1
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Sibert BS, Kim JY, Yang JE, Ke Z, Stobart CC, Moore ML, Wright ER. Assembly of respiratory syncytial virus matrix protein lattice and its coordination with fusion glycoprotein trimers. Nat Commun 2024; 15:5923. [PMID: 39004634 PMCID: PMC11247094 DOI: 10.1038/s41467-024-50162-x] [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: 10/22/2021] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Respiratory syncytial virus (RSV) is an enveloped, filamentous, negative-strand RNA virus that causes significant respiratory illness worldwide. RSV vaccines are available, however there is still significant need for research to support the development of vaccines and therapeutics against RSV and related Mononegavirales viruses. Individual virions vary in size, with an average diameter of ~130 nm and ranging from ~500 nm to over 10 µm in length. Though the general arrangement of structural proteins in virions is known, we use cryo-electron tomography and sub-tomogram averaging to determine the molecular organization of RSV structural proteins. We show that the peripheral membrane-associated RSV matrix (M) protein is arranged in a packed helical-like lattice of M-dimers. We report that RSV F glycoprotein is frequently observed as pairs of trimers oriented in an anti-parallel conformation to support potential interactions between trimers. Our sub-tomogram averages indicate the positioning of F-trimer pairs is correlated with the underlying M lattice. These results provide insight into RSV virion organization and may aid in the development of RSV vaccines and anti-viral targets.
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Affiliation(s)
- Bryan S Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Joseph Y Kim
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Zunlong Ke
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | | | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
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2
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Galaz-Montoya JG. The advent of preventive high-resolution structural histopathology by artificial-intelligence-powered cryogenic electron tomography. Front Mol Biosci 2024; 11:1390858. [PMID: 38868297 PMCID: PMC11167099 DOI: 10.3389/fmolb.2024.1390858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/08/2024] [Indexed: 06/14/2024] Open
Abstract
Advances in cryogenic electron microscopy (cryoEM) single particle analysis have revolutionized structural biology by facilitating the in vitro determination of atomic- and near-atomic-resolution structures for fully hydrated macromolecular complexes exhibiting compositional and conformational heterogeneity across a wide range of sizes. Cryogenic electron tomography (cryoET) and subtomogram averaging are rapidly progressing toward delivering similar insights for macromolecular complexes in situ, without requiring tags or harsh biochemical purification. Furthermore, cryoET enables the visualization of cellular and tissue phenotypes directly at molecular, nanometric resolution without chemical fixation or staining artifacts. This forward-looking review covers recent developments in cryoEM/ET and related technologies such as cryogenic focused ion beam milling scanning electron microscopy and correlative light microscopy, increasingly enhanced and supported by artificial intelligence algorithms. Their potential application to emerging concepts is discussed, primarily the prospect of complementing medical histopathology analysis. Machine learning solutions are poised to address current challenges posed by "big data" in cryoET of tissues, cells, and macromolecules, offering the promise of enabling novel, quantitative insights into disease processes, which may translate into the clinic and lead to improved diagnostics and targeted therapeutics.
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Affiliation(s)
- Jesús G. Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, United States
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3
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Perez D, Dowlatshahi DP, Azaldegui CA, Dahlberg PD, Moerner WE. Exploring transient states of PAmKate to enable improved cryogenic single-molecule imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590965. [PMID: 38712218 PMCID: PMC11071506 DOI: 10.1101/2024.04.24.590965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Super-resolved cryogenic correlative light and electron microscopy is a powerful approach which combines the single-molecule specificity and sensitivity of fluorescence imaging with the nano-scale resolution of cryogenic electron tomography. Key to this method is active control over the emissive state of fluorescent labels to ensure sufficient sparsity to localize individual emitters. Recent work has identified fluorescent proteins (FPs) which photoactivate or photoswitch efficiently at cryogenic temperatures, but long on-times due to reduced quantum yield of photobleaching remains a challenge for imaging structures with a high density of localizations. In this work, we explore the photophysical properties of the red photoactivatable FP PAmKate and identify a 2-color process leading to enhanced turn-off of active emitters, improving localization rate. Specifically, after excitation of ground state molecules, we find a transient state forms with a lifetime of ~2 ms which can be bleached by exposure to a second wavelength. We measure the response of the transient state to different wavelengths, demonstrate how this mechanism can be used to improve imaging, and provide a blueprint for study of other FPs at cryogenic temperatures.
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Affiliation(s)
- Davis Perez
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Dara P Dowlatshahi
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
- Department of Structural Biology, Stanford University, Stanford, California 94305, United States
| | - Christopher A Azaldegui
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Peter D Dahlberg
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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4
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Last MGF, Voortman LM, Sharp TH. Imaging intracellular components in situ using super-resolution cryo-correlative light and electron microscopy. Methods Cell Biol 2024; 187:223-248. [PMID: 38705626 DOI: 10.1016/bs.mcb.2024.02.027] [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
Super-resolution cryo-correlative light and electron microscopy (SRcryoCLEM) is emerging as a powerful method to enable targeted in situ structural studies of biological samples. By combining the high specificity and localization accuracy of single-molecule localization microscopy (cryoSMLM) with the high resolution of cryo-electron tomography (cryoET), this method enables accurately targeted data acquisition and the observation and identification of biomolecules within their natural cellular context. Despite its potential, the adaptation of SRcryoCLEM has been hindered by the need for specialized equipment and expertise. In this chapter, we outline a workflow for cryoSMLM and cryoET-based SRcryoCLEM, and we demonstrate that, given the right tools, it is possible to incorporate cryoSMLM into an established cryoET workflow. Using Vimentin as an exemplary target of interest, we demonstrate all stages of an SRcryoCLEM experiment: performing cryoSMLM, targeting cryoET acquisition based on single-molecule localization maps, and correlation of cryoSMLM and cryoET datasets using scNodes, a software package dedicated to SRcryoCLEM. By showing how SRcryoCLEM enables the imaging of specific intracellular components in situ, we hope to facilitate adoption of the technique within the field of cryoEM.
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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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5
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Kim JY, Yang JE, Mitchell JW, English LA, Yang SZ, Tenpas T, Dent EW, Wildonger J, Wright ER. Handling Difficult Cryo-ET Samples: A Study with Primary Neurons from Drosophila melanogaster. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:2127-2148. [PMID: 37966978 PMCID: PMC11168236 DOI: 10.1093/micmic/ozad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 11/17/2023]
Abstract
Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons having been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
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Affiliation(s)
- Joseph Y. Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Josephine W. Mitchell
- Department of Chemistry and Biochemistry, Kalamazoo College, Kalamazoo, MI 49006, USA
| | - Lauren A. English
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sihui Z. Yang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Tanner Tenpas
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Erik W. Dent
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jill Wildonger
- Departments of Pediatrics and Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, USA
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6
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Sáenz-de-Santa-María I, Henderson JM, Pepe A, Zurzolo C. Identification and Characterization of Tunneling Nanotubes for Intercellular Trafficking. Curr Protoc 2023; 3:e939. [PMID: 37994667 DOI: 10.1002/cpz1.939] [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: 11/24/2023]
Abstract
Tunneling nanotubes (TNTs) are thin membranous channels providing a direct cytoplasmic connection between remote cells. They are commonly observed in different cell cultures and increasing evidence supports their role in intercellular communication, and pathogen and amyloid protein transfer. However, the study of TNTs presents several pitfalls (e.g., difficulty in preserving such delicate structures, possible confusion with other protrusions, structural and functional heterogeneity, etc.) and therefore requires thoroughly designed approaches. The methods described in this protocol represent a guideline for the characterization of TNTs (or TNT-like structures) in cell culture. Specifically, optimized protocols to (1) identify TNTs and the cytoskeletal elements present inside them; (2) evaluate TNT frequency in cell culture; (3) unambiguously distinguish them from other cellular connections or protrusions; (4) monitor their formation in living cells; (5) characterize TNTs by a micropatterning approach; and (6) investigate TNT ultrastructure by cryo-EM are provided. Finally, this article describes how to assess TNT-mediated cell-to-cell transfer of cellular components, which is a fundamental criterion for identifying functional TNTs. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Identification of tunneling nanotubes Alternate Protocol 1: Identifying the cytoskeletal elements present in tunneling nanotubes Alternate Protocol 2: Distinguishing tunneling nanotubes from intercellular bridges formed during cell division Basic Protocol 2: Deciphering tunneling nanotube formation and lifetime by live fluorescent microscopy Alternate Protocol 3: Deciphering tunneling nanotube formation using a live-compatible dye Basic Protocol 3: Assessing tunneling nanotubes functionality in intercellular transfer Alternate Protocol 4: Flow cytometry approach to quantify the rate of vesicle or mitochondria transfer Support Protocol: Controls to support TNT-mediated transfer Basic Protocol 4: Studies of tunneling nanotubes by cell micropatterning Basic Protocol 5: Characterization of the ultrastructure of tunneling nanotubes by cryo-EM.
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Affiliation(s)
- Inés Sáenz-de-Santa-María
- Unité de Trafic Membranaire et Pathogénèse, Département de Biologie Cellulaire et Infection, Institut Pasteur, CNRS UMR3691, Paris, France
| | - J Michael Henderson
- Unité de Trafic Membranaire et Pathogénèse, Département de Biologie Cellulaire et Infection, Institut Pasteur, CNRS UMR3691, Paris, France
| | - Anna Pepe
- Unité de Trafic Membranaire et Pathogénèse, Département de Biologie Cellulaire et Infection, Institut Pasteur, CNRS UMR3691, Paris, France
| | - Chiara Zurzolo
- Unité de Trafic Membranaire et Pathogénèse, Département de Biologie Cellulaire et Infection, Institut Pasteur, CNRS UMR3691, Paris, France
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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7
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Kumar I, Paudyal A, Kádková A, Stewart M, Sørensen JB, Radecke J. An Improved Method for Growing Primary Neurons on Electron Microscopy Grids Co-Cultured with Astrocytes. Int J Mol Sci 2023; 24:15191. [PMID: 37894872 PMCID: PMC10606997 DOI: 10.3390/ijms242015191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
With the increasing popularity of cryo-electron tomography (cryo-ET) in recent years, the quest to establish a method for growing primary neurons directly on electron microscopy grids (EM grids) has been ongoing. Here we describe a straightforward way to establish a mature neuronal network on EM grids, which includes formation of synaptic contacts. These synapses were thin enough to allow for direct visualization of small filaments such as SNARE proteins tethering the synaptic vesicle (SV) to the active zone plasma membrane on a Titan Krios without prior focused ion-beam milling.
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Affiliation(s)
- Ishika Kumar
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK;
| | - Anju Paudyal
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Becquerel Ave, Didcot OX11 ORD, UK; (A.P.); (M.S.)
| | - Anna Kádková
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark (J.B.S.)
| | - Michelle Stewart
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Becquerel Ave, Didcot OX11 ORD, UK; (A.P.); (M.S.)
| | - Jakob Balslev Sørensen
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark (J.B.S.)
| | - Julika Radecke
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK;
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark (J.B.S.)
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8
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Yang JE, Larson MR, Sibert BS, Kim JY, Parrell D, Sanchez JC, Pappas V, Kumar A, Cai K, Thompson K, Wright ER. Correlative montage parallel array cryo-tomography for in situ structural cell biology. Nat Methods 2023; 20:1537-1543. [PMID: 37723245 PMCID: PMC10555823 DOI: 10.1038/s41592-023-01999-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/08/2023] [Indexed: 09/20/2023]
Abstract
Imaging large fields of view while preserving high-resolution structural information remains a challenge in low-dose cryo-electron tomography. Here we present robust tools for montage parallel array cryo-tomography (MPACT) tailored for vitrified specimens. The combination of correlative cryo-fluorescence microscopy, focused-ion-beam milling, substrate micropatterning, and MPACT supports studies that contextually define the three-dimensional architecture of cells. To further extend the flexibility of MPACT, tilt series may be processed in their entirety or as individual tiles suitable for sub-tomogram averaging, enabling efficient data processing and analysis.
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Affiliation(s)
- Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Matthew R Larson
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Bryan S Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Joseph Y Kim
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Daniel Parrell
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA
| | - Juan C Sanchez
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Biophysics Graduate Program, University of Wisconsin, Madison, WI, USA
| | - Victoria Pappas
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Biophysics Graduate Program, University of Wisconsin, Madison, WI, USA
| | - Anil Kumar
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Kai Cai
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Keith Thompson
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
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9
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Golyshev SA, Kazakov EP, Kireev II, Reunov DG, Malyshev IV. Soft X-ray Microscopy in Cell Biology: Current Status, Contributions and Prospects. Acta Naturae 2023; 15:32-43. [PMID: 38234603 PMCID: PMC10790358 DOI: 10.32607/actanaturae.26551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/27/2023] [Indexed: 01/19/2024] Open
Abstract
The recent advances achieved in microscopy technology have led to a significant breakthrough in biological research. Super-resolution fluorescent microscopy now allows us to visualize subcellular structures down to the pin-pointing of the single molecules in them, while modern electron microscopy has opened new possibilities in the study of protein complexes in their native, intracellular environment at near-atomic resolution. Nonetheless, both fluorescent and electron microscopy have remained beset by their principal shortcomings: the reliance on labeling procedures and severe sample volume limitations, respectively. Soft X-ray microscopy is a candidate method that can compensate for the shortcomings of both technologies by making possible observation of the entirety of the cellular interior without chemical fixation and labeling with an isotropic resolution of 40-70 nm. This will thus bridge the resolution gap between light and electron microscopy (although this gap is being narrowed, it still exists) and resolve the issue of compatibility with the former, and possibly in the near future, the latter methods. This review aims to assess the current state of soft X-ray microscopy and its impact on our understanding of the subcellular organization. It also attempts to look into the future of X-ray microscopy, particularly as relates to its seamless integration into the cell biology toolkit.
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Affiliation(s)
- S. A. Golyshev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russian Federation
| | - E. P. Kazakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russian Federation
| | - I. I. Kireev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russian Federation
| | - D. G. Reunov
- Institute of Physics of Microstructures RAS, Nizhny Novgorod, 603950 Russian Federation
| | - I. V. Malyshev
- Institute of Physics of Microstructures RAS, Nizhny Novgorod, 603950 Russian Federation
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10
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Uryu K, Soplop N, Sheahan TP, Catanese MT, Huynh C, Pena J, Boudreau N, Matei I, Kenific C, Hashimoto A, Hoshino A, Rice CM, Lyden D. Advancement in Cellular Topographic and Nanoparticle Capture Imaging by High Resolution Microscopy Incorporating a Freeze-Drying and Gaseous Nitrogen-based Approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.559906. [PMID: 37808646 PMCID: PMC10557753 DOI: 10.1101/2023.09.28.559906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Scanning electron microscopy (SEM) offers an unparalleled view of the membrane topography of mammalian cells by using a conventional osmium (OsO4) and ethanol-based tissue preparation. However, conventional SEM methods limit optimal resolution due to ethanol and lipid interactions and interfere with visualization of fluorescent reporter proteins. Therefore, SEM correlative light and electron microscopy (CLEM) has been hindered by the adverse effects of ethanol and OsO4 on retention of fluorescence signals. To overcome this technological gap in achieving high-resolution SEM and retain fluorescent reporter signals, we developed a freeze-drying method with gaseous nitrogen (FDGN). We demonstrate that FDGN preserves cyto-architecture to allow visualization of detailed membrane topography while retaining fluorescent signals and that FDGN processing can be used in conjunction with a variety of high-resolution imaging systems to enable collection and validation of unique, high-quality data from these approaches. In particular, we show that FDGN coupled with high resolution microscopy provided detailed insight into viral or tumor-derived extracellular vesicle (TEV)-host cell interactions and may aid in designing new approaches to intervene during viral infection or to harness TEVs as therapeutic agents.
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Affiliation(s)
- Kunihiro Uryu
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
- Janelia Rearch Campsu, Ashuburn, Virginia, 20147, USA
| | - Nadine Soplop
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Timothy P. Sheahan
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065 USA
| | - Maria-Teresa Catanese
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065 USA
| | - Chuong Huynh
- Ion Microscopy Innovation Center, Zeiss Microscopy LLC, Peabody, MA 01960, USA
| | - John Pena
- Sonder Research X, Cornell University, Ithaca, NY 14853, USA
| | - Nancy Boudreau
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065 USA
| | - Irina Matei
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065 USA
| | - Candia Kenific
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065 USA
| | - Ayako Hashimoto
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065 USA
| | - Ayuko Hoshino
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065 USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065 USA
| | - David Lyden
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065 USA
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11
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Yang J, Vrbovská V, Franke T, Sibert B, Larson M, Coomes T, Rigort A, Mitchels J, Wright ER. Precise 3D Localization by Integrated Fluorescence Microscopy (iFLM) for Cryo-FIB-milling and In-situ Cryo-ET. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1055-1057. [PMID: 37613109 DOI: 10.1093/micmic/ozad067.541] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Jae Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
| | | | | | - Bryan Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
| | - Matt Larson
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
| | - Tom Coomes
- Thermo Fisher Scientific, Hillsboro, OR, United States
| | | | | | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Morgridge Institute for Research, Madison, WI, United States
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12
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Yang J, Vrbovská V, Franke T, Sibert B, Larson M, Hall A, Rigort A, Mitchels J, Wright ER. Integrated Fluorescence Microscopy (iFLM) for Cryo-FIB-milling and In-situ Cryo-ET. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548578. [PMID: 37502891 PMCID: PMC10369943 DOI: 10.1101/2023.07.11.548578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Correlative cryo-FLM-FIB milling is a powerful sample preparation technique for in situ cryo-ET. However, correlative workflows that incorporate precise targeting remain challenging. Here, we demonstrate the development and use of an integrated Fluorescence Light Microscope (iFLM) module within a cryo-FIB-SEM to enable a coordinate-based two-point 3D correlative workflow. The iFLM guided targeting of regions of interest coupled with an automated milling process of the cryo-FIB-SEM instrument allows for the efficient preparation of 9-12 ∼200 nm thick lamellae within 24 hours. Using regular and montage-cryo-ET data collection schemes, we acquired data from FIB-milled lamellae of HeLa cells to examine cellular ultrastructure. Overall, this workflow facilitates on-the-fly targeting and automated FIB-milling of cryo-preserved cells, bacteria, and possibly high pressure frozen tissue, to produce lamellae for downstream cryo-ET data collection.
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Affiliation(s)
- Jae Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI USA
| | | | | | - Bryan Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI USA
| | - Matthew Larson
- Department of Biochemistry, University of Wisconsin, Madison, WI USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI USA
| | - Alex Hall
- Thermo Fisher Scientific Brno, Brno, Czech Republic
| | - Alex Rigort
- Thermo Fisher Scientific Brno, Brno, Czech Republic
| | | | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI USA
- Morgridge Institute for Research, Madison, WI, USA
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13
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Kim JY, Yang JE, Mitchell JW, English LA, Yang SZ, Tenpas T, Dent EW, Wildonger J, Wright ER. Handling difficult cryo-ET samples: A study with primary neurons from Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548468. [PMID: 37502991 PMCID: PMC10369871 DOI: 10.1101/2023.07.10.548468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
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Affiliation(s)
- Joseph Y. Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Josephine W. Mitchell
- Department of Chemistry and Biochemistry, Kalamazoo College, Kalamazoo, MI, 49006, USA
| | - Lauren A. English
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Sihui Z. Yang
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Tanner Tenpas
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Erik W. Dent
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Jill Wildonger
- Departments of Pediatrics and Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53715, USA
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14
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Li S, Jia X, Niu T, Zhang X, Qi C, Xu W, Deng H, Sun F, Ji G. HOPE-SIM, a cryo-structured illumination fluorescence microscopy system for accurately targeted cryo-electron tomography. Commun Biol 2023; 6:474. [PMID: 37120442 PMCID: PMC10148829 DOI: 10.1038/s42003-023-04850-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/18/2023] [Indexed: 05/01/2023] Open
Abstract
Cryo-focused ion beam (cryo-FIB) milling technology has been developed for the fabrication of cryo-lamella of frozen native specimens for study by in situ cryo-electron tomography (cryo-ET). However, the precision of the target of interest is still one of the major bottlenecks limiting application. Here, we have developed a cryo-correlative light and electron microscopy (cryo-CLEM) system named HOPE-SIM by incorporating a 3D structured illumination fluorescence microscopy (SIM) system and an upgraded high-vacuum stage to achieve efficiently targeted cryo-FIB. With the 3D super resolution of cryo-SIM as well as our cryo-CLEM software, 3D-View, the correlation precision of targeting region of interest can reach to 110 nm enough for the subsequent cryo-lamella fabrication. We have successfully utilized the HOPE-SIM system to prepare cryo-lamellae targeting mitochondria, centrosomes of HeLa cells and herpesvirus assembly compartment of infected BHK-21 cells, which suggests the high potency of the HOPE-SIM system for future in situ cryo-ET workflows.
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Affiliation(s)
- Shuoguo Li
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xing Jia
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Tongxin Niu
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiaoyun Zhang
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Chen Qi
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Wei Xu
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Hongyu Deng
- University of Chinese Academy of Sciences, 100049, Beijing, China
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Fei Sun
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Gang Ji
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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15
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Li S, Wang Z, Jia X, Niu T, Zhang J, Yin G, Zhang X, Zhu Y, Ji G, Sun F. ELI trifocal microscope: a precise system to prepare target cryo-lamellae for in situ cryo-ET study. Nat Methods 2023; 20:276-283. [PMID: 36646897 PMCID: PMC9911351 DOI: 10.1038/s41592-022-01748-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/06/2022] [Indexed: 01/18/2023]
Abstract
Cryo-electron tomography (cryo-ET) has become a powerful approach to study the high-resolution structure of cellular macromolecular machines in situ. However, the current correlative cryo-fluorescence and electron microscopy lacks sufficient accuracy and efficiency to precisely prepare cryo-lamellae of target locations for subsequent cryo-ET. Here we describe a precise cryogenic fabrication system, ELI-TriScope, which sets electron (E), light (L) and ion (I) beams at the same focal point to achieve accurate and efficient preparation of a target cryo-lamella. ELI-TriScope uses a commercial dual-beam scanning electron microscope modified to incorporate a cryo-holder-based transfer system and embed an optical imaging system just underneath the vitrified specimen. Cryo-focused ion beam milling can be accurately navigated by monitoring the real-time fluorescence signal of the target molecule. Using ELI-TriScope, we prepared a batch of cryo-lamellae of HeLa cells targeting the centrosome with a success rate of ~91% and discovered new in situ structural features of the human centrosome by cryo-ET.
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Affiliation(s)
- Shuoguo Li
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziyan Wang
- University of Chinese Academy of Sciences, Beijing, China
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xing Jia
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tongxin Niu
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianguo Zhang
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guoliang Yin
- University of Chinese Academy of Sciences, Beijing, China
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyun Zhang
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yun Zhu
- University of Chinese Academy of Sciences, Beijing, China.
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Gang Ji
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Fei Sun
- Center for Biological Imaging, Core Facilities for Protein Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
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16
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Vijayakrishnan S. In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview. Subcell Biochem 2023; 106:3-36. [PMID: 38159222 DOI: 10.1007/978-3-031-40086-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Cryo-electron tomography (cryo-ET) has emerged as a powerful tool in structural biology to study viruses and is undergoing a resolution revolution. Enveloped viruses comprise several RNA and DNA pleomorphic viruses that are pathogens of clinical importance to humans and animals. Considerable efforts in cryogenic correlative light and electron microscopy (cryo-CLEM), cryogenic focused ion beam milling (cryo-FIB), and integrative structural techniques are helping to identify virus structures within cells leading to a rise of in situ discoveries shedding light on how viruses interact with their hosts during different stages of infection. This chapter reviews recent advances in the application of cryo-ET in imaging enveloped viruses and the structural and mechanistic insights revealed studying the viral infection cycle within their eukaryotic cellular hosts, with particular attention to viral entry, replication, assembly, and egress during infection.
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Affiliation(s)
- Swetha Vijayakrishnan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Glasgow, Scotland, UK.
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17
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Tikhonova TN, Kolmogorov VS, Timoshenko RV, Vaneev AN, Cohen-Gerassi D, Osminkina LA, Gorelkin PV, Erofeev AS, Sysoev NN, Adler-Abramovich L, Shirshin EA. Sensing Cells-Peptide Hydrogel Interaction In Situ via Scanning Ion Conductance Microscopy. Cells 2022; 11:cells11244137. [PMID: 36552900 PMCID: PMC9776472 DOI: 10.3390/cells11244137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Peptide-based hydrogels were shown to serve as good matrices for 3D cell culture and to be applied in the field of regenerative medicine. The study of the cell-matrix interaction is important for the understanding of cell attachment, proliferation, and migration, as well as for the improvement of the matrix. Here, we used scanning ion conductance microscopy (SICM) to study the growth of cells on self-assembled peptide-based hydrogels. The hydrogel surface topography, which changes during its formation in an aqueous solution, were studied at nanoscale resolution and compared with fluorescence lifetime imaging microscopy (FLIM). Moreover, SICM demonstrated the ability to map living cells inside the hydrogel. A zwitterionic label-free pH nanoprobe with a sensitivity > 0.01 units was applied for the investigation of pH mapping in the hydrogel to estimate the hydrogel applicability for cell growth. The SICM technique that was applied here to evaluate the cell growth on the peptide-based hydrogel can be used as a tool to study functional living cells.
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Affiliation(s)
- Tatiana N. Tikhonova
- Department of Physics, M.V. Lomonosov Moscow State University, Leninskie Gory 1/2, 119991 Moscow, Russia
| | - Vasilii S. Kolmogorov
- Laboratory of Biophysics, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Roman V. Timoshenko
- Laboratory of Biophysics, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Alexander N. Vaneev
- Laboratory of Biophysics, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Dana Cohen-Gerassi
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, The Center for Nanoscience and Nanotechnology, The Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 69978, Israel
| | - Liubov A. Osminkina
- Department of Physics, M.V. Lomonosov Moscow State University, Leninskie Gory 1/2, 119991 Moscow, Russia
| | - Petr V. Gorelkin
- Laboratory of Biophysics, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Alexander S. Erofeev
- Laboratory of Biophysics, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Nikolay N. Sysoev
- Department of Physics, M.V. Lomonosov Moscow State University, Leninskie Gory 1/2, 119991 Moscow, Russia
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, The Center for Nanoscience and Nanotechnology, The Center for the Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 69978, Israel
| | - Evgeny A. Shirshin
- Department of Physics, M.V. Lomonosov Moscow State University, Leninskie Gory 1/2, 119991 Moscow, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 8-2 Trubetskaya St., 119991 Moscow, Russia
- Correspondence: ; Tel.: +7-4959391104
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18
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Lowery AW, Ambi A, Miller LM, Boreyko JB. Reducing Frost during Cryoimaging Using a Hygroscopic Ice Frame. ACS OMEGA 2022; 7:43421-43431. [PMID: 36506191 PMCID: PMC9730467 DOI: 10.1021/acsomega.2c03083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/13/2022] [Indexed: 06/17/2023]
Abstract
Cryomicroscopy is commonly hampered by frost accumulation, reducing the visual clarity of the specimen. Pulling a vacuum or purging with nitrogen gas can greatly reduce the sample chamber's humidity, but at cryogenic temperatures, even minute concentrations of water vapor can still result in frost deposition. Here, a hygroscopic ice frame was created around the specimen to suppress frost growth during cryomicroscopy. Specifically, fluorescently tagged rat brain vessels were frozen on a silicon nitride window with an ice frame, and the luminescence of the fluorescent tag was improved by a factor of 6 compared to a similar specimen in only a nitrogen purge environment. These findings suggest that the simple implementation of a hygroscopic ice frame surrounding the specimen can substantially improve the visual clarity for cryomicroscopy, beyond that of a vacuum or nitrogen purge system.
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Affiliation(s)
- Adam W. Lowery
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
- National
Synchrotron Light Source II, Brookhaven
National Laboratory, Upton, New York 11973, United States
| | - Ashwin Ambi
- National
Synchrotron Light Source II, Brookhaven
National Laboratory, Upton, New York 11973, United States
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Lisa M. Miller
- National
Synchrotron Light Source II, Brookhaven
National Laboratory, Upton, New York 11973, United States
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Jonathan B. Boreyko
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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19
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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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20
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Dahlberg PD, Perez D, Hecksel CW, Chiu W, Moerner WE. Metallic support films reduce optical heating in cryogenic correlative light and electron tomography. J Struct Biol 2022; 214:107901. [PMID: 36191745 PMCID: PMC9729463 DOI: 10.1016/j.jsb.2022.107901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/28/2022] [Accepted: 09/26/2022] [Indexed: 12/30/2022]
Abstract
Super-resolved cryogenic correlative light and electron tomography is an emerging method that provides both the single-molecule sensitivity and specificity of fluorescence imaging, and the molecular scale resolution and detailed cellular context of tomography, all in vitrified cells preserved in their native hydrated state. Technical hurdles that limit these correlative experiments need to be overcome for the full potential of this approach to be realized. Chief among these is sample heating due to optical excitation which leads to devitrification, a phase transition from amorphous to crystalline ice. Here we show that much of this heating is due to the material properties of the support film of the electron microscopy grid, specifically the absorptivity and thermal conductivity. We demonstrate through experiment and simulation that the properties of the standard holey carbon electron microscopy grid lead to substantial heating under optical excitation. In order to avoid devitrification, optical excitation intensities must be kept orders of magnitude lower than the intensities commonly employed in room temperature super-resolution experiments. We further show that the use of metallic films, either holey gold grids, or custom made holey silver grids, alleviate much of this heating. For example, the holey silver grids permit 20× the optical intensities used on the standard holey carbon grids. Super-resolution correlative experiments conducted on holey silver grids under these increased optical excitation intensities have a corresponding increase in the rate of single-molecule fluorescence localizations. This results in an increased density of localizations and improved correlative imaging without deleterious effects from sample heating.
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Affiliation(s)
- Peter D Dahlberg
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Davis Perez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Corey W Hecksel
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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21
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Gaietta G, Kai F, Swift MF, Weaver VM, Volkmann N, Hanein D. Novel cryo-tomography workflow reveals nanometer-scale responses of epithelial cells to matrix stiffness and dimensionality. Mol Biol Cell 2022; 33:br28. [PMID: 36287913 PMCID: PMC9727794 DOI: 10.1091/mbc.e22-03-0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Matrix stiffness and dimensionality have been shown to be major determinants of cell behavior. However, a workflow for examining nanometer-scale responses of the associated molecular machinery is not available. Here, we describe a comprehensive, quantitative workflow that permits the analysis of cells responding to mechanical and dimensionality cues in their native state at nanometer scale by cryogenic electron tomography. Using this approach, we quantified distinct cytoskeletal nanoarchitectures and vesicle phenotypes induced in human mammary epithelial cells in response to stiffness and dimensionality of reconstituted basement membrane. Our workflow closely recapitulates the microenvironment associated with acinar morphogenesis and identified distinct differences in situ at nanometer scale. Using drug treatment, we showed that molecular events and nanometer-scale rearrangements triggered by engagement of apical cell receptors with reconstituted basement membrane correspond to changes induced by reduction of cortical tension. Our approach is fully adaptable to any kind of stiffness regime, extracellular matrix composition, and drug treatment.
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Affiliation(s)
- Guido Gaietta
- Scintillon Institute, San Diego, CA 92121,*Address correspondence to: Dorit Hanein (); Guido Gaietta (); Niels Volkmann ()
| | - Fuiboon Kai
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, CA 94143
| | | | - Valerie M. Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, CA 94143
| | - Niels Volkmann
- Scintillon Institute, San Diego, CA 92121,Structural Image Analysis Unit, Université de Paris Cité, F-75015 Paris, France,*Address correspondence to: Dorit Hanein (); Guido Gaietta (); Niels Volkmann ()
| | - Dorit Hanein
- Scintillon Institute, San Diego, CA 92121,Structural Studies of Macromolecular Machines in Cellulo Unit, Institut Pasteur, CNRS UMR3528, Université de Paris Cité, F-75015 Paris, France,*Address correspondence to: Dorit Hanein (); Guido Gaietta (); Niels Volkmann ()
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22
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Abstract
Single-pass transmembrane receptors (SPTMRs) represent a diverse group of integral membrane proteins that are involved in many essential cellular processes, including signal transduction, cell adhesion, and transmembrane transport of materials. Dysregulation of the SPTMRs is linked with many human diseases. Despite extensive efforts in past decades, the mechanisms of action of the SPTMRs remain incompletely understood. One major hurdle is the lack of structures of the full-length SPTMRs in different functional states. Such structural information is difficult to obtain by traditional structural biology methods such as X-ray crystallography and nuclear magnetic resonance (NMR). The recent rapid development of single-particle cryo-electron microscopy (cryo-EM) has led to an exponential surge in the number of high-resolution structures of integral membrane proteins, including SPTMRs. Cryo-EM structures of SPTMRs solved in the past few years have tremendously improved our understanding of how SPTMRs function. In this review, we will highlight these progresses in the structural studies of SPTMRs by single-particle cryo-EM, analyze important structural details of each protein involved, and discuss their implications on the underlying mechanisms. Finally, we also briefly discuss remaining challenges and exciting opportunities in the field.
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Affiliation(s)
- Kai Cai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
| | - Xuewu Zhang
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xuewu Zhang, Department of pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Xiao-chen Bai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xiao-chen Bai, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA;
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23
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Sibert BS, Kim JY, Yang JE, Wright ER. Micropatterning Transmission Electron Microscopy Grids to Direct Cell Positioning within Whole-Cell Cryo-Electron Tomography Workflows. J Vis Exp 2021. [PMID: 34570100 PMCID: PMC8601404 DOI: 10.3791/62992] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Whole-cell cryo-electron tomography (cryo-ET) is a powerful technology that is used to produce nanometer-level resolution structures of macromolecules present in the cellular context and preserved in a near-native frozen-hydrated state. However, there are challenges associated with culturing and/or adhering cells onto TEM grids in a manner that is suitable for tomography while retaining the cells in their physiological state. Here, a detailed step-by-step protocol is presented on the use of micropatterning to direct and promote eukaryotic cell growth on TEM grids. During micropatterning, cell growth is directed by depositing extra-cellular matrix (ECM) proteins within specified patterns and positions on the foil of the TEM grid while the other areas remain coated with an anti-fouling layer. Flexibility in the choice of surface coating and pattern design makes micropatterning broadly applicable for a wide range of cell types. Micropatterning is useful for studies of structures within individual cells as well as more complex experimental systems such as host-pathogen interactions or differentiated multi-cellular communities. Micropatterning may also be integrated into many downstream whole-cell cryo-ET workflows, including correlative light and electron microscopy (cryo-CLEM) and focused-ion beam milling (cryo-FIB).
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Affiliation(s)
- Bryan S Sibert
- Department of Biochemistry, University of Wisconsin, Madison; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison
| | - Joseph Y Kim
- Department of Biochemistry, University of Wisconsin, Madison; Department of Chemistry, University of Wisconsin, Madison
| | - Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison; Morgridge Institute for Research;
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24
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Jiang J, Cheong KY, Falkowski PG, Dai W. Integrating on-grid immunogold labeling and cryo-electron tomography to reveal photosystem II structure and spatial distribution in thylakoid membranes. J Struct Biol 2021; 213:107746. [PMID: 34010667 PMCID: PMC8577061 DOI: 10.1016/j.jsb.2021.107746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 11/17/2022]
Abstract
A long-standing challenge in cell biology is elucidating the structure and spatial distribution of individual membrane-bound proteins, protein complexes and their interactions in their native environment. Here, we describe a workflow that combines on-grid immunogold labeling, followed by cryo-electron tomography (cryoET) imaging and structural analyses to identify and characterize the structure of photosystem II (PSII) complexes. Using an antibody specific to a core subunit of PSII, the D1 protein (uniquely found in the water splitting complex in all oxygenic photoautotrophs), we identified PSII complexes in biophysically active thylakoid membranes isolated from a model marine diatom Phaeodactylum tricornutum. Subsequent cryoET analyses of these protein complexes resolved two PSII structures: supercomplexes and dimeric cores. Our integrative approach establishes the structural signature of multimeric membrane protein complexes in their native environment and provides a pathway to elucidate their high-resolution structures.
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Affiliation(s)
- Jennifer Jiang
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States
| | - Kuan Yu Cheong
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, United States; Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, United States
| | - Paul G Falkowski
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States; Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, United States; Department of Earth and Planetary Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States
| | - Wei Dai
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States.
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25
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Hurley ME, Sheard TMD, Norman R, Kirton HM, Shah SS, Pervolaraki E, Yang Z, Gamper N, White E, Steele D, Jayasinghe I. A correlative super-resolution protocol to visualise structural underpinnings of fast second-messenger signalling in primary cell types. Methods 2021; 193:27-37. [PMID: 33059034 DOI: 10.1016/j.ymeth.2020.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/28/2020] [Accepted: 10/07/2020] [Indexed: 10/24/2022] Open
Abstract
Nanometre-scale cellular information obtained through super-resolution microscopies are often unaccompanied by functional information, particularly transient and diffusible signals through which life is orchestrated in the nano-micrometre spatial scale. We describe a correlative imaging protocol which allows the ubiquitous intracellular second messenger, calcium (Ca2+), to be directly visualised against nanoscale patterns of the ryanodine receptor (RyR) Ca2+ channels which give rise to these Ca2+ signals in wildtype primary cells. This was achieved by combining total internal reflection fluorescence (TIRF) imaging of the elementary Ca2+ signals, with the subsequent DNA-PAINT imaging of the RyRs. We report a straightforward image analysis protocol of feature extraction and image alignment between correlative datasets and demonstrate how such data can be used to visually identify the ensembles of Ca2+ channels that are locally activated during the genesis of cytoplasmic Ca2+ signals.
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Affiliation(s)
- Miriam E Hurley
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Thomas M D Sheard
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Ruth Norman
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Hannah M Kirton
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Shihab S Shah
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Eleftheria Pervolaraki
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Zhaokang Yang
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Nikita Gamper
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Ed White
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Derek Steele
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Izzy Jayasinghe
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Department of Molecular Biology and Biotechnology, Faculty of Science, The University of Sheffield, S10 2TN, UK.
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26
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Bäuerlein FJB, Baumeister W. Towards Visual Proteomics at High Resolution. J Mol Biol 2021; 433:167187. [PMID: 34384780 DOI: 10.1016/j.jmb.2021.167187] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/02/2021] [Accepted: 08/02/2021] [Indexed: 11/24/2022]
Abstract
Traditionally, structural biologists approach the complexity of cellular proteomes in a reductionist manner. Proteomes are fractionated, their molecular components purified and studied one-by-one using the experimental methods for structure determination at their disposal. Visual proteomics aims at obtaining a holistic picture of cellular proteomes by studying them in situ, ideally in unperturbed cellular environments. The method that enables doing this at highest resolution is cryo-electron tomography. It allows to visualize cellular landscapes with molecular resolution generating maps or atlases revealing the interaction networks which underlie cellular functions in health and in disease states. Current implementations of cryo ET do not yet realize the full potential of the method in terms of resolution and interpretability. To this end, further improvements in technology and methodology are needed. This review describes the state of the art as well as measures which we expect will help overcoming current limitations.
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Affiliation(s)
- Felix J B Bäuerlein
- Max-Planck-Institute of Biochemistry, Department for Molecular Structural Biology, Am Klopferspitz 18, 82152 Planegg, Germany; Georg-August-University, Institute for Neuropathology, Robert-Koch-Strasse 40, 37075 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany.
| | - Wolfgang Baumeister
- Max-Planck-Institute of Biochemistry, Department for Molecular Structural Biology, Am Klopferspitz 18, 82152 Planegg, Germany.
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27
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Skaar EP. Imaging Infection Across Scales of Size: From Whole Animals to Single Molecules. Annu Rev Microbiol 2021; 75:407-426. [PMID: 34343016 DOI: 10.1146/annurev-micro-041521-121457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Infectious diseases are a leading cause of global morbidity and mortality, and the threat of infectious diseases to human health is steadily increasing as new diseases emerge, existing diseases reemerge, and antimicrobial resistance expands. The application of imaging technology to the study of infection biology has the potential to uncover new factors that are critical to the outcome of host-pathogen interactions and to lead to innovations in diagnosis and treatment of infectious diseases. This article reviews current and future opportunities for the application of imaging to the study of infectious diseases, with a particular focus on the power of imaging objects across a broad range of sizes to expand the utility of these approaches. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Eric P Skaar
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA;
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28
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An overview of the recent advances in cryo-electron microscopy for life sciences. Emerg Top Life Sci 2021; 5:151-168. [PMID: 33760078 DOI: 10.1042/etls20200295] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 01/18/2023]
Abstract
Cryo-electron microscopy (CryoEM) has superseded X-ray crystallography and NMR to emerge as a popular and effective tool for structure determination in recent times. It has become indispensable for the characterization of large macromolecular assemblies, membrane proteins, or samples that are limited, conformationally heterogeneous, and recalcitrant to crystallization. Besides, it is the only tool capable of elucidating high-resolution structures of macromolecules and biological assemblies in situ. A state-of-the-art electron microscope operable at cryo-temperature helps preserve high-resolution details of the biological sample. The structures can be determined, either in isolation via single-particle analysis (SPA) or helical reconstruction, electron diffraction (ED) or within the cellular environment via cryo-electron tomography (cryoET). All the three streams of SPA, ED, and cryoET (along with subtomogram averaging) have undergone significant advancements in recent times. This has resulted in breaking the boundaries with respect to both the size of the macromolecules/assemblies whose structures could be determined along with the visualization of atomic details at resolutions unprecedented for cryoEM. In addition, the collection of larger datasets combined with the ability to sort and process multiple conformational states from the same sample are providing the much-needed link between the protein structures and their functions. In overview, these developments are helping scientists decipher the molecular mechanism of critical cellular processes, solve structures of macromolecules that were challenging targets for structure determination until now, propelling forward the fields of biology and biomedicine. Here, we summarize recent advances and key contributions of the three cryo-electron microscopy streams of SPA, ED, and cryoET.
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29
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Okolo CA, Kounatidis I, Groen J, Nahas KL, Balint S, Fish TM, Koronfel MA, Cortajarena AL, Dobbie IM, Pereiro E, Harkiolaki M. Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures. Nat Protoc 2021; 16:2851-2885. [PMID: 33990802 DOI: 10.1038/s41596-021-00522-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
3D correlative microscopy methods have revolutionized biomedical research, allowing the acquisition of multidimensional information to gain an in-depth understanding of biological systems. With the advent of relevant cryo-preservation methods, correlative imaging of cryogenically preserved samples has led to nanometer resolution imaging (2-50 nm) under harsh imaging regimes such as electron and soft X-ray tomography. These methods have now been combined with conventional and super-resolution fluorescence imaging at cryogenic temperatures to augment information content from a given sample, resulting in the immediate requirement for protocols that facilitate hassle-free, unambiguous cross-correlation between microscopes. We present here sample preparation strategies and a direct comparison of different working fiducialization regimes that facilitate 3D correlation of cryo-structured illumination microscopy and cryo-soft X-ray tomography. Our protocol has been tested at two synchrotron beamlines (B24 at Diamond Light Source in the UK and BL09 Mistral at ALBA in Spain) and has led to the development of a decision aid that facilitates experimental design with the strategic use of markers based on project requirements. This protocol takes between 1.5 h and 3.5 d to complete, depending on the cell populations used (adherent cells may require several days to grow on sample carriers).
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Affiliation(s)
- Chidinma A Okolo
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Ilias Kounatidis
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | | | - Kamal L Nahas
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.,Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Stefan Balint
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Thomas M Fish
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Mohamed A Koronfel
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Ian M Dobbie
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Eva Pereiro
- Beamline 09-MISTRAL, ALBA Synchrotron, Barcelona, Spain
| | - Maria Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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30
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Banerjee A, Bhakta S, Sengupta J. Integrative approaches in cryogenic electron microscopy: Recent advances in structural biology and future perspectives. iScience 2021; 24:102044. [PMID: 33532719 PMCID: PMC7829201 DOI: 10.1016/j.isci.2021.102044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cellular factories engage numerous highly complex "molecular machines" to perform pivotal biological functions. 3D structural visualization is an effective way to understand the functional mechanisms of these biomacromolecules. The "resolution revolution" has established cryogenic electron microscopy (cryo-EM) as a preferred structural biology tool. In parallel with the advances in cryo-EM methodologies aiming at atomic resolution, several innovative approaches have started emerging where other techniques are sensibly integrated with cryo-EM to obtain additional insights into the biological processes. For example, combining the time-resolved technique with high-resolution cryo-EM enables discerning structures of short-lived intermediates in the functional pathway of a biomolecule. Likewise, integrating mass spectrometry (MS) techniques with cryo-EM allows deciphering structural organizations of large molecular assemblies. Here, we discuss how the data generated upon combining either time resolve or MS techniques with cryo-EM supplement structural elucidations with in-depth understanding of the function of cellular macromolecules when they participate in fundamental biological processes.
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Affiliation(s)
- Aneek Banerjee
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sayan Bhakta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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31
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Yang JE, Larson MR, Sibert BS, Shrum S, Wright ER. CorRelator: Interactive software for real-time high precision cryo-correlative light and electron microscopy. J Struct Biol 2021; 213:107709. [PMID: 33610654 PMCID: PMC8601405 DOI: 10.1016/j.jsb.2021.107709] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/06/2021] [Accepted: 02/11/2021] [Indexed: 12/31/2022]
Abstract
Cryo-correlative light and electron microscopy (CLEM) is a technique that uses the spatiotemporal cues from fluorescence light microscopy (FLM) to investigate the high-resolution ultrastructure of biological samples by cryo-electron microscopy (cryo-EM). Cryo-CLEM provides advantages for identifying and distinguishing fluorescently labeled proteins, macromolecular complexes, and organelles from the cellular environment. Challenges remain on how correlation workflows and software tools are implemented on different microscope platforms to support automated cryo-EM data acquisition. Here, we present CorRelator: an open-source desktop application that bridges between cryo-FLM and real-time cryo-EM/ET automated data collection. CorRelator implements a pixel-coordinate-to-stage-position transformation for flexible, high accuracy on-the-fly and post-acquisition correlation. CorRelator can be integrated into cryo-CLEM workflows and easily adapted to standard fluorescence and transmission electron microscope (TEM) system configurations. CorRelator was benchmarked under live-cell and cryogenic conditions using several FLM and TEM instruments, demonstrating that CorRelator reliably supports real-time, automated correlative cryo-EM/ET acquisition, through a combination of software-aided and interactive alignment. CorRelator is a cross-platform software package featuring an intuitive Graphical User Interface (GUI) that guides the user through the correlation process. CorRelator source code is available at: https://github.com/wright-cemrc-projects/corr.
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Affiliation(s)
- Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Matthew R Larson
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Bryan S Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Samantha Shrum
- Biophysics Graduate Program, University of Wisconsin, Madison, WI 53706, United States
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Biophysics Graduate Program, University of Wisconsin, Madison, WI 53706, United States; Morgridge Institute for Research, Madison, WI, 53715, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States.
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32
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Heiligenstein X, de Beer M, Heiligenstein J, Eyraud F, Manet L, Schmitt F, Lamers E, Lindenau J, Kea-Te Lindert M, Salamero J, Raposo G, Sommerdijk N, Belle M, Akiva A. HPM live μ for a full CLEM workflow. Methods Cell Biol 2021; 162:115-149. [PMID: 33707009 DOI: 10.1016/bs.mcb.2020.10.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
With the development of advanced imaging methods that took place in the last decade, the spatial correlation of microscopic and spectroscopic information-known as multimodal imaging or correlative microscopy (CM)-has become a broadly applied technique to explore biological and biomedical materials at different length scales. Among the many different combinations of techniques, Correlative Light and Electron Microscopy (CLEM) has become the flagship of this revolution. Where light (mainly fluorescence) microscopy can be used directly for the live imaging of cells and tissues, for almost all applications, electron microscopy (EM) requires fixation of the biological materials. Although sample preparation for EM is traditionally done by chemical fixation and embedding in a resin, rapid cryogenic fixation (vitrification) has become a popular way to avoid the formation of artifacts related to the chemical fixation/embedding procedures. During vitrification, the water in the sample transforms into an amorphous ice, keeping the ultrastructure of the biological sample as close as possible to the native state. One immediate benefit of this cryo-arrest is the preservation of protein fluorescence, allowing multi-step multi-modal imaging techniques for CLEM. To minimize the delay separating live imaging from cryo-arrest, we developed a high-pressure freezing (HPF) system directly coupled to a light microscope. We address the optimization of sample preservation and the time needed to capture a biological event, going from live imaging to cryo-arrest using HPF. To further explore the potential of cryo-fixation related to the forthcoming transition from imaging 2D (cell monolayers) to imaging 3D samples (tissue) and the associated importance of homogeneous deep vitrification, the HPF core technology has been revisited to allow easy modification of the environmental parameters during vitrification. Lastly, we will discuss the potential of our HPM within CLEM protocols especially for correlating live imaging using the Zeiss LSM900 with electron microscopy.
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Affiliation(s)
| | - Marit de Beer
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Cell Biology, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Biochemistry, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | | | | | | | | | - Mariska Kea-Te Lindert
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Cell Biology, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jean Salamero
- SERPICO Inria Team/UMR 144 CNRS & National Biology and Health Infrastructure "France Bioimaging", Institut Curie, Paris, France
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France; Institut Curie, PSL Research University, CNRS, UMR144, Structure and Membrane Compartments, Paris, France
| | - Nico Sommerdijk
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Biochemistry, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Anat Akiva
- Electron Microscopy Center, Radboudumc Technology Center Microscopy, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Cell Biology, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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33
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Jiménez-Ortigosa C, Jiang J, Chen M, Kuang X, Healey KR, Castellano P, Boparai N, Ludtke SJ, Perlin DS, Dai W. Cryo-Electron Tomography of Candida glabrata Plasma Membrane Proteins. J Fungi (Basel) 2021; 7:120. [PMID: 33562124 PMCID: PMC7914498 DOI: 10.3390/jof7020120] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/18/2022] Open
Abstract
Fungal plasma membrane proteins have long been recognized as targets for the development of antifungal agents. Despite recent progress in experimental approaches and computational structural predictions, our knowledge of the structural dynamics and spatial distribution of these membrane proteins in the context of their native lipid environment remains limited. By applying cryo-electron tomography (cryoET) and subtomogram analysis, we aim to characterize the structural characteristics and spatial distribution of membrane proteins present in Candida glabrata plasma membranes. This study has resulted in the identification of the membrane-embedded structure of the fungal H+-ATPase, Pma1. Tomograms of the plasma membrane revealed that Pma1 complexes are heterogeneously distributed as hexamers that cluster into distinct membrane microdomains. This study characterizes fungal membrane proteins in the native cellular landscape and highlights the unique potential of cryoET to advance our understanding of cellular biology and biological systems.
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Affiliation(s)
- Cristina Jiménez-Ortigosa
- Hackensack Meridian Health-Center for Discovery and Innovation, 111 Ideation Way, Nutley, NJ 07110, USA;
| | - Jennifer Jiang
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA; (J.J.); (X.K.); (P.C.); (N.B.)
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Muyuan Chen
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; (M.C.); (S.J.L.)
| | - Xuyuan Kuang
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA; (J.J.); (X.K.); (P.C.); (N.B.)
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
- Department of Hyperbaric Oxygen, Central South University, Changsha 410008, China
| | - Kelley R. Healey
- Department of Biology, William Paterson University, 300 Pompton Road, Wayne, NJ 07470, USA;
| | - Paul Castellano
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA; (J.J.); (X.K.); (P.C.); (N.B.)
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Nikpreet Boparai
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA; (J.J.); (X.K.); (P.C.); (N.B.)
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Steven J. Ludtke
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; (M.C.); (S.J.L.)
| | - David S. Perlin
- Hackensack Meridian Health-Center for Discovery and Innovation, 111 Ideation Way, Nutley, NJ 07110, USA;
| | - Wei Dai
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA; (J.J.); (X.K.); (P.C.); (N.B.)
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
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Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies. Commun Biol 2021; 4:137. [PMID: 33514845 PMCID: PMC7846596 DOI: 10.1038/s42003-020-01567-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/04/2020] [Indexed: 11/12/2022] Open
Abstract
Lamellar bodies (LBs) are surfactant-rich organelles in alveolar cells. LBs disassemble into a lipid-protein network that reduces surface tension and facilitates gas exchange in the alveolar cavity. Current knowledge of LB architecture is predominantly based on electron microscopy studies using disruptive sample preparation methods. We established and validated a post-correlation on-lamella cryo-correlative light and electron microscopy approach for cryo-FIB milled cells to structurally characterize and validate the identity of LBs in their unperturbed state. Using deconvolution and 3D image registration, we were able to identify fluorescently labeled membrane structures analyzed by cryo-electron tomography. In situ cryo-electron tomography of A549 cells as well as primary Human Small Airway Epithelial Cells revealed that LBs are composed of membrane sheets frequently attached to the limiting membrane through “T”-junctions. We report a so far undescribed outer membrane dome protein complex (OMDP) on the limiting membrane of LBs. Our data suggest that LB biogenesis is driven by parallel membrane sheet import and by the curvature of the limiting membrane to maximize lipid storage capacity. Using the post-correlation on-lamella cryo-CLEM workflow, Klein, Wimmer et al. show that lamellar bodies (LBs) are composed of membrane sheets frequently attached to the limiting membrane through T-junctions in ABCA3 overexpressing cells and in primary human small airway epithelial cells. This study provides insights into LB biogenesis and membrane packing inside the LB.
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Abstract
Cryo-electron tomography (cryo-ET) is an extremely powerful tool which is used to image cellular features in their close-to-native environment at a resolution where both protein structure and membrane morphology can be revealed. Compared to conventional electron microscopy methods for biology, cryo-ET does not include the use of potentially artifact generating agents for sample fixation or visualization. Despite its obvious advantages, cryo-ET has not been widely adopted by cell biologists. This might originate from the overwhelming and constantly growing number of complex ways to record and process data as well as the numerous methods available for sample preparation. In this chapter, we will take one step back and guide the reader through the essential steps of sample preparation using mammalian cells, as well as the basic steps involved in data recording and processing. The described protocol will allow the reader to obtain data that can be used for morphological analysis and precise measurements of biological structures in their cellular environment. Furthermore, this data can be used for more elaborate structural analysis by applying further image processing steps like subtomogram averaging, which is required to determine the structure of proteins.
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Wu GH, Mitchell PG, Galaz-Montoya JG, Hecksel CW, Sontag EM, Gangadharan V, Marshman J, Mankus D, Bisher ME, Lytton-Jean AKR, Frydman J, Czymmek K, Chiu W. Multi-scale 3D Cryo-Correlative Microscopy for Vitrified Cells. Structure 2020; 28:1231-1237.e3. [PMID: 32814034 PMCID: PMC7642057 DOI: 10.1016/j.str.2020.07.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/10/2020] [Accepted: 07/29/2020] [Indexed: 10/23/2022]
Abstract
Three-dimensional (3D) visualization of vitrified cells can uncover structures of subcellular complexes without chemical fixation or staining. Here, we present a pipeline integrating three imaging modalities to visualize the same specimen at cryogenic temperature at different scales: cryo-fluorescence confocal microscopy, volume cryo-focused ion beam scanning electron microscopy, and transmission cryo-electron tomography. Our proof-of-concept benchmark revealed the 3D distribution of organelles and subcellular structures in whole heat-shocked yeast cells, including the ultrastructure of protein inclusions that recruit fluorescently-labeled chaperone Hsp104. Since our workflow efficiently integrates imaging at three different scales and can be applied to other types of cells, it could be used for large-scale phenotypic studies of frozen-hydrated specimens in a variety of healthy and diseased conditions with and without treatments.
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Affiliation(s)
- Gong-Her Wu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Patrick G Mitchell
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jesus G Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Corey W Hecksel
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Emily M Sontag
- Department of Biology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | | | - Jeffrey Marshman
- Zeiss Research Microscopy Solutions, White Plains, NY 10601, USA
| | - David Mankus
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Margaret E Bisher
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Abigail K R Lytton-Jean
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Judith Frydman
- Department of Biology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Kirk Czymmek
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Wah Chiu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA; Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
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Zhang M, Guan Y, Dang Z, Zhang P, Zheng Z, Chen L, Kuang W, Wang C, Liang G. Directly observing intracellular nanoparticle formation with nanocomputed tomography. SCIENCE ADVANCES 2020; 6:6/43/eaba3190. [PMID: 33097531 PMCID: PMC7608822 DOI: 10.1126/sciadv.aba3190] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 09/01/2020] [Indexed: 05/10/2023]
Abstract
Directly observing intracellular nanostructure formation remains challenging. In this work, using a rationally designed small-molecule 4-nitrobenzyl carbamate-Cys(SEt)-Asp-Asp-Phe(iodine)-2-cyano-benzothiazole (NBC-Iod-CBT), we directly observed intracellular nanoparticle formation with nanocomputed tomography (nano-CT). In vitro, upon glutathione reduction and nitroreductase (NTR) cleavage, NBC-Iod-CBT undergoes a CBT-Cys click condensation reaction to self-assemble nanoparticles Iod-CBT-NPs with an average linear absorption coefficient (LAC) value of 0.182 ± 0.078 μm-1 to x-ray. Nano-CT imaging of the NBC-Iod-CBT-treated, NTR-overexpressing HeLa cells showed the existence of Iod-CBT-NPs in their cytoplasm with an average LAC value of 0.172 ± 0.032 μm-1 We anticipate that our strategy could help people to deeply understand the formation mechanism of intracellular nanostructures in the near future.
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Affiliation(s)
- Miaomiao Zhang
- Hefei National Laboratory of Physical Sciences at Microscale, Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Yong Guan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, 42 Hezuohua South Road, Hefei, Anhui 230029, China
| | - Zheng Dang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, 42 Hezuohua South Road, Hefei, Anhui 230029, China
| | - Pinggen Zhang
- School of Life Sciences, University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui 230027, China
| | - Zhen Zheng
- Hefei National Laboratory of Physical Sciences at Microscale, Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Liang Chen
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, 42 Hezuohua South Road, Hefei, Anhui 230029, China
| | - Wen Kuang
- Hefei National Laboratory of Physical Sciences at Microscale, Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Chenchen Wang
- Hefei National Laboratory of Physical Sciences at Microscale, Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Gaolin Liang
- Hefei National Laboratory of Physical Sciences at Microscale, Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China.
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing, Jiangsu 210096, China
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Quemin ERJ, Machala EA, Vollmer B, Pražák V, Vasishtan D, Rosch R, Grange M, Franken LE, Baker LA, Grünewald K. Cellular Electron Cryo-Tomography to Study Virus-Host Interactions. Annu Rev Virol 2020; 7:239-262. [PMID: 32631159 DOI: 10.1146/annurev-virology-021920-115935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses are obligatory intracellular parasites that reprogram host cells upon infection to produce viral progeny. Here, we review recent structural insights into virus-host interactions in bacteria, archaea, and eukaryotes unveiled by cellular electron cryo-tomography (cryoET). This advanced three-dimensional imaging technique of vitreous samples in near-native state has matured over the past two decades and proven powerful in revealing molecular mechanisms underlying viral replication. Initial studies were restricted to cell peripheries and typically focused on early infection steps, analyzing surface proteins and viral entry. Recent developments including cryo-thinning techniques, phase-plate imaging, and correlative approaches have been instrumental in also targeting rare events inside infected cells. When combined with advances in dedicated image analyses and processing methods, details of virus assembly and egress at (sub)nanometer resolution were uncovered. Altogether, we provide a historical and technical perspective and discuss future directions and impacts of cryoET for integrative structural cell biology analyses of viruses.
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Affiliation(s)
- Emmanuelle R J Quemin
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Emily A Machala
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Benjamin Vollmer
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Vojtěch Pražák
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Daven Vasishtan
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Rene Rosch
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Michael Grange
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Linda E Franken
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Lindsay A Baker
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Kay Grünewald
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
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KUBA JAKUB, MITCHELS JOHN, HOVORKA MILOŠ, ERDMANN PHILIPP, BERKA LUKÁŠ, KIRMSE ROBERT, KÖNIG JULIA, DE BOCK JAN, GOETZE BERNHARD, RIGORT ALEXANDER. Advanced cryo‐tomography workflow developments – correlative microscopy, milling automation and cryo‐lift‐out. J Microsc 2020; 281:112-124. [DOI: 10.1111/jmi.12939] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/22/2020] [Accepted: 06/16/2020] [Indexed: 01/13/2023]
Affiliation(s)
- JAKUB KUBA
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | - JOHN MITCHELS
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | - MILOŠ HOVORKA
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | - PHILIPP ERDMANN
- Department of Molecular Structural Biology Max Planck Institute of Biochemistry Martinsried Germany
| | - LUKÁŠ BERKA
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | | | | | - JAN DE BOCK
- Leica Microsystems CMS GmbH Mannheim Germany
| | - BERNHARD GOETZE
- Thermo Fisher Scientific FEI Deutschland GmbH Planegg Germany
| | - ALEXANDER RIGORT
- Department of Molecular Structural Biology Max Planck Institute of Biochemistry Martinsried Germany
- Thermo Fisher Scientific FEI Deutschland GmbH Planegg Germany
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40
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Ganeva I, Kukulski W. Membrane Architecture in the Spotlight of Correlative Microscopy. Trends Cell Biol 2020; 30:577-587. [DOI: 10.1016/j.tcb.2020.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/19/2022]
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Wagner FR, Watanabe R, Schampers R, Singh D, Persoon H, Schaffer M, Fruhstorfer P, Plitzko J, Villa E. Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography. Nat Protoc 2020; 15:2041-2070. [PMID: 32405053 PMCID: PMC8053421 DOI: 10.1038/s41596-020-0320-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/06/2020] [Indexed: 12/31/2022]
Abstract
Recent advances have made cryogenic (cryo) electron microscopy a key technique to achieve near-atomic-resolution structures of biochemically isolated macromolecular complexes. Cryo-electron tomography (cryo-ET) can give unprecedented insight into these complexes in the context of their natural environment. However, the application of cryo-ET is limited to samples that are thinner than most cells, thereby considerably reducing its applicability. Cryo-focused-ion-beam (cryo-FIB) milling has been used to carve (micromachining) out 100-250-nm-thin regions (called lamella) in the intact frozen cells. This procedure opens a window into the cells for high-resolution cryo-ET and structure determination of biomolecules in their native environment. Further combination with fluorescence microscopy allows users to determine cells or regions of interest for the targeted fabrication of lamellae and cryo-ET imaging. Here, we describe how to prepare lamellae using a microscope equipped with both FIB and scanning electron microscopy modalities. Such microscopes (Aquilos Cryo-FIB/Scios/Helios or CrossBeam) are routinely referred to as dual-beam microscopes, and they are equipped with a cryo-stage for all operations in cryogenic conditions. The basic principle of the described methodologies is also applicable for other types of dual-beam microscopes equipped with a cryo-stage. We also briefly describe how to integrate fluorescence microscopy data for targeted milling and critical considerations for cryo-ET data acquisition of the lamellae. Users familiar with cryo-electron microscopy who get basic training in dual-beam microscopy can complete the protocol within 2-3 d, allowing for several pause points during the procedure.
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Affiliation(s)
- Felix R Wagner
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Reika Watanabe
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Digvijay Singh
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Hans Persoon
- Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Peter Fruhstorfer
- Thermo Fisher Scientific, Eindhoven, the Netherlands
- Eppendorf AG, Hamburg, Germany
| | - Jürgen Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elizabeth Villa
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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42
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Jun S, Ro HJ, Bharda A, Kim SI, Jeoung D, Jung HS. Advances in Cryo-Correlative Light and Electron Microscopy: Applications for Studying Molecular and Cellular Events. Protein J 2020; 38:609-615. [PMID: 31396855 DOI: 10.1007/s10930-019-09856-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cryo-correlative light and electron microscopy (Cryo-CLEM) is materializing as a widespread approach amalgamating the advantages of both fluorescence light microscopy (FLM) as well as three dimensional (3D) cryo-electron tomography (cryo-ET) to reveal the ultrastructure of significant target molecules with specific cellular functions. Cryo-CLEM allows imaging of cells by means of fluorescence microscopy exhibiting the location of the destined molecule at high temporal and spatial resolution while cryo-ET is employed to analyze the 3D structure at a molecular resolution in close-to-physiological condition. Present review focuses upon the practical strategies for Cryo-CLEM and recent technical developments that will assist the broad implementation of this technique to investigate and answer questions pertaining to various biological events occurring in the cell.
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Affiliation(s)
- Sangmi Jun
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea. .,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea. .,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea.
| | - Hyun-Joo Ro
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Anahita Bharda
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea
| | - Seung Il Kim
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Dooil Jeoung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea.
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Abstract
Viruses are obligatory parasites that take advantage of intracellular niches to replicate. During infection, their genomes are carried in capsids across the membranes of host cells to sites of virion production by exploiting cellular behaviour and resources to guide and achieve all aspects of delivery and the downstream virus manufacturing process. Successful entry hinges on execution of a precisely tuned viral uncoating program where incoming capsids disassemble in consecutive steps to ensure that genomes are released at the right time, and in the right place for replication to occur. Each step of disassembly is cell-assisted, involving individual pathways that transmit signals to regulate discrete functions, but at the same time, these signalling pathways are organized into larger networks, which communicate back and forth in complex ways in response to the presence of virus. In this review, we consider the elegant strategy by which adenoviruses (AdVs) target and navigate cellular networks to initiate the production of progeny virions. There are many remarkable aspects about the AdV entry program; for example, the virus gains targeted control of a large well-defined local network neighbourhood by coupling several interacting processes (including endocytosis, autophagy and microtubule trafficking) around a collective reference state centred on the interactional topology and multifunctional nature of protein VI. Understanding the network targeting activity of protein VI, as well as other built-in mechanisms that allow AdV particles to be efficient at navigating the subsystems of the cell, can be used to improve viral vectors, but also has potential to be incorporated for use in entirely novel delivery systems.
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Affiliation(s)
- Justin W Flatt
- Faculty of Biological and Environmental Sciences and HiLIFE-Institute of Biotechnology, University of Helsinki , 00790 Helsinki , Finland
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences and HiLIFE-Institute of Biotechnology, University of Helsinki , 00790 Helsinki , Finland
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44
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Affiliation(s)
- Ian M Dobbie
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
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45
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Flow Cytometry Analysis of HIV-1 Env Conformations at the Surface of Infected Cells and Virions: Role of Nef, CD4, and SERINC5. J Virol 2020; 94:JVI.01783-19. [PMID: 31852789 DOI: 10.1128/jvi.01783-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022] Open
Abstract
The HIV-1 Env protein is exposed at the surface of virions and infected cells. Env fluctuates between different closed and open structural states and these conformations influence both viral infectivity and sensitivity to antibody binding and neutralization. We established a flow virometry assay to visualize Env proteins at the surface of human immunodeficiency virus type 1 (HIV-1) virions. The assay is performed on ultracentrifuged fluorescent viral particles that are stained with a panel of broadly neutralizing antibodies (bNAbs) and nonneutralizing antibodies (nnAbs) that probe different epitopes of Env. We used this assay to compare Env at the surface of producer cells and viral particles and to analyze the effect of Nef, CD4, and SERINC5 on Env accessibility to antibodies. We studied the laboratory-adapted strain NL4-3 and two transmitted/founder viruses, THRO and CH058. We confirm that antibody accessibility varies between viral strains and show that Nef, CD4, and SERINC5 additively impact Env conformations. We further demonstrate that the Env accessibility profile on virions is globally similar to that observed on HIV-1-infected cells, with some noticeable differences. For instance, nnAbs bind to virions more efficiently than to producer cells, likely reflecting changes in Env conformational states on mature viral particles. This test complements other techniques and provides a convenient and simple tool for quantifying and probing the structure of Env at the virion surface and to analyze the impact of viral and cellular proteins on these parameters.IMPORTANCE HIV-1 Env conformation is one of the key parameters determining viral infectivity. The flow virometry-based assay developed in this study allows for the characterization of proteins incorporated in HIV-1 particles. We studied the conformation of HIV-1 Env and the impact that the viral protein Nef and the cellular proteins CD4 and SERINC5 have on Env accessibility to antibodies. Our assay permitted us to highlight some noticeable differences in the conformation of Env between producer cells and viral particles. It contributes to a better understanding of the actual composition of HIV-1 particles.
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Luque D, Castón JR. Cryo-electron microscopy for the study of virus assembly. Nat Chem Biol 2020; 16:231-239. [PMID: 32080621 DOI: 10.1038/s41589-020-0477-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
Abstract
Although viruses are extremely diverse in shape and size, evolution has led to a limited number of viral classes or lineages, which is probably linked to the assembly constraints of a viable capsid. Viral assembly mechanisms are restricted to two general pathways, (i) co-assembly of capsid proteins and single-stranded nucleic acids and (ii) a sequential mechanism in which scaffolding-mediated capsid precursor assembly is followed by genome packaging. Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), which are revolutionizing structural biology, are central to determining the high-resolution structures of many viral assemblies as well as those of assembly intermediates. This wealth of cryo-EM data has also led to the development and redesign of virus-based platforms for biomedical and biotechnological applications. In this Review, we will discuss recent viral assembly analyses by cryo-EM and cryo-ET showing how natural assembly mechanisms are used to encapsulate heterologous cargos including chemicals, enzymes, and/or nucleic acids for a variety of nanotechnological applications.
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Affiliation(s)
- Daniel Luque
- Centro Nacional de Microbiología/ISCIII, Majadahonda, Madrid, Spain
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus Cantoblanco, Madrid, Spain.
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47
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Ng CT, Gan L. Investigating eukaryotic cells with cryo-ET. Mol Biol Cell 2020; 31:87-100. [PMID: 31935172 PMCID: PMC6960407 DOI: 10.1091/mbc.e18-05-0329] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 01/06/2023] Open
Abstract
The interior of eukaryotic cells is mysterious. How do the large communities of macromolecular machines interact with each other? How do the structures and positions of these nanoscopic entities respond to new stimuli? Questions like these can now be answered with the help of a method called electron cryotomography (cryo-ET). Cryo-ET will ultimately reveal the inner workings of a cell at the protein, secondary structure, and perhaps even side-chain levels. Combined with genetic or pharmacological perturbation, cryo-ET will allow us to answer previously unimaginable questions, such as how structure, biochemistry, and forces are related in situ. Because it bridges structural biology and cell biology, cryo-ET is indispensable for structural cell biology-the study of the 3-D macromolecular structure of cells. Here we discuss some of the key ideas, strategies, auxiliary techniques, and innovations that an aspiring structural cell biologist will consider when planning to ask bold questions.
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Affiliation(s)
- Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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48
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Toro-Nahuelpan M, Zagoriy I, Senger F, Blanchoin L, Théry M, Mahamid J. Tailoring cryo-electron microscopy grids by photo-micropatterning for in-cell structural studies. Nat Methods 2020; 17:50-54. [PMID: 31740821 PMCID: PMC6949126 DOI: 10.1038/s41592-019-0630-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023]
Abstract
Spatially controlled cell adhesion on electron microscopy supports remains a bottleneck in specimen preparation for cellular cryo-electron tomography. Here, we describe contactless and mask-free photo-micropatterning of electron microscopy grids for site-specific deposition of extracellular matrix-related proteins. We attained refined cell positioning for micromachining by cryo-focused ion beam milling. Complex micropatterns generated predictable intracellular organization, allowing direct correlation between cell architecture and in-cell three-dimensional structural characterization of the underlying molecular machinery.
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Affiliation(s)
- Mauricio Toro-Nahuelpan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fabrice Senger
- CytomorphoLab, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes/CEA/CNRS/INRA, Grenoble, France
| | - Laurent Blanchoin
- CytomorphoLab, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes/CEA/CNRS/INRA, Grenoble, France
- CytomorphoLab, Hôpital Saint Louis, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Manuel Théry
- CytomorphoLab, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes/CEA/CNRS/INRA, Grenoble, France
- CytomorphoLab, Hôpital Saint Louis, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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Hamilton GL, Alper J, Sanabria H. Reporting on the future of integrative structural biology ORAU workshop. FRONT BIOSCI-LANDMRK 2020; 25:43-68. [PMID: 31585877 PMCID: PMC7323472 DOI: 10.2741/4794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Integrative and hybrid methods have the potential to bridge long-standing knowledge gaps in structural biology. These methods will have a prominent role in the future of the field as we make advances toward a complete, unified representation of biology that spans the molecular and cellular scales. The Department of Physics and Astronomy at Clemson University hosted The Future of Integrative Structural Biology workshop on April 29, 2017 and partially sponsored by partially sponsored by a program of the Oak Ridge Associated Universities (ORAU). The workshop brought experts from multiple structural biology disciplines together to discuss near-term steps toward the goal of a molecular atlas of the cell. The discussion focused on the types of structural data that should be represented, how this data should be represented, and how the time domain might be incorporated into such an atlas. The consensus was that an explorable, map-like Virtual Cell, containing both spatial and temporal data bridging the atomic and cellular length scales obtained by multiple experimental methods, represents the best path toward a complete atlas of the cell.
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Affiliation(s)
- George L Hamilton
- Physics and Astronomy, Clemson University, 216 Kinard Lab, Clemson, S.C. USA
| | - Joshua Alper
- Physics and Astronomy, Clemson University, 302B Kinard Lab, Clemson, S.C. 29634-0978. USA
| | - Hugo Sanabria
- Physics and Astronomy, Clemson University, 214 Kinard Lab, Clemson, S.C. 29634-0978. USA,
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50
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Toro-Nahuelpan M, Zagoriy I, Senger F, Blanchoin L, Théry M, Mahamid J. Tailoring cryo-electron microscopy grids by photo-micropatterning for in-cell structural studies. Nat Methods 2020; 17:50-54. [PMID: 31740821 DOI: 10.21203/rs.2.12377/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/07/2019] [Indexed: 05/22/2023]
Abstract
Spatially controlled cell adhesion on electron microscopy supports remains a bottleneck in specimen preparation for cellular cryo-electron tomography. Here, we describe contactless and mask-free photo-micropatterning of electron microscopy grids for site-specific deposition of extracellular matrix-related proteins. We attained refined cell positioning for micromachining by cryo-focused ion beam milling. Complex micropatterns generated predictable intracellular organization, allowing direct correlation between cell architecture and in-cell three-dimensional structural characterization of the underlying molecular machinery.
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Affiliation(s)
- Mauricio Toro-Nahuelpan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fabrice Senger
- CytomorphoLab, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes/CEA/CNRS/INRA, Grenoble, France
| | - Laurent Blanchoin
- CytomorphoLab, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes/CEA/CNRS/INRA, Grenoble, France
- CytomorphoLab, Hôpital Saint Louis, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Manuel Théry
- CytomorphoLab, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes/CEA/CNRS/INRA, Grenoble, France
- CytomorphoLab, Hôpital Saint Louis, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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