1
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Perez D, Dowlatshahi DP, Azaldegui CA, Ansell TB, Dahlberg PD, Moerner WE. Exploring Transient States of PAmKate to Enable Improved Cryogenic Single-Molecule Imaging. J Am Chem Soc 2024. [PMID: 39388715 DOI: 10.1021/jacs.4c05632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
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 nanoscale 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) that photoactivate or photoswitch efficiently at cryogenic temperatures, but long on-times due to reduced quantum yield of photobleaching remain 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 that a transient state forms with a lifetime of ∼2 ms under cryogenic conditions, 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 the 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
| | - T Bertie Ansell
- 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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2
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Pierson JA, Yang JE, Wright ER. Recent advances in correlative cryo-light and electron microscopy. Curr Opin Struct Biol 2024; 89:102934. [PMID: 39366119 DOI: 10.1016/j.sbi.2024.102934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 10/06/2024]
Abstract
Correlative light and electron microscopy (CLEM) pipelines serve to integrate the imaging modalities of fluorescence light microscopy (FLM) and cryogenic electron microscopy (cryo-EM) to produce contextually relevant high-resolution structural snapshots of biological systems. Innovations in sample preparation, instrumentation, imaging, and data processing have advanced the field of cryo-EM. This review focuses on prior work and recent developments in the field of cryo- EM that support further integration of technologies for correlative microscopy workflows.
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Affiliation(s)
- Joshua A Pierson
- Department of Biochemistry, 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
| | - 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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3
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Perez D, Dowlatshahi DP, Azaldegui CA, Ansell TB, 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 nanoscale 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 under cryogenic conditions 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
| | - T. Bertie Ansell
- 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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Noble AJ, de Marco A. Cryo-focused ion beam for in situ structural biology: State of the art, challenges, and perspectives. Curr Opin Struct Biol 2024; 87:102864. [PMID: 38901373 DOI: 10.1016/j.sbi.2024.102864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 06/22/2024]
Abstract
Cryogenic-focused ion beam (cryo-FIB) instruments became essential for high-resolution imaging in cryo-preserved cells and tissues. Cryo-FIBs use accelerated ions to thin samples that would otherwise be too thick for cryo-electron microscopy (cryo-EM). This allows visualizing cellular ultrastructures in near-native frozen hydrated states. This review describes the current state-of-the-art capabilities of cryo-FIB technology and its applications in structural cell and tissue biology. We discuss recent advances in instrumentation, imaging modalities, automation, sample preparation protocols, and targeting techniques. We outline remaining challenges and future directions to make cryo-FIB more precise, enable higher throughput, and be widely accessible. Further improvements in targeting, efficiency, robust sample preparation, emerging ion sources, automation, and downstream electron tomography have the potential to reveal intricate molecular architectures across length scales inside cells and tissues. Cryo-FIB is poised to become an indispensable tool for preparing native biological systems in situ for high-resolution 3D structural analysis.
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Affiliation(s)
- Alex J Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue New York, NY, 10027, USA. https://twitter.com/alexjamesnoble
| | - Alex de Marco
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue New York, NY, 10027, USA.
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5
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Dutta M, Acharya P. Cryo-electron microscopy in the study of virus entry and infection. Front Mol Biosci 2024; 11:1429180. [PMID: 39114367 PMCID: PMC11303226 DOI: 10.3389/fmolb.2024.1429180] [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: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses have been responsible for many epidemics and pandemics that have impacted human life globally. The COVID-19 pandemic highlighted both our vulnerability to viral outbreaks, as well as the mobilization of the scientific community to come together to combat the unprecedented threat to humanity. Cryo-electron microscopy (cryo-EM) played a central role in our understanding of SARS-CoV-2 during the pandemic and continues to inform about this evolving pathogen. Cryo-EM with its two popular imaging modalities, single particle analysis (SPA) and cryo-electron tomography (cryo-ET), has contributed immensely to understanding the structure of viruses and interactions that define their life cycles and pathogenicity. Here, we review how cryo-EM has informed our understanding of three distinct viruses, of which two - HIV-1 and SARS-CoV-2 infect humans, and the third, bacteriophages, infect bacteria. For HIV-1 and SARS-CoV-2 our focus is on the surface glycoproteins that are responsible for mediating host receptor binding, and host and cell membrane fusion, while for bacteriophages, we review their structure, capsid maturation, attachment to the bacterial cell surface and infection initiation mechanism.
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Affiliation(s)
- Moumita Dutta
- Duke Human Vaccine Institute, Durham, NC, United States
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Surgery, Durham, NC, United States
- Department of Biochemistry, Duke University, Durham, NC, United States
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6
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Hale VL, Hooker J, Russo CJ, Löwe J. Honeycomb gold specimen supports enabling orthogonal focussed ion beam-milling of elongated cells for cryo-ET. J Struct Biol 2024; 216:108097. [PMID: 38772448 PMCID: PMC7616276 DOI: 10.1016/j.jsb.2024.108097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 05/11/2024] [Accepted: 05/18/2024] [Indexed: 05/23/2024]
Abstract
Cryo-focussed ion beam (FIB)-milling is a powerful technique that opens up thick, cellular specimens to high-resolution structural analysis by electron cryotomography (cryo-ET). FIB-milled lamellae can be produced from cells on grids, or cut from thicker, high-pressure frozen specimens. However, these approaches can put geometrical constraints on the specimen that may be unhelpful, particularly when imaging structures within the cell that have a very defined orientation. For example, plunge frozen rod-shaped bacteria orient parallel to the plane of the grid, yet the Z-ring, a filamentous structure of the tubulin-like protein FtsZ and the key organiser of bacterial division, runs around the circumference of the cell such that it is perpendicular to the imaging plane. It is therefore difficult or impractical to image many complete rings with current technologies. To circumvent this problem, we have fabricated monolithic gold specimen supports with a regular array of cylindrical wells in a honeycomb geometry, which trap bacteria in a vertical orientation. These supports, which we call "honeycomb gold discs", replace standard EM grids and when combined with FIB-milling enable the production of lamellae containing cross-sections through cells. The resulting lamellae are more stable and resistant to breakage and charging than conventional lamellae. The design of the honeycomb discs can be modified according to need and so will also enable cryo-ET and cryo-EM imaging of other specimens in otherwise difficult to obtain orientations.
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Affiliation(s)
| | - James Hooker
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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7
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Chen T, Giannone G. Single molecule imaging unveils cellular architecture, dynamics and mechanobiology. Curr Opin Cell Biol 2024; 88:102369. [PMID: 38759257 DOI: 10.1016/j.ceb.2024.102369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/19/2024]
Abstract
The biomechanical regulation of the cytoskeleton and cell adhesions underlies various essential cellular functions. Studying them requires visualizing their nanostructure and molecular dynamics with evermore precise spatio-temporal resolution. In this review we will focus on the recent advances in single molecule fluorescence imaging techniques and discuss how they improve our understanding of mechanically sensitive cellular structures such as adhesions and the cytoskeleton. We will also discuss future directions for research, emphasizing on the 3D nature of cellular structures and tissues, their mechanical regulation at the molecule level, as well as how super-resolution microscopy will enhance our knowledge on protein structure and conformational changes in the cellular context.
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Affiliation(s)
- Tianchi Chen
- Interdisciplinary Institute for Neuroscience, Université Bordeaux, CNRS, UMR 5297, 33000 Bordeaux, France
| | - Grégory Giannone
- Interdisciplinary Institute for Neuroscience, Université Bordeaux, CNRS, UMR 5297, 33000 Bordeaux, France.
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8
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Oz S, Saar G, Olszakier S, Heinrich R, Kompanets MO, Berlin S. Revealing the MRI-Contrast in Optically Cleared Brains. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400316. [PMID: 38647385 PMCID: PMC11165557 DOI: 10.1002/advs.202400316] [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: 01/09/2024] [Revised: 04/10/2024] [Indexed: 04/25/2024]
Abstract
The current consensus holds that optically-cleared specimens are unsuitable for Magnetic Resonance Imaging (MRI); exhibiting absence of contrast. Prior studies combined MRI with tissue-clearing techniques relying on the latter's ability to eliminate lipids, thereby fostering the assumption that lipids constitute the primary source of ex vivo MRI-contrast. Nevertheless, these findings contradict an extensive body of literature that underscores the contribution of other features to contrast. Furthermore, it remains unknown whether non-delipidating clearing methods can produce MRI-compatible specimens or whether MRI-contrast can be re-established. These limitations hinder the development of multimodal MRI-light-microscopy (LM) imaging approaches. This study assesses the relation between MRI-contrast, and delipidation in optically-cleared whole brains following different tissue-clearing approaches. It is demonstrated that uDISCO and ECi-brains are MRI-compatible upon tissue rehydration, despite both methods' substantial delipidating-nature. It is also demonstrated that, whereas Scale-clearing preserves most lipids, Scale-cleared brain lack MRI-contrast. Furthermore, MRI-contrast is restored to lipid-free CLARITY-brains without introducing lipids. Our results thereby dissociate between the essentiality of lipids to MRI-contrast. A tight association is found between tissue expansion, hyperhydration and loss of MRI-contrast. These findings then enabled us to develop a multimodal MRI-LM-imaging approach, opening new avenues to bridge between the micro- and mesoscale for biomedical research and clinical applications.
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Affiliation(s)
- Shimrit Oz
- Department of NeuroscienceFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
| | - Galit Saar
- Biomedical Core FacilityFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
| | - Shunit Olszakier
- Department of NeuroscienceFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
| | - Ronit Heinrich
- Department of NeuroscienceFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
| | - Mykhail O. Kompanets
- L.M. Litvinenko Institute of Physico‐Organic Chemistry and Coal ChemistryNational Academy of Sciences of UkraineKyivUkraine
| | - Shai Berlin
- Department of NeuroscienceFaculty of MedicineTechnion‐Israel Institute of TechnologyHaifa3525433Israel
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9
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Nogales E, Mahamid J. Bridging structural and cell biology with cryo-electron microscopy. Nature 2024; 628:47-56. [PMID: 38570716 PMCID: PMC11211576 DOI: 10.1038/s41586-024-07198-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/13/2024] [Indexed: 04/05/2024]
Abstract
Most life scientists would agree that understanding how cellular processes work requires structural knowledge about the macromolecules involved. For example, deciphering the double-helical nature of DNA revealed essential aspects of how genetic information is stored, copied and repaired. Yet, being reductionist in nature, structural biology requires the purification of large amounts of macromolecules, often trimmed off larger functional units. The advent of cryogenic electron microscopy (cryo-EM) greatly facilitated the study of large, functional complexes and generally of samples that are hard to express, purify and/or crystallize. Nevertheless, cryo-EM still requires purification and thus visualization outside of the natural context in which macromolecules operate and coexist. Conversely, cell biologists have been imaging cells using a number of fast-evolving techniques that keep expanding their spatial and temporal reach, but always far from the resolution at which chemistry can be understood. Thus, structural and cell biology provide complementary, yet unconnected visions of the inner workings of cells. Here we discuss how the interplay between cryo-EM and cryo-electron tomography, as a connecting bridge to visualize macromolecules in situ, holds great promise to create comprehensive structural depictions of macromolecules as they interact in complex mixtures or, ultimately, inside the cell itself.
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Affiliation(s)
- Eva Nogales
- Molecular and Cell Biology Department, Institute for Quantitative Biomedicine, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, Berkeley, CA, USA.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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10
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Pepe A, Groen J, Zurzolo C, Sartori-Rupp A. Correlative cryo-microscopy pipelines for in situ cellular studies. Methods Cell Biol 2024; 187:175-203. [PMID: 38705624 DOI: 10.1016/bs.mcb.2024.02.038] [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
Correlative cryo-microscopy pipelines combining light and electron microscopy and tomography in cryogenic conditions (cryoCLEM) on the same sample are powerful methods for investigating the structure of specific cellular targets identified by a fluorescent tag within their unperturbed cellular environment. CryoCLEM approaches circumvent one of the inherent limitations of cryo EM, and specifically cryo electron tomography (cryoET), of identifying the imaged structures in the crowded 3D environment of cells. Whereas several cryoCLEM approaches are based on thinning the sample by cryo FIB milling, here we present detailed protocols of two alternative cryoCLEM approaches for in situ studies of adherent cells at the single-cell level without the need for such cryo-thinning. The first approach is a complete cryogenic pipeline in which both fluorescence and electronic imaging are performed on frozen-hydrated samples, the second is a hybrid cryoCLEM approach in which fluorescence imaging is performed at room temperature, followed by rapid freezing and subsequent cryoEM imaging. We provide a detailed description of the two methods we have employed for imaging fluorescently labeled cellular structures with thickness below 350-500nm, such as cell protrusions and organelles located in the peripheral areas of the cells.
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Affiliation(s)
- Anna Pepe
- Membrane Traffic and Pathogenesis, Institut Pasteur, Paris, France
| | - Johannes Groen
- NanoImaging Core Facility, Institut Pasteur, Paris, France; Dynamics of Host-Pathogen Interactions, Institut Pasteur, Paris, France
| | - Chiara Zurzolo
- Membrane Traffic and Pathogenesis, Institut Pasteur, Paris, France
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11
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Franek M, Koptašíková L, Mikšátko J, Liebl D, Macíčková E, Pospíšil J, Esner M, Dvořáčková M, Fajkus J. In-section Click-iT detection and super-resolution CLEM analysis of nucleolar ultrastructure and replication in plants. Nat Commun 2024; 15:2445. [PMID: 38503728 PMCID: PMC10950858 DOI: 10.1038/s41467-024-46324-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Correlative light and electron microscopy (CLEM) is an important tool for the localisation of target molecule(s) and their spatial correlation with the ultrastructural map of subcellular features at the nanometre scale. Adoption of these advanced imaging methods has been limited in plant biology, due to challenges with plant tissue permeability, fluorescence labelling efficiency, indexing of features of interest throughout the complex 3D volume and their re-localization on micrographs of ultrathin cross-sections. Here, we demonstrate an imaging approach based on tissue processing and embedding into methacrylate resin followed by imaging of sections by both, single-molecule localization microscopy and transmission electron microscopy using consecutive CLEM and same-section CLEM correlative workflow. Importantly, we demonstrate that the use of a particular type of embedding resin is not only compatible with single-molecule localization microscopy but shows improvements in the fluorophore blinking behavior relative to the whole-mount approaches. Here, we use a commercially available Click-iT ethynyl-deoxyuridine cell proliferation kit to visualize the DNA replication sites of wild-type Arabidopsis thaliana seedlings, as well as fasciata1 and nucleolin1 plants and apply our in-section CLEM imaging workflow for the analysis of S-phase progression and nucleolar organization in mutant plants with aberrant nucleolar phenotypes.
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Affiliation(s)
- Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic.
| | - Lenka Koptašíková
- Charles University, Faculty of Science, Biology Section, Imaging Methods Core Facility at BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
- University of Exeter, Faculty of Health and Life Sciences, Bioimaging Centre, Geoffrey Pope Building, Stocker Road, EX4 4QD, Exeter, UK
| | - Jíří Mikšátko
- Charles University, Faculty of Science, Biology Section, Imaging Methods Core Facility at BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - David Liebl
- Charles University, Faculty of Science, Biology Section, Imaging Methods Core Facility at BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Eliška Macíčková
- Charles University, Faculty of Science, Biology Section, Imaging Methods Core Facility at BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Jakub Pospíšil
- Cellular Imaging Core Facility CELLIM, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology Masaryk University (CEITEC MU), Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Milan Esner
- Cellular Imaging Core Facility CELLIM, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology Masaryk University (CEITEC MU), Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic.
| | - Jíří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-61137, Brno, Czech Republic
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12
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Last MGF, Voortman LM, Sharp TH. Building a super-resolution fluorescence cryomicroscope. Methods Cell Biol 2024; 187:205-222. [PMID: 38705625 DOI: 10.1016/bs.mcb.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Correlated super-resolution fluorescence microscopy and cryo-electron microscopy enables imaging with both high labeling specificity and high resolution. Naturally, combining two sophisticated imaging techniques within one workflow also introduces new requirements on hardware, such as the need for a super-resolution fluorescence capable microscope that can be used to image cryogenic samples. In this chapter, we describe the design and use of the "cryoscope"; a microscope designed for single-molecule localization microscopy (SMLM) of cryoEM samples that fits right into established cryoEM workflows. We demonstrate the results that can be achieved with our microscope by imaging fluorescently labeled vimentin, an intermediate filament, within U2OS cells grown on EM grids, and we provide detailed 3d models that encompass the entire design of the microscope.
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Affiliation(s)
- Mart G F Last
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands; School of Biochemistry, University of Bristol, Bristol, United Kingdom.
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13
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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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14
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Gee M, Atai K, Coller HA, Yeates TO, Castells-Graells R. Designed fluorescent protein cages as fiducial markers for targeted cell imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582585. [PMID: 38464160 PMCID: PMC10925312 DOI: 10.1101/2024.02.28.582585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Understanding how proteins function within their cellular environments is essential for cellular biology and biomedical research. However, current imaging techniques exhibit limitations, particularly in the study of small complexes and individual proteins within cells. Previously, protein cages have been employed as imaging scaffolds to study purified small proteins using cryo-electron microscopy (cryo-EM). Here we demonstrate an approach to deliver designed protein cages - endowed with fluorescence and targeted binding properties - into cells, thereby serving as fiducial markers for cellular imaging. We used protein cages with anti-GFP DARPin domains to target a mitochondrial protein (MFN1) expressed in mammalian cells, which was genetically fused to GFP. We demonstrate that the protein cages can penetrate cells, are directed to specific subcellular locations, and are detectable with confocal microscopy. This innovation represents a milestone in developing tools for in-depth cellular exploration, especially in conjunction with methods such as cryo-correlative light and electron microscopy (cryo-CLEM).
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Affiliation(s)
- Morgan Gee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | - Kaiser Atai
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Hilary A Coller
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA 90095
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA 90095
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15
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Palao L, Murakami K, Chang YW. Combining per-particle cryo-ET and cryo-EM single particle analysis to elucidate heterogeneous DNA-protein organization. Curr Opin Struct Biol 2024; 84:102765. [PMID: 38181688 PMCID: PMC10922635 DOI: 10.1016/j.sbi.2023.102765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
Cryo-electron microscopy single particle analysis (cryo-EM SPA) and cryo-electron tomography (cryo-ET) have historically been employed as distinct approaches for investigating molecular structures of disparate sample types, focusing on highly purified biological macromolecules and in situ cellular contexts, respectively. However, these techniques offer inherently complementary structural insights that, when combined, provide a more comprehensive understanding of complex biological systems. For example, if both techniques are applied to the same purified biological macromolecules, cryo-ET has the ability to resolve highly flexible yet strong signal features on an individual target molecule which will not be preserved in the high-resolution cryo-EM SPA results. In this review, we highlight recent achievements utilizing such applications to unveil new insights into the chromatin assembly and activities of DNA-protein assemblies. This convergence of cryo-EM SPA and cryo-ET holds great promise for elucidating new structural aspects of these essential molecular processes.
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Affiliation(s)
- Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, PA, USA
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, PA, USA; Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, PA, USA; Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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16
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Faber T, McConville JT, Lamprecht A. Focused ion beam-scanning electron microscopy provides novel insights of drug delivery phenomena. J Control Release 2024; 366:312-327. [PMID: 38161031 DOI: 10.1016/j.jconrel.2023.12.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Scanning electron microscopy (SEM) has long been a standard tool for morphological analyses, providing sub micrometer resolution of pharmaceutical formulations. However, analysis of internal morphologies of such formulations can often be biased due to the introduction of artifacts that originate from sample preparation. A recent advancement in SEM, is the focused ion beam scanning electron microscopy (FIB-SEM). This technique uses a focused ion beam (FIB) to remove material with nanometer precision, to provide virtually sample-independent access to sub-surface structures. The FIB can be combined with SEM imaging capabilities within the same instrumentation. As a powerful analytical tool, electron microscopy and FIB-milling are performed sequentially to produce high-resolution 3D models of structural peculiarities of diverse drug delivery systems or their behavior in a biological environment, i.e. intracellular or -tissue distribution. This review paper briefly describes the technical background of the method, outlines a wide array of potential uses within the drug delivery field, and focuses on intracellular transport where high-resolution images are an essential tool for mechanistical insights.
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Affiliation(s)
- Thilo Faber
- Department of Pharmaceutics, Institute of Pharmacy, University of Bonn, Bonn, Germany
| | - Jason T McConville
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, USA
| | - Alf Lamprecht
- Department of Pharmaceutics, Institute of Pharmacy, University of Bonn, Bonn, Germany; Université de Franche-Comté, INSERM UMR1098 Right, Besançon, France.
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17
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Asarnow D, Becker VA, Bobe D, Dubbledam C, Johnston JD, Kopylov M, Lavoie NR, Li Q, Mattingly JM, Mendez JH, Paraan M, Turner J, Upadhye V, Walsh RM, Gupta M, Eng ET. Recent advances in infectious disease research using cryo-electron tomography. Front Mol Biosci 2024; 10:1296941. [PMID: 38288336 PMCID: PMC10822977 DOI: 10.3389/fmolb.2023.1296941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/07/2023] [Indexed: 01/31/2024] Open
Abstract
With the increasing spread of infectious diseases worldwide, there is an urgent need for novel strategies to combat them. Cryogenic sample electron microscopy (cryo-EM) techniques, particularly electron tomography (cryo-ET), have revolutionized the field of infectious disease research by enabling multiscale observation of biological structures in a near-native state. This review highlights the recent advances in infectious disease research using cryo-ET and discusses the potential of this structural biology technique to help discover mechanisms of infection in native environments and guiding in the right direction for future drug discovery.
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Affiliation(s)
- Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Vada A. Becker
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States
| | - Daija Bobe
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Charlie Dubbledam
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Jake D. Johnston
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States
| | - Mykhailo Kopylov
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Nathalie R. Lavoie
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, MA, United States
| | - Qiuye Li
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Jacob M. Mattingly
- Department of Chemistry, College of Arts and Sciences, Emory University, Atlanta, GA, United States
| | - Joshua H. Mendez
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Mohammadreza Paraan
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Jack Turner
- European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Viraj Upadhye
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Richard M. Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology and Harvard Medical School, Boston, MA, United States
| | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
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18
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Ching C, Maufront J, di Cicco A, Lévy D, Dezi M. C ool-contacts: Cryo-Electron Microscopy of Membrane Contact Sites and Their Components. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2024; 7:25152564241231364. [PMID: 38410695 PMCID: PMC10895918 DOI: 10.1177/25152564241231364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024]
Abstract
Electron microscopy has played a pivotal role in elucidating the ultrastructure of membrane contact sites between cellular organelles. The advent of cryo-electron microscopy has ushered in the ability to determine atomic models of constituent proteins or protein complexes within sites of membrane contact through single particle analysis. Furthermore, it enables the visualization of the three-dimensional architecture of membrane contact sites, encompassing numerous copies of proteins, whether in vitro reconstituted or directly observed in situ using cryo-electron tomography. Nevertheless, there exists a scarcity of cryo-electron microscopy studies focused on the site of membrane contact and their constitutive proteins. This review provides an overview of the contributions made by cryo-electron microscopy to our understanding of membrane contact sites, outlines the associated limitations, and explores prospects in this field.
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Affiliation(s)
- Cyan Ching
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Julien Maufront
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Aurélie di Cicco
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Daniel Lévy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Manuela Dezi
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
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19
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Mazal H, Wieser FF, Sandoghdar V. Insights into protein structure using cryogenic light microscopy. Biochem Soc Trans 2023; 51:2041-2059. [PMID: 38015555 PMCID: PMC10754291 DOI: 10.1042/bst20221246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Fluorescence microscopy has witnessed many clever innovations in the last two decades, leading to new methods such as structured illumination and super-resolution microscopies. The attainable resolution in biological samples is, however, ultimately limited by residual motion within the sample or in the microscope setup. Thus, such experiments are typically performed on chemically fixed samples. Cryogenic light microscopy (Cryo-LM) has been investigated as an alternative, drawing on various preservation techniques developed for cryogenic electron microscopy (Cryo-EM). Moreover, this approach offers a powerful platform for correlative microscopy. Another key advantage of Cryo-LM is the strong reduction in photobleaching at low temperatures, facilitating the collection of orders of magnitude more photons from a single fluorophore. This results in much higher localization precision, leading to Angstrom resolution. In this review, we discuss the general development and progress of Cryo-LM with an emphasis on its application in harnessing structural information on proteins and protein complexes.
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Affiliation(s)
- Hisham Mazal
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
| | - Franz-Ferdinand Wieser
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
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20
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Last MGF, Noteborn WEM, Voortman LM, Sharp TH. Super-resolution fluorescence imaging of cryosamples does not limit achievable resolution in cryoEM. J Struct Biol 2023; 215:108040. [PMID: 37918761 DOI: 10.1016/j.jsb.2023.108040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Correlated super-resolution cryo-fluorescence and cryo-electron microscopy (cryoEM) has been gaining popularity as a method to investigate biological samples with high resolution and specificity. A concern in this combined method (called SR-cryoCLEM), however, is whether and how fluorescence imaging prior to cryoEM acquisition is detrimental to sample integrity. In this report, we investigated the effect of high-dose laser light (405, 488, and 561 nm) irradiation on apoferritin samples prepared for cryoEM with excitation wavelengths commonly used in fluorescence microscopy, and compared these samples to controls that were kept in the dark. We found that laser illumination, of equal duration and intensity as used in cryo-single molecule localization microscopy (cryoSMLM) and in the presence of high concentrations of fluorescent protein, did not affect the achievable resolution in cryoEM, with final reconstructions reaching resolutions of ∼ 1.8 Å regardless of the laser illumination. The finding that super-resolution fluorescence imaging of cryosamples prior to cryoEM data acquisition does not limit the achievable resolution suggests that super-resolution cryo-fluorescence microscopy and in situ structural biology using cryoEM are entirely compatible.
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Affiliation(s)
- Mart G F Last
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Willem E M Noteborn
- Netherlands Centre for Electron Nanoscopy, Leiden University, 2333 AL Leiden, The Netherlands
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands.
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21
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Ochner H, Bharat TAM. Charting the molecular landscape of the cell. Structure 2023; 31:1297-1305. [PMID: 37699393 PMCID: PMC7615466 DOI: 10.1016/j.str.2023.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023]
Abstract
Biological function of macromolecules is closely tied to their cellular location, as well as to interactions with other molecules within the native environment of the cell. Therefore, to obtain detailed mechanistic insights into macromolecular functionality, one of the outstanding targets for structural biology is to produce an atomic-level understanding of the cell. One structural biology technique that has already been used to directly derive atomic models of macromolecules from cells, without any additional external information, is electron cryotomography (cryoET). In this perspective article, we discuss possible routes to chart the molecular landscape of the cell by advancing cryoET imaging as well as by embedding cryoET into correlative imaging workflows.
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Affiliation(s)
- Hannah Ochner
- Structural Studies Division, MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK.
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22
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Beatty KE, López CS. Characteristics of genetic tags for correlative light and electron microscopy. Curr Opin Chem Biol 2023; 76:102369. [PMID: 37453163 DOI: 10.1016/j.cbpa.2023.102369] [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: 05/01/2023] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Fluorescence microscopy is indispensable in live cell studies of fluorescently-labeled proteins, but has limited resolution and context. Electron microscopy offers high-resolution imaging of cellular ultrastructure, including membranes, organelles, and other nanoscale features. However, identifying proteins by EM remains a substantial challenge. There is potential to combine the strengths of both FM and EM through correlative light and EM (CLEM), and bridging the two modalities enables new discoveries and biological insights. CLEM enables cellular proteins to be observed dynamically, across size scales, and in relationship to sub-cellular structures. A central limitation to using CLEM is the scarcity of methods for labeling proteins with CLEM reporters. This review will describe the characteristics of genetic tags for CLEM that are available today, including fixation-resistant fluorescent proteins, 3,3'-diaminobenzidine (DAB)-based tags, metal-chelating tags, DNA origami tags, and VIP tags.
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Affiliation(s)
- Kimberly E Beatty
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
| | - Claudia S López
- Department of Biomedical Engineering Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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23
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Last MGF, Voortman LM, Sharp TH. scNodes: a correlation and processing toolkit for super-resolution fluorescence and electron microscopy. Nat Methods 2023; 20:1445-1446. [PMID: 37596472 DOI: 10.1038/s41592-023-01991-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Affiliation(s)
- Mart G F Last
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
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24
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Kirchweger P, Mullick D, Swain PP, Wolf SG, Elbaum M. Correlating cryo-super resolution radial fluctuations and dual-axis cryo-scanning transmission electron tomography to bridge the light-electron resolution gap. J Struct Biol 2023; 215:107982. [PMID: 37268154 DOI: 10.1016/j.jsb.2023.107982] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/05/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Visualization of organelles and their interactions with other features in the native cell remains a challenge in modern biology. We have introduced cryo-scanning transmission electron tomography (CSTET), which can access 3D volumes on the scale of 1 micron with a resolution of nanometers, making it ideal for this task. Here we introduce two relevant advances: (a) we demonstrate the utility of multi-color super-resolution radial fluctuation light microscopy under cryogenic conditions (cryo-SRRF), and (b) we extend the use of deconvolution processing for dual-axis CSTET data. We show that cryo-SRRF nanoscopy is able to reach resolutions in the range of 100 nm, using commonly available fluorophores and a conventional widefield microscope for cryo-correlative light-electron microscopy. Such resolution aids in precisely identifying regions of interest before tomographic acquisition and enhances precision in localizing features of interest within the 3D reconstruction. Dual-axis CSTET tilt series data and application of entropy regularized deconvolution during post-processing results in close-to-isotropic resolution in the reconstruction without averaging. The integration of cryo-SRRF with deconvolved dual-axis CSTET provides a versatile workflow for studying unique objects in a cell.
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Affiliation(s)
- Peter Kirchweger
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Debakshi Mullick
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Prabhu Prasad Swain
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel; School of Physical Sciences, UM-DAE Centre for Excellence in Basic Sciences, Mumbai 400098, India
| | - Sharon G Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michael Elbaum
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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25
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Lin C, Zhang L, Zhang Z, Jiang Y, Li X. Locating cellular contents during cryoFIB milling using cellular secondary-electron imaging. J Struct Biol 2023; 215:108005. [PMID: 37495195 DOI: 10.1016/j.jsb.2023.108005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 07/19/2023] [Accepted: 07/23/2023] [Indexed: 07/28/2023]
Abstract
Cryo-electron tomography (cryoET) is a powerful technology that allows in-situ observation of the molecular structure of tissues and cells. Cryo-focused ion beam (cryoFIB) milling plays an important role in the preparation of high-quality thin lamellar samples for cryoET studies, thus, promoting the rapid development of cryoET in recent years. However, locating the regions of interest in a large cell or tissue during cryoFIB milling remains a major challenge limiting cryoET applications on arbitrary biological samples. Here, we report an on-the-fly localization method based on cellular secondary electron imaging (CSEI), which is derived from a basic imaging function of the cryoFIB instruments and enables high-contrast imaging of the cellular contents of frozen-hydrated biological samples. Moreover, CSEI does not require fluorescent labels and additional devices. The present study discusses the imaging principles and settings for optimizing CSEI. Tests on several commercially available cryoFIB instruments demonstrated that CSEI was feasible on mainstream instruments to observe all types of cellular contents and reliable under different milling conditions. We established a simple milling-localization workflow and tested it using the basal body of Chlamydomonas reinhardtii.
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Affiliation(s)
- Chao Lin
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Beijing 100084, China; Advanced Innovation Center for Structural Biology, Beijing 100084, China
| | - Li Zhang
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Beijing 100084, China; Advanced Innovation Center for Structural Biology, Beijing 100084, China
| | - Ziying Zhang
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Beijing 100084, China; Advanced Innovation Center for Structural Biology, Beijing 100084, China
| | - Yifeng Jiang
- ZEISS Microscopy Customer Center, Beijing laboratory, Beijing 100088, China
| | - Xueming Li
- Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Beijing 100084, China; Advanced Innovation Center for Structural Biology, Beijing 100084, China.
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26
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Rane L, Wulffele J, Bourgeois D, Glushonkov O, Mantovanelli AMR, Zala N, Byrdin M. Light-Induced Forward and Reverse Intersystem Crossing in Green Fluorescent Proteins at Cryogenic Temperatures. J Phys Chem B 2023. [PMID: 37235526 DOI: 10.1021/acs.jpcb.3c02971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Combining fluorescence and phosphorescence kinetics, we characterize forward and reverse intersystem crossing (FISC and RISC, respectively) between the singlet and triplet manifolds S ↔ T in photoswitchable (rsEGFP2) and non-photoswitchable (EGFP) green fluorescent proteins upon continuous 488 nm laser excitation at cryogenic temperatures (CTs). Both proteins behave very similarly, with T1 absorption spectra showing a visible peak at 490 nm (10 mM-1 cm-1) and a vibrational progression in the near-infrared (720 to 905 nm). The dark lifetime of T1 is 21-24 ms at 100 K and very weakly temperature-dependent up to 180 K. Above 180 K, T1 lifetimes reduce rapidly to few milliseconds as found at room temperature (RT). FISC and RISC quantum yields are 0.3 and 0.1%, respectively, for both proteins. The light-induced RISC channel becomes faster than the dark reversal at power densities as low as 20 W cm-2. We discuss implications for fluorescence (super resolution-) microscopy at CT and RT.
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Affiliation(s)
- Lukas Rane
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Jip Wulffele
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Oleksandr Glushonkov
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Angela M R Mantovanelli
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Ninon Zala
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Martin Byrdin
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
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27
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Last MGF, Tuijtel MW, Voortman LM, Sharp TH. Selecting optimal support grids for super-resolution cryogenic correlated light and electron microscopy. Sci Rep 2023; 13:8270. [PMID: 37217690 DOI: 10.1038/s41598-023-35590-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/20/2023] [Indexed: 05/24/2023] Open
Abstract
Cryogenic transmission electron microscopy (cryo-TEM) and super-resolution fluorescence microscopy are two popular and ever improving methods for high-resolution imaging of biological samples. In recent years, the combination of these two techniques into one correlated workflow has gained attention as a promising route towards contextualizing and enriching cryo-TEM imagery. A problem that is often encountered in the combination of these methods is that of light-induced damage to the sample during fluorescence imaging that renders the sample structure unsuitable for TEM imaging. In this paper, we describe how absorption of light by TEM sample support grids leads to sample damage, and we systematically explore the importance of parameters of grid design. We explain how, by changing the grid geometry and materials, one can increase the maximum illumination power density in fluorescence microscopy by up to an order of magnitude. Finally, we demonstrate the significant improvements in super-resolution image quality that are enabled by the selection of support grids that are optimally suited for correlated cryo-microscopy.
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Affiliation(s)
- Mart G F Last
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC, Leiden, The Netherlands
| | - Maarten W Tuijtel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt Am Main, Germany
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre, 2300 RC, Leiden, The Netherlands.
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28
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de Beer M, Daviran D, Roverts R, Rutten L, Macías-Sánchez E, Metz JR, Sommerdijk N, Akiva A. Precise targeting for 3D cryo-correlative light and electron microscopy volume imaging of tissues using a FinderTOP. Commun Biol 2023; 6:510. [PMID: 37169904 PMCID: PMC10175257 DOI: 10.1038/s42003-023-04887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/28/2023] [Indexed: 05/13/2023] Open
Abstract
Cryo-correlative light and electron microscopy (cryoCLEM) is a powerful strategy to high resolution imaging in the unperturbed hydrated state. In this approach fluorescence microscopy aids localizing the area of interest, and cryogenic focused ion beam/scanning electron microscopy (cryoFIB/SEM) allows preparation of thin cryo-lamellae for cryoET. However, the current method cannot be accurately applied on bulky (3D) samples such as tissues and organoids. 3D cryo-correlative imaging of large volumes is needed to close the resolution gap between cryo-light microscopy and cryoET, placing sub-nanometer observations in a larger biological context. Currently technological hurdles render 3D cryoCLEM an unexplored approach. Here we demonstrate a cryoCLEM workflow for tissues, correlating cryo-Airyscan confocal microscopy with 3D cryoFIB/SEM volume imaging. Accurate correlation is achieved by imprinting a FinderTOP pattern in the sample surface during high pressure freezing, and allows precise targeting for cryoFIB/SEM volume imaging.
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Affiliation(s)
- Marit de Beer
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Deniz Daviran
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rona Roverts
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Luco Rutten
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elena Macías-Sánchez
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Stratigraphy and Paleontology, University of Granada, Granada, Spain
| | - Juriaan R Metz
- Department of Animal Ecology and Physiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Nico Sommerdijk
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Anat Akiva
- Electron Microscopy Center, Radboud Technology Center Microscopy, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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29
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Berger C, Premaraj N, Ravelli RBG, Knoops K, López-Iglesias C, Peters PJ. Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology. Nat Methods 2023; 20:499-511. [PMID: 36914814 DOI: 10.1038/s41592-023-01783-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/20/2023] [Indexed: 03/16/2023]
Abstract
Cryogenic electron microscopy and data processing enable the determination of structures of isolated macromolecules to near-atomic resolution. However, these data do not provide structural information in the cellular environment where macromolecules perform their native functions, and vital molecular interactions can be lost during the isolation process. Cryogenic focused ion beam (FIB) fabrication generates thin lamellae of cellular samples and tissues, enabling structural studies on the near-native cellular interior and its surroundings by cryogenic electron tomography (cryo-ET). Cellular cryo-ET benefits from the technological developments in electron microscopes, detectors and data processing, and more in situ structures are being obtained and at increasingly higher resolution. In this Review, we discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamellae, tomography, data processing and correlative light and electron microscopy that have enabled these studies. Finally, we explore the future of cryo-ET in terms of both methods development and biological application.
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Affiliation(s)
- Casper Berger
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Navya Premaraj
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Kèvin Knoops
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Carmen López-Iglesias
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands.
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30
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Tortarolo G, Manley S. Optical microscopy gets down to angstroms. Nat Biotechnol 2023; 41:473-474. [PMID: 36344839 DOI: 10.1038/s41587-022-01544-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Giorgio Tortarolo
- École Polytechnique Fédérale de Lausanne, Laboratory of Experimental Biophysics, Lausanne, Switzerland
| | - Suliana Manley
- École Polytechnique Fédérale de Lausanne, Laboratory of Experimental Biophysics, Lausanne, Switzerland.
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31
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Pope I, Tanner H, Masia F, Payne L, Arkill KP, Mantell J, Langbein W, Borri P, Verkade P. Correlative light-electron microscopy using small gold nanoparticles as single probes. LIGHT, SCIENCE & APPLICATIONS 2023; 12:80. [PMID: 36977682 PMCID: PMC10050153 DOI: 10.1038/s41377-023-01115-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/09/2023] [Accepted: 02/21/2023] [Indexed: 05/25/2023]
Abstract
Correlative light-electron microscopy (CLEM) requires the availability of robust probes which are visible both in light and electron microscopy. Here we demonstrate a CLEM approach using small gold nanoparticles as a single probe. Individual gold nanoparticles bound to the epidermal growth factor protein were located with nanometric precision background-free in human cancer cells by light microscopy using resonant four-wave mixing (FWM), and were correlatively mapped with high accuracy to the corresponding transmission electron microscopy images. We used nanoparticles of 10 nm and 5 nm radius, and show a correlation accuracy below 60 nm over an area larger than 10 µm size, without the need for additional fiducial markers. Correlation accuracy was improved to below 40 nm by reducing systematic errors, while the localisation precision is below 10 nm. Polarisation-resolved FWM correlates with nanoparticle shapes, promising for multiplexing by shape recognition in future applications. Owing to the photostability of gold nanoparticles and the applicability of FWM microscopy to living cells, FWM-CLEM opens up a powerful alternative to fluorescence-based methods.
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Affiliation(s)
- Iestyn Pope
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Hugh Tanner
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
- Department of Chemistry, Umeå University, Umeå, 90187, Sweden
| | - Francesco Masia
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Lukas Payne
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Kenton Paul Arkill
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
- School of Medicine, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Judith Mantell
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
| | - Wolfgang Langbein
- School of Physics and Astronomy, Cardiff University, The Parade, Cardiff, CF24 3AA, UK
| | - Paola Borri
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - Paul Verkade
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK.
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32
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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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33
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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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34
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Wilkinson EM, Spenkelink LM, van Oijen AM. Observing protein dynamics during DNA-lesion bypass by the replisome. Front Mol Biosci 2022; 9:968424. [PMID: 36213113 PMCID: PMC9534484 DOI: 10.3389/fmolb.2022.968424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Faithful DNA replication is essential for all life. A multi-protein complex called the replisome contains all the enzymatic activities required to facilitate DNA replication, including unwinding parental DNA and synthesizing two identical daughter molecules. Faithful DNA replication can be challenged by both intrinsic and extrinsic factors, which can result in roadblocks to replication, causing incomplete replication, genomic instability, and an increased mutational load. This increased mutational load can ultimately lead to a number of diseases, a notable example being cancer. A key example of a roadblock to replication is chemical modifications in the DNA caused by exposure to ultraviolet light. Protein dynamics are thought to play a crucial role to the molecular pathways that occur in the presence of such DNA lesions, including potential damage bypass. Therefore, many assays have been developed to study these dynamics. In this review, we discuss three methods that can be used to study protein dynamics during replisome–lesion encounters in replication reactions reconstituted from purified proteins. Specifically, we focus on ensemble biochemical assays, single-molecule fluorescence, and cryo-electron microscopy. We discuss two key model DNA replication systems, derived from Escherichia coli and Saccharomyces cerevisiae. The main methods of choice to study replication over the last decades have involved biochemical assays that rely on ensemble averaging. While these assays do not provide a direct readout of protein dynamics, they can often be inferred. More recently, single-molecule techniques including single-molecule fluorescence microscopy have been used to visualize replisomes encountering lesions in real time. In these experiments, individual proteins can be fluorescently labeled in order to observe the dynamics of specific proteins during DNA replication. Finally, cryo-electron microscopy can provide detailed structures of individual replisome components, which allows functional data to be interpreted in a structural context. While classic cryo-electron microscopy approaches provide static information, recent developments such as time-resolved cryo-electron microscopy help to bridge the gap between static structures and dynamic single-molecule techniques by visualizing sequential steps in biochemical pathways. In combination, these techniques will be capable of visualizing DNA replication and lesion encounter dynamics in real time, whilst observing the structural changes that facilitate these dynamics.
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Affiliation(s)
- Elise M. Wilkinson
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Lisanne M. Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- *Correspondence: Lisanne M. Spenkelink, ; Antoine M. van Oijen,
| | - Antoine M. van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- *Correspondence: Lisanne M. Spenkelink, ; Antoine M. van Oijen,
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35
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Piper SJ, Johnson RM, Wootten D, Sexton PM. Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM. Chem Rev 2022; 122:13989-14017. [PMID: 35849490 PMCID: PMC9480104 DOI: 10.1021/acs.chemrev.1c00837] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 11/29/2022]
Abstract
Membrane proteins are highly diverse in both structure and function and can, therefore, present different challenges for structure determination. They are biologically important for cells and organisms as gatekeepers for information and molecule transfer across membranes, but each class of membrane proteins can present unique obstacles to structure determination. Historically, many membrane protein structures have been investigated using highly engineered constructs or using larger fusion proteins to improve solubility and/or increase particle size. Other strategies included the deconstruction of the full-length protein to target smaller soluble domains. These manipulations were often required for crystal formation to support X-ray crystallography or to circumvent lower resolution due to high noise and dynamic motions of protein subdomains. However, recent revolutions in membrane protein biochemistry and cryo-electron microscopy now provide an opportunity to solve high resolution structures of both large, >1 megadalton (MDa), and small, <100 kDa (kDa), drug targets in near-native conditions, routinely reaching resolutions around or below 3 Å. This review provides insights into how the recent advances in membrane biology and biochemistry, as well as technical advances in cryo-electron microscopy, help us to solve structures of a large variety of membrane protein groups, from small receptors to large transporters and more complex machineries.
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Affiliation(s)
- Sarah J. Piper
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Rachel M. Johnson
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Denise Wootten
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Patrick M. Sexton
- Drug
Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- ARC
Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute
of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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36
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Gold nanomaterials and their potential use as cryo-electron tomography labels. J Struct Biol 2022; 214:107880. [PMID: 35809758 DOI: 10.1016/j.jsb.2022.107880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 12/14/2022]
Abstract
Rapid advances in cryo-electron tomography (cryo-ET) are driving a revolution in cellular structural biology. However, unambiguous identification of specific biomolecules within cellular tomograms remains challenging. Overcoming this obstacle and reliably identifying targets in the crowded cellular environment is of major importance for the understanding of cellular function and is a pre-requisite for high-resolution structural analysis. The use of highly-specific, readily visualised and adjustable labels would help mitigate this issue, improving both data quality and sample throughput. While progress has been made in cryo-CLEM and in the development of cloneable high-density tags, technical issues persist and a robust 'cryo-GFP' remains elusive. Readily-synthesized gold nanomaterials conjugated to small 'affinity modules' may represent a solution. The synthesis of materials including gold nanoclusters (AuNCs) and gold nanoparticles (AuNPs) is increasingly well understood and is now within the capabilities of non-specialist laboratories. The remarkable chemical and photophysical properties of <3nm diameter nanomaterials and their emergence as tools with widespread biomedical application presents significant opportunities to the cryo-microscopy community. In this review, we will outline developments in the synthesis, functionalisation and labelling uses of both AuNPs and AuNCs in cryo-ET, while discussing their potential as multi-modal probes for cryo-CLEM.
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37
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Chua EYD, Mendez JH, Rapp M, Ilca SL, Tan YZ, Maruthi K, Kuang H, Zimanyi CM, Cheng A, Eng ET, Noble AJ, Potter CS, Carragher B. Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy. Annu Rev Biochem 2022; 91:1-32. [PMID: 35320683 PMCID: PMC10393189 DOI: 10.1146/annurev-biochem-032620-110705] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cryo-electron microscopy (cryo-EM) continues its remarkable growth as a method for visualizing biological objects, which has been driven by advances across the entire pipeline. Developments in both single-particle analysis and in situ tomography have enabled more structures to be imaged and determined to better resolutions, at faster speeds, and with more scientists having improved access. This review highlights recent advances at each stageof the cryo-EM pipeline and provides examples of how these techniques have been used to investigate real-world problems, including antibody development against the SARS-CoV-2 spike during the recent COVID-19 pandemic.
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Affiliation(s)
- Eugene Y D Chua
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Joshua H Mendez
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Micah Rapp
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Serban L Ilca
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, Singapore;
- Disease Intervention Technology Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kashyap Maruthi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Christina M Zimanyi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Anchi Cheng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Edward T Eng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Alex J Noble
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Clinton S Potter
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Bridget Carragher
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
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38
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Automated vitrification of cryo-EM samples with controllable sample thickness using suction and real-time optical inspection. Nat Commun 2022; 13:2985. [PMID: 35624105 PMCID: PMC9142589 DOI: 10.1038/s41467-022-30562-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/26/2022] [Indexed: 12/13/2022] Open
Abstract
The speed and efficiency of data collection and image processing in cryo-electron microscopy have increased over the last decade. However, cryo specimen preparation techniques have lagged and faster, more reproducible specimen preparation devices are needed. Here, we present a vitrification device with highly automated sample handling, requiring only limited user interaction. Moreover, the device allows inspection of thin films using light microscopy, since the excess liquid is removed through suction by tubes, not blotting paper. In combination with dew-point control, this enables thin film preparation in a controlled and reproducible manner. The advantage is that the quality of the prepared cryo specimen is characterized before electron microscopy data acquisition. The practicality and performance of the device are illustrated with experimental results obtained by vitrification of protein suspensions, lipid vesicles, bacterial and human cells, followed by imaged using single particle analysis, cryo-electron tomography, and cryo correlated light and electron microscopy. Faster cryo specimen preparation can advance cryo electron microscopy (cryoEM). Here, the authors present a vitrification device with automated sample handling for cryoEM of proteins, suspensions and cells, enabling blot-free sample thinning, dew-point control and characterization of cryo grids prior to data acquisition.
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39
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Mazal H, Wieser FF, Sandoghdar V. Deciphering a hexameric protein complex with Angstrom optical resolution. eLife 2022; 11:76308. [PMID: 35616526 PMCID: PMC9142145 DOI: 10.7554/elife.76308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/12/2022] [Indexed: 12/24/2022] Open
Abstract
Cryogenic optical localization in three dimensions (COLD) was recently shown to resolve up to four binding sites on a single protein. However, because COLD relies on intensity fluctuations that result from the blinking behavior of fluorophores, it is limited to cases where individual emitters show different brightness. This significantly lowers the measurement yield. To extend the number of resolved sites as well as the measurement yield, we employ partial labeling and combine it with polarization encoding in order to identify single fluorophores during their stochastic blinking. We then use a particle classification scheme to identify and resolve heterogenous subsets and combine them to reconstruct the three-dimensional arrangement of large molecular complexes. We showcase this method (polarCOLD) by resolving the trimer arrangement of proliferating cell nuclear antigen (PCNA) and six different sites of the hexamer protein Caseinolytic Peptidase B (ClpB) of Thermus thermophilus in its quaternary structure, both with Angstrom resolution. The combination of polarCOLD and single-particle cryogenic electron microscopy (cryoEM) promises to provide crucial insight into intrinsic heterogeneities of biomolecular structures. Furthermore, our approach is fully compatible with fluorescent protein labeling and can, thus, be used in a wide range of studies in cell and membrane biology.
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Affiliation(s)
- Hisham Mazal
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Franz-Ferdinand Wieser
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.,Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
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40
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Hinterer F, Schneider MC, Hubmer S, López-Martinez M, Zelger P, Jesacher A, Ramlau R, Schütz GJ. Robust and bias-free localization of individual fixed dipole emitters achieving the Cramér Rao bound for applications in cryo-single molecule localization microscopy. PLoS One 2022; 17:e0263500. [PMID: 35120171 PMCID: PMC8815875 DOI: 10.1371/journal.pone.0263500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 01/20/2022] [Indexed: 11/18/2022] Open
Abstract
Single molecule localization microscopy (SMLM) has the potential to resolve structural details of biological samples at the nanometer length scale. Compared to room temperature experiments, SMLM performed under cryogenic temperature achieves higher photon yields and, hence, higher localization precision. However, to fully exploit the resolution it is crucial to account for the anisotropic emission characteristics of fluorescence dipole emitters with fixed orientation. In case of slight residual defocus, localization estimates may well be biased by tens of nanometers. We show here that astigmatic imaging in combination with information about the dipole orientation allows to extract the position of the dipole emitters without localization bias and down to a precision of 1 nm, thereby reaching the corresponding Cramér Rao bound. The approach is showcased with simulated data for various dipole orientations, and parameter settings realistic for real life experiments.
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Affiliation(s)
- Fabian Hinterer
- Institute of Industrial Mathematics, Johannes Kepler University Linz, Linz, Austria
| | | | | | | | - Philipp Zelger
- Division for Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander Jesacher
- Division for Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - Ronny Ramlau
- Institute of Industrial Mathematics, Johannes Kepler University Linz, Linz, Austria
- Johann Radon Institute Linz, Linz, Austria
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41
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Parasitology meets cryo-electron tomography – exciting prospects await. Trends Parasitol 2022; 38:365-378. [DOI: 10.1016/j.pt.2022.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 12/27/2022]
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42
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Anton L, Cobb DW, Ho CM. Structural parasitology of the malaria parasite Plasmodium falciparum. Trends Biochem Sci 2022; 47:149-159. [PMID: 34887149 PMCID: PMC11236216 DOI: 10.1016/j.tibs.2021.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/20/2021] [Accepted: 10/25/2021] [Indexed: 12/25/2022]
Abstract
The difficulty of faithfully recapitulating malarial protein complexes in heterologous expression systems has long impeded structural study for much of the Plasmodium falciparum proteome. However, recent advances in single-particle cryo electron microscopy (cryoEM) now enable structure determination at atomic resolution with significantly reduced requirements for both sample quantity and purity. Combined with recent developments in gene editing, these advances open the door to structure determination and structural proteomics of macromolecular complexes enriched directly from P. falciparum parasites. Furthermore, the combination of cryoEM with the rapidly emerging use of in situ cryo electron tomography (cryoET) to directly visualize ultrastructures and protein complexes in the native cellular context will yield exciting new insights into the molecular machinery underpinning malaria parasite biology and pathogenesis.
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Affiliation(s)
- Leonie Anton
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - David W Cobb
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Chi-Min Ho
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.
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43
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Lane R, Wolters AHG, Giepmans BNG, Hoogenboom JP. Integrated Array Tomography for 3D Correlative Light and Electron Microscopy. Front Mol Biosci 2022; 8:822232. [PMID: 35127826 PMCID: PMC8809480 DOI: 10.3389/fmolb.2021.822232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022] Open
Abstract
Volume electron microscopy (EM) of biological systems has grown exponentially in recent years due to innovative large-scale imaging approaches. As a standalone imaging method, however, large-scale EM typically has two major limitations: slow rates of acquisition and the difficulty to provide targeted biological information. We developed a 3D image acquisition and reconstruction pipeline that overcomes both of these limitations by using a widefield fluorescence microscope integrated inside of a scanning electron microscope. The workflow consists of acquiring large field of view fluorescence microscopy (FM) images, which guide to regions of interest for successive EM (integrated correlative light and electron microscopy). High precision EM-FM overlay is achieved using cathodoluminescent markers. We conduct a proof-of-concept of our integrated workflow on immunolabelled serial sections of tissues. Acquisitions are limited to regions containing biological targets, expediting total acquisition times and reducing the burden of excess data by tens or hundreds of GBs.
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Affiliation(s)
- Ryan Lane
- Imaging Physics, Delft University of Technology, Delft, Netherlands
| | - Anouk H. G. Wolters
- Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ben N. G. Giepmans
- Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, Groningen, Netherlands
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44
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Saibil HR. Cryo-EM in molecular and cellular biology. Mol Cell 2022; 82:274-284. [DOI: 10.1016/j.molcel.2021.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022]
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45
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Tian B, Xu X, Xue Y, Ji W, Xu T. Cryogenic superresolution correlative light and electron microscopy on the frontier of subcellular imaging. Biophys Rev 2021; 13:1163-1171. [DOI: 10.1007/s12551-021-00851-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/03/2021] [Indexed: 12/22/2022] Open
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46
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Parlanti P, Cappello V. Microscopes, tools, probes, and protocols: A guide in the route of correlative microscopy for biomedical investigation. Micron 2021; 152:103182. [PMID: 34801960 DOI: 10.1016/j.micron.2021.103182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 12/11/2022]
Abstract
In the last decades, the advancements of microscopes technology, together with the development of new imaging approaches, are trying to address some biological questions that have been unresolved in the past: the need to combine in the same analysis temporal, functional and morphological information on the biological sample has become pressing. For this reason, the use of correlative microscopy, in which two or more imaging techniques are combined in the same analysis, is getting increasingly widespread. In fact, correlative microscopy can overcome limitations of a single imaging method, giving access to a larger amount of information from the same specimen. However, correlative microscopy can be challenging, and appropriate protocols for sample preparation and imaging methods must be selected. Here we review the state of the art of correlating electron microscopy with different imaging methods, focusing on sample preparation, tools, and labeling methods, with the aim to provide a comprehensive guide for those scientists who are approaching the field of correlative methods.
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Affiliation(s)
- Paola Parlanti
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, I-56025, Pontedera (PI), Italy.
| | - Valentina Cappello
- Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography, Viale Rinaldo Piaggio 34, I-56025, Pontedera (PI), Italy.
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47
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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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48
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Andrian T, Delcanale P, Pujals S, Albertazzi L. Correlating Super-Resolution Microscopy and Transmission Electron Microscopy Reveals Multiparametric Heterogeneity in Nanoparticles. NANO LETTERS 2021; 21:5360-5368. [PMID: 34125548 PMCID: PMC8227466 DOI: 10.1021/acs.nanolett.1c01666] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/03/2021] [Indexed: 05/22/2023]
Abstract
The functionalization of nanoparticles with functional moieties is a key strategy to achieve cell targeting in nanomedicine. The interplay between size and ligand number is crucial for the formulation performance and needs to be properly characterized to understand nanoparticle structure-activity relations. However, there is a lack of methods able to measure both size and ligand number at the same time and at the single particle level. Here, we address this issue by introducing a correlative light and electron microscopy (CLEM) method combining super-resolution microscopy (SRM) and transmission electron microscopy (TEM) imaging. We apply our super-resCLEM method to characterize the relationship between size and ligand number and density in PLGA-PEG nanoparticles. We highlight how heterogeneity found in size can impact ligand distribution and how a significant part of the nanoparticle population goes completely undetected in the single-technique analysis. Super-resCLEM holds great promise for the multiparametric analysis of other parameters and nanomaterials.
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Affiliation(s)
- Teodora Andrian
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 15-21, 08028 Barcelona, Spain
| | - Pietro Delcanale
- Dipartimento
di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco area delle Scienze 7/A, 43124 Parma, Italy
| | - Silvia Pujals
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 15-21, 08028 Barcelona, Spain
- Department
of Electronics and Biomedical Engineering, Faculty of Physics, Universitat de Barcelona, Avenido Diagonal 647, 08028, Barcelona, Spain
| | - Lorenzo Albertazzi
- Institute
for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 15-21, 08028 Barcelona, Spain
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
- ;
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49
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Konen T, Stumpf D, Grotjohann T, Jansen I, Bossi M, Weber M, Jensen N, Hell SW, Jakobs S. The Positive Switching Fluorescent Protein Padron2 Enables Live-Cell Reversible Saturable Optical Linear Fluorescence Transitions (RESOLFT) Nanoscopy without Sequential Illumination Steps. ACS NANO 2021; 15:9509-9521. [PMID: 34019380 PMCID: PMC8291764 DOI: 10.1021/acsnano.0c08207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Reversibly switchable fluorescent proteins (RSFPs) can be repeatedly transferred between a fluorescent on- and a nonfluorescent off-state by illumination with light of different wavelengths. Negative switching RSFPs are switched from the on- to the off-state with the same wavelength that also excites fluorescence. Positive switching RSFPs have a reversed light response, where the fluorescence excitation wavelength induces the transition from the off- to the on-state. Reversible saturable optical linear (fluorescence) transitions (RESOLFT) nanoscopy utilizes these switching states to achieve diffraction-unlimited resolution but so far has primarily relied on negative switching RSFPs by using time sequential switching schemes. On the basis of the green fluorescent RSFP Padron, we engineered the positive switching RSFP Padron2. Compared to its predecessor, it can undergo 50-fold more switching cycles while displaying a contrast ratio between the on- and the off-states of more than 100:1. Because of its robust switching behavior, Padron2 supports a RESOLFT imaging scheme that entirely refrains from sequential switching as it only requires beam scanning of two spatially overlaid light distributions. Using Padron2, we demonstrate live-cell RESOLFT nanoscopy without sequential illumination steps.
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Affiliation(s)
- Timo Konen
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Daniel Stumpf
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Tim Grotjohann
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Isabelle Jansen
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Mariano Bossi
- Department
of Optical Nanoscopy, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Michael Weber
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Nickels Jensen
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stefan W. Hell
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
- Department
of Optical Nanoscopy, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Stefan Jakobs
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
- Clinic
of Neurology, University of Göttingen, 37075 Göttingen, Germany
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50
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Abstract
The application of cryo-correlative light and cryo-electron microscopy (cryo-CLEM) gives us a way to locate structures of interest in the electron microscope. In brief, the structures of interest are fluorescently tagged, and images from the cryo-fluorescent microscope (cryo-FM) maps are superimposed on those from the cryo-electron microscope (cryo-EM). By enhancing cryo-FM to include single-molecule localization microscopy (SMLM), we can achieve much better localization. The introduction of cryo-SMLM increased the yield of photons from fluorophores, which can benefit localization efforts. Dahlberg and Moerner (2021, Annual Review of Physical Chemistry, 72, 253-278) have a recent broad and elegant review of super-resolution cryo-CLEM. This paper focuses on cryo(F)PALM/STORM for the cryo-electron tomography community. I explore the current challenges to increase the accuracy of localization by SMLM and the mapping of those positions onto cryo-EM images and maps. There is much to consider: we need to know if the excitation of fluorophores damages the structures we seek to visualize. We need to determine if higher numerical aperture (NA) objectives, which add complexity to image analysis but increase resolution and the efficiency of photon collection, are better than lower NA objectives, which pose fewer problems. We need to figure out the best way to determine the axial position of fluorophores. We need to have better ways of aligning maps determined by FM with those determined by EM. We need to improve the instrumentation to be easier to use, more accurate, and ice-contamination free. The bottom line is that we have more work to do.
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