing so, is a principal determinant in the emerging properties of epithelial tissues. Mechanical force, when applied to the lateral cell-cell interface, can modulate the strength of adhesion and influence intercellular dynamics. Yet the relationship between mechanical force and epithelial cell behavior is complex and not completely understood. This commentary aims to provide an investigative look at the usage of cellular forces at the epithelial cell-cell adhesion interface.
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Affiliation(s)
- Vivian W Tang
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL, 61801, USA
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Yi X, Zou G, Gao H. Mechanics of cellular packing of nanorods with finite and non-uniform diameters. NANOSCALE 2018; 10:14090-14099. [PMID: 29999084 DOI: 10.1039/c8nr04110e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To understand the mechanics of cellular/intracellular packing of one-dimensional nanomaterials, we performed theoretical analysis and molecular dynamics simulations to investigate how the morphology and mechanical behaviors of a lipid vesicle are regulated by encapsulated rigid nanorods of finite and non-uniform diameters, including a cylindrical rod, a rod with widened ends, a cone-shaped rod, and a screwdriver-shaped rod. As the rod length increases, the vesicle evolves from a sphere into different shapes, such as a lemon, a conga drum, a cherry, a bowling pin, or a tubular shape for long and thick rods. The contact between the vesicle protrusion and the rod plays an important role in regulating the vesicle tubulation, membrane tension, and axial contact force on the rod. Our analysis provides a theoretical basis to understand a wide range of experiments on morphological transitions that occur in cellular packing of actin or microtubule bundles, mitotic cell division, and intracellular packing of carbon nanotubes.
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Affiliation(s)
- Xin Yi
- Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing 100871, China and Beijing Innovation Center for Engineering Science and Advanced Technology, Peking University, Beijing 100871, China.
| | - Guijin Zou
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA.
| | - Huajian Gao
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA.
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Tailoring the appearance: what will synthetic cells look like? Curr Opin Biotechnol 2018; 51:47-56. [DOI: 10.1016/j.copbio.2017.11.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/23/2022]
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Abstract
How do the cells in our body reconfigure their shape to achieve complex tasks like migration and mitosis, yet maintain their shape in response to forces exerted by, for instance, blood flow and muscle action? Cell shape control is defined by a delicate mechanical balance between active force generation and passive material properties of the plasma membrane and the cytoskeleton. The cytoskeleton forms a space-spanning fibrous network comprising three subsystems: actin, microtubules and intermediate filaments. Bottom-up reconstitution of minimal synthetic cells where these cytoskeletal subsystems are encapsulated inside a lipid vesicle provides a powerful avenue to dissect the force balance that governs cell shape control. Although encapsulation is technically demanding, a steady stream of advances in this technique has made the reconstitution of shape-changing minimal cells increasingly feasible. In this topical review we provide a route-map of the recent advances in cytoskeletal encapsulation techniques and outline recent reports that demonstrate shape change phenomena in simple biomimetic vesicle systems. We end with an outlook toward the next steps required to achieve more complex shape changes with the ultimate aim of building a fully functional synthetic cell with the capability to autonomously grow, divide and move.
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Affiliation(s)
- Yuval Mulla
- These authors contributed equally to this work
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45
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Li B, Abel SM. Shaping membrane vesicles by adsorption of a semiflexible polymer. SOFT MATTER 2018; 14:185-193. [PMID: 29143046 DOI: 10.1039/c7sm01751k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The adsorption of polymers onto fluid membranes is a problem of fundamental interest in biology and soft materials, in part because the flexibility of membranes can lead to nontrivial coupling between polymer and membrane configurations. Here, we use Monte Carlo computer simulations to study the adsorption of a semiflexible polymer onto a fluid membrane vesicle. Polymer adsorption can significantly impact both the vesicle and polymer shapes, and we identify distinct classes of configurations that emerge as a function of polymer persistence length, membrane bending rigidity, adsorption strength, and vesicle size. Large-scale deformations of the vesicle include invaginations of the membrane that internalize the polymer in a membrane bud. The buds range from disk-like shapes surrounding a collapsed polymer to tubular deformations enveloping rod-like polymers. For small vesicles, polymer adsorption also induces dumbbell-like vesicle shapes with a narrow membrane constriction circled by the polymer. Vesicles with sufficiently small or large bending rigidities adopt configurations similar to those without the polymer present. We further characterize statistical properties of the membrane and polymer configurations and identify distinct classes of polymer configurations that emerge within membrane buds. Analysis of idealized polymer-membrane configurations provides additional insight into transitions between bud shapes.
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Affiliation(s)
- Bing Li
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA.
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Fujiwara I, Narita A. Keeping the focus on biophysics and actin filaments in Nagoya: A report of the 2016 "now in actin" symposium. Cytoskeleton (Hoboken) 2017; 74:450-464. [PMID: 28681410 DOI: 10.1002/cm.21384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 01/01/2023]
Abstract
Regulatory systems in living cells are highly organized, enabling cells to response to various changes in their environments. Actin polymerization and depolymerization are crucial to establish cytoskeletal networks to maintain muscle contraction, cell motility, cell division, adhesion, organism development and more. To share and promote the biophysical understanding of such mechanisms in living creatures, the "Now in Actin Study: -Motor protein research reaching a new stage-" symposium was organized at Nagoya University, Japan on 12 and 13, December 2016. The organizers invited emeritus professor of Nagoya and Osaka Universities Fumio Oosawa and leading scientists worldwide as keynote speakers, in addition to poster presentations on cell motility studies by many researchers. Studies employing various biophysical, biochemical, cell and molecular biological and mathematical approaches provided the latest understanding of mechanisms of cell motility functions driven by actin, microtubules, actin-binding proteins, and other motor proteins.
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Affiliation(s)
- Ikuko Fujiwara
- Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan
| | - Akihiro Narita
- Structural Biology Research Center and Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Nagoya 464-8601, Japan
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Yamamoto T, Schiessel H. Transcription Driven Phase Separation in Chromatin Brush. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:3036-3044. [PMID: 26974855 DOI: 10.1021/acs.langmuir.6b00442] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We theoretically predict the local density of nucleosomes on DNA brushes in a solution of molecules, which are necessary for transcription and the assembly of nucleosomes. Our theory predicts that in a confined space, DNA brushes show phase separation, where a region of relatively large nucleosomal occupancy coexists with a region of smaller nucleosomal occupancy. This phase separation is driven by an instability arising from the fact that the rate of transcription increases as the nucleosomal occupancy decreases due to the excluded volume interactions between nucleosomes and RNA polymerase during thermal diffusion and, in turn, nucleosomes are (in some cases) desorbed from DNA when RNA polymerase collides with nucleosomes during transcription. The miscibility phase diagram shows critical points, which are sensitive to the rate constants involved in transcription, the changes of interactions of DNA chain segments by assembling nucleosomes, and pressures that are applied to the brushes.
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Affiliation(s)
- Tetsuya Yamamoto
- National Composite Center, Nagoya University Furo-cho , Chikusa-ku, Nagoya 464-8603, Japan
| | - Helmut Schiessel
- Instituut-Lorentz for Theoretical Physics , Niels Bohrweg 2, Leiden, NL-2333 CA, The Netherlands
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