1
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Gemin O, Gluc M, Rosa H, Purdy M, Niemann M, Peskova Y, Mattei S, Jomaa A. Ribosomes hibernate on mitochondria during cellular stress. Nat Commun 2024; 15:8666. [PMID: 39379376 PMCID: PMC11461667 DOI: 10.1038/s41467-024-52911-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 09/23/2024] [Indexed: 10/10/2024] Open
Abstract
Cell survival under nutrient-deprived conditions relies on cells' ability to adapt their organelles and rewire their metabolic pathways. In yeast, glucose depletion induces a stress response mediated by mitochondrial fragmentation and sequestration of cytosolic ribosomes on mitochondria. This cellular adaptation promotes survival under harsh environmental conditions; however, the underlying mechanism of this response remains unknown. Here, we demonstrate that upon glucose depletion protein synthesis is halted. Cryo-electron microscopy structure of the ribosomes show that they are devoid of both tRNA and mRNA, and a subset of the particles depicted a conformational change in rRNA H69 that could prevent tRNA binding. Our in situ structural analyses reveal that the hibernating ribosomes tether to fragmented mitochondria and establish eukaryotic-specific, higher-order storage structures by assembling into oligomeric arrays on the mitochondrial surface. Notably, we show that hibernating ribosomes exclusively bind to the outer mitochondrial membrane via the small ribosomal subunit during cellular stress. We identify the ribosomal protein Cpc2/RACK1 as the molecule mediating ribosomal tethering to mitochondria. This study unveils the molecular mechanism connecting mitochondrial stress with the shutdown of protein synthesis and broadens our understanding of cellular responses to nutrient scarcity and cell quiescence.
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Affiliation(s)
- Olivier Gemin
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, Heidelberg, Germany
| | - Maciej Gluc
- Department of Molecular Physiology and Biological Physics and Center for Cell and Membrane Physiology, School of Medicine, University of Virginia, Charlottesville, USA
| | - Higor Rosa
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, Heidelberg, Germany
| | - Michael Purdy
- Department of Molecular Physiology and Biological Physics and Center for Cell and Membrane Physiology, School of Medicine, University of Virginia, Charlottesville, USA
| | - Moritz Niemann
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, Heidelberg, Germany
| | - Yelena Peskova
- Department of Molecular Physiology and Biological Physics and Center for Cell and Membrane Physiology, School of Medicine, University of Virginia, Charlottesville, USA
| | - Simone Mattei
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, Heidelberg, Germany.
- European Molecular Biology Laboratory, Imaging Centre, Meyerhofstraße 1, Heidelberg, Germany.
| | - Ahmad Jomaa
- Department of Molecular Physiology and Biological Physics and Center for Cell and Membrane Physiology, School of Medicine, University of Virginia, Charlottesville, USA.
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, USA.
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2
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Matsko NB, Schorb M, Schwab Y. Selective signal enhancement in Fourier space as a tool for discovering ultrastructural organization of macromolecules from in situ TEM. J Struct Biol 2024; 216:108128. [PMID: 39284397 DOI: 10.1016/j.jsb.2024.108128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 09/10/2024] [Accepted: 09/12/2024] [Indexed: 10/01/2024]
Abstract
We present a Fourier transform (FT) based analytical method that allows to obtain of ultrastructural details from TEM images at sub-nanometer scale applying a selective filtering for singular macromolecule electron microscopy density information. It can be applied to high-pressure frozen, frozen hydrated and epoxy freeze substituted and embedded biological species. Both 2D projections and orthoslices from reconstructed tomograms can be used as a source of structural information. The key to the method is to select the macromolecule or organelle of interest with an accuracy of ≥ 7 - 3 nm (depending on pixel size of initial tilt series or singular image acquisition) and explore both the central low frequency FT intensity and diffraction regions to obtain the spatial structural organization and its dimensional characteristics, respectively. We also introduce a structure-specific selective mask FT filtering approach that can significantly improve image information even in poorly contrasted TEM of resin sections without heavy metal been used. The described method elucidates chromatin architecture without the need of averaging. A zigzag symmetry of 30 nm diameter chromatin fibers which in general is a controversial topic of research has been identified for C. elegans cells in vivo with sub-nanometer details being preserved in the images.
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Affiliation(s)
- Nadejda B Matsko
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Max-Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Jahn-Str. 29, D-69120 Heidelberg, Germany.
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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3
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Parkhurst JM, Varslot T, Dumoux M, Siebert CA, Darrow M, Basham M, Kirkland A, Grange M, Evans G, Naismith JH. Pillar data-acquisition strategies for cryo-electron tomography of beam-sensitive biological samples. Acta Crystallogr D Struct Biol 2024; 80:421-438. [PMID: 38829361 PMCID: PMC11154591 DOI: 10.1107/s2059798324004546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
For cryo-electron tomography (cryo-ET) of beam-sensitive biological specimens, a planar sample geometry is typically used. As the sample is tilted, the effective thickness of the sample along the direction of the electron beam increases and the signal-to-noise ratio concomitantly decreases, limiting the transfer of information at high tilt angles. In addition, the tilt range where data can be collected is limited by a combination of various sample-environment constraints, including the limited space in the objective lens pole piece and the possible use of fixed conductive braids to cool the specimen. Consequently, most tilt series are limited to a maximum of ±70°, leading to the presence of a missing wedge in Fourier space. The acquisition of cryo-ET data without a missing wedge, for example using a cylindrical sample geometry, is hence attractive for volumetric analysis of low-symmetry structures such as organelles or vesicles, lysis events, pore formation or filaments for which the missing information cannot be compensated by averaging techniques. Irrespective of the geometry, electron-beam damage to the specimen is an issue and the first images acquired will transfer more high-resolution information than those acquired last. There is also an inherent trade-off between higher sampling in Fourier space and avoiding beam damage to the sample. Finally, the necessity of using a sufficient electron fluence to align the tilt images means that this fluence needs to be fractionated across a small number of images; therefore, the order of data acquisition is also a factor to consider. Here, an n-helix tilt scheme is described and simulated which uses overlapping and interleaved tilt series to maximize the use of a pillar geometry, allowing the entire pillar volume to be reconstructed as a single unit. Three related tilt schemes are also evaluated that extend the continuous and classic dose-symmetric tilt schemes for cryo-ET to pillar samples to enable the collection of isotropic information across all spatial frequencies. A fourfold dose-symmetric scheme is proposed which provides a practical compromise between uniform information transfer and complexity of data acquisition.
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Affiliation(s)
- James M. Parkhurst
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Trond Varslot
- Thermo Fisher Scientific, Vlastimila Pecha, Brno, Czechia
| | - Maud Dumoux
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - C. Alistair Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Michele Darrow
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Mark Basham
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Angus Kirkland
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Electron Physical Science Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
| | - Michael Grange
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Gwyndaf Evans
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James H. Naismith
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
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4
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Galaz-Montoya JG. The advent of preventive high-resolution structural histopathology by artificial-intelligence-powered cryogenic electron tomography. Front Mol Biosci 2024; 11:1390858. [PMID: 38868297 PMCID: PMC11167099 DOI: 10.3389/fmolb.2024.1390858] [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: 02/24/2024] [Accepted: 05/08/2024] [Indexed: 06/14/2024] Open
Abstract
Advances in cryogenic electron microscopy (cryoEM) single particle analysis have revolutionized structural biology by facilitating the in vitro determination of atomic- and near-atomic-resolution structures for fully hydrated macromolecular complexes exhibiting compositional and conformational heterogeneity across a wide range of sizes. Cryogenic electron tomography (cryoET) and subtomogram averaging are rapidly progressing toward delivering similar insights for macromolecular complexes in situ, without requiring tags or harsh biochemical purification. Furthermore, cryoET enables the visualization of cellular and tissue phenotypes directly at molecular, nanometric resolution without chemical fixation or staining artifacts. This forward-looking review covers recent developments in cryoEM/ET and related technologies such as cryogenic focused ion beam milling scanning electron microscopy and correlative light microscopy, increasingly enhanced and supported by artificial intelligence algorithms. Their potential application to emerging concepts is discussed, primarily the prospect of complementing medical histopathology analysis. Machine learning solutions are poised to address current challenges posed by "big data" in cryoET of tissues, cells, and macromolecules, offering the promise of enabling novel, quantitative insights into disease processes, which may translate into the clinic and lead to improved diagnostics and targeted therapeutics.
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Affiliation(s)
- Jesús G. Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, United States
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5
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Cruz-León S, Majtner T, Hoffmann PC, Kreysing JP, Kehl S, Tuijtel MW, Schaefer SL, Geißler K, Beck M, Turoňová B, Hummer G. High-confidence 3D template matching for cryo-electron tomography. Nat Commun 2024; 15:3992. [PMID: 38734767 PMCID: PMC11088655 DOI: 10.1038/s41467-024-47839-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/12/2024] [Indexed: 05/13/2024] Open
Abstract
Visual proteomics attempts to build atlases of the molecular content of cells but the automated annotation of cryo electron tomograms remains challenging. Template matching (TM) and methods based on machine learning detect structural signatures of macromolecules. However, their applicability remains limited in terms of both the abundance and size of the molecular targets. Here we show that the performance of TM is greatly improved by using template-specific search parameter optimization and by including higher-resolution information. We establish a TM pipeline with systematically tuned parameters for the automated, objective and comprehensive identification of structures with confidence 10 to 100-fold above the noise level. We demonstrate high-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, fatty acid synthases, lipid membranes and microtubules, and individual subunits inside crowded eukaryotic cells. We provide software tools for the generic implementation of our method that is broadly applicable towards realizing visual proteomics.
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Affiliation(s)
- Sergio Cruz-León
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Tomáš Majtner
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Patrick C Hoffmann
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Jan Philipp Kreysing
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Sebastian Kehl
- Max Planck Computing and Data Facility, Gießenbachstraße 2, 85748, Garching, Germany
| | - Maarten W Tuijtel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Stefan L Schaefer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Katharina Geißler
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
- Institute of Biochemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
- Institute of Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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6
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Tuijtel MW, Cruz-León S, Kreysing JP, Welsch S, Hummer G, Beck M, Turoňová B. Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging. SCIENCE ADVANCES 2024; 10:eadk6285. [PMID: 38669330 PMCID: PMC11051657 DOI: 10.1126/sciadv.adk6285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
Cryo-electron tomography (cryo-ET) is a powerful method to elucidate subcellular architecture and to structurally analyze biomolecules in situ by subtomogram averaging, yet data quality critically depends on specimen thickness. Cells that are too thick for transmission imaging can be thinned into lamellae by cryo-focused ion beam (cryo-FIB) milling. Despite being a crucial parameter directly affecting attainable resolution, optimal lamella thickness has not been systematically investigated nor the extent of structural damage caused by gallium ions used for FIB milling. We thus systematically determined how resolution is affected by these parameters. We find that ion-induced damage does not affect regions more than 30 nanometers from either lamella surface and that up to ~180-nanometer lamella thickness does not negatively affect resolution. This shows that there is no need to generate very thin lamellae and lamella thickness can be chosen such that it captures cellular features of interest, thereby opening cryo-ET also for studies of large complexes.
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Affiliation(s)
- Maarten W. Tuijtel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Sergio Cruz-León
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Jan Philipp Kreysing
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute of Biochemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
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7
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Liang LY, Geoghegan ND, Mlodzianoski M, Leis A, Whitehead LW, Surudoi MG, Young SN, Janes P, Shepherd D, Ghosal D, Rogers KL, Murphy JM, Lucet IS. Co-clustering of EphB6 and ephrinB1 in trans restrains cancer cell invasion. Commun Biol 2024; 7:461. [PMID: 38627519 PMCID: PMC11021433 DOI: 10.1038/s42003-024-06118-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
EphB6 is an understudied ephrin receptor tyrosine pseudokinase that is downregulated in multiple types of metastatic cancers. Unlike its kinase-active counterparts which autophosphorylate and transmit signals upon intercellular interaction, little is known about how EphB6 functions in the absence of intrinsic kinase activity. Here, we unveil a molecular mechanism of cell-cell interaction driven by EphB6. We identify ephrinB1 as a cognate ligand of EphB6 and show that in trans interaction of EphB6 with ephrinB1 on neighboring cells leads to the formation of large co-clusters at the plasma membrane. These co-clusters exhibit a decreased propensity towards endocytosis, suggesting a unique characteristic for this type of cell-cell interaction. Using lattice light-sheet microscopy, 3D structured illumination microscopy and cryo-electron tomography techniques, we show that co-clustering of EphB6 and ephrinB1 promotes the formation of double-membrane tubular structures between cells. Importantly, we also demonstrate that these intercellular structures stabilize cell-cell adhesion, leading to a reduction in the invasive behavior of cancer cells. Our findings rationalize a role for EphB6 pseudokinase as a tumor suppressor when interacting with its ligands in trans.
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Affiliation(s)
- Lung-Yu Liang
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Niall D Geoghegan
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Michael Mlodzianoski
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Andrew Leis
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Lachlan W Whitehead
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Minglyanna G Surudoi
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Peter Janes
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, Level 5, ONJ Centre, 145 Studley Rd, Heidelberg, VIC, 3084, Australia
| | - Doulin Shepherd
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Kelly L Rogers
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
| | - Isabelle S Lucet
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia.
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8
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Homola M, Büttner CR, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. SCIENCE ADVANCES 2024; 10:eadk1954. [PMID: 38598627 PMCID: PMC11006232 DOI: 10.1126/sciadv.adk1954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth's climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus' inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum-derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which enables the continuous release of virions by exocytosis.
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Affiliation(s)
- Miroslav Homola
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Carina R. Büttner
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tibor Füzik
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavel Křepelka
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Radka Holbová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Marten L. Chaillet
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Jakub Žák
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Danyil Grybchuk
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Friedrich Förster
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - William H. Wilson
- Marine Biological Association, Plymouth, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | | | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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9
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Powell BM, Brant TS, Davis JH, Mosalaganti S. Rapid structural analysis of bacterial ribosomes in situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586148. [PMID: 38585831 PMCID: PMC10996489 DOI: 10.1101/2024.03.22.586148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Rapid structural analysis of purified proteins and their complexes has become increasingly common thanks to key methodological advances in cryo-electron microscopy (cryo-EM) and associated data processing software packages. In contrast, analogous structural analysis in cells via cryo-electron tomography (cryo-ET) remains challenging due to critical technical bottlenecks, including low-throughput sample preparation and imaging, and laborious data processing methods. Here, we describe the development of a rapid in situ cryo-ET sample preparation and data analysis workflow that results in the routine determination of sub-nm resolution ribosomal structures. We apply this workflow to E. coli, producing a 5.8 Å structure of the 70S ribosome from cells in less than 10 days, and we expect this workflow will be widely applicable to related bacterial samples.
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Affiliation(s)
- Barrett M. Powell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Tyler S. Brant
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Joseph H. Davis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Shyamal Mosalaganti
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109
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10
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Connolly SM, Erwin AL, Sabb M, Hanks JL, Chang L, Torrez RM, Caso GC, Campbell AM, Mosalaganti S, Cover TL, Ohi MD. Structural Analysis of Membrane-associated Forms of Helicobacter pylori VacA Toxin. J Mol Biol 2024; 436:168432. [PMID: 38161000 PMCID: PMC11090358 DOI: 10.1016/j.jmb.2023.168432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Helicobacter pylori colonizes the stomach in about half of the human population, leading to an increased risk of peptic ulcer disease and gastric cancer. H. pylori secretes an 88 kDa VacA toxin that contributes to pathogenesis. VacA assembles into oligomeric complexes in solution and forms anion-selective channels in cell membranes. Cryo-electron microscopy (cryo-EM) analyses of VacA oligomers in solution provided insights into VacA oligomerization but failed to reveal the structure of the hydrophobic N-terminal region predicted to be a pore-forming domain. In this study, we incubated VacA with liposomes and used single particle cryo-EM to analyze detergent-extracted VacA oligomers. A 3D structure of detergent-solubilized VacA hexamers revealed the presence of six α-helices extending from the center of the oligomers, a feature not observed in previous studies of water-soluble VacA oligomers. Cryo-electron tomography analysis and 2D averages of VacA associated with liposomes confirmed that central regions of the membrane-associated VacA oligomers can insert into the lipid bilayer. However, insertion is heterogenous, with some membrane-associated oligomers appearing only partially inserted and others sitting on top of the bilayer. These studies indicate that VacA undergoes a conformational change when contacting the membrane and reveal an α-helical region positioned to extend into the membrane. Although the reported VacA 3D structure does not represent a selective anion channel, our combined single particle 3D analysis, cryo-electron tomography, and modeling allow us to propose a model for the structural organization of the VacA N-terminus in the context of a hexamer as it inserts into the membrane.
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Affiliation(s)
- Sarah M Connolly
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Amanda L Erwin
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Megan Sabb
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jessica L Hanks
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Louise Chang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Rachel M Torrez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Georgia C Caso
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Anne M Campbell
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shyamal Mosalaganti
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Timothy L Cover
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA.
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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11
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Bauda E, Gallet B, Moravcova J, Effantin G, Chan H, Novacek J, Jouneau PH, Rodrigues CDA, Schoehn G, Moriscot C, Morlot C. Ultrastructure of macromolecular assemblies contributing to bacterial spore resistance revealed by in situ cryo-electron tomography. Nat Commun 2024; 15:1376. [PMID: 38355696 PMCID: PMC10867305 DOI: 10.1038/s41467-024-45770-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
Bacterial spores owe their incredible resistance capacities to molecular structures that protect the cell content from external aggressions. Among the determinants of resistance are the quaternary structure of the chromosome and an extracellular shell made of proteinaceous layers (the coat), the assembly of which remains poorly understood. Here, in situ cryo-electron tomography on lamellae generated by cryo-focused ion beam micromachining provides insights into the ultrastructural organization of Bacillus subtilis sporangia. The reconstructed tomograms reveal that early during sporulation, the chromosome in the forespore adopts a toroidal structure harboring 5.5-nm thick fibers. At the same stage, coat proteins at the surface of the forespore form a stack of amorphous or structured layers with distinct electron density, dimensions and organization. By analyzing mutant strains using cryo-electron tomography and transmission electron microscopy on resin sections, we distinguish seven nascent coat regions with different molecular properties, and propose a model for the contribution of coat morphogenetic proteins.
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Affiliation(s)
- Elda Bauda
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Benoit Gallet
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Jana Moravcova
- CEITEC-Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | | | - Helena Chan
- University of Technology Sydney, 2007, Ultimo, NSW, Australia
| | - Jiri Novacek
- CEITEC-Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | | | | | - Guy Schoehn
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | | | - Cecile Morlot
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France.
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12
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Ochner H, Bharat TAM. Charting the molecular landscape of the cell. Structure 2023; 31:1297-1305. [PMID: 37699393 PMCID: PMC7615466 DOI: 10.1016/j.str.2023.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023]
Abstract
Biological function of macromolecules is closely tied to their cellular location, as well as to interactions with other molecules within the native environment of the cell. Therefore, to obtain detailed mechanistic insights into macromolecular functionality, one of the outstanding targets for structural biology is to produce an atomic-level understanding of the cell. One structural biology technique that has already been used to directly derive atomic models of macromolecules from cells, without any additional external information, is electron cryotomography (cryoET). In this perspective article, we discuss possible routes to chart the molecular landscape of the cell by advancing cryoET imaging as well as by embedding cryoET into correlative imaging workflows.
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Affiliation(s)
- Hannah Ochner
- Structural Studies Division, MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK.
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13
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Lewis GR, Ringe E, Midgley PA. Cones and spirals: Multi-axis acquisition for scalar and vector electron tomography. Ultramicroscopy 2023; 252:113775. [PMID: 37295062 DOI: 10.1016/j.ultramic.2023.113775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
Electron tomography (ET) has become an important tool for understanding the 3D nature of nanomaterials, with recent developments enabling not only scalar reconstructions of electron density, but also vector reconstructions of magnetic fields. However, whilst new signals have been incorporated into the ET toolkit, the acquisition schemes have largely kept to conventional single-axis tilt series for scalar ET, and dual-axis schemes for magnetic vector ET. In this work, we explore the potential of using multi-axis tilt schemes including conical and spiral tilt schemes to improve reconstruction fidelity in scalar and magnetic vector ET. Through a combination of systematic simulations and a proof-of-concept experiment, we show that spiral and conical tilt schemes have the potential to produce substantially improved reconstructions, laying the foundations of a new approach to electron tomography acquisition and reconstruction.
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Affiliation(s)
- George R Lewis
- Department of Materials Science and Metallurgy, University of Cambridge, Charles Babbage Road, Cambridge CB3 0FS, UK; Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK.
| | - Emilie Ringe
- Department of Materials Science and Metallurgy, University of Cambridge, Charles Babbage Road, Cambridge CB3 0FS, UK; Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
| | - Paul A Midgley
- Department of Materials Science and Metallurgy, University of Cambridge, Charles Babbage Road, Cambridge CB3 0FS, UK
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14
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Abstract
Recent advances in cryo-electron microscopy have marked only the beginning of the potential of this technique. To bring structure into cell biology, the modality of cryo-electron tomography has fast developed into a bona fide in situ structural biology technique where structures are determined in their native environment, the cell. Nearly every step of the cryo-focused ion beam-assisted electron tomography (cryo-FIB-ET) workflow has been improved upon in the past decade, since the first windows were carved into cells, unveiling macromolecular networks in near-native conditions. By bridging structural and cell biology, cryo-FIB-ET is advancing our understanding of structure-function relationships in their native environment and becoming a tool for discovering new biology.
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Affiliation(s)
- Lindsey N Young
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
| | - Elizabeth Villa
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, USA
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15
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Shah PNM, Gilchrist JB, Forsberg BO, Burt A, Howe A, Mosalaganti S, Wan W, Radecke J, Chaban Y, Sutton G, Stuart DI, Boyce M. Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography. Cell Host Microbe 2023; 31:604-615.e4. [PMID: 36996819 PMCID: PMC7615348 DOI: 10.1016/j.chom.2023.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/27/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023]
Abstract
Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and visualization of the assembly process has been hampered by the inaccessibility of unstable intermediates. We characterize the assembly pathway of group A rotaviruses observed in situ within cryo-preserved infected cells through the use of cryoelectron tomography of cellular lamellae. Our findings demonstrate that the viral polymerase VP1 recruits viral genomes during particle assembly, as revealed by infecting with a conditionally lethal mutant. Additionally, pharmacological inhibition to arrest the transiently enveloped stage uncovered a unique conformation of the VP4 spike. Subtomogram averaging provided atomic models of four intermediate states, including a pre-packaging single-layered intermediate, the double-layered particle, the transiently enveloped double-layered particle, and the fully assembled triple-layered virus particle. In summary, these complementary approaches enable us to elucidate the discrete steps involved in forming an intracellular rotavirus particle.
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Affiliation(s)
- Pranav N M Shah
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK; CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford, UK.
| | - James B Gilchrist
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Björn O Forsberg
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK; Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Alister Burt
- Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Andrew Howe
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Shyamal Mosalaganti
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - William Wan
- Vanderbilt University Center for Structural Biology, PMB 407917, 465 21st Ave S, 5140 MRB3, Nashville, TN, USA
| | - Julika Radecke
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Yuriy Chaban
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Geoff Sutton
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK; CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Mark Boyce
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
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16
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Berger C, Premaraj N, Ravelli RBG, Knoops K, López-Iglesias C, Peters PJ. Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology. Nat Methods 2023; 20:499-511. [PMID: 36914814 DOI: 10.1038/s41592-023-01783-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/20/2023] [Indexed: 03/16/2023]
Abstract
Cryogenic electron microscopy and data processing enable the determination of structures of isolated macromolecules to near-atomic resolution. However, these data do not provide structural information in the cellular environment where macromolecules perform their native functions, and vital molecular interactions can be lost during the isolation process. Cryogenic focused ion beam (FIB) fabrication generates thin lamellae of cellular samples and tissues, enabling structural studies on the near-native cellular interior and its surroundings by cryogenic electron tomography (cryo-ET). Cellular cryo-ET benefits from the technological developments in electron microscopes, detectors and data processing, and more in situ structures are being obtained and at increasingly higher resolution. In this Review, we discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamellae, tomography, data processing and correlative light and electron microscopy that have enabled these studies. Finally, we explore the future of cryo-ET in terms of both methods development and biological application.
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Affiliation(s)
- Casper Berger
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Navya Premaraj
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Kèvin Knoops
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Carmen López-Iglesias
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands.
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17
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Khavnekar S, Wan W, Majumder P, Wietrzynski W, Erdmann PS, Plitzko JM. Multishot tomography for high-resolution in situ subtomogram averaging. J Struct Biol 2023; 215:107911. [PMID: 36343843 DOI: 10.1016/j.jsb.2022.107911] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/29/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) can resolve protein complexes at near atomic resolution, and when combined with focused ion beam (FIB) milling, macromolecules can be observed within their native context. Unlike single particle acquisition (SPA), cryo-ET can be slow, which may reduce overall project throughput. We here propose a fast, multi-position tomographic acquisition scheme based on beam-tilt corrected beam-shift imaging along the tilt axis, which yields sub-nanometer in situ STA averages.
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Affiliation(s)
| | - W Wan
- Vanderbilt University, United States
| | | | | | - P S Erdmann
- MPI for Biochemistry, Germany; Human Technopole, Italy.
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18
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Seifer S. Sampling theory perspective on tomographic tilt increment schemes. Ultramicroscopy 2023; 245:113669. [PMID: 36566528 DOI: 10.1016/j.ultramic.2022.113669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/26/2022] [Accepted: 12/17/2022] [Indexed: 12/23/2022]
Abstract
Given a limited radiation exposure to be distributed over a discrete number of tilted projections in tomography, the optimal collection of information depends on the tilt increment scheme. Relying on principles of sampling theory, several tilt increment schemes can be compared and quantified. Following reasoning of Saxton, a revised scheme is offered in which the tilt angle increments Δθn are proportional to 1/cosθn. The revised scheme is preferable according to matrix analysis and simulations of geometrical optics. For thin specimens, applying a cosine sampling grid similar to Hoppe's scheme can improve the results. A realistic case is examined by Dr. Probe simulation of a scanning transmission electron microscope (STEM) for an atomic model adapted from the Ferritin protein molecule. Optimal reconstruction methods that are tested include the direct algebraic method, iterative reconstruction, and a new deconvolution-based weighted back-projection, which resembles the correction filter technique in signal recovery from sub-sampled data. A non-linear correction may be accounted for by iteration of the simulation with an ad-hoc atomic model.
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Affiliation(s)
- Shahar Seifer
- Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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19
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Tollervey F, Zhang X, Bose M, Sachweh J, Woodruff JB, Franzmann TM, Mahamid J. Cryo-Electron Tomography of Reconstituted Biomolecular Condensates. Methods Mol Biol 2023; 2563:297-324. [PMID: 36227480 DOI: 10.1007/978-1-0716-2663-4_15] [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] [Indexed: 06/16/2023]
Abstract
The assembly of membraneless compartments by phase separation has recently been recognized as a mechanism for spatial and temporal organization of biomolecules within the cell. The functions of such mesoscale assemblies, termed biomolecular condensates, depend on networks of multivalent interactions between proteins, their structured and disordered domains, and commonly also include nucleic acids. Cryo-electron tomography is an ideal tool to investigate the three-dimensional architecture of such pleomorphic interaction networks at nanometer resolution and thus form inferences about function. However, preparation of suitable cryo-electron microscopy samples of condensates may be prone to protein denaturation, low retention of material on the sample carrier, and contamination associated with cryo-sample preparation and transfers. Here, we describe a series of protocols designed to obtain high-quality cryo-electron tomography data of biomolecular condensates reconstituted in vitro. These include critical screening by light microscopy, cryo-fixation by plunge freezing, sample loading into an electron microscope operated at liquid nitrogen temperature, data collection, processing of the data into three-dimensional tomograms, and their interpretation.
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Affiliation(s)
- Fergus Tollervey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for Joint PhD Between EMBL and Heidelberg University Faculty of Biosciences, Heidelberg, Germany
| | - Xiaojie Zhang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mainak Bose
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jenny Sachweh
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Jeffrey B Woodruff
- Department of Cell Biology, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Titus M Franzmann
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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20
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de Teresa-Trueba I, Goetz SK, Mattausch A, Stojanovska F, Zimmerli CE, Toro-Nahuelpan M, Cheng DWC, Tollervey F, Pape C, Beck M, Diz-Muñoz A, Kreshuk A, Mahamid J, Zaugg JB. Convolutional networks for supervised mining of molecular patterns within cellular context. Nat Methods 2023; 20:284-294. [PMID: 36690741 PMCID: PMC9911354 DOI: 10.1038/s41592-022-01746-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/02/2022] [Indexed: 01/24/2023]
Abstract
Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning framework for supervised segmentation and macromolecular complex localization in cryo-electron tomography. To train and benchmark DeePiCt on experimental data, we comprehensively annotated 20 tomograms of Schizosaccharomyces pombe for ribosomes, fatty acid synthases, membranes, nuclear pore complexes, organelles, and cytosol. By comparing DeePiCt to state-of-the-art approaches on this dataset, we show its unique ability to identify low-abundance and low-density complexes. We use DeePiCt to study compositionally distinct subpopulations of cellular ribosomes, with emphasis on their contextual association with mitochondria and the endoplasmic reticulum. Finally, applying pre-trained networks to a HeLa cell tomogram demonstrates that DeePiCt achieves high-quality predictions in unseen datasets from different biological species in a matter of minutes. The comprehensively annotated experimental data and pre-trained networks are provided for immediate use by the community.
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Affiliation(s)
- Irene de Teresa-Trueba
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,Present Address: Computer Science and Artificial Intelligence Lab, ENGIE Lab Crigen, Stains, France
| | - Sara K. Goetz
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Alexander Mattausch
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Frosina Stojanovska
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Christian E. Zimmerli
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.419494.50000 0001 1018 9466Present Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Mauricio Toro-Nahuelpan
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,Present Address: Santiago GmbH & Co. KG, Willich, Germany
| | - Dorothy W. C. Cheng
- grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fergus Tollervey
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Constantin Pape
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7450.60000 0001 2364 4210Present Address: Institute for Computer Science, Universität Göttingen, Göttingen, Germany
| | - Martin Beck
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.419494.50000 0001 1018 9466Present Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Alba Diz-Muñoz
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna Kreshuk
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Judith B. Zaugg
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XGenome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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21
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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: 21] [Impact Index Per Article: 10.5] [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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22
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Hrebík D, Gondová M, Valentová L, Füzik T, Přidal A, Nováček J, Plevka P. Polyelectrolyte coating of cryo-EM grids improves lateral distribution and prevents aggregation of macromolecules. Acta Crystallogr D Struct Biol 2022; 78:1337-1346. [PMID: 36322417 PMCID: PMC9629489 DOI: 10.1107/s2059798322009299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) is one of the primary methods used to determine the structures of macromolecules and their complexes. With the increased availability of cryo-electron microscopes, the preparation of high-quality samples has become a bottleneck in the cryo-EM structure-determination pipeline. Macromolecules can be damaged during the purification or preparation of vitrified samples for cryo-EM, making them prone to binding to the grid support, to aggregation or to the adoption of preferential orientations at the air-water interface. Here, it is shown that coating cryo-EM grids with a negatively charged polyelectrolyte, such as single-stranded DNA, before applying the sample reduces the aggregation of macromolecules and improves their distribution. The single-stranded DNA-coated grids enabled the determination of high-resolution structures from samples that aggregated on conventional grids. The polyelectrolyte coating reduces the diffusion of macromolecules and thus may limit the negative effects of the contact of macromolecules with the grid support and blotting paper, as well as of the shear forces on macromolecules during grid blotting. Coating grids with polyelectrolytes can readily be employed in any laboratory dealing with cryo-EM sample preparation, since it is fast, simple, inexpensive and does not require specialized equipment.
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Affiliation(s)
- Dominik Hrebík
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Mária Gondová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lucie Valentová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tibor Füzik
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Antonín Přidal
- Faculty of Agronomy, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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23
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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24
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Martinez M, Chen WD, Cova MM, Molnár P, Mageswaran SK, Guérin A, John ARO, Lebrun M, Chang YW. Rhoptry secretion system structure and priming in Plasmodium falciparum revealed using in situ cryo-electron tomography. Nat Microbiol 2022; 7:1230-1238. [PMID: 35817892 PMCID: PMC7613239 DOI: 10.1038/s41564-022-01171-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/07/2022] [Indexed: 01/13/2023]
Abstract
Apicomplexan parasites secrete contents of the rhoptries, club-shaped organelles in the apical region, into host cells to permit their invasion and establishment of infection. The rhoptry secretory apparatus (RSA), which is critical for rhoptry secretion, was recently discovered in Toxoplasma and Cryptosporidium. It is unknown whether a similar molecular machinery exists in the malaria parasite Plasmodium. In this study, we use in situ cryo-electron tomography to investigate the rhoptry secretion system in P. falciparum merozoites. We identify the presence of an RSA at the cell apex and a morphologically distinct apical vesicle docking the tips of the two rhoptries to the RSA. We also discover two additional rhoptry organizations that lack the apical vesicle. Using subtomogram averaging, we reveal different conformations of the RSA structure corresponding to different rhoptry organizations. Our results highlight previously unknown steps in the process of rhoptry secretion and indicate a regulatory role for the conserved apical vesicle in host invasion by apicomplexan parasites.
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Affiliation(s)
- Matthew Martinez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - William David Chen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Petra Molnár
- Department of Pediatrics, Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shrawan Kumar Mageswaran
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amandine Guérin
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Audrey R Odom John
- Department of Pediatrics, Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maryse Lebrun
- LPHI, UMR 5235 CNRS, Université de Montpellier, Montpellier, France
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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25
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Schneider J, Jasnin M. Capturing actin assemblies in cells using in situ cryo-electron tomography. Eur J Cell Biol 2022; 101:151224. [PMID: 35500467 DOI: 10.1016/j.ejcb.2022.151224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Actin contributes to an exceptionally wide range of cellular processes through the assembly and disassembly of highly dynamic and ordered structures. Visualizing these structures in cells can help us understand how the molecular players of the actin machinery work together to produce force-generating systems. In recent years, cryo-electron tomography (cryo-ET) has become the method of choice for structural analysis of the cell interior at the molecular scale. Here we review advances in cryo-ET workflows that have enabled this transformation, especially the automation of sample preparation procedures, data collection, and processing. We discuss new structural analyses of dynamic actin assemblies in cryo-preserved cells, which have provided mechanistic insights into actin assembly and function at the nanoscale. Finally, we highlight the latest visual proteomics studies of actin filaments and their interactors reaching sub-nanometer resolutions in cells.
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Affiliation(s)
- Jonathan Schneider
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Marion Jasnin
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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26
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Jenkins J, Worrall L, Strynadka N. Recent structural advances towards understanding of the bacterial type III secretion injectisome. Trends Biochem Sci 2022; 47:795-809. [DOI: 10.1016/j.tibs.2022.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 04/01/2022] [Accepted: 04/25/2022] [Indexed: 12/22/2022]
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27
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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28
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Obr M, JH Hagen W, Dick RA, Yu L, Kotecha A, KM Schur F. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. J Struct Biol 2022; 214:107852. [DOI: 10.1016/j.jsb.2022.107852] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 01/26/2023]
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29
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Vankadari N, Shepherd DC, Carter SD, Ghosal D. Three-dimensional insights into human enveloped viruses in vitro and in situ. Biochem Soc Trans 2022; 50:95-105. [PMID: 35076655 PMCID: PMC9022983 DOI: 10.1042/bst20210433] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022]
Abstract
Viruses can be enveloped or non-enveloped, and require a host cell to replicate and package their genomes into new virions to infect new cells. To accomplish this task, viruses hijack the host-cell machinery to facilitate their replication by subverting and manipulating normal host cell function. Enveloped viruses can have severe consequences for human health, causing various diseases such as acquired immunodeficiency syndrome (AIDS), seasonal influenza, COVID-19, and Ebola virus disease. The complex arrangement and pleomorphic architecture of many enveloped viruses pose a challenge for the more widely used structural biology techniques, such as X-ray crystallography. Cryo-electron tomography (cryo-ET), however, is a particularly well-suited tool for overcoming the limitations associated with visualizing the irregular shapes and morphology enveloped viruses possess at macromolecular resolution. The purpose of this review is to explore the latest structural insights that cryo-ET has revealed about enveloped viruses, with particular attention given to their architectures, mechanisms of entry, replication, assembly, maturation and egress during infection. Cryo-ET is unique in its ability to visualize cellular landscapes at 3-5 nanometer resolution. Therefore, it is the most suited technique to study asymmetric elements and structural rearrangements of enveloped viruses during infection in their native cellular context.
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Affiliation(s)
- Naveen Vankadari
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Doulin C. Shepherd
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Stephen D. Carter
- Centre for Virus Research, Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, U.K
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
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30
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Saibil HR. Cryo-EM in molecular and cellular biology. Mol Cell 2022; 82:274-284. [DOI: 10.1016/j.molcel.2021.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022]
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31
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Zimmerli CE, Allegretti M, Rantos V, Goetz SK, Obarska-Kosinska A, Zagoriy I, Halavatyi A, Hummer G, Mahamid J, Kosinski J, Beck M. Nuclear pores dilate and constrict in cellulo. Science 2021; 374:eabd9776. [PMID: 34762489 DOI: 10.1126/science.abd9776] [Citation(s) in RCA: 151] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Christian E Zimmerli
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Matteo Allegretti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vasileios Rantos
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany.,EMBL Hamburg, 22607 Hamburg, Germany
| | - Sara K Goetz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Agnieszka Obarska-Kosinska
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,EMBL Hamburg, 22607 Hamburg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | | | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany.,EMBL Hamburg, 22607 Hamburg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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32
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He Y, Jiang L, Chen T, Xu Y, Jia H, Yi R, Xue D, Song M, Genc A, Bouchet-Marquis C, Pullan L, Tessner T, Yoo J, Li X, Zhang JG, Zhang S, Wang C. Progressive growth of the solid-electrolyte interphase towards the Si anode interior causes capacity fading. NATURE NANOTECHNOLOGY 2021; 16:1113-1120. [PMID: 34326526 DOI: 10.1038/s41565-021-00947-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 06/16/2021] [Indexed: 05/24/2023]
Abstract
The solid-electrolyte interphase (SEI), a layer formed on the electrode surface, is essential for electrochemical reactions in batteries and critically governs the battery stability. Active materials, especially those with extremely high energy density, such as silicon (Si), often inevitably undergo a large volume swing upon ion insertion and extraction, raising a critical question as to how the SEI interactively responds to and evolves with the material and consequently controls the cycling stability of the battery. Here, by integrating sensitive elemental tomography, an advanced algorithm and cryogenic scanning transmission electron microscopy, we unveil, in three dimensions, a correlated structural and chemical evolution of Si and SEI. Corroborated with a chemomechanical model, we demonstrate progressive electrolyte permeation and SEI growth along the percolation channel of the nanovoids due to vacancy injection and condensation during the delithiation process. Consequently, the Si-SEI spatial configuration evolves from the classic 'core-shell' structure in the first few cycles to a 'plum-pudding' structure following extended cycling, featuring the engulfing of Si domains by the SEI, which leads to the disruption of electron conduction pathways and formation of dead Si, contributing to capacity loss. The spatially coupled interactive evolution model of SEI and active materials, in principle, applies to a broad class of high-capacity electrode materials, leading to a critical insight for remedying the fading of high-capacity electrodes.
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Affiliation(s)
- Yang He
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
- Beijing University of Science and Technology, Beijing, China
| | - Lin Jiang
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Hillsboro, OR, USA
| | - Tianwu Chen
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA
| | - Yaobin Xu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Haiping Jia
- Energy and Environmental Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ran Yi
- Energy and Environmental Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Dingchuan Xue
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA
| | - Miao Song
- Physical and Computational Science Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Arda Genc
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Hillsboro, OR, USA
| | - Cedric Bouchet-Marquis
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Hillsboro, OR, USA
| | - Lee Pullan
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Hillsboro, OR, USA
| | - Ted Tessner
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Hillsboro, OR, USA
| | - Jinkyoung Yoo
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Xiaolin Li
- Energy and Environmental Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Ji-Guang Zhang
- Energy and Environmental Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sulin Zhang
- Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA, USA.
| | - Chongmin Wang
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
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33
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Parkhurst JM, Dumoux M, Basham M, Clare D, Siebert CA, Varslot T, Kirkland A, Naismith JH, Evans G. Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography. Open Biol 2021; 11:210160. [PMID: 34699732 PMCID: PMC8548082 DOI: 10.1098/rsob.210160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a 'digital twin' software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured.
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Affiliation(s)
- James M. Parkhurst
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Maud Dumoux
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Mark Basham
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Daniel Clare
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - C. Alistair Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Trond Varslot
- Thermo Fisher Scientific, Vlastimila Pecha, Brno, Czech Republic
| | - Angus Kirkland
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Electron Physical Science Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK,Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, UK
| | - James H. Naismith
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Gwyndaf Evans
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK,Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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34
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Abstract
Cryo-electron tomography has stepped fully into the spotlight. Enthusiasm is high. Fortunately for us, this is an exciting time to be a cryotomographer, but there is still a way to go before declaring victory. Despite its potential, cryo-electron tomography possesses many inherent challenges. How do we image through thick cell samples, and possibly even tissue? How do we identify a protein of interest amidst the noisy, crowded environment of the cytoplasm? How do we target specific moments of a dynamic cellular process for tomographic imaging? In this review, we cover the history of cryo-electron tomography and how it came to be, roughly speaking, as well as the many approaches that have been developed to overcome its intrinsic limitations.
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Affiliation(s)
- Ryan K. Hylton
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Matthew T. Swulius
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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35
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Li S. Cryo-electron tomography of enveloped viruses. Trends Biochem Sci 2021; 47:173-186. [PMID: 34511334 DOI: 10.1016/j.tibs.2021.08.005] [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] [Received: 05/20/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Viruses are macromolecular machineries that hijack cellular metabolism for replication. Enveloped viruses comprise a large variety of RNA and DNA viruses, many of which are notorious human or animal pathogens. Despite their importance, the presence of lipid bilayers in their assembly has made most enveloped viruses too pleomorphic to be reconstructed as a whole by traditional structural biology methods. Furthermore, structural biology of the viral lifecycle was hindered by the sample thickness. Here, I review the recent advances in the applications of cryo-electron tomography (cryo-ET) on enveloped viral structures and intracellular viral activities.
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Affiliation(s)
- Sai Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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36
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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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Winter SL, Chlanda P. Dual-axis Volta phase plate cryo-electron tomography of Ebola virus-like particles reveals actin-VP40 interactions. J Struct Biol 2021; 213:107742. [PMID: 33971285 DOI: 10.1016/j.jsb.2021.107742] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/17/2021] [Accepted: 05/03/2021] [Indexed: 12/20/2022]
Abstract
Cryo-electron tomography (cryo-ET) is a pivotal imaging technique for studying the structure of pleomorphic enveloped viruses and their interactions with the host at native conditions. Owing to the limited tilting range of samples with a slab geometry, electron tomograms suffer from so-called missing wedge information in Fourier space. In dual-axis cryo-ET, two tomograms reconstructed from orthogonally oriented tilt series are combined into a tomogram with improved resolution as the missing wedge information is reduced to a pyramid. Volta phase plate (VPP) allows to perform in-focus cryo-ET with high contrast transfer at low-resolution frequencies and thus its application may improve the quality of dual-axis tomograms. Here, we compare dual-axis cryo-ET with and without VPP on Ebola virus-like particles to visualize and segment viral and host cell proteins within the membrane-enveloped filamentous particles. Dual-axis VPP cryo-ET reduces the missing wedge information and ray artifacts arising from the weighted back-projection during tomogram reconstruction, thereby minimizing ambiguity in the analysis of crowded environments and facilitating 3D segmentation. We show that dual-axis VPP tomograms provide a comprehensive description of macromolecular organizations such as nucleocapsid assembly states, the distribution of glycoproteins on the viral envelope and asymmetric arrangements of the VP40 layer in non-filamentous regions of virus-like particles. Our data reveal actin filaments within virus-like particles in close proximity to the viral VP40 scaffold, suggesting a direct interaction between VP40 and actin filaments. Dual-axis VPP cryo-ET provides more complete 3D information at high contrast and allows for better interpretation of macromolecule interactions and pleomorphic organizations.
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Affiliation(s)
- Sophie L Winter
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany; Research Group "Membrane Biology of Viral Infection", Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany; Research Group "Membrane Biology of Viral Infection", Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.
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Zhang X, Mahamid J. Addressing the challenge of in situ structural studies of RNP granules in light of emerging opportunities. Curr Opin Struct Biol 2020; 65:149-158. [DOI: 10.1016/j.sbi.2020.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/01/2020] [Accepted: 06/16/2020] [Indexed: 01/23/2023]
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Basanta B, Chowdhury S, Lander GC, Grotjahn DA. A guided approach for subtomogram averaging of challenging macromolecular assemblies. J Struct Biol X 2020; 4:100041. [PMID: 33319208 PMCID: PMC7724198 DOI: 10.1016/j.yjsbx.2020.100041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 10/13/2020] [Accepted: 11/18/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
- Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research, HZ 175, 10550 N Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Saikat Chowdhury
- Department of Biochemistry and Cell Biology, 144 Center for Molecular Medicine, Stony Brook University, Stony Brook, NY 11794, United States
| | - Gabriel C. Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, HZ 175, 10550 N Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Danielle A. Grotjahn
- Department of Integrative Structural and Computational Biology, Scripps Research, HZ 175, 10550 N Torrey Pines Rd., La Jolla, CA 92037, United States
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40
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Turk M, Baumeister W. The promise and the challenges of cryo-electron tomography. FEBS Lett 2020; 594:3243-3261. [PMID: 33020915 DOI: 10.1002/1873-3468.13948] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 01/11/2023]
Abstract
Structural biologists have traditionally approached cellular complexity in a reductionist manner in which the cellular molecular components are fractionated and purified before being studied individually. This 'divide and conquer' approach has been highly successful. However, awareness has grown in recent years that biological functions can rarely be attributed to individual macromolecules. Most cellular functions arise from their concerted action, and there is thus a need for methods enabling structural studies performed in situ, ideally in unperturbed cellular environments. Cryo-electron tomography (Cryo-ET) combines the power of 3D molecular-level imaging with the best structural preservation that is physically possible to achieve. Thus, it has a unique potential to reveal the supramolecular architecture or 'molecular sociology' of cells and to discover the unexpected. Here, we review state-of-the-art Cryo-ET workflows, provide examples of biological applications, and discuss what is needed to realize the full potential of Cryo-ET.
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Affiliation(s)
- Martin Turk
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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41
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Turoňová B, Sikora M, Schürmann C, Hagen WJH, Welsch S, Blanc FEC, von Bülow S, Gecht M, Bagola K, Hörner C, van Zandbergen G, Landry J, de Azevedo NTD, Mosalaganti S, Schwarz A, Covino R, Mühlebach MD, Hummer G, Krijnse Locker J, Beck M. In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science 2020; 370:203-208. [PMID: 32817270 DOI: 10.1101/2020.06.26.173476] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/13/2020] [Indexed: 05/24/2023]
Abstract
The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo-electron tomography, subtomogram averaging, and molecular dynamics simulations to structurally analyze S in situ. Compared with the recombinant S, the viral S was more heavily glycosylated and occurred mostly in the closed prefusion conformation. We show that the stalk domain of S contains three hinges, giving the head unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and potentially to the development of safe vaccines.
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Affiliation(s)
- Beata Turoňová
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Christoph Schürmann
- Division of Veterinary Medicine, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany
| | - Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Florian E C Blanc
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Michael Gecht
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Katrin Bagola
- Division of Immunology, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany
| | - Cindy Hörner
- Division of Veterinary Medicine, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany
- German Center for Infection Research, Gießen-Marburg-Langen, Germany
| | - Ger van Zandbergen
- Division of Immunology, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany
- Institute for Immunology, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Jonathan Landry
- Genomics Core Facility, EMBL, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | | | - Shyamal Mosalaganti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Andre Schwarz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Roberto Covino
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Germany
| | - Michael D Mühlebach
- Division of Veterinary Medicine, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany
- German Center for Infection Research, Gießen-Marburg-Langen, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany.
- Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Jacomine Krijnse Locker
- Electron Microscopy of Pathogens Unit, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany.
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany.
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
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42
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Turoňová B, Sikora M, Schürmann C, Hagen WJH, Welsch S, Blanc FEC, von Bülow S, Gecht M, Bagola K, Hörner C, van Zandbergen G, Landry J, de Azevedo NTD, Mosalaganti S, Schwarz A, Covino R, Mühlebach MD, Hummer G, Krijnse Locker J, Beck M. In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science 2020; 370:203-208. [PMID: 32817270 PMCID: PMC7665311 DOI: 10.1126/science.abd5223] [Citation(s) in RCA: 446] [Impact Index Per Article: 111.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022]
Abstract
The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo-electron tomography, subtomogram averaging, and molecular dynamics simulations to structurally analyze S in situ. Compared with the recombinant S, the viral S was more heavily glycosylated and occurred mostly in the closed prefusion conformation. We show that the stalk domain of S contains three hinges, giving the head unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and potentially to the development of safe vaccines.
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Affiliation(s)
- Beata Turoňová
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Christoph Schürmann
- Division of Veterinary Medicine, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany
| | - Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Florian E C Blanc
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Michael Gecht
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Katrin Bagola
- Division of Immunology, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany
| | - Cindy Hörner
- Division of Veterinary Medicine, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany.,German Center for Infection Research, Gießen-Marburg-Langen, Germany
| | - Ger van Zandbergen
- Division of Immunology, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany.,Institute for Immunology, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany.,Research Center for Immunotherapy (FZI), University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Jonathan Landry
- Genomics Core Facility, EMBL, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | | | - Shyamal Mosalaganti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Andre Schwarz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Roberto Covino
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany.,Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Germany
| | - Michael D Mühlebach
- Division of Veterinary Medicine, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany.,German Center for Infection Research, Gießen-Marburg-Langen, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany. .,Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Jacomine Krijnse Locker
- Electron Microscopy of Pathogens Unit, Paul Ehrlich Institute, Paul Ehrlich Strasse 51-59, 63225 Langen, Germany.
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany. .,Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
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43
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Sanchez RM, Zhang Y, Chen W, Dietrich L, Kudryashev M. Subnanometer-resolution structure determination in situ by hybrid subtomogram averaging - single particle cryo-EM. Nat Commun 2020; 11:3709. [PMID: 32709843 PMCID: PMC7381653 DOI: 10.1038/s41467-020-17466-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/30/2020] [Indexed: 11/09/2022] Open
Abstract
Cryo-electron tomography combined with subtomogram averaging (StA) has yielded high-resolution structures of macromolecules in their native context. However, high-resolution StA is not commonplace due to beam-induced sample drift, images with poor signal-to-noise ratios (SNR), challenges in CTF correction, and limited particle number. Here we address these issues by collecting tilt series with a higher electron dose at the zero-degree tilt. Particles of interest are then located within reconstructed tomograms, processed by conventional StA, and then re-extracted from the high-dose images in 2D. Single particle analysis tools are then applied to refine the 2D particle alignment and generate a reconstruction. Use of our hybrid StA (hStA) workflow improved the resolution for tobacco mosaic virus from 7.2 to 4.4 Å and for the ion channel RyR1 in crowded native membranes from 12.9 to 9.1 Å. These resolution gains make hStA a promising approach for other StA projects aimed at achieving subnanometer resolution.
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Affiliation(s)
- Ricardo M Sanchez
- Max Planck Institute for Biophysics, Max-von-Laue Strasse, 3, 60348, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt am Main, Max-von-Laue Strasse, 15, 60348, Frankfurt am Main, Germany
| | - Yingyi Zhang
- Max Planck Institute for Biophysics, Max-von-Laue Strasse, 3, 60348, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt am Main, Max-von-Laue Strasse, 15, 60348, Frankfurt am Main, Germany
| | - Wenbo Chen
- Max Planck Institute for Biophysics, Max-von-Laue Strasse, 3, 60348, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt am Main, Max-von-Laue Strasse, 15, 60348, Frankfurt am Main, Germany
| | - Lea Dietrich
- Department of Structural Biology, Max Planck Institute for Biophysics, Max-von-Laue Strasse, 3, 60348, Frankfurt am Main, Germany
| | - Mikhail Kudryashev
- Max Planck Institute for Biophysics, Max-von-Laue Strasse, 3, 60348, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt am Main, Max-von-Laue Strasse, 15, 60348, Frankfurt am Main, Germany.
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44
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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: 23] [Impact Index Per Article: 5.8] [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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