1
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Swaminathan U, Pucadyil TJ. Reconstituting membrane fission using a high content and throughput assay. Biochem Soc Trans 2024; 52:1449-1457. [PMID: 38747723 DOI: 10.1042/bst20231325] [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] [Received: 03/13/2024] [Revised: 04/21/2024] [Accepted: 05/01/2024] [Indexed: 06/27/2024]
Abstract
Protein-mediated membrane fission has been analyzed both in bulk and at the single event resolution. Studies on membrane fission in vitro using tethers have provided fundamental insights into the process but are low in throughput. In recent years, supported membrane template (SMrT) have emerged as a facile and convenient assay system for membrane fission. SMrTs provide useful information on intermediates in the pathway to fission and are therefore high in content. They are also high in throughput because numerous fission events can be monitored in a single experiment. This review discusses the utility of SMrTs in providing insights into fission pathways and its adaptation to annotate membrane fission functions in proteins.
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Affiliation(s)
- Uma Swaminathan
- Indian Institute of Science Education and Research, Pune, India
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2
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Tsai FC, Guérin G, Pernier J, Bassereau P. Actin-membrane linkers: Insights from synthetic reconstituted systems. Eur J Cell Biol 2024; 103:151402. [PMID: 38461706 DOI: 10.1016/j.ejcb.2024.151402] [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] [Received: 12/03/2023] [Revised: 02/10/2024] [Accepted: 02/28/2024] [Indexed: 03/12/2024] Open
Abstract
At the cell surface, the actin cytoskeleton and the plasma membrane interact reciprocally in a variety of processes related to the remodeling of the cell surface. The actin cytoskeleton has been known to modulate membrane organization and reshape the membrane. To this end, actin-membrane linking molecules play a major role in regulating actin assembly and spatially direct the interaction between the actin cytoskeleton and the membrane. While studies in cells have provided a wealth of knowledge on the molecular composition and interactions of the actin-membrane interface, the complex molecular interactions make it challenging to elucidate the precise actions of the actin-membrane linkers at the interface. Synthetic reconstituted systems, consisting of model membranes and purified proteins, have been a powerful approach to elucidate how actin-membrane linkers direct actin assembly to drive membrane shape changes. In this review, we will focus only on several actin-membrane linkers that have been studied by using reconstitution systems. We will discuss the design principles of these reconstitution systems and how they have contributed to the understanding of the cellular functions of actin-membrane linkers. Finally, we will provide a perspective on future research directions in understanding the intricate actin-membrane interaction.
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Affiliation(s)
- Feng-Ching Tsai
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris 75005, France.
| | - Gwendal Guérin
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris 75005, France
| | - Julien Pernier
- Tumor Cell Dynamics Unit, Inserm U1279, Gustave Roussy Institute, Université Paris-Saclay, Villejuif 94800, France
| | - Patricia Bassereau
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris 75005, France.
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3
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Huster D, Maiti S, Herrmann A. Phospholipid Membranes as Chemically and Functionally Tunable Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312898. [PMID: 38456771 DOI: 10.1002/adma.202312898] [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: 11/29/2023] [Revised: 02/12/2024] [Indexed: 03/09/2024]
Abstract
The sheet-like lipid bilayer is the fundamental structural component of all cell membranes. Its building blocks are phospholipids and cholesterol. Their amphiphilic structure spontaneously leads to the formation of a bilayer in aqueous environment. Lipids are not just structural elements. Individual lipid species, the lipid membrane structure, and lipid dynamics influence and regulate membrane protein function. An exciting field is emerging where the membrane-associated material properties of different bilayer systems are used in designing innovative solutions for widespread applications across various fields, such as the food industry, cosmetics, nano- and biomedicine, drug storage and delivery, biotechnology, nano- and biosensors, and computing. Here, the authors summarize what is known about how lipids determine the properties and functions of biological membranes and how this has been or can be translated into innovative applications. Based on recent progress in the understanding of membrane structure, dynamics, and physical properties, a perspective is provided on how membrane-controlled regulation of protein functions can extend current applications and even offer new applications.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, D-04107, Leipzig, Germany
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, 400 005, India
| | - Andreas Herrmann
- Freie Universität Berlin, Department Chemistry and Biochemistry, SupraFAB, Altensteinstr. 23a, D-14195, Berlin, Germany
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4
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Ruppelt D, Trollmann MFW, Dema T, Wirtz SN, Flegel H, Mönnikes S, Grond S, Böckmann RA, Steinem C. The antimicrobial fibupeptide lugdunin forms water-filled channel structures in lipid membranes. Nat Commun 2024; 15:3521. [PMID: 38664456 PMCID: PMC11045845 DOI: 10.1038/s41467-024-47803-6] [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: 06/13/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Recently, a novel cyclo-heptapeptide composed of alternating D,L-amino acids and a unique thiazolidine heterocycle, called lugdunin, was discovered, which is produced by the nasal and skin commensal Staphylococcus lugdunensis. Lugdunin displays potent antimicrobial activity against a broad spectrum of Gram-positive bacteria, including challenging-to-treat methicillin-resistant Staphylococcus aureus (MRSA). Lugdunin specifically inhibits target bacteria by dissipating their membrane potential. However, the precise mode of action of this new class of fibupeptides remains largely elusive. Here, we disclose the mechanism by which lugdunin rapidly destabilizes the bacterial membrane potential using an in vitro approach. The peptide strongly partitions into lipid compositions resembling Gram-positive bacterial membranes but less in those harboring the eukaryotic membrane component cholesterol. Upon insertion, lugdunin forms hydrogen-bonded antiparallel β-sheets by the formation of peptide nanotubes, as demonstrated by ATR-FTIR spectroscopy and molecular dynamics simulations. These hydrophilic nanotubes filled with a water wire facilitate not only the translocation of protons but also of monovalent cations as demonstrated by voltage-clamp experiments on black lipid membranes. Collectively, our results provide evidence that the natural fibupeptide lugdunin acts as a peptidic channel that is spontaneously formed by an intricate stacking mechanism, leading to the dissipation of a bacterial cell's membrane potential.
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Affiliation(s)
- Dominik Ruppelt
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstraße 2, 37077, Göttingen, Germany
| | - Marius F W Trollmann
- Computational Biology, Department Biologie & Erlangen National High Perfomance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany
| | - Taulant Dema
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Sebastian N Wirtz
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Hendrik Flegel
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstraße 2, 37077, Göttingen, Germany
| | - Sophia Mönnikes
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstraße 2, 37077, Göttingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department Biologie & Erlangen National High Perfomance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany.
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität, Tammannstraße 2, 37077, Göttingen, Germany.
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077, Göttingen, Germany.
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5
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Hsu YY, Hwang SW, Chen SJ, Alsberg E, Liu AP. Development of mechanosensitive synthetic cells for biomedical applications. SLAS Technol 2024; 29:100095. [PMID: 37385542 DOI: 10.1016/j.slast.2023.06.004] [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] [Received: 04/21/2023] [Revised: 06/08/2023] [Accepted: 06/22/2023] [Indexed: 07/01/2023]
Abstract
The ability of cells to sense and respond to their physical environment plays a fundamental role in a broad spectrum of biological processes. As one of the most essential molecular force sensors and transducers found in cell membranes, mechanosensitive (MS) ion channels can convert mechanical inputs into biochemical or electrical signals to mediate a variety of sensations. The bottom-up construction of cell-sized compartments displaying cell-like organization, behaviors, and complexity, also known as synthetic cells, has gained popularity as an experimental platform to characterize biological functions in isolation. By reconstituting MS channels in the synthetic lipid bilayers, we envision using mechanosensitive synthetic cells for several medical applications. Here, we describe three different concepts for using ultrasound, shear stress, and compressive stress as mechanical stimuli to activate drug release from mechanosensitive synthetic cells for disease treatments.
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Affiliation(s)
- Yen-Yu Hsu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sung-Won Hwang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Samuel J Chen
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eben Alsberg
- Richard and Loan Hill Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL 60612, USA; Departments of Mechanical & Industrial Engineering, Orthopaedic Surgery, and Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.
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6
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Sherer LA, Mahanta B, Courtemanche N. Computational tools for quantifying actin filament numbers, lengths, and bundling. Biol Open 2024; 13:bio060267. [PMID: 38372564 PMCID: PMC10924227 DOI: 10.1242/bio.060267] [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: 12/01/2023] [Accepted: 02/08/2024] [Indexed: 02/20/2024] Open
Abstract
The actin cytoskeleton is a dynamic filamentous network that assembles into specialized structures to enable cells to perform essential processes. Direct visualization of fluorescently-labeled cytoskeletal proteins has provided numerous insights into the dynamic processes that govern the assembly of actin-based structures. However, accurate analysis of these experiments is often complicated by the interdependent and kinetic natures of the reactions involved. It is often challenging to disentangle these processes to accurately track their evolution over time. Here, we describe two programs written in the MATLAB programming language that facilitate counting, length measurements, and quantification of bundling of actin filaments visualized in fluorescence micrographs. To demonstrate the usefulness of our programs, we describe their application to the analysis of two representative reactions: (1) a solution of pre-assembled filaments under equilibrium conditions, and (2) a reaction in which actin filaments are crosslinked together over time. We anticipate that these programs can be applied to extract equilibrium and kinetic information from a broad range of actin-based reactions, and that their usefulness can be expanded further to investigate the assembly of other biopolymers.
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Affiliation(s)
- Laura A. Sherer
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Biswaprakash Mahanta
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Naomi Courtemanche
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
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7
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Nishikawa S, Sato G, Takada S, Kohyama S, Honda G, Yanagisawa M, Hori Y, Doi N, Yoshinaga N, Fujiwara K. Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell-Size Space. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308030. [PMID: 38054641 PMCID: PMC10853730 DOI: 10.1002/advs.202308030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/22/2023] [Indexed: 12/07/2023]
Abstract
Cells are small, closed spaces filled with various types of macromolecules. Although it is shown that the characteristics of biochemical reactions in vitro are quite different from those in living cells, the role of the co-existence of various macromolecules in cell-size space remains still elusive. Here, using a constructive approach, it is demonstrated that the co-existence of various macromolecules themselves has the ability to tune protein localization for spatiotemporal regulation and a biochemical reaction system in a cell-size space. Both experimental and theoretical analyses reveal that enhancement of interfacial effects by a large surface-area-to-volume ratio facilitates membrane localization of molecules in the cell-size space, and the interfacial effects are alleviated by competitive binding to lipid membranes among multiple proteins even if their membrane affinities are weak. These results indicate that competition for membrane binding among various macromolecules in the cell-size space plays a role in regulating the spatiotemporal molecular organization and biochemical reaction networks. These findings shed light on the importance of surrounding molecules for biochemical reactions using purified elements in small spaces.
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Affiliation(s)
- Saki Nishikawa
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Gaku Sato
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Sakura Takada
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Shunshi Kohyama
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
- Present address:
Department for Cellular and Molecular BiophysicsMax Planck Institute for BiochemistryAm Klopferspitz 18D‐82152MartinsriedGermany
| | - Gen Honda
- Komaba Institute for ScienceGraduate School of Arts and SciencesThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
| | - Miho Yanagisawa
- Komaba Institute for ScienceGraduate School of Arts and SciencesThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
- Graduate School of ScienceThe University of TokyoHongo 7‐3‐1BunkyoTokyo113‐0033Japan
- Center for Complex Systems BiologyUniversal Biology InstituteThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
| | - Yutaka Hori
- Department of Applied Physics and Physico‐informaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Nobuhide Doi
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Natsuhiko Yoshinaga
- WPI Advanced Institute for Materials Research (WPI‐AIMR)Tohoku UniversityKatahira 2‐1‐1, Aoba‐KuSendai980‐8577Japan
- MathAM‐OILAISTSendai980‐8577Japan
| | - Kei Fujiwara
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
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8
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Hoffmann C, Milovanovic D. Dipping contacts - a novel type of contact site at the interface between membraneless organelles and membranes. J Cell Sci 2023; 136:jcs261413. [PMID: 38149872 PMCID: PMC10785658 DOI: 10.1242/jcs.261413] [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] [Indexed: 12/28/2023] Open
Abstract
Liquid-liquid phase separation is a major mechanism for organizing macromolecules, particularly proteins with intrinsically disordered regions, in compartments not limited by a membrane or a scaffold. The cell can therefore be perceived as a complex emulsion containing many of these membraneless organelles, also referred to as biomolecular condensates, together with numerous membrane-bound organelles. It is currently unclear how such a complex concoction operates to allow for intracellular trafficking, signaling and metabolic processes to occur with high spatiotemporal precision. Based on experimental observations of synaptic vesicle condensates - a membraneless organelle that is in fact packed with membranes - we present here the framework of dipping contacts: a novel type of contact site between membraneless organelles and membranes. In this Hypothesis, we propose that our framework of dipping contacts can serve as a foundation to investigate the interface that couples the diffusion and material properties of condensates to biochemical processes occurring in membranes. The identity and regulation of this interface is especially critical in the case of neurodegenerative diseases, where aberrant inclusions of misfolded proteins and damaged organelles underlie cellular pathology.
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Affiliation(s)
- Christian Hoffmann
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Dragomir Milovanovic
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- National Center for X-ray Tomography, Advanced Light Source, Berkeley, CA 94720, USA
- Einstein Center for Neuroscience, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Berlin and Berlin Institute of Health, 10117 Berlin, Germany
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9
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Kandiyoth FB, Michelot A. Reconstitution of actin-based cellular processes: Why encapsulation changes the rules. Eur J Cell Biol 2023; 102:151368. [PMID: 37922812 DOI: 10.1016/j.ejcb.2023.151368] [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] [Received: 07/05/2023] [Revised: 10/02/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023] Open
Abstract
While in vitro reconstitution of cellular processes is progressing rapidly, the encapsulation of biomimetic systems to reproduce the cellular environment is a major challenge. Here we review the difficulties, using reconstitution of processes dependent on actin polymerization as an example. Some of the problems are purely technical, due to the need for engineering strategies to encapsulate concentrated solutions in micrometer-sized compartments. However, other significant issues arise from the reduction of experimental volumes, which alters the chemical evolution of these non-equilibrium systems. Important parameters to consider for successful reconstitutions are the amount of each component, their consumption and renewal rates to guarantee their continuous availability.
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Affiliation(s)
| | - Alphée Michelot
- Aix Marseille Univ, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France.
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10
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Liebe NL, Mey I, Vuong L, Shikho F, Geil B, Janshoff A, Steinem C. Bioinspired Membrane Interfaces: Controlling Actomyosin Architecture and Contractility. ACS APPLIED MATERIALS & INTERFACES 2023; 15:11586-11598. [PMID: 36848241 PMCID: PMC9999349 DOI: 10.1021/acsami.3c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The creation of biologically inspired artificial lipid bilayers on planar supports provides a unique platform to study membrane-confined processes in a well-controlled setting. At the plasma membrane of mammalian cells, the linkage of the filamentous (F)-actin network is of pivotal importance leading to cell-specific and dynamic F-actin architectures, which are essential for the cell's shape, mechanical resilience, and biological function. These networks are established through the coordinated action of diverse actin-binding proteins and the presence of the plasma membrane. Here, we established phosphatidylinositol-4,5-bisphosphate (PtdIns[4,5]P2)-doped supported planar lipid bilayers to which contractile actomyosin networks were bound via the membrane-actin linker ezrin. This membrane system, amenable to high-resolution fluorescence microscopy, enabled us to analyze the connectivity and contractility of the actomyosin network. We found that the network architecture and dynamics are not only a function of the PtdIns[4,5]P2 concentration but also depend on the presence of negatively charged phosphatidylserine (PS). PS drives the attached network into a regime, where low but physiologically relevant connectivity to the membrane results in strong contractility of the actomyosin network, emphasizing the importance of the lipid composition of the membrane interface.
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Affiliation(s)
- Nils L. Liebe
- Institut
für Organische und Biomolekulare Chemie, Georg-August Universität, Tammannstr. 2, Göttingen 37077, Germany
| | - Ingo Mey
- Institut
für Organische und Biomolekulare Chemie, Georg-August Universität, Tammannstr. 2, Göttingen 37077, Germany
| | - Loan Vuong
- Institut
für Organische und Biomolekulare Chemie, Georg-August Universität, Tammannstr. 2, Göttingen 37077, Germany
| | - Fadi Shikho
- Institut
für Organische und Biomolekulare Chemie, Georg-August Universität, Tammannstr. 2, Göttingen 37077, Germany
| | - Burkhard Geil
- Institut
für Physikalische Chemie, Georg-August
Universität, Tammannstr. 6, Göttingen 37077, Germany
| | - Andreas Janshoff
- Institut
für Physikalische Chemie, Georg-August
Universität, Tammannstr. 6, Göttingen 37077, Germany
| | - Claudia Steinem
- Institut
für Organische und Biomolekulare Chemie, Georg-August Universität, Tammannstr. 2, Göttingen 37077, Germany
- Max-Planck-Institut
für Dynamik und Selbstorganisation, Am Fassberg 17, Göttingen 37077, Germany
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11
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Jukic N, Perrino AP, Redondo-Morata L, Scheuring S. Structure and dynamics of ESCRT-III membrane remodeling proteins by high-speed atomic force microscopy. J Biol Chem 2023; 299:104575. [PMID: 36870686 PMCID: PMC10074808 DOI: 10.1016/j.jbc.2023.104575] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Endosomal Sorting Complex Required for Transport (ESCRT) proteins assemble on the cytoplasmic leaflet of membranes and remodel them. ESCRT is involved in biological processes where membranes are bent away from the cytosol, constricted, and finally severed, such as in multi-vesicular body formation (in the endosomal pathway for protein sorting) or abscission during cell division. The ESCRT system is hijacked by enveloped viruses to allow buds of nascent virions to be constricted, severed and released. ESCRT-III proteins, the most downstream components of the ESCRT system, are monomeric and cytosolic in their autoinhibited conformation. They share a common architecture, a four-helix bundle with a fifth helix that interacts with this bundle to prevent polymerizing. Upon binding to negatively charged membranes, the ESCRT-III components adopt an activated state that allows them to polymerize into filaments and spirals, and to interact with the AAA-ATPase Vps4 for polymer remodeling. ESCRT-III has been studied with electron microscopy (EM) and fluorescence microscopy (FM); these methods provided invaluable information about ESCRT assembly structures or their dynamics, respectively, but neither approach provides detailed insights into both aspects simultaneously. High-speed atomic force microscopy (HS-AFM) has overcome this shortcoming, providing movies at high spatio-temporal resolution of biomolecular processes, significantly increasing our understanding of ESCRT-III structure and dynamics. Here, we review the contributions of HS-AFM in the analysis of ESCRT-III, focusing on recent developments of non-planar and deformable HS-AFM supports. We divide the HS-AFM observations into four sequential steps in the ESCRT-III lifecycle: 1) polymerization, 2) morphology, 3) dynamics, and 4) depolymerization.
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Affiliation(s)
- Nebojsa Jukic
- Weill Cornell Medicine, Physiology, Biophysics and Systems Biology Graduate Program, New York, NY 10065, USA
| | - Alma P Perrino
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065, USA
| | - Lorena Redondo-Morata
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, F-59000 Lille, France
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065, USA; Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York, NY 14853, USA.
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12
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Ferreras S, Singh NP, Le Borgne R, Bun P, Binz T, Parton RG, Verbavatz JM, Vannier C, Galli T. A synthetic organelle approach to probe SNARE-mediated membrane fusion in a bacterial host. J Biol Chem 2023; 299:102974. [PMID: 36738791 PMCID: PMC10011478 DOI: 10.1016/j.jbc.2023.102974] [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] [Received: 08/02/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
In vivo and in vitro assays, particularly reconstitution using artificial membranes, have established the role of synaptic soluble N-Ethylmaleimide-sensitive attachment protein receptors (SNAREs) VAMP2, Syntaxin-1A, and SNAP-25 in membrane fusion. However, using artificial membranes requires challenging protein purifications that could be avoided in a cell-based assay. Here, we developed a synthetic biological approach based on the generation of membrane cisternae by the integral membrane protein Caveolin in Escherichia coli and coexpression of SNAREs. Syntaxin-1A/SNAP-25/VAMP-2 complexes were formed and regulated by SNARE partner protein Munc-18a in the presence of Caveolin. Additionally, Syntaxin-1A/SNAP-25/VAMP-2 synthesis provoked increased length of E. coli only in the presence of Caveolin. We found that cell elongation required SNAP-25 and was inhibited by tetanus neurotoxin. This elongation was not a result of cell division arrest. Furthermore, electron and super-resolution microscopies showed that synaptic SNAREs and Caveolin coexpression led to the partial loss of the cisternae, suggesting their fusion with the plasma membrane. In summary, we propose that this assay reconstitutes membrane fusion in a simple organism with an easy-to-observe phenotype and is amenable to structure-function studies of SNAREs.
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Affiliation(s)
- Soledad Ferreras
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France
| | - Neha Pratap Singh
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France
| | - Remi Le Borgne
- Université Paris Cité, CNRS, UMR7592, Institut Jacques Monod, Paris, France
| | - Philippe Bun
- Université Paris Cité, NeurImag, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris, France
| | - Thomas Binz
- Institute of Cell Biochemistry, Hannover Medical School, Hannover, Germany
| | - Robert G Parton
- The University of Queensland, Institute for Molecular Bioscience and Centre for Microscopy and Microanalysis, Qld, Brisbane, Australia
| | | | - Christian Vannier
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France.
| | - Thierry Galli
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM, Membrane Traffic in Healthy & Diseased Brain, Paris, France; GHU Paris psychiatrie neurosciences, Paris, France.
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13
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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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14
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Avalos-Padilla Y, Georgiev VN, Ewins E, Robinson T, Orozco E, Lipowsky R, Dimova R. Stepwise remodeling and subcompartment formation in individual vesicles by three ESCRT-III proteins. iScience 2022; 26:105765. [PMID: 36590172 PMCID: PMC9800321 DOI: 10.1016/j.isci.2022.105765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/21/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The endosomal sorting complex required for transport (ESCRT) is a multi-protein machinery involved in several membrane remodeling processes. Different approaches have been used to resolve how ESCRT proteins scission membranes. However, the underlying mechanisms generating membrane deformations are still a matter of debate. Here, giant unilamellar vesicles, microfluidic technology, and micropipette aspiration are combined to continuously follow the ESCRT-III-mediated membrane remodeling on the single-vesicle level for the first time. With this approach, we identify different mechanisms by which a minimal set of three ESCRT-III proteins from Entamoeba histolytica reshape the membrane. These proteins modulate the membrane stiffness and spontaneous curvature to regulate bud size and generate intraluminal vesicles even in the absence of ATP. We demonstrate that the bud stability depends on the protein concentration and membrane tension. The approaches introduced here should open the road to diverse applications in synthetic biology for establishing artificial cells with several membrane compartments.
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Affiliation(s)
- Yunuen Avalos-Padilla
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany,Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, ES-08028 Barcelona, Spain,Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-Universitat de Barcelona), Rosselló 149-153, ES-08036 Barcelona, Spain
| | - Vasil N. Georgiev
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Eleanor Ewins
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Tom Robinson
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV IPN, 07360 Ciudad de México, México
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany,Corresponding author
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15
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Kai L, Sonal, Heermann T, Schwille P. Reconstitution of a Reversible Membrane Switch via Prenylation by One-Pot Cell-Free Expression. ACS Synth Biol 2022; 12:108-119. [PMID: 36445320 PMCID: PMC9872162 DOI: 10.1021/acssynbio.2c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reversible membrane targeting of proteins is one of the key regulators of cellular interaction networks, for example, for signaling and polarization. So-called "membrane switches" are thus highly attractive targets for the design of minimal cells but have so far been tricky to reconstitute in vitro. Here, we introduce cell-free prenylated protein synthesis (CFpPS), which enables the synthesis and membrane targeting of proteins in a single reaction mix including the prenylation machinery. CFpPS can confer membrane affinity to any protein via addition of a 4-peptide motif to its C-terminus and offers robust production of prenylated proteins not only in their soluble forms but also in the direct vicinity of biomimetic membranes. Thus, CFpPS enabled us to reconstitute the prenylated polarity hub Cdc42 and its regulatory protein in vitro, implementing a key membrane switch. We propose CFpPS to be a versatile and effective platform for engineering complex features, such as polarity induction, in synthetic cells.
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Affiliation(s)
- Lei Kai
- Department
of Cellular and Molecular Biophysics, Max
Planck Institute of Biochemistry, D-82152 Martinsried, Germany,School
of Life Sciences, Jiangsu Normal University, Shanghai Road 101, 221116 Xuzhou, P. R. China,. Phone: +86 15852001351
| | - Sonal
- Department
of Cellular and Molecular Biophysics, Max
Planck Institute of Biochemistry, D-82152 Martinsried, Germany,Biosciences
Division, University College London, Gower Street, WC1E 6BT London, U.K.
| | - Tamara Heermann
- Department
of Cellular and Molecular Biophysics, Max
Planck Institute of Biochemistry, D-82152 Martinsried, Germany
| | - Petra Schwille
- Department
of Cellular and Molecular Biophysics, Max
Planck Institute of Biochemistry, D-82152 Martinsried, Germany,. Phone: +49 89 8578 2900
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16
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Pinglay S, Bulajić M, Rahe DP, Huang E, Brosh R, Mamrak NE, King BR, German S, Cadley JA, Rieber L, Easo N, Lionnet T, Mahony S, Maurano MT, Holt LJ, Mazzoni EO, Boeke JD. Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation. Science 2022; 377:eabk2820. [PMID: 35771912 PMCID: PMC9648154 DOI: 10.1126/science.abk2820] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Precise Hox gene expression is crucial for embryonic patterning. Intra-Hox transcription factor binding and distal enhancer elements have emerged as the major regulatory modules controlling Hox gene expression. However, quantifying their relative contributions has remained elusive. Here, we introduce "synthetic regulatory reconstitution," a conceptual framework for studying gene regulation, and apply it to the HoxA cluster. We synthesized and delivered variant rat HoxA clusters (130 to 170 kilobases) to an ectopic location in the mouse genome. We found that a minimal HoxA cluster recapitulated correct patterns of chromatin remodeling and transcription in response to patterning signals, whereas the addition of distal enhancers was needed for full transcriptional output. Synthetic regulatory reconstitution could provide a generalizable strategy for deciphering the regulatory logic of gene expression in complex genomes.
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Affiliation(s)
- Sudarshan Pinglay
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Milica Bulajić
- Department of Biology, New York University, New York, NY 10003, USA
| | - Dylan P. Rahe
- Department of Biology, New York University, New York, NY 10003, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Nicholas E. Mamrak
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Benjamin R. King
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Sergei German
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - John A. Cadley
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Lila Rieber
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Nicole Easo
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Timothée Lionnet
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Cell Biology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew T. Maurano
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Liam J. Holt
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | | | - Jef D. Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
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17
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Zubaite G, Hindley JW, Ces O, Elani Y. Dynamic Reconfiguration of Subcompartment Architectures in Artificial Cells. ACS NANO 2022; 16:9389-9400. [PMID: 35695383 PMCID: PMC9245354 DOI: 10.1021/acsnano.2c02195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/27/2022] [Indexed: 06/01/2023]
Abstract
Artificial cells are minimal structures constructed from biomolecular building blocks designed to mimic cellular processes, behaviors, and architectures. One near-ubiquitous feature of cellular life is the spatial organization of internal content. We know from biology that organization of content (including in membrane-bound organelles) is linked to cellular functions and that this feature is dynamic: the presence, location, and degree of compartmentalization changes over time. Vesicle-based artificial cells, however, are not currently able to mimic this fundamental cellular property. Here, we describe an artificial cell design strategy that addresses this technological bottleneck. We create a series of artificial cell architectures which possess multicompartment assemblies localized either on the inner or on the outer surface of the artificial cell membrane. Exploiting liquid-liquid phase separation, we can also engineer spatially segregated regions of condensed subcompartments attached to the cell surface, aligning with coexisting membrane domains. These structures can sense changes in environmental conditions and respond by reversibly transitioning from condensed multicompartment layers on the membrane surface to a dispersed state in the cell lumen, mimicking the dynamic compartmentalization found in biological cells. Likewise, we engineer exosome-like subcompartments that can be released to the environment. We can achieve this by using two types of triggers: chemical (addition of salts) and mechanical (by pulling membrane tethers using optical traps). These approaches allow us to control the compartmentalization state of artificial cells on population and single-cell levels.
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Affiliation(s)
- Greta Zubaite
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- Department
of Chemical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - James W. Hindley
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, 82 Wood Lane, London W12
0BZ, United Kingdom
| | - Oscar Ces
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, 82 Wood Lane, London W12
0BZ, United Kingdom
| | - Yuval Elani
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, 82 Wood Lane, London W12
0BZ, United Kingdom
- Department
of Chemical Engineering, Imperial College
London, Exhibition Road, London SW7 2AZ, United Kingdom
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18
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Yang S, Joesaar A, Bögels BWA, Mann S, de Greef TFA. Protocellular CRISPR/Cas‐Based Diffusive Communication Using Transcriptional RNA Signaling. Angew Chem Int Ed Engl 2022; 61:e202202436. [PMID: 35385207 PMCID: PMC9320857 DOI: 10.1002/anie.202202436] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Indexed: 11/29/2022]
Abstract
Protocells containing enzyme‐driven biomolecular circuits that can process and exchange information offer a promising approach for mimicking cellular features and developing molecular information platforms. Here, we employ synthetic transcriptional circuits together with CRISPR/Cas‐based DNA processing inside semipermeable protein‐polymer microcompartments. We first establish a transcriptional protocell that can be activated by external DNA strands and produce functional RNA aptamers. Subsequently, we engineer a transcriptional module to generate RNA strands functioning as diffusive signals that can be sensed by neighboring protocells and trigger the activation of internalized DNA probes or localization of Cas nucleases. Our results highlight the opportunities to combine CRISPR/Cas machinery and DNA nanotechnology for protocellular communication and provide a step towards the development of protocells capable of distributed molecular information processing.
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Affiliation(s)
- Shuo Yang
- Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Alex Joesaar
- Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology 2629 HZ Delft The Netherlands
| | - Bas W. A. Bögels
- Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry School of Chemistry and Max Planck-Bristol Centre for Minimal Biology School of Chemistry, University of Bristol Bristol BS8 1TS UK
- School of Materials Science and Engineering Institute of Molecular Medicine (IMM) Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Tom F. A. de Greef
- Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
- Computational Biology group Department of Biomedical Engineering Eindhoven University of Technology The Netherlands
- Institute for Molecules and Materials Faculty of Science Radboud University Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Center for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht Princetonlaan 6 3584 CB Utrecht The Netherlands
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19
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Yang S, Joesaar A, Bögels BWA, Mann S, Greef T. Protocellular CRISPR/Cas‐based Diffusive Communication Using Transcriptional RNA Signaling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shuo Yang
- Eindhoven University of Technology: Technische Universiteit Eindhoven Biomedical Engineering NETHERLANDS
| | - Alex Joesaar
- Eindhoven University of Technology: Technische Universiteit Eindhoven Biomedical Engineering NETHERLANDS
| | - Bas W. A. Bögels
- Eindhoven University of Technology: Technische Universiteit Eindhoven Biomedical Engineering NETHERLANDS
| | - Stephen Mann
- Bristol University School of Chemistry UNITED KINGDOM
| | - Tom Greef
- Eindhoven University of Technology Den Dolech 2CE 1.44B 5612 AZ Eindhoven NETHERLANDS
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20
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Arribas Perez M, Beales PA. Biomimetic Curvature and Tension-Driven Membrane Fusion Induced by Silica Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:13917-13931. [PMID: 34788054 DOI: 10.1021/acs.langmuir.1c02492] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fusion events in living cells are intricate phenomena that require the coordinate action of multicomponent protein complexes. However, simpler synthetic tools to control membrane fusion in artificial cells are highly desirable. Native membrane fusion machinery mediates fusion, driving a delicate balance of membrane curvature and tension between two closely apposed membranes. Here, we show that silica nanoparticles (SiO2 NPs) at a size close to the cross-over between tension-driven and curvature-driven interaction regimes initiate efficient fusion of biomimetic model membranes. Fusion efficiency and mechanisms are studied by Förster resonance energy transfer and confocal fluorescence microscopy. SiO2 NPs induce a slight increase in lipid packing likely to increase the lateral tension of the membrane. We observe a connection between membrane tension and fusion efficiency. Finally, real-time confocal fluorescence microscopy reveals three distinct mechanistic pathways for membrane fusion. SiO2 NPs show significant potential for inclusion in the synthetic biology toolkit for membrane remodeling and fusion in artificial cells.
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Affiliation(s)
- Marcos Arribas Perez
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
| | - Paul A Beales
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
- Bragg Centre for Materials Research, University of Leeds, Leeds LS2 9JT, U.K
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21
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Tivony R, Fletcher M, Al Nahas K, Keyser UF. A Microfluidic Platform for Sequential Assembly and Separation of Synthetic Cell Models. ACS Synth Biol 2021; 10:3105-3116. [PMID: 34761904 PMCID: PMC8609574 DOI: 10.1021/acssynbio.1c00371] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Cell-sized vesicles
like giant unilamellar vesicles (GUVs) are
established as a promising biomimetic model for studying cellular
phenomena in isolation. However, the presence of residual components
and byproducts, generated during vesicles preparation and manipulation,
severely limits the utility of GUVs in applications like synthetic
cells. Therefore, with the rapidly growing field of synthetic biology,
there is an emergent demand for techniques that can continuously purify
cell-like vesicles from diverse residues, while GUVs are being simultaneously
synthesized and manipulated. We have developed a microfluidic platform
capable of purifying GUVs through stream bifurcation, where a vesicles
suspension is partitioned into three fractions: purified GUVs, residual
components, and a washing solution. Using our purification approach,
we show that giant vesicles can be separated from various residues—which
range in size and chemical composition—with a very high efficiency
(e = 0.99), based on size and deformability of the
filtered objects. In addition, by incorporating the purification module
with a microfluidic-based GUV-formation method, octanol-assisted liposome
assembly (OLA), we established an integrated production-purification
microfluidic unit that sequentially produces, manipulates, and purifies
GUVs. We demonstrate the applicability of the integrated device to
synthetic biology through sequentially fusing SUVs with freshly prepared
GUVs and separating the fused GUVs from extraneous SUVs and oil droplets
at the same time.
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Affiliation(s)
- Ran Tivony
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Marcus Fletcher
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Kareem Al Nahas
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Ulrich F. Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
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22
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Kinetic and structural roles for the surface in guiding SAS-6 self-assembly to direct centriole architecture. Nat Commun 2021; 12:6180. [PMID: 34702818 PMCID: PMC8548535 DOI: 10.1038/s41467-021-26329-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 09/24/2021] [Indexed: 11/24/2022] Open
Abstract
Discovering mechanisms governing organelle assembly is a fundamental pursuit in biology. The centriole is an evolutionarily conserved organelle with a signature 9-fold symmetrical chiral arrangement of microtubules imparted onto the cilium it templates. The first structure in nascent centrioles is a cartwheel, which comprises stacked 9-fold symmetrical SAS-6 ring polymers emerging orthogonal to a surface surrounding each resident centriole. The mechanisms through which SAS-6 polymerization ensures centriole organelle architecture remain elusive. We deploy photothermally-actuated off-resonance tapping high-speed atomic force microscopy to decipher surface SAS-6 self-assembly mechanisms. We show that the surface shifts the reaction equilibrium by ~104 compared to solution. Moreover, coarse-grained molecular dynamics and atomic force microscopy reveal that the surface converts the inherent helical propensity of SAS-6 polymers into 9-fold rings with residual asymmetry, which may guide ring stacking and impart chiral features to centrioles and cilia. Overall, our work reveals fundamental design principles governing centriole assembly. The centriole exhibits an evolutionarily conserved 9-fold radial symmetry that stems from a cartwheel containing vertically stacked ring polymers that harbor 9 homodimers of the protein SAS-6. Here the authors show how dual properties inherent to surface-guided SAS-6 self-assembly possess spatial information that dictates correct scaffolding of centriole architecture.
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23
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Through the looking glass: milestones on the road towards mirroring life. Trends Biochem Sci 2021; 46:931-943. [PMID: 34294544 DOI: 10.1016/j.tibs.2021.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/05/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022]
Abstract
Naturally occurring DNA, RNA, and proteins predominantly exist in only one enantiomeric form (homochirality). Advances in biotechnology and chemical synthesis allow the production of the respective alternate enantiomeric form, enabling access to mirror-image versions of these natural biopolymers. Exploiting the unique properties of such mirror molecules has already led to many applications, such as biostable and nonimmunogenic therapeutics or sensors. However, a 'roadblock' for unlocking the mirror world is the lack of biological systems capable of synthesizing critical building blocks including mirror oligonucleotides and oligopeptides to reducing cost and improve purity. Here, we provide an overview of the current progress, applications, and challenges of the molecular mirror world by identifying milestones towards mirroring life.
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24
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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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25
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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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26
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The state of F-BAR domains as membrane-bound oligomeric platforms. Trends Cell Biol 2021; 31:644-655. [PMID: 33888395 DOI: 10.1016/j.tcb.2021.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/16/2022]
Abstract
Fes/Cip4 homology Bin/amphiphysin/Rvs (F-BAR) domains, like all BAR domains, are dimeric units that oligomerize and bind membranes. F-BAR domains are generally coupled to additional domains that function in protein binding or have enzymatic activity. Because of their crescent shape and ability to oligomerize, F-BAR domains have been traditionally viewed as membrane-deformation modules. However, multiple independent studies have provided no evidence that certain F-BAR domains are able to tubulate membrane. Instead, a growing body of literature featuring structural, biochemical, biophysical, and microscopy-based studies supports the idea that the F-BAR domain family can be unified only by their ability to form oligomeric assemblies on membranes to provide platforms for molecular assembly.
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27
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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: 63] [Impact Index Per Article: 21.0] [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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28
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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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29
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Lin DW, Liu Y, Lee YQ, Yang PJ, Ho CT, Hong JC, Hsiao JC, Liao DC, Liang AJ, Hung TC, Chen YC, Tu HL, Hsu CP, Huang HC. Construction of intracellular asymmetry and asymmetric division in Escherichia coli. Nat Commun 2021; 12:888. [PMID: 33563962 PMCID: PMC7873278 DOI: 10.1038/s41467-021-21135-1] [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: 09/07/2019] [Accepted: 01/09/2021] [Indexed: 01/23/2023] Open
Abstract
The design principle of establishing an intracellular protein gradient for asymmetric cell division is a long-standing fundamental question. While the major molecular players and their interactions have been elucidated via genetic approaches, the diversity and redundancy of natural systems complicate the extraction of critical underlying features. Here, we take a synthetic cell biology approach to construct intracellular asymmetry and asymmetric division in Escherichia coli, in which division is normally symmetric. We demonstrate that the oligomeric PopZ from Caulobacter crescentus can serve as a robust polarized scaffold to functionalize RNA polymerase. Furthermore, by using another oligomeric pole-targeting DivIVA from Bacillus subtilis, the newly synthesized protein can be constrained to further establish intracellular asymmetry, leading to asymmetric division and differentiation. Our findings suggest that the coupled oligomerization and restriction in diffusion may be a strategy for generating a spatial gradient for asymmetric cell division.
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Affiliation(s)
- Da-Wei Lin
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Yang Liu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Yue-Qi Lee
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Po-Jiun Yang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Chia-Tse Ho
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Jui-Chung Hong
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | | | - Der-Chien Liao
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - An-Jou Liang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Tzu-Chiao Hung
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Yu-Chuan Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
| | - Chao-Ping Hsu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
| | - Hsiao-Chun Huang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan.
- Department of Life Science, National Taiwan University, Taipei, Taiwan.
- Graduate Institute of Electronics Engineering, National Taiwan University, Taipei, Taiwan.
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30
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Franquelim HG, Dietz H, Schwille P. Reversible membrane deformations by straight DNA origami filaments. SOFT MATTER 2021; 17:276-287. [PMID: 32406895 DOI: 10.1039/d0sm00150c] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Membrane-active cytoskeletal elements, such as FtsZ, septin or actin, form filamentous polymers able to induce and stabilize curvature on cellular membranes. In order to emulate the characteristic dynamic self-assembly properties of cytoskeletal subunits in vitro, biomimetic synthetic scaffolds were here developed using DNA origami. In contrast to our earlier work with pre-curved scaffolds, we specifically assessed the potential of origami mimicking straight filaments, such as actin and microtubules, by origami presenting cholesteryl anchors for membrane binding and additional blunt end stacking interactions for controllable polymerization into linear filaments. By assessing the interaction of our DNA nanostructures with model membranes using fluorescence microscopy, we show that filaments can be formed, upon increasing MgCl2 in solution, for structures displaying blunt ends; and can subsequently depolymerize, by decreasing the concentration of MgCl2. Distinctive spike-like membrane protrusions were generated on giant unilamellar vesicles at high membrane-bound filament densities, and the presence of such deformations was reversible and shown to correlate with the MgCl2-triggered polymerization of DNA origami subunits into filamentous aggregates. In the end, our approach reveals the formation of membrane-bound filaments as a minimal requirement for membrane shaping by straight cytoskeletal-like objects.
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Affiliation(s)
| | - Hendrik Dietz
- Technical University of Munich, Garching Near Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried near Munich, Germany.
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31
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Gonzales DT, Zechner C, Tang TYD. Building synthetic multicellular systems using bottom–up approaches. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.coisb.2020.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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32
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Ganzinger KA, Merino‐Salomón A, García‐Soriano DA, Butterfield AN, Litschel T, Siedler F, Schwille P. FtsZ Reorganization Facilitates Deformation of Giant Vesicles in Microfluidic Traps**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Kristina A. Ganzinger
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
- Living Matter AMOLF P.O. Box 41883-1009 DB Amsterdam The Netherlands
| | - Adrián Merino‐Salomón
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Daniela A. García‐Soriano
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - A. Nelson Butterfield
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Thomas Litschel
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Frank Siedler
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
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33
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Ganzinger KA, Merino‐Salomón A, García‐Soriano DA, Butterfield AN, Litschel T, Siedler F, Schwille P. FtsZ Reorganization Facilitates Deformation of Giant Vesicles in Microfluidic Traps*. Angew Chem Int Ed Engl 2020; 59:21372-21376. [PMID: 32735732 PMCID: PMC7756778 DOI: 10.1002/anie.202001928] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/27/2020] [Indexed: 12/23/2022]
Abstract
The geometry of reaction compartments can affect the local outcome of interface-restricted reactions. Giant unilamellar vesicles (GUVs) are commonly used to generate cell-sized, membrane-bound reaction compartments, which are, however, always spherical. Herein, we report the development of a microfluidic chip to trap and reversibly deform GUVs into cigar-like shapes. When trapping and elongating GUVs that contain the primary protein of the bacterial Z ring, FtsZ, we find that membrane-bound FtsZ filaments align preferentially with the short GUV axis. When GUVs are released from this confinement and membrane tension is relaxed, FtsZ reorganizes reversibly from filaments into dynamic rings that stabilize membrane protrusions; a process that allows reversible GUV deformation. We conclude that microfluidic traps are useful for manipulating both geometry and tension of GUVs, and for investigating how both affect the outcome of spatially-sensitive reactions inside them, such as that of protein self-organization.
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Affiliation(s)
- Kristina A. Ganzinger
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
- Living MatterAMOLFP.O. Box 41883-1009 DBAmsterdamThe Netherlands
| | - Adrián Merino‐Salomón
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Daniela A. García‐Soriano
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - A. Nelson Butterfield
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Thomas Litschel
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Frank Siedler
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Petra Schwille
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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34
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Johnston CA. A Cell Adhesion-Based Reconstitution Method for Studying Cell Polarity. Front Cell Dev Biol 2020; 8:598492. [PMID: 33195282 PMCID: PMC7649242 DOI: 10.3389/fcell.2020.598492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/07/2020] [Indexed: 11/24/2022] Open
Abstract
Cell polarity is an evolutionarily conserved process of asymmetric spatial organization within cells and is essential to tissue structure, signal transduction, cell migration, and cell division. The establishment and maintenance of polarity typically involves extensive protein-protein interactions that can be made further intricate by cell cycle-dependent regulation. These aspects can make interpreting phenotypes within traditional in vivo genetic systems challenging due to pleiotropic effects in loss-of-function experiments. Minimal reconstitution methods offer investigators the advantage of stricter control of otherwise complex systems and allow for more direct assessment of the role of individual components to the process of interest. Here I provide a detailed protocol for a cell adhesion-based method of inducing cell polarity within non-polarized Drosophila S2 cells. This technique is simple, cost effective, moderate throughput, and amenable to RNAi-based loss-of-function studies. The ability to “plug-and-play” genes of interest allows investigators to easily assess the contribution of individual protein domains and post-translational modifications to their function. The system is ideally suited to test not only the requirement of individual components but also their sufficiency, and can provide important insight into the epistatic relationship among multiple components in a protein complex. Although designed for use within Drosophila cells, the general premise and protocol should be easily adapted to mammalian cell culture or other systems that may better suit the interests of potential users.
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35
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Gubieda AG, Packer JR, Squires I, Martin J, Rodriguez J. Going with the flow: insights from Caenorhabditis elegans zygote polarization. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190555. [PMID: 32829680 PMCID: PMC7482210 DOI: 10.1098/rstb.2019.0555] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2020] [Indexed: 12/12/2022] Open
Abstract
Cell polarity is the asymmetric distribution of cellular components along a defined axis. Polarity relies on complex signalling networks between conserved patterning proteins, including the PAR (partitioning defective) proteins, which become segregated in response to upstream symmetry breaking cues. Although the mechanisms that drive the asymmetric localization of these proteins are dependent upon cell type and context, in many cases the regulation of actomyosin cytoskeleton dynamics is central to the transport, recruitment and/or stabilization of these polarity effectors into defined subcellular domains. The transport or advection of PAR proteins by an actomyosin flow was first observed in the Caenorhabditis elegans zygote more than a decade ago. Since then a multifaceted approach, using molecular methods, high-throughput screens, and biophysical and computational models, has revealed further aspects of this flow and how polarity regulators respond to and modulate it. Here, we review recent findings on the interplay between actomyosin flow and the PAR patterning networks in the polarization of the C. elegans zygote. We also discuss how these discoveries and developed methods are shaping our understanding of other flow-dependent polarizing systems. This article is part of a discussion meeting issue 'Contemporary morphogenesis'.
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Affiliation(s)
| | | | | | | | - Josana Rodriguez
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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36
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Gires PY, Thampi M, Weiss M. Quantifying active diffusion in an agitated fluid. Phys Chem Chem Phys 2020; 22:21678-21684. [PMID: 32966453 DOI: 10.1039/d0cp03629c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mixing of reactants in microdroplets predominantly relies on diffusional motion due to small Reynolds numbers and the resulting absence of turbulent flows. Enhancing diffusion in microdroplets by an auxiliary noise source is therefore a topical problem. Here we report on how the diffusional motion of tracer beads is enhanced upon agitating the surrounding aqueous fluid with miniaturized magnetic stir bars that are compatible with microdroplets and microfluidic devices. Using single-particle tracking, we demonstrate via a broad palette of measures that local stirring of the fluid at different frequencies leads to an enhanced but apparently normal and homogenous diffusion process, i.e. diffusional steps follow the anticipated Gaussian distribution and no ballistic motion is observed whereas diffusion coefficients are significantly increased. The signature of stirring is, however, visible in the power-spectral density and in the velocity autocorrelation function of trajectories. Our data therefore demonstrate that diffusive mixing can be locally enhanced with miniaturized stir bars while only moderately affecting the ambient noise properties. The latter may also facilitate the controlled addition of nonequilibrium noise to complex fluids in future applications.
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Affiliation(s)
- Pierre-Yves Gires
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany.
| | - Mithun Thampi
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany.
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany.
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37
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Vutukuri HR, Hoore M, Abaurrea-Velasco C, van Buren L, Dutto A, Auth T, Fedosov DA, Gompper G, Vermant J. Active particles induce large shape deformations in giant lipid vesicles. Nature 2020; 586:52-56. [PMID: 32999485 DOI: 10.1038/s41586-020-2730-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 07/24/2020] [Indexed: 11/09/2022]
Abstract
Biological cells generate intricate structures by sculpting their membrane from within to actively sense and respond to external stimuli or to explore their environment1-4. Several pathogenic bacteria also provide examples of how localized forces strongly deform cell membranes from inside, leading to the invasion of neighbouring healthy mammalian cells5. Giant unilamellar vesicles have been successfully used as a minimal model system with which to mimic biological cells6-11, but the realization of a minimal system with localized active internal forces that can strongly deform lipid membranes from within and lead to dramatic shape changes remains challenging. Here we present a combined experimental and simulation study that demonstrates how self-propelled particles enclosed in giant unilamellar vesicles can induce a plethora of non-equilibrium shapes and active membrane fluctuations. Using confocal microscopy, in the experiments we explore the membrane response to local forces exerted by self-phoretic Janus microswimmers. To quantify dynamic membrane changes, we perform Langevin dynamics simulations of active Brownian particles enclosed in thin membrane shells modelled by dynamically triangulated surfaces. The most pronounced shape changes are observed at low and moderate particle loadings, with the formation of tether-like protrusions and highly branched, dendritic structures, whereas at high volume fractions globally deformed vesicle shapes are observed. The resulting state diagram predicts the conditions under which local internal forces generate various membrane shapes. A controlled realization of such distorted vesicle morphologies could improve the design of artificial systems such as small-scale soft robots and synthetic cells.
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Affiliation(s)
| | - Masoud Hoore
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich, Germany
| | - Clara Abaurrea-Velasco
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich, Germany
| | - Lennard van Buren
- Soft Materials, Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Alessandro Dutto
- Soft Materials, Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Thorsten Auth
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich, Germany
| | - Dmitry A Fedosov
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich, Germany.
| | - Jan Vermant
- Soft Materials, Department of Materials, ETH Zürich, Zürich, Switzerland
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38
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Mandal S, Kurzthaler C, Franosch T, Löwen H. Crowding-Enhanced Diffusion: An Exact Theory for Highly Entangled Self-Propelled Stiff Filaments. PHYSICAL REVIEW LETTERS 2020; 125:138002. [PMID: 33034497 DOI: 10.1103/physrevlett.125.138002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/14/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
We study a strongly interacting crowded system of self-propelled stiff filaments by event-driven Brownian dynamics simulations and an analytical theory to elucidate the intricate interplay of crowding and self-propulsion. We find a remarkable increase of the effective diffusivity upon increasing the filament number density by more than one order of magnitude. This counterintuitive "crowded is faster" behavior can be rationalized by extending the concept of a confining tube pioneered by Doi and Edwards for highly entangled, crowded, passive to active systems. We predict a scaling theory for the effective diffusivity as a function of the Péclet number and the filament number density. Subsequently, we show that an exact expression derived for a single self-propelled filament with motility parameters as input can predict the nontrivial spatiotemporal dynamics over the entire range of length and timescales. In particular, our theory captures short-time diffusion, directed swimming motion at intermediate times, and the transition to complete orientational relaxation at long times.
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Affiliation(s)
- Suvendu Mandal
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
| | - Christina Kurzthaler
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, USA
- Institut für Theoretische Physik, Universität Innsbruck, A-6020 Innsbruck, Austria
| | - Thomas Franosch
- Institut für Theoretische Physik, Universität Innsbruck, A-6020 Innsbruck, Austria
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
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39
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Farhadi L, Ricketts SN, Rust MJ, Das M, Robertson-Anderson RM, Ross JL. Actin and microtubule crosslinkers tune mobility and control co-localization in a composite cytoskeletal network. SOFT MATTER 2020; 16:7191-7201. [PMID: 32207504 DOI: 10.1039/c9sm02400j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Actin and microtubule filaments, with their auxiliary proteins, enable the cytoskeleton to carry out vital processes in the cell by tuning the organizational and mechanical properties of the network. Despite their critical importance and interactions in cells, we are only beginning to uncover information about the composite network. The challenge is due to the high complexity of combining actin, microtubules, and their hundreds of known associated proteins. Here, we use fluorescence microscopy, fluctuation, and cross-correlation analysis to examine the role of actin and microtubules in the presence of an antiparallel microtubule crosslinker, MAP65, and a generic, strong actin crosslinker, biotin-NeutrAvidin. For a fixed ratio of actin and microtubule filaments, we vary the amount of each crosslinker and measure the organization and fluctuations of the filaments. We find that the microtubule crosslinker plays the principle role in the organization of the system, while, actin crosslinking dictates the mobility of the filaments. We have previously demonstrated that the fluctuations of filaments are related to the mechanics, implying that actin crosslinking controls the mechanical properties of the network, independent of the microtubule-driven re-organization.
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Affiliation(s)
- Leila Farhadi
- Department of Physics, University of Massachusetts, Amherst, 666 N. Pleasant St., Amherst, MA 01003, USA.
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40
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Miniaturized magnetic stir bars for controlled agitation of aqueous microdroplets. Sci Rep 2020; 10:10911. [PMID: 32616786 PMCID: PMC7331805 DOI: 10.1038/s41598-020-67767-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/08/2020] [Indexed: 12/19/2022] Open
Abstract
Controlled stirring of tiny volumes of aqueous fluids is of particular importance in the life sciences, e.g. in the context of microfluidic and lab-on-chip applications. Local stirring not only accelerates fluid mixing and diffusion-limited processes, but it also allows for adding controlled active noise to the fluid. Here we report on the synthesis and characterization of magnetic nano-stir bars (MNBs) with which these features can be achieved in a straightforward fashion. We also demonstrate the applicability of MNBs to cell extract droplets in microfluidic channels and we show that they can introduce active noise to cell extracts as evidenced by altered fluctuations of ensembles of cytoskeletal filaments.
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41
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Jose AM. The analysis of living systems can generate both knowledge and illusions. eLife 2020; 9:56354. [PMID: 32553111 PMCID: PMC7302876 DOI: 10.7554/elife.56354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/12/2020] [Indexed: 12/20/2022] Open
Abstract
Life relies on phenomena that range from changes in molecules that occur within nanoseconds to changes in populations that occur over millions of years. Researchers have developed a vast range of experimental techniques to analyze living systems, but a given technique usually only works over a limited range of length or time scales. Therefore, gaining a full understanding of a living system usually requires the integration of information obtained at multiple different scales by two or more techniques. This approach has undoubtedly led to a much better understanding of living systems but, equally, the staggering complexity of these systems, the sophistication and limitations of the techniques available in modern biology, and the need to use two or more techniques, can lead to persistent illusions of knowledge. Here, in an effort to make better use of the experimental techniques we have at our disposal, I propose a broad classification of techniques into six complementary approaches: perturbation, visualization, substitution, characterization, reconstitution, and simulation. Such a taxonomy might also help increase the reproducibility of inferences and improve peer review.
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Affiliation(s)
- Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
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42
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Laohakunakorn N, Grasemann L, Lavickova B, Michielin G, Shahein A, Swank Z, Maerkl SJ. Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:213. [PMID: 32266240 PMCID: PMC7105575 DOI: 10.3389/fbioe.2020.00213] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-free systems offer a promising approach to engineer biology since their open nature allows for well-controlled and characterized reaction conditions. In this review, we discuss the history and recent developments in engineering recombinant and crude extract systems, as well as breakthroughs in enabling technologies, that have facilitated increased throughput, compartmentalization, and spatial control of cell-free protein synthesis reactions. Combined with a deeper understanding of the cell-free systems themselves, these advances improve our ability to address a range of scientific questions. By mastering control of the cell-free platform, we will be in a position to construct increasingly complex biomolecular systems, and approach natural biological complexity in a bottom-up manner.
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Affiliation(s)
- Nadanai Laohakunakorn
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura Grasemann
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbora Lavickova
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Grégoire Michielin
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Amir Shahein
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zoe Swank
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J. Maerkl
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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43
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Göpfrich K, Urban MJ, Frey C, Platzman I, Spatz JP, Liu N. Dynamic Actuation of DNA-Assembled Plasmonic Nanostructures in Microfluidic Cell-Sized Compartments. NANO LETTERS 2020; 20:1571-1577. [PMID: 32083879 PMCID: PMC7307956 DOI: 10.1021/acs.nanolett.9b04217] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been integrated or operated inside synthetic cells toward the goal of realizing artificial biological systems entirely from the bottom-up. In this Letter, we encapsulate and actuate DNA-assembled dynamic nanostructures inside cell-sized microfluidic compartments. These encapsulated DNA nanostructures not only exhibit structural reconfigurability owing to their pH-sensitive molecular switches upon external stimuli but also possess optical feedback enabled by the integrated plasmonic probes. In particular, we demonstrate the power of microfluidic compartmentalization for achieving on-chip plasmonic enantiomer separation and substrate filtration. Our work exemplifies that the two unique tools, droplet-based microfluidics and DNA technology, offering high precision on the microscale and nanoscale, respectively, can be brought together to greatly enrich the complexity and diversity of functional synthetic systems.
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Affiliation(s)
- Kerstin Göpfrich
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, 69120 Heidelberg, Germany
| | - Maximilian J. Urban
- Max
Planck Institute for Intelligent Systems, Heisenbergstraße 3, 70569 Stuttgart, Germany
- Kirchhoff
Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Christoph Frey
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Department
of Biophysical Chemistry, Heidelberg University, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Ilia Platzman
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Department
of Biophysical Chemistry, Heidelberg University, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Joachim P. Spatz
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Department
of Biophysical Chemistry, Heidelberg University, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
- Max
Planck School Matter to Life, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Na Liu
- Max
Planck Institute for Intelligent Systems, Heisenbergstraße 3, 70569 Stuttgart, Germany
- Kirchhoff
Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Max
Planck School Matter to Life, Jahnstraße 29, 69120 Heidelberg, Germany
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44
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Banerjee S, Gardel ML, Schwarz US. The Actin Cytoskeleton as an Active Adaptive Material. ANNUAL REVIEW OF CONDENSED MATTER PHYSICS 2020; 11:421-439. [PMID: 33343823 PMCID: PMC7748259 DOI: 10.1146/annurev-conmatphys-031218-013231] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Actin is the main protein used by biological cells to adapt their structure and mechanics to their needs. Cellular adaptation is made possible by molecular processes that strongly depend on mechanics. The actin cytoskeleton is also an active material that continuously consumes energy. This allows for dynamical processes that are possible only out of equilibrium and opens up the possibility for multiple layers of control that have evolved around this single protein.Here we discuss the actin cytoskeleton from the viewpoint of physics as an active adaptive material that can build structures superior to man-made soft matter systems. Not only can actin be used to build different network architectures on demand and in an adaptive manner, but it also exhibits the dynamical properties of feedback systems, like excitability, bistability, or oscillations. Therefore, it is a prime example of how biology couples physical structure and information flow and a role model for biology-inspired metamaterials.
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Affiliation(s)
- Shiladitya Banerjee
- Department of Physics and Astronomy and Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Margaret L Gardel
- Department of Physics, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
| | - Ulrich S Schwarz
- Institute for Theoretical Physics and BioQuant, Heidelberg University, 69120 Heidelberg, Germany
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45
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Beckers D, Urbancic D, Sezgin E. Impact of Nanoscale Hindrances on the Relationship between Lipid Packing and Diffusion in Model Membranes. J Phys Chem B 2020; 124:1487-1494. [PMID: 32026676 PMCID: PMC7050011 DOI: 10.1021/acs.jpcb.0c00445] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Membrane
models have allowed for precise study of the plasma membrane’s
biophysical properties, helping to unravel both structural and dynamic
motifs within cell biology. Freestanding and supported bilayer systems
are popular models to reconstitute membrane-related processes. Although
it is well-known that each have their advantages and limitations,
comprehensive comparison of their biophysical properties is still
lacking. Here, we compare the diffusion and lipid packing in giant
unilamellar vesicles, planar and spherical supported membranes, and
cell-derived giant plasma membrane vesicles. We apply florescence
correlation spectroscopy (FCS), spectral imaging, and super-resolution
stimulated emission depletion FCS to study the diffusivity, lipid
packing, and nanoscale architecture of these membrane systems, respectively.
Our data show that lipid packing and diffusivity is tightly correlated
in freestanding bilayers. However, nanoscale interactions in the supported
bilayers cause deviation from this correlation. These data are essential
to develop accurate theoretical models of the plasma membrane and
will serve as a guideline for suitable model selection in future studies
to reconstitute biological processes.
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Affiliation(s)
- Daniel Beckers
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine , University of Oxford , Oxford OX3 9DS , U.K
| | - Dunja Urbancic
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine , University of Oxford , Oxford OX3 9DS , U.K.,Faculty of Pharmacy , University of Ljubljana , Askerceva cesta 7 , 1000 Ljubljana , Slovenia
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine , University of Oxford , Oxford OX3 9DS , U.K.,Science for Life Laboratory, Department of Women's and Children's Health , Karolinska Institutet , Solna , Sweden
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Pollard LW, Garabedian MV, Alioto SL, Shekhar S, Goode BL. Genetically inspired in vitro reconstitution of Saccharomyces cerevisiae actin cables from seven purified proteins. Mol Biol Cell 2020; 31:335-347. [PMID: 31913750 PMCID: PMC7183793 DOI: 10.1091/mbc.e19-10-0576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A major goal of synthetic biology is to define the minimal cellular machinery required to assemble a biological structure in its simplest form. Here, we focused on Saccharomyces cerevisiae actin cables, which provide polarized tracks for intracellular transport and maintain defined lengths while continuously undergoing rapid assembly and turnover. Guided by the genetic requirements for proper cable assembly and dynamics, we show that seven evolutionarily conserved S. cerevisiae proteins (actin, formin, profilin, tropomyosin, capping protein, cofilin, and AIP1) are sufficient to reconstitute the formation of cables that undergo polarized turnover and maintain steady-state lengths similar to actin cables in vivo. Further, the removal of individual proteins from this simple in vitro reconstitution system leads to cable defects that closely approximate in vivo cable phenotypes caused by disrupting the corresponding genes. Thus, a limited set of molecular components is capable of self-organizing into dynamic, micron-scale actin structures with features similar to cables in living cells.
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Affiliation(s)
| | | | | | | | - Bruce L Goode
- Department of Biology, Brandeis University, Waltham, MA 02454
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47
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Illukkumbura R, Bland T, Goehring NW. Patterning and polarization of cells by intracellular flows. Curr Opin Cell Biol 2019; 62:123-134. [PMID: 31760155 PMCID: PMC6968950 DOI: 10.1016/j.ceb.2019.10.005] [Citation(s) in RCA: 30] [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: 08/02/2019] [Revised: 10/11/2019] [Accepted: 10/16/2019] [Indexed: 11/19/2022]
Abstract
Beginning with Turing’s seminal work [1], decades of research have demonstrated the fundamental ability of biochemical networks to generate and sustain the formation of patterns. However, it is increasingly appreciated that biochemical networks both shape and are shaped by physical and mechanical processes [2, 3, 4]. One such process is fluid flow. In many respects, the cytoplasm, membrane and actin cortex all function as fluids, and as they flow, they drive bulk transport of molecules throughout the cell. By coupling biochemical activity to long range molecular transport, flows can shape the distributions of molecules in space. Here we review the various types of flows that exist in cells, with the aim of highlighting recent advances in our understanding of how flows are generated and how they contribute to intracellular patterning processes, such as the establishment of cell polarity.
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Affiliation(s)
| | - Tom Bland
- The Francis Crick Institute, London, UK; Institute for the Physics of Living Systems, University College London, London, UK
| | - Nathan W Goehring
- The Francis Crick Institute, London, UK; Institute for the Physics of Living Systems, University College London, London, UK; MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
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48
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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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49
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Bhattacharya S, Phatake RS, Nabha Barnea S, Zerby N, Zhu JJ, Shikler R, Lemcoff NG, Jelinek R. Fluorescent Self-Healing Carbon Dot/Polymer Gels. ACS NANO 2019; 13:7396-7401. [PMID: 30615415 DOI: 10.1021/acsnano.9b05112] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Multicolor, fluorescent self-healing gels were constructed through reacting carbon dots produced from different aldehyde precursors with branched polyethylenimine. The self-healing gels were formed through Schiff base reaction between the aldehyde units displayed upon the carbon dots' surface and primary amine residues within the polyethylenimine network, generating imine bonds. The dynamic covalent imine bonds between the carbon dots and polymeric matrix endowed the gels with both excellent self-healing properties as well as high mechanical strength. Moreover, the viscoelastic properties of the gels could be intimately modulated by controlling the ratio between the carbon dots and polymer. The distinct fluorescence emissions of the gels, originating from the specific carbon dot constituents, were employed for fabrication of light emitters at different colors, particularly generating white light.
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Affiliation(s)
- Sagarika Bhattacharya
- Department of Chemistry , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
| | | | - Shiran Nabha Barnea
- Department of Electrical and Computer Engineering , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
| | - Nicholas Zerby
- Department of Chemistry , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Rafi Shikler
- Department of Electrical and Computer Engineering , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
| | - Norberto Gabriel Lemcoff
- Department of Chemistry , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
- Ilse Katz Institute for Nanotechnology , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
| | - Raz Jelinek
- Department of Chemistry , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
- Ilse Katz Institute for Nanotechnology , Ben Gurion University of the Negev , Beer Sheva 84105 , Israel
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