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Eisenstein F, Fukuda Y, Danev R. Smart parallel automated cryo-electron tomography. Nat Methods 2024:10.1038/s41592-024-02373-9. [PMID: 39117874 DOI: 10.1038/s41592-024-02373-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 06/20/2024] [Indexed: 08/10/2024]
Abstract
In situ cryo-electron tomography enables investigation of macromolecules in their native cellular environment. Samples have become more readily available owing to recent software and hardware advancements. Data collection, however, still requires an experienced operator and appreciable microscope time to carefully select targets for high-throughput tilt series acquisition. Here, we developed smart parallel automated cryo-electron tomography (SPACEtomo), a workflow using machine learning approaches to fully automate the entire cryo-electron tomography process, including lamella detection, biological feature segmentation, target selection and parallel tilt series acquisition, all without the need for human intervention. This degree of automation will be essential for obtaining statistically relevant datasets and high-resolution structures of macromolecules in their native context.
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Affiliation(s)
- Fabian Eisenstein
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
| | - Yoshiyuki Fukuda
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan.
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2
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Watson AJI, Bartesaghi A. Advances in cryo-ET data processing: meeting the demands of visual proteomics. Curr Opin Struct Biol 2024; 87:102861. [PMID: 38889501 PMCID: PMC11283971 DOI: 10.1016/j.sbi.2024.102861] [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: 02/13/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
Abstract
Cryogenic electron tomography (cryo-ET), a method that enables the viewing of biomolecules in near-native environments at high resolution, is rising in accessibility and applicability. Over the past several years, once slow sample preparation and data collection procedures have seen innovations which enable rapid collection of the large datasets required for attaining high resolution structures. Increased data availability has provided a driving force for exciting improvements in cryo-ET data processing methodologies throughout the entire processing pipeline and the development of accessible graphical user interfaces (GUIs) that enable individuals inexperienced in computational fields to convert raw tilt series into 3D structures. These advances in data processing are enabling cryo-ET to attain higher resolution and extending its applicability to more complex samples.
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Affiliation(s)
- Abigail J I Watson
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Alberto Bartesaghi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Computer Science, Duke University, Durham, NC, 27708, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA.
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3
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Noble AJ, de Marco A. Cryo-focused ion beam for in situ structural biology: State of the art, challenges, and perspectives. Curr Opin Struct Biol 2024; 87:102864. [PMID: 38901373 DOI: 10.1016/j.sbi.2024.102864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 06/22/2024]
Abstract
Cryogenic-focused ion beam (cryo-FIB) instruments became essential for high-resolution imaging in cryo-preserved cells and tissues. Cryo-FIBs use accelerated ions to thin samples that would otherwise be too thick for cryo-electron microscopy (cryo-EM). This allows visualizing cellular ultrastructures in near-native frozen hydrated states. This review describes the current state-of-the-art capabilities of cryo-FIB technology and its applications in structural cell and tissue biology. We discuss recent advances in instrumentation, imaging modalities, automation, sample preparation protocols, and targeting techniques. We outline remaining challenges and future directions to make cryo-FIB more precise, enable higher throughput, and be widely accessible. Further improvements in targeting, efficiency, robust sample preparation, emerging ion sources, automation, and downstream electron tomography have the potential to reveal intricate molecular architectures across length scales inside cells and tissues. Cryo-FIB is poised to become an indispensable tool for preparing native biological systems in situ for high-resolution 3D structural analysis.
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Affiliation(s)
- Alex J Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue New York, NY, 10027, USA. https://twitter.com/alexjamesnoble
| | - Alex de Marco
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue New York, NY, 10027, USA.
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4
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Hale VL, Hooker J, Russo CJ, Löwe J. Honeycomb gold specimen supports enabling orthogonal focussed ion beam-milling of elongated cells for cryo-ET. J Struct Biol 2024; 216:108097. [PMID: 38772448 PMCID: PMC7616276 DOI: 10.1016/j.jsb.2024.108097] [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: 12/29/2023] [Revised: 05/11/2024] [Accepted: 05/18/2024] [Indexed: 05/23/2024]
Abstract
Cryo-focussed ion beam (FIB)-milling is a powerful technique that opens up thick, cellular specimens to high-resolution structural analysis by electron cryotomography (cryo-ET). FIB-milled lamellae can be produced from cells on grids, or cut from thicker, high-pressure frozen specimens. However, these approaches can put geometrical constraints on the specimen that may be unhelpful, particularly when imaging structures within the cell that have a very defined orientation. For example, plunge frozen rod-shaped bacteria orient parallel to the plane of the grid, yet the Z-ring, a filamentous structure of the tubulin-like protein FtsZ and the key organiser of bacterial division, runs around the circumference of the cell such that it is perpendicular to the imaging plane. It is therefore difficult or impractical to image many complete rings with current technologies. To circumvent this problem, we have fabricated monolithic gold specimen supports with a regular array of cylindrical wells in a honeycomb geometry, which trap bacteria in a vertical orientation. These supports, which we call "honeycomb gold discs", replace standard EM grids and when combined with FIB-milling enable the production of lamellae containing cross-sections through cells. The resulting lamellae are more stable and resistant to breakage and charging than conventional lamellae. The design of the honeycomb discs can be modified according to need and so will also enable cryo-ET and cryo-EM imaging of other specimens in otherwise difficult to obtain orientations.
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Affiliation(s)
| | - James Hooker
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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5
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Xia X, Sung PY, Martynowycz MW, Gonen T, Roy P, Zhou ZH. RNA genome packaging and capsid assembly of bluetongue virus visualized in host cells. Cell 2024; 187:2236-2249.e17. [PMID: 38614100 PMCID: PMC11182334 DOI: 10.1016/j.cell.2024.03.007] [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: 01/17/2023] [Revised: 10/18/2023] [Accepted: 03/07/2024] [Indexed: 04/15/2024]
Abstract
Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques of high-resolution cryoelectron microscopy (cryo-EM), cellular cryoelectron tomography (cryo-ET), and structure-guided mutagenesis to investigate genome packaging and capsid assembly of bluetongue virus (BTV), a member of the Reoviridae family of dsRNA viruses. A total of eleven assembly states of BTV capsid were captured, with resolutions up to 2.8 Å, with most visualized in the host cytoplasm. ATPase VP6 was found underneath the vertices of capsid shell protein VP3 as an RNA-harboring pentamer, facilitating RNA packaging. RNA packaging expands the VP3 shell, which then engages middle- and outer-layer proteins to generate infectious virions. These revealed "duality" characteristics of the BTV assembly mechanism reconcile previous contradictory co-assembly and core-filling models and provide insights into the mysterious RNA packaging and capsid assembly of Reoviridae members and beyond.
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Affiliation(s)
- Xian Xia
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Po-Yu Sung
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Michael W Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Polly Roy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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6
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Comet M, Dijkman PM, Boer Iwema R, Franke T, Masiulis S, Schampers R, Raschdorf O, Grollios F, Pryor EE, Drulyte I. Tomo Live: an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows. Acta Crystallogr D Struct Biol 2024; 80:247-258. [PMID: 38512070 PMCID: PMC10994173 DOI: 10.1107/s2059798324001840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
Data acquisition and processing for cryo-electron tomography can be a significant bottleneck for users. To simplify and streamline the cryo-ET workflow, Tomo Live, an on-the-fly solution that automates the alignment and reconstruction of tilt-series data, enabling real-time data-quality assessment, has been developed. Through the integration of Tomo Live into the data-acquisition workflow for cryo-ET, motion correction is performed directly after each of the acquired tilt angles. Immediately after the tilt-series acquisition has completed, an unattended tilt-series alignment and reconstruction into a 3D volume is performed. The results are displayed in real time in a dedicated remote web platform that runs on the microscope hardware. Through this web platform, users can review the acquired data (aligned stack and 3D volume) and several quality metrics that are obtained during the alignment and reconstruction process. These quality metrics can be used for fast feedback for subsequent acquisitions to save time. Parameters such as Alignment Accuracy, Deleted Tilts and Tilt Axis Correction Angle are visualized as graphs and can be used as filters to export only the best tomograms (raw data, reconstruction and intermediate data) for further processing. Here, the Tomo Live algorithms and workflow are described and representative results on several biological samples are presented. The Tomo Live workflow is accessible to both expert and non-expert users, making it a valuable tool for the continued advancement of structural biology, cell biology and histology.
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Affiliation(s)
- Maxime Comet
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Patricia M. Dijkman
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Reint Boer Iwema
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Tilman Franke
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Simonas Masiulis
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Ruud Schampers
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Oliver Raschdorf
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Fanis Grollios
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Edward E. Pryor
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Ieva Drulyte
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
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7
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Zhao J, Yu X, Shentu X, Li D. The application and development of electron microscopy for three-dimensional reconstruction in life science: a review. Cell Tissue Res 2024; 396:1-18. [PMID: 38416172 DOI: 10.1007/s00441-024-03878-7] [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: 10/17/2023] [Accepted: 02/13/2024] [Indexed: 02/29/2024]
Abstract
Imaging technologies have played a pivotal role in advancing biological research by enabling visualization of biological structures and processes. While traditional electron microscopy (EM) produces two-dimensional images, emerging techniques now allow high-resolution three-dimensional (3D) characterization of specimens in situ, meeting growing needs in molecular and cellular biology. Combining transmission electron microscopy (TEM) with serial sectioning inaugurated 3D imaging, attracting biologists seeking to explore cell ultrastructure and driving advancement of 3D EM reconstruction. By comprehensively and precisely rendering internal structure and distribution, 3D TEM reconstruction provides unparalleled ultrastructural insights into cells and molecules, holding tremendous value for elucidating structure-function relationships and broadly propelling structural biology. Here, we first introduce the principle of 3D reconstruction of cells and tissues by classical approaches in TEM and then discuss modern technologies utilizing TEM and on new SEM-based as well as cryo-electron microscope (cryo-EM) techniques. 3D reconstruction techniques from serial sections, electron tomography (ET), and the recent single-particle analysis (SPA) are examined; the focused ion beam scanning electron microscopy (FIB-SEM), the serial block-face scanning electron microscopy (SBF-SEM), and automatic tape-collecting lathe ultramicrotome (ATUM-SEM) for 3D reconstruction of large volumes are discussed. Finally, we review the challenges and development prospects of these technologies in life science. It aims to provide an informative reference for biological researchers.
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Affiliation(s)
- Jingjing Zhao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China
| | - Danting Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China.
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8
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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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9
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Last MGF, Voortman LM, Sharp TH. Building a super-resolution fluorescence cryomicroscope. Methods Cell Biol 2024; 187:205-222. [PMID: 38705625 DOI: 10.1016/bs.mcb.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Correlated super-resolution fluorescence microscopy and cryo-electron microscopy enables imaging with both high labeling specificity and high resolution. Naturally, combining two sophisticated imaging techniques within one workflow also introduces new requirements on hardware, such as the need for a super-resolution fluorescence capable microscope that can be used to image cryogenic samples. In this chapter, we describe the design and use of the "cryoscope"; a microscope designed for single-molecule localization microscopy (SMLM) of cryoEM samples that fits right into established cryoEM workflows. We demonstrate the results that can be achieved with our microscope by imaging fluorescently labeled vimentin, an intermediate filament, within U2OS cells grown on EM grids, and we provide detailed 3d models that encompass the entire design of the microscope.
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Affiliation(s)
- Mart G F Last
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands; School of Biochemistry, University of Bristol, Bristol, United Kingdom.
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10
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Beggs KW, Kassab AJ, Colletta M, Yu Y, Kourkoutis LF, Darwish AA, Giannuzzi LA. Conjugate Multimode Heat Transfer Analysis of Cryogenic EXLO Manipulation. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024; 30:66-76. [PMID: 38180779 DOI: 10.1093/micmic/ozad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/05/2023] [Accepted: 11/13/2023] [Indexed: 01/06/2024]
Abstract
In this study, a conjugate radiation/conduction multimode heat transfer analysis of cryogenic focused ion beam (FIB) milling steps necessary for producing ex situ lift out specimens under cryogenic conditions (cryo-EXLO) is performed. Using finite volume for transient heat conduction and enclosure theory for radiation heat transfer, the analysis shows that as long as the specimen is attached or touching the FIB side wall trenches, the specimen will remain vitreous indefinitely, while actively cooled at liquid nitrogen (LN2) temperatures. To simulate the time needed to perform a transfer step to move the bulk sample containing the FIB-thinned specimen from the cryo-FIB to the cryo-EXLO cryostat, the LN2 temperature active cooling is turned off after steady-state conditions are reached and the specimen is monitored over time until the critical devitrification temperature is reached. Under these conditions, the sample will remain vitreous for >3 min, which is more than enough time needed to perform the cryo-transfer step from the FIB to the cryostat, which takes only ∼10 s. Cryo-transmission electron microscopy images of a manipulated cryo-EXLO yeast specimen prepared with cryo-FIB corroborates the heat transfer analysis.
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Affiliation(s)
- Kyle W Beggs
- Centecorp LLC, 147 Parsons Rd, Longwood, FL 32779, USA
| | | | - Michael Colletta
- Applied and Engineering Physics, Clark Hall, Cornell University, Ithaca, NY, USA
| | - Yue Yu
- Applied and Engineering Physics, Clark Hall, Cornell University, Ithaca, NY, USA
| | - Lena F Kourkoutis
- Applied and Engineering Physics, Clark Hall, Cornell University, Ithaca, NY, USA
- Kavli Institute at Cornell for Nanoscale Science, Physical Sciences Building, Cornell University, Ithaca, NY, USA
| | - Ahmed A Darwish
- EXpressLO LLC, 5483 Lee St, Unit 12, Lehigh Acres, FL 33971, USA
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11
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McCafferty CL, Klumpe S, Amaro RE, Kukulski W, Collinson L, Engel BD. Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell 2024; 187:563-584. [PMID: 38306982 DOI: 10.1016/j.cell.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.
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Affiliation(s)
| | - Sven Klumpe
- Research Group CryoEM Technology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Rommie E Amaro
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Wanda Kukulski
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Benjamin D Engel
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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12
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Sitsel O, Wang Z, Janning P, Kroczek L, Wagner T, Raunser S. Yersinia entomophaga Tc toxin is released by T10SS-dependent lysis of specialized cell subpopulations. Nat Microbiol 2024; 9:390-404. [PMID: 38238469 PMCID: PMC10847048 DOI: 10.1038/s41564-023-01571-z] [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: 03/28/2023] [Accepted: 11/29/2023] [Indexed: 02/04/2024]
Abstract
Disease-causing bacteria secrete numerous toxins to invade and subjugate their hosts. Unlike many smaller toxins, the secretion machinery of most large toxins remains enigmatic. By combining genomic editing, proteomic profiling and cryo-electron tomography of the insect pathogen Yersinia entomophaga, we demonstrate that a specialized subset of these cells produces a complex toxin cocktail, including the nearly ribosome-sized Tc toxin YenTc, which is subsequently exported by controlled cell lysis using a transcriptionally coupled, pH-dependent type 10 secretion system (T10SS). Our results dissect the Tc toxin export process by a T10SS, identifying that T10SSs operate via a previously unknown lytic mode of action and establishing them as crucial players in the size-insensitive release of cytoplasmically folded toxins. With T10SSs directly embedded in Tc toxin operons of major pathogens, we anticipate that our findings may model an important aspect of pathogenesis in bacteria with substantial impact on agriculture and healthcare.
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Affiliation(s)
- Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Zhexin Wang
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Petra Janning
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Lara Kroczek
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Thorsten Wagner
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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13
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Eskelinen EL. Novel insights into autophagosome biogenesis revealed by cryo-electron tomography. FEBS Lett 2024; 598:9-16. [PMID: 37625816 DOI: 10.1002/1873-3468.14726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Autophagosome biogenesis, from the appearance of the phagophore to elongation and closure into an autophagosome, is one of the long-lasting open questions in the autophagy field. Recent studies utilising cryo-electron tomography and detailed analysis of the image data have revealed new information on the membrane dynamics of these events, including the shape and dimensions of omegasomes, phagophores and autophagosomes, and their relationships with the organelles around them. One of the important predictions from the new results is that 60-80% of the autophagosome membrane area is delivered by direct lipid transfer or lipid synthesis. Cryo-electron tomography can be expected to provide new directions for autophagy research in the near future.
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14
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Berkamp S, Daviran D, Smeets M, Caignard A, Jani RA, Sundermeyer P, Jonker C, Gerlach S, Hoffmann B, Lau K, Sachse C. Correlative Light and Electron Cryo-Microscopy Workflow Combining Micropatterning, Ice Shield, and an In-Chamber Fluorescence Light Microscope. Bio Protoc 2023; 13:e4901. [PMID: 38156035 PMCID: PMC10751236 DOI: 10.21769/bioprotoc.4901] [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: 08/10/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 12/30/2023] Open
Abstract
In situ cryo-electron tomography (cryo-ET) is the most current, state-of-the-art technique to study cell machinery in its hydrated near-native state. The method provides ultrastructural details at sub-nanometer resolution for many components within the cellular context. Making use of recent advances in sample preparation techniques and combining this method with correlative light and electron microscopy (CLEM) approaches have enabled targeted molecular visualization. Nevertheless, the implementation has also added to the complexity of the workflow and introduced new obstacles in the way of streamlining and achieving high throughput, sample yield, and sample quality. Here, we report a detailed protocol by combining multiple newly available technologies to establish an integrated, high-throughput, optimized, and streamlined cryo-CLEM workflow for improved sample yield. Key features • PRIMO micropatterning allows precise cell positioning and maximum number of cell targets amenable to thinning with cryo focused-ion-beam-scanning electron microscopy. • CERES ice shield ensures that the lamellae remain free of ice contamination during the batch milling process. • METEOR in-chamber fluorescence microscope facilitates the targeted cryo focused-ion-beam (cryo FIB) milling of these targets. • Combining the three technologies into one cryo-CLEM workflow maximizes sample yield, throughput, and efficiency. Graphical overview.
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Affiliation(s)
- Sabrina Berkamp
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing, IBI-6: Structural Cell Biology, Forschungszentrum Jülich, Jülich, Germany
| | | | | | | | | | - Pia Sundermeyer
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing, IBI-6: Structural Cell Biology, Forschungszentrum Jülich, Jülich, Germany
| | | | - Sven Gerlach
- Institute of Biological Information Processing, IBI-2: Mechanobiology Forschungszentrum Jülich, Jülich, Germany
| | - Bernd Hoffmann
- Institute of Biological Information Processing, IBI-2: Mechanobiology Forschungszentrum Jülich, Jülich, Germany
| | | | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing, IBI-6: Structural Cell Biology, Forschungszentrum Jülich, Jülich, Germany
- Department of Biology, Heinrich Heine University, Düsseldorf, Germany
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15
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Schiøtz OH, Kaiser CJO, Klumpe S, Morado DR, Poege M, Schneider J, Beck F, Klebl DP, Thompson C, Plitzko JM. Serial Lift-Out: sampling the molecular anatomy of whole organisms. Nat Methods 2023:10.1038/s41592-023-02113-5. [PMID: 38110637 DOI: 10.1038/s41592-023-02113-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/25/2023] [Indexed: 12/20/2023]
Abstract
Cryo-focused ion beam milling of frozen-hydrated cells and subsequent cryo-electron tomography (cryo-ET) has enabled the structural elucidation of macromolecular complexes directly inside cells. Application of the technique to multicellular organisms and tissues, however, is still limited by sample preparation. While high-pressure freezing enables the vitrification of thicker samples, it prolongs subsequent preparation due to increased thinning times and the need for extraction procedures. Additionally, thinning removes large portions of the specimen, restricting the imageable volume to the thickness of the final lamella, typically <300 nm. Here we introduce Serial Lift-Out, an enhanced lift-out technique that increases throughput and obtainable contextual information by preparing multiple sections from single transfers. We apply Serial Lift-Out to Caenorhabditis elegans L1 larvae, yielding a cryo-ET dataset sampling the worm's anterior-posterior axis, and resolve its ribosome structure to 7 Å and a subregion of the 11-protofilament microtubule to 13 Å, illustrating how Serial Lift-Out enables the study of multicellular molecular anatomy.
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Affiliation(s)
- Oda Helene Schiøtz
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christoph J O Kaiser
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sven Klumpe
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Dustin R Morado
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department for Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Matthias Poege
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jonathan Schneider
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Beck
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David P Klebl
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christopher Thompson
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Jürgen M Plitzko
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany.
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16
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Liu HF, Zhou Y, Huang Q, Piland J, Jin W, Mandel J, Du X, Martin J, Bartesaghi A. nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography. Nat Methods 2023; 20:1909-1919. [PMID: 37884796 PMCID: PMC10703682 DOI: 10.1038/s41592-023-02045-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023]
Abstract
Single-particle cryo-electron tomography is an emerging technique capable of determining the structure of proteins imaged within the native context of cells at molecular resolution. While high-throughput techniques for sample preparation and tilt-series acquisition are beginning to provide sufficient data to allow structural studies of proteins at physiological concentrations, the complex data analysis pipeline and the demanding storage and computational requirements pose major barriers for the development and broader adoption of this technology. Here, we present a scalable, end-to-end framework for single-particle cryo-electron tomography data analysis from on-the-fly pre-processing of tilt series to high-resolution refinement and classification, which allows efficient analysis and visualization of datasets with hundreds of tilt series and hundreds of thousands of particles. We validate our approach using in vitro and cellular datasets, demonstrating its effectiveness at achieving high-resolution and revealing conformational heterogeneity in situ. The framework is made available through an intuitive and easy-to-use computer application, nextPYP ( http://nextpyp.app ).
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Affiliation(s)
- Hsuan-Fu Liu
- Department of Biochemistry, Duke University, Durham, NC, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Qinwen Huang
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Jonathan Piland
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA
| | - Weisheng Jin
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Justin Mandel
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Xiaochen Du
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey Martin
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Alberto Bartesaghi
- Department of Biochemistry, Duke University, Durham, NC, USA.
- Department of Computer Science, Duke University, Durham, NC, USA.
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA.
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17
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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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18
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Tamborrini D, Wang Z, Wagner T, Tacke S, Stabrin M, Grange M, Kho AL, Rees M, Bennett P, Gautel M, Raunser S. Structure of the native myosin filament in the relaxed cardiac sarcomere. Nature 2023; 623:863-871. [PMID: 37914933 PMCID: PMC10665186 DOI: 10.1038/s41586-023-06690-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023]
Abstract
The thick filament is a key component of sarcomeres, the basic units of striated muscle1. Alterations in thick filament proteins are associated with familial hypertrophic cardiomyopathy and other heart and muscle diseases2. Despite the central importance of the thick filament, its molecular organization remains unclear. Here we present the molecular architecture of native cardiac sarcomeres in the relaxed state, determined by cryo-electron tomography. Our reconstruction of the thick filament reveals the three-dimensional organization of myosin, titin and myosin-binding protein C (MyBP-C). The arrangement of myosin molecules is dependent on their position along the filament, suggesting specialized capacities in terms of strain susceptibility and force generation. Three pairs of titin-α and titin-β chains run axially along the filament, intertwining with myosin tails and probably orchestrating the length-dependent activation of the sarcomere. Notably, whereas the three titin-α chains run along the entire length of the thick filament, titin-β chains do not. The structure also demonstrates that MyBP-C bridges thin and thick filaments, with its carboxy-terminal region binding to the myosin tails and directly stabilizing the OFF state of the myosin heads in an unforeseen manner. These results provide a foundation for future research investigating muscle disorders involving sarcomeric components.
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Affiliation(s)
- Davide Tamborrini
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Zhexin Wang
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Thorsten Wagner
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sebastian Tacke
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Markus Stabrin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Michael Grange
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Ay Lin Kho
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, Kings College London BHF Centre of Research Excellence, London, UK
| | - Martin Rees
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, Kings College London BHF Centre of Research Excellence, London, UK
| | - Pauline Bennett
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, Kings College London BHF Centre of Research Excellence, London, UK
| | - Mathias Gautel
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, Kings College London BHF Centre of Research Excellence, London, UK
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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19
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Wu Y, Qin C, Du W, Guo Z, Chen L, Guo Q. A practical multicellular sample preparation pipeline broadens the application of in situ cryo-electron tomography. J Struct Biol 2023; 215:107971. [PMID: 37201639 DOI: 10.1016/j.jsb.2023.107971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/28/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
The structural studies of macromolecules in their physiological context, particularly in tissue, is constrained by the bottleneck of sample preparation. In this study, we present a practical pipeline for preparing multicellular samples for cryo-electron tomography. The pipeline comprises sample isolation, vitrification, and lift-out-based lamella preparation using commercially available instruments. We demonstrate the efficacy of our pipeline by visualizing pancreatic β cells from mouse islets at the molecular level. This pipeline enables the determination of the properties of insulin crystals in situ for the first time, using unperturbed samples.
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Affiliation(s)
- Yichun Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China
| | - Changdong Qin
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenjing Du
- State Key Laboratory of Protein and Plant Gene Research, Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China
| | - Zhenxi Guo
- School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Center for Life Sciences, College of Future Technology, Peking University, Beijing 100871, China
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
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20
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Tan ZY, Cai S, Noble AJ, Chen JK, Shi J, Gan L. Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ. eLife 2023; 12:RP87672. [PMID: 37503920 PMCID: PMC10382156 DOI: 10.7554/elife.87672] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ (inside cells) resembles the canonical structure determined in vitro 25 years ago. Nucleosome structure in situ is otherwise poorly understood. Using cryo-electron tomography (cryo-ET) and 3D classification analysis of budding yeast cells, here we find that canonical nucleosomes account for less than 10% of total nucleosomes expected in situ. In a strain in which H2A-GFP is the sole source of histone H2A, class averages that resemble canonical nucleosomes both with and without GFP densities are found ex vivo (in nuclear lysates), but not in situ. These data suggest that the budding yeast intranuclear environment favors multiple non-canonical nucleosome conformations. Using the structural observations here and the results of previous genomics and biochemical studies, we propose a model in which the average budding yeast nucleosome's DNA is partially detached in situ.
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Affiliation(s)
- Zhi Yang Tan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Shujun Cai
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Alex J Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Jon K Chen
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Jian Shi
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Lu Gan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
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21
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Smeets M, Lau K. Improving Cryo-Electron Tomography Data Quality and Throughput by Streamlining the Workflow. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1054. [PMID: 37613115 DOI: 10.1093/micmic/ozad067.540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Marit Smeets
- Delmic B.V. , Life Sciences, Delft, The Netherlands
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22
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Chang ML, Erwin AL, Mosalaganti S. Image Processing Pipeline for In Situ Structural Characterization of Filaments. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:952-953. [PMID: 37613656 DOI: 10.1093/micmic/ozad067.475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Matthew L Chang
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States
| | - Amanda L Erwin
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
- Departments of Cell and Developmental Biology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Shyamal Mosalaganti
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
- Departments of Cell and Developmental Biology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, United States
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States
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23
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Rice G, Wagner T, Stabrin M, Sitsel O, Prumbaum D, Raunser S. TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining. Nat Methods 2023:10.1038/s41592-023-01878-z. [PMID: 37188953 DOI: 10.1038/s41592-023-01878-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023]
Abstract
Cryogenic-electron tomography enables the visualization of cellular environments in extreme detail, however, tools to analyze the full amount of information contained within these densely packed volumes are still needed. Detailed analysis of macromolecules through subtomogram averaging requires particles to first be localized within the tomogram volume, a task complicated by several factors including a low signal to noise ratio and crowding of the cellular space. Available methods for this task suffer either from being error prone or requiring manual annotation of training data. To assist in this crucial particle picking step, we present TomoTwin: an open source general picking model for cryogenic-electron tomograms based on deep metric learning. By embedding tomograms in an information-rich, high-dimensional space that separates macromolecules according to their three-dimensional structure, TomoTwin allows users to identify proteins in tomograms de novo without manually creating training data or retraining the network to locate new proteins.
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Affiliation(s)
- Gavin Rice
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Thorsten Wagner
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Markus Stabrin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Daniel Prumbaum
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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24
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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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25
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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: 28] [Impact Index Per Article: 28.0] [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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26
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Berger C, Dumoux M, Glen T, Yee NBY, Mitchels JM, Patáková Z, Darrow MC, Naismith JH, Grange M. Plasma FIB milling for the determination of structures in situ. Nat Commun 2023; 14:629. [PMID: 36746945 PMCID: PMC9902539 DOI: 10.1038/s41467-023-36372-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Structural biology studies inside cells and tissues require methods to thin vitrified specimens to electron transparency. Until now, focused ion beams based on gallium have been used. However, ion implantation, changes to surface chemistry and an inability to access high currents limit gallium application. Here, we show that plasma-coupled ion sources can produce cryogenic lamellae of vitrified human cells in a robust and automated manner, with quality sufficient for pseudo-atomic structure determination. Lamellae were produced in a prototype microscope equipped for long cryogenic run times (> 1 week) and with multi-specimen support fully compatible with modern-day transmission electron microscopes. We demonstrate that plasma ion sources can be used for structural biology within cells, determining a structure in situ to 4.9 Å, and characterise the resolution dependence on particle distance from the lamella edge. We describe a workflow upon which different plasmas can be examined to further streamline lamella fabrication.
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Affiliation(s)
- Casper Berger
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, Oxford, United Kingdom
| | - Maud Dumoux
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - Thomas Glen
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - Neville B-Y Yee
- Artificial Intelligence & Informatics, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - John M Mitchels
- Thermo Fisher Scientific Brno s.r.o, Brno, 627 00, Czech Republic
| | - Zuzana Patáková
- Thermo Fisher Scientific Brno s.r.o, Brno, 627 00, Czech Republic
| | - Michele C Darrow
- Artificial Intelligence & Informatics, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - James H Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, Oxford, United Kingdom
| | - Michael Grange
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom. .,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, Oxford, United Kingdom.
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27
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Capitanio C, Bieber A, Wilfling F. How Membrane Contact Sites Shape the Phagophore. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231162495. [PMID: 37366413 PMCID: PMC10243513 DOI: 10.1177/25152564231162495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/15/2023] [Accepted: 02/18/2023] [Indexed: 06/28/2023]
Abstract
During macroautophagy, phagophores establish multiple membrane contact sites (MCSs) with other organelles that are pivotal for proper phagophore assembly and growth. In S. cerevisiae, phagophore contacts have been observed with the vacuole, the ER, and lipid droplets. In situ imaging studies have greatly advanced our understanding of the structure and function of these sites. Here, we discuss how in situ structural methods like cryo-CLEM can give unprecedented insights into MCSs, and how they help to elucidate the structural arrangements of MCSs within cells. We further summarize the current knowledge of the contact sites in autophagy, focusing on autophagosome biogenesis in the model organism S. cerevisiae.
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Affiliation(s)
- Cristina Capitanio
- Department of Molecular Machines and
Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Aligning Science Across Parkinson's (ASAP)
Collaborative Research Network, Chevy Chase, MD, USA
| | - Anna Bieber
- Department of Molecular Machines and
Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Aligning Science Across Parkinson's (ASAP)
Collaborative Research Network, Chevy Chase, MD, USA
| | - Florian Wilfling
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt a. M., Germany
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28
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Eisenstein F, Yanagisawa H, Kashihara H, Kikkawa M, Tsukita S, Danev R. Parallel cryo electron tomography on in situ lamellae. Nat Methods 2023; 20:131-138. [PMID: 36456783 DOI: 10.1038/s41592-022-01690-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/28/2022] [Indexed: 12/05/2022]
Abstract
In situ cryo electron tomography of cryo focused ion beam milled samples has emerged in recent years as a powerful technique for structural studies of macromolecular complexes in their native cellular environment. However, the possibilities for recording tomographic tilt series in a high-throughput manner are limited, in part by the lamella-shaped samples. Here we utilize a geometrical sample model and optical image shift to record tens of tilt series in parallel, thereby saving time and gaining access to sample areas conventionally used for tracking specimen movement. The parallel cryo electron tomography (PACE-tomo) method achieves a throughput faster than 5 min per tilt series and allows for the collection of sample areas that were previously unreachable, thus maximizing the amount of data from each lamella. Performance testing with ribosomes in vitro and in situ on state-of-the-art and general-purpose microscopes demonstrated the high throughput and quality of PACE-tomo.
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Affiliation(s)
| | | | - Hiroka Kashihara
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
| | | | - Sachiko Tsukita
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan.
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29
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Guaita M, Watters SC, Loerch S. Recent advances and current trends in cryo-electron microscopy. Curr Opin Struct Biol 2022; 77:102484. [PMID: 36323134 DOI: 10.1016/j.sbi.2022.102484] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/13/2022] [Accepted: 09/21/2022] [Indexed: 12/14/2022]
Abstract
All steps of cryogenic electron-microscopy (cryo-EM) workflows have rapidly evolved over the last decade. Advances in both single-particle analysis (SPA) cryo-EM and cryo-electron tomography (cryo-ET) have facilitated the determination of high-resolution biomolecular structures that are not tractable with other methods. However, challenges remain. For SPA, these include improved resolution in an additional dimension: time. For cryo-ET, these include accessing difficult-to-image areas of a cell and finding rare molecules. Finally, there is a need for automated and faster workflows, as many projects are limited by throughput. Here, we review current developments in SPA cryo-EM and cryo-ET that push these boundaries. Collectively, these advances are poised to propel our spatial and temporal understanding of macromolecular processes.
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Affiliation(s)
- Margherita Guaita
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Scott C Watters
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Sarah Loerch
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA.
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30
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Rodríguez de Francisco B, Bezault A, Xu XP, Hanein D, Volkmann N. MEPSi: A tool for simulating tomograms of membrane-embedded proteins. J Struct Biol 2022; 214:107921. [PMID: 36372192 DOI: 10.1016/j.jsb.2022.107921] [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: 07/31/2022] [Revised: 10/27/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022]
Abstract
The throughput and fidelity of cryogenic cellular electron tomography (cryo-ET) is constantly increasing through advances in cryogenic electron microscope hardware, direct electron detection devices, and powerful image processing algorithms. However, the need for careful optimization of sample preparations and for access to expensive, high-end equipment, make cryo-ET a costly and time-consuming technique. Generally, only after the last step of the cryo-ET workflow, when reconstructed tomograms are available, it becomes clear whether the chosen imaging parameters were suitable for a specific type of sample in order to answer a specific biological question. Tools for a-priory assessment of the feasibility of samples to answer biological questions and how to optimize imaging parameters to do so would be a major advantage. Here we describe MEPSi (Membrane Embedded Protein Simulator), a simulation tool aimed at rapid and convenient evaluation and optimization of cryo-ET data acquisition parameters for studies of transmembrane proteins in their native environment. We demonstrate the utility of MEPSi by showing how to detangle the influence of different data collection parameters and different orientations in respect to tilt axis and electron beam for two examples: (1) simulated plasma membranes with embedded single-pass transmembrane αIIbβ3 integrin receptors and (2) simulated virus membranes with embedded SARS-CoV-2 spike proteins.
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Affiliation(s)
- Borja Rodríguez de Francisco
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France
| | - Armel Bezault
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France
| | | | - Dorit Hanein
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Studies of Macromolecular Machines in Cellulo Unit, Paris, France; Scintillon Institute, San Diego, CA 92121, USA
| | - Niels Volkmann
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Image Analysis Unit, Paris, France.
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31
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Franken LE, Rosch R, Laugks U, Grünewald K. Protocol for live-cell fluorescence-guided cryoFIB-milling and electron cryo-tomography of virus-infected cells. STAR Protoc 2022; 3:101696. [PMID: 36149798 PMCID: PMC9508610 DOI: 10.1016/j.xpro.2022.101696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/13/2022] [Accepted: 08/17/2022] [Indexed: 01/25/2023] Open
Abstract
Here, we present a protocol for assessing virus-infected cells using electron cryo-tomography (cryoET). It includes the basic workflows of seeding cells, plunge-freezing, clipping, cryo-focused ion beam milling (cryoFIB-milling), and cryoET, as well as two optional modules: micropatterning and live-cell fluorescence microscopy. We use an A549 human cell line and the virus HAdV5-pIX-mcherry in this protocol, but the comprehensive workflow can be easily transferred to other cell types and different types of virus infection or treatment. For complete details on the use and execution of this protocol, please refer to Pfitzner et al. (2021).
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Affiliation(s)
- Linda E. Franken
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251 Hamburg, Germany,Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany,Corresponding author
| | - Rene Rosch
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251 Hamburg, Germany,Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany,Universität Hamburg, Institute for Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ulrike Laugks
- Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany,Universität Hamburg, Institute for Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Kay Grünewald
- Leibniz Institute of Virology (LIV), Martinistraße 52, 20251 Hamburg, Germany,Centre for Structural Systems Biology, Notkestraße 85, 22607 Hamburg, Germany,Universität Hamburg, Institute for Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany,Corresponding author
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32
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Abstract
The three-dimensional organization of biomolecules important for the functioning of all living systems can be determined by cryo-electron tomography imaging under native biological contexts. Cryo-electron tomography is continually expanding and evolving, and the development of new methods that use the latest technology for sample thinning is enabling the visualization of ever larger and more complex biological systems, allowing imaging across scales. Quantitative cryo-electron tomography possesses the capability of visualizing the impact of molecular and environmental perturbations in subcellular structure and function to understand fundamental biological processes. This review provides an overview of current hardware and software developments that allow quantitative cryo-electron tomography studies and their limitations and how overcoming them may allow us to unleash the full power of cryo-electron tomography.
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Affiliation(s)
- Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
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33
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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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34
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Functional Remodeling of the Contractile Smooth Muscle Cell Cortex, a Provocative Concept, Supported by Direct Visualization of Cortical Remodeling. BIOLOGY 2022; 11:biology11050662. [PMID: 35625390 PMCID: PMC9138025 DOI: 10.3390/biology11050662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/06/2022] [Accepted: 04/24/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary As a key element of the smooth muscle cell contractile apparatus, the actin cytoskeleton participates in the development of force by acting as a molecular track for the myosin cross bridge motor. At the same time, the actin cytoskeleton must transmit the force developed during contraction to the extracellular matrix and, thus, to neighboring cells. This propagation of force to the cell periphery and beyond is initiated in part on specifically localized cellular cortical actin filaments also involved in mechano-chemical transduction. During the contractile process itself and in response to extracellular structural and chemical alterations, the smooth muscle actin cytoskeletal remodels. This indicates that the cytoskeleton is a dynamic cellular organelle that adapts to the changes in cell shape and chemical cues. Current evidence connecting contractile function and mechano-transduction mechanisms to the plasticity of the vascular smooth muscle actin cytoskeleton is reviewed; we then describe new evidence for cytoskeletal remodeling in vascular smooth muscle cells. Here, using immunoelectron microscopy, we visualize the actin binding proteins filamin A, zyxin and talin in these cells and show that they participate in the cortical cell cytoskeletal alteration, thus supporting the premise that smooth muscle cell remodeling occurs during contraction. Abstract Considerable controversy has surrounded the functional anatomy of the cytoskeleton of the contractile vascular smooth muscle cell. Recent studies have suggested a dynamic nature of the cortical cytoskeleton of these cells, but direct proof has been lacking. Here, we review past studies in this area suggesting a plasticity of smooth muscle cells. We also present images testing these suggestions by using the technique of immunoelectron microscopy of metal replicas to directly visualize the cortical actin cytoskeleton of the contractile smooth muscle cell along with interactions by representative cytoskeletal binding proteins. We find the cortical cytoskeletal matrix to be a branched, interconnected network of linear actin bundles. Here, the focal adhesion proteins talin and zyxin were localized with nanometer accuracy. Talin is reported in past studies to span the integrin–cytoplasm distance in fibroblasts and zyxin is known to be an adaptor protein between alpha-actinin and VASP. In response to activation of signal transduction with the alpha-agonist phenylephrine, we found that no movement of talin was detectable but that the zyxin-zyxin spacing was statistically significantly decreased in the smooth muscle cells examined. Contractile smooth muscle is often assumed to have a fixed cytoskeletal structure. Thus, the results included here are important in that they directly support the concept at the electron microscopic level that the focal adhesion of the contractile smooth muscle cell has a dynamic nature and that the protein–protein interfaces showing plasticity are protein-specific.
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35
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Waffle Method: A general and flexible approach for improving throughput in FIB-milling. Nat Commun 2022; 13:1857. [PMID: 35387991 PMCID: PMC8987090 DOI: 10.1038/s41467-022-29501-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 03/17/2022] [Indexed: 12/29/2022] Open
Abstract
Cryo-FIB/SEM combined with cryo-ET has emerged from within the field of cryo-EM as the method for obtaining the highest resolution structural information of complex biological samples in-situ in native and non-native environments. However, challenges remain in conventional cryo-FIB/SEM workflows, including milling thick specimens with vitrification issues, specimens with preferred orientation, low-throughput when milling small and/or low concentration specimens, and specimens that distribute poorly across grid squares. Here we present a general approach called the ‘Waffle Method’ which leverages high-pressure freezing to address these challenges. We illustrate the mitigation of these challenges by applying the Waffle Method and cryo-ET to reveal the macrostructure of the polar tube in microsporidian spores in multiple complementary orientations, which was previously not possible due to preferred orientation. We demonstrate the broadness of the Waffle Method by applying it to three additional cellular samples and a single particle sample using a variety of cryo-FIB-milling hardware, with manual and automated approaches. We also present a unique and critical stress-relief gap designed specifically for waffled lamellae. We propose the Waffle Method as a way to achieve many advantages of cryo-liftout on the specimen grid while avoiding the long, challenging, and technically-demanding process required for cryo-liftout. Here the authors describe the Waffle Method, aimed at increasing the throughput of and solves several challenges present in cryo-FIB/SEM sample preparation for cryo-ET analysis — the highest-resolution method for obtaining 3D views of native biological specimens in-situ.
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36
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Liedtke J, Depelteau JS, Briegel A. How advances in cryo-electron tomography have contributed to our current view of bacterial cell biology. J Struct Biol X 2022; 6:100065. [PMID: 35252838 PMCID: PMC8894267 DOI: 10.1016/j.yjsbx.2022.100065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
Advancements in the field of cryo-electron tomography have greatly contributed to our current understanding of prokaryotic cell organization and revealed intracellular structures with remarkable architecture. In this review, we present some of the prominent advancements in cryo-electron tomography, illustrated by a subset of structural examples to demonstrate the power of the technique. More specifically, we focus on technical advances in automation of data collection and processing, sample thinning approaches, correlative cryo-light and electron microscopy, and sub-tomogram averaging methods. In turn, each of these advances enabled new insights into bacterial cell architecture, cell cycle progression, and the structure and function of molecular machines. Taken together, these significant advances within the cryo-electron tomography workflow have led to a greater understanding of prokaryotic biology. The advances made the technique available to a wider audience and more biological questions and provide the basis for continued advances in the near future.
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Affiliation(s)
- Janine Liedtke
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Jamie S Depelteau
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ariane Briegel
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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37
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Wang Z, Grange M, Pospich S, Wagner T, Kho AL, Gautel M, Raunser S. Structures from intact myofibrils reveal mechanism of thin filament regulation through nebulin. Science 2022; 375:eabn1934. [PMID: 35175800 DOI: 10.1126/science.abn1934] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In skeletal muscle, nebulin stabilizes and regulates the length of thin filaments, but the underlying mechanism remains nebulous. In this work, we used cryo-electron tomography and subtomogram averaging to reveal structures of native nebulin bound to thin filaments within intact sarcomeres. This in situ reconstruction provided high-resolution details of the interaction between nebulin and actin, demonstrating the stabilizing role of nebulin. Myosin bound to the thin filaments exhibited different conformations of the neck domain, highlighting its inherent structural variability in muscle. Unexpectedly, nebulin did not interact with myosin or tropomyosin, but it did interact with a troponin T linker through two potential binding motifs on nebulin, explaining its regulatory role. Our structures support the role of nebulin as a thin filament "molecular ruler" and provide a molecular basis for studying nemaline myopathies.
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Affiliation(s)
- Zhexin Wang
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Michael Grange
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Sabrina Pospich
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Thorsten Wagner
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Ay Lin Kho
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, Kings College London BHF Centre of Research Excellence, Guy's Campus, London SE1 1UL, UK
| | - Mathias Gautel
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, Kings College London BHF Centre of Research Excellence, Guy's Campus, London SE1 1UL, UK
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
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38
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Parasitology meets cryo-electron tomography – exciting prospects await. Trends Parasitol 2022; 38:365-378. [DOI: 10.1016/j.pt.2022.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 12/27/2022]
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39
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Klykov O, Kopylov M, Carragher B, Heck AJR, Noble AJ, Scheltema RA. Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology. Mol Cell 2022; 82:285-303. [PMID: 35063097 PMCID: PMC8842845 DOI: 10.1016/j.molcel.2021.12.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Combining diverse experimental structural and interactomic methods allows for the construction of comprehensible molecular encyclopedias of biological systems. Typically, this involves merging several independent approaches that provide complementary structural and functional information from multiple perspectives and at different resolution ranges. A particularly potent combination lies in coupling structural information from cryoelectron microscopy or tomography (cryo-EM or cryo-ET) with interactomic and structural information from mass spectrometry (MS)-based structural proteomics. Cryo-EM/ET allows for sub-nanometer visualization of biological specimens in purified and near-native states, while MS provides bioanalytical information for proteins and protein complexes without introducing additional labels. Here we highlight recent achievements in protein structure and interactome determination using cryo-EM/ET that benefit from additional MS analysis. We also give our perspective on how combining cryo-EM/ET and MS will continue bridging gaps between molecular and cellular studies by capturing and describing 3D snapshots of proteomes and interactomes.
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Affiliation(s)
- Oleg Klykov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Mykhailo Kopylov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Bridget Carragher
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Alex J Noble
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands.
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40
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Boltje DB, Hoogenboom JP, Jakobi AJ, Jensen GJ, Jonker CTH, Kaag MJ, Koster AJ, Last MGF, de Agrela Pinto C, Plitzko JM, Raunser S, Tacke S, Wang Z, van der Wee EB, Wepf R, den Hoedt S. A cryogenic, coincident fluorescence, electron, and ion beam microscope. eLife 2022; 11:82891. [PMID: 36305590 PMCID: PMC9714966 DOI: 10.7554/elife.82891] [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: 08/23/2022] [Accepted: 10/25/2022] [Indexed: 02/04/2023] Open
Abstract
Cryogenic electron tomography (cryo-ET) combined with subtomogram averaging, allows in situ visualization and structure determination of macromolecular complexes at subnanometre resolution. Cryogenic focused ion beam (cryo-FIB) micromachining is used to prepare a thin lamella-shaped sample out of a frozen-hydrated cell for cryo-ET imaging, but standard cryo-FIB fabrication is blind to the precise location of the structure or proteins of interest. Fluorescence-guided focused ion beam (FIB) milling at target locations requires multiple sample transfers prone to contamination, and relocation and registration accuracy is often insufficient for 3D targeting. Here, we present in situ fluorescence microscopy-guided FIB fabrication of a frozen-hydrated lamella to address this problem: we built a coincident three-beam cryogenic correlative microscope by retrofitting a compact cryogenic microcooler, custom positioning stage, and an inverted widefield fluorescence microscope (FM) on an existing FIB scanning electron microscope. We show FM controlled targeting at every milling step in the lamella fabrication process, validated with transmission electron microscope tomogram reconstructions of the target regions. The ability to check the lamella during and after the milling process results in a higher success rate in the fabrication process and will increase the throughput of fabrication for lamellae suitable for high-resolution imaging.
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Affiliation(s)
- Daan B Boltje
- Department of Imaging Physic, Delft University of TechnologyDelftNetherlands,Delmic B.VDelftNetherlands
| | - Jacob P Hoogenboom
- Department of Imaging Physic, Delft University of TechnologyDelftNetherlands
| | - Arjen J Jakobi
- Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Grant J Jensen
- California Institute of TechnologyPasadenaUnited States,Brigham Young UniversityProvoUnited States
| | | | - Max J Kaag
- Department of Imaging Physic, Delft University of TechnologyDelftNetherlands
| | - Abraham J Koster
- Department of Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Mart GF Last
- Delmic B.VDelftNetherlands,Department of Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | | | - Jürgen M Plitzko
- CryoEM Technology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular PhysiologyDortmundGermany
| | - Sebastian Tacke
- Department of Structural Biochemistry, Max Planck Institute of Molecular PhysiologyDortmundGermany
| | - Zhexin Wang
- Department of Structural Biochemistry, Max Planck Institute of Molecular PhysiologyDortmundGermany
| | | | - Roger Wepf
- Centre for Microscopy and Microanalysis, University of QueenslandBrisbaneAustralia
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41
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Klumpe S, Fung HKH, Goetz SK, Zagoriy I, Hampoelz B, Zhang X, Erdmann PS, Baumbach J, Müller CW, Beck M, Plitzko JM, Mahamid J. A modular platform for automated cryo-FIB workflows. eLife 2021; 10:e70506. [PMID: 34951584 PMCID: PMC8769651 DOI: 10.7554/elife.70506] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/23/2021] [Indexed: 11/22/2022] Open
Abstract
Lamella micromachining by focused ion beam milling at cryogenic temperature (cryo-FIB) has matured into a preparation method widely used for cellular cryo-electron tomography. Due to the limited ablation rates of low Ga+ ion beam currents required to maintain the structural integrity of vitreous specimens, common preparation protocols are time-consuming and labor intensive. The improved stability of new-generation cryo-FIB instruments now enables automated operations. Here, we present an open-source software tool, SerialFIB, for creating automated and customizable cryo-FIB preparation protocols. The software encompasses a graphical user interface for easy execution of routine lamellae preparations, a scripting module compatible with available Python packages, and interfaces with three-dimensional correlative light and electron microscopy (CLEM) tools. SerialFIB enables the streamlining of advanced cryo-FIB protocols such as multi-modal imaging, CLEM-guided lamella preparation and in situ lamella lift-out procedures. Our software therefore provides a foundation for further development of advanced cryogenic imaging and sample preparation protocols.
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Affiliation(s)
- Sven Klumpe
- Department Molecular Structural Biology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Herman KH Fung
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Sara K Goetz
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of BiosciencesHeidelbergGermany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Bernhard Hampoelz
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Xiaojie Zhang
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Philipp S Erdmann
- Department Molecular Structural Biology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Janina Baumbach
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
- Cell Biology and Biophysics Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Jürgen M Plitzko
- Department Molecular Structural Biology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
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