1
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Zhao DY, Bäuerlein FJB, Saha I, Hartl FU, Baumeister W, Wilfling F. Autophagy preferentially degrades non-fibrillar polyQ aggregates. Mol Cell 2024; 84:1980-1994.e8. [PMID: 38759629 DOI: 10.1016/j.molcel.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
Aggregation of proteins containing expanded polyglutamine (polyQ) repeats is the cytopathologic hallmark of a group of dominantly inherited neurodegenerative diseases, including Huntington's disease (HD). Huntingtin (Htt), the disease protein of HD, forms amyloid-like fibrils by liquid-to-solid phase transition. Macroautophagy has been proposed to clear polyQ aggregates, but the efficiency of aggrephagy is limited. Here, we used cryo-electron tomography to visualize the interactions of autophagosomes with polyQ aggregates in cultured cells in situ. We found that an amorphous aggregate phase exists next to the radially organized polyQ fibrils. Autophagosomes preferentially engulfed this amorphous material, mediated by interactions between the autophagy receptor p62/SQSTM1 and the non-fibrillar aggregate surface. In contrast, amyloid fibrils excluded p62 and evaded clearance, resulting in trapping of autophagic structures. These results suggest that the limited efficiency of autophagy in clearing polyQ aggregates is due to the inability of autophagosomes to interact productively with the non-deformable, fibrillar disease aggregates.
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Affiliation(s)
- Dorothy Y Zhao
- Max Planck Institute of Biochemistry, Molecular Machines and Signaling, 82152 Martinsried, Germany; Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; Max Planck Institute of Biophysics, Mechanisms of Cellular Quality Control, 60438 Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Felix J B Bäuerlein
- Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; University Medical Center Göttingen, Institute of Neuropathology, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany
| | - Itika Saha
- Max Planck Institute of Biochemistry, Cellular Biochemistry, 82152 Martinsried, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - F Ulrich Hartl
- Max Planck Institute of Biochemistry, Cellular Biochemistry, 82152 Martinsried, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Wolfgang Baumeister
- Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Florian Wilfling
- Max Planck Institute of Biochemistry, Molecular Machines and Signaling, 82152 Martinsried, Germany; Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; Max Planck Institute of Biophysics, Mechanisms of Cellular Quality Control, 60438 Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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2
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Valdebenito S, Ajasin D, Prideaux B, Eugenin EA. Correlative Imaging to Detect Rare HIV Reservoirs and Associated Damage in Tissues. Methods Mol Biol 2024; 2807:93-110. [PMID: 38743223 DOI: 10.1007/978-1-0716-3862-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Correlative light-electron microscopy (CLEM) has evolved in the last decades, especially after significant developments in sample preparation, imaging acquisition, software, spatial resolution, and equipment, including confocal, live-cell, super-resolution, and electron microscopy (scanning, transmission, focused ion beam, and cryo-electron microscopy). However, the recent evolution of different laser-related techniques, such as mass spectrometry imaging (MSI) and laser capture microdissection, could further expand spatial imaging capabilities into high-resolution OMIC approaches such as proteomic, lipidomics, small molecule, and drug discovery. Here, we will describe a protocol to integrate the detection of rare viral reservoirs with imaging mass spectrometry.
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Affiliation(s)
- Silvana Valdebenito
- Department of Neurobiology, The University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - David Ajasin
- Department of Neurobiology, The University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Brendan Prideaux
- Department of Neurobiology, The University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Eliseo A Eugenin
- Department of Neurobiology, The University of Texas Medical Branch (UTMB), Galveston, TX, USA.
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3
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Schiøtz OH, Kaiser CJO, Klumpe S, Morado DR, Poege M, Schneider J, Beck F, Klebl DP, Thompson C, Plitzko JM. Serial Lift-Out: sampling the molecular anatomy of whole organisms. Nat Methods 2023:10.1038/s41592-023-02113-5. [PMID: 38110637 DOI: 10.1038/s41592-023-02113-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/25/2023] [Indexed: 12/20/2023]
Abstract
Cryo-focused ion beam milling of frozen-hydrated cells and subsequent cryo-electron tomography (cryo-ET) has enabled the structural elucidation of macromolecular complexes directly inside cells. Application of the technique to multicellular organisms and tissues, however, is still limited by sample preparation. While high-pressure freezing enables the vitrification of thicker samples, it prolongs subsequent preparation due to increased thinning times and the need for extraction procedures. Additionally, thinning removes large portions of the specimen, restricting the imageable volume to the thickness of the final lamella, typically <300 nm. Here we introduce Serial Lift-Out, an enhanced lift-out technique that increases throughput and obtainable contextual information by preparing multiple sections from single transfers. We apply Serial Lift-Out to Caenorhabditis elegans L1 larvae, yielding a cryo-ET dataset sampling the worm's anterior-posterior axis, and resolve its ribosome structure to 7 Å and a subregion of the 11-protofilament microtubule to 13 Å, illustrating how Serial Lift-Out enables the study of multicellular molecular anatomy.
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Affiliation(s)
- Oda Helene Schiøtz
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christoph J O Kaiser
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sven Klumpe
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Dustin R Morado
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department for Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Matthias Poege
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jonathan Schneider
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Beck
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David P Klebl
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christopher Thompson
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Jürgen M Plitzko
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.
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4
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Last MGF, Noteborn WEM, Voortman LM, Sharp TH. Super-resolution fluorescence imaging of cryosamples does not limit achievable resolution in cryoEM. J Struct Biol 2023; 215:108040. [PMID: 37918761 DOI: 10.1016/j.jsb.2023.108040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Correlated super-resolution cryo-fluorescence and cryo-electron microscopy (cryoEM) has been gaining popularity as a method to investigate biological samples with high resolution and specificity. A concern in this combined method (called SR-cryoCLEM), however, is whether and how fluorescence imaging prior to cryoEM acquisition is detrimental to sample integrity. In this report, we investigated the effect of high-dose laser light (405, 488, and 561 nm) irradiation on apoferritin samples prepared for cryoEM with excitation wavelengths commonly used in fluorescence microscopy, and compared these samples to controls that were kept in the dark. We found that laser illumination, of equal duration and intensity as used in cryo-single molecule localization microscopy (cryoSMLM) and in the presence of high concentrations of fluorescent protein, did not affect the achievable resolution in cryoEM, with final reconstructions reaching resolutions of ∼ 1.8 Å regardless of the laser illumination. The finding that super-resolution fluorescence imaging of cryosamples prior to cryoEM data acquisition does not limit the achievable resolution suggests that super-resolution cryo-fluorescence microscopy and in situ structural biology using cryoEM are entirely compatible.
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Affiliation(s)
- Mart G F Last
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Willem E M Noteborn
- Netherlands Centre for Electron Nanoscopy, Leiden University, 2333 AL Leiden, The Netherlands
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands.
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5
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Kirchweger P, Mullick D, Swain PP, Wolf SG, Elbaum M. Correlating cryo-super resolution radial fluctuations and dual-axis cryo-scanning transmission electron tomography to bridge the light-electron resolution gap. J Struct Biol 2023; 215:107982. [PMID: 37268154 DOI: 10.1016/j.jsb.2023.107982] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/05/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Visualization of organelles and their interactions with other features in the native cell remains a challenge in modern biology. We have introduced cryo-scanning transmission electron tomography (CSTET), which can access 3D volumes on the scale of 1 micron with a resolution of nanometers, making it ideal for this task. Here we introduce two relevant advances: (a) we demonstrate the utility of multi-color super-resolution radial fluctuation light microscopy under cryogenic conditions (cryo-SRRF), and (b) we extend the use of deconvolution processing for dual-axis CSTET data. We show that cryo-SRRF nanoscopy is able to reach resolutions in the range of 100 nm, using commonly available fluorophores and a conventional widefield microscope for cryo-correlative light-electron microscopy. Such resolution aids in precisely identifying regions of interest before tomographic acquisition and enhances precision in localizing features of interest within the 3D reconstruction. Dual-axis CSTET tilt series data and application of entropy regularized deconvolution during post-processing results in close-to-isotropic resolution in the reconstruction without averaging. The integration of cryo-SRRF with deconvolved dual-axis CSTET provides a versatile workflow for studying unique objects in a cell.
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Affiliation(s)
- Peter Kirchweger
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Debakshi Mullick
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Prabhu Prasad Swain
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel; School of Physical Sciences, UM-DAE Centre for Excellence in Basic Sciences, Mumbai 400098, India
| | - Sharon G Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michael Elbaum
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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6
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Perez D, Dahlberg PD, Moerner WE. Advanced Cryogenic Light Microscopy Stage to Enable 3D Super-resolved Cryogenic Correlative Light and Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1941. [PMID: 37612900 DOI: 10.1093/micmic/ozad067.1005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Davis Perez
- Department of Chemistry, Stanford University, Stanford, CA, United States
| | - Peter D Dahlberg
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, United States
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, United States
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7
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Zimmermann L, Chlanda P. Cryo-electron tomography of viral infection - from applications to biosafety. Curr Opin Virol 2023; 61:101338. [PMID: 37348443 DOI: 10.1016/j.coviro.2023.101338] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/25/2023] [Accepted: 05/28/2023] [Indexed: 06/24/2023]
Abstract
Cellular cryo-electron tomography (cryo-ET) offers 3D snapshots at molecular resolution capturing pivotal steps during viral infection. However, tomogram quality depends on the vitrification level of the sample and its thickness. In addition, mandatory inactivation protocols to assure biosafety when handling highly pathogenic viruses during cryo-ET can compromise sample preservation. Here, we focus on different strategies applied in cryo-ET and discuss their advantages and limitations with reference to severe acute respiratory syndrome coronavirus 2 studies. We highlight the importance of virus-like particle (VLP) and replicon systems to study virus assembly and replication in a cellular context without inactivation protocols. We discuss the application of chemical fixation and different irradiation methods in cryo-ET sample preparation and acquisition workflows.
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Affiliation(s)
- Liv Zimmermann
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
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8
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Bagrov DV, Adlerberg VV, Skryabin GO, Nikishin II, Galetsky SA, Tchevkina EM, Kirpichnikov MP, Shaitan KV. AFM-TEM correlation microscopy and its application to lipid nanoparticles. Microsc Res Tech 2023. [PMID: 37125595 DOI: 10.1002/jemt.24336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/04/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
So far, only a few articles have demonstrated the possibility of correlated AFM-TEM imaging - sequential imaging of the same individual objects using atomic-force microscopy (AFM) and transmission electron microscopy (TEM). The current work contributes to the development of this approach by giving a step-by-step procedure, which yields pairs of correlated AFM-TEM images. We describe the application of correlation AFM-TEM microscopy to lipid nanoparticles (small extracellular vesicles and liposomes). The sizes of individual particles measured by the two methods were in good agreement, taking the tip broadening into account. The correlated AFM-TEM imaging can be valuable for single-particle analysis and nanometrology.
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Affiliation(s)
- Dmitry V Bagrov
- Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir V Adlerberg
- Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Gleb O Skryabin
- Department of oncogene regulation, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Igor I Nikishin
- Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Sergey A Galetsky
- Department of oncogene regulation, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Elena M Tchevkina
- Department of oncogene regulation, Institute of Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Mikhail P Kirpichnikov
- Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin V Shaitan
- Department of Bioengineering, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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9
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Klein S, Golani G, Lolicato F, Lahr C, Beyer D, Herrmann A, Wachsmuth-Melm M, Reddmann N, Brecht R, Hosseinzadeh M, Kolovou A, Makroczyova J, Peterl S, Schorb M, Schwab Y, Brügger B, Nickel W, Schwarz US, Chlanda P. IFITM3 blocks influenza virus entry by sorting lipids and stabilizing hemifusion. Cell Host Microbe 2023; 31:616-633.e20. [PMID: 37003257 DOI: 10.1016/j.chom.2023.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/15/2022] [Accepted: 03/06/2023] [Indexed: 04/03/2023]
Abstract
Interferon-induced transmembrane protein 3 (IFITM3) inhibits the entry of numerous viruses through undefined molecular mechanisms. IFITM3 localizes in the endosomal-lysosomal system and specifically affects virus fusion with target cell membranes. We found that IFITM3 induces local lipid sorting, resulting in an increased concentration of lipids disfavoring viral fusion at the hemifusion site. This increases the energy barrier for fusion pore formation and the hemifusion dwell time, promoting viral degradation in lysosomes. In situ cryo-electron tomography captured IFITM3-mediated arrest of influenza A virus membrane fusion. Observation of hemifusion diaphragms between viral particles and late endosomal membranes confirmed hemifusion stabilization as a molecular mechanism of IFITM3. The presence of the influenza fusion protein hemagglutinin in post-fusion conformation close to hemifusion sites further indicated that IFITM3 does not interfere with the viral fusion machinery. Collectively, these findings show that IFITM3 induces lipid sorting to stabilize hemifusion and prevent virus entry into target cells.
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Affiliation(s)
- Steffen Klein
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Gonen Golani
- BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany; Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany; Department of Physics, University of Helsinki, Helsinki, Finland
| | - Carmen Lahr
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Daniel Beyer
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Alexia Herrmann
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Moritz Wachsmuth-Melm
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Nina Reddmann
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Romy Brecht
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Mehdi Hosseinzadeh
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Androniki Kolovou
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Jana Makroczyova
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Sarah Peterl
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Yannick Schwab
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Ulrich S Schwarz
- BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany; Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany.
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10
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Wang C, Wojtynek M, Medalia O. Structural investigation of eukaryotic cells: From the periphery to the interior by cryo-electron tomography. Adv Biol Regul 2023; 87:100923. [PMID: 36280452 DOI: 10.1016/j.jbior.2022.100923] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
Cryo-electron tomography (cryo-ET) combines a close-to-life preservation of the cell with high-resolution three-dimensional (3D) imaging. This allows to study the molecular architecture of the cellular landscape and provides unprecedented views on biological processes and structures. In this review we mainly focus on the application of cryo-ET to visualize and structurally characterize eukaryotic cells - from the periphery to the cellular interior. We discuss strategies that can be employed to investigate the structure of challenging targets in their cellular environment as well as the application of complimentary approaches in conjunction with cryo-ET.
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Affiliation(s)
- Chunyang Wang
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Matthias Wojtynek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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11
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Dow LP, Gaietta G, Kaufman Y, Swift MF, Lemos M, Lane K, Hopcroft M, Bezault A, Sauvanet C, Volkmann N, Pruitt BL, Hanein D. Morphological control enables nanometer-scale dissection of cell-cell signaling complexes. Nat Commun 2022; 13:7831. [PMID: 36539423 PMCID: PMC9768166 DOI: 10.1038/s41467-022-35409-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Protein micropatterning enables robust control of cell positioning on electron-microscopy substrates for cryogenic electron tomography (cryo-ET). However, the combination of regulated cell boundaries and the underlying electron-microscopy substrate (EM-grids) provides a poorly understood microenvironment for cell biology. Because substrate stiffness and morphology affect cellular behavior, we devised protocols to characterize the nanometer-scale details of the protein micropatterns on EM-grids by combining cryo-ET, atomic force microscopy, and scanning electron microscopy. Measuring force displacement characteristics of holey carbon EM-grids, we found that their effective spring constant is similar to physiological values expected from skin tissues. Despite their apparent smoothness at light-microscopy resolution, spatial boundaries of the protein micropatterns are irregular at nanometer scale. Our protein micropatterning workflow provides the means to steer both positioning and morphology of cell doublets to determine nanometer details of punctate adherens junctions. Our workflow serves as the foundation for studying the fundamental structural changes governing cell-cell signaling.
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Affiliation(s)
- Liam P. Dow
- grid.133342.40000 0004 1936 9676Mechanical Engineering and Biomolecular Science and Engineering, University of California, Santa Barbara, CA USA
| | - Guido Gaietta
- grid.465257.70000 0004 5913 8442Scintillon Institute, San Diego, CA USA
| | - Yair Kaufman
- grid.133342.40000 0004 1936 9676Mechanical Engineering and Biomolecular Science and Engineering, University of California, Santa Barbara, CA USA
| | - Mark F. Swift
- grid.465257.70000 0004 5913 8442Scintillon Institute, San Diego, CA USA
| | - Moara Lemos
- grid.428999.70000 0001 2353 6535Institut Pasteur, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, F-75015 Paris, France
| | - Kerry Lane
- grid.133342.40000 0004 1936 9676Mechanical Engineering and Biomolecular Science and Engineering, University of California, Santa Barbara, CA USA
| | - Matthew Hopcroft
- grid.133342.40000 0004 1936 9676Mechanical Engineering and Biomolecular Science and Engineering, University of California, Santa Barbara, CA USA
| | - Armel Bezault
- grid.428999.70000 0001 2353 6535Institut Pasteur, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, F-75015 Paris, France
| | - Cécile Sauvanet
- grid.428999.70000 0001 2353 6535Institut Pasteur, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, F-75015 Paris, France
| | - Niels Volkmann
- grid.465257.70000 0004 5913 8442Scintillon Institute, San Diego, CA USA ,Institut Pasteur, Université de Paris, CNRS UMR3528, Structural Image Analysis Unit, Paris, France
| | - Beth L. Pruitt
- grid.133342.40000 0004 1936 9676Mechanical Engineering and Biomolecular Science and Engineering, University of California, Santa Barbara, CA USA
| | - Dorit Hanein
- grid.465257.70000 0004 5913 8442Scintillon Institute, San Diego, CA USA ,grid.428999.70000 0001 2353 6535Institut Pasteur, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, F-75015 Paris, France ,grid.133342.40000 0004 1936 9676Present Address: Department of Chemistry and Biochemistry, and of Biomedical Engineering, University of California, Santa Barbara, CA USA
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12
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Zabeo D, Davies KM. Studying membrane modulation mechanisms by electron cryo-tomography. Curr Opin Struct Biol 2022; 77:102464. [PMID: 36174286 DOI: 10.1016/j.sbi.2022.102464] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 12/14/2022]
Abstract
Membrane modulation is a key part of cellular life. Critical to processes like energy production, cell division, trafficking, migration and even pathogen entry, defects in membrane modulation are often associated with diseases. Studying the molecular mechanisms of membrane modulation is challenging due to the highly dynamic nature of the oligomeric assemblies involved, which adopt multiple conformations depending on the precise event they are participating in. With the development of electron cryo-tomography and subtomogram averaging, many of these challenges are being resolved as it is now possible to observe complex macromolecular assemblies inside a cell at nanometre to sub-nanometre resolutions. Here, we review the different ways electron cryo-tomography is being used to help uncover the molecular mechanisms used by cells to shape their membranes.
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Affiliation(s)
- Davide Zabeo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Karen M Davies
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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13
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Guaita M, Watters SC, Loerch S. Recent advances and current trends in cryo-electron microscopy. Curr Opin Struct Biol 2022; 77:102484. [PMID: 36323134 DOI: 10.1016/j.sbi.2022.102484] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/13/2022] [Accepted: 09/21/2022] [Indexed: 12/14/2022]
Abstract
All steps of cryogenic electron-microscopy (cryo-EM) workflows have rapidly evolved over the last decade. Advances in both single-particle analysis (SPA) cryo-EM and cryo-electron tomography (cryo-ET) have facilitated the determination of high-resolution biomolecular structures that are not tractable with other methods. However, challenges remain. For SPA, these include improved resolution in an additional dimension: time. For cryo-ET, these include accessing difficult-to-image areas of a cell and finding rare molecules. Finally, there is a need for automated and faster workflows, as many projects are limited by throughput. Here, we review current developments in SPA cryo-EM and cryo-ET that push these boundaries. Collectively, these advances are poised to propel our spatial and temporal understanding of macromolecular processes.
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Affiliation(s)
- Margherita Guaita
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Scott C Watters
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Sarah Loerch
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA.
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14
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Franken LE, Rosch R, Laugks U, Grünewald K. Protocol for live-cell fluorescence-guided cryoFIB-milling and electron cryo-tomography of virus-infected cells. STAR Protoc 2022; 3:101696. [PMID: 36149798 PMCID: PMC9508610 DOI: 10.1016/j.xpro.2022.101696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/13/2022] [Accepted: 08/17/2022] [Indexed: 01/25/2023] Open
Abstract
Here, we present a protocol for assessing virus-infected cells using electron cryo-tomography (cryoET). It includes the basic workflows of seeding cells, plunge-freezing, clipping, cryo-focused ion beam milling (cryoFIB-milling), and cryoET, as well as two optional modules: micropatterning and live-cell fluorescence microscopy. We use an A549 human cell line and the virus HAdV5-pIX-mcherry in this protocol, but the comprehensive workflow can be easily transferred to other cell types and different types of virus infection or treatment. For complete details on the use and execution of this protocol, please refer to Pfitzner et al. (2021).
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Affiliation(s)
- Linda E. Franken
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251 Hamburg, Germany,Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany,Corresponding author
| | - Rene Rosch
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251 Hamburg, Germany,Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany,Universität Hamburg, Institute for Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ulrike Laugks
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany,Universität Hamburg, Institute for Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Kay Grünewald
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251 Hamburg, Germany,Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany,Universität Hamburg, Institute for Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany,Corresponding author
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15
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Direct Capsid Labeling of Infectious HIV-1 by Genetic Code Expansion Allows Detection of Largely Complete Nuclear Capsids and Suggests Nuclear Entry of HIV-1 Complexes via Common Routes. mBio 2022; 13:e0195922. [PMID: 35972146 PMCID: PMC9600849 DOI: 10.1128/mbio.01959-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The cone-shaped mature HIV-1 capsid is the main orchestrator of early viral replication. After cytosolic entry, it transports the viral replication complex along microtubules toward the nucleus. While it was initially believed that the reverse transcribed genome is released from the capsid in the cytosol, recent observations indicate that a high amount of capsid protein (CA) remains associated with subviral complexes during import through the nuclear pore complex (NPC). Observation of postentry events via microscopic detection of HIV-1 CA is challenging, since epitope shielding limits immunodetection and the genetic fragility of CA hampers direct labeling approaches. Here, we present a minimally invasive strategy based on genetic code expansion and click chemistry that allows for site-directed fluorescent labeling of HIV-1 CA, while retaining virus morphology and infectivity. Thereby, we could directly visualize virions and subviral complexes using advanced microscopy, including nanoscopy and correlative imaging. Quantification of signal intensities of subviral complexes revealed an amount of CA associated with nuclear complexes in HeLa-derived cells and primary T cells consistent with a complete capsid and showed that treatment with the small molecule inhibitor PF74 did not result in capsid dissociation from nuclear complexes. Cone-shaped objects detected in the nucleus by electron tomography were clearly identified as capsid-derived structures by correlative microscopy. High-resolution imaging revealed dose-dependent clustering of nuclear capsids, suggesting that incoming particles may follow common entry routes.
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16
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Abstract
The three-dimensional organization of biomolecules important for the functioning of all living systems can be determined by cryo-electron tomography imaging under native biological contexts. Cryo-electron tomography is continually expanding and evolving, and the development of new methods that use the latest technology for sample thinning is enabling the visualization of ever larger and more complex biological systems, allowing imaging across scales. Quantitative cryo-electron tomography possesses the capability of visualizing the impact of molecular and environmental perturbations in subcellular structure and function to understand fundamental biological processes. This review provides an overview of current hardware and software developments that allow quantitative cryo-electron tomography studies and their limitations and how overcoming them may allow us to unleash the full power of cryo-electron tomography.
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Affiliation(s)
- Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
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17
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Gold nanomaterials and their potential use as cryo-electron tomography labels. J Struct Biol 2022; 214:107880. [PMID: 35809758 DOI: 10.1016/j.jsb.2022.107880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 12/14/2022]
Abstract
Rapid advances in cryo-electron tomography (cryo-ET) are driving a revolution in cellular structural biology. However, unambiguous identification of specific biomolecules within cellular tomograms remains challenging. Overcoming this obstacle and reliably identifying targets in the crowded cellular environment is of major importance for the understanding of cellular function and is a pre-requisite for high-resolution structural analysis. The use of highly-specific, readily visualised and adjustable labels would help mitigate this issue, improving both data quality and sample throughput. While progress has been made in cryo-CLEM and in the development of cloneable high-density tags, technical issues persist and a robust 'cryo-GFP' remains elusive. Readily-synthesized gold nanomaterials conjugated to small 'affinity modules' may represent a solution. The synthesis of materials including gold nanoclusters (AuNCs) and gold nanoparticles (AuNPs) is increasingly well understood and is now within the capabilities of non-specialist laboratories. The remarkable chemical and photophysical properties of <3nm diameter nanomaterials and their emergence as tools with widespread biomedical application presents significant opportunities to the cryo-microscopy community. In this review, we will outline developments in the synthesis, functionalisation and labelling uses of both AuNPs and AuNCs in cryo-ET, while discussing their potential as multi-modal probes for cryo-CLEM.
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18
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Fermie J, de Jager L, Foster HE, Veenendaal T, de Heus C, van Dijk S, ten Brink C, Oorschot V, Yang L, Li W, Müller WH, Howes S, Carter AP, Förster F, Posthuma G, Gerritsen HC, Klumperman J, Liv N. Bimodal endocytic probe for three-dimensional correlative light and electron microscopy. CELL REPORTS METHODS 2022; 2:100220. [PMID: 35637912 PMCID: PMC9142762 DOI: 10.1016/j.crmeth.2022.100220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 02/04/2022] [Accepted: 04/26/2022] [Indexed: 12/03/2022]
Abstract
We present a bimodal endocytic tracer, fluorescent BSA-gold (fBSA-Au), as a fiducial marker for 2D and 3D correlative light and electron microscopy (CLEM) applications. fBSA-Au consists of colloidal gold (Au) particles stabilized with fluorescent BSA. The conjugate is efficiently endocytosed and distributed throughout the 3D endolysosomal network of cells and has an excellent visibility in both fluorescence microscopy (FM) and electron microscopy (EM). We demonstrate that fBSA-Au facilitates rapid registration in several 2D and 3D CLEM applications using Tokuyasu cryosections, resin-embedded material, and cryoelectron microscopy (cryo-EM). Endocytosed fBSA-Au benefits from a homogeneous 3D distribution throughout the endosomal system within the cell, does not obscure any cellular ultrastructure, and enables accurate (50-150 nm) correlation of fluorescence to EM data. The broad applicability and visibility in both modalities makes fBSA-Au an excellent endocytic fiducial marker for 2D and 3D (cryo)CLEM applications.
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Affiliation(s)
- Job Fermie
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands
| | - Leanne de Jager
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Helen E. Foster
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Cambridge, UK
| | - Tineke Veenendaal
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Cecilia de Heus
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Suzanne van Dijk
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Corlinda ten Brink
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Viola Oorschot
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lin Yang
- Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- Institute of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wally H. Müller
- Microbiology, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Stuart Howes
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Andrew P. Carter
- Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Cambridge, UK
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - George Posthuma
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Hans C. Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, the Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Nalan Liv
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
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19
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Scher N, Rechav K, Paul-Gilloteaux P, Avinoam O. Sample preparation and image registration for correlative cryo-FM and cryo-FIB-SEM of plunge-frozen mammalian cells. STAR Protoc 2022; 3:101142. [PMID: 35199027 PMCID: PMC8844706 DOI: 10.1016/j.xpro.2022.101142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
We recently demonstrated how lipid droplets can serve as in situ fiducials for correlating cryo-fluorescence microscopy (cryo-FM) and cryo-focused ion beam scanning electron microscopy (cryo-FIB-SEM) datasets of mammalian cells grown on grids. Here we describe a step-by-step protocol for correlative cryo-FM and cryo-FIB-SEM, starting from sample preparation of C2C12 cell line, followed by imaging with cryo-FM and cryo-FIB-SEM. Finally, we detail how to perform the 3D-correlation with sub-micron accuracy. For complete details on the use and execution of this profile, please refer to Scher et al. (2021).
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Affiliation(s)
- Nadav Scher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Perrine Paul-Gilloteaux
- Structure Fédérative de Recherche François Bonamy, INSERM, CNRS, Université de Nantes, Nantes, France
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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20
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Klumpe S, Fung HKH, Goetz SK, Zagoriy I, Hampoelz B, Zhang X, Erdmann PS, Baumbach J, Müller CW, Beck M, Plitzko JM, Mahamid J. A modular platform for automated cryo-FIB workflows. eLife 2021; 10:e70506. [PMID: 34951584 PMCID: PMC8769651 DOI: 10.7554/elife.70506] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/23/2021] [Indexed: 11/22/2022] Open
Abstract
Lamella micromachining by focused ion beam milling at cryogenic temperature (cryo-FIB) has matured into a preparation method widely used for cellular cryo-electron tomography. Due to the limited ablation rates of low Ga+ ion beam currents required to maintain the structural integrity of vitreous specimens, common preparation protocols are time-consuming and labor intensive. The improved stability of new-generation cryo-FIB instruments now enables automated operations. Here, we present an open-source software tool, SerialFIB, for creating automated and customizable cryo-FIB preparation protocols. The software encompasses a graphical user interface for easy execution of routine lamellae preparations, a scripting module compatible with available Python packages, and interfaces with three-dimensional correlative light and electron microscopy (CLEM) tools. SerialFIB enables the streamlining of advanced cryo-FIB protocols such as multi-modal imaging, CLEM-guided lamella preparation and in situ lamella lift-out procedures. Our software therefore provides a foundation for further development of advanced cryogenic imaging and sample preparation protocols.
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Affiliation(s)
- Sven Klumpe
- Department Molecular Structural Biology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Herman KH Fung
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Sara K Goetz
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of BiosciencesHeidelbergGermany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Bernhard Hampoelz
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Xiaojie Zhang
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Philipp S Erdmann
- Department Molecular Structural Biology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Janina Baumbach
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
- Cell Biology and Biophysics Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Jürgen M Plitzko
- Department Molecular Structural Biology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
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21
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Bäuerlein FJB, Baumeister W. Towards Visual Proteomics at High Resolution. J Mol Biol 2021; 433:167187. [PMID: 34384780 DOI: 10.1016/j.jmb.2021.167187] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/02/2021] [Accepted: 08/02/2021] [Indexed: 11/24/2022]
Abstract
Traditionally, structural biologists approach the complexity of cellular proteomes in a reductionist manner. Proteomes are fractionated, their molecular components purified and studied one-by-one using the experimental methods for structure determination at their disposal. Visual proteomics aims at obtaining a holistic picture of cellular proteomes by studying them in situ, ideally in unperturbed cellular environments. The method that enables doing this at highest resolution is cryo-electron tomography. It allows to visualize cellular landscapes with molecular resolution generating maps or atlases revealing the interaction networks which underlie cellular functions in health and in disease states. Current implementations of cryo ET do not yet realize the full potential of the method in terms of resolution and interpretability. To this end, further improvements in technology and methodology are needed. This review describes the state of the art as well as measures which we expect will help overcoming current limitations.
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Affiliation(s)
- Felix J B Bäuerlein
- Max-Planck-Institute of Biochemistry, Department for Molecular Structural Biology, Am Klopferspitz 18, 82152 Planegg, Germany; Georg-August-University, Institute for Neuropathology, Robert-Koch-Strasse 40, 37075 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany.
| | - Wolfgang Baumeister
- Max-Planck-Institute of Biochemistry, Department for Molecular Structural Biology, Am Klopferspitz 18, 82152 Planegg, Germany.
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22
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Abstract
The application of cryo-correlative light and cryo-electron microscopy (cryo-CLEM) gives us a way to locate structures of interest in the electron microscope. In brief, the structures of interest are fluorescently tagged, and images from the cryo-fluorescent microscope (cryo-FM) maps are superimposed on those from the cryo-electron microscope (cryo-EM). By enhancing cryo-FM to include single-molecule localization microscopy (SMLM), we can achieve much better localization. The introduction of cryo-SMLM increased the yield of photons from fluorophores, which can benefit localization efforts. Dahlberg and Moerner (2021, Annual Review of Physical Chemistry, 72, 253-278) have a recent broad and elegant review of super-resolution cryo-CLEM. This paper focuses on cryo(F)PALM/STORM for the cryo-electron tomography community. I explore the current challenges to increase the accuracy of localization by SMLM and the mapping of those positions onto cryo-EM images and maps. There is much to consider: we need to know if the excitation of fluorophores damages the structures we seek to visualize. We need to determine if higher numerical aperture (NA) objectives, which add complexity to image analysis but increase resolution and the efficiency of photon collection, are better than lower NA objectives, which pose fewer problems. We need to figure out the best way to determine the axial position of fluorophores. We need to have better ways of aligning maps determined by FM with those determined by EM. We need to improve the instrumentation to be easier to use, more accurate, and ice-contamination free. The bottom line is that we have more work to do.
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23
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Scher N, Rechav K, Paul-Gilloteaux P, Avinoam O. In situ fiducial markers for 3D correlative cryo-fluorescence and FIB-SEM imaging. iScience 2021; 24:102714. [PMID: 34258551 PMCID: PMC8253967 DOI: 10.1016/j.isci.2021.102714] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/12/2021] [Accepted: 06/08/2021] [Indexed: 11/26/2022] Open
Abstract
Imaging of cells and tissues has improved significantly over the last decade. Dual-beam instruments with a focused ion beam mounted on a scanning electron microscope (FIB-SEM), offering high-resolution 3D imaging of large volumes and fields-of-view are becoming widely used in the life sciences. FIB-SEM has most recently been implemented on fully hydrated, cryo-immobilized, biological samples. Correlative light and electron microscopy workflows combining fluorescence microscopy (FM) with FIB-SEM imaging exist, whereas workflows combining cryo-FM and cryo-FIB-SEM imaging are not yet commonly available. Here, we demonstrate that fluorescently labeled lipid droplets can serve as in situ fiducial markers for correlating cryo-FM and FIB-SEM datasets and that this approach can be used to target the acquisition of large FIB-SEM stacks spanning tens of microns under cryogenic conditions. We also show that cryo-FIB-SEM imaging is particularly informative for questions related to organelle structure and inter-organellar contacts, nuclear organization, and mineral deposits in cells.
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Affiliation(s)
- Nadav Scher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Katya Rechav
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Perrine Paul-Gilloteaux
- Structure Fédérative de Recherche François Bonamy, INSERM, CNRS, Université de Nantes, Nantes, France
| | - Ori Avinoam
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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24
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Müller TG, Zila V, Peters K, Schifferdecker S, Stanic M, Lucic B, Laketa V, Lusic M, Müller B, Kräusslich HG. HIV-1 uncoating by release of viral cDNA from capsid-like structures in the nucleus of infected cells. eLife 2021; 10:64776. [PMID: 33904396 PMCID: PMC8169111 DOI: 10.7554/elife.64776] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
HIV-1 replication commences inside the cone-shaped viral capsid, but timing, localization, and mechanism of uncoating are under debate. We adapted a strategy to visualize individual reverse-transcribed HIV-1 cDNA molecules and their association with viral and cellular proteins using fluorescence and correlative-light-and-electron-microscopy (CLEM). We specifically detected HIV-1 cDNA inside nuclei, but not in the cytoplasm. Nuclear cDNA initially co-localized with a fluorescent integrase fusion (IN-FP) and the viral CA (capsid) protein, but cDNA-punctae separated from IN-FP/CA over time. This phenotype was conserved in primary HIV-1 target cells, with nuclear HIV-1 complexes exhibiting strong CA-signals in all cell types. CLEM revealed cone-shaped HIV-1 capsid-like structures and apparently broken capsid-remnants at the position of IN-FP signals and elongated chromatin-like structures in the position of viral cDNA punctae lacking IN-FP. Our data argue for nuclear uncoating by physical disruption rather than cooperative disassembly of the CA-lattice, followed by physical separation from the pre-integration complex.
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Affiliation(s)
- Thorsten G Müller
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vojtech Zila
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Kyra Peters
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Sandra Schifferdecker
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mia Stanic
- Department of Infectious Diseases Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Bojana Lucic
- Department of Infectious Diseases Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Vibor Laketa
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, partner site Heidelberg, Heidelberg, Germany
| | - Marina Lusic
- Department of Infectious Diseases Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, partner site Heidelberg, Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research, partner site Heidelberg, Heidelberg, Germany
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25
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Dahlberg PD, Moerner WE. Cryogenic Super-Resolution Fluorescence and Electron Microscopy Correlated at the Nanoscale. Annu Rev Phys Chem 2021; 72:253-278. [PMID: 33441030 PMCID: PMC8877847 DOI: 10.1146/annurev-physchem-090319-051546] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
We review the emerging method of super-resolved cryogenic correlative light and electron microscopy (srCryoCLEM). Super-resolution (SR) fluorescence microscopy and cryogenic electron tomography (CET) are both powerful techniques for observing subcellular organization, but each approach has unique limitations. The combination of the two brings the single-molecule sensitivity and specificity of SR to the detailed cellular context and molecular scale resolution of CET. The resulting correlative data is more informative than the sum of its parts. The correlative images can be used to pinpoint the positions of fluorescently labeled proteins in the high-resolution context of CET with nanometer-scale precision and/or to identify proteins in electron-dense structures. The execution of srCryoCLEM is challenging and the approach is best described as a method that is still in its infancy with numerous technical challenges. In this review, we describe state-of-the-art srCryoCLEM experiments, discuss the most pressing challenges, and give a brief outlook on future applications.
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Affiliation(s)
- Peter D Dahlberg
- Department of Chemistry, Stanford University, Stanford, California 94305, USA;
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA;
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26
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Yang JE, Larson MR, Sibert BS, Shrum S, Wright ER. CorRelator: Interactive software for real-time high precision cryo-correlative light and electron microscopy. J Struct Biol 2021; 213:107709. [PMID: 33610654 PMCID: PMC8601405 DOI: 10.1016/j.jsb.2021.107709] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/06/2021] [Accepted: 02/11/2021] [Indexed: 12/31/2022]
Abstract
Cryo-correlative light and electron microscopy (CLEM) is a technique that uses the spatiotemporal cues from fluorescence light microscopy (FLM) to investigate the high-resolution ultrastructure of biological samples by cryo-electron microscopy (cryo-EM). Cryo-CLEM provides advantages for identifying and distinguishing fluorescently labeled proteins, macromolecular complexes, and organelles from the cellular environment. Challenges remain on how correlation workflows and software tools are implemented on different microscope platforms to support automated cryo-EM data acquisition. Here, we present CorRelator: an open-source desktop application that bridges between cryo-FLM and real-time cryo-EM/ET automated data collection. CorRelator implements a pixel-coordinate-to-stage-position transformation for flexible, high accuracy on-the-fly and post-acquisition correlation. CorRelator can be integrated into cryo-CLEM workflows and easily adapted to standard fluorescence and transmission electron microscope (TEM) system configurations. CorRelator was benchmarked under live-cell and cryogenic conditions using several FLM and TEM instruments, demonstrating that CorRelator reliably supports real-time, automated correlative cryo-EM/ET acquisition, through a combination of software-aided and interactive alignment. CorRelator is a cross-platform software package featuring an intuitive Graphical User Interface (GUI) that guides the user through the correlation process. CorRelator source code is available at: https://github.com/wright-cemrc-projects/corr.
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Affiliation(s)
- Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Matthew R Larson
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Bryan S Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Samantha Shrum
- Biophysics Graduate Program, University of Wisconsin, Madison, WI 53706, United States
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Biophysics Graduate Program, University of Wisconsin, Madison, WI 53706, United States; Morgridge Institute for Research, Madison, WI, 53715, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States.
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Zila V, Margiotta E, Turoňová B, Müller TG, Zimmerli CE, Mattei S, Allegretti M, Börner K, Rada J, Müller B, Lusic M, Kräusslich HG, Beck M. Cone-shaped HIV-1 capsids are transported through intact nuclear pores. Cell 2021; 184:1032-1046.e18. [PMID: 33571428 PMCID: PMC7895898 DOI: 10.1016/j.cell.2021.01.025] [Citation(s) in RCA: 158] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/20/2020] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid is generally believed to exceed the diameter of the nuclear pore complex (NPC), indicating that capsid uncoating has to occur prior to nuclear import. Here, we combined correlative light and electron microscopy with subtomogram averaging to capture the structural status of reverse transcription-competent HIV-1 complexes in infected T cells. We demonstrated that the diameter of the NPC in cellulo is sufficient for the import of apparently intact, cone-shaped capsids. Subsequent to nuclear import, we detected disrupted and empty capsid fragments, indicating that uncoating of the replication complex occurs by breaking the capsid open, and not by disassembly into individual subunits. Our data directly visualize a key step in HIV-1 replication and enhance our mechanistic understanding of the viral life cycle.
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Affiliation(s)
- Vojtech Zila
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Erica Margiotta
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Beata Turoňová
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Thorsten G Müller
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Christian E Zimmerli
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Simone Mattei
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland; European Molecular Biology Laboratory, Imaging Center, 69117 Heidelberg, Germany
| | - Matteo Allegretti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Kathleen Börner
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany; German Center for Infection Research, partner site Heidelberg, 69120 Heidelberg, Germany
| | - Jona Rada
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Marina Lusic
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany; German Center for Infection Research, partner site Heidelberg, 69120 Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany; German Center for Infection Research, partner site Heidelberg, 69120 Heidelberg, Germany.
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Max Planck Institute of Biophysics, Department of Molecular Sociology, 60438 Frankfurt, Germany.
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28
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Cryo-correlative light and electron microscopy workflow for cryo-focused ion beam milled adherent cells. Methods Cell Biol 2021; 162:273-302. [PMID: 33707016 DOI: 10.1016/bs.mcb.2020.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In situ cryo-electron tomography of cryo-focused ion beam (cryo-FIB) milled cells enables the study of cellular organelles in unperturbed conditions and close to the molecular resolution. However, due to the crowdedness of the cellular environment, the identification of individual macromolecular complexes either on organelles or inside the cytosol in cryo-electron tomograms is challenging. Cryo-correlative light and electron microscopy (cryo-CLEM) employs a fluorescently labeled feature of interest imaged by cryo-light microscopy that is correlated to cryo-electron microscopy maps of cryo-FIB milled lamellae using correlation markers discernable by both imaging methods. Here, we provide a protocol for a post-correlation on-lamella cryo-CLEM approach for localization of fluorescently labeled organelles of interest in cryo-lamellae after cryo-FIB milling and tomography of adherent plunge frozen cells.
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29
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Weiner A. Step-by-step guide to post-acquisition correlation of confocal and FIB/SEM volumes using Amira software. Methods Cell Biol 2020; 162:333-351. [PMID: 33707018 DOI: 10.1016/bs.mcb.2020.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In recent years new methodologies and workflow pipelines for acquiring correlated fluorescence microscopy and volume electron microscopy datasets have been extensively described and made accessible to users of different levels. Post-acquisition image processing, and particularly correlation of the optical and electron data in a single integrated three-dimensional framework can be key for extracting valuable information, especially when imaging large sample volumes such as whole cells or tissues. These tasks remain challenging and are often rate-limiting to most users. Here we provide a step-by-step guide to image processing and manual correlation using ImageJ and Amira software of a confocal microscopy stack and a focused ion beam/scanning electron microscopy (FIB/SEM) tomogram acquired using a correlative pipeline. These previously published datasets capture a highly transient invasion event by the bacterium Shigella flexneri infecting an epithelial cell grown in culture, and are made available here in their pre-processed form for readers who wish to gain hands-on experience in image processing and correlation using existing data. In this guide we describe a simple protocol for correlation based on internal sample features clearly visible by both fluorescence and electron microscopy, which is normally sufficient when correlating standard fluorescence microscopy stacks with FIB/SEM data. While the guide describes the treatment of specific datasets, it is applicable to a wide variety of samples and different microscopy approaches that require basic correlation and visualization of two or more datasets in a single integrated framework.
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Affiliation(s)
- Allon Weiner
- Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, Inserm, Sorbonne Université, Paris, France.
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30
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Chang IY, Rahman M, Harned A, Cohen-Fix O, Narayan K. Cryo-fluorescence microscopy of high-pressure frozen C. elegans enables correlative FIB-SEM imaging of targeted embryonic stages in the intact worm. Methods Cell Biol 2020; 162:223-252. [PMID: 33707014 PMCID: PMC9472676 DOI: 10.1016/bs.mcb.2020.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Rapidly changing features in an intact biological sample are challenging to efficiently trap and image by conventional electron microscopy (EM). For example, the model organism C. elegans is widely used to study embryonic development and differentiation, yet the fast kinetics of cell division makes the targeting of specific developmental stages for ultrastructural study difficult. We set out to image the condensed metaphase chromosomes of an early embryo in the intact worm in 3-D. To achieve this, one must capture this transient structure, then locate and subsequently image the corresponding volume by EM in the appropriate context of the organism, all while minimizing a variety of artifacts. In this methodological advance, we report on the high-pressure freezing of spatially constrained whole C. elegans hermaphrodites in a combination of cryoprotectants to identify embryonic cells in metaphase by in situ cryo-fluorescence microscopy. The screened worms were then freeze substituted, resin embedded and further prepared such that the targeted cells were successfully located and imaged by focused ion beam scanning electron microscopy (FIB-SEM). We reconstructed the targeted metaphase structure and also correlated an intriguing punctate fluorescence signal to a H2B-enriched putative polar body autophagosome in an adjacent cell undergoing telophase. By enabling cryo-fluorescence microscopy of thick samples, our workflow can thus be used to trap and image transient structures in C. elegans or similar organisms in a near-native state, and then reconstruct their corresponding cellular architectures at high resolution and in 3-D by correlative volume EM.
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Affiliation(s)
- Irene Y Chang
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Mohammad Rahman
- The Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Adam Harned
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Orna Cohen-Fix
- The Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States.
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31
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Buerger K, Schmidt KN, Fokkema J, Gerritsen HC, Maier O, de Vries U, Zaytseva Y, Rachel R, Witzgall R. On-section correlative light and electron microscopy of large cellular volumes using STEM tomography. Methods Cell Biol 2020; 162:171-203. [PMID: 33707012 DOI: 10.1016/bs.mcb.2020.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The application of both fluorescence and electron microscopy results in a powerful combination of imaging modalities called "correlative light and electron microscopy" (CLEM). Whereas conventional transmission electron microscopy (TEM) tomography is only able to image sections up to a thickness of ~300nm, scanning transmission electron microscopy (STEM) tomography at 200kV allows the analysis of sections up to a thickness of 900nm in three dimensions. In the current study we have successfully integrated STEM tomography into CLEM as demonstrated for human retinal pigment epithelial 1 (RPE1) cells expressing various fluorescent fusion proteins which were high-pressure frozen and then embedded in Lowicryl HM20. Fluorescently labeled gold nanoparticles were applied onto resin sections and imaged by fluorescence and electron microscopy. STEM tomograms were recorded at regions of interest, and overlays were generated using the eC-CLEM software package. Through the nuclear staining of living cells, the use of fluorescently labeled gold fiducials for the generation of overlays, and the integration of STEM tomography we have markedly extended the application of the Kukulski protocol (Kukulski et al., 2011, 2012). Various fluorescently tagged proteins localizing to different cellular organelles could be assigned to their ultrastructural compartments. By combining STEM tomography with on-section CLEM, fluorescently tagged proteins can be localized in three-dimensional ultrastructural environments with a volume of at least 2.7×2.7×0.5μm.
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Affiliation(s)
- Korbinian Buerger
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Regensburg, Germany.
| | - Kerstin N Schmidt
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Regensburg, Germany
| | - Jantina Fokkema
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Hans C Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Olga Maier
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Regensburg, Germany
| | - Uwe de Vries
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Regensburg, Germany
| | - Yulia Zaytseva
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Regensburg, Germany
| | - Reinhard Rachel
- Center for Electron Microscopy, University of Regensburg, Regensburg, Germany
| | - Ralph Witzgall
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Regensburg, Germany.
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32
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Li X, Park D, Chang Y, Radhakrishnan A, Wu H, Wang P, Liu J. A mammalian system for high-resolution imaging of intact cells by cryo-electron tomography. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 160:87-96. [PMID: 33058942 DOI: 10.1016/j.pbiomolbio.2020.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 09/17/2020] [Accepted: 09/20/2020] [Indexed: 10/23/2022]
Abstract
Mammalian cells contain an elaborate network of organelles and molecular machines that orchestrate essential cellular processes. Visualization of this network at a molecular level is vital for understanding these cellular processes. Here we present a model system based on nerve growth factor (NGF)-differentiated PC12 cells (PC12+) and suitable for high resolution imaging of organelles and molecular machines in situ. We detail an optimized imaging pipeline that effectively combines correlative light and electron microscopy (CLEM), cryo-focused ion beam (cryo-FIB), cryo-electron tomography (cryo-ET), and sub-tomogram averaging to produce three-dimensional and molecular resolution snapshots of organelles and molecular machines in near-native cellular environments. Our studies demonstrate that cryo-ET imaging of PC12+ systems provides an accessible and highly efficient avenue for dissecting specific cellular processes in mammalian cells at high resolution.
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Affiliation(s)
- Xia Li
- Department of Microbial Pathogenesis and Microbial Science Institute, Yale School of Medicine, New Haven, CT, 06516, USA; Institute of Special Environmental Medicine and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, 226000, China.
| | - Donghyun Park
- Department of Microbial Pathogenesis and Microbial Science Institute, Yale School of Medicine, New Haven, CT, 06516, USA
| | - Yunjie Chang
- Department of Microbial Pathogenesis and Microbial Science Institute, Yale School of Medicine, New Haven, CT, 06516, USA
| | | | - Hangjun Wu
- Center of Cryo Electron Microscopy and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Pei Wang
- Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China
| | - Jun Liu
- Department of Microbial Pathogenesis and Microbial Science Institute, Yale School of Medicine, New Haven, CT, 06516, USA.
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33
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Abstract
Correlative light and electron microscopy (CLEM) combines the strengths of light microscopy (LM) and electron microscopy (EM) to pin-point and visualize cellular or macromolecular structures. However, there are many different imaging modalities that can be combined in a CLEM workflow, creating a vast number of combinations that can overwhelm new-comers to the field. Here, we offer a conceptual framework to help guide the decision-making process for choosing the CLEM workflow that can best address your research question, based on the answer to five questions.
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34
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KUBA JAKUB, MITCHELS JOHN, HOVORKA MILOŠ, ERDMANN PHILIPP, BERKA LUKÁŠ, KIRMSE ROBERT, KÖNIG JULIA, DE BOCK JAN, GOETZE BERNHARD, RIGORT ALEXANDER. Advanced cryo‐tomography workflow developments – correlative microscopy, milling automation and cryo‐lift‐out. J Microsc 2020; 281:112-124. [DOI: 10.1111/jmi.12939] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/22/2020] [Accepted: 06/16/2020] [Indexed: 01/13/2023]
Affiliation(s)
- JAKUB KUBA
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | - JOHN MITCHELS
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | - MILOŠ HOVORKA
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | - PHILIPP ERDMANN
- Department of Molecular Structural Biology Max Planck Institute of Biochemistry Martinsried Germany
| | - LUKÁŠ BERKA
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | | | | | - JAN DE BOCK
- Leica Microsystems CMS GmbH Mannheim Germany
| | - BERNHARD GOETZE
- Thermo Fisher Scientific FEI Deutschland GmbH Planegg Germany
| | - ALEXANDER RIGORT
- Department of Molecular Structural Biology Max Planck Institute of Biochemistry Martinsried Germany
- Thermo Fisher Scientific FEI Deutschland GmbH Planegg Germany
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35
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Ganeva I, Kukulski W. Membrane Architecture in the Spotlight of Correlative Microscopy. Trends Cell Biol 2020; 30:577-587. [DOI: 10.1016/j.tcb.2020.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/19/2022]
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36
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Böhning J, Bharat TAM. Towards high-throughput in situ structural biology using electron cryotomography. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 160:97-103. [PMID: 32579969 DOI: 10.1016/j.pbiomolbio.2020.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 01/11/2023]
Abstract
Electron cryotomography is a rapidly evolving method for imaging macromolecules directly within the native environment of cells and tissues. Combined with sub-tomogram averaging, it allows structural and cell biologists to obtain sub-nanometre resolution structures in situ. However, low throughput in cryo-ET sample preparation and data acquisition, as well as difficulties in target localisation and sub-tomogram averaging image processing, limit its widespread usability. In this review, we discuss new advances in the field that address these throughput and technical problems. We focus on recent efforts made to resolve issues in sample thinning, improvement in data collection speed at the microscope, strategies for localisation of macromolecules using correlated light and electron microscopy and advancements made to improve resolution in sub-tomogram averaging. These advances will considerably decrease the amount of time and effort required for cryo-ET and sub-tomogram averaging, ushering in a new era of structural biology where in situ macromolecular structure determination will be routine.
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Affiliation(s)
- Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom.
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37
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Jun S, Ro HJ, Bharda A, Kim SI, Jeoung D, Jung HS. Advances in Cryo-Correlative Light and Electron Microscopy: Applications for Studying Molecular and Cellular Events. Protein J 2020; 38:609-615. [PMID: 31396855 DOI: 10.1007/s10930-019-09856-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cryo-correlative light and electron microscopy (Cryo-CLEM) is materializing as a widespread approach amalgamating the advantages of both fluorescence light microscopy (FLM) as well as three dimensional (3D) cryo-electron tomography (cryo-ET) to reveal the ultrastructure of significant target molecules with specific cellular functions. Cryo-CLEM allows imaging of cells by means of fluorescence microscopy exhibiting the location of the destined molecule at high temporal and spatial resolution while cryo-ET is employed to analyze the 3D structure at a molecular resolution in close-to-physiological condition. Present review focuses upon the practical strategies for Cryo-CLEM and recent technical developments that will assist the broad implementation of this technique to investigate and answer questions pertaining to various biological events occurring in the cell.
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Affiliation(s)
- Sangmi Jun
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea. .,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea. .,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea.
| | - Hyun-Joo Ro
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Anahita Bharda
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea
| | - Seung Il Kim
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Dooil Jeoung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea.
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38
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Zachs T, Schertel A, Medeiros J, Weiss GL, Hugener J, Matos J, Pilhofer M. Fully automated, sequential focused ion beam milling for cryo-electron tomography. eLife 2020; 9:e52286. [PMID: 32149604 PMCID: PMC7082125 DOI: 10.7554/elife.52286] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/07/2020] [Indexed: 11/13/2022] Open
Abstract
Cryo-electron tomography (cryoET) has become a powerful technique at the interface of structural biology and cell biology, due to its unique ability for imaging cells in their native state and determining structures of macromolecular complexes in their cellular context. A limitation of cryoET is its restriction to relatively thin samples. Sample thinning by cryo-focused ion beam (cryoFIB) milling has significantly expanded the range of samples that can be analyzed by cryoET. Unfortunately, cryoFIB milling is low-throughput, time-consuming and manual. Here, we report a method for fully automated sequential cryoFIB preparation of high-quality lamellae, including rough milling and polishing. We reproducibly applied this method to eukaryotic and bacterial model organisms, and show that the resulting lamellae are suitable for cryoET imaging and subtomogram averaging. Since our method reduces the time required for lamella preparation and minimizes the need for user input, we envision the technique will render previously inaccessible projects feasible.
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Affiliation(s)
- Tobias Zachs
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Andreas Schertel
- Carl Zeiss Microscopy GmbH, Zeiss Customer Center EuropeOberkochenGermany
| | - João Medeiros
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Gregor L Weiss
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Jannik Hugener
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
- Institute of Biochemistry, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Joao Matos
- Institute of Biochemistry, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule ZürichZürichSwitzerland
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39
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Fu X, Ning J, Zhong Z, Ambrose Z, Charles Watkins S, Zhang P. AutoCLEM: An Automated Workflow for Correlative Live-Cell Fluorescence Microscopy and Cryo-Electron Tomography. Sci Rep 2019; 9:19207. [PMID: 31844138 PMCID: PMC6915765 DOI: 10.1038/s41598-019-55766-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 12/02/2019] [Indexed: 01/06/2023] Open
Abstract
Correlative light and electron microscopy (CLEM) combines the strengths of both light and electron imaging modalities and enables linking of biological spatiotemporal information from live-cell fluorescence light microscopy (fLM) to high-resolution cellular ultra-structures from cryo-electron microscopy and tomography (cryoEM/ET). This has been previously achieved by using fLM signals to localize the regions of interest under cryogenic conditions. The correlation process, however, is often tedious and time-consuming with low throughput and limited accuracy, because multiple correlation steps at different length scales are largely carried out manually. Here, we present an experimental workflow, AutoCLEM, which overcomes the existing limitations and improves the performance and throughput of CLEM methods, and associated software. The AutoCLEM system encompasses a high-speed confocal live-cell imaging module to acquire an automated fLM grid atlas that is linked to the cryoEM grid atlas, followed by cryofLM imaging after freezing. The fLM coordinates of the targeted areas are automatically converted to cryoEM/ET and refined using fluorescent fiducial beads. This AutoCLEM workflow significantly accelerates the correlation efficiency between live-cell fluorescence imaging and cryoEM/ET structural analysis, as demonstrated by visualizing human immunodeficiency virus type 1 (HIV-1) interacting with host cells.
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Affiliation(s)
- Xiaofeng Fu
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Jiying Ning
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Zhou Zhong
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Zandrea Ambrose
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Simon Charles Watkins
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA. .,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. .,Electron Bio-Imaging Centre, Diamond Light Sources, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
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40
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Hoffmann PC, Bharat TAM, Wozny MR, Boulanger J, Miller EA, Kukulski W. Tricalbins Contribute to Cellular Lipid Flux and Form Curved ER-PM Contacts that Are Bridged by Rod-Shaped Structures. Dev Cell 2019; 51:488-502.e8. [PMID: 31743663 PMCID: PMC6863393 DOI: 10.1016/j.devcel.2019.09.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 08/06/2019] [Accepted: 09/25/2019] [Indexed: 11/25/2022]
Abstract
Lipid flow between cellular organelles occurs via membrane contact sites. Extended-synaptotagmins, known as tricalbins in yeast, mediate lipid transfer between the endoplasmic reticulum (ER) and plasma membrane (PM). How these proteins regulate membrane architecture to transport lipids across the aqueous space between bilayers remains unknown. Using correlative microscopy, electron cryo-tomography, and high-throughput genetics, we address the interplay of architecture and function in budding yeast. We find that ER-PM contacts differ in protein composition and membrane morphology, not in intermembrane distance. In situ electron cryo-tomography reveals the molecular organization of tricalbin-mediated contacts, suggesting a structural framework for putative lipid transfer. Genetic analysis uncovers functional overlap with cellular lipid routes, such as maintenance of PM asymmetry. Further redundancies are suggested for individual tricalbin protein domains. We propose a modularity of molecular and structural functions of tricalbins and of their roles within the cellular network of lipid distribution pathways.
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Affiliation(s)
- Patrick C Hoffmann
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, UK
| | - Michael R Wozny
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jerome Boulanger
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Elizabeth A Miller
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Wanda Kukulski
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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41
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Asam C, Buerger K, Felthaus O, Brébant V, Rachel R, Prantl L, Witzgall R, Haerteis S, Aung T. Subcellular localization of the chemotherapeutic agent doxorubicin in renal epithelial cells and in tumor cells using correlative light and electron microscopy. Clin Hemorheol Microcirc 2019; 73:157-167. [DOI: 10.3233/ch-199212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Claudia Asam
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Germany
| | - Korbinian Buerger
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Germany
| | - Oliver Felthaus
- Centre of Plastic, Aesthetic, Hand and Reconstructive Surgery, University of Regensburg, Regensburg, Germany
| | - Vanessa Brébant
- Centre of Plastic, Aesthetic, Hand and Reconstructive Surgery, University of Regensburg, Regensburg, Germany
| | - Reinhard Rachel
- Centre for Electron Microscopy, Faculty of Biology and Preclinical Medicine, University of Regensburg, Germany
| | - Lukas Prantl
- Centre of Plastic, Aesthetic, Hand and Reconstructive Surgery, University of Regensburg, Regensburg, Germany
| | - Ralph Witzgall
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Germany
| | - Silke Haerteis
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Germany
| | - Thiha Aung
- Centre of Plastic, Aesthetic, Hand and Reconstructive Surgery, University of Regensburg, Regensburg, Germany
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42
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Engel L, Gaietta G, Dow LP, Swift MF, Pardon G, Volkmann N, Weis WI, Hanein D, Pruitt BL. Extracellular matrix micropatterning technology for whole cell cryogenic electron microscopy studies. JOURNAL OF MICROMECHANICS AND MICROENGINEERING : STRUCTURES, DEVICES, AND SYSTEMS 2019; 29:115018. [PMID: 32879557 PMCID: PMC7457726 DOI: 10.1088/1361-6439/ab419a] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cryogenic electron tomography is the highest resolution tool available for structural analysis of macromolecular organization inside cells. Micropatterning of extracellular matrix (ECM) proteins is an established in vitro cell culture technique used to control cell shape. Recent traction force microscopy studies have shown correlation between cell morphology and the regulation of force transmission. However, it remains unknown how cells sustain increased strain energy states and localized stresses at the supramolecular level. Here, we report a technology to enable direct observation of mesoscale organization in epithelial cells under morphological modulation, using a maskless protein photopatterning method (PRIMO) to confine cells to ECM micropatterns on electron microscopy substrates. These micropatterned cell culture substrates can be used in mechanobiology research to correlate changes in nanometer-scale organization at cell-cell and cell-ECM contacts to strain energy states and traction stress distribution in the cell.
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Affiliation(s)
- Leeya Engel
- Department of Bioengineering, Stanford University, Stanford, California
- Correspondence:
| | - Guido Gaietta
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Liam P. Dow
- Department of Bioengineering, Stanford University, Stanford, California
- Biomolecular Science and Engineering Program, University of California, Santa Barbara
| | - Mark F. Swift
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Gaspard Pardon
- Department of Bioengineering, Stanford University, Stanford, California
| | - Niels Volkmann
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - William I. Weis
- Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine
| | - Dorit Hanein
- Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Beth L. Pruitt
- Department of Bioengineering, Stanford University, Stanford, California
- Biomolecular Science and Engineering Program, University of California, Santa Barbara
- Departments of Mechanical Engineering and Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara
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43
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Andronov L, Michalon J, Ouararhni K, Orlov I, Hamiche A, Vonesch JL, Klaholz BP. 3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations. Bioinformatics 2019; 34:3004-3012. [PMID: 29635310 DOI: 10.1093/bioinformatics/bty200] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 04/02/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Single-molecule localization microscopy (SMLM) can play an important role in integrated structural biology approaches to identify, localize and determine the 3D structure of cellular structures. While many tools exist for the 3D analysis and visualization of crystal or cryo-EM structures little exists for 3D SMLM data, which can provide unique insights but are particularly challenging to analyze in three dimensions especially in a dense cellular context. Results We developed 3DClusterViSu, a method based on 3D Voronoi tessellations that allows local density estimation, segmentation and quantification of 3D SMLM data and visualization of protein clusters within a 3D tool. We show its robust performance on microtubules and histone proteins H2B and CENP-A with distinct spatial distributions. 3DClusterViSu will favor multi-scale and multi-resolution synergies to allow integrating molecular and cellular levels in the analysis of macromolecular complexes. Availability and impementation 3DClusterViSu is available under http://cbi-dev.igbmc.fr/cbi/voronoi3D. Supplementary information Supplementary figures are available at Bioinformatics online.
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Affiliation(s)
- Leonid Andronov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jonathan Michalon
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Khalid Ouararhni
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Igor Orlov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Ali Hamiche
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jean-Luc Vonesch
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France.,Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
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44
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Otegui MS, Pennington JG. Electron tomography in plant cell biology. Microscopy (Oxf) 2019; 68:69-79. [PMID: 30452668 DOI: 10.1093/jmicro/dfy133] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/15/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022] Open
Abstract
Electron tomography (ET) approaches are based on the imaging of a biological specimen at different tilt angles by transmission electron microscopy (TEM). ET can be applied to both plastic-embedded and frozen samples. Technological advancements in TEM, direct electron detection, automated image collection, and imaging processing algorithms allow for 2-7-nm scale axial resolution in tomographic reconstructions of cells and organelles. In this review, we discussed the application of ET in plant cell biology and new opportunities for imaging plant cells by cryo-ET and other 3D electron microscopy approaches.
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Affiliation(s)
- Marisa S Otegui
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison WI, USA.,Laboratory of Molecular and Cellular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison WI, USA.,Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison WI, USA
| | - Jannice G Pennington
- Institute for Molecular Virology, University of Wisconsin-Madison, 1525 Linden Drive, Madison WI, USA.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, USA
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45
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Metskas LA, Briggs JAG. Fluorescence-Based Detection of Membrane Fusion State on a Cryo-EM Grid using Correlated Cryo-Fluorescence and Cryo-Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2019; 25:942-949. [PMID: 31084637 PMCID: PMC6624127 DOI: 10.1017/s1431927619000606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Correlated light and electron microscopy (CLEM) has become a popular technique for combining the protein-specific labeling of fluorescence with electron microscopy, both at room and cryogenic temperatures. Fluorescence applications at cryo-temperatures have typically been limited to localization of tagged protein oligomers due to known issues of extended triplet state duration, spectral shifts, and reduced photon capture through cryo-CLEM objectives. Here, we consider fluorophore characteristics and behaviors that could enable more extended applications. We describe how dialkylcarbocanine DiD, and its autoquenching by resonant energy transfer (RET), can be used to distinguish the fusion state of a lipid bilayer at cryo-temperatures. By adapting an established fusion assay to work under cryo-CLEM conditions, we identified areas of fusion between influenza virus-like particles and fluorescently labeled lipid vesicles on a cryo-EM grid. This result demonstrates that cryo-CLEM can be used to localize functions in addition to tagged proteins, and that fluorescence autoquenching by RET can be incorporated successfully into cryo-CLEM approaches. In the case of membrane fusion applications, this method provides both an orthogonal confirmation of functional state independent of the morphological description from cryo-EM and a way to bridge room-temperature kinetic assays and the cryo-EM images.
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Affiliation(s)
- Lauren Ann Metskas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory,69117 Heidelberg,Germany
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory,69117 Heidelberg,Germany
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46
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Imaging of post-mortem human brain tissue using electron and X-ray microscopy. Curr Opin Struct Biol 2019; 58:138-148. [PMID: 31349127 DOI: 10.1016/j.sbi.2019.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/26/2019] [Accepted: 06/10/2019] [Indexed: 12/12/2022]
Abstract
Electron microscopy imaging of post-mortem human brain (PMHB) comes with a unique set of challenges due to numerous parameters beyond the researcher's control. Nevertheless, the wealth of information provided by the ultrastructural analysis of PMHB is proving crucial in our understanding of neurodegenerative diseases. This review highlights the importance of such studies and covers challenges, limitations and recent developments in the application of current EM imaging, including cryo-ET and correlative hybrid techniques, on PMHB.
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47
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Touve MA, Wright DB, Mu C, Sun H, Park C, Gianneschi NC. Block Copolymer Amphiphile Phase Diagrams by High-Throughput Transmission Electron Microscopy. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00563] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | | | - Chen Mu
- Department of Industrial & Manufacturing Engineering, Florida State University, Tallahassee, Florida 32310, United States
| | | | - Chiwoo Park
- Department of Industrial & Manufacturing Engineering, Florida State University, Tallahassee, Florida 32310, United States
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48
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Eltsov M, Grewe D, Lemercier N, Frangakis A, Livolant F, Leforestier A. Nucleosome conformational variability in solution and in interphase nuclei evidenced by cryo-electron microscopy of vitreous sections. Nucleic Acids Res 2019; 46:9189-9200. [PMID: 30053160 PMCID: PMC6158616 DOI: 10.1093/nar/gky670] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/13/2018] [Indexed: 01/04/2023] Open
Abstract
In Eukaryotes, DNA is wound around the histone octamer forming the basic chromatin unit, the nucleosome. Atomic structures have been obtained from crystallography and single particle cryo-electron microscopy (cryoEM) of identical engineered particles. But native nucleosomes are dynamical entities with diverse DNA sequence and histone content, and little is known about their conformational variability, especially in the cellular context. Using cryoEM and tomography of vitreous sections we analyse native nucleosomes, both in vitro, using purified particles solubilized at physiologically relevant concentrations (25–50%), and in situ, within interphase nuclei. We visualize individual nucleosomes at a level of detail that allows us to measure the distance between the DNA gyres wrapped around. In concentrated solutions, we demonstrate a salt-dependent transition, with a high salt compact conformation resembling the canonical nucleosome and an open low salt one, closer to nuclear nucleosomes. Although further particle characterization and cartography are needed to understand the relationship between this conformational variability and chromatin functional states, this work opens a route to chromatin exploration in situ.
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Affiliation(s)
- Mikhail Eltsov
- Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Diana Grewe
- Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Nicolas Lemercier
- Laboratoire de Physique des Solides, UMR 8502 CNRS, Université Paris-Sud, Université Paris-Saclay, Bat 510, 91405 Orsay Cedex, France
| | - Achilleas Frangakis
- Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Françoise Livolant
- Laboratoire de Physique des Solides, UMR 8502 CNRS, Université Paris-Sud, Université Paris-Saclay, Bat 510, 91405 Orsay Cedex, France
| | - Amélie Leforestier
- Laboratoire de Physique des Solides, UMR 8502 CNRS, Université Paris-Sud, Université Paris-Saclay, Bat 510, 91405 Orsay Cedex, France
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49
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Cryo-SOFI enabling low-dose super-resolution correlative light and electron cryo-microscopy. Proc Natl Acad Sci U S A 2019; 116:4804-4809. [PMID: 30808803 PMCID: PMC6421404 DOI: 10.1073/pnas.1810690116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Correlative light and electron cryo-microscopy (cryo-CLEM) combines information from the specific labeling of fluorescence cryo-microscopy (cryo-FM) with the high resolution in environmental context of electron cryo-microscopy (cryo-EM). Exploiting super-resolution methods for cryo-FM is advantageous, as it enables the identification of rare events within the environmental background of cryo-EM at a sensitivity and resolution beyond that of conventional methods. However, due to the need for relatively high laser intensities, current super-resolution cryo-CLEM methods require cryo-protectants or support films which can severely reduce image quality in cryo-EM and are not compatible with many samples, such as mammalian cells. Here, we introduce cryogenic super-resolution optical fluctuation imaging (cryo-SOFI), a low-dose super-resolution imaging scheme based on the SOFI principle. As cryo-SOFI does not require special sample preparation, it is fully compatible with conventional cryo-EM specimens, and importantly, it does not affect the quality of cryo-EM imaging. By applying cryo-SOFI to a variety of biological application examples, we demonstrate resolutions up to ∼135 nm, an improvement of up to three times compared with conventional cryo-FM, while maintaining the specimen in a vitrified state for subsequent cryo-EM. Cryo-SOFI presents a general solution to the problem of specimen devitrification in super-resolution cryo-CLEM. It does not require a complex optical setup and can easily be implemented in any existing cryo-FM system.
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50
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Correlative cryo super-resolution light and electron microscopy on mammalian cells using fluorescent proteins. Sci Rep 2019; 9:1369. [PMID: 30718653 PMCID: PMC6362030 DOI: 10.1038/s41598-018-37728-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/12/2018] [Indexed: 11/22/2022] Open
Abstract
Sample fixation by vitrification is critical for the optimal structural preservation of biomolecules and subsequent high-resolution imaging by cryo-correlative light and electron microscopy (cryoCLEM). There is a large resolution gap between cryo fluorescence microscopy (cryoFLM), ~400-nm, and the sub-nanometre resolution achievable with cryo-electron microscopy (cryoEM), which hinders interpretation of cryoCLEM data. Here, we present a general approach to increase the resolution of cryoFLM using cryo-super-resolution (cryoSR) microscopy that is compatible with successive cryoEM investigation in the same region. We determined imaging parameters to avoid devitrification of the cryosamples without the necessity for cryoprotectants. Next, we examined the applicability of various fluorescent proteins (FPs) for single-molecule localisation cryoSR microscopy and found that all investigated FPs display reversible photoswitchable behaviour, and demonstrated cryoSR on lipid nanotubes labelled with rsEGFP2 and rsFastLime. Finally, we performed SR-cryoCLEM on mammalian cells expressing microtubule-associated protein-2 fused to rsEGFP2 and performed 3D cryo-electron tomography on the localised areas. The method we describe exclusively uses commercially available equipment to achieve a localisation precision of 30-nm. Furthermore, all investigated FPs displayed behaviour compatible with cryoSR microscopy, making this technique broadly available without requiring specialised equipment and will improve the applicability of this emerging technique for cellular and structural biology.
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