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Wu H, Fujioka Y, Sakaguchi S, Suzuki Y, Nakano T. Electron Tomography as a Tool to Study SARS-CoV-2 Morphology. Int J Mol Sci 2024; 25:11762. [PMID: 39519314 PMCID: PMC11547116 DOI: 10.3390/ijms252111762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 10/29/2024] [Accepted: 10/30/2024] [Indexed: 11/16/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel betacoronavirus, is the causative agent of COVID-19, which has caused economic and social disruption worldwide. To date, many drugs and vaccines have been developed for the treatment and prevention of COVID-19 and have effectively controlled the global epidemic of SARS-CoV-2. However, SARS-CoV-2 is highly mutable, leading to the emergence of new variants that may counteract current therapeutic measures. Electron microscopy (EM) is a valuable technique for obtaining ultrastructural information about the intracellular process of virus replication. In particular, EM allows us to visualize the morphological and subcellular changes during virion formation, which would provide a promising avenue for the development of antiviral agents effective against new SARS-CoV-2 variants. In this review, we present our recent findings using transmission electron microscopy (TEM) combined with electron tomography (ET) to reveal the morphologically distinct types of SARS-CoV-2 particles, demonstrating that TEM and ET are valuable tools for visually understanding the maturation status of SARS-CoV-2 in infected cells. This review also discusses the application of EM analysis to the evaluation of genetically engineered RNA viruses.
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Affiliation(s)
- Hong Wu
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka 565-0871, Japan; (Y.F.); (S.S.); (T.N.)
| | | | | | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka 565-0871, Japan; (Y.F.); (S.S.); (T.N.)
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2
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Castón JR, Luque D. Conventional Electron Microscopy, Cryogenic Electron Microscopy, and Cryogenic Electron Tomography of Viruses. Subcell Biochem 2024; 105:81-134. [PMID: 39738945 DOI: 10.1007/978-3-031-65187-8_3] [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: 01/02/2025]
Abstract
Electron microscopy (EM) techniques have been crucial for understanding the structure of biological specimens such as cells, tissues and macromolecular assemblies. Viruses and related viral assemblies are ideal targets for structural studies that help to define essential biological functions. Whereas conventional EM methods use chemical fixation, dehydration, and staining of the specimens, cryogenic electron microscopy (cryo-EM) preserves the native hydrated state. Combined with image processing and three-dimensional reconstruction techniques, cryo-EM provides three-dimensional maps of these macromolecular complexes from projection images, at atomic or near-atomic resolutions. Cryo-EM is also a major technique in structural biology for dynamic studies of functional complexes, which are often unstable, flexible, scarce, or transient in their native environments. State-of-the-art techniques in structural virology now extend beyond purified symmetric capsids and focus on the asymmetric elements such as the packaged genome and minor structural proteins that were previously missed. As a tool, cryo-EM also complements high-resolution techniques such as X-ray diffraction and NMR spectroscopy; these synergistic hybrid approaches provide important new information. Three-dimensional cryogenic electron tomography (cryo-ET), a variation of cryo-EM, goes further, and allows the study of pleomorphic and complex viruses not only in their physiological state but also in their natural environment in the cell, thereby bridging structural studies at the molecular and cellular levels. Cryo-EM and cryo-ET have been applied successfully in basic research, shedding light on fundamental aspects of virus biology and providing insights into threatening viruses, including SARS-CoV-2, responsible for the COVID-19 pandemic.
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Affiliation(s)
- José R Castón
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
- Nanobiotechnology Associated Unit CNB-CSIC-IMDEA, Madrid, Spain.
| | - Daniel Luque
- School of Biomedical Sciences, The University of New South Wales, Sydney, NSW, Australia.
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW, Australia.
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3
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Evans SL, Al-Hazeem MMJ, Mann D, Smetacek N, Beavil AJ, Sun Y, Chen T, Dykes GF, Liu LN, Bergeron JRC. Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome. Structure 2023; 31:677-688.e4. [PMID: 37015227 PMCID: PMC10689251 DOI: 10.1016/j.str.2023.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/19/2023] [Accepted: 03/09/2023] [Indexed: 04/05/2023]
Abstract
Carboxysomes are proteinaceous bacterial microcompartments that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, encapsulating several enzymes, including ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for the first step of the Calvin-Benson-Bassham cycle. Despite their significance in carbon fixation and great bioengineering potentials, the structural understanding of native carboxysomes is currently limited to low-resolution studies. Here, we report the characterization of a native α-carboxysome from a marine cyanobacterium by single-particle cryoelectron microscopy (cryo-EM). We have determined the structure of its RuBisCO enzyme, and obtained low-resolution maps of its icosahedral shell, and of its concentric interior organization. Using integrative modeling approaches, we have proposed a complete atomic model of an intact carboxysome, providing insight into its organization and assembly. This is critical for a better understanding of the carbon fixation mechanism and toward repurposing carboxysomes in synthetic biology for biotechnological applications.
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Affiliation(s)
- Sasha L Evans
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Monsour M J Al-Hazeem
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniel Mann
- Ernst-Ruska Centre 3, Forschungszentrum Jülich, Jülich, Germany
| | - Nicolas Smetacek
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - Andrew J Beavil
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, Shandong, China.
| | - Julien R C Bergeron
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK; Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK.
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Burton-Smith RN, Murata K. Cryo-electron Microscopy of Protein Cages. Methods Mol Biol 2023; 2671:173-210. [PMID: 37308646 DOI: 10.1007/978-1-0716-3222-2_11] [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: 06/14/2023]
Abstract
Protein cages are one of the most widely studied objects in the field of cryogenic electron microscopy-encompassing natural and synthetic constructs, from enzymes assisting protein folding such as chaperonin to virus capsids. Tremendous diversity of morphology and function is demonstrated by the structure and role of proteins, some of which are nearly ubiquitous, while others are present in few organisms. Protein cages are often highly symmetrical, which helps improve the resolution obtained by cryo-electron microscopy (cryo-EM). Cryo-EM is the study of vitrified samples using an electron probe to image the subject. A sample is rapidly frozen in a thin layer on a porous grid, attempting to keep the sample as close to a native state as possible. This grid is kept at cryogenic temperatures throughout imaging in an electron microscope. Once image acquisition is complete, a variety of software packages may be employed to carry out analysis and reconstruction of three-dimensional structures from the two-dimensional micrograph images. Cryo-EM can be used on samples that are too large or too heterogeneous to be amenable to other structural biology techniques like NMR or X-ray crystallography. In recent years, advances in both hardware and software have provided significant improvements to the results obtained using cryo-EM, recently demonstrating true atomic resolution from vitrified aqueous samples. Here, we review these advances in cryo-EM, especially in that of protein cages, and introduce several tips for situations we have experienced.
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Affiliation(s)
- Raymond N Burton-Smith
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute for Natural Sciences, Okazaki, Aichi, Japan
- National Institute for Physiological Sciences (NIPS), National Institute for Natural Sciences, Okazaki, Aichi, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute for Natural Sciences, Okazaki, Aichi, Japan.
- National Institute for Physiological Sciences (NIPS), National Institute for Natural Sciences, Okazaki, Aichi, Japan.
- Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan.
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Cheng A, Kim PT, Kuang H, Mendez JH, Chua EYD, Maruthi K, Wei H, Sawh A, Aragon MF, Serbynovskyi V, Neselu K, Eng ET, Potter CS, Carragher B, Bepler T, Noble AJ. Fully automated multi-grid cryoEM screening using Smart Leginon. IUCRJ 2023; 10:77-89. [PMID: 36598504 PMCID: PMC9812217 DOI: 10.1107/s2052252522010624] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Single-particle cryo-electron microscopy (cryoEM) is a swiftly growing method for understanding protein structure. With increasing demand for high-throughput, high-resolution cryoEM services comes greater demand for rapid and automated cryoEM grid and sample screening. During screening, optimal grids and sample conditions are identified for subsequent high-resolution data collection. Screening is a major bottleneck for new cryoEM projects because grids must be optimized for several factors, including grid type, grid hole size, sample concentration, buffer conditions, ice thickness and particle behavior. Even for mature projects, multiple grids are commonly screened to select a subset for high-resolution data collection. Here, machine learning and novel purpose-built image-processing and microscope-handling algorithms are incorporated into the automated data-collection software Leginon, to provide an open-source solution for fully automated high-throughput grid screening. This new version, broadly called Smart Leginon, emulates the actions of an operator in identifying areas on the grid to explore as potentially useful for data collection. Smart Leginon Autoscreen sequentially loads and examines grids from an automated specimen-exchange system to provide completely unattended grid screening across a set of grids. Comparisons between a multi-grid autoscreen session and conventional manual screening by 5 expert microscope operators are presented. On average, Autoscreen reduces operator time from ∼6 h to <10 min and provides a percentage of suitable images for evaluation comparable to the best operator. The ability of Smart Leginon to target holes that are particularly difficult to identify is analyzed. Finally, the utility of Smart Leginon is illustrated with three real-world multi-grid user screening/collection sessions, demonstrating the efficiency and flexibility of the software package. The fully automated functionality of Smart Leginon significantly reduces the burden on operator screening time, improves the throughput of screening and recovers idle microscope time, thereby improving availability of cryoEM services.
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Affiliation(s)
- Anchi Cheng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Paul T. Kim
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| | - Huihui Kuang
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Joshua H. Mendez
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Eugene Y. D. Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Kashyap Maruthi
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Hui Wei
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Anjelique Sawh
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Mahira F. Aragon
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | | | - Kasahun Neselu
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Clinton S. Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tristan Bepler
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| | - Alex J. Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
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A novel capsid protein network allows the characteristic internal membrane structure of Marseilleviridae giant viruses. Sci Rep 2022; 12:21428. [PMID: 36504202 PMCID: PMC9742146 DOI: 10.1038/s41598-022-24651-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 11/18/2022] [Indexed: 12/14/2022] Open
Abstract
Marseilleviridae is a family of giant viruses, showing a characteristic internal membrane with extrusions underneath the icosahedral vertices. However, such large objects, with a maximum diameter of 250 nm are technically difficult to examine at sub-nanometre resolution by cryo-electron microscopy. Here, we tested the utility of 1 MV high-voltage cryo-EM (cryo-HVEM) for single particle structural analysis (SPA) of giant viruses using tokyovirus, a species of Marseilleviridae, and revealed the capsid structure at 7.7 Å resolution. The capsid enclosing the viral DNA consisted primarily of four layers: (1) major capsid proteins (MCPs) and penton proteins, (2) minor capsid proteins (mCPs), (3) scaffold protein components (ScPCs), and (4) internal membrane. The mCPs showed a novel capsid lattice consisting of eight protein components. ScPCs connecting the icosahedral vertices supported the formation of the membrane extrusions, and possibly act like tape measure proteins reported in other giant viruses. The density on top of the MCP trimer was suggested to include glycoproteins. This is the first attempt at cryo-HVEM SPA. We found the primary limitations to be the lack of automated data acquisition and software support for collection and processing and thus achievable resolution. However, the results pave the way for using cryo-HVEM for structural analysis of larger biological specimens.
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Watanabe R, Song C, Kayama Y, Takemura M, Murata K. Particle Morphology of Medusavirus Inside and Outside the Cells Reveals a New Maturation Process of Giant Viruses. J Virol 2022; 96:e0185321. [PMID: 35297671 PMCID: PMC9006890 DOI: 10.1128/jvi.01853-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/14/2022] [Indexed: 01/01/2023] Open
Abstract
Medusavirus, a giant virus, is phylogenetically closer to eukaryotes than the other giant viruses and has been recently classified as an independent species. However, details of its morphology and maturation process in host cells remain unclear. Here, we investigated the particle morphology of medusavirus inside and outside infected cells using conventional transmission electron microscopy (C-TEM) and cryo-electron microscopy (cryo-EM). The C-TEM of amoebae infected with the medusavirus showed four types of particles, i.e., pseudo-DNA-empty (p-Empty), DNA-empty (Empty), semi-DNA-full (s-Full), and DNA-full (Full). Time-dependent changes in the four types of particles and their intracellular localization suggested a new maturation process for the medusavirus. Viral capsids and viral DNAs are produced independently in the cytoplasm and nucleus, respectively, and only the empty particles located near the host nucleus can incorporate the viral DNA into the capsid. Therefore, all four types of particles were found outside the cells. The cryo-EM of these particles showed that the intact virus structure, covered with three different types of spikes, was preserved among all particle types, although with minor size-related differences. The internal membrane exhibited a structural array similar to that of the capsid, interacted closely with the capsid, and displayed open membrane structures in the Empty and p-Empty particles. The results suggest that these open structures in the internal membrane are used for an exchange of scaffold proteins and viral DNA during the maturation process. This new model of the maturation process of medusavirus provides insight into the structural and behavioral diversity of giant viruses. IMPORTANCE Giant viruses exhibit diverse morphologies and maturation processes. In this study, medusavirus showed four types of particle morphologies, both inside and outside the infected cells, when propagated in amoeba culture. Time-course analysis and intracellular localization of the medusavirus in the infected cells suggested a new maturation process via the four types of particles. Like the previously reported pandoravirus, the viral DNA of medusavirus is replicated in the host's nucleus. However, viral capsids are produced independently in the host cytoplasm, and only empty capsids near the nucleus can take up viral DNA. As a result, many immature particles were released from the host cell along with the mature particles. The capsid structure is well conserved among the four types of particles, except for the open membrane structures in the empty particles, suggesting that they are used to exchange scaffold proteins for viral DNAs. These findings indicate that medusavirus has a unique maturation process.
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Affiliation(s)
- Ryoto Watanabe
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Aichi, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Chihong Song
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Aichi, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Yoko Kayama
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Terabase, Inc., Okazaki, Aichi, Japan
| | - Masaharu Takemura
- Institute of Arts and Sciences, Tokyo University of Science, Shinjuku, Tokyo, Japan
| | - Kazuyoshi Murata
- School of Life Science, The Graduate University for Advanced Studies, Okazaki, Aichi, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
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