151
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Meister A, Blume A. (Cryo)Transmission Electron Microscopy of Phospholipid Model Membranes Interacting with Amphiphilic and Polyphilic Molecules. Polymers (Basel) 2017; 9:E521. [PMID: 30965829 PMCID: PMC6418595 DOI: 10.3390/polym9100521] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 10/12/2017] [Accepted: 10/13/2017] [Indexed: 11/16/2022] Open
Abstract
Lipid membranes can incorporate amphiphilic or polyphilic molecules leading to specific functionalities and to adaptable properties of the lipid bilayer host. The insertion of guest molecules into membranes frequently induces changes in the shape of the lipid matrix that can be visualized by transmission electron microscopy (TEM) techniques. Here, we review the use of stained and vitrified specimens in (cryo)TEM to characterize the morphology of amphiphilic and polyphilic molecules upon insertion into phospholipid model membranes. Special emphasis is placed on the impact of novel synthetic amphiphilic and polyphilic bolalipids and polymers on membrane integrity and shape stability.
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Affiliation(s)
- Annette Meister
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany.
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany.
| | - Alfred Blume
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany.
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152
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Lemercier N, Middel V, Hentsch D, Taubert S, Takamiya M, Beil T, Vonesch JL, Baumbach T, Schultz P, Antony C, Strähle U. Microtome-integrated microscope system for high sensitivity tracking of in-resin fluorescence in blocks and ultrathin sections for correlative microscopy. Sci Rep 2017; 7:13583. [PMID: 29051533 PMCID: PMC5648784 DOI: 10.1038/s41598-017-13348-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/22/2017] [Indexed: 12/02/2022] Open
Abstract
Many areas of biological research demand the combined use of different imaging modalities to cover a wide range of magnifications and measurements or to place fluorescent patterns into an ultrastructural context. A technically difficult problem is the efficient specimen transfer between different imaging modalities without losing the coordinates of the regions-of-interest (ROI). Here, we report a new and highly sensitive integrated system that combines a custom designed microscope with an ultramicrotome for in-resin-fluorescence detection in blocks, ribbons and sections on EM-grids. Although operating with long-distance lenses, this system achieves a very high light sensitivity. Our instrumental set-up and operating workflow are designed to investigate rare events in large tissue volumes. Applications range from studies of individual immune, stem and cancer cells to the investigation of non-uniform subcellular processes. As a use case, we present the ultrastructure of a single membrane repair patch on a muscle fiber in intact muscle in a whole animal context.
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Affiliation(s)
- Nicolas Lemercier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 1, rue Laurent Fries, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 1, rue Laurent Fries, 67404, Illkirch, France.,Université de Strasbourg, 1, rue Laurent Fries, 67404, Illkirch, France
| | - Volker Middel
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Didier Hentsch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 1, rue Laurent Fries, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 1, rue Laurent Fries, 67404, Illkirch, France.,Université de Strasbourg, 1, rue Laurent Fries, 67404, Illkirch, France
| | - Serge Taubert
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 1, rue Laurent Fries, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 1, rue Laurent Fries, 67404, Illkirch, France.,Université de Strasbourg, 1, rue Laurent Fries, 67404, Illkirch, France
| | - Masanari Takamiya
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Tanja Beil
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Jean-Luc Vonesch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 1, rue Laurent Fries, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 1, rue Laurent Fries, 67404, Illkirch, France.,Université de Strasbourg, 1, rue Laurent Fries, 67404, Illkirch, France
| | - Tilo Baumbach
- Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
| | - Patrick Schultz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, 67404, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, 1, rue Laurent Fries, 67404, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U964, 1, rue Laurent Fries, 67404, Illkirch, France. .,Université de Strasbourg, 1, rue Laurent Fries, 67404, Illkirch, France.
| | - Claude Antony
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 1, rue Laurent Fries, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 1, rue Laurent Fries, 67404, Illkirch, France.,Université de Strasbourg, 1, rue Laurent Fries, 67404, Illkirch, France.,Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Uwe Strähle
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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153
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Adell MAY, Migliano SM, Upadhyayula S, Bykov YS, Sprenger S, Pakdel M, Vogel GF, Jih G, Skillern W, Behrouzi R, Babst M, Schmidt O, Hess MW, Briggs JA, Kirchhausen T, Teis D. Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for reverse membrane budding. eLife 2017; 6:31652. [PMID: 29019322 PMCID: PMC5665648 DOI: 10.7554/elife.31652] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 09/25/2017] [Indexed: 12/18/2022] Open
Abstract
The ESCRT machinery mediates reverse membrane scission. By quantitative fluorescence lattice light-sheet microscopy, we have shown that ESCRT-III subunits polymerize rapidly on yeast endosomes, together with the recruitment of at least two Vps4 hexamers. During their 3–45 s lifetimes, the ESCRT-III assemblies accumulated 75–200 Snf7 and 15–50 Vps24 molecules. Productive budding events required at least two additional Vps4 hexamers. Membrane budding was associated with continuous, stochastic exchange of Vps4 and ESCRT-III components, rather than steady growth of fixed assemblies, and depended on Vps4 ATPase activity. An all-or-none step led to final release of ESCRT-III and Vps4. Tomographic electron microscopy demonstrated that acute disruption of Vps4 recruitment stalled membrane budding. We propose a model in which multiple Vps4 hexamers (four or more) draw together several ESCRT-III filaments. This process induces cargo crowding and inward membrane buckling, followed by constriction of the nascent bud neck and ultimately ILV generation by vesicle fission.
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Affiliation(s)
- Manuel Alonso Y Adell
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Simona M Migliano
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Srigokul Upadhyayula
- Department of Pediatrics, Harvard Medical School, Boston, United States.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Yury S Bykov
- Structural and Computational Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Simon Sprenger
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Mehrshad Pakdel
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Georg F Vogel
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.,Division of Histology and Embryology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gloria Jih
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Wesley Skillern
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States
| | - Reza Behrouzi
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Markus Babst
- Department of Biology, University of Utah, Utah, United States.,Center for Cell and Genome Science, University of Utah, Utah, United States
| | - Oliver Schmidt
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael W Hess
- Division of Histology and Embryology, Medical University of Innsbruck, Innsbruck, Austria
| | - John Ag Briggs
- Structural and Computational Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tomas Kirchhausen
- Department of Pediatrics, Harvard Medical School, Boston, United States.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - David Teis
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.,Austrian Drug Screening Institute, Innsbruck, Austria
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154
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Zhou H, Gang Y, Chen S, Wang Y, Xiong Y, Li L, Yin F, Liu Y, Liu X, Zeng S. Development of a neutral embedding resin for optical imaging of fluorescently labeled biological tissue. JOURNAL OF BIOMEDICAL OPTICS 2017; 22:1-7. [PMID: 29076308 DOI: 10.1117/1.jbo.22.10.106015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/02/2017] [Indexed: 06/07/2023]
Abstract
Plastic embedding is widely applied in light microscopy analyses. Previous studies have shown that embedding agents and related techniques can greatly affect the quality of biological tissue embedding and fluorescent imaging. Specifically, it is difficult to preserve endogenous fluorescence using currently available acidic commercial embedding resins and related embedding techniques directly. Here, we developed a neutral embedding resin that improved the green fluorescent protein (GFP), yellow fluorescent protein (YFP), and DsRed fluorescent intensity without adjusting the pH value of monomers or reactivating fluorescence in lye. The embedding resin had a high degree of polymerization, and its fluorescence preservation ratios for GFP, YFP, and DsRed were 126.5%, 155.8%, and 218.4%, respectively.
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Affiliation(s)
- Hongfu Zhou
- Huazhong University of Science and Technology, Collaborative Innovation Center for Biomedical Engine, China
- Huazhong University of Science and Technology, School of Engineering Sciences, Britton Chance Center, China
| | - Yadong Gang
- Huazhong University of Science and Technology, Collaborative Innovation Center for Biomedical Engine, China
- Huazhong University of Science and Technology, School of Engineering Sciences, Britton Chance Center, China
| | - Shenghua Chen
- Huazhong University of Science and Technology, Collaborative Innovation Center for Biomedical Engine, China
- Huazhong University of Science and Technology, School of Engineering Sciences, Britton Chance Center, China
| | - Yu Wang
- Huazhong University of Science and Technology, Collaborative Innovation Center for Biomedical Engine, China
- Huazhong University of Science and Technology, School of Engineering Sciences, Britton Chance Center, China
| | - Yumiao Xiong
- Huazhong University of Science and Technology, Collaborative Innovation Center for Biomedical Engine, China
- Huazhong University of Science and Technology, School of Engineering Sciences, Britton Chance Center, China
| | - Longhui Li
- Huazhong University of Science and Technology, Collaborative Innovation Center for Biomedical Engine, China
- Huazhong University of Science and Technology, School of Engineering Sciences, Britton Chance Center, China
| | - Fangfang Yin
- Huazhong University of Science and Technology, Collaborative Innovation Center for Biomedical Engine, China
- Huazhong University of Science and Technology, School of Engineering Sciences, Britton Chance Center, China
| | - Yue Liu
- Huazhong University of Science and Technology, Collaborative Innovation Center for Biomedical Engine, China
- Huazhong University of Science and Technology, School of Engineering Sciences, Britton Chance Center, China
| | - Xiuli Liu
- Huazhong University of Science and Technology, Collaborative Innovation Center for Biomedical Engine, China
- Huazhong University of Science and Technology, School of Engineering Sciences, Britton Chance Center, China
| | - Shaoqun Zeng
- Huazhong University of Science and Technology, Collaborative Innovation Center for Biomedical Engine, China
- Huazhong University of Science and Technology, School of Engineering Sciences, Britton Chance Center, China
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155
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Inducing fluorescence of uranyl acetate as a dual-purpose contrast agent for correlative light-electron microscopy with nanometre precision. Sci Rep 2017; 7:10442. [PMID: 28874723 PMCID: PMC5585351 DOI: 10.1038/s41598-017-10905-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/16/2017] [Indexed: 01/24/2023] Open
Abstract
Correlative light-electron microscopy (CLEM) combines the high spatial resolution of transmission electron microscopy (TEM) with the capability of fluorescence light microscopy (FLM) to locate rare or transient cellular events within a large field of view. CLEM is therefore a powerful technique to study cellular processes. Aligning images derived from both imaging modalities is a prerequisite to correlate the two microscopy data sets, and poor alignment can limit interpretability of the data. Here, we describe how uranyl acetate, a commonly-used contrast agent for TEM, can be induced to fluoresce brightly at cryogenic temperatures (−195 °C) and imaged by cryoFLM using standard filter sets. This dual-purpose contrast agent can be used as a general tool for CLEM, whereby the equivalent staining allows direct correlation between fluorescence and TEM images. We demonstrate the potential of this approach by performing multi-colour CLEM of cells containing equine arteritis virus proteins tagged with either green- or red-fluorescent protein, and achieve high-precision localization of virus-induced intracellular membrane modifications. Using uranyl acetate as a dual-purpose contrast agent, we achieve an image alignment precision of ~30 nm, twice as accurate as when using fiducial beads, which will be essential for combining TEM with the evolving field of super-resolution light microscopy.
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156
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Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells. Nat Protoc 2017; 12:1792-1816. [PMID: 28796234 DOI: 10.1038/nprot.2017.065] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Electron microscopy (EM) is the premiere technique for high-resolution imaging of cellular ultrastructure. Unambiguous identification of specific proteins or cellular compartments in electron micrographs, however, remains challenging because of difficulties in delivering electron-dense contrast agents to specific subcellular targets within intact cells. We recently reported enhanced ascorbate peroxidase 2 (APEX2) as a broadly applicable genetic tag that generates EM contrast on a specific protein or subcellular compartment of interest. This protocol provides guidelines for designing and validating APEX2 fusion constructs, along with detailed instructions for cell culture, transfection, fixation, heavy-metal staining, embedding in resin, and EM imaging. Although this protocol focuses on EM in cultured mammalian cells, APEX2 is applicable to many cell types and contexts, including intact tissues and organisms, and is useful for numerous applications beyond EM, including live-cell proteomic mapping. This protocol, which describes procedures for sample preparation from cell monolayers and cell pellets, can be completed in 10 d, including time for APEX2 fusion construct validation, cell growth, and solidification of embedding resins. Notably, the only additional steps required relative to a standard EM sample preparation are cell transfection and a 2- to 45-min staining period with 3,3-diaminobenzidine (DAB) and hydrogen peroxide (H2O2).
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157
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Kuri P, Schieber NL, Thumberger T, Wittbrodt J, Schwab Y, Leptin M. Dynamics of in vivo ASC speck formation. J Cell Biol 2017; 216:2891-2909. [PMID: 28701426 PMCID: PMC5584180 DOI: 10.1083/jcb.201703103] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/31/2017] [Accepted: 06/13/2017] [Indexed: 12/18/2022] Open
Abstract
The inflammasome adaptor ASC forms enormous intracellular complexes called specks. Live imaging of endogenous ASC in keratinocytes reveals speck formation dynamics and their lethal effects, as well as macrophages’ engulfment and digestion of the specks left behind by dead cells. Activated danger or pathogen sensors trigger assembly of the inflammasome adaptor ASC into specks, large signaling platforms considered hallmarks of inflammasome activation. Because a lack of in vivo tools has prevented the study of endogenous ASC dynamics, we generated a live ASC reporter through CRISPR/Cas9 tagging of the endogenous gene in zebrafish. We see strong ASC expression in the skin and other epithelia that act as barriers to insult. A toxic stimulus triggered speck formation and rapid pyroptosis in keratinocytes in vivo. Macrophages engulfed and digested that speck-containing, pyroptotic debris. A three-dimensional, ultrastructural reconstruction, based on correlative light and electron microscopy of the in vivo assembled specks revealed a compact network of highly intercrossed filaments, whereas pyrin domain (PYD) or caspase activation and recruitment domain alone formed filamentous aggregates. The effector caspase is recruited through PYD, whose overexpression induced pyroptosis but only after substantial delay. Therefore, formation of a single, compact speck and rapid cell-death induction in vivo requires a full-length ASC.
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Affiliation(s)
- Paola Kuri
- Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nicole L Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maria Leptin
- Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany .,Institute of Genetics, University of Cologne, Cologne, Germany.,European Molecular Biology Organization, Heidelberg, Germany
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158
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Marion J, Le Bars R, Satiat-Jeunemaitre B, Boulogne C. Optimizing CLEM protocols for plants cells: GMA embedding and cryosections as alternatives for preservation of GFP fluorescence in Arabidopsis roots. J Struct Biol 2017; 198:196-202. [DOI: 10.1016/j.jsb.2017.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 03/23/2017] [Indexed: 12/21/2022]
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159
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Correlative super-resolution fluorescence and electron microscopy using conventional fluorescent proteins in vacuo. J Struct Biol 2017; 199:120-131. [PMID: 28576556 PMCID: PMC5531056 DOI: 10.1016/j.jsb.2017.05.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 04/27/2017] [Accepted: 05/29/2017] [Indexed: 12/12/2022]
Abstract
Super-resolution light microscopy, correlative light and electron microscopy, and volume electron microscopy are revolutionising the way in which biological samples are examined and understood. Here, we combine these approaches to deliver super-accurate correlation of fluorescent proteins to cellular structures. We show that YFP and GFP have enhanced blinking properties when embedded in acrylic resin and imaged under partial vacuum, enabling in vacuo single molecule localisation microscopy. In conventional section-based correlative microscopy experiments, the specimen must be moved between imaging systems and/or further manipulated for optimal viewing. These steps can introduce undesirable alterations in the specimen, and complicate correlation between imaging modalities. We avoided these issues by using a scanning electron microscope with integrated optical microscope to acquire both localisation and electron microscopy images, which could then be precisely correlated. Collecting data from ultrathin sections also improved the axial resolution and signal-to-noise ratio of the raw localisation microscopy data. Expanding data collection across an array of sections will allow 3-dimensional correlation over unprecedented volumes. The performance of this technique is demonstrated on vaccinia virus (with YFP) and diacylglycerol in cellular membranes (with GFP).
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160
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Li S, Raychaudhuri S, Watanabe S. Flash-and-Freeze: A Novel Technique to Capture Membrane Dynamics with Electron Microscopy. J Vis Exp 2017. [PMID: 28518090 PMCID: PMC5565139 DOI: 10.3791/55664] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cells constantly change their membrane architecture and protein distribution, but it is extremely difficult to visualize these events at a temporal and spatial resolution on the order of ms and nm, respectively. We have developed a time-resolved electron microscopy technique, "flash-and-freeze," that induces cellular events with optogenetics and visualizes the resulting membrane dynamics by freezing cells at defined time points after stimulation. To demonstrate this technique, we expressed channelrhodopsin, a light-sensitive cation channel, in mouse hippocampal neurons. A flash of light stimulates neuronal activity and induces neurotransmitter release from synaptic terminals through the fusion of synaptic vesicles. The optogenetic stimulation of neurons is coupled with high-pressure freezing to follow morphological changes during synaptic transmission. Using a commercial instrument, we captured the fusion of synaptic vesicles and the recovery of the synaptic vesicle membrane. To visualize the sequence of events, large datasets were generated and analyzed blindly, since morphological changes were followed in different cells over time. Nevertheless, flash-and-freeze allows the visualization of membrane dynamics in electron micrographs with ms temporal resolution.
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Affiliation(s)
- Shuo Li
- Department of Cell Biology, Johns Hopkins School of Medicine; Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health
| | | | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins School of Medicine; Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine;
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161
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Janel S, Werkmeister E, Bongiovanni A, Lafont F, Barois N. CLAFEM: Correlative light atomic force electron microscopy. Methods Cell Biol 2017; 140:165-185. [PMID: 28528632 DOI: 10.1016/bs.mcb.2017.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Atomic force microscopy (AFM) is becoming increasingly used in the biology field. It can give highly accurate topography and biomechanical quantitative data, such as adhesion, elasticity, and viscosity, on living samples. Nowadays, correlative light electron microscopy is a must-have tool in the biology field that combines different microscopy techniques to spatially and temporally analyze the structure and function of a single sample. Here, we describe the combination of AFM with superresolution light microscopy and electron microscopy. We named this technique correlative light atomic force electron microscopy (CLAFEM) in which AFM can be used on fixed and living cells in association with superresolution light microscopy and further processed for transmission or scanning electron microscopy. We herein illustrate this approach to observe cellular bacterial infection and cytoskeleton. We show that CLAFEM brings complementary information at the cellular level, from on the one hand protein distribution and topography at the nanometer scale and on the other hand elasticity at the piconewton scales to fine ultrastructural details.
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Affiliation(s)
- Sébastien Janel
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Elisabeth Werkmeister
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Antonino Bongiovanni
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Frank Lafont
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Nicolas Barois
- Univ. Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille - CIIL - Center for Infection and Immunity of Lille, Lille, France
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162
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Markert SM, Bauer V, Muenz TS, Jones NG, Helmprobst F, Britz S, Sauer M, Rössler W, Engstler M, Stigloher C. 3D subcellular localization with superresolution array tomography on ultrathin sections of various species. Methods Cell Biol 2017; 140:21-47. [PMID: 28528634 DOI: 10.1016/bs.mcb.2017.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Array Tomography (AT) is a relatively easy-to-use and yet powerful method to put molecular identity in its full ultrastructural context. Ultrathin sections are stained with fluorophores and then imaged by light and afterward by electron microscopy to obtain a correlated view of a region of interest: its ultrastructure and specific staining. By combining AT with high-pressure freezing for superior structural preservation and superresolution light microscopy, even small subcellular structures can be mapped in 3D. We established protocols for the application of superresolution AT on ultrathin plastic sections of Caenorhabditis elegans, Trypanosoma brucei, and brain tissue of Cataglyphis fortis and Apis mellifera. All steps are described in detail from sample preparation to 3D reconstruction, including species-specific modifications. We thus showcase the versatility of our protocol and give some examples for biological questions that can be answered with this technique. We offer a step-by-step recipe for superresolution AT that can be easily applied for C. elegans, T. brucei, C. fortis, and A. mellifera and adapted for other model systems.
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163
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Hemelaar SR, de Boer P, Chipaux M, Zuidema W, Hamoh T, Martinez FP, Nagl A, Hoogenboom JP, Giepmans BNG, Schirhagl R. Nanodiamonds as multi-purpose labels for microscopy. Sci Rep 2017; 7:720. [PMID: 28389652 PMCID: PMC5429637 DOI: 10.1038/s41598-017-00797-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/13/2017] [Indexed: 11/09/2022] Open
Abstract
Nanodiamonds containing fluorescent nitrogen-vacancy centers are increasingly attracting interest for use as a probe in biological microscopy. This interest stems from (i) strong resistance to photobleaching allowing prolonged fluorescence observation times; (ii) the possibility to excite fluorescence using a focused electron beam (cathodoluminescence; CL) for high-resolution localization; and (iii) the potential use for nanoscale sensing. For all these schemes, the development of versatile molecular labeling using relatively small diamonds is essential. Here, we show the direct targeting of a biological molecule with nanodiamonds as small as 70 nm using a streptavidin conjugation and standard antibody labelling approach. We also show internalization of 40 nm sized nanodiamonds. The fluorescence from the nanodiamonds survives osmium-fixation and plastic embedding making them suited for correlative light and electron microscopy. We show that CL can be observed from epon-embedded nanodiamonds, while surface-exposed nanoparticles also stand out in secondary electron (SE) signal due to the exceptionally high diamond SE yield. Finally, we demonstrate the magnetic read-out using fluorescence from diamonds prior to embedding. Thus, our results firmly establish nanodiamonds containing nitrogen-vacancy centers as unique, versatile probes for combining and correlating different types of microscopy, from fluorescence imaging and magnetometry to ultrastructural investigation using electron microscopy.
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Affiliation(s)
- S R Hemelaar
- Groningen University, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - P de Boer
- Groningen University, University Medical Center Groningen, Department of Cell Biology, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - M Chipaux
- Groningen University, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - W Zuidema
- Delft University of Technology, Dept. Imaging Physics, Lorentzweg 1, 2628, CJ, Delft, The Netherlands
| | - T Hamoh
- Groningen University, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - F Perona Martinez
- Groningen University, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - A Nagl
- Groningen University, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - J P Hoogenboom
- Delft University of Technology, Dept. Imaging Physics, Lorentzweg 1, 2628, CJ, Delft, The Netherlands
| | - B N G Giepmans
- Groningen University, University Medical Center Groningen, Department of Cell Biology, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands
| | - R Schirhagl
- Groningen University, University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713, AW, Groningen, The Netherlands.
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164
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Using integrated correlative cryo-light and electron microscopy to directly observe syntaphilin-immobilized neuronal mitochondria in situ. BIOPHYSICS REPORTS 2017; 3:8-16. [PMID: 28781997 PMCID: PMC5515996 DOI: 10.1007/s41048-017-0035-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/28/2016] [Indexed: 01/05/2023] Open
Abstract
Correlative cryo-fluorescence and cryo-electron microscopy (cryo-CLEM) system has been fast becoming a powerful technique with the advantage to allow the fluorescent labeling and direct visualization of the close-to-physiologic ultrastructure in cells at the same time, offering unique insights into the ultrastructure with specific cellular function. There have been various engineered ways to achieve cryo-CLEM including the commercial FEI iCorr system that integrates fluorescence microscope into the column of transmission electron microscope. In this study, we applied the approach of the cryo-CLEM-based iCorr to image the syntaphilin-immobilized neuronal mitochondria in situ to test the performance of the FEI iCorr system and determine its correlation accuracy. Our study revealed the various morphologies of syntaphilin-immobilized neuronal mitochondria that interact with microtubules and suggested that the cryo-CLEM procedure by the FEI iCorr system is suitable with a half micron-meter correlation accuracy to study the cellular organelles that have a discrete distribution and large size, e.g. mitochondrion, Golgi complex, lysosome, etc.
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165
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Miles BT, Greenwood AB, Benito-Alifonso D, Tanner H, Galan MC, Verkade P, Gersen H. Direct Evidence of Lack of Colocalisation of Fluorescently Labelled Gold Labels Used in Correlative Light Electron Microscopy. Sci Rep 2017; 7:44666. [PMID: 28317888 PMCID: PMC5357795 DOI: 10.1038/srep44666] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/13/2017] [Indexed: 12/16/2022] Open
Abstract
Fluorescently labelled nanoparticles are routinely used in Correlative Light Electron Microscopy (CLEM) to combine the capabilities of two separate microscope platforms: fluorescent light microscopy (LM) and electron microscopy (EM). The inherent assumption is that the fluorescent label observed under LM colocalises well with the electron dense nanoparticle observed in EM. Herein we show, by combining single molecule fluorescent imaging with optical detection of the scattering from single gold nanoparticles, that for a commercially produced sample of 10 nm gold nanoparticles tagged to Alexa-633 there is in fact no colocalisation between the fluorescent signatures of Alexa-633 and the scattering associated with the gold nanoparticle. This shows that the attached gold nanoparticle quenches the fluorescent signal by ~95%, or less likely that the complex has dissociated. In either scenario, the observed fluorescent signal in fact arises from a large population of untagged fluorophores; rendering these labels potentially ineffective and misleading to the field.
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Affiliation(s)
- Benjamin T. Miles
- Nanophotonics and Nanophysics Group, H.H. Wills Physics Laboratory, University of Bristol, Bristol, BS8 1TL, UK
| | - Alexander B. Greenwood
- Nanophotonics and Nanophysics Group, H.H. Wills Physics Laboratory, University of Bristol, Bristol, BS8 1TL, UK
| | | | - Hugh Tanner
- Bristol Centre for Functional Nanomaterials, H.H. Wills Physics Laboratory, University of Bristol, Bristol, BS8 1TL, UK
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - M. Carmen Galan
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
| | - Paul Verkade
- Wolfson Bioimaging Facility, University of Bristol, Bristol, BS8 1TD, UK
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Henkjan Gersen
- Nanophotonics and Nanophysics Group, H.H. Wills Physics Laboratory, University of Bristol, Bristol, BS8 1TL, UK
- Bristol Centre for Functional Nanomaterials, H.H. Wills Physics Laboratory, University of Bristol, Bristol, BS8 1TL, UK
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166
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Abstract
Super-resolution fluorescence imaging by photoactivation or photoswitching of single fluorophores and position determination (single-molecule localization microscopy, SMLM) provides microscopic images with subdiffraction spatial resolution. This technology has enabled new insights into how proteins are organized in a cellular context, with a spatial resolution approaching virtually the molecular level. A unique strength of SMLM is that it delivers molecule-resolved information, along with super-resolved images of cellular structures. This allows quantitative access to cellular structures, for example, how proteins are distributed and organized and how they interact with other biomolecules. Ultimately, it is even possible to determine protein numbers in cells and the number of subunits in a protein complex. SMLM thus has the potential to pave the way toward a better understanding of how cells function at the molecular level. In this review, we describe how SMLM has contributed new knowledge in eukaryotic biology, and we specifically focus on quantitative biological data extracted from SMLM images.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology & Biophysics, Julius-Maximilian-University of Würzburg , 97074 Würzburg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt , 60438 Frankfurt, Germany
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167
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Haring MT, Liv N, Zonnevylle AC, Narvaez AC, Voortman LM, Kruit P, Hoogenboom JP. Automated sub-5 nm image registration in integrated correlative fluorescence and electron microscopy using cathodoluminescence pointers. Sci Rep 2017; 7:43621. [PMID: 28252673 PMCID: PMC5333625 DOI: 10.1038/srep43621] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/26/2017] [Indexed: 11/09/2022] Open
Abstract
In the biological sciences, data from fluorescence and electron microscopy is correlated to allow fluorescence biomolecule identification within the cellular ultrastructure and/or ultrastructural analysis following live-cell imaging. High-accuracy (sub-100 nm) image overlay requires the addition of fiducial markers, which makes overlay accuracy dependent on the number of fiducials present in the region of interest. Here, we report an automated method for light-electron image overlay at high accuracy, i.e. below 5 nm. Our method relies on direct visualization of the electron beam position in the fluorescence detection channel using cathodoluminescence pointers. We show that image overlay using cathodoluminescence pointers corrects for image distortions, is independent of user interpretation, and does not require fiducials, allowing image correlation with molecular precision anywhere on a sample.
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Affiliation(s)
- Martijn T. Haring
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Nalan Liv
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | | | - Angela C. Narvaez
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | | | - Pieter Kruit
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Jacob P. Hoogenboom
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
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168
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Müller A, Neukam M, Ivanova A, Sönmez A, Münster C, Kretschmar S, Kalaidzidis Y, Kurth T, Verbavatz JM, Solimena M. A Global Approach for Quantitative Super Resolution and Electron Microscopy on Cryo and Epoxy Sections Using Self-labeling Protein Tags. Sci Rep 2017; 7:23. [PMID: 28154417 PMCID: PMC5428382 DOI: 10.1038/s41598-017-00033-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 12/20/2016] [Indexed: 01/19/2023] Open
Abstract
Correlative light and electron microscopy (CLEM) is a powerful approach to investigate the molecular ultrastructure of labeled cell compartments. However, quantitative CLEM studies are rare, mainly due to small sample sizes and the sensitivity of fluorescent proteins to strong fixatives and contrasting reagents for EM. Here, we show that fusion of a self-labeling protein to insulin allows for the quantification of age-distinct insulin granule pools in pancreatic beta cells by a combination of super resolution and transmission electron microscopy on Tokuyasu cryosections. In contrast to fluorescent proteins like GFP organic dyes covalently bound to self-labeling proteins retain their fluorescence also in epoxy resin following high pressure freezing and freeze substitution, or remarkably even after strong chemical fixation. This enables for the assessment of age-defined granule morphology and degradation. Finally, we demonstrate that this CLEM protocol is highly versatile, being suitable for single and dual fluorescent labeling and detection of different proteins with optimal ultrastructure preservation and contrast.
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Affiliation(s)
- Andreas Müller
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.,Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
| | - Martin Neukam
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.,Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
| | - Anna Ivanova
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.,Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
| | - Anke Sönmez
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.,Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
| | - Carla Münster
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.,Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany
| | - Susanne Kretschmar
- Center for Regenerative Therapies Dresden (CRTD), TU Dresden, Dresden, Germany.,Biotechnology Center of the TU Dresden (BIOTEC), Dresden, Germany
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.,Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Thomas Kurth
- Center for Regenerative Therapies Dresden (CRTD), TU Dresden, Dresden, Germany.,Biotechnology Center of the TU Dresden (BIOTEC), Dresden, Germany
| | - Jean-Marc Verbavatz
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.,Institut Jacques Monod, Université Paris Diderot, Paris, France
| | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany. .,Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany. .,Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
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169
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Trifunctional lipid probes for comprehensive studies of single lipid species in living cells. Proc Natl Acad Sci U S A 2017; 114:1566-1571. [PMID: 28154130 DOI: 10.1073/pnas.1611096114] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Lipid-mediated signaling events regulate many cellular processes. Investigations of the complex underlying mechanisms are difficult because several different methods need to be used under varying conditions. Here we introduce multifunctional lipid derivatives to study lipid metabolism, lipid-protein interactions, and intracellular lipid localization with a single tool per target lipid. The probes are equipped with two photoreactive groups to allow photoliberation (uncaging) and photo-cross-linking in a sequential manner, as well as a click-handle for subsequent functionalization. We demonstrate the versatility of the design for the signaling lipids sphingosine and diacylglycerol; uncaging of the probe for these two species triggered calcium signaling and intracellular protein translocation events, respectively. We performed proteomic screens to map the lipid-interacting proteome for both lipids. Finally, we visualized a sphingosine transport deficiency in patient-derived Niemann-Pick disease type C fibroblasts by fluorescence as well as correlative light and electron microscopy, pointing toward the diagnostic potential of such tools. We envision that this type of probe will become important for analyzing and ultimately understanding lipid signaling events in a comprehensive manner.
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170
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Morphew MK, Giddings TH, McIntosh JR. Immunolocalization of Proteins in Fission Yeast by Electron Microscopy. Cold Spring Harb Protoc 2017; 2017:2017/1/pdb.prot091322. [PMID: 28049778 DOI: 10.1101/pdb.prot091322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Electron microscopy (EM) immunolocalization of antigens in fission yeast can be accomplished with cells processed by rapid freezing and freeze-substitution followed by embedding in acrylic or methacrylate resins. Microtome sections of embedded cells are collected onto EM grids. Primary antibodies to the antigen of interest, followed by secondary antibodies conjugated to colloidal gold, are allowed to bind to antigens at the surface of these plastic sections. This type of postembed labeling provides information on antigen localization to a resolution of 10-20 nm, depending on the size of the metal particle used, the form of the antibody (Fab vs. complete IgG or IgM), and whether direct or indirect labeling is used. The method has the potential to map macromolecules in three dimensions in a relatively large volume when thin (30-60-nm) serial sections are labeled, imaged, aligned, and modeled to create a representative volume. The biggest challenge of this technique is the necessary compromise between the preservation of cellular ultrastructure and the preservation of antigen reactivity. The protocols described here show how to immunolabel samples for EM and include suggestions for overcoming challenges related to antigen preservation.
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Affiliation(s)
- Mary K Morphew
- Laboratory for 3D Electron Microscopy, University of Colorado, Boulder, Colorado 80309-0347
| | - Thomas H Giddings
- Laboratory for 3D Electron Microscopy, University of Colorado, Boulder, Colorado 80309-0347
| | - J Richard McIntosh
- Laboratory for 3D Electron Microscopy, University of Colorado, Boulder, Colorado 80309-0347.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
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171
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McIntosh JR, Morphew MK, Giddings TH. Electron Microscopy of Fission Yeast. Cold Spring Harb Protoc 2017; 2017:2017/1/pdb.top079822. [PMID: 28049809 DOI: 10.1101/pdb.top079822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Electron microscopy (EM) can provide images of cells with a spatial resolution that significantly surpasses that available from light microscopy (LM), even with modern methods that give LM "super resolution." However, EM resolution comes with costs in time spent with sample preparation, expense of instrumentation, and concerns regarding sample preparation artifacts. It is therefore important to know the limitations of EM as well as its strengths. Here we describe the most reliable methods for the preservation of fission yeast cells currently available. We describe the properties of images obtained by transmission EM (TEM) and contrast them with images from scanning EM (SEM). We also show how one can make three-dimensional TEM images and discuss several approaches to address the problem of localizing specific proteins within cells. We give references to work by others who have pursued similar goals with different methods, and we discuss briefly the complex subject of image interpretation.
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Affiliation(s)
- J Richard McIntosh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
- Laboratory for 3D Electron Microscopy, University of Colorado, Boulder, Colorado 80309-0347
| | - Mary K Morphew
- Laboratory for 3D Electron Microscopy, University of Colorado, Boulder, Colorado 80309-0347
| | - Thomas H Giddings
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
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172
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173
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Schorb M, Sieckmann F. Matrix MAPS—an intuitive software to acquire, analyze, and annotate light microscopy data for CLEM. Methods Cell Biol 2017; 140:321-333. [DOI: 10.1016/bs.mcb.2017.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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174
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Schieber NL, Machado P, Markert SM, Stigloher C, Schwab Y, Steyer AM. Minimal resin embedding of multicellular specimens for targeted FIB-SEM imaging. Methods Cell Biol 2017; 140:69-83. [DOI: 10.1016/bs.mcb.2017.03.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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175
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176
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Johnson E, Kaufmann R. Preserving the photoswitching ability of standard fluorescent proteins for correlative in-resin super-resolution and electron microscopy. Methods Cell Biol 2017; 140:49-67. [DOI: 10.1016/bs.mcb.2017.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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177
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Brama E, Peddie CJ, Wilkes G, Gu Y, Collinson LM, Jones ML. ultraLM and miniLM: Locator tools for smart tracking of fluorescent cells in correlative light and electron microscopy. Wellcome Open Res 2016; 1:26. [PMID: 28090593 PMCID: PMC5234702 DOI: 10.12688/wellcomeopenres.10299.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In-resin fluorescence (IRF) protocols preserve fluorescent proteins in resin-embedded cells and tissues for correlative light and electron microscopy, aiding interpretation of macromolecular function within the complex cellular landscape. Dual-contrast IRF samples can be imaged in separate fluorescence and electron microscopes, or in dual-modality integrated microscopes for high resolution correlation of fluorophore to organelle. IRF samples also offer a unique opportunity to automate correlative imaging workflows. Here we present two new locator tools for finding and following fluorescent cells in IRF blocks, enabling future automation of correlative imaging. The ultraLM is a fluorescence microscope that integrates with an ultramicrotome, which enables ‘smart collection’ of ultrathin sections containing fluorescent cells or tissues for subsequent transmission electron microscopy or array tomography. The miniLM is a fluorescence microscope that integrates with serial block face scanning electron microscopes, which enables ‘smart tracking’ of fluorescent structures during automated serial electron image acquisition from large cell and tissue volumes.
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Affiliation(s)
- Elisabeth Brama
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Christopher J Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Gary Wilkes
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Yan Gu
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Lucy M Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Martin L Jones
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
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178
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Zachman MJ, Asenath-Smith E, Estroff LA, Kourkoutis LF. Site-Specific Preparation of Intact Solid-Liquid Interfaces by Label-Free In Situ Localization and Cryo-Focused Ion Beam Lift-Out. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:1338-1349. [PMID: 27869059 DOI: 10.1017/s1431927616011892] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Scanning transmission electron microscopy (STEM) allows atomic scale characterization of solid-solid interfaces, but has seen limited applications to solid-liquid interfaces due to the volatility of liquids in the microscope vacuum. Although cryo-electron microscopy is routinely used to characterize hydrated samples stabilized by rapid freezing, sample thinning is required to access the internal interfaces of thicker specimens. Here, we adapt cryo-focused ion beam (FIB) "lift-out," a technique recently developed for biological specimens, to prepare intact internal solid-liquid interfaces for high-resolution structural and chemical analysis by cryo-STEM. To guide the milling process we introduce a label-free in situ method of localizing subsurface structures in suitable materials by energy dispersive X-ray spectroscopy (EDX). Monte Carlo simulations are performed to evaluate the depth-probing capability of the technique, and show good qualitative agreement with experiment. We also detail procedures to produce homogeneously thin lamellae, which enable nanoscale structural, elemental, and chemical analysis of intact solid-liquid interfaces by analytical cryo-STEM. This work demonstrates the potential of cryo-FIB lift-out and cryo-STEM for understanding physical and chemical processes at solid-liquid interfaces.
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Affiliation(s)
- Michael J Zachman
- 1School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | - Emily Asenath-Smith
- 3Department of Materials Science and Engineering,Cornell University,Ithaca,NY 14853,USA
| | - Lara A Estroff
- 2Kavli Institute at Cornell for Nanoscale Science,Cornell University,Ithaca,NY 14853,USA
| | - Lena F Kourkoutis
- 1School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
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179
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Karreman MA, Hyenne V, Schwab Y, Goetz JG. Intravital Correlative Microscopy: Imaging Life at the Nanoscale. Trends Cell Biol 2016; 26:848-863. [DOI: 10.1016/j.tcb.2016.07.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 01/04/2023]
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180
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Markert SM, Britz S, Proppert S, Lang M, Witvliet D, Mulcahy B, Sauer M, Zhen M, Bessereau JL, Stigloher C. Filling the gap: adding super-resolution to array tomography for correlated ultrastructural and molecular identification of electrical synapses at the C. elegans connectome. NEUROPHOTONICS 2016; 3:041802. [PMID: 27175373 PMCID: PMC4855082 DOI: 10.1117/1.nph.3.4.041802] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/08/2016] [Indexed: 06/02/2023]
Abstract
Correlating molecular labeling at the ultrastructural level with high confidence remains challenging. Array tomography (AT) allows for a combination of fluorescence and electron microscopy (EM) to visualize subcellular protein localization on serial EM sections. Here, we describe an application for AT that combines near-native tissue preservation via high-pressure freezing and freeze substitution with super-resolution light microscopy and high-resolution scanning electron microscopy (SEM) analysis on the same section. We established protocols that combine SEM with structured illumination microscopy (SIM) and direct stochastic optical reconstruction microscopy (dSTORM). We devised a method for easy, precise, and unbiased correlation of EM images and super-resolution imaging data using endogenous cellular landmarks and freely available image processing software. We demonstrate that these methods allow us to identify and label gap junctions in Caenorhabditis elegans with precision and confidence, and imaging of even smaller structures is feasible. With the emergence of connectomics, these methods will allow us to fill in the gap-acquiring the correlated ultrastructural and molecular identity of electrical synapses.
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Affiliation(s)
| | - Sebastian Britz
- University of Würzburg, Biocenter, Division of Electron Microscopy, Am Hubland, Würzburg 97074, Germany
| | - Sven Proppert
- University of Würzburg, Department of Biotechnology and Biophysics, Am Hubland, Würzburg 97074, Germany
- University of Würzburg, Department of Neurophysiology, Institute of Physiology, Röntgenring 9, Würzburg 97070, Germany
| | - Marietta Lang
- University of Würzburg, Biocenter, Division of Electron Microscopy, Am Hubland, Würzburg 97074, Germany
| | - Daniel Witvliet
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- University of Toronto, Department of Molecular Genetics, Physiology and Institute of Medical Science, 1 King's College Cir, Toronto, Ontario M5S 1A8, Canada
| | - Ben Mulcahy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- University of Toronto, Department of Molecular Genetics, Physiology and Institute of Medical Science, 1 King's College Cir, Toronto, Ontario M5S 1A8, Canada
| | - Markus Sauer
- University of Würzburg, Department of Biotechnology and Biophysics, Am Hubland, Würzburg 97074, Germany
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- University of Toronto, Department of Molecular Genetics, Physiology and Institute of Medical Science, 1 King's College Cir, Toronto, Ontario M5S 1A8, Canada
| | - Jean-Louis Bessereau
- Institut NeuroMyoGene, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U1217, 16 rue R. Dubois, Villeurbanne Cedex F-69622, France
| | - Christian Stigloher
- University of Würzburg, Biocenter, Division of Electron Microscopy, Am Hubland, Würzburg 97074, Germany
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181
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Otsuka S, Bui KH, Schorb M, Hossain MJ, Politi AZ, Koch B, Eltsov M, Beck M, Ellenberg J. Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope. eLife 2016; 5. [PMID: 27630123 PMCID: PMC5065316 DOI: 10.7554/elife.19071] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/13/2016] [Indexed: 01/01/2023] Open
Abstract
The nuclear pore complex (NPC) mediates nucleocytoplasmic transport through the nuclear envelope. How the NPC assembles into this double membrane boundary has remained enigmatic. Here, we captured temporally staged assembly intermediates by correlating live cell imaging with high-resolution electron tomography and super-resolution microscopy. Intermediates were dome-shaped evaginations of the inner nuclear membrane (INM), that grew in diameter and depth until they fused with the flat outer nuclear membrane. Live and super-resolved fluorescence microscopy revealed the molecular maturation of the intermediates, which initially contained the nuclear and cytoplasmic ring component Nup107, and only later the cytoplasmic filament component Nup358. EM particle averaging showed that the evagination base was surrounded by an 8-fold rotationally symmetric ring structure from the beginning and that a growing mushroom-shaped density was continuously associated with the deforming membrane. Quantitative structural analysis revealed that interphase NPC assembly proceeds by an asymmetric inside-out extrusion of the INM.
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Affiliation(s)
- Shotaro Otsuka
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Khanh Huy Bui
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Schorb
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - M Julius Hossain
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antonio Z Politi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Birgit Koch
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail Eltsov
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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182
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Three-dimensional and immune electron microscopic analysis of the secretory pathway in Saccharomyces cerevisiae. Histochem Cell Biol 2016; 146:515-527. [DOI: 10.1007/s00418-016-1483-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2016] [Indexed: 01/07/2023]
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183
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Begemann I, Galic M. Correlative Light Electron Microscopy: Connecting Synaptic Structure and Function. Front Synaptic Neurosci 2016; 8:28. [PMID: 27601992 PMCID: PMC4993758 DOI: 10.3389/fnsyn.2016.00028] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/12/2016] [Indexed: 11/20/2022] Open
Abstract
Many core paradigms of contemporary neuroscience are based on information obtained by electron or light microscopy. Intriguingly, these two imaging techniques are often viewed as complementary, yet separate entities. Recent technological advancements in microscopy techniques, labeling tools, and fixation or preparation procedures have fueled the development of a series of hybrid approaches that allow correlating functional fluorescence microscopy data and ultrastructural information from electron micrographs from a singular biological event. As correlative light electron microscopy (CLEM) approaches become increasingly accessible, long-standing neurobiological questions regarding structure-function relation are being revisited. In this review, we will survey what developments in electron and light microscopy have spurred the advent of correlative approaches, highlight the most relevant CLEM techniques that are currently available, and discuss its potential and limitations with respect to neuronal and synapse-specific applications.
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Affiliation(s)
- Isabell Begemann
- DFG Cluster of Excellence 'Cells in Motion', (EXC 1003), University of Muenster, MuensterGermany; Institute of Medical Physics and Biophysics, University Hospital Münster, University of Muenster, MuensterGermany
| | - Milos Galic
- DFG Cluster of Excellence 'Cells in Motion', (EXC 1003), University of Muenster, MuensterGermany; Institute of Medical Physics and Biophysics, University Hospital Münster, University of Muenster, MuensterGermany
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184
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Chang HF, Bzeih H, Schirra C, Chitirala P, Halimani M, Cordat E, Krause E, Rettig J, Pattu V. Endocytosis of Cytotoxic Granules Is Essential for Multiple Killing of Target Cells by T Lymphocytes. THE JOURNAL OF IMMUNOLOGY 2016; 197:2473-84. [PMID: 27527597 DOI: 10.4049/jimmunol.1600828] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/20/2016] [Indexed: 11/19/2022]
Abstract
CTLs are serial killers that kill multiple target cells via exocytosis of cytotoxic granules (CGs). CG exocytosis is tightly regulated and has been investigated in great detail; however, whether CG proteins are endocytosed following exocytosis and contribute to serial killing remains unknown. By using primary CTLs derived from a knock-in mouse of the CG membrane protein Synaptobrevin2, we show that CGs are endocytosed in a clathrin- and dynamin-dependent manner. Following acidification, endocytosed CGs are recycled through early and late, but not recycling endosomes. CGs are refilled with granzyme B at the late endosome stage and polarize to subsequent synapses formed between the CTL and new target cells. Importantly, inhibiting CG endocytosis in CTLs results in a significant reduction of their cytotoxic activity. Thus, our data demonstrate that continuous endocytosis of CG membrane proteins is a prerequisite for efficient serial killing of CTLs and identify key events in this process.
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Affiliation(s)
- Hsin-Fang Chang
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421 Homburg/Saar, Germany; and
| | - Hawraa Bzeih
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421 Homburg/Saar, Germany; and
| | - Claudia Schirra
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421 Homburg/Saar, Germany; and
| | - Praneeth Chitirala
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421 Homburg/Saar, Germany; and
| | - Mahantappa Halimani
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421 Homburg/Saar, Germany; and
| | - Emmanuelle Cordat
- Department of Physiology, University of Alberta, Edmonton T6G 2H7, Alberta, Canada
| | - Elmar Krause
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421 Homburg/Saar, Germany; and
| | - Jens Rettig
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421 Homburg/Saar, Germany; and
| | - Varsha Pattu
- Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421 Homburg/Saar, Germany; and
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185
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Killingsworth MC, Bobryshev YV. Correlative Light- and Electron Microscopy Using Quantum Dot Nanoparticles. J Vis Exp 2016. [PMID: 27584907 DOI: 10.3791/54307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
A method is described whereby quantum dot (QD) nanoparticles can be used for correlative immunocytochemical studies of human pathology tissue using widefield fluorescence light microscopy and transmission electron microscopy (TEM). To demonstrate the protocol we have immunolabeled ultrathin epoxy sections of human somatostatinoma tumor using a primary antibody to somatostatin, followed by a biotinylated secondary antibody and visualization with streptavidin conjugated 585 nm cadmium-selenium (CdSe) quantum dots (QDs). The sections are mounted on a TEM specimen grid then placed on a glass slide for observation by widefield fluorescence light microscopy. Light microscopy reveals 585 nm QD labeling as bright orange fluorescence forming a granular pattern within the tumor cell cytoplasm. At low to mid-range magnification by light microscopy the labeling pattern can be easily recognized and the level of non-specific or background labeling assessed. This is a critical step for subsequent interpretation of the immunolabeling pattern by TEM and evaluation of the morphological context. The same section is then blotted dry and viewed by TEM. QD probes are seen to be attached to amorphous material contained in individual secretory granules. Images are acquired from the same region of interest (ROI) seen by light microscopy for correlative analysis. Corresponding images from each modality may then be blended to overlay fluorescence data on TEM ultrastructure of the corresponding region.
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Affiliation(s)
- Murray C Killingsworth
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales Australia; School of Medicine, Western Sydney University; Correlative Microscopy Group, Ingham Institute for Applied Medical Research; Electron Microscopy Laboratory, Department of Anatomical Pathology, Sydney South West Pathology Service, New South Wales Health Pathology;
| | - Yuri V Bobryshev
- Correlative Microscopy Group, Ingham Institute for Applied Medical Research; Electron Microscopy Laboratory, Department of Anatomical Pathology, Sydney South West Pathology Service, New South Wales Health Pathology; School of Medical Sciences, Faculty of Medicine, University of New South Wales Australia
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186
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Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M. Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development. Cell 2016; 166:664-678. [PMID: 27397507 PMCID: PMC4967450 DOI: 10.1016/j.cell.2016.06.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 04/15/2016] [Accepted: 06/03/2016] [Indexed: 11/30/2022]
Abstract
Nuclear pore complexes (NPCs) span the nuclear envelope (NE) and mediate nucleocytoplasmic transport. In metazoan oocytes and early embryos, NPCs reside not only within the NE, but also at some endoplasmic reticulum (ER) membrane sheets, termed annulate lamellae (AL). Although a role for AL as NPC storage pools has been discussed, it remains controversial whether and how they contribute to the NPC density at the NE. Here, we show that AL insert into the NE as the ER feeds rapid nuclear expansion in Drosophila blastoderm embryos. We demonstrate that NPCs within AL resemble pore scaffolds that mature only upon insertion into the NE. We delineate a topological model in which NE openings are critical for AL uptake that nevertheless occurs without compromising the permeability barrier of the NE. We finally show that this unanticipated mode of pore insertion is developmentally regulated and operates prior to gastrulation. Annulate lamellae (AL) NPCs insert into the nuclear envelope during interphase AL-NPCs are pore scaffolds devoid of most transport channel nucleoporins NE-openings enable AL insertion, yet the permeability barrier remains unperturbed AL-NPC insertion operates only before gastrulation
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Affiliation(s)
- Bernhard Hampoelz
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Marie-Therese Mackmull
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Pedro Machado
- European Molecular Biology Laboratory, Electron Microscopy Core Facility, 69117 Heidelberg, Germany
| | - Paolo Ronchi
- European Molecular Biology Laboratory, Electron Microscopy Core Facility, 69117 Heidelberg, Germany
| | - Khanh Huy Bui
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Nicole Schieber
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany
| | | | - Aleksandar Necakov
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Amparo Andrés-Pons
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | | | - Thomas Lecuit
- Aix-Marseille Université, CNRS, IBDM UMR 7288, 13009 Marseille, France
| | - Yannick Schwab
- European Molecular Biology Laboratory, Electron Microscopy Core Facility, 69117 Heidelberg, Germany; European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany.
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187
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Schorb M, Gaechter L, Avinoam O, Sieckmann F, Clarke M, Bebeacua C, Bykov YS, Sonnen AFP, Lihl R, Briggs JAG. New hardware and workflows for semi-automated correlative cryo-fluorescence and cryo-electron microscopy/tomography. J Struct Biol 2016; 197:83-93. [PMID: 27368127 PMCID: PMC5287355 DOI: 10.1016/j.jsb.2016.06.020] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/17/2016] [Accepted: 06/27/2016] [Indexed: 12/17/2022]
Abstract
Correlative light and electron microscopy allows features of interest defined by fluorescence signals to be located in an electron micrograph of the same sample. Rare dynamic events or specific objects can be identified, targeted and imaged by electron microscopy or tomography. To combine it with structural studies using cryo-electron microscopy or tomography, fluorescence microscopy must be performed while maintaining the specimen vitrified at liquid-nitrogen temperatures and in a dry environment during imaging and transfer. Here we present instrumentation, software and an experimental workflow that improves the ease of use, throughput and performance of correlated cryo-fluorescence and cryo-electron microscopy. The new cryo-stage incorporates a specially modified high-numerical aperture objective lens and provides a stable and clean imaging environment. It is combined with a transfer shuttle for contamination-free loading of the specimen. Optimized microscope control software allows automated acquisition of the entire specimen area by cryo-fluorescence microscopy. The software also facilitates direct transfer of the fluorescence image and associated coordinates to the cryo-electron microscope for subsequent fluorescence-guided automated imaging. Here we describe these technological developments and present a detailed workflow, which we applied for automated cryo-electron microscopy and tomography of various specimens.
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Affiliation(s)
- Martin Schorb
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Electron Microscopy Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Leander Gaechter
- Leica Microsystems (Schweiz) AG, Max Schmidheiny-Strasse 201, 9435 Heerbrugg, Switzerland
| | - Ori Avinoam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Frank Sieckmann
- Leica Microsystems GmbH, Am Friedensplatz 3, 68165 Mannheim, Germany
| | - Mairi Clarke
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Cecilia Bebeacua
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Yury S Bykov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Andreas F-P Sonnen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, EMBL/Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Reinhard Lihl
- Leica Mikrosysteme GmbH, Hernalser Hauptstraße 219, 1170 Vienna, Austria
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Molecular Medicine Partnership Unit, EMBL/Universitätsklinikum Heidelberg, Heidelberg, Germany.
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188
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Kukulski W, Picco A, Specht T, Briggs JA, Kaksonen M. Clathrin modulates vesicle scission, but not invagination shape, in yeast endocytosis. eLife 2016; 5. [PMID: 27341079 PMCID: PMC4945154 DOI: 10.7554/elife.16036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/23/2016] [Indexed: 01/18/2023] Open
Abstract
In a previous paper (Picco et al., 2015), the dynamic architecture of the protein machinery during clathrin-mediated endocytosis was visualized using a new live imaging and particle tracking method. Here, by combining this approach with correlative light and electron microscopy, we address the role of clathrin in this process. During endocytosis, clathrin forms a cage-like coat around the membrane and associated protein components. There is growing evidence that clathrin does not determine the membrane morphology of the invagination but rather modulates the progression of endocytosis. We investigate how the deletion of clathrin heavy chain impairs the dynamics and the morphology of the endocytic membrane in budding yeast. Our results show that clathrin is not required for elongating or shaping the endocytic membrane invagination. Instead, we find that clathrin contributes to the regularity of vesicle scission and thereby to controlling vesicle size. DOI:http://dx.doi.org/10.7554/eLife.16036.001
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Affiliation(s)
- Wanda Kukulski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Andrea Picco
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Tanja Specht
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - John Ag Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marko Kaksonen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Biochemistry, University of Geneva, Geneva, Switzerland
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189
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Shemesh M, Addadi S, Milstein Y, Geiger B, Addadi L. Study of Osteoclast Adhesion to Cortical Bone Surfaces: A Correlative Microscopy Approach for Concomitant Imaging of Cellular Dynamics and Surface Modifications. ACS APPLIED MATERIALS & INTERFACES 2016; 8:14932-43. [PMID: 26682493 PMCID: PMC4919753 DOI: 10.1021/acsami.5b08126] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bone remodeling relies on the coordinated functioning of osteoblasts, bone-forming cells, and osteoclasts, bone-resorbing cells. The effects of specific chemical and physical bone features on the osteoclast adhesive apparatus, the sealing zone ring, and their relation to resorption functionality are still not well-understood. We designed and implemented a correlative imaging method that enables monitoring of the same area of bone surface by time-lapse light microscopy, electron microscopy, and atomic force microscopy before, during, and after exposure to osteoclasts. We show that sealing zone rings preferentially develop around surface protrusions, with lateral dimensions of several micrometers, and ∼1 μm height. Direct overlay of sealing zone rings onto resorption pits on the bone surface shows that the rings adapt to pit morphology. The correlative procedure presented here is noninvasive and performed under ambient conditions, without the need for sample labeling. It can potentially be applied to study various aspects of cell-matrix interactions.
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Affiliation(s)
- Michal Shemesh
- Department
of Structural Biology and Department of Molecular Cell Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | | | | | - Benjamin Geiger
- Department
of Structural Biology and Department of Molecular Cell Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Lia Addadi
- Department
of Structural Biology and Department of Molecular Cell Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
- E-mail: . Phone: +972-8-934 2228
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190
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Bertipaglia C, Schneider S, Jakobi AJ, Tarafder AK, Bykov YS, Picco A, Kukulski W, Kosinski J, Hagen WJ, Ravichandran AC, Wilmanns M, Kaksonen M, Briggs JA, Sachse C. Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle. EMBO Rep 2016; 17:1044-60. [PMID: 27266708 PMCID: PMC4931565 DOI: 10.15252/embr.201541960] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/02/2016] [Indexed: 11/09/2022] Open
Abstract
Selective autophagy is the mechanism by which large cargos are specifically sequestered for degradation. The structural details of cargo and receptor assembly giving rise to autophagic vesicles remain to be elucidated. We utilize the yeast cytoplasm-to-vacuole targeting (Cvt) pathway, a prototype of selective autophagy, together with a multi-scale analysis approach to study the molecular structure of Cvt vesicles. We report the oligomeric nature of the major Cvt cargo Ape1 with a combined 2.8 Å X-ray and negative stain EM structure, as well as the secondary cargo Ams1 with a 6.3 Å cryo-EM structure. We show that the major dodecameric cargo prApe1 exhibits a tendency to form higher-order chain structures that are broken upon interaction with the receptor Atg19 in vitro The stoichiometry of these cargo-receptor complexes is key to maintaining the size of the Cvt aggregate in vivo Using correlative light and electron microscopy, we further visualize key stages of Cvt vesicle biogenesis. Our findings suggest that Atg19 interaction limits Ape1 aggregate size while serving as a vehicle for vacuolar delivery of tetrameric Ams1.
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Affiliation(s)
- Chiara Bertipaglia
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sarah Schneider
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Arjen J Jakobi
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Hamburg Unit, European Molecular Biology Laboratory, Hamburg, Germany
| | - Abul K Tarafder
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yury S Bykov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andrea Picco
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Wanda Kukulski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Wim Jh Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Arvind C Ravichandran
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthias Wilmanns
- Hamburg Unit, European Molecular Biology Laboratory, Hamburg, Germany
| | - Marko Kaksonen
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - John Ag Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Carsten Sachse
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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191
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Hanne J, Zila V, Heilemann M, Müller B, Kräusslich HG. Super-resolved insights into human immunodeficiency virus biology. FEBS Lett 2016; 590:1858-76. [PMID: 27117435 DOI: 10.1002/1873-3468.12186] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/13/2016] [Accepted: 04/21/2016] [Indexed: 11/06/2022]
Abstract
The recent development of fluorescence microscopy approaches overcoming the diffraction limit of light microscopy opened possibilities for studying small-scale cellular processes. The spatial resolution achieved by these novel techniques, together with the possibility to perform live-cell and multicolor imaging, make them ideally suited for visualization of native viruses and subviral structures within the complex environment of a host cell or organ, thus providing fundamentally new possibilities for investigating virus-cell interactions. Here, we review the use of super-resolution microscopy approaches to study virus-cell interactions, and discuss recent insights into human immunodeficiency virus biology obtained by exploiting these novel techniques.
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Affiliation(s)
- Janina Hanne
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany.,Optical Nanoscopy Division, German Cancer Research Center, Heidelberg, Germany
| | - Vojtech Zila
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
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192
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Curwin AJ, Brouwers N, Alonso Y Adell M, Teis D, Turacchio G, Parashuraman S, Ronchi P, Malhotra V. ESCRT-III drives the final stages of CUPS maturation for unconventional protein secretion. eLife 2016; 5. [PMID: 27115345 PMCID: PMC4868542 DOI: 10.7554/elife.16299] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 04/25/2016] [Indexed: 01/05/2023] Open
Abstract
The unconventional secretory pathway exports proteins that bypass the endoplasmic reticulum. In Saccharomyces cerevisiae, conditions that trigger Acb1 secretion via this pathway generate a Grh1 containing compartment composed of vesicles and tubules surrounded by a cup-shaped membrane and collectively called CUPS. Here we report a quantitative assay for Acb1 secretion that reveals requirements for ESCRT-I, -II, and -III but, surprisingly, without the involvement of the Vps4 AAA-ATPase. The major ESCRT-III subunit Snf7 localizes transiently to CUPS and this was accelerated in vps4Δ cells, correlating with increased Acb1 secretion. Microscopic analysis suggests that, instead of forming intraluminal vesicles with the help of Vps4, ESCRT-III/Snf7 promotes direct engulfment of preexisting Grh1 containing vesicles and tubules into a saccule to generate a mature Acb1 containing compartment. This novel multivesicular / multilamellar compartment, we suggest represents the stable secretory form of CUPS that is competent for the release of Acb1 to cells exterior. DOI:http://dx.doi.org/10.7554/eLife.16299.001 Cells produce thousands of different proteins with a variety of different roles in the body. Some proteins, for example the hormone insulin, perform roles outside of the cell and are released from cells in a process that has several stages. In the first step, newly-made insulin and many other “secretory” proteins enter a compartment called the endoplasmic reticulum. Once inside, these proteins can then be loaded into other compartments and transported to the edge of the cell. There is another class of secretory proteins that are released from the cell without first entering the endoplasmic reticulum, in a process termed “unconventional protein secretion”. A protein called Acb1 is released from yeast cells in this manner. Previous research identified a compartment that might be involved in this process. However, it is not clear how this compartment (named CUPS) forms, and what role it plays in unconventional protein secretion. Curwin et al. investigated how CUPS form in yeast cells, and whether the compartment contains Acb1 proteins. The experiments reveal that after CUPS form they need to mature into a form that is involved in the release of Acb1 proteins from the cell. This maturation process involves some, but not all, of the same genes as those involved in producing another type of compartment in cells called a multivesicular body. Acb1 is only found in the mature CUPS and multivesicular bodies are not involved in the release of this protein from the cell. Curwin et al.’s findings shed some light on how Acb1 and other secretory proteins can be released from cells without involving the endoplasmic reticulum. Future challenges are to reveal how CUPS capture cargo and find out how Acb1 leaves the CUPS to exit the cell. DOI:http://dx.doi.org/10.7554/eLife.16299.002
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Affiliation(s)
- Amy J Curwin
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Nathalie Brouwers
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Manuel Alonso Y Adell
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - David Teis
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriele Turacchio
- Institute of Protein Biochemistry, National Research Council of Italy, Naples, Italy
| | | | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vivek Malhotra
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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193
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Bykov YS, Cortese M, Briggs JAG, Bartenschlager R. Correlative light and electron microscopy methods for the study of virus-cell interactions. FEBS Lett 2016; 590:1877-95. [PMID: 27008928 DOI: 10.1002/1873-3468.12153] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 03/09/2016] [Accepted: 03/22/2016] [Indexed: 12/21/2022]
Abstract
Electron microscopy (EM) is an invaluable tool to study the interactions of viruses with cells, and the ultrastructural changes induced in host cells by virus infection. Light microscopy (LM) is a complementary tool with the potential to locate rare events, label specific components, and obtain dynamic information. The combination of LM and EM in correlative light and electron microscopy (CLEM) is particularly powerful. It can be used to complement a static EM image with dynamic data from live imaging, identify the ultrastructure observed in LM, or, conversely, provide molecular specificity data for a known ultrastructure. Here, we describe methods and strategies for CLEM, discuss their advantages and limitations, and review applications of CLEM to study virus-host interactions.
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Affiliation(s)
- Yury S Bykov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Germany
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Germany
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194
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van der Hoeven B, Oudshoorn D, Koster AJ, Snijder EJ, Kikkert M, Bárcena M. Biogenesis and architecture of arterivirus replication organelles. Virus Res 2016; 220:70-90. [PMID: 27071852 PMCID: PMC7111217 DOI: 10.1016/j.virusres.2016.04.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 02/06/2023]
Abstract
Arterivirus RNA synthesis presumably is associated with double-membrane vesicles (DMVs). Putative intermediates in DMV formation were detected in infected cells. Arterivirus-induced DMVs form a highly interconnected reticulovesicular network (RVN). Expression of the nsp2-3 replicase polyprotein fragment induces a comparable RVN. Nsp2-7 expression results in smaller DMVs, closer in size to DMVs found in infection.
All eukaryotic positive-stranded RNA (+RNA) viruses appropriate host cell membranes and transform them into replication organelles, specialized micro-environments that are thought to support viral RNA synthesis. Arteriviruses (order Nidovirales) belong to the subset of +RNA viruses that induce double-membrane vesicles (DMVs), similar to the structures induced by e.g. coronaviruses, picornaviruses and hepatitis C virus. In the last years, electron tomography has revealed substantial differences between the structures induced by these different virus groups. Arterivirus-induced DMVs appear to be closed compartments that are continuous with endoplasmic reticulum membranes, thus forming an extensive reticulovesicular network (RVN) of intriguing complexity. This RVN is remarkably similar to that described for the distantly related coronaviruses (also order Nidovirales) and sets them apart from other DMV-inducing viruses analysed to date. We review here the current knowledge and open questions on arterivirus replication organelles and discuss them in the light of the latest studies on other DMV-inducing viruses, particularly coronaviruses. Using the equine arteritis virus (EAV) model system and electron tomography, we present new data regarding the biogenesis of arterivirus-induced DMVs and uncover numerous putative intermediates in DMV formation. We generated cell lines that can be induced to express specific EAV replicase proteins and showed that DMVs induced by the transmembrane proteins nsp2 and nsp3 form an RVN and are comparable in topology and architecture to those formed during viral infection. Co-expression of the third EAV transmembrane protein (nsp5), expressed as part of a self-cleaving polypeptide that mimics viral polyprotein processing in infected cells, led to the formation of DMVs whose size was more homogenous and closer to what is observed upon EAV infection, suggesting a regulatory role for nsp5 in modulating membrane curvature and DMV formation.
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Affiliation(s)
- Barbara van der Hoeven
- Electron Microscopy Section, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Diede Oudshoorn
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Abraham J Koster
- Electron Microscopy Section, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Montserrat Bárcena
- Electron Microscopy Section, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands.
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195
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Yamauchi Y, Greber UF. Principles of Virus Uncoating: Cues and the Snooker Ball. Traffic 2016; 17:569-92. [PMID: 26875443 PMCID: PMC7169695 DOI: 10.1111/tra.12387] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/10/2016] [Accepted: 02/10/2016] [Indexed: 12/17/2022]
Abstract
Viruses are spherical or complex shaped carriers of proteins, nucleic acids and sometimes lipids and sugars. They are metastable and poised for structural changes. These features allow viruses to communicate with host cells during entry, and to release the viral genome, a process known as uncoating. Studies have shown that hundreds of host factors directly or indirectly support this process. The cell provides molecules that promote stepwise virus uncoating, and direct the virus to the site of replication. It acts akin to a snooker player who delivers accurate and timely shots (cues) to the ball (virus) to score. The viruses, on the other hand, trick (snooker) the host, hijack its homeostasis systems, and dampen innate immune responses directed against danger signals. In this review, we discuss how cellular cues, facilitators, and built‐in viral mechanisms promote uncoating. Cues come from receptors, enzymes and chemicals that act directly on the virus particle to alter its structure, trafficking and infectivity. Facilitators are defined as host factors that are involved in processes which indirectly enhance entry or uncoating. Unraveling the mechanisms of virus uncoating will continue to enhance understanding of cell functions, and help counteracting infections with chemicals and vaccines.
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Affiliation(s)
- Yohei Yamauchi
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Urs F Greber
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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196
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Abstract
A quiet revolution is under way in technologies used for nanoscale cellular imaging. Focused ion beams, previously restricted to the materials sciences and semiconductor fields, are rapidly becoming powerful tools for ultrastructural imaging of biological samples. Cell and tissue architecture, as preserved in plastic-embedded resin or in plunge-frozen form, can be investigated in three dimensions by scanning electron microscopy imaging of freshly created surfaces that result from the progressive removal of material using a focused ion beam. The focused ion beam can also be used as a sculpting tool to create specific specimen shapes such as lamellae or needles that can be analyzed further by transmission electron microscopy or by methods that probe chemical composition. Here we provide an in-depth primer to the application of focused ion beams in biology, including a guide to the practical aspects of using the technology, as well as selected examples of its contribution to the generation of new insights into subcellular architecture and mechanisms underlying host-pathogen interactions.
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197
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Hogstrom LJ, Guo SM, Murugadoss K, Bathe M. Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length scales. Interface Focus 2016; 6:20150081. [PMID: 26855758 DOI: 10.1098/rsfs.2015.0081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Brain function emerges from hierarchical neuronal structure that spans orders of magnitude in length scale, from the nanometre-scale organization of synaptic proteins to the macroscopic wiring of neuronal circuits. Because the synaptic electrochemical signal transmission that drives brain function ultimately relies on the organization of neuronal circuits, understanding brain function requires an understanding of the principles that determine hierarchical neuronal structure in living or intact organisms. Recent advances in fluorescence imaging now enable quantitative characterization of neuronal structure across length scales, ranging from single-molecule localization using super-resolution imaging to whole-brain imaging using light-sheet microscopy on cleared samples. These tools, together with correlative electron microscopy and magnetic resonance imaging at the nanoscopic and macroscopic scales, respectively, now facilitate our ability to probe brain structure across its full range of length scales with cellular and molecular specificity. As these imaging datasets become increasingly accessible to researchers, novel statistical and computational frameworks will play an increasing role in efforts to relate hierarchical brain structure to its function. In this perspective, we discuss several prominent experimental advances that are ushering in a new era of quantitative fluorescence-based imaging in neuroscience along with novel computational and statistical strategies that are helping to distil our understanding of complex brain structure.
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Affiliation(s)
- L J Hogstrom
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
| | - S M Guo
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
| | - K Murugadoss
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
| | - M Bathe
- Department of Biological Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue, Building 16, Room 255, Cambridge, MA 02139 , USA
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198
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Leo-Macias A, Agullo-Pascual E, Sanchez-Alonso JL, Keegan S, Lin X, Arcos T, Feng-Xia-Liang, Korchev YE, Gorelik J, Fenyö D, Rothenberg E, Rothenberg E, Delmar M. Nanoscale visualization of functional adhesion/excitability nodes at the intercalated disc. Nat Commun 2016; 7:10342. [PMID: 26787348 PMCID: PMC4735805 DOI: 10.1038/ncomms10342] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 12/01/2015] [Indexed: 02/06/2023] Open
Abstract
Intercellular adhesion and electrical excitability are considered separate cellular properties. Studies of myelinated fibres, however, show that voltage-gated sodium channels (VGSCs) aggregate with cell adhesion molecules at discrete subcellular locations, such as the nodes of Ranvier. Demonstration of similar macromolecular organization in cardiac muscle is missing. Here we combine nanoscale-imaging (single-molecule localization microscopy; electron microscopy; and ‘angle view' scanning patch clamp) with mathematical simulations to demonstrate distinct hubs at the cardiac intercalated disc, populated by clusters of the adhesion molecule N-cadherin and the VGSC NaV1.5. We show that the N-cadherin-NaV1.5 association is not random, that NaV1.5 molecules in these clusters are major contributors to cardiac sodium current, and that loss of NaV1.5 expression reduces intercellular adhesion strength. We speculate that adhesion/excitability nodes are key sites for crosstalk of the contractile and electrical molecular apparatus and may represent the structural substrate of cardiomyopathies in patients with mutations in molecules of the VGSC complex. In myelinated fibres conduction and adhesion proteins aggregate at discrete foci, but it is unclear if this organization is present in other excitable cells. Using nanoscale visualization and in silico techniques, the authors show that adhesion/excitability nodes exist at the intercalated discs of adult cardiac muscle.
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Affiliation(s)
- Alejandra Leo-Macias
- The Leon H Charney Division of Cardiology, New York University School of Medicine (NYU-SoM), 522 First Avenue, Smilow 805, New York, New York 10016, USA
| | - Esperanza Agullo-Pascual
- The Leon H Charney Division of Cardiology, New York University School of Medicine (NYU-SoM), 522 First Avenue, Smilow 805, New York, New York 10016, USA
| | - Jose L Sanchez-Alonso
- Imperial College, National Heart and Lung Institute, Department of Cardiac Medicine, Imperial Center for Translational and Experimental Medicine, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Sarah Keegan
- Center for Health Informatics and Bioinformatics, NYU-SoM, Translational Research Building, 227 East 30th Street, New York, New York 10016, USA
| | - Xianming Lin
- The Leon H Charney Division of Cardiology, New York University School of Medicine (NYU-SoM), 522 First Avenue, Smilow 805, New York, New York 10016, USA
| | - Tatiana Arcos
- The Leon H Charney Division of Cardiology, New York University School of Medicine (NYU-SoM), 522 First Avenue, Smilow 805, New York, New York 10016, USA
| | - Feng-Xia-Liang
- Microscopy Core, NYU-SoM, 522 First Avenue, Skirball Institute, 2nd Floor, New York, New York 10016, USA
| | - Yuri E Korchev
- Division of Medicine, Imperial College, Hammersmith Campus, Du Cane Road, London, London W12 0NN, UK
| | - Julia Gorelik
- Imperial College, National Heart and Lung Institute, Department of Cardiac Medicine, Imperial Center for Translational and Experimental Medicine, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - David Fenyö
- Center for Health Informatics and Bioinformatics, NYU-SoM, Translational Research Building, 227 East 30th Street, New York, New York 10016, USA
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, NYU-SoM, 522 First Avenue, MSB 3rd Floor, New York, New York 10016, USA
| | | | - Mario Delmar
- The Leon H Charney Division of Cardiology, New York University School of Medicine (NYU-SoM), 522 First Avenue, Smilow 805, New York, New York 10016, USA
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199
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Follain G, Mercier L, Osmani N, Harlepp S, Goetz JG. Seeing is believing: multi-scale spatio-temporal imaging towards in vivo cell biology. J Cell Sci 2016; 130:23-38. [DOI: 10.1242/jcs.189001] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
ABSTRACT
Life is driven by a set of biological events that are naturally dynamic and tightly orchestrated from the single molecule to entire organisms. Although biochemistry and molecular biology have been essential in deciphering signaling at a cellular and organismal level, biological imaging has been instrumental for unraveling life processes across multiple scales. Imaging methods have considerably improved over the past decades and now allow to grasp the inner workings of proteins, organelles, cells, organs and whole organisms. Not only do they allow us to visualize these events in their most-relevant context but also to accurately quantify underlying biomechanical features and, so, provide essential information for their understanding. In this Commentary, we review a palette of imaging (and biophysical) methods that are available to the scientific community for elucidating a wide array of biological events. We cover the most-recent developments in intravital imaging, light-sheet microscopy, super-resolution imaging, and correlative light and electron microscopy. In addition, we illustrate how these technologies have led to important insights in cell biology, from the molecular to the whole-organism resolution. Altogether, this review offers a snapshot of the current and state-of-the-art imaging methods that will contribute to the understanding of life and disease.
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Affiliation(s)
- Gautier Follain
- Microenvironmental Niche in Tumorigenesis and Targeted Therapy, Inserm U1109, MN3T, Strasbourg F-67200, France
- Université de Strasbourg, Strasbourg F-67000, France
- LabEx Medalis, Université de Strasbourg, Strasbourg, F-67000, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg F-67000, France
| | - Luc Mercier
- Microenvironmental Niche in Tumorigenesis and Targeted Therapy, Inserm U1109, MN3T, Strasbourg F-67200, France
- Université de Strasbourg, Strasbourg F-67000, France
- LabEx Medalis, Université de Strasbourg, Strasbourg, F-67000, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg F-67000, France
| | - Naël Osmani
- Microenvironmental Niche in Tumorigenesis and Targeted Therapy, Inserm U1109, MN3T, Strasbourg F-67200, France
- Université de Strasbourg, Strasbourg F-67000, France
- LabEx Medalis, Université de Strasbourg, Strasbourg, F-67000, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg F-67000, France
| | - Sébastien Harlepp
- Université de Strasbourg, Strasbourg F-67000, France
- DON: Optique ultrarapide et nanophotonique, IPCMS UMR7504, Strasbourg 67000, France
- LabEx NIE, Université de Strasbourg, Strasbourg F-67000, France
| | - Jacky G. Goetz
- Microenvironmental Niche in Tumorigenesis and Targeted Therapy, Inserm U1109, MN3T, Strasbourg F-67200, France
- Université de Strasbourg, Strasbourg F-67000, France
- LabEx Medalis, Université de Strasbourg, Strasbourg, F-67000, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg F-67000, France
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200
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van Elsland DM, Bos E, de Boer W, Overkleeft HS, Koster AJ, van Kasteren SI. Detection of bioorthogonal groups by correlative light and electron microscopy allows imaging of degraded bacteria in phagocytes. Chem Sci 2016; 7:752-758. [PMID: 28791116 PMCID: PMC5529995 DOI: 10.1039/c5sc02905h] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/21/2015] [Indexed: 01/07/2023] Open
Abstract
The interaction between parasites and phagocytic immune cells is a key inter-species interaction in biology. Normally, phagocytosis results in the killing of invaders, but obligate intracellular parasites hijack the pathway to ensure their survival and replication. The in situ study of these parasites in the phagocytic pathway is very difficult, as genetic modification is often complicated and, if successful, only allows the tracking of pathogen phagocytosis up until the degradation of the engineered reporter constructs. Here we combine bioorthogonal chemistry with correlative light-electron microscopy (CLEM) to follow bacterial processing in the phagolysosomal system. Labelled bacteria are produced using bioorthogonal non-canonical amino tagging (BONCAT), precluding the need for any genetic modification. The bacterial proteome - even during degradation - was then visualised using a novel CLEM-based approach. This allowed us to obtain high resolution information about the subcellular location of the degrading bacteria, even after the proteolytic degradation of reporter constructs. To further explore the potential of CLEM-based imaging of bioorthogonal functionalities, azide-labelled glycans were imaged by this same approach, as well as active-subpopulations of enzymes using a 2-step activity-based protein profiling strategy.
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Affiliation(s)
- Daphne M van Elsland
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
| | - Erik Bos
- Department of Molecular Cell Biology , Section Electron Microscopy , Leiden University Medical Center , Leiden , The Netherlands .
| | - Wouter de Boer
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
| | - Herman S Overkleeft
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
| | - Abraham J Koster
- Department of Molecular Cell Biology , Section Electron Microscopy , Leiden University Medical Center , Leiden , The Netherlands .
| | - Sander I van Kasteren
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
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