251
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Idrissi FZ, Geli MI. Zooming in on the molecular mechanisms of endocytic budding by time-resolved electron microscopy. Cell Mol Life Sci 2014; 71:641-57. [PMID: 24002236 PMCID: PMC11113444 DOI: 10.1007/s00018-013-1452-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 07/17/2013] [Accepted: 08/08/2013] [Indexed: 12/31/2022]
Abstract
Endocytic budding implies the remodeling of a plasma membrane portion from a flat sheet to a closed vesicle. Clathrin- and actin-mediated endocytosis in yeast has proven a very powerful model to study this process, with more than 60 evolutionarily conserved proteins involved in fashioning primary endocytic vesicles. Major progress in the field has been made during the last decades by defining the sequential recruitment of the endocytic machinery at the cell cortex using live-cell fluorescence microscopy. Higher spatial resolution has been recently achieved by developing time-resolved electron microscopy methods, allowing for the first time the visualization of changes in the plasma membrane shape, coupled to the dynamics of the endocytic machinery. Here, we highlight these advances and review recent findings from yeast and mammals that have increased our understanding of where and how endocytic proteins may apply force to remodel the plasma membrane during different stages of the process.
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Affiliation(s)
- Fatima-Zahra Idrissi
- Department of Cell Biology, Instituto de Biología Molecular de Barcelona (CSIC), Baldiri i Reixac 15, 08028, Barcelona, Spain,
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252
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McDonald KL. Rapid embedding methods into epoxy and LR White resins for morphological and immunological analysis of cryofixed biological specimens. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2014; 20:152-163. [PMID: 24252586 DOI: 10.1017/s1431927613013846] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A variety of specimens including bacteria, ciliates, choanoflagellates (Salpingoeca rosetta), zebrafish (Danio rerio) embryos, nematode worms (Caenorhabditis elegans), and leaves of white clover (Trifolium repens) plants were high pressure frozen, freeze-substituted, infiltrated with either Epon, Epon-Araldite, or LR White resins, and polymerized. Total processing time from freezing to blocks ready to section was about 6 h. For epoxy embedding the specimens were freeze-substituted in 1% osmium tetroxide plus 0.1% uranyl acetate in acetone. For embedding in LR White the freeze-substitution medium was 0.2% uranyl acetate in acetone. Rapid infiltration was achieved by centrifugation through increasing concentrations of resin followed by polymerization at 100°C for 1.5-2 h. The preservation of ultrastructure was comparable to standard freeze substitution and resin embedding methods that take days to complete. On-section immunolabeling results for actin and tubulin molecules were positive with very low background labeling. The LR White methods offer a safer, quicker, and less-expensive alternative to Lowicryl embedding of specimens processed for on-section immunolabeling without traditional aldehyde fixatives.
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Affiliation(s)
- Kent L McDonald
- Electron Microscope Laboratory, University of California, Berkeley, CA 94720, USA
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253
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Abstract
In this chapter we describe three different approaches for three-dimensional imaging of electron microscopic samples: serial sectioning transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM) tomography, and focused ion beam/scanning electron microscopy (FIB/SEM) tomography. With these methods, relatively large volumes of resin-embedded biological structures can be analyzed at resolutions of a few nm within a reasonable expenditure of time. The traditional method is serial sectioning and imaging the same area in all sections. Another method is TEM tomography that involves tilting a section in the electron beam and then reconstruction of the volume by back projection of the images. When the scanning transmission (STEM) mode is used, thicker sections (up to 1 μm) can be analyzed. The third approach presented here is focused ion beam/scanning electron microscopy (FIB/SEM) tomography, in which a sample is repeatedly milled with a focused ion beam (FIB) and each newly produced block face is imaged with the scanning electron microscope (SEM). This process can be repeated ad libitum in arbitrary small increments allowing 3D analysis of relatively large volumes such as eukaryotic cells. We show that resolution of this approach is considerably improved when the secondary electron signal is used. However, the most important prerequisite for three-dimensional imaging is good specimen preparation. For all three imaging methods, cryo-fixed (high-pressure frozen) and freeze-substituted samples have been used.
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254
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Koning RI, Celler K, Willemse J, Bos E, van Wezel GP, Koster AJ. Correlative cryo-fluorescence light microscopy and cryo-electron tomography of Streptomyces. Methods Cell Biol 2014; 124:217-39. [PMID: 25287843 DOI: 10.1016/b978-0-12-801075-4.00010-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Light microscopy and electron microscopy are complementary techniques that in a correlative approach enable identification and targeting of fluorescently labeled structures in situ for three-dimensional imaging at nanometer resolution. Correlative imaging allows electron microscopic images to be positioned in a broader temporal and spatial context. We employed cryo-correlative light and electron microscopy (cryo-CLEM), combining cryo-fluorescence light microscopy and cryo-electron tomography, on vitrified Streptomyces bacteria to study cell division. Streptomycetes are mycelial bacteria that grow as long hyphae and reproduce via sporulation. On solid media, Streptomyces subsequently form distinct aerial mycelia where cell division leads to the formation of unigenomic spores which separate and disperse to form new colonies. In liquid media, only vegetative hyphae are present divided by noncell separating crosswalls. Their multicellular life style makes them exciting model systems for the study of bacterial development and cell division. Complex intracellular structures have been visualized with transmission electron microscopy. Here, we describe the methods for cryo-CLEM that we applied for studying Streptomyces. These methods include cell growth, fluorescent labeling, cryo-fixation by vitrification, cryo-light microscopy using a Linkam cryo-stage, image overlay and relocation, cryo-electron tomography using a Titan Krios, and tomographic reconstruction. Additionally, methods for segmentation, volume rendering, and visualization of the correlative data are described.
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Affiliation(s)
- Roman I Koning
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, Leiden, The Netherlands
| | - Katherine Celler
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, The Netherlands
| | - Joost Willemse
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, The Netherlands
| | - Erik Bos
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, The Netherlands
| | - Abraham J Koster
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, Leiden, The Netherlands
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255
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Correlative light and electron microscopy: from live cell dynamic to 3D ultrastructure. Methods Mol Biol 2014; 1117:485-501. [PMID: 24357376 DOI: 10.1007/978-1-62703-776-1_21] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Correlative light and electron microscopy (CLEM) aims at combining data acquired from the same sample through both imaging modalities. Many combinations can be found in the literature where almost any kind of light microscopy (LM) has been associated to different processing in electron microscopy (EM) and applied to a wide variety of specimen, from cultured cells to multicellular organisms. In this chapter, we focus on a technique that intends to combine LM acquisition on living cells with transmission EM (TEM) analysis. A specific attention is given to the description of a method to bring precise coordinates to the object of interest, to allow a straightforward correlation between LM and EM. Moreover, we describe how, by using high-pressure freezing as a fixation technique, dynamic events observed at the LM are captured and studied at the ultrastructural level.
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256
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Fernández de Castro I, Sanz-Sánchez L, Risco C. Metallothioneins for correlative light and electron microscopy. Methods Cell Biol 2014; 124:55-70. [PMID: 25287836 DOI: 10.1016/b978-0-12-801075-4.00003-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Structural biologists have been working for decades on new strategies to identify proteins in cells unambiguously. We recently explored the possibilities of using the small metal-binding protein, metallothionein (MT), as a tag to detect proteins in transmission electron microscopy. It had been reported that, when fused with a protein of interest and treated in vitro with gold salts, a single MT tag will build an electron-dense gold cluster ~1 nm in diameter; we provided proof of this principle by demonstrating that MT can be used to detect intracellular proteins in bacteria and eukaryotic cells. The method, which is compatible with a variety of sample processing techniques, allows specific detection of proteins in cells with exceptional sensitivity. We illustrated the applicability of the technique in a series of studies to visualize the intracellular distribution of bacterial and viral proteins. Immunogold labeling was fundamental to confirm the specificity of the MT-gold method. When proteins were double-tagged with green fluorescent protein and MT, direct correlative light and electron microscopy allowed visualization of the same macromolecular complexes with different spatial resolutions. MT-gold tagging might also become a useful tool for mapping proteins into the 3D-density maps produced by (cryo)-electron tomography. New protocols will be needed for double or multiple labeling of proteins, using different versions of MT with fluorophores of different colors. Further research is also necessary to render the MT-gold labeling procedure compatible with immunogold labeling on Tokuyasu cryosections and with cryo-electron microscopy of vitreous sections.
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Affiliation(s)
- Isabel Fernández de Castro
- Cell Structure Laboratory, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Cantoblanco, Madrid, Spain
| | - Laura Sanz-Sánchez
- Cell Structure Laboratory, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Cantoblanco, Madrid, Spain
| | - Cristina Risco
- Cell Structure Laboratory, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Cantoblanco, Madrid, Spain
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257
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Oorschot VMJ, Sztal TE, Bryson-Richardson RJ, Ramm G. Immuno correlative light and electron microscopy on Tokuyasu cryosections. Methods Cell Biol 2014; 124:241-58. [PMID: 25287844 DOI: 10.1016/b978-0-12-801075-4.00011-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Finding a rare structure by electron microscopy is the equivalent of finding a "needle in a haystack." Correlative light- and immunoelectron microscopy (CLEM) on Tokuyasu cryosections is a sophisticated technique to address this challenge. Hereby, fluorescently labeled structures of interest are identified in an overview image by light microscopy and subsequently traced in electron microscopy. While the direct transfer and imaging of the same sections from optical to electron microscopy enables straightforward correlation, the sample preparation is crucial and technically demanding. We provide a detailed guide outlining the critical steps for sample embedding, cryosectioning, immunolabeling, and imaging. In the example provided, we use CLEM to trace aggregates formed in a zebrafish myopathy model expressing enhanced green fluorescent protein (eGFP) tagged actin. In our case, only a few muscle fibers express eGFP-actin with a subset of fibers containing aggregates. By fluorescence microscopy, we are able to identify the aggregates in the zebrafish tissue, and we subsequently, use immunoelectron microscopy to image the same structures at high resolution. The CLEM method described here using Tokuyasu cryosections can be applied to a large range of samples including small organisms, tissue samples, and cells.
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Affiliation(s)
| | - Tamar E Sztal
- School of Biological Sciences, Faculty of Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Georg Ramm
- Monash Micro Imaging, Monash University, Melbourne, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
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258
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Johannes L, Wunder C, Bassereau P. Bending "on the rocks"--a cocktail of biophysical modules to build endocytic pathways. Cold Spring Harb Perspect Biol 2014; 6:6/1/a016741. [PMID: 24384570 DOI: 10.1101/cshperspect.a016741] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Numerous biological processes rely on endocytosis. The construction of endocytic pits is achieved by a bewildering complexity of biochemical factors that function in clathrin-dependent and -independent pathways. In this review, we argue that this complexity can be conceptualized by a deceptively small number of physical principles that fall into two broad categories: passive mechanisms, such as asymmetric transbilayer stress, scaffolding, line tension, and crowding, and active mechanisms driven by mechanochemical enzymes and/or cytoskeleton. We illustrate how the functional identity of biochemical modules depends on system parameters such as local protein density on membranes, thus explaining some of the controversy in the field. Different modules frequently operate in parallel in the same step and often are shared by apparently divergent uptake processes. The emergence of a novel endocytic classification system may thus be envisioned in which functional modules are the elementary bricks.
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Affiliation(s)
- Ludger Johannes
- Institut Curie-Centre de Recherche, Traffic, Signaling and Delivery Group, 75248 Paris Cedex 05, France
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259
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Abstract
More than 30 years ago two groups independently reported the vitrification of pure water, which was until then regarded as impossible without a cryoprotectant [1, 2]. This opened the opportunity to cryo-electron microscopy (cryo-EM) to observe biological samples at nanometer scale, close to their native state. However, poor electron penetration through biological samples sets the limit for sample thickness to less than the average size of the mammalian cell. In order to image bulky specimens at the cell or tissue level in transmission electron microscopy (TEM), a sample has to be either thinned by focused ion beam or mechanically sectioned. The latter technique, Cryo-Electron Microscopy of Vitreous Section (CEMOVIS), employs cryo-ultramicrotomy to produce sections with thicknesses of 40-100 μm of vitreous biological material suitable for cryo-EM. CEMOVIS consists of trimming and sectioning a sample with a diamond knife, placing and attaching the section onto an electron microscopy grid, transferring the grid to the cryo-electron microscope and imaging. All steps must be carried on below devitrification temperature to obtain successful results. In this chapter we provide a step-by-step guide to produce and image vitreous sections of a biological sample.
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Affiliation(s)
- Petr Chlanda
- National Institute of Health, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
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260
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Abstract
In correlative microscopy, light microscopy provides the overview and orientation of the complex cells and tissue, while electron microscopy offers the detailed localization and correlation of subcellular structures. In this chapter we offer detailed high-quality electron microscopical preparation methods for optimum preservation of the cellular ultrastructure. From such preparations serial thin sections are collected and used for comparative histochemical, immunofluorescence, and immunogold staining.In light microscopy histological stains identify the orientation of the sample and immunofluorescence labeling facilitates to find the region of interest, namely, the labeled cells expressing the macromolecule under investigation. Sections, labeled with immunogold are analyzed by electron microscopy in order to identify the label within the cellular architecture at high resolution.
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Affiliation(s)
- Heinz Schwarz
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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261
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Gibson KH, Vorkel D, Meissner J, Verbavatz JM. Fluorescing the electron: strategies in correlative experimental design. Methods Cell Biol 2014; 124:23-54. [PMID: 25287835 DOI: 10.1016/b978-0-12-801075-4.00002-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Correlative light and electron microscopy (CLEM) encompasses a growing number of imaging techniques aiming to combine the benefits of light microscopy, which allows routine labeling of molecules and live-cell imaging of fluorescently tagged proteins with the resolution and ultrastructural detail provided by electron microscopy (EM). Here we review three different strategies that are commonly used in CLEM and we illustrate each approach with one detailed example of their application. The focus is on different options for sample preparation with their respective benefits as well as on the imaging workflows that can be used. The three strategies cover: (1) the combination of live-cell imaging with the high resolution of EM (time-resolved CLEM), (2) the need to identify a fluorescent cell of interest for further exploration by EM (cell sorting), and (3) the subcellular correlation of a fluorescent feature in a cell with its associated ultrastructural features (spatial CLEM). Finally, we discuss future directions for CLEM exploring the possibilities for combining super-resolution microscopy with EM.
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Affiliation(s)
- Kimberley H Gibson
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Daniela Vorkel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jana Meissner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jean-Marc Verbavatz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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262
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Peddie CJ, Liv N, Hoogenboom JP, Collinson LM. Integrated Light and Scanning Electron Microscopy of GFP-Expressing Cells. Methods Cell Biol 2014; 124:363-89. [DOI: 10.1016/b978-0-12-801075-4.00017-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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263
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Correlative Light Microscopy and Electron Tomography to Study Von Willebrand Factor Exocytosis from Vascular Endothelial Cells. Methods Cell Biol 2014; 124:71-92. [DOI: 10.1016/b978-0-12-801075-4.00004-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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264
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265
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Malatesta M, Pellicciari C, Cisterna B, Costanzo M, Galimberti V, Biggiogera M, Zancanaro C. Tracing nanoparticles and photosensitizing molecules at transmission electron microscopy by diaminobenzidine photo-oxidation. Micron 2013; 59:44-51. [PMID: 24530364 DOI: 10.1016/j.micron.2013.12.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/12/2013] [Accepted: 12/12/2013] [Indexed: 11/29/2022]
Abstract
During the last three decades, diaminobenzidine photo-oxidation has been applied in a variety of studies to correlate light and electron microscopy. Actually, when a fluorophore is excited by light, it can induce the oxidation of diaminobenzidine into an electron-dense osmiophilic product, which precipitates in close proximity to the fluorophore, thereby allowing its ultrastructural detection. This method has very recently been developed for two innovative applications: tracking the fate of fluorescently labeled nanoparticles in single cells, and detecting the subcellular location of photo-active molecules suitable for photodynamic therapy. These studies established that the cytochemical procedures exploiting diaminobenzidine photo-oxidation represent a reliable tool for detecting, inside the cells, with high sensitivity fluorescing molecules. These procedures are trustworthy even if the fluorescing molecules are present in very low amounts, either inside membrane-bounded organelles, or at the surface of the plasma membrane, or free in the cytosol. In particular, diaminobenzidine photo-oxidation allowed elucidating the mechanisms responsible for nanoparticles internalization in neuronal cells and for their escape from lysosomal degradation. As for the photo-active molecules, their subcellular distribution at the ultrastructural level provided direct evidence for the lethal multiorganelle photo-damage occurring after cell photo-sensitization. In addition, DAB photo-oxidized samples are suitable for the ultrastructural detection of organelle-specific molecules by post-embedding gold immunolabeling.
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Affiliation(s)
- M Malatesta
- Department of Neurological and Movement Sciences (Anatomy and Histology Section), University of Verona, Strada Le Grazie 8, 37134 Verona, Italy.
| | - C Pellicciari
- Department of Biology and Biotechnology "Lazzaro Spallanzani" (Laboratory of Cell Biology and Neurobiology), University of Pavia, Via A. Ferrata, 9, 27100 Pavia, Italy.
| | - B Cisterna
- Department of Neurological and Movement Sciences (Anatomy and Histology Section), University of Verona, Strada Le Grazie 8, 37134 Verona, Italy.
| | - M Costanzo
- Department of Neurological and Movement Sciences (Anatomy and Histology Section), University of Verona, Strada Le Grazie 8, 37134 Verona, Italy.
| | - V Galimberti
- Department of Biology and Biotechnology "Lazzaro Spallanzani" (Laboratory of Cell Biology and Neurobiology), University of Pavia, Via A. Ferrata, 9, 27100 Pavia, Italy.
| | - M Biggiogera
- Department of Biology and Biotechnology "Lazzaro Spallanzani" (Laboratory of Cell Biology and Neurobiology), University of Pavia, Via A. Ferrata, 9, 27100 Pavia, Italy.
| | - C Zancanaro
- Department of Neurological and Movement Sciences (Anatomy and Histology Section), University of Verona, Strada Le Grazie 8, 37134 Verona, Italy.
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266
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Schorb M, Briggs JAG. Correlated cryo-fluorescence and cryo-electron microscopy with high spatial precision and improved sensitivity. Ultramicroscopy 2013; 143:24-32. [PMID: 24275379 DOI: 10.1016/j.ultramic.2013.10.015] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/29/2013] [Accepted: 10/31/2013] [Indexed: 01/24/2023]
Abstract
Performing fluorescence microscopy and electron microscopy on the same sample allows fluorescent signals to be used to identify and locate features of interest for subsequent imaging by electron microscopy. To carry out such correlative microscopy on vitrified samples appropriate for structural cryo-electron microscopy it is necessary to perform fluorescence microscopy at liquid-nitrogen temperatures. Here we describe an adaptation of a cryo-light microscopy stage to permit use of high-numerical aperture objectives. This allows high-sensitivity and high-resolution fluorescence microscopy of vitrified samples. We describe and apply a correlative cryo-fluorescence and cryo-electron microscopy workflow together with a fiducial bead-based image correlation procedure. This procedure allows us to locate fluorescent bacteriophages in cryo-electron microscopy images with an accuracy on the order of 50 nm, based on their fluorescent signal. It will allow the user to precisely and unambiguously identify and locate objects and events for subsequent high-resolution structural study, based on fluorescent signals.
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Affiliation(s)
- Martin Schorb
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.
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267
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Bhave M, Papanikou E, Iyer P, Pandya K, Jain BK, Ganguly A, Sharma C, Pawar K, Austin J, Day KJ, Rossanese OW, Glick BS, Bhattacharyya D. Golgi enlargement in Arf-depleted yeast cells is due to altered dynamics of cisternal maturation. J Cell Sci 2013; 127:250-7. [PMID: 24190882 DOI: 10.1242/jcs.140996] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Regulation of the size and abundance of membrane compartments is a fundamental cellular activity. In Saccharomyces cerevisiae, disruption of the ADP-ribosylation factor 1 (ARF1) gene yields larger and fewer Golgi cisternae by partially depleting the Arf GTPase. We observed a similar phenotype with a thermosensitive mutation in Nmt1, which myristoylates and activates Arf. Therefore, partial depletion of Arf is a convenient tool for dissecting mechanisms that regulate Golgi structure. We found that in arf1Δ cells, late Golgi structure is particularly abnormal, with the number of late Golgi cisternae being severely reduced. This effect can be explained by selective changes in cisternal maturation kinetics. The arf1Δ mutation causes early Golgi cisternae to mature more slowly and less frequently, but does not alter the maturation of late Golgi cisternae. These changes quantitatively explain why late Golgi cisternae are fewer in number and correspondingly larger. With a stacked Golgi, similar changes in maturation kinetics could be used by the cell to modulate the number of cisternae per stack. Thus, the rates of processes that transform a maturing compartment can determine compartmental size and copy number.
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Affiliation(s)
- Madhura Bhave
- Advanced Centre for Treatment Research & Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, 410210 MH, India
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268
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Kopek BG, Shtengel G, Grimm JB, Clayton DA, Hess HF. Correlative photoactivated localization and scanning electron microscopy. PLoS One 2013; 8:e77209. [PMID: 24204771 PMCID: PMC3808397 DOI: 10.1371/journal.pone.0077209] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/03/2013] [Indexed: 11/26/2022] Open
Abstract
The ability to localize proteins precisely within subcellular space is crucial to understanding the functioning of biological systems. Recently, we described a protocol that correlates a precise map of fluorescent fusion proteins localized using three-dimensional super-resolution optical microscopy with the fine ultrastructural context of three-dimensional electron micrographs. While it achieved the difficult simultaneous objectives of high photoactivated fluorophore preservation and ultrastructure preservation, it required a super-resolution optical and specialized electron microscope that is not available to many researchers. We present here a faster and more practical protocol with the advantage of a simpler two-dimensional optical (Photoactivated Localization Microscopy (PALM)) and scanning electron microscope (SEM) system that retains the often mutually exclusive attributes of fluorophore preservation and ultrastructure preservation. As before, cryosections were prepared using the Tokuyasu protocol, but the staining protocol was modified to be amenable for use in a standard SEM without the need for focused ion beam ablation. We show the versatility of this technique by labeling different cellular compartments and structures including mitochondrial nucleoids, peroxisomes, and the nuclear lamina. We also demonstrate simultaneous two-color PALM imaging with correlated electron micrographs. Lastly, this technique can be used with small-molecule dyes as demonstrated with actin labeling using phalloidin conjugated to a caged dye. By retaining the dense protein labeling expected for super-resolution microscopy combined with ultrastructural preservation, simplifying the tools required for correlative microscopy, and expanding the number of useful labels we expect this method to be accessible and valuable to a wide variety of researchers.
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Affiliation(s)
- Benjamin G. Kopek
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
- * E-mail:
| | - Gleb Shtengel
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Jonathan B. Grimm
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - David A. Clayton
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Harald F. Hess
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
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269
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Schellenberger P, Kaufmann R, Siebert CA, Hagen C, Wodrich H, Grünewald K. High-precision correlative fluorescence and electron cryo microscopy using two independent alignment markers. Ultramicroscopy 2013; 143:41-51. [PMID: 24262358 PMCID: PMC4045203 DOI: 10.1016/j.ultramic.2013.10.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 11/29/2022]
Abstract
Correlative light and electron microscopy (CLEM) is an emerging technique which combines functional information provided by fluorescence microscopy (FM) with the high-resolution structural information of electron microscopy (EM). So far, correlative cryo microscopy of frozen-hydrated samples has not reached better than micrometre range accuracy. Here, a method is presented that enables the correlation between fluorescently tagged proteins and electron cryo tomography (cryoET) data with nanometre range precision. Specifically, thin areas of vitrified whole cells are examined by correlative fluorescence cryo microscopy (cryoFM) and cryoET. Novel aspects of the presented cryoCLEM workflow not only include the implementation of two independent electron dense fluorescent markers to improve the precision of the alignment, but also the ability of obtaining an estimate of the correlation accuracy for each individual object of interest. The correlative workflow from plunge-freezing to cryoET is detailed step-by-step for the example of locating fluorescence-labelled adenovirus particles trafficking inside a cell. Vitrified mammalian cell were imaged by fluorescence and electron cryo microscopy. TetraSpeck fluorescence markers were added to correct shifts between cryo fluorescence channels. FluoSpheres fiducials were used as reference points to assign new coordinates to cryoEM images. Adenovirus particles were localised with an average correlation precision of 63 nm.
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Affiliation(s)
- Pascale Schellenberger
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Rainer Kaufmann
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - C Alistair Siebert
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christoph Hagen
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Harald Wodrich
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, University of Bordeaux SEGALEN, 146 rue Leo Seignat, 33076 Bordeaux, France
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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270
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Opening windows into the cell: focused-ion-beam milling for cryo-electron tomography. Curr Opin Struct Biol 2013; 23:771-7. [DOI: 10.1016/j.sbi.2013.08.006] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/12/2013] [Accepted: 08/29/2013] [Indexed: 11/16/2022]
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271
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Malatesta M, Zancanaro C, Costanzo M, Cisterna B, Pellicciari C. Simultaneous ultrastructural analysis of fluorochrome-photoconverted diaminobenzidine and gold immunolabelling in cultured cells. Eur J Histochem 2013; 57:e26. [PMID: 24085275 PMCID: PMC3794357 DOI: 10.4081/ejh.2013.e26] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 08/02/2013] [Accepted: 08/07/2013] [Indexed: 12/19/2022] Open
Abstract
Diaminobenzidine photoconversion is a technique by which a fluorescent dye is transformed into a stably insoluble, brown, electrondense signal, thus enabling examination at both bright field light microscopy and transmission electron microscopy. In this work, a procedure is proposed for combining photoconversion and immunoelectron microscopy: in vitro cell cultures have been first submitted to photoconversion to analyse the intracellular fate of either fluorescent nanoparticles or photosensitizing molecules, then processed for transmission electron microscopy; different fixative solutions and embedding media have been used, and the ultrathin sections were finally submitted to post-embedding immunogold cytochemistry. Under all conditions the photoconversion reaction product and the target antigen were properly detected in the same section; Epon-embedded, osmicated samples required a pre-treatment with sodium metaperiodate to unmask the antigenic sites. This simple and reliable procedure exploits a single sample to simultaneously localise the photoconversion product and a variety of antigens allowing a specific identification of subcellular organelles at the ultrastructural level.
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Affiliation(s)
- M Malatesta
- Dipartimento di Scienze Neurologiche e del Movimento, sezione di Anatomia e Istologia, Università di Verona.
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272
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Müller B, Heilemann M. Shedding new light on viruses: super-resolution microscopy for studying human immunodeficiency virus. Trends Microbiol 2013; 21:522-33. [PMID: 23916730 DOI: 10.1016/j.tim.2013.06.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/20/2013] [Accepted: 06/27/2013] [Indexed: 01/09/2023]
Abstract
For more than 70 years electron microscopy (EM) techniques have played an important role in investigating structures of enveloped viruses. By contrast, use of fluorescence microscopy (FM) methods for this purpose was limited by the fact that the size of virus particles is generally around or below the diffraction limit of light microscopy. Various super-resolution (SR) fluorescence imaging techniques developed over the past two decades bypass the diffraction limit of light microscopy, allowing visualization of subviral details and bridging the gap between conventional FM and EM methods. We summarize here findings on human immunodeficiency virus (HIV-1) obtained using SR-FM techniques. Although the number of published studies is currently limited and some of the pioneering analyses also covered methodological or descriptive aspects, recent publications clearly indicate the potential to approach open questions in HIV-1 replication from a new angle.
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Affiliation(s)
- Barbara Müller
- Department of Infectious Diseases, Virology, University of Heidelberg, Germany.
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273
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ZONNEVYLLE A, VAN TOL R, LIV N, NARVAEZ A, EFFTING A, KRUIT P, HOOGENBOOM J. Integration of a high-NA light microscope in a scanning electron microscope. J Microsc 2013; 252:58-70. [DOI: 10.1111/jmi.12071] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 06/25/2013] [Indexed: 11/28/2022]
Affiliation(s)
- A.C. ZONNEVYLLE
- Department of Imaging Science and Technology; Faculty of Applied Sciences; Delft University of Technology; Lorentzweg the Netherlands
| | - R.F.C. VAN TOL
- Electronic and Mechanical Services (DEMO); Delft University of Technology; Mekelweg the Netherlands
| | - N. LIV
- Department of Imaging Science and Technology; Faculty of Applied Sciences; Delft University of Technology; Lorentzweg the Netherlands
| | - A.C. NARVAEZ
- Department of Imaging Science and Technology; Faculty of Applied Sciences; Delft University of Technology; Lorentzweg the Netherlands
| | | | - P. KRUIT
- Department of Imaging Science and Technology; Faculty of Applied Sciences; Delft University of Technology; Lorentzweg the Netherlands
| | - J.P. HOOGENBOOM
- Department of Imaging Science and Technology; Faculty of Applied Sciences; Delft University of Technology; Lorentzweg the Netherlands
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274
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Briggs J. John Briggs: a closer look at HIV and coated vesicles. Interview by Caitlin Sedgwick. J Cell Biol 2013; 201:966-7. [PMID: 23798726 PMCID: PMC3691461 DOI: 10.1083/jcb.2017pi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Briggs studies the organization of viral and cellular coat proteins using cryo-electron microscopy.
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275
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Aricescu AR, Owens RJ. Expression of recombinant glycoproteins in mammalian cells: towards an integrative approach to structural biology. Curr Opin Struct Biol 2013; 23:345-56. [PMID: 23623336 DOI: 10.1016/j.sbi.2013.04.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 03/30/2013] [Accepted: 04/02/2013] [Indexed: 01/26/2023]
Abstract
Mammalian cells are rapidly becoming the system of choice for the production of recombinant glycoproteins for structural biology applications. Their use has enabled the structural investigation of a whole new set of targets including large, multi-domain and highly glycosylated eukaryotic cell surface receptors and their supra-molecular assemblies. We summarize the technical advances that have been made in mammalian expression technology and highlight some of the structural insights that have been obtained using these methods. Looking forward, it is clear that mammalian cell expression will provide exciting and unique opportunities for an integrative approach to the structural study of proteins, especially of human origin and medically relevant, by bridging the gap between the purified state and the cellular context.
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Affiliation(s)
- A Radu Aricescu
- Division of Structural Biology, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
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276
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Yang Z, Hu B, Zhang Y, Luo Q, Gong H. Development of a plastic embedding method for large-volume and fluorescent-protein-expressing tissues. PLoS One 2013; 8:e60877. [PMID: 23577174 PMCID: PMC3618106 DOI: 10.1371/journal.pone.0060877] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 03/04/2013] [Indexed: 02/02/2023] Open
Abstract
Fluorescent proteins serve as important biomarkers for visualizing both subcellular organelles in living cells and structural and functional details in large-volume tissues or organs. However, current techniques for plastic embedding are limited in their ability to preserve fluorescence while remaining suitable for micro-optical sectioning tomography of large-volume samples. In this study, we quantitatively evaluated the fluorescence preservation and penetration time of several commonly used resins in a Thy1-eYFP-H transgenic whole mouse brain, including glycol methacrylate (GMA), LR White, hydroxypropyl methacrylate (HPMA) and Unicryl. We found that HMPA embedding doubled the eYFP fluorescence intensity but required long durations of incubation for whole brain penetration. GMA, Unicryl and LR White each penetrated the brain rapidly but also led to variable quenching of eYFP fluorescence. Among the fast-penetrating resins, GMA preserved fluorescence better than LR White and Unicryl. We found that we could optimize the GMA formulation by reducing the polymerization temperature, removing 4-methoxyphenol and adjusting the pH of the resin solution to be alkaline. By optimizing the GMA formulation, we increased percentage of eYFP fluorescence preservation in GMA-embedded brains nearly two-fold. These results suggest that modified GMA is suitable for embedding large-volume tissues such as whole mouse brain and provide a novel approach for visualizing brain-wide networks.
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Affiliation(s)
- Zhongqin Yang
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Bihe Hu
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhui Zhang
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China
- * E-mail:
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277
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Buser C, Drubin DG. Ultrastructural imaging of endocytic sites in Saccharomyces cerevisiae by transmission electron microscopy and immunolabeling. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2013; 19:381-92. [PMID: 23458500 PMCID: PMC4113337 DOI: 10.1017/s1431927612014304] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Defining the ultrastructure of endocytic sites and localization of endocytic proteins in Saccharomyces cerevisiae by immunoelectron microscopy is central in understanding the mechanisms of membrane deformation and scission during endocytosis. We show that an improved sample preparation protocol based on high-pressure freezing, freeze substitution, and low-temperature embedding allows us to maintain the cellular fine structure and to immunolabel green fluorescent protein-tagged endocytic proteins or actin in the same sections. Using this technique we analyzed the stepwise deformation of endocytic membranes and immunolocalized the endocytic proteins Abp1p, Sla1p, Rvs167p, and actin, and were able to draw a clear ultrastructural distinction between endocytic sites and eisosomes by immunolocalizing Pil1p. In addition to defining the geometry and the fine structure of budding yeast endocytic sites, we observed associated actin filaments forming a cage-like meshwork around the endocytic membrane.
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Affiliation(s)
- Christopher Buser
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David G. Drubin
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
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278
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Hanssen E, Dekiwadia C, Riglar DT, Rug M, Lemgruber L, Cowman AF, Cyrklaff M, Kudryashev M, Frischknecht F, Baum J, Ralph SA. Electron tomography of Plasmodium falciparum merozoites reveals core cellular events that underpin erythrocyte invasion. Cell Microbiol 2013; 15:1457-72. [PMID: 23461734 DOI: 10.1111/cmi.12132] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 11/29/2022]
Abstract
Erythrocyte invasion by merozoites forms of the malaria parasite is a key step in the establishment of human malaria disease. To date, efforts to understand cellular events underpinning entry have been limited to insights from non-human parasites, with no studies at sub-micrometer resolution undertaken using the most virulent human malaria parasite, Plasmodium falciparum. This leaves our understanding of the dynamics of merozoite sub-cellular compartments during infectionincomplete, in particular that of the secretory organelles. Using advances in P. falciparum merozoite isolation and new imaging techniques we present a three-dimensional study of invasion using electron microscopy, cryo-electron tomography and cryo-X-ray tomography. We describe the core architectural features of invasion and identify fusion between rhoptries at the commencement of invasion as a hitherto overlooked event that likely provides a critical step that initiates entry. Given the centrality of merozoite organelle proteins to vaccine development, these insights provide a mechanistic framework to understand therapeutic strategies targeted towards the cellular events of invasion.
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Affiliation(s)
- Eric Hanssen
- Advanced Microscopy Facility and Center of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic., 3010, Australia
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279
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Cortese K, Vicidomini G, Gagliani MC, Boccacci P, Diaspro A, Tacchetti C. High data output method for 3-D correlative light-electron microscopy using ultrathin cryosections. Methods Mol Biol 2013; 950:417-37. [PMID: 23086888 DOI: 10.1007/978-1-62703-137-0_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Investigation of intracellular dynamics requires a detailed description of the molecular topography and ultrastructural morphology of the cell, for example, the position of a protein in relation to a given compartment of the cell and the morphology of the compartment. Standard fluorescence light microscopy (FLM) localizes proteins in living or fixed cells with a resolution of few hundreds of nanometers, but the unlabeled cellular context is partially missing. Electron microscopy (EM) techniques, such as immuno-EM, reveal protein topology with a few tens of nanometer resolution and retain the cellular context. However, EM analysis shows shortcomings compared to FLM, such as, lower statistical output, applicability only to fixed cells, and higher technical difficulties. To bridge the gap between fluorescent cell imaging and EM, several laboratories have developed methods for correlative light-electron microscopy (CLEM). In CLEM, a limited number of fluorescently labeled cell compartments are first imaged by light microscopy and then visualized and analyzed by EM. Recently, two different CLEM approaches using the EM cryo-immunogold method have been developed to extend the analysis to a high number of regions of interest and to correlate the topology of specific antigens. In this chapter, we describe one of these methods, the High Data Output CLEM (HDO-CLEM) approach. The major benefits of HDO-CLEM are the possibility to (1) correlate several hundreds of events at the same time, (2) perform three-dimensional (3D) correlation, (3) immunolabel both endogenous and recombinantly tagged proteins at the same time, and (4) combine the high data analysis capability of FLM with the high precision-accuracy of transmission electron microscopy in a CLEM hybrid morphometric analysis. We have identified and optimized critical steps in sample preparation, defined routines for sample analysis and retracing of regions of interest, developed software for semi/fully automatic 3D FLM reconstruction and defined preliminary conditions for a hybrid light/electron microscopy morphometry approach.
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Affiliation(s)
- Katia Cortese
- MicroscoBio Research Center, Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
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280
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Tranfield EM, Walker DC. The ultrastructure of animal atherosclerosis: What has been done, and the electron microscopy advancements that could help scientists answer new biological questions. Micron 2013; 46:1-11. [DOI: 10.1016/j.micron.2012.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 12/01/2012] [Indexed: 12/20/2022]
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281
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Faas F, Bárcena M, Agronskaia A, Gerritsen H, Moscicka K, Diebolder C, van Driel L, Limpens R, Bos E, Ravelli R, Koning R, Koster A. Localization of fluorescently labeled structures in frozen-hydrated samples using integrated light electron microscopy. J Struct Biol 2013; 181:283-90. [DOI: 10.1016/j.jsb.2012.12.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 12/05/2012] [Accepted: 12/10/2012] [Indexed: 10/27/2022]
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282
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Liv N, Zonnevylle AC, Narvaez AC, Effting APJ, Voorneveld PW, Lucas MS, Hardwick JC, Wepf RA, Kruit P, Hoogenboom JP. Simultaneous correlative scanning electron and high-NA fluorescence microscopy. PLoS One 2013; 8:e55707. [PMID: 23409024 PMCID: PMC3568124 DOI: 10.1371/journal.pone.0055707] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 12/28/2012] [Indexed: 02/04/2023] Open
Abstract
Correlative light and electron microscopy (CLEM) is a unique method for investigating biological structure-function relations. With CLEM protein distributions visualized in fluorescence can be mapped onto the cellular ultrastructure measured with electron microscopy. Widespread application of correlative microscopy is hampered by elaborate experimental procedures related foremost to retrieving regions of interest in both modalities and/or compromises in integrated approaches. We present a novel approach to correlative microscopy, in which a high numerical aperture epi-fluorescence microscope and a scanning electron microscope illuminate the same area of a sample at the same time. This removes the need for retrieval of regions of interest leading to a drastic reduction of inspection times and the possibility for quantitative investigations of large areas and datasets with correlative microscopy. We demonstrate Simultaneous CLEM (SCLEM) analyzing cell-cell connections and membrane protrusions in whole uncoated colon adenocarcinoma cell line cells stained for actin and cortactin with AlexaFluor488. SCLEM imaging of coverglass-mounted tissue sections with both electron-dense and fluorescence staining is also shown.
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Affiliation(s)
- Nalan Liv
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - A. Christiaan Zonnevylle
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Angela C. Narvaez
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | | | - Philip W. Voorneveld
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Miriam S. Lucas
- Electron Microscopy ETH Zurich - EMEZ, ETH Zurich, Zurich, Switzerland
| | - James C. Hardwick
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Roger A. Wepf
- Electron Microscopy ETH Zurich - EMEZ, ETH Zurich, Zurich, Switzerland
| | - Pieter Kruit
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Jacob P. Hoogenboom
- Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
- * E-mail:
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283
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Guerrero-Ferreira RC, Wright ER. Cryo-electron tomography of bacterial viruses. Virology 2013; 435:179-86. [PMID: 23217626 DOI: 10.1016/j.virol.2012.08.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/08/2012] [Accepted: 08/19/2012] [Indexed: 01/15/2023]
Abstract
Bacteriophage particles contain both simple and complex macromolecular assemblages and machines that enable them to regulate the infection process under diverse environmental conditions with a broad range of bacterial hosts. Recent developments in cryo-electron tomography (cryo-ET) make it possible to observe the interactions of bacteriophages with their host cells under native-state conditions at unprecedented resolution and in three-dimensions. This review describes the application of cryo-ET to studies of bacteriophage attachment, genome ejection, assembly and egress. Current topics of investigation and future directions in the field are also discussed.
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Affiliation(s)
- Ricardo C Guerrero-Ferreira
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
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284
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Badia-Martinez D, Oksanen HM, Stuart DI, Abrescia NGA. Combined approaches to study virus structures. Subcell Biochem 2013; 68:203-246. [PMID: 23737053 DOI: 10.1007/978-94-007-6552-8_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A virus particle must work as a safe box for protecting its genome, but at the same time it has to undergo dramatic conformational changes in order to preserve itself by propagating in a cell infection. Thus, viruses are miniaturized wonders whose structural complexity requires them to be investigated by a combination of different techniques that can tackle both static and dynamic processes. In this chapter we will illustrate how major structural techniques such as X-ray crystallography and electron microscopy have been and can be combined with other techniques to determine the structure of complex viruses. The power of these hybrid method approaches are revealed through the various examples provided.
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Affiliation(s)
- Daniel Badia-Martinez
- Structural Biology Unit, CICbioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain
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285
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Microscopy: Progress and prospect. J Microsc Ultrastruct 2013. [DOI: 10.1016/j.jmau.2013.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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286
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Kruhlak MJ. Correlative fluorescence and EFTEM imaging of the organized components of the mammalian nucleus. Methods Mol Biol 2013; 950:397-416. [PMID: 23086887 PMCID: PMC7581281 DOI: 10.1007/978-1-62703-137-0_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The cell nucleus contains many distinct subnuclear compartments, domains, and bodies that vary in their composition, structure, and function. While the cellular constituents that occupy the subnuclear regions may be well known, defining the structural details of the molecular assembly of the constituents has been more difficult. A correlative fluorescence and energy-filtering transmission electron microscopy (EFTEM) imaging method has the ability to provide these details. The correlative microscopy method described here allows the tracking of subnuclear structures from specific cells by fluorescence microscopy and then, using electron energy loss imaging in the transmission electron microscope, reveals the ultrastructural features of the nuclear components along with endogenous elemental information that relates directly to the biochemical composition of the structure. The ultrastructural features and composition of well-characterized PML bodies and interchromatin granule clusters are compared to those of ligand-activated glucocorticoid receptor (GR) foci, with GR foci containing fibrogranular nucleic acid-containing features and PML bodies being devoid of nucleic acid.
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Affiliation(s)
- Michael J Kruhlak
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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287
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Pellicciari C, Giagnacovo M, Cisterna B, Costanzo M, Croce AC, Bottiroli G, Malatesta M. Ultrastructural detection of photosensitizing molecules by fluorescence photoconversion of diaminobenzidine. Histochem Cell Biol 2012; 139:863-71. [DOI: 10.1007/s00418-012-1071-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2012] [Indexed: 12/14/2022]
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288
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Karreman MA, Van Donselaar EG, Agronskaia AV, Verrips CT, Gerritsen HC. Novel contrasting and labeling procedures for correlative microscopy of thawed cryosections. J Histochem Cytochem 2012; 61:236-47. [PMID: 23264637 DOI: 10.1369/0022155412473756] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
One of the major challenges for correlative microscopy is the preparation of the sample; the protocols for transmission electron microscopy (TEM) and fluorescence microscopy (FM) often prove to be incompatible. Here, we introduce 2+Staining: an improved contrasting procedure for Tokuyasu sections that yields both excellent positive membrane contrast in the TEM and bright fluorescence of the probe labeled on the section. 2+Staining involves the contrasting of the immunolabeled sections with 1% osmium tetroxide, 2% uranyl acetate and lead citrate in sequential steps, followed by embedding in 1.8% methyl cellulose. In addition, we demonstrate an amplification of the fluorescent signal by introducing additional antibody incubation steps to the immunolabeling procedure. The methods were validated using the integrated laser and electron microscope (iLEM), a novel tool for correlative microscopy combining FM and TEM in a single setup. The approaches were tested on HL-60 cells labeled for lysosomal-associated membrane protein 2 (LAMP-2) and on sections of muscle from a facioscapulohumeral dystrophy mouse model. Yielding excellent results and greatly expediting the workflow, the methods are of great value for those working in the field of correlative microscopy and indispensible for future users of integrated correlative microscopy.
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289
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Takizawa T, Robinson JM. Correlative fluorescence and transmission electron microscopy in tissues. Methods Cell Biol 2012; 111:37-57. [PMID: 22857922 DOI: 10.1016/b978-0-12-416026-2.00003-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Correlative microscopy has meant different things over the years; currently, this term refers to imaging the same exact structures with two or more imaging modalities. This commonly involves combining fluorescence and electron microscopy. Much of the recent work related to correlative microscopy has been done using cell culture models. However, many biological questions cannot be addressed in these models, but require instead the 3-dimensional organization of cells found in tissues. Herein, we discuss some of the issues related to correlative microscopy of tissues including the major reporter systems presently available for correlative microscopy. We present data from our own work in which we have focused on the use of ultrathin cryosections of tissues as the substrate for immunolabeling to combine immunofluorescence and electron microscopy of the same sub-cellular structures.
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Affiliation(s)
- Toshihiro Takizawa
- Department of Molecular Anatomy, Nippon Medical School, Tokyo 113-8602, Japan
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290
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Watanabe S, Richards J, Hollopeter G, Hobson RJ, Davis WM, Jorgensen EM. Nano-fEM: protein localization using photo-activated localization microscopy and electron microscopy. J Vis Exp 2012:e3995. [PMID: 23242070 DOI: 10.3791/3995] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mapping the distribution of proteins is essential for understanding the function of proteins in a cell. Fluorescence microscopy is extensively used for protein localization, but subcellular context is often absent in fluorescence images. Immuno-electron microscopy, on the other hand, can localize proteins, but the technique is limited by a lack of compatible antibodies, poor preservation of morphology and because most antigens are not exposed to the specimen surface. Correlative approaches can acquire the fluorescence image from a whole cell first, either from immuno-fluorescence or genetically tagged proteins. The sample is then fixed and embedded for electron microscopy, and the images are correlated (1-3). However, the low-resolution fluorescence image and the lack of fiducial markers preclude the precise localization of proteins. Alternatively, fluorescence imaging can be done after preserving the specimen in plastic. In this approach, the block is sectioned, and fluorescence images and electron micrographs of the same section are correlated (4-7). However, the diffraction limit of light in the correlated image obscures the locations of individual molecules, and the fluorescence often extends beyond the boundary of the cell. Nano-resolution fluorescence electron microscopy (nano-fEM) is designed to localize proteins at nano-scale by imaging the same sections using photo-activated localization microscopy (PALM) and electron microscopy. PALM overcomes the diffraction limit by imaging individual fluorescent proteins and subsequently mapping the centroid of each fluorescent spot (8-10). We outline the nano-fEM technique in five steps. First, the sample is fixed and embedded using conditions that preserve the fluorescence of tagged proteins. Second, the resin blocks are sectioned into ultrathin segments (70-80 nm) that are mounted on a cover glass. Third, fluorescence is imaged in these sections using the Zeiss PALM microscope. Fourth, electron dense structures are imaged in these same sections using a scanning electron microscope. Fifth, the fluorescence and electron micrographs are aligned using gold particles as fiducial markers. In summary, the subcellular localization of fluorescently tagged proteins can be determined at nanometer resolution in approximately one week.
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Affiliation(s)
- Shigeki Watanabe
- Department of Biology, Howard Hughes Medical Institute, University of Utah
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291
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Powis K, Schrul B, Tienson H, Gostimskaya I, Breker M, High S, Schuldiner M, Jakob U, Schwappach B. Get3 is a holdase chaperone and moves to deposition sites for aggregated proteins when membrane targeting is blocked. J Cell Sci 2012. [PMID: 23203805 PMCID: PMC3613179 DOI: 10.1242/jcs.112151] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The endomembrane system of yeast contains different tail-anchored proteins that are post-translationally targeted to membranes via their C-terminal transmembrane domain. This hydrophobic segment could be hazardous in the cytosol if membrane insertion fails, resulting in the need for energy-dependent chaperoning and the degradation of aggregated tail-anchored proteins. A cascade of GET proteins cooperates in a conserved pathway to accept newly synthesized tail-anchored proteins from ribosomes and guide them to a receptor at the endoplasmic reticulum, where membrane integration takes place. It is, however, unclear how the GET system reacts to conditions of energy depletion that might prevent membrane insertion and hence lead to the accumulation of hydrophobic proteins in the cytosol. Here we show that the ATPase Get3, which accommodates the hydrophobic tail anchor of clients, has a dual function: promoting tail-anchored protein insertion when glucose is abundant and serving as an ATP-independent holdase chaperone during energy depletion. Like the generic chaperones Hsp42, Ssa2, Sis1 and Hsp104, we found that Get3 moves reversibly to deposition sites for protein aggregates, hence supporting the sequestration of tail-anchored proteins under conditions that prevent tail-anchored protein insertion. Our findings support a ubiquitous role for the cytosolic GET complex as a triaging platform involved in cellular proteostasis.
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Affiliation(s)
- Katie Powis
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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292
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Plasma membrane reshaping during endocytosis is revealed by time-resolved electron tomography. Cell 2012; 150:508-20. [PMID: 22863005 DOI: 10.1016/j.cell.2012.05.046] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 04/04/2012] [Accepted: 05/17/2012] [Indexed: 12/22/2022]
Abstract
Endocytosis, like many dynamic cellular processes, requires precise temporal and spatial orchestration of complex protein machinery to mediate membrane budding. To understand how this machinery works, we directly correlated fluorescence microscopy of key protein pairs with electron tomography. We systematically located 211 endocytic intermediates, assigned each to a specific time window in endocytosis, and reconstructed their ultrastructure in 3D. The resulting virtual ultrastructural movie defines the protein-mediated membrane shape changes during endocytosis in budding yeast. It reveals that clathrin is recruited to flat membranes and does not initiate curvature. Instead, membrane invagination begins upon actin network assembly followed by amphiphysin binding to parallel membrane segments, which promotes elongation of the invagination into a tubule. Scission occurs on average 9 s after initial bending when invaginations are ∼100 nm deep, releasing nonspherical vesicles with 6,400 nm2 mean surface area. Direct correlation of protein dynamics with ultrastructure provides a quantitative 4D resource.
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293
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Chojnacki J, Müller B. Investigation of HIV-1 assembly and release using modern fluorescence imaging techniques. Traffic 2012; 14:15-24. [PMID: 22957540 DOI: 10.1111/tra.12006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/04/2012] [Accepted: 09/07/2012] [Indexed: 12/17/2022]
Abstract
The replication of HIV-1, like that of all viruses, is intimately connected with cellular structures and pathways. For many years, bulk biochemical and cell biological methods were the main approaches employed to investigate interactions between HIV-1 and its host cell. However, during the past decade advancements in fluorescence imaging technologies opened new possibilities for the direct visualization of individual steps occurring throughout the viral replication cycle. Electron microscopy (EM) methods, which have traditionally been employed for the study of viruses, are complemented by fluorescence microscopy (FM) techniques that allow us to follow the dynamics of virus-cell interaction. Subdiffraction fluorescence microscopy, as well as correlative EM/FM approaches, are narrowing the fundamental gap between the high structural resolution provided by EM and the high temporal resolution and throughput accomplished by FM. The application of modern microscopy to the study of HIV-1-host cell interactions has provided insights into the biology of the virus which could not easily, or not at all, have been gained by other methods. Here, we review how modern fluorescence imaging techniques enhanced our knowledge of the dynamic and structural changes involved in HIV-1 particle formation.
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Affiliation(s)
- Jakub Chojnacki
- Department of Infectious Diseases, Virology, University Hospital of Heidelberg, Heidelberg, Germany
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294
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Idrissi FZ, Blasco A, Espinal A, Geli MI. Ultrastructural dynamics of proteins involved in endocytic budding. Proc Natl Acad Sci U S A 2012; 109:E2587-94. [PMID: 22949647 PMCID: PMC3465411 DOI: 10.1073/pnas.1202789109] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorescence live-cell imaging has temporally resolved the conserved choreography of more than 30 proteins involved in clathrin and actin-mediated endocytic budding from the plasma membrane. However, the resolution of these studies is insufficient to unveil how the endocytic machinery actually drives membrane deformation in vivo. In this study, we use quantitative immuno-EM to introduce the temporal dimension to the ultrastructural analysis of membrane budding and define changes in the topography of the lipid bilayer coupled to the dynamics of endocytic proteins with unprecedented spatiotemporal resolution. Using this approach, we frame the emergence of membrane curvature with respect to the recruitment of endocytic factors and show that constriction of the invaginations correlates with translocation of membrane-sculpting proteins. Furthermore, we show that initial bending of the plasma membrane is independent of actin and clathrin polymerization and precedes building of an actin cap branched by the Arp2/3 complex. Finally, our data indicate that constriction and additional elongation of the endocytic profiles require the mechanochemical activity of the myosins-I. Altogether, this work provides major insights into the molecular mechanisms driving membrane deformation in a cellular context.
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Affiliation(s)
- Fatima-Zahra Idrissi
- Department of Cell Biology, Instituto de Biología Molecular de Barcelona (CSIC), 08028 Barcelona, Spain; and
| | - Anabel Blasco
- Servei d´Estadística, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Anna Espinal
- Servei d´Estadística, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - María Isabel Geli
- Department of Cell Biology, Instituto de Biología Molecular de Barcelona (CSIC), 08028 Barcelona, Spain; and
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295
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Karreman MA, Agronskaia AV, van Donselaar EG, Vocking K, Fereidouni F, Humbel BM, Verrips CT, Verkleij AJ, Gerritsen HC. Optimizing immuno-labeling for correlative fluorescence and electron microscopy on a single specimen. J Struct Biol 2012; 180:382-6. [PMID: 22982545 DOI: 10.1016/j.jsb.2012.09.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 08/28/2012] [Accepted: 09/03/2012] [Indexed: 11/28/2022]
Abstract
Correlative fluorescence and electron microscopy has become an indispensible tool for research in cell biology. The integrated Laser and Electron Microscope (iLEM) combines a Fluorescence Microscope (FM) and a Transmission Electron Microscope (TEM) within one set-up. This unique imaging tool allows for rapid identification of a region of interest with the FM, and subsequent high resolution TEM imaging of this area. Sample preparation is one of the major challenges in correlative microscopy of a single specimen; it needs to be apt for both FM and TEM imaging. For iLEM, the performance of the fluorescent probe should not be impaired by the vacuum of the TEM. In this technical note, we have compared the fluorescence intensity of six fluorescent probes in a dry, oxygen free environment relative to their performance in water. We demonstrate that the intensity of some fluorophores is strongly influenced by its surroundings, which should be taken into account in the design of the experiment. Furthermore, a freeze-substitution and Lowicryl resin embedding protocol is described that yields excellent membrane contrast in the TEM but prevents quenching of the fluorescent immuno-labeling. The embedding protocol results in a single specimen preparation procedure that performs well in both FM and TEM. Such procedures are not only essential for the iLEM, but also of great value to other correlative microscopy approaches.
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Affiliation(s)
- Matthia A Karreman
- Molecular Biophysics, Department of Physics and Astronomy, Utrecht University, Princetonplein 1, Utrecht, The Netherlands.
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296
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Abstract
Endocytosis includes a number of processes by which cells internalize segments of their plasma membrane, enclosing a wide variety of material from outside the cell. Endocytosis can contribute to uptake of nutrients, regulation of signaling molecules, control of osmotic pressure, and function of synapses. The actin cytoskeleton plays an essential role in several of these processes. Actin assembly can create protrusions that encompass extracellular materials. Actin can also support the processes of invagination of a membrane segment into the cytoplasm, elongation of the invagination, scission of the new vesicle from the plasma membrane, and movement of the vesicle away from the membrane. We briefly discuss various types of endocytosis, including phagocytosis, macropinocytosis, and clathrin-independent endocytosis. We focus mainly on new findings on the relative importance of actin in clathrin-mediated endocytosis (CME) in yeast versus mammalian cells.
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Affiliation(s)
- Olivia L Mooren
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA.
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297
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Faas FG, Avramut MC, M. van den Berg B, Mommaas AM, Koster AJ, Ravelli RB. Virtual nanoscopy: generation of ultra-large high resolution electron microscopy maps. J Cell Biol 2012; 198:457-69. [PMID: 22869601 PMCID: PMC3413355 DOI: 10.1083/jcb.201201140] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 06/27/2012] [Indexed: 12/23/2022] Open
Abstract
A key obstacle in uncovering the orchestration between molecular and cellular events is the vastly different length scales on which they occur. We describe here a methodology for ultrastructurally mapping regions of cells and tissue as large as 1 mm(2) at nanometer resolution. Our approach employs standard transmission electron microscopy, rapid automated data collection, and stitching to create large virtual slides. It greatly facilitates correlative light-electron microscopy studies to relate structure and function and provides a genuine representation of ultrastructural events. The method is scalable as illustrated by slides up to 281 gigapixels in size. Here, we applied virtual nanoscopy in a correlative light-electron microscopy study to address the role of the endothelial glycocalyx in protein leakage over the glomerular filtration barrier, in an immunogold labeling study of internalization of oncolytic reovirus in human dendritic cells, in a cryo-electron microscopy study of intact vitrified mouse embryonic cells, and in an ultrastructural mapping of a complete zebrafish embryo slice.
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Affiliation(s)
- Frank G.A. Faas
- Department of Molecular Cell Biology and Department of Nephrology, Leiden University Medical Center (LUMC), 2300 RC Leiden, Netherlands
| | - M. Cristina Avramut
- Department of Molecular Cell Biology and Department of Nephrology, Leiden University Medical Center (LUMC), 2300 RC Leiden, Netherlands
| | - Bernard M. van den Berg
- Department of Molecular Cell Biology and Department of Nephrology, Leiden University Medical Center (LUMC), 2300 RC Leiden, Netherlands
| | - A. Mieke Mommaas
- Department of Molecular Cell Biology and Department of Nephrology, Leiden University Medical Center (LUMC), 2300 RC Leiden, Netherlands
| | - Abraham J. Koster
- Department of Molecular Cell Biology and Department of Nephrology, Leiden University Medical Center (LUMC), 2300 RC Leiden, Netherlands
| | - Raimond B.G. Ravelli
- Department of Molecular Cell Biology and Department of Nephrology, Leiden University Medical Center (LUMC), 2300 RC Leiden, Netherlands
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298
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Phan S, Lawrence A, Molina T, Lanman J, Berlanga M, Terada M, Kulungowski A, Obayashi J, Ellisman M. TxBR montage reconstruction for large field electron tomography. J Struct Biol 2012; 180:154-64. [PMID: 22749959 DOI: 10.1016/j.jsb.2012.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Revised: 06/05/2012] [Accepted: 06/12/2012] [Indexed: 11/18/2022]
Abstract
Electron tomography (ET) has been proven an essential technique for imaging the structure of cells beyond the range of the light microscope down to the molecular level. Large-field high-resolution views of biological specimens span more than four orders of magnitude in spatial scale, and, as a consequence, are rather difficult to generate directly. Various techniques have been developed towards generating those views, from increasing the sensor array size to implementing serial sectioning and montaging. Datasets and reconstructions obtained by the latter techniques generate multiple three-dimensional (3D) reconstructions, that need to be combined together to provide all the multiscale information. In this work, we show how to implement montages within TxBR, a tomographic reconstruction software package. This work involves some new application of mathematical concepts related to volume preserving transformations and issues of gauge ambiguity, which are essential problems arising from the nature of the observation in an electron microscope. The purpose of TxBR is to handle those issues as generally as possible in order to correct for most distortions in the 3D reconstructions and allow for a seamless recombination of ET montages.
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Affiliation(s)
- Sébastien Phan
- National Center For Microscopy and Imaging Research, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0608, USA
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299
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Lidke DS, Lidke KA. Advances in high-resolution imaging--techniques for three-dimensional imaging of cellular structures. J Cell Sci 2012; 125:2571-80. [PMID: 22685332 DOI: 10.1242/jcs.090027] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A fundamental goal in biology is to determine how cellular organization is coupled to function. To achieve this goal, a better understanding of organelle composition and structure is needed. Although visualization of cellular organelles using fluorescence or electron microscopy (EM) has become a common tool for the cell biologist, recent advances are providing a clearer picture of the cell than ever before. In particular, advanced light-microscopy techniques are achieving resolutions below the diffraction limit and EM tomography provides high-resolution three-dimensional (3D) images of cellular structures. The ability to perform both fluorescence and electron microscopy on the same sample (correlative light and electron microscopy, CLEM) makes it possible to identify where a fluorescently labeled protein is located with respect to organelle structures visualized by EM. Here, we review the current state of the art in 3D biological imaging techniques with a focus on recent advances in electron microscopy and fluorescence super-resolution techniques.
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Affiliation(s)
- Diane S Lidke
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131, USA
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300
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Baumgärtel V, Müller B, Lamb DC. Quantitative live-cell imaging of human immunodeficiency virus (HIV-1) assembly. Viruses 2012; 4:777-99. [PMID: 22754649 PMCID: PMC3386619 DOI: 10.3390/v4050777] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 04/24/2012] [Indexed: 11/16/2022] Open
Abstract
Advances in fluorescence methodologies make it possible to investigate biological systems in unprecedented detail. Over the last few years, quantitative live-cell imaging has increasingly been used to study the dynamic interactions of viruses with cells and is expected to become even more indispensable in the future. Here, we describe different fluorescence labeling strategies that have been used to label HIV-1 for live cell imaging and the fluorescence based methods used to visualize individual aspects of virus-cell interactions. This review presents an overview of experimental methods and recent experiments that have employed quantitative microscopy in order to elucidate the dynamics of late stages in the HIV-1 replication cycle. This includes cytosolic interactions of the main structural protein, Gag, with itself and the viral RNA genome, the recruitment of Gag and RNA to the plasma membrane, virion assembly at the membrane and the recruitment of cellular proteins involved in HIV-1 release to the nascent budding site.
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Affiliation(s)
- Viola Baumgärtel
- Department of Chemistry, Center for NanoScience (CeNS) and Center for Integrated Protein Science, Munich (CIPSM), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, D-81377 München, Germany;
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany
- Authors to whom correspondence should be addressed; (B.M.); (D.C.L.); Tel.: +49-6221-56-1325 (B.M.); +49-89-2180-77564 (D.C.L.); Fax: +49-6221-56-5003 (B.M.); +49-89-2180-77560 (D.C.L.)
| | - Don C. Lamb
- Department of Chemistry, Center for NanoScience (CeNS) and Center for Integrated Protein Science, Munich (CIPSM), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, D-81377 München, Germany;
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
- Authors to whom correspondence should be addressed; (B.M.); (D.C.L.); Tel.: +49-6221-56-1325 (B.M.); +49-89-2180-77564 (D.C.L.); Fax: +49-6221-56-5003 (B.M.); +49-89-2180-77560 (D.C.L.)
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