1
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Groza R, Schmidt KV, Müller PM, Ronchi P, Schlack-Leigers C, Neu U, Puchkov D, Dimova R, Matthaeus C, Taraska J, Weikl TR, Ewers H. Adhesion energy controls lipid binding-mediated endocytosis. Nat Commun 2024; 15:2767. [PMID: 38553473 PMCID: PMC10980822 DOI: 10.1038/s41467-024-47109-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
Several bacterial toxins and viruses can deform membranes through multivalent binding to lipids for clathrin-independent endocytosis. However, it remains unclear, how membrane deformation and endocytic internalization are mechanistically linked. Here we show that many lipid-binding virions induce membrane deformation and clathrin-independent endocytosis, suggesting a common mechanism based on multivalent lipid binding by globular particles. We create a synthetic cellular system consisting of a lipid-anchored receptor in the form of GPI-anchored anti-GFP nanobodies and a multivalent globular binder exposing 180 regularly-spaced GFP molecules on its surface. We show that these globular, 40 nm diameter, particles bind to cells expressing the receptor, deform the plasma membrane upon adhesion and become endocytosed in a clathrin-independent manner. We explore the role of the membrane adhesion energy in endocytosis by using receptors with affinities varying over 7 orders of magnitude. Using this system, we find that once a threshold in adhesion energy is overcome to allow for membrane deformation, endocytosis occurs reliably. Multivalent, binding-induced membrane deformation by globular binders is thus sufficient for internalization to occur and we suggest it is the common, purely biophysical mechanism for lipid-binding mediated endocytosis of toxins and pathogens.
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Affiliation(s)
- Raluca Groza
- Institute of Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Kita Valerie Schmidt
- Institute of Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
- Max Planck Institute of Colloids and Interfaces, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Paul Markus Müller
- Institute of Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Claire Schlack-Leigers
- Institute of Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Ursula Neu
- Institute of Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Dmytro Puchkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125, Berlin, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Claudia Matthaeus
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Institute for Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
| | - Justin Taraska
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thomas R Weikl
- Max Planck Institute of Colloids and Interfaces, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Helge Ewers
- Institute of Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany.
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2
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Zhu X, Chen Q, Zhao H, Yang Q, Goudappagouda, Gelléri M, Ritz S, Ng D, Koynov K, Parekh SH, Chetty VK, Thakur BK, Cremer C, Landfester K, Müllen K, Terenzio M, Bonn M, Narita A, Liu X. Intrinsic Burst-Blinking Nanographenes for Super-Resolution Bioimaging. J Am Chem Soc 2024; 146:5195-5203. [PMID: 38275287 PMCID: PMC10910517 DOI: 10.1021/jacs.3c11152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
Single-molecule localization microscopy (SMLM) is a powerful technique to achieve super-resolution imaging beyond the diffraction limit. Although various types of blinking fluorophores are currently considered for SMLM, intrinsic blinking fluorophores remain rare at the single-molecule level. Here, we report the synthesis of nanographene-based intrinsic burst-blinking fluorophores for highly versatile SMLM. We image amyloid fibrils in air and in various pH solutions without any additive and lysosome dynamics in live mammalian cells under physiological conditions. In addition, the single-molecule labeling of nascent proteins in primary sensory neurons was achieved with azide-functionalized nanographenes via click chemistry. SMLM imaging reveals higher local translation at axonal branching with unprecedented detail, while the size of translation foci remained similar throughout the entire network. These various results demonstrate the potential of nanographene-based fluorophores to drastically expand the applicability of super-resolution imaging.
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Affiliation(s)
- Xingfu Zhu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Qiang Chen
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Hao Zhao
- Organic
and Carbon Nanomaterials Unit, Okinawa Institute
of Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
| | - Qiqi Yang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Goudappagouda
- Organic
and Carbon Nanomaterials Unit, Okinawa Institute
of Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
| | - Márton Gelléri
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Sandra Ritz
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
| | - David Ng
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kaloian Koynov
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sapun H. Parekh
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | | | - Basant Kumar Thakur
- Department
of Pediatrics III, University Hospital Essen, 45147 Essen, Germany
| | - Christoph Cremer
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Katharina Landfester
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Klaus Müllen
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Marco Terenzio
- Molecular
Neuroscience Unit, Okinawa Institute of
Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Akimitsu Narita
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Organic
and Carbon Nanomaterials Unit, Okinawa Institute
of Science and Technology Graduate University, Kunigami-gun, Okinawa 904-0495, Japan
| | - Xiaomin Liu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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3
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Luo H, Jiang C, Wen Y, Wang X, Wang F, Liu L, Yu H. Correlative super-resolution bright-field and fluorescence imaging by microsphere assisted microscopy. NANOSCALE 2024; 16:1703-1710. [PMID: 38099700 DOI: 10.1039/d3nr04096h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
The resolution of fluorescence imaging has been significantly enhanced with the development of super-resolution imaging techniques, surpassing the diffraction limit and reaching sub-diffraction scales of tens of nanometers. However, the resolution of the bright-field images of cells is restricted by the diffraction limit, leading to a significant gap between the resolutions of fluorescence and bright-field imaging, which hinders the research of the precise distribution of intracellular nanostructures. A microsphere superlens offers a promising solution by providing label-free super-resolution imaging capabilities compatible with fluorescence super-resolution imaging. In this study, we used microsphere superlenses to simultaneously enhance the resolution of bright-field and fluorescence imaging, achieving correlated super-resolution bright-field and fluorescence imaging. Compared to conventional bright-field images, we improved the imaging resolution from λ/1.3 to λ/4.2. A correlative super-resolution of mouse skeletal muscle cells was achieved, enabling the clear observation of the precise distribution of nanoparticles in mouse skeletal muscle cells. Furthermore, microsphere superlenses inherit the advantages of optical imaging, which is expected to enable the capturing of ultrafast biological activity within living cells with extremely high temporal resolutions.
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Affiliation(s)
- Hao Luo
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaodi Jiang
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
- Shenyang Jianzhu University, Shenyang 110168, China
| | - Yangdong Wen
- Institute of Urban Rail Transportation, Southwest Jiaotong University, Chengdu 610000, China
| | - Xiaoduo Wang
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110016, China
| | - Feifei Wang
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong 999077, Hong Kong
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110016, China
| | - Haibo Yu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110016, China
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4
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Puchkov D, Müller PM, Lehmann M, Matthaeus C. Analyzing the cellular plasma membrane by fast and efficient correlative STED and platinum replica EM. Front Cell Dev Biol 2023; 11:1305680. [PMID: 38099299 PMCID: PMC10720448 DOI: 10.3389/fcell.2023.1305680] [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: 10/02/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
The plasma membrane of mammalian cells links transmembrane receptors, various structural components, and membrane-binding proteins to subcellular processes, allowing inter- and intracellular communication. Therefore, membrane-binding proteins, together with structural components such as actin filaments, modulate the cell membrane in their flexibility, stiffness, and curvature. Investigating membrane components and curvature in cells remains challenging due to the diffraction limit in light microscopy. Preparation of 5-15-nm-thin plasma membrane sheets and subsequent inspection by metal replica transmission electron microscopy (TEM) reveal detailed information about the cellular membrane topology, including the structure and curvature. However, electron microscopy cannot identify proteins associated with specific plasma membrane domains. Here, we describe a novel adaptation of correlative super-resolution light microscopy and platinum replica TEM (CLEM-PREM), allowing the analysis of plasma membrane sheets with respect to their structural details, curvature, and associated protein composition. We suggest a number of shortcuts and troubleshooting solutions to contemporary PREM protocols. Thus, implementation of super-resolution stimulated emission depletion (STED) microscopy offers significant reduction in sample preparation time and reduced technical challenges for imaging and analysis. Additionally, highly technical challenges associated with replica preparation and transfer on a TEM grid can be overcome by scanning electron microscopy (SEM) imaging. The combination of STED microscopy and platinum replica SEM or TEM provides the highest spatial resolution of plasma membrane proteins and their underlying membrane and is, therefore, a suitable method to study cellular events like endocytosis, membrane trafficking, or membrane tension adaptations.
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Affiliation(s)
- Dmytro Puchkov
- Cellular Imaging Facility, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Paul Markus Müller
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Martin Lehmann
- Cellular Imaging Facility, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Claudia Matthaeus
- Cellular Physiology of Nutrition, Institute for Nutritional Science, University of Potsdam, Potsdam, Germany
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5
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Sochacki KA, Sun WW, Michalak DJ, Kunamaneni P, Hinshaw JE, Taraska JW. Toward Plasma Membrane Visual Proteomics: Developing a Correlative Cryo-electron Tomography Pipeline for Isolated Plasma Membranes. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:898. [PMID: 37613816 DOI: 10.1093/micmic/ozad067.445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Kem A Sochacki
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Willy W Sun
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Dennis J Michalak
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Prasanthi Kunamaneni
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jenny E Hinshaw
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Justin W Taraska
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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6
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Groza R, Schmidt KV, Müller PM, Ronchi P, Schlack-Leigers C, Neu U, Puchkov D, Dimova R, Matthäus C, Taraska J, Weikl TR, Ewers H. Adhesion energy controls lipid binding-mediated endocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.23.546235. [PMID: 37503169 PMCID: PMC10370163 DOI: 10.1101/2023.06.23.546235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Several bacterial toxins and viruses can deform membranes through multivalent binding to lipids for clathrin-independent endocytosis. However, it remains unclear, how membrane deformation and endocytic internalization are mechanistically linked. Here we show that many lipid-binding virions induce membrane deformation and clathrin-independent endocytosis, suggesting a common mechanism based on multivalent lipid binding by globular particles. We create a synthetic cellular system consisting of a lipid-anchored receptor in the form of GPI-anchored anti-GFP nanobodies and a multivalent globular binder exposing 180 regularly-spaced GFP molecules on its surface. We show that these globular, 40 nm diameter, particles bind to cells expressing the receptor, deform the plasma membrane upon adhesion and become endocytosed in a clathrin-independent manner. We explore the role of the membrane adhesion energy in endocytosis by using receptors with affinities varying over 7 orders of magnitude. Using this system, we find that once a threshold in adhesion energy is overcome to allow for membrane deformation, endocytosis occurs reliably. Multivalent, binding-induced membrane deformation by globular binders is thus sufficient for internalization to occur and we suggest it is the common, purely biophysical mechanism for lipid-binding mediated endocytosis of toxins and pathogens.
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7
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Gong J, Jin Z, Chen H, He J, Zhang Y, Yang X. Super-resolution fluorescence microscopic imaging in pathogenesis and drug treatment of neurological disease. Adv Drug Deliv Rev 2023; 196:114791. [PMID: 37004939 DOI: 10.1016/j.addr.2023.114791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/16/2023] [Accepted: 03/19/2023] [Indexed: 04/03/2023]
Abstract
Since super-resolution fluorescence microscopic technology breaks the diffraction limit that has existed for a long time in optical imaging, it can observe the process of synapses formed between nerve cells and the protein aggregation related to neurological disease. Thus, super-resolution fluorescence microscopic imaging has significantly impacted several industries, including drug development and pathogenesis research, and it is anticipated that it will significantly alter the future of life science research. Here, we focus on several typical super-resolution fluorescence microscopic technologies, introducing their benefits and drawbacks, as well as applications in several common neurological diseases, in the hope that their services will be expanded and improved in the pathogenesis and drug treatment of neurological diseases.
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8
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A conformational switch in clathrin light chain regulates lattice structure and endocytosis at the plasma membrane of mammalian cells. Nat Commun 2023; 14:732. [PMID: 36759616 PMCID: PMC9911608 DOI: 10.1038/s41467-023-36304-7] [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: 05/05/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Conformational changes in endocytic proteins are regulators of clathrin-mediated endocytosis. Three clathrin heavy chains associated with clathrin light chains (CLC) assemble into triskelia that link into a geometric lattice that curves to drive endocytosis. Structural changes in CLC have been shown to regulate triskelia assembly in solution, yet the nature of these changes, and their effects on lattice growth, curvature, and endocytosis in cells are unknown. Here, we develop a new correlative fluorescence resonance energy transfer (FRET) and platinum replica electron microscopy method, named FRET-CLEM. With FRET-CLEM, we measure conformational changes in clathrin at thousands of individual morphologically distinct clathrin-coated structures. We discover that the N-terminus of CLC repositions away from the plasma membrane and triskelia vertex as coats curve. Preventing this conformational switch with chemical tools increases lattice sizes and inhibits endocytosis. Thus, a specific conformational switch in the light chain regulates lattice curvature and endocytosis in mammalian cells.
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9
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Riachy L, Ferrand T, Chasserot-Golaz S, Galas L, Alexandre S, Montero-Hadjadje M. Advanced Imaging Approaches to Reveal Molecular Mechanisms Governing Neuroendocrine Secretion. Neuroendocrinology 2023; 113:107-119. [PMID: 34915491 DOI: 10.1159/000521457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/09/2021] [Indexed: 11/19/2022]
Abstract
Identification of the molecular mechanisms governing neuroendocrine secretion and resulting intercellular communication is one of the great challenges of cell biology to better understand organism physiology and neurosecretion disruption-related pathologies such as hypertension, neurodegenerative, or metabolic diseases. To visualize molecule distribution and dynamics at the nanoscale, many imaging approaches have been developed and are still emerging. In this review, we provide an overview of the pioneering studies using transmission electron microscopy, atomic force microscopy, total internal reflection microscopy, and super-resolution microscopy in neuroendocrine cells to visualize molecular mechanisms driving neurosecretion processes, including exocytosis and associated fusion pores, endocytosis and associated recycling vesicles, and protein-protein or protein-lipid interactions. Furthermore, the potential and the challenges of these different advanced imaging approaches for application in the study of neuroendocrine cell biology are discussed, aiming to guide researchers to select the best approach for their specific purpose around the crucial but not yet fully understood neurosecretion process.
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Affiliation(s)
- Lina Riachy
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, Institut de Recherche et d'Innovation Biomédicale de Normandie, Normandie University, UNIROUEN, INSERM, U1239, Rouen, France
| | - Thomas Ferrand
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, Institut de Recherche et d'Innovation Biomédicale de Normandie, Normandie University, UNIROUEN, INSERM, U1239, Rouen, France
| | - Sylvette Chasserot-Golaz
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique, Strasbourg University, Strasbourg, France
| | - Ludovic Galas
- Normandie University, UNIROUEN, INSERM, PRIMACEN, Rouen, France
| | - Stéphane Alexandre
- Polymères, Biopolymères, Surfaces Laboratory, CNRS, Normandie University, UNIROUEN, UMR 6270, Rouen, France
| | - Maité Montero-Hadjadje
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, Institut de Recherche et d'Innovation Biomédicale de Normandie, Normandie University, UNIROUEN, INSERM, U1239, Rouen, France
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10
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Matthaeus C, Sochacki KA, Dickey AM, Puchkov D, Haucke V, Lehmann M, Taraska JW. The molecular organization of differentially curved caveolae indicates bendable structural units at the plasma membrane. Nat Commun 2022; 13:7234. [PMID: 36433988 PMCID: PMC9700719 DOI: 10.1038/s41467-022-34958-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022] Open
Abstract
Caveolae are small coated plasma membrane invaginations with diverse functions. Caveolae undergo curvature changes. Yet, it is unclear which proteins regulate this process. To address this gap, we develop a correlative stimulated emission depletion (STED) fluorescence and platinum replica electron microscopy imaging (CLEM) method to image proteins at single caveolae. Caveolins and cavins are found at all caveolae, independent of curvature. EHD2 is detected at both low and highly curved caveolae. Pacsin2 associates with low curved caveolae and EHBP1 with mostly highly curved caveolae. Dynamin is absent from caveolae. Cells lacking dynamin show no substantial changes to caveolae, suggesting that dynamin is not directly involved in caveolae curvature. We propose a model where caveolins, cavins, and EHD2 assemble as a cohesive structural unit regulated by intermittent associations with pacsin2 and EHBP1. These coats can flatten and curve to enable lipid traffic, signaling, and changes to the surface area of the cell.
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Affiliation(s)
- Claudia Matthaeus
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kem A Sochacki
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrea M Dickey
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dmytro Puchkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Faculty of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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11
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Yang C, Colosi P, Hugelier S, Zabezhinsky D, Lakadamyali M, Svitkina T. Actin polymerization promotes invagination of flat clathrin-coated lattices in mammalian cells by pushing at lattice edges. Nat Commun 2022; 13:6127. [PMID: 36253374 PMCID: PMC9576739 DOI: 10.1038/s41467-022-33852-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) requires energy input from actin polymerization in mechanically challenging conditions. The roles of actin in CME are poorly understood due to inadequate knowledge of actin organization at clathrin-coated structures (CCSs). Using platinum replica electron microscopy of mammalian cells, we show that Arp2/3 complex-dependent branched actin networks, which often emerge from microtubule tips, assemble along the CCS perimeter, lack interaction with the apical clathrin lattice, and have barbed ends oriented toward the CCS. This structure is hardly compatible with the widely held "apical pulling" model describing actin functions in CME. Arp2/3 complex inhibition or epsin knockout produce large flat non-dynamic CCSs, which split into invaginating subdomains upon recovery from Arp2/3 inhibition. Moreover, epsin localization to CCSs depends on Arp2/3 activity. We propose an "edge pushing" model for CME, wherein branched actin polymerization promotes severing and invagination of flat CCSs in an epsin-dependent manner by pushing at the CCS boundary, thus releasing forces opposing the intrinsic curvature of clathrin lattices.
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Affiliation(s)
- Changsong Yang
- grid.25879.310000 0004 1936 8972Department of Biology, University of Pennsylvania, Philadelphia, PA USA
| | - Patricia Colosi
- grid.25879.310000 0004 1936 8972Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Siewert Hugelier
- grid.25879.310000 0004 1936 8972Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Daniel Zabezhinsky
- grid.25879.310000 0004 1936 8972Department of Biology, University of Pennsylvania, Philadelphia, PA USA
| | - Melike Lakadamyali
- grid.25879.310000 0004 1936 8972Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Tatyana Svitkina
- grid.25879.310000 0004 1936 8972Department of Biology, University of Pennsylvania, Philadelphia, PA USA
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12
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Coexistence of vitreous and crystalline phases of H 2O at ambient temperature. Proc Natl Acad Sci U S A 2022; 119:e2117281119. [PMID: 35763575 PMCID: PMC9271169 DOI: 10.1073/pnas.2117281119] [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: 11/18/2022] Open
Abstract
Understanding the phase behavior of H2O is essential in geoscience, extreme biology, biological imaging, chemistry, and physics. Vitreous phases of H2O are of particular importance since these phases avoid the typical expansion of H2O during ice-crystal formation. Here, we confirm the existence of vitreous ice and ice VI in mixed-phase samples of H2O at room temperature and high pressure. We show how Raman scattering and X-ray diffraction alone lead to misleading characterization and understanding of the mixed-phase material, a conclusion supported by molecular dynamics simulations. The coexistence of vitreous and crystalline components of H2O under these conditions is crucial for experimental studies of biological systems. The results have implications for related metastable transitions in other materials under pressure. Formation of vitreous ice during rapid compression of water at room temperature is important for biology and the study of biological systems. Here, we show that Raman spectra of rapidly compressed water at greater than 1 GPa at room temperature exhibits the signature of high-density amorphous ice, whereas the X-ray diffraction (XRD) pattern is dominated by crystalline ice VI. To resolve this apparent contradiction, we used molecular dynamics simulations to calculate full vibrational spectra and diffraction patterns of mixtures of vitreous ice and ice VI, including embedded interfaces between the two phases. We show quantitatively that Raman spectra, which probe the local polarizability with respect to atomic displacements, are dominated by the vitreous phase, whereas a small amount of the crystalline component is readily apparent by XRD. The results of our combined experimental and theoretical studies have implications for detecting vitreous phases of water, survival of biological systems under extreme conditions, and biological imaging. The results provide additional insight into the stable and metastable phases of H2O as a function of pressure and temperature, as well as of other materials undergoing pressure-induced amorphization and other metastable transitions.
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13
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van den Dries K, Fransen J, Cambi A. Fluorescence CLEM in biology: historic developments and current super-resolution applications. FEBS Lett 2022; 596:2486-2496. [PMID: 35674424 DOI: 10.1002/1873-3468.14421] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022]
Abstract
Correlative light and electron microscopy (CLEM) is a powerful imaging approach that allows the direct correlation of information obtained on a light and an electron microscope. There is a growing interest in the application of CLEM in biology, mainly attributable to technical advances in field of fluorescence microscopy in the past two decades. In this review, we summarize the important developments in CLEM for biological applications, focusing on the combination of fluorescence microscopy and electron microscopy. We first provide a brief overview of the early days of fluorescence CLEM usage starting with the initial rise in the late 1970s and the subsequent optimization of CLEM workflows during the following two decades. Next, we describe how the engineering of fluorescent proteins and the development of super-resolution fluorescence microscopy have significantly renewed the interest in CLEM resulting in the present application of fluorescence CLEM in many different areas of cellular and molecular biology. Lastly, we present the promises and challenges for the future of fluorescence CLEM discussing novel workflows, probe development and quantification possibilities.
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Affiliation(s)
- Koen van den Dries
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Jack Fransen
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands.,Microscopic Imaging Center, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Alessandra Cambi
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
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14
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Jeong D, Kim D. Recent Developments in Correlative Super-Resolution Fluorescence Microscopy and Electron Microscopy. Mol Cells 2022; 45:41-50. [PMID: 35114646 PMCID: PMC8819494 DOI: 10.14348/molcells.2021.5011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/31/2021] [Accepted: 12/31/2021] [Indexed: 11/27/2022] Open
Abstract
The recently developed correlative super-resolution fluorescence microscopy (SRM) and electron microscopy (EM) is a hybrid technique that simultaneously obtains the spatial locations of specific molecules with SRM and the context of the cellular ultrastructure by EM. Although the combination of SRM and EM remains challenging owing to the incompatibility of samples prepared for these techniques, the increasing research attention on these methods has led to drastic improvements in their performances and resulted in wide applications. Here, we review the development of correlative SRM and EM (sCLEM) with a focus on the correlation of EM with different SRM techniques. We discuss the limitations of the integration of these two microscopy techniques and how these challenges can be addressed to improve the quality of correlative images. Finally, we address possible future improvements and advances in the continued development and wide application of sCLEM approaches.
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Affiliation(s)
- Dokyung Jeong
- Department of Chemistry, Hanyang University, Seoul 04763, Korea
| | - Doory Kim
- Department of Chemistry, Hanyang University, Seoul 04763, Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Korea
- Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
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15
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Abstract
The cytoskeleton is a complex of detergent-insoluble components of the cytoplasm playing critical roles in cell motility, shape generation, and mechanical properties of a cell. Fibrillar polymers-actin filaments, microtubules, and intermediate filaments-are major constituents of the cytoskeleton, which constantly change their organization during cellular activities. The actin cytoskeleton is especially polymorphic, as actin filaments can form multiple higher-order assemblies performing different functions. Structural information about cytoskeleton organization is critical for understanding its functions and mechanisms underlying various forms of cellular activity. Because of the nanometer-scale thickness of cytoskeletal fibers, electron microscopy (EM) is a key tool to determine the structure of the cytoskeleton.This article describes application of rotary shadowing (or platinum replica ) EM (PREM) for visualization of the cytoskeleton . The procedure is applicable to thin cultured cells growing on glass coverslips and consists of detergent extraction (or mechanical "unroofing") of cells to expose their cytoskeleton , chemical fixation to provide stability, ethanol dehydration and critical point drying to preserve three-dimensionality, rotary shadowing with platinum to create contrast, and carbon coating to stabilize replicas. This technique provides easily interpretable three-dimensional images, in which individual cytoskeletal fibers are clearly resolved and individual proteins can be identified by immunogold labeling. More importantly, PREM is easily compatible with live cell imaging, so that one can correlate the dynamics of a cell or its components, e.g., expressed fluorescent proteins, with high-resolution structural organization of the cytoskeleton in the same cell.
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Affiliation(s)
- Tatyana Svitkina
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
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16
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Clathrin-mediated endocytosis cooperates with bulk endocytosis to generate vesicles. iScience 2022; 25:103809. [PMID: 35198874 PMCID: PMC8841809 DOI: 10.1016/j.isci.2022.103809] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/02/2021] [Accepted: 01/20/2022] [Indexed: 11/25/2022] Open
Abstract
Clathrin-mediated endocytosis, the most prominent endocytic mode, is thought to be generated primarily from relatively flat patches of the plasma membrane. By employing conventional and platinum replica electron microscopy and super-resolution STED microscopy in neuroendocrine chromaffin cells, we found that large Ω-shaped or dome-shaped plasma membrane invaginations, previously thought of as the precursor of bulk endocytosis, are primary sites for clathrin-coated pit generation after depolarization. Clathrin-coated pits are more densely packed at invaginations rather than flat membranes, suggesting that invaginations are preferred sites for clathrin-coated pit formation, likely because their positive curvature facilitates coated-pit formation. Thus, clathrin-mediated endocytosis closely collaborates with bulk endocytosis to enhance endocytic capacity in active secretory cells. This direct collaboration between two classically independent endocytic pathways is of broad importance given the central role of both clathrin-mediated endocytosis and bulk endocytosis in neurons, endocrine cells, immune cells, and many other cell types throughout the body. Bulk membrane invaginations are primary sites for clathrin-coated pit formation Invaginations are preferred over flat membrane for clathrin-coated pit formation Clathrin-coated vesicle formation from membrane invagination is suggested Clathrin-mediated and bulk endocytosis collaborate to enhance endocytic capacity
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17
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Anderson RH, Sochacki KA, Vuppula H, Scott BL, Bailey EM, Schultz MM, Kerkvliet JG, Taraska JW, Hoppe AD, Francis KR. Sterols lower energetic barriers of membrane bending and fission necessary for efficient clathrin-mediated endocytosis. Cell Rep 2021; 37:110008. [PMID: 34788623 PMCID: PMC8620193 DOI: 10.1016/j.celrep.2021.110008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/03/2021] [Accepted: 10/26/2021] [Indexed: 01/16/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) is critical for cellular signal transduction, receptor recycling, and membrane homeostasis in mammalian cells. Acute depletion of cholesterol disrupts CME, motivating analysis of CME dynamics in the context of human disorders of cholesterol metabolism. We report that inhibition of post-squalene cholesterol biosynthesis impairs CME. Imaging of membrane bending dynamics and the CME pit ultrastructure reveals prolonged clathrin pit lifetimes and shallow clathrin-coated structures, suggesting progressive impairment of curvature generation correlates with diminishing sterol abundance. Sterol structural requirements for efficient CME include 3′ polar head group and B-ring conformation, resembling the sterol structural prerequisites for tight lipid packing and polarity. Furthermore, Smith-Lemli-Opitz fibroblasts with low cholesterol abundance exhibit deficits in CME-mediated transferrin internalization. We conclude that sterols lower the energetic costs of membrane bending during pit formation and vesicular scission during CME and suggest that reduced CME activity may contribute to cellular phenotypes observed within disorders of cholesterol metabolism. Anderson et al. demonstrate that sterol abundance and identity play a dominant role in facilitating clathrin-mediated endocytosis. Detailed analyses of clathrin-coated pits under sterol depletion support a requirement for sterol-mediated membrane bending during multiple stages of endocytosis, implicating endocytic dysfunction within the pathogenesis of disorders of cholesterol metabolism.
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Affiliation(s)
- Ruthellen H Anderson
- Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105, USA; Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD 57104, USA
| | - Kem A Sochacki
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Harika Vuppula
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, USA; BioSystems Networks and Translational Research Center, Brookings, SD 57007, USA
| | - Brandon L Scott
- Nanoscience and Nanoengineering, South Dakota School of Mines & Technology, Rapid City, SD 57701, USA
| | - Elizabeth M Bailey
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, USA; BioSystems Networks and Translational Research Center, Brookings, SD 57007, USA
| | - Maycie M Schultz
- Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD 57104, USA
| | - Jason G Kerkvliet
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, USA; BioSystems Networks and Translational Research Center, Brookings, SD 57007, USA
| | - Justin W Taraska
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Adam D Hoppe
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, USA; BioSystems Networks and Translational Research Center, Brookings, SD 57007, USA.
| | - Kevin R Francis
- Cellular Therapies and Stem Cell Biology Group, Sanford Research, Sioux Falls, SD 57104, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105, USA.
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18
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Prasai B, Haber GJ, Strub MP, Ahn R, Ciemniecki JA, Sochacki KA, Taraska JW. The nanoscale molecular morphology of docked exocytic dense-core vesicles in neuroendocrine cells. Nat Commun 2021; 12:3970. [PMID: 34172739 PMCID: PMC8233335 DOI: 10.1038/s41467-021-24167-9] [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: 08/26/2020] [Accepted: 06/04/2021] [Indexed: 12/31/2022] Open
Abstract
Rab-GTPases and their interacting partners are key regulators of secretory vesicle trafficking, docking, and fusion to the plasma membrane in neurons and neuroendocrine cells. Where and how these proteins are positioned and organized with respect to the vesicle and plasma membrane are unknown. Here, we use correlative super-resolution light and platinum replica electron microscopy to map Rab-GTPases (Rab27a and Rab3a) and their effectors (Granuphilin-a, Rabphilin3a, and Rim2) at the nanoscale in 2D. Next, we apply a targetable genetically-encoded electron microscopy labeling method that uses histidine based affinity-tags and metal-binding gold-nanoparticles to determine the 3D axial location of these exocytic proteins and two SNARE proteins (Syntaxin1A and SNAP25) using electron tomography. Rab proteins are distributed across the entire surface and t-SNARE proteins at the base of docked vesicles. We propose that the circumferential distribution of Rabs and Rab-effectors could aid in the efficient transport, capture, docking, and rapid fusion of calcium-triggered exocytic vesicles in excitable cells.
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Affiliation(s)
- Bijeta Prasai
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gideon J Haber
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marie-Paule Strub
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Regina Ahn
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - John A Ciemniecki
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kem A Sochacki
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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19
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Okolo CA, Kounatidis I, Groen J, Nahas KL, Balint S, Fish TM, Koronfel MA, Cortajarena AL, Dobbie IM, Pereiro E, Harkiolaki M. Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures. Nat Protoc 2021; 16:2851-2885. [PMID: 33990802 DOI: 10.1038/s41596-021-00522-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
3D correlative microscopy methods have revolutionized biomedical research, allowing the acquisition of multidimensional information to gain an in-depth understanding of biological systems. With the advent of relevant cryo-preservation methods, correlative imaging of cryogenically preserved samples has led to nanometer resolution imaging (2-50 nm) under harsh imaging regimes such as electron and soft X-ray tomography. These methods have now been combined with conventional and super-resolution fluorescence imaging at cryogenic temperatures to augment information content from a given sample, resulting in the immediate requirement for protocols that facilitate hassle-free, unambiguous cross-correlation between microscopes. We present here sample preparation strategies and a direct comparison of different working fiducialization regimes that facilitate 3D correlation of cryo-structured illumination microscopy and cryo-soft X-ray tomography. Our protocol has been tested at two synchrotron beamlines (B24 at Diamond Light Source in the UK and BL09 Mistral at ALBA in Spain) and has led to the development of a decision aid that facilitates experimental design with the strategic use of markers based on project requirements. This protocol takes between 1.5 h and 3.5 d to complete, depending on the cell populations used (adherent cells may require several days to grow on sample carriers).
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Affiliation(s)
- Chidinma A Okolo
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Ilias Kounatidis
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | | | - Kamal L Nahas
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.,Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Stefan Balint
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Thomas M Fish
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Mohamed A Koronfel
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Ian M Dobbie
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Eva Pereiro
- Beamline 09-MISTRAL, ALBA Synchrotron, Barcelona, Spain
| | - Maria Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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20
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Dahlberg PD, Moerner WE. Cryogenic Super-Resolution Fluorescence and Electron Microscopy Correlated at the Nanoscale. Annu Rev Phys Chem 2021; 72:253-278. [PMID: 33441030 PMCID: PMC8877847 DOI: 10.1146/annurev-physchem-090319-051546] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
We review the emerging method of super-resolved cryogenic correlative light and electron microscopy (srCryoCLEM). Super-resolution (SR) fluorescence microscopy and cryogenic electron tomography (CET) are both powerful techniques for observing subcellular organization, but each approach has unique limitations. The combination of the two brings the single-molecule sensitivity and specificity of SR to the detailed cellular context and molecular scale resolution of CET. The resulting correlative data is more informative than the sum of its parts. The correlative images can be used to pinpoint the positions of fluorescently labeled proteins in the high-resolution context of CET with nanometer-scale precision and/or to identify proteins in electron-dense structures. The execution of srCryoCLEM is challenging and the approach is best described as a method that is still in its infancy with numerous technical challenges. In this review, we describe state-of-the-art srCryoCLEM experiments, discuss the most pressing challenges, and give a brief outlook on future applications.
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Affiliation(s)
- Peter D Dahlberg
- Department of Chemistry, Stanford University, Stanford, California 94305, USA;
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA;
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21
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Sochacki KA, Heine BL, Haber GJ, Jimah JR, Prasai B, Alfonzo-Méndez MA, Roberts AD, Somasundaram A, Hinshaw JE, Taraska JW. The structure and spontaneous curvature of clathrin lattices at the plasma membrane. Dev Cell 2021; 56:1131-1146.e3. [PMID: 33823128 PMCID: PMC8081270 DOI: 10.1016/j.devcel.2021.03.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 01/19/2021] [Accepted: 03/11/2021] [Indexed: 01/10/2023]
Abstract
Clathrin-mediated endocytosis is the primary pathway for receptor and cargo internalization in eukaryotic cells. It is characterized by a polyhedral clathrin lattice that coats budding membranes. The mechanism and control of lattice assembly, curvature, and vesicle formation at the plasma membrane has been a matter of long-standing debate. Here, we use platinum replica and cryoelectron microscopy and tomography to present a structural framework of the pathway. We determine the shape and size parameters common to clathrin-mediated endocytosis. We show that clathrin sites maintain a constant surface area during curvature across multiple cell lines. Flat clathrin is present in all cells and spontaneously curves into coated pits without additional energy sources or recruited factors. Finally, we attribute curvature generation to loosely connected and pentagon-containing flat lattices that can rapidly curve when a flattening force is released. Together, these data present a universal mechanistic model of clathrin-mediated endocytosis.
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Affiliation(s)
- Kem A Sochacki
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Bridgette L Heine
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gideon J Haber
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - John R Jimah
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bijeta Prasai
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marco A Alfonzo-Méndez
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Aleah D Roberts
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Agila Somasundaram
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jenny E Hinshaw
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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22
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Find your coat: Using correlative light and electron microscopy to study intracellular protein coats. Curr Opin Cell Biol 2021; 71:21-28. [PMID: 33684808 DOI: 10.1016/j.ceb.2021.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/14/2022]
Abstract
Protein coats, important for vesicular trafficking in eukaryotic cells, help shape membranes and package cargo. But their dynamic construction cannot be fully understood until the distinct steps of their assembly in their native intracellular context at molecular resolution can be visualized. For this, correlative light and electron microscopy (CLEM) is an essential tool. Here, we discuss how emerging CLEM techniques have been used to study the assembly of protein coats inside cells. We review how current and developing CLEM technologies are poised to answer fundamental questions of protein coat architecture at the nanoscale.
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23
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Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffié J, Manley S, Jungmann R, Sauer M, Lakadamyali M, Zimmer C. Single-molecule localization microscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:39. [PMID: 35663461 PMCID: PMC9160414 DOI: 10.1038/s43586-021-00038-x] [Citation(s) in RCA: 269] [Impact Index Per Article: 89.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM.
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Affiliation(s)
- Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
| | - Melina T. Gyparaki
- Department of Biology, University of Pennsylvania,
Philadelphia, PA, USA
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
- ;
;
;
;
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
- ;
;
;
;
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
- ;
;
;
;
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- ;
;
;
;
| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
- ;
;
;
;
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24
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Roberts AD, Davenport TM, Dickey AM, Ahn R, Sochacki KA, Taraska JW. Structurally distinct endocytic pathways for B cell receptors in B lymphocytes. Mol Biol Cell 2020; 31:2826-2840. [PMID: 33085561 PMCID: PMC7851864 DOI: 10.1091/mbc.e20-08-0532] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
B lymphocytes play a critical role in adaptive immunity. On antigen binding, B cell receptors (BCR) cluster on the plasma membrane and are internalized by endocytosis. In this process, B cells capture diverse antigens in various contexts and concentrations. However, it is unclear whether the mechanism of BCR endocytosis changes in response to these factors. Here, we studied the mechanism of soluble antigen-induced BCR clustering and internalization in a cultured human B cell line using correlative superresolution fluorescence and platinum replica electron microscopy. First, by visualizing nanoscale BCR clusters, we provide direct evidence that BCR cluster size increases with F(ab’)2 concentration. Next, we show that the physical mechanism of internalization switches in response to BCR cluster size. At low concentrations of antigen, B cells internalize small BCR clusters by classical clathrin-mediated endocytosis. At high antigen concentrations, when cluster size increases beyond the size of a single clathrin-coated pit, B cells retrieve receptor clusters using large invaginations of the plasma membrane capped with clathrin. At these sites, we observed early and sustained recruitment of actin and an actin polymerizing protein FCHSD2. We further show that actin recruitment is required for the efficient generation of these novel endocytic carriers and for their capture into the cytosol. We propose that in B cells, the mechanism of endocytosis switches to accommodate large receptor clusters formed when cells encounter high concentrations of soluble antigen. This mechanism is regulated by the organization and dynamics of the cortical actin cytoskeleton.
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Affiliation(s)
- Aleah D Roberts
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Thaddeus M Davenport
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Andrea M Dickey
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Regina Ahn
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Kem A Sochacki
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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25
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Abstract
Correlative light and electron microscopy (CLEM) combines the strengths of light microscopy (LM) and electron microscopy (EM) to pin-point and visualize cellular or macromolecular structures. However, there are many different imaging modalities that can be combined in a CLEM workflow, creating a vast number of combinations that can overwhelm new-comers to the field. Here, we offer a conceptual framework to help guide the decision-making process for choosing the CLEM workflow that can best address your research question, based on the answer to five questions.
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26
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An accelerated procedure for approaching and imaging of optically branded region of interest in tissue. Methods Cell Biol 2020; 162:205-221. [PMID: 33707013 DOI: 10.1016/bs.mcb.2020.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Many areas of biology have benefited from advances in light microscopy (LM). However, one limitation of the LM approach is that numerous critically important aspects of subcellular machineries are well beyond the resolution of conventional LM. For studying these, electron microscopy (EM) remains the technique of choice to visualize and identify macromolecules at the ultrastructural level. The most powerful approach is combining both techniques, LM and EM (i.e., to apply correlative light/electron microscopy, CLEM) to image exactly the same region of interest. This combination allows, for example, to immuno-localize proteins by LM and then to visualize the ultrastructural context of the same region of the sample. However, the identification and correlation of the regions of interest (ROIs) at the levels of LM and EM remains a major challenge, mostly due to the difficulties with correlation along the Z-axis for both modalities. In this chapter, we address this difficulty and describe an approach for performing CLEM in tissue samples using marks from near-infrared branding as indicators of a ROI, and then using serial block face-scanning electron microscopy (SBF-SEM) to identify and approach this ROI. Once a ROI has been approached, serial sections are collected on grids for high-resolution imaging by transmission EM, and subsequent correlation with LM images showing labeled proteins.
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27
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Wagner FR, Watanabe R, Schampers R, Singh D, Persoon H, Schaffer M, Fruhstorfer P, Plitzko J, Villa E. Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography. Nat Protoc 2020; 15:2041-2070. [PMID: 32405053 PMCID: PMC8053421 DOI: 10.1038/s41596-020-0320-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/06/2020] [Indexed: 12/31/2022]
Abstract
Recent advances have made cryogenic (cryo) electron microscopy a key technique to achieve near-atomic-resolution structures of biochemically isolated macromolecular complexes. Cryo-electron tomography (cryo-ET) can give unprecedented insight into these complexes in the context of their natural environment. However, the application of cryo-ET is limited to samples that are thinner than most cells, thereby considerably reducing its applicability. Cryo-focused-ion-beam (cryo-FIB) milling has been used to carve (micromachining) out 100-250-nm-thin regions (called lamella) in the intact frozen cells. This procedure opens a window into the cells for high-resolution cryo-ET and structure determination of biomolecules in their native environment. Further combination with fluorescence microscopy allows users to determine cells or regions of interest for the targeted fabrication of lamellae and cryo-ET imaging. Here, we describe how to prepare lamellae using a microscope equipped with both FIB and scanning electron microscopy modalities. Such microscopes (Aquilos Cryo-FIB/Scios/Helios or CrossBeam) are routinely referred to as dual-beam microscopes, and they are equipped with a cryo-stage for all operations in cryogenic conditions. The basic principle of the described methodologies is also applicable for other types of dual-beam microscopes equipped with a cryo-stage. We also briefly describe how to integrate fluorescence microscopy data for targeted milling and critical considerations for cryo-ET data acquisition of the lamellae. Users familiar with cryo-electron microscopy who get basic training in dual-beam microscopy can complete the protocol within 2-3 d, allowing for several pause points during the procedure.
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Affiliation(s)
- Felix R Wagner
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Reika Watanabe
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Digvijay Singh
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Hans Persoon
- Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Peter Fruhstorfer
- Thermo Fisher Scientific, Eindhoven, the Netherlands
- Eppendorf AG, Hamburg, Germany
| | - Jürgen Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elizabeth Villa
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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28
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Jun S, Ro HJ, Bharda A, Kim SI, Jeoung D, Jung HS. Advances in Cryo-Correlative Light and Electron Microscopy: Applications for Studying Molecular and Cellular Events. Protein J 2020; 38:609-615. [PMID: 31396855 DOI: 10.1007/s10930-019-09856-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cryo-correlative light and electron microscopy (Cryo-CLEM) is materializing as a widespread approach amalgamating the advantages of both fluorescence light microscopy (FLM) as well as three dimensional (3D) cryo-electron tomography (cryo-ET) to reveal the ultrastructure of significant target molecules with specific cellular functions. Cryo-CLEM allows imaging of cells by means of fluorescence microscopy exhibiting the location of the destined molecule at high temporal and spatial resolution while cryo-ET is employed to analyze the 3D structure at a molecular resolution in close-to-physiological condition. Present review focuses upon the practical strategies for Cryo-CLEM and recent technical developments that will assist the broad implementation of this technique to investigate and answer questions pertaining to various biological events occurring in the cell.
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Affiliation(s)
- Sangmi Jun
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea. .,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea. .,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea.
| | - Hyun-Joo Ro
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Anahita Bharda
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea
| | - Seung Il Kim
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Dooil Jeoung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea.
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29
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Huang R, Feng FP, Huang CH, Mao L, Tang M, Yan ZY, Shao B, Qin L, Xu T, Xue YH, Zhu BZ. Chiral Os(II) Polypyridyl Complexes as Enantioselective Nuclear DNA Imaging Agents Especially Suitable for Correlative High-Resolution Light and Electron Microscopy Studies. ACS APPLIED MATERIALS & INTERFACES 2020; 12:3465-3473. [PMID: 31913004 DOI: 10.1021/acsami.9b19776] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The high-resolution technique transmission electron microscopy (TEM), with OsO4 as the traditional fixative, is an essential tool for cell biology and medicine. Although OsO4 has been extensively used, it is far from perfect because of its high volatility and toxicity. Os(II) polypyridyl complexes like [Os(phen)2(dppz)]2+ (phen = 1,10-phenanthroline; dppz = dipyridophenazine) are not only the well-known molecular DNA "light-switches" but also the potential ideal candidates for TEM studies. Here, we report that the cell-impermeable cationic [Os(phen)2(dppz)]2+ can be preferentially delivered into the live-cell nucleus through ion-pairing with chlorophenolate counter-anions, where it functions as an unparalleled enantioselective nuclear DNA imaging reagent especially suitable for correlative light and electron microscopy (CLEM) studies in both living and fixed cells, which can clearly visualize chromosome aggregation and decondensation during mitosis simultaneously. We propose that the chiral Os(II) polypyridyl complexes can be used as a distinctive group of enantioselective high-resolution CLEM imaging probes for live-cell nuclear DNA studies.
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Affiliation(s)
- Rong Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Feng-Ping Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
| | - Chun-Hua Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Li Mao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Miao Tang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zhu-Ying Yan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Bo Shao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Li Qin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Tao Xu
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
| | - Yan-Hong Xue
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
| | - Ben-Zhan Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
- Joint Institute for Environmental Science , Research Center for Eco-Environmental Sciences and Hong Kong Baptist University , Kowloon 999077 , Hong Kong
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30
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Hoffman DP, Shtengel G, Xu CS, Campbell KR, Freeman M, Wang L, Milkie DE, Pasolli HA, Iyer N, Bogovic JA, Stabley DR, Shirinifard A, Pang S, Peale D, Schaefer K, Pomp W, Chang CL, Lippincott-Schwartz J, Kirchhausen T, Solecki DJ, Betzig E, Hess HF. Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. Science 2020; 367:eaaz5357. [PMID: 31949053 PMCID: PMC7339343 DOI: 10.1126/science.aaz5357] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/20/2019] [Indexed: 12/27/2022]
Abstract
Within cells, the spatial compartmentalization of thousands of distinct proteins serves a multitude of diverse biochemical needs. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) can elucidate protein spatial relationships to global ultrastructure, but has suffered from tradeoffs of structure preservation, fluorescence retention, resolution, and field of view. We developed a platform for three-dimensional cryogenic SR and focused ion beam-milled block-face EM across entire vitreously frozen cells. The approach preserves ultrastructure while enabling independent SR and EM workflow optimization. We discovered unexpected protein-ultrastructure relationships in mammalian cells including intranuclear vesicles containing endoplasmic reticulum-associated proteins, web-like adhesions between cultured neurons, and chromatin domains subclassified on the basis of transcriptional activity. Our findings illustrate the value of a comprehensive multimodal view of ultrastructural variability across whole cells.
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Affiliation(s)
- David P Hoffman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Gleb Shtengel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Kirby R Campbell
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Melanie Freeman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Lei Wang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - H Amalia Pasolli
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Nirmala Iyer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - John A Bogovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Daniel R Stabley
- Neuroimaging Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Abbas Shirinifard
- Bioimage Analysis Core, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Song Pang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - David Peale
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Kathy Schaefer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Wim Pomp
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Chi-Lun Chang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | | | - Tom Kirchhausen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - David J Solecki
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Physics, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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31
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Vassilopoulos S, Gibaud S, Jimenez A, Caillol G, Leterrier C. Ultrastructure of the axonal periodic scaffold reveals a braid-like organization of actin rings. Nat Commun 2019; 10:5803. [PMID: 31862971 PMCID: PMC6925202 DOI: 10.1038/s41467-019-13835-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022] Open
Abstract
Recent super-resolution microscopy studies have unveiled a periodic scaffold of actin rings regularly spaced by spectrins under the plasma membrane of axons. However, ultrastructural details are unknown, limiting a molecular and mechanistic understanding of these enigmatic structures. Here, we combine platinum-replica electron and optical super-resolution microscopy to investigate the cortical cytoskeleton of axons at the ultrastructural level. Immunogold labeling and correlative super-resolution/electron microscopy allow us to unambiguously resolve actin rings as braids made of two long, intertwined actin filaments connected by a dense mesh of aligned spectrins. This molecular arrangement contrasts with the currently assumed model of actin rings made of short, capped actin filaments. Along the proximal axon, we resolved the presence of phospho-myosin light chain and the scaffold connection with microtubules via ankyrin G. We propose that braided rings explain the observed stability of the actin-spectrin scaffold and ultimately participate in preserving the axon integrity.
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Affiliation(s)
- Stéphane Vassilopoulos
- Sorbonne Université, INSERM, Institute of Myology, Centre of Research in Myology, UMRS 974, Paris, France.
| | - Solène Gibaud
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | - Angélique Jimenez
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | - Ghislaine Caillol
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
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32
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Interferometric fluorescence cross correlation spectroscopy. PLoS One 2019; 14:e0225797. [PMID: 31851670 PMCID: PMC6919592 DOI: 10.1371/journal.pone.0225797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/12/2019] [Indexed: 11/20/2022] Open
Abstract
Measuring transport properties like diffusion and directional flow is essential for understanding dynamics within heterogeneous systems including living cells and novel materials. Fluorescent molecules traveling within these inhomogeneous environments under the forces of Brownian motion and flow exhibit fluctuations in their concentration, which are directly linked to the transport properties. We present a method utilizing single photon interference and fluorescence correlation spectroscopy (FCS) to simultaneously measure transport of fluorescent molecules within aqueous samples. Our method, within seconds, measures transport in thousands of homogenous voxels (100 nm)3 and under certain conditions, eliminates photo-physical artifacts associated with blinking of fluorescent molecules. A comprehensive theoretical framework is presented and validated by measuring transport of quantum dots, associated with VSV-G receptor along cellular membranes as well as within viscous gels.
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33
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Chen Y, Yong J, Martínez-Sánchez A, Yang Y, Wu Y, De Camilli P, Fernández-Busnadiego R, Wu M. Dynamic instability of clathrin assembly provides proofreading control for endocytosis. J Cell Biol 2019; 218:3200-3211. [PMID: 31451612 PMCID: PMC6781453 DOI: 10.1083/jcb.201804136] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/03/2019] [Accepted: 08/01/2019] [Indexed: 12/18/2022] Open
Abstract
Chen et al. reconstitute endocytosis in a cell-free system and show that cargo sorting requires the dynamic dissociation of clathrin during the growth phase of the clathrin-coated pit formation. Clathrin-mediated endocytosis depends on the formation of functional clathrin-coated pits that recruit cargos and mediate the uptake of those cargos into the cell. However, it remains unclear whether the cargos in the growing clathrin-coated pits are actively monitored by the coat assembly machinery. Using a cell-free reconstitution system, we report that clathrin coat formation and cargo sorting can be uncoupled, indicating that a checkpoint is required for functional cargo incorporation. We demonstrate that the ATPase Hsc70 and a dynamic exchange of clathrin during assembly are required for this checkpoint. In the absence of Hsc70 function, clathrin assembles into pits but fails to enrich cargo. Using single-molecule imaging, we further show that uncoating takes place throughout the lifetime of the growing clathrin-coated pits. Our results suggest that the dynamic exchange of clathrin, at the cost of the reduced overall assembly rates, primarily serves as a proofreading mechanism for quality control of endocytosis.
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Affiliation(s)
- Yan Chen
- Centre for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore
| | - Jeffery Yong
- Centre for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore
| | | | - Yang Yang
- Centre for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore
| | - Yumei Wu
- Howard Hughes Medical Institute, Department of Cell Biology and Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
| | - Pietro De Camilli
- Howard Hughes Medical Institute, Department of Cell Biology and Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
| | - Rubén Fernández-Busnadiego
- Max Planck Institute for Biochemistry, Martinsried, Germany.,Department of Neuropathology, University Medical Center, Georg-August University Göttingen, Göttingen, Germany
| | - Min Wu
- Centre for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore .,Mechanobiology Institute, National University of Singapore, Singapore
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34
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Taraska JW. A primer on resolving the nanoscale structure of the plasma membrane with light and electron microscopy. J Gen Physiol 2019; 151:974-985. [PMID: 31253697 PMCID: PMC6683668 DOI: 10.1085/jgp.201812227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Taraska reviews the imaging methods that are being used to understand the structure of the plasma membrane at the molecular level. The plasma membrane separates a cell from its external environment. All materials and signals that enter or leave the cell must cross this hydrophobic barrier. Understanding the architecture and dynamics of the plasma membrane has been a central focus of general cellular physiology. Both light and electron microscopy have been fundamental in this endeavor and have been used to reveal the dense, complex, and dynamic nanoscale landscape of the plasma membrane. Here, I review classic and recent developments in the methods used to image and study the structure of the plasma membrane, particularly light, electron, and correlative microscopies. I will discuss their history and use for mapping the plasma membrane and focus on how these tools have provided a structural framework for understanding the membrane at the scale of molecules. Finally, I will describe how these studies provide a roadmap for determining the nanoscale architecture of other organelles and entire cells in order to bridge the gap between cellular form and function.
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Affiliation(s)
- Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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35
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Reinhard S, Aufmkolk S, Sauer M, Doose S. Registration and Visualization of Correlative Super-Resolution Microscopy Data. Biophys J 2019; 116:2073-2078. [PMID: 31103233 DOI: 10.1016/j.bpj.2019.04.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 11/28/2022] Open
Abstract
We introduce a method for registration and visualization of correlative super-resolution microscopy images from different microscopy techniques. We established an automated registration procedure based on the generalized Hough transform. We developed a software tool to apply this algorithm and visualize correlated images from structured illumination microscopy (SIM) and direct stochastic optical reconstruction microscopy (dSTORM). To demonstrate the potential of this super-resolution correlator, we visualize the distribution of the presynaptic protein bassoon in the active zones of synapses in the molecular layer of the mouse cerebellum. First, a multiple labeled sample is imaged by SIM, followed by imaging of one of the fluorescent labels by dSTORM. To avoid the use of artificial fiducial markers, we used the signal of Alexa Fluor 647 recorded in switching buffer on the two microscopes for image superposition. We recorded multicolor SIM images in 20-μm thick brain slices to identify synapses in the dendritic system of Purkinje cells and put higher-resolved dSTORM images of the synaptic distribution of bassoon in registry.
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Affiliation(s)
- Sebastian Reinhard
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany
| | - Sarah Aufmkolk
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany; Department of Neurology & Neurosurgery, Montréal Neurological Institute, Montréal, Québec, Canada; Department of Chemistry, McGill University, Montréal, Québec, Canada
| | - Markus Sauer
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany.
| | - Sören Doose
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany.
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36
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Prigozhin MB, Maurer PC, Courtis AM, Liu N, Wisser MD, Siefe C, Tian B, Chan E, Song G, Fischer S, Aloni S, Ogletree DF, Barnard ES, Joubert LM, Rao J, Alivisatos AP, Macfarlane RM, Cohen BE, Cui Y, Dionne JA, Chu S. Bright sub-20-nm cathodoluminescent nanoprobes for electron microscopy. NATURE NANOTECHNOLOGY 2019; 14:420-425. [PMID: 30833691 PMCID: PMC6786485 DOI: 10.1038/s41565-019-0395-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/28/2019] [Indexed: 05/19/2023]
Abstract
Electron microscopy has been instrumental in our understanding of complex biological systems. Although electron microscopy reveals cellular morphology with nanoscale resolution, it does not provide information on the location of different types of proteins. An electron-microscopy-based bioimaging technology capable of localizing individual proteins and resolving protein-protein interactions with respect to cellular ultrastructure would provide important insights into the molecular biology of a cell. Here, we synthesize small lanthanide-doped nanoparticles and measure the absolute photon emission rate of individual nanoparticles resulting from a given electron excitation flux (cathodoluminescence). Our results suggest that the optimization of nanoparticle composition, synthesis protocols and electron imaging conditions can lead to sub-20-nm nanolabels that would enable high signal-to-noise localization of individual biomolecules within a cellular context. In ensemble measurements, these labels exhibit narrow spectra of nine distinct colours, so the imaging of biomolecules in a multicolour electron microscopy modality may be possible.
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Affiliation(s)
| | - Peter C Maurer
- Department of Physics, Stanford University, Stanford, CA, USA
| | - Alexandra M Courtis
- Department of Chemistry, University of California at Berkeley, Berkeley, CA, USA
| | - Nian Liu
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Michael D Wisser
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Chris Siefe
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Bining Tian
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emory Chan
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guosheng Song
- Department of Radiology, Stanford University, Stanford, CA, USA
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Stefan Fischer
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Shaul Aloni
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - D Frank Ogletree
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Edward S Barnard
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Lydia-Marie Joubert
- CSIF Beckman Center, Stanford University, Stanford, CA, USA
- EM Unit, Central Analytical Facilities, Stellenbosch University, Stellenbosch, South Africa
| | - Jianghong Rao
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - A Paul Alivisatos
- Department of Chemistry, University of California at Berkeley, Berkeley, CA, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Materials Science and Engineering, University of California, Berkeley, CA, USA
- Kavli Energy NanoScience Institute, Berkeley, CA, USA
| | | | - Bruce E Cohen
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yi Cui
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Jennifer A Dionne
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Steven Chu
- Department of Physics, Stanford University, Stanford, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.
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37
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Ali T, Bednarska J, Vassilopoulos S, Tran M, Diakonov IA, Ziyadeh-Isleem A, Guicheney P, Gorelik J, Korchev YE, Reilly MM, Bitoun M, Shevchuk A. Correlative SICM-FCM reveals changes in morphology and kinetics of endocytic pits induced by disease-associated mutations in dynamin. FASEB J 2019; 33:8504-8518. [PMID: 31017801 PMCID: PMC6593877 DOI: 10.1096/fj.201802635r] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Dynamin 2 (DNM2) is a GTP-binding protein that controls endocytic vesicle scission and defines a whole class of dynamin-dependent endocytosis, including clathrin-mediated endocytosis by caveoli. It has been suggested that mutations in the DNM2 gene, associated with 3 inherited diseases, disrupt endocytosis. However, how exactly mutations affect the nanoscale morphology of endocytic machinery has never been studied. In this paper, we used live correlative scanning ion conductance microscopy (SICM) and fluorescence confocal microscopy (FCM) to study how disease-associated mutations affect the morphology and kinetics of clathrin-coated pits (CCPs) by directly following their dynamics of formation, maturation, and internalization in skin fibroblasts from patients with centronuclear myopathy (CNM) and in Cos-7 cells expressing corresponding dynamin mutants. Using SICM-FCM, which we have developed, we show how p.R465W mutation disrupts pit structure, preventing its maturation and internalization, and significantly increases the lifetime of CCPs. Differently, p.R522H slows down the formation of CCPs without affecting their internalization. We also found that CNM mutations in DNM2 affect the distribution of caveoli and reduce dorsal ruffling in human skin fibroblasts. Collectively, our SICM-FCM findings at single CCP level, backed up by electron microscopy data, argue for the impairment of several forms of endocytosis in DNM2-linked CNM.-Ali, T., Bednarska, J., Vassilopoulos, S., Tran, M., Diakonov, I. A., Ziyadeh-Isleem, A., Guicheney, P., Gorelik, J., Korchev, Y. E., Reilly, M. M., Bitoun, M., Shevchuk, A. Correlative SICM-FCM reveals changes in morphology and kinetics of endocytic pits induced by disease-associated mutations in dynamin.
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Affiliation(s)
- Tayyibah Ali
- Division of Experimental Medicine, Department of Medicine, Imperial College London, London, United Kingdom
| | - Joanna Bednarska
- Division of Experimental Medicine, Department of Medicine, Imperial College London, London, United Kingdom
| | - Stéphane Vassilopoulos
- Research Center for Myology, Institut de Myologie, UMRS 974, INSERM, Sorbonne Université, Paris, France
| | - Martin Tran
- Division of Experimental Medicine, Department of Medicine, Imperial College London, London, United Kingdom
| | - Ivan A Diakonov
- Department of Cardiac Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Azza Ziyadeh-Isleem
- UMRS 1166, INSERM, Institute of Cardiometabolism and Nutrition (ICAN), Paris, France.,UMRS 1166, Sorbonne Universités-Pierre and Marie Curie University (UPMC), Paris, France
| | - Pascale Guicheney
- UMRS 1166, INSERM, Institute of Cardiometabolism and Nutrition (ICAN), Paris, France.,UMRS 1166, Sorbonne Universités-Pierre and Marie Curie University (UPMC), Paris, France
| | - Julia Gorelik
- Department of Cardiac Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Yuri E Korchev
- Division of Experimental Medicine, Department of Medicine, Imperial College London, London, United Kingdom
| | - Mary M Reilly
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square London, United Kingdom
| | - Marc Bitoun
- Research Center for Myology, Institut de Myologie, UMRS 974, INSERM, Sorbonne Université, Paris, France
| | - Andrew Shevchuk
- Division of Experimental Medicine, Department of Medicine, Imperial College London, London, United Kingdom
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38
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Krystofiak ES, Heymann JB, Kachar B. Carbon replicas reveal double stranded structure of tight junctions in phase-contrast electron microscopy. Commun Biol 2019; 2:98. [PMID: 30886907 PMCID: PMC6414538 DOI: 10.1038/s42003-019-0319-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
Replica-based freeze-fracture and freeze-etching electron microscopy methods provide surface topography information, particularly suited to studying membrane protein complexes in their native context. The fidelity and resolution of metal replicas is limited by the inherent property of metal atoms to crystallize. To overcome the limitations of metal replicas, we combined amorphous carbon replicas with phase-contrast electron microscopy. Using this approach, tight junction intramembrane fibrils were shown to have a double stranded morphology.
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Affiliation(s)
- Evan S Krystofiak
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA.,Cell Imaging Shared Resource, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - J Bernard Heymann
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bechara Kachar
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA.
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39
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Mohammadian S, Fokkema J, Agronskaia AV, Liv N, de Heus C, van Donselaar E, Blab GA, Klumperman J, Gerritsen HC. High accuracy, fiducial marker-based image registration of correlative microscopy images. Sci Rep 2019; 9:3211. [PMID: 30824844 PMCID: PMC6397213 DOI: 10.1038/s41598-019-40098-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 01/28/2019] [Indexed: 12/03/2022] Open
Abstract
Fluorescence microscopy (FM) and electron microscopy (EM) are complementary techniques. FM affords examination of large fields of view and identifying regions of interest but has a low resolution. EM exhibits excellent resolution over a limited field of view. The combination of these two techniques, correlative microscopy, received considerable interest in the past years and has proven its potential in biology and material science. Accurate correlation of FM and EM images is, however, challenging due to the differences in contrast mechanism, size of field of view and resolution. We report an accurate, fast and robust method to correlate FM and EM images using low densities of fiducial markers. Here, 120 nm diameter fiducial markers consisting of fluorescently labelled silica coated gold nanoparticles are used. The method relies on recording FM, low magnification EM and high magnification EM images. Two linear transformation matrices are constructed, FM to low magnification EM and low magnification EM to high magnification EM. Combination of these matrices results in a high accuracy transformation of FM to high magnification EM coordinates. The method was tested using two different transmission electron microscopes and different Tokuyasu and Lowicryl sections. The overall accuracy of the correlation method is high, 5-30 nm.
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Affiliation(s)
- Sajjad Mohammadian
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Jantina Fokkema
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Alexandra V Agronskaia
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cecilia de Heus
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elly van Donselaar
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gerhard A Blab
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hans C Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
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40
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Pujals S, Feiner-Gracia N, Delcanale P, Voets I, Albertazzi L. Super-resolution microscopy as a powerful tool to study complex synthetic materials. Nat Rev Chem 2019. [DOI: 10.1038/s41570-018-0070-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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41
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Galvanetto N. Single-cell unroofing: probing topology and nanomechanics of native membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2532-2538. [DOI: 10.1016/j.bbamem.2018.09.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/19/2018] [Accepted: 09/26/2018] [Indexed: 10/28/2022]
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42
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Baumgart F, Arnold AM, Rossboth BK, Brameshuber M, Schütz GJ. What we talk about when we talk about nanoclusters. Methods Appl Fluoresc 2018; 7:013001. [PMID: 30412469 DOI: 10.1088/2050-6120/aaed0f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Superresolution microscopy results have sparked the idea that many membrane proteins are not randomly distributed across the plasma membrane but are instead arranged in nanoclusters. Frequently, these new results seemed to confirm older data based on biochemical and electron microscopy experiments. Recently, however, it was recognized that multiple countings of the very same fluorescently labeled protein molecule can be easily confused with true protein clusters. Various strategies have been developed, which are intended to solve the problem of discriminating true protein clusters from imaging artifacts. We believe that there is currently no perfect algorithm for this problem; instead, different approaches have different strengths and weaknesses. In this review, we discuss single molecule localization microscopy in view of its ability to detect nanoclusters of membrane proteins. To capture the different views on nanoclustering, we chose an unconventional style for this article: we placed its scientific content in the setting of a fictive conference, where five researchers from different fields discuss the problem of detecting and quantifying nanoclusters. Using this style, we feel that the different approaches common for different research areas can be well illustrated. Similarities to a short story by Raymond Carver are not unintentional.
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43
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Joosten B, Willemse M, Fransen J, Cambi A, van den Dries K. Super-Resolution Correlative Light and Electron Microscopy (SR-CLEM) Reveals Novel Ultrastructural Insights Into Dendritic Cell Podosomes. Front Immunol 2018; 9:1908. [PMID: 30186284 PMCID: PMC6113363 DOI: 10.3389/fimmu.2018.01908] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/02/2018] [Indexed: 12/17/2022] Open
Abstract
Podosomes are multimolecular cytoskeletal structures that coordinate the migration of tissue-resident dendritic cells (DCs). They consist of a protrusive actin-rich core and an adhesive integrin-rich ring that contains adaptor proteins such as vinculin and zyxin. Individual podosomes are typically interconnected by a dense network of actin filaments giving rise to large podosome clusters. The actin density in podosome clusters complicates the analysis of podosomes by light microscopy alone. Here, we present an optimized procedure for performing super-resolution correlative light and electron microscopy (SR-CLEM) to study the organization of multiple proteins with respect to actin in podosome clusters at the ventral plasma membrane of DCs. We demonstrate that our procedure is suited to correlate at least three colors in super-resolution Airyscan microscopy with scanning electron microscopy (SEM). Using this procedure, we first reveal an intriguing complexity in the organization of ventral and radiating actin filaments in clusters formed by DCs which was not properly detected before by light microscopy alone. Next, we demonstrate a differential organization of vinculin and zyxin with respect to the actin filaments at podosomes. While vinculin mostly resides at sites where the actin filaments connect to the cell membrane, zyxin is primarily associated with filaments close to and on top of the core. Finally, we reveal a novel actin-based structure with SEM that connects closely associated podosome cores and which may be important for podosome topography sensing. Interestingly, these interpodosomal connections, in contrast to the radiating and ventral actin filaments appear to be insensitive to inhibition of actin polymerization suggesting that these pools of actin are not dynamically coupled. Together, our work demonstrates the power of correlating different imaging modalities for studying multimolecular cellular structures and could potentially be further exploited to study processes at the ventral plasma membrane of immune cells such as clathrin-mediated endocytosis or immune synapse formation.
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Affiliation(s)
- Ben Joosten
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marieke Willemse
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Microscopic Imaging Center, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jack Fransen
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Microscopic Imaging Center, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alessandra Cambi
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Koen van den Dries
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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44
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Picco A, Kaksonen M. Quantitative imaging of clathrin-mediated endocytosis. Curr Opin Cell Biol 2018; 53:105-110. [PMID: 30025292 DOI: 10.1016/j.ceb.2018.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/24/2018] [Accepted: 06/11/2018] [Indexed: 11/29/2022]
Abstract
Clathrin-mediated endocytosis is a process by which eukaryotic cells bend a small region of their plasma membrane to form a transport vesicle that carries specific cargo molecules into the cell. Endocytosis controls the composition of the plasma membrane, imports nutrients and regulates many signalling pathways. The roles of most of the proteins involved in endocytosis have been thoroughly characterised. However, how these proteins cooperate in the cell to drive the endocytic process is not well understood. Microscopy methods have been instrumental in describing the dynamics and the molecular mechanism of endocytosis. Here, we will review the challenges and the recent advances in visualising the endocytic machinery and we will reflect on how the integration of current imaging technologies can lead us toward a quantitative understanding of the molecular mechanisms of endocytosis.
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Affiliation(s)
- Andrea Picco
- Department of Biochemistry and NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Marko Kaksonen
- Department of Biochemistry and NCCR Chemical Biology, University of Geneva, Geneva, Switzerland.
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45
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Clarke NI, Royle SJ. FerriTag is a new genetically-encoded inducible tag for correlative light-electron microscopy. Nat Commun 2018; 9:2604. [PMID: 29973588 PMCID: PMC6031641 DOI: 10.1038/s41467-018-04993-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 05/24/2018] [Indexed: 01/20/2023] Open
Abstract
A current challenge is to develop tags to precisely visualize proteins in cells by light and electron microscopy. Here, we introduce FerriTag, a genetically-encoded chemically-inducible tag for correlative light-electron microscopy. FerriTag is a fluorescent recombinant electron-dense ferritin particle that can be attached to a protein-of-interest using rapamycin-induced heterodimerization. We demonstrate the utility of FerriTag for correlative light-electron microscopy by labeling proteins associated with various intracellular structures including mitochondria, plasma membrane, and clathrin-coated pits and vesicles. FerriTagging has a good signal-to-noise ratio and a labeling resolution of approximately 10 nm. We demonstrate how FerriTagging allows nanoscale mapping of protein location relative to a subcellular structure, and use it to detail the distribution and conformation of huntingtin-interacting protein 1 related (HIP1R) in and around clathrin-coated pits.
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Affiliation(s)
- Nicholas I Clarke
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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46
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van Elsland DM, Pujals S, Bakkum T, Bos E, Oikonomeas‐Koppasis N, Berlin I, Neefjes J, Meijer AH, Koster AJ, Albertazzi L, van Kasteren SI. Ultrastructural Imaging of Salmonella-Host Interactions Using Super-resolution Correlative Light-Electron Microscopy of Bioorthogonal Pathogens. Chembiochem 2018; 19:1766-1770. [PMID: 29869826 PMCID: PMC6120560 DOI: 10.1002/cbic.201800230] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Indexed: 01/06/2023]
Abstract
The imaging of intracellular pathogens inside host cells is complicated by the low resolution and sensitivity of fluorescence microscopy and by the lack of ultrastructural information to visualize the pathogens. Herein, we present a new method to visualize these pathogens during infection that circumvents these problems: by using a metabolic hijacking approach to bioorthogonally label the intracellular pathogen Salmonella Typhimurium and by using these bioorthogonal groups to introduce fluorophores compatible with stochastic optical reconstruction microscopy (STORM) and placing this in a correlative light electron microscopy (CLEM) workflow, the pathogen can be imaged within its host cell context Typhimurium with a resolution of 20 nm. This STORM-CLEM approach thus presents a new approach to understand these pathogens during infection.
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Affiliation(s)
- Daphne M. van Elsland
- Leiden Institute of Chemistry andThe Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 55, 2333CCLeidenThe Netherlands
- Department of Cell and Chemical BiologyInstitute for Chemical ImmunologyLeiden University Medical Center LUMCEinthovenweg 222333 ZCLeidenThe Netherlands
| | - Sílvia Pujals
- Department of Nanoscopy for NanomedicineInstitute of Bioengineering of Catalonia (IBEC)Barcelona Institute of Science and Technology08028BarcelonaSpain
| | - Thomas Bakkum
- Leiden Institute of Chemistry andThe Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 55, 2333CCLeidenThe Netherlands
| | - Erik Bos
- Department of Electron MicroscopyLeiden University Medical Center LUMCEinthovenweg 222333 ZCLeidenThe Netherlands
| | - Nikolaos Oikonomeas‐Koppasis
- Leiden Institute of Chemistry andThe Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 55, 2333CCLeidenThe Netherlands
| | - Ilana Berlin
- Department of Cell and Chemical BiologyInstitute for Chemical ImmunologyLeiden University Medical Center LUMCEinthovenweg 222333 ZCLeidenThe Netherlands
| | - Jacques Neefjes
- Department of Cell and Chemical BiologyInstitute for Chemical ImmunologyLeiden University Medical Center LUMCEinthovenweg 222333 ZCLeidenThe Netherlands
| | - Annemarie H. Meijer
- Institute of Biology LeidenLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - Abraham J. Koster
- Department of Electron MicroscopyLeiden University Medical Center LUMCEinthovenweg 222333 ZCLeidenThe Netherlands
| | - Lorenzo Albertazzi
- Department of Nanoscopy for NanomedicineInstitute of Bioengineering of Catalonia (IBEC)Barcelona Institute of Science and Technology08028BarcelonaSpain
- Department of Biomedical Engineering and Institute of Complex Molecular SystemsEindhoven University of Technology5600 MBEindhovenThe Netherlands
| | - Sander I. van Kasteren
- Leiden Institute of Chemistry andThe Institute for Chemical ImmunologyLeiden UniversityEinsteinweg 55, 2333CCLeidenThe Netherlands
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47
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Buttler CA, Pezeshkian N, Fernandez MV, Aaron J, Norman S, Freed EO, van Engelenburg SB. Single molecule fate of HIV-1 envelope reveals late-stage viral lattice incorporation. Nat Commun 2018; 9:1861. [PMID: 29748537 PMCID: PMC5945595 DOI: 10.1038/s41467-018-04220-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/09/2018] [Indexed: 11/09/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) assembly occurs on the inner leaflet of the host cell plasma membrane, incorporating the essential viral envelope glycoprotein (Env) within a budding lattice of HIV-1 Gag structural proteins. The mechanism by which Env incorporates into viral particles remains poorly understood. To determine the mechanism of recruitment of Env to assembly sites, we interrogate the subviral angular distribution of Env on cell-associated virus using multicolor, three-dimensional (3D) superresolution microscopy. We demonstrate that, in a manner dependent on cell type and on the long cytoplasmic tail of Env, the distribution of Env is biased toward the necks of cell-associated particles. We postulate that this neck-biased distribution is regulated by vesicular retention and steric complementarity of Env during independent Gag lattice formation.
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Affiliation(s)
- Carmen A Buttler
- Molecular and Cellular Biophysics Program, Department of Biological Sciences, University of Denver, Denver, CO, 80210, USA
| | - Nairi Pezeshkian
- Molecular and Cellular Biophysics Program, Department of Biological Sciences, University of Denver, Denver, CO, 80210, USA
| | - Melissa V Fernandez
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Jesse Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Sofya Norman
- Molecular and Cellular Biophysics Program, Department of Biological Sciences, University of Denver, Denver, CO, 80210, USA
| | - Eric O Freed
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Schuyler B van Engelenburg
- Molecular and Cellular Biophysics Program, Department of Biological Sciences, University of Denver, Denver, CO, 80210, USA.
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48
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Bucher D, Frey F, Sochacki KA, Kummer S, Bergeest JP, Godinez WJ, Kräusslich HG, Rohr K, Taraska JW, Schwarz US, Boulant S. Clathrin-adaptor ratio and membrane tension regulate the flat-to-curved transition of the clathrin coat during endocytosis. Nat Commun 2018; 9:1109. [PMID: 29549258 PMCID: PMC5856840 DOI: 10.1038/s41467-018-03533-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/15/2018] [Indexed: 12/03/2022] Open
Abstract
Although essential for many cellular processes, the sequence of structural and molecular events during clathrin-mediated endocytosis remains elusive. While it was long believed that clathrin-coated pits grow with a constant curvature, it was recently suggested that clathrin first assembles to form flat structures that then bend while maintaining a constant surface area. Here, we combine correlative electron and light microscopy and mathematical growth laws to study the ultrastructural rearrangements of the clathrin coat during endocytosis in BSC-1 mammalian cells. We confirm that clathrin coats initially grow flat and demonstrate that curvature begins when around 70% of the final clathrin content is acquired. We find that this transition is marked by a change in the clathrin to clathrin-adaptor protein AP2 ratio and that membrane tension suppresses this transition. Our results support the notion that BSC-1 mammalian cells dynamically regulate the flat-to-curved transition in clathrin-mediated endocytosis by both biochemical and mechanical factors. The sequence of structural and molecular events during clathrin-mediated endocytosis is unclear. Here the authors combine correlative microscopy and simple mathematical growth laws to demonstrate that the flat patch starts to curve when around 70% of the final clathrin content is reached.
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Affiliation(s)
- Delia Bucher
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Felix Frey
- BioQuant Center, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany
| | - Kem A Sochacki
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Susann Kummer
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Jan-Philip Bergeest
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.,BioQuant Center, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), Department of Bioinformatics and Functional Genomics, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| | - William J Godinez
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.,BioQuant Center, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), Department of Bioinformatics and Functional Genomics, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Karl Rohr
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.,BioQuant Center, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), Department of Bioinformatics and Functional Genomics, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| | - Justin W Taraska
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ulrich S Schwarz
- BioQuant Center, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany. .,Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany.
| | - Steeve Boulant
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany. .,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.
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49
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Howes SC, Koning RI, Koster AJ. Correlative microscopy for structural microbiology. Curr Opin Microbiol 2018; 43:132-138. [PMID: 29414444 DOI: 10.1016/j.mib.2018.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/12/2018] [Accepted: 01/14/2018] [Indexed: 10/18/2022]
Abstract
Understanding how microbes utilize their environment is aided by visualizing them in their natural context at high resolution. Correlative imaging enables efficient targeting and identification of labelled viral and bacterial components by light microscopy combined with high resolution imaging by electron microscopy. Advances in genetic and bioorthogonal labelling, improved workflows for targeting and image correlation, and large-scale data collection are increasing the applicability of correlative imaging methods. Furthermore, developments in mass spectroscopy and soft X-ray imaging are expanding the correlative imaging modalities available. Investigating the structure and organization of microbes within their host by combined imaging methods provides important insights into mechanisms of infection and disease which cannot be obtained by other techniques.
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Affiliation(s)
- Stuart C Howes
- Leiden University Medical Centre, Department of Molecular Cell Biology, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Roman I Koning
- Leiden University Medical Centre, Department of Molecular Cell Biology, PO Box 9600, 2300 RC Leiden, The Netherlands; Netherlands Centre for Electron Nanoscopy, Institute of Biology, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Abraham J Koster
- Leiden University Medical Centre, Department of Molecular Cell Biology, PO Box 9600, 2300 RC Leiden, The Netherlands; Netherlands Centre for Electron Nanoscopy, Institute of Biology, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands.
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Miller H, Zhou Z, Shepherd J, Wollman AJM, Leake MC. Single-molecule techniques in biophysics: a review of the progress in methods and applications. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:024601. [PMID: 28869217 DOI: 10.1088/1361-6633/aa8a02] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.
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Affiliation(s)
- Helen Miller
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, United Kingdom
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