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Hutchings J, Villa E. Expanding insights from in situ cryo-EM. Curr Opin Struct Biol 2024; 88:102885. [PMID: 38996624 DOI: 10.1016/j.sbi.2024.102885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/28/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
The combination of cryo-electron tomography and subtomogram analysis affords 3D high-resolution views of biological macromolecules in their native cellular environment, or in situ. Streamlined methods for acquiring and processing these data are advancing attainable resolutions into the realm of drug discovery. Yet regardless of resolution, structure prediction driven by artificial intelligence (AI) combined with subtomogram analysis is becoming powerful in understanding macromolecular assemblies. Automated and AI-assisted data mining is increasingly necessary to cope with the growing wealth of tomography data and to maximize the information obtained from them. Leveraging developments from AI and single-particle analysis could be essential in fulfilling the potential of in situ cryo-EM. Here, we highlight new developments for in situ cryo-EM and the emerging potential for AI in this process.
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Affiliation(s)
- Joshua Hutchings
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA.
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2
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Yoniles J, Summers JA, Zielinski KA, Antolini C, Panjalingam M, Lisova S, Moss FR, Di Perna MA, Kupitz C, Hunter MS, Pollack L, Wakatsuki S, Dahlberg PD. Time-resolved cryogenic electron tomography for the study of transient cellular processes. Mol Biol Cell 2024; 35:mr4. [PMID: 38717434 PMCID: PMC11244162 DOI: 10.1091/mbc.e24-01-0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/15/2024] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
Cryogenic electron tomography (cryo-ET) is the highest resolution imaging technique applicable to the life sciences, enabling subnanometer visualization of specimens preserved in their near native states. The rapid plunge freezing process used to prepare samples lends itself to time-resolved studies, which researchers have pursued for in vitro samples for decades. Here, we focus on developing a freezing apparatus for time-resolved studies in situ. The device mixes cellular samples with solution-phase stimulants before spraying them directly onto an electron microscopy grid that is transiting into cryogenic liquid ethane. By varying the flow rates of cell and stimulant solutions within the device, we can control the reaction time from tens of milliseconds to over a second before freezing. In a proof-of-principle demonstration, the freezing method is applied to a model bacterium, Caulobacter crescentus, mixed with an acidic buffer. Through cryo-ET we resolved structural changes throughout the cell, including surface-layer protein dissolution, outer membrane deformation, and cytosolic rearrangement, all within 1.5 s of reaction time. This new approach, Time-Resolved cryo-ET (TR-cryo-ET), enhances the capabilities of cryo-ET by incorporating a subsecond temporal axis and enables the visualization of induced structural changes at the molecular, organelle, or cellular level.
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Affiliation(s)
- Joseph Yoniles
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305
| | - Jacob A. Summers
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Kara A. Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Cali Antolini
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | | | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Frank R. Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | | | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Peter D. Dahlberg
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
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3
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Galaz-Montoya JG. The advent of preventive high-resolution structural histopathology by artificial-intelligence-powered cryogenic electron tomography. Front Mol Biosci 2024; 11:1390858. [PMID: 38868297 PMCID: PMC11167099 DOI: 10.3389/fmolb.2024.1390858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/08/2024] [Indexed: 06/14/2024] Open
Abstract
Advances in cryogenic electron microscopy (cryoEM) single particle analysis have revolutionized structural biology by facilitating the in vitro determination of atomic- and near-atomic-resolution structures for fully hydrated macromolecular complexes exhibiting compositional and conformational heterogeneity across a wide range of sizes. Cryogenic electron tomography (cryoET) and subtomogram averaging are rapidly progressing toward delivering similar insights for macromolecular complexes in situ, without requiring tags or harsh biochemical purification. Furthermore, cryoET enables the visualization of cellular and tissue phenotypes directly at molecular, nanometric resolution without chemical fixation or staining artifacts. This forward-looking review covers recent developments in cryoEM/ET and related technologies such as cryogenic focused ion beam milling scanning electron microscopy and correlative light microscopy, increasingly enhanced and supported by artificial intelligence algorithms. Their potential application to emerging concepts is discussed, primarily the prospect of complementing medical histopathology analysis. Machine learning solutions are poised to address current challenges posed by "big data" in cryoET of tissues, cells, and macromolecules, offering the promise of enabling novel, quantitative insights into disease processes, which may translate into the clinic and lead to improved diagnostics and targeted therapeutics.
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Affiliation(s)
- Jesús G. Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, United States
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4
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Grillová L, Romeis E, Lieberman NAP, Tantalo LC, Xu LH, Molini B, Trejos AT, Lacey G, Goulding D, Thomson NR, Greninger AL, Giacani L. Bright New Resources for Syphilis Research: Genetically Encoded Fluorescent Tags for Treponema pallidum and Sf1Ep Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596454. [PMID: 38854070 PMCID: PMC11160695 DOI: 10.1101/2024.05.29.596454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The recently discovered methodologies to cultivate and genetically manipulate Treponema pallidum subsp. pallidum ( T. pallidum ) have significantly helped syphilis research, allowing the in vitro evaluation of antibiotic efficacy, performance of controlled studies to assess differential treponemal gene expression, and generation of loss-of-function mutants to evaluate the contribution of specific genetic loci to T. pallidum virulence. Building on this progress, we engineered the T. pallidum SS14 strain to express a red-shifted Green Fluorescent Protein (GFP) and Sf1Ep cells to express mCherry and blue fluorescent protein (BFP) for enhanced visualization. These new resources improve microscopy- and cell sorting-based applications for T. pallidum , better capturing the physical interaction between the host and pathogen, among other possibilities. Continued efforts to develop and share new tools and resources are required to help our overall knowledge of T. pallidum biology and syphilis pathogenesis reach that of other bacterial pathogens, including spirochetes. Graphical abstract By employing genetic engineering, T. pallidum was modified to express GFP, and Sf1Ep cells to express mCherry on the cytoplasmic membrane and BFP in the nucleus. These new resources for syphilis research will facilitate experimental designs to better define the complex interplay between T. pallidum and the host during infection.
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5
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Perez D, Dowlatshahi DP, Azaldegui CA, Dahlberg PD, Moerner WE. Exploring transient states of PAmKate to enable improved cryogenic single-molecule imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590965. [PMID: 38712218 PMCID: PMC11071506 DOI: 10.1101/2024.04.24.590965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Super-resolved cryogenic correlative light and electron microscopy is a powerful approach which combines the single-molecule specificity and sensitivity of fluorescence imaging with the nano-scale resolution of cryogenic electron tomography. Key to this method is active control over the emissive state of fluorescent labels to ensure sufficient sparsity to localize individual emitters. Recent work has identified fluorescent proteins (FPs) which photoactivate or photoswitch efficiently at cryogenic temperatures, but long on-times due to reduced quantum yield of photobleaching remains a challenge for imaging structures with a high density of localizations. In this work, we explore the photophysical properties of the red photoactivatable FP PAmKate and identify a 2-color process leading to enhanced turn-off of active emitters, improving localization rate. Specifically, after excitation of ground state molecules, we find a transient state forms with a lifetime of ~2 ms which can be bleached by exposure to a second wavelength. We measure the response of the transient state to different wavelengths, demonstrate how this mechanism can be used to improve imaging, and provide a blueprint for study of other FPs at cryogenic temperatures.
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Affiliation(s)
- Davis Perez
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Dara P Dowlatshahi
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
- Department of Structural Biology, Stanford University, Stanford, California 94305, United States
| | - Christopher A Azaldegui
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Peter D Dahlberg
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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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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Zhou Q, Liu Q, Wang Y, Chen J, Schmid O, Rehberg M, Yang L. Bridging Smart Nanosystems with Clinically Relevant Models and Advanced Imaging for Precision Drug Delivery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308659. [PMID: 38282076 PMCID: PMC11005737 DOI: 10.1002/advs.202308659] [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: 11/12/2023] [Indexed: 01/30/2024]
Abstract
Intracellular delivery of nano-drug-carriers (NDC) to specific cells, diseased regions, or solid tumors has entered the era of precision medicine that requires systematic knowledge of nano-biological interactions from multidisciplinary perspectives. To this end, this review first provides an overview of membrane-disruption methods such as electroporation, sonoporation, photoporation, microfluidic delivery, and microinjection with the merits of high-throughput and enhanced efficiency for in vitro NDC delivery. The impact of NDC characteristics including particle size, shape, charge, hydrophobicity, and elasticity on cellular uptake are elaborated and several types of NDC systems aiming for hierarchical targeting and delivery in vivo are reviewed. Emerging in vitro or ex vivo human/animal-derived pathophysiological models are further explored and highly recommended for use in NDC studies since they might mimic in vivo delivery features and fill the translational gaps from animals to humans. The exploration of modern microscopy techniques for precise nanoparticle (NP) tracking at the cellular, organ, and organismal levels informs the tailored development of NDCs for in vivo application and clinical translation. Overall, the review integrates the latest insights into smart nanosystem engineering, physiological models, imaging-based validation tools, all directed towards enhancing the precise and efficient intracellular delivery of NDCs.
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Affiliation(s)
- Qiaoxia Zhou
- Institute of Lung Health and Immunity (LHI), Helmholtz MunichComprehensive Pneumology Center (CPC‐M)Member of the German Center for Lung Research (DZL)85764MunichGermany
- Department of Forensic PathologyWest China School of Preclinical and Forensic MedicineSichuan UniversityNo. 17 Third Renmin Road NorthChengdu610041China
- Burning Rock BiotechBuilding 6, Phase 2, Standard Industrial Unit, No. 7 LuoXuan 4th Road, International Biotech IslandGuangzhou510300China
| | - Qiongliang Liu
- Institute of Lung Health and Immunity (LHI), Helmholtz MunichComprehensive Pneumology Center (CPC‐M)Member of the German Center for Lung Research (DZL)85764MunichGermany
- Department of Thoracic SurgeryShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai200080China
| | - Yan Wang
- Qingdao Central HospitalUniversity of Health and Rehabilitation Sciences (Qingdao Central Medical Group)Qingdao266042China
| | - Jie Chen
- Department of Respiratory MedicineNational Key Clinical SpecialtyBranch of National Clinical Research Center for Respiratory DiseaseXiangya HospitalCentral South UniversityChangshaHunan410008China
- Center of Respiratory MedicineXiangya HospitalCentral South UniversityChangshaHunan410008China
- Clinical Research Center for Respiratory Diseases in Hunan ProvinceChangshaHunan410008China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory DiseaseChangshaHunan410008China
- National Clinical Research Center for Geriatric DisordersXiangya HospitalChangshaHunan410008P. R. China
| | - Otmar Schmid
- Institute of Lung Health and Immunity (LHI), Helmholtz MunichComprehensive Pneumology Center (CPC‐M)Member of the German Center for Lung Research (DZL)85764MunichGermany
| | - Markus Rehberg
- Institute of Lung Health and Immunity (LHI), Helmholtz MunichComprehensive Pneumology Center (CPC‐M)Member of the German Center for Lung Research (DZL)85764MunichGermany
| | - Lin Yang
- Institute of Lung Health and Immunity (LHI), Helmholtz MunichComprehensive Pneumology Center (CPC‐M)Member of the German Center for Lung Research (DZL)85764MunichGermany
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8
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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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9
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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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10
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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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11
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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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12
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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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13
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Taraska JW. Genetically encoded shape probes for cryogenic electron tomography. Nat Methods 2023; 20:1874-1876. [PMID: 37932396 DOI: 10.1038/s41592-023-02044-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Affiliation(s)
- Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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14
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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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15
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Marin Z, Fuentes LA, Bewersdorf J, Baddeley D. Extracting nanoscale membrane morphology from single-molecule localizations. Biophys J 2023; 122:3022-3030. [PMID: 37355772 PMCID: PMC10432223 DOI: 10.1016/j.bpj.2023.06.010] [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: 03/08/2023] [Revised: 05/17/2023] [Accepted: 06/15/2023] [Indexed: 06/26/2023] Open
Abstract
Membrane surface reconstruction at the nanometer scale is required for understanding mechanisms of subcellular shape change. This historically has been the domain of electron microscopy, but extraction of surfaces from specific labels is a difficult task in this imaging modality. Existing methods for extracting surfaces from fluorescence microscopy have poor resolution or require high-quality super-resolution data that are manually cleaned and curated. Here, we present NanoWrap, a new method for extracting surfaces from generalized single-molecule localization microscopy data. This makes it possible to study the shape of specifically labeled membranous structures inside cells. We validate NanoWrap using simulations and demonstrate its reconstruction capabilities on single-molecule localization microscopy data of the endoplasmic reticulum and mitochondria. NanoWrap is implemented in the open-source Python Microscopy Environment.
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Affiliation(s)
- Zach Marin
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand; Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut; Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Lukas A Fuentes
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut; Department of Biomedical Engineering, Yale University, New Haven, Connecticut; Department of Physics, Yale University, New Haven, Connecticut
| | - David Baddeley
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand; Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut.
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16
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Perez D, Dahlberg PD, Moerner WE. Advanced Cryogenic Light Microscopy Stage to Enable 3D Super-resolved Cryogenic Correlative Light and Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1941. [PMID: 37612900 DOI: 10.1093/micmic/ozad067.1005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Davis Perez
- Department of Chemistry, Stanford University, Stanford, CA, United States
| | - Peter D Dahlberg
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, United States
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, United States
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17
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Zimmermann L, Chlanda P. Cryo-electron tomography of viral infection - from applications to biosafety. Curr Opin Virol 2023; 61:101338. [PMID: 37348443 DOI: 10.1016/j.coviro.2023.101338] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/25/2023] [Accepted: 05/28/2023] [Indexed: 06/24/2023]
Abstract
Cellular cryo-electron tomography (cryo-ET) offers 3D snapshots at molecular resolution capturing pivotal steps during viral infection. However, tomogram quality depends on the vitrification level of the sample and its thickness. In addition, mandatory inactivation protocols to assure biosafety when handling highly pathogenic viruses during cryo-ET can compromise sample preservation. Here, we focus on different strategies applied in cryo-ET and discuss their advantages and limitations with reference to severe acute respiratory syndrome coronavirus 2 studies. We highlight the importance of virus-like particle (VLP) and replicon systems to study virus assembly and replication in a cellular context without inactivation protocols. We discuss the application of chemical fixation and different irradiation methods in cryo-ET sample preparation and acquisition workflows.
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Affiliation(s)
- Liv Zimmermann
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
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18
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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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19
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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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20
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Burgers TCQ, Vlijm R. Fluorescence-based super-resolution-microscopy strategies for chromatin studies. Chromosoma 2023:10.1007/s00412-023-00792-9. [PMID: 37000292 PMCID: PMC10356683 DOI: 10.1007/s00412-023-00792-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/28/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023]
Abstract
Super-resolution microscopy (SRM) is a prime tool to study chromatin organisation at near biomolecular resolution in the native cellular environment. With fluorescent labels DNA, chromatin-associated proteins and specific epigenetic states can be identified with high molecular specificity. The aim of this review is to introduce the field of diffraction-unlimited SRM to enable an informed selection of the most suitable SRM method for a specific chromatin-related research question. We will explain both diffraction-unlimited approaches (coordinate-targeted and stochastic-localisation-based) and list their characteristic spatio-temporal resolutions, live-cell compatibility, image-processing, and ability for multi-colour imaging. As the increase in resolution, compared to, e.g. confocal microscopy, leads to a central role of the sample quality, important considerations for sample preparation and concrete examples of labelling strategies applicable to chromatin research are discussed. To illustrate how SRM-based methods can significantly improve our understanding of chromatin functioning, and to serve as an inspiring starting point for future work, we conclude with examples of recent applications of SRM in chromatin research.
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Affiliation(s)
- Thomas C Q Burgers
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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21
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Sartor A, Dahlberg PD, Perez D, Moerner WE. Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms. J Phys Chem B 2023; 127:2690-2700. [PMID: 36943356 PMCID: PMC10069424 DOI: 10.1021/acs.jpcb.2c08995] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/01/2023] [Indexed: 03/23/2023]
Abstract
Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. We find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.
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Affiliation(s)
- Annina
M. Sartor
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Division
of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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22
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Marin Z, Fuentes LA, Bewersdorf J, Baddeley D. Extracting nanoscale membrane morphology from single-molecule localizations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525798. [PMID: 36945449 PMCID: PMC10028748 DOI: 10.1101/2023.01.26.525798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Membrane surface reconstruction at the nanometer scale is required for understanding mechanisms of subcellular shape change. This historically has been the domain of electron microscopy, but extraction of surfaces from specific labels is a difficult task in this imaging modality. Existing methods for extracting surfaces from fluorescence microscopy have poor resolution or require high-quality super-resolution data that is manually cleaned and curated. Here we present a new method for extracting surfaces from generalized single-molecule localization microscopy (SMLM) data. This makes it possible to study the shape of specifically-labelled membraneous structures inside of cells. We validate our method using simulations and demonstrate its reconstruction capabilities on SMLM data of the endoplasmic reticulum and mitochondria. Our method is implemented in the open-source Python Microscopy Environment. SIGNIFICANCE We introduce a novel tool for reconstruction of subcellular membrane surfaces from single-molecule localization microscopy data and use it to visualize and quantify local shape and membrane-membrane interactions. We benchmark its performance on simulated data and demonstrate its fidelity to experimental data.
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23
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Zabeo D, Davies KM. Studying membrane modulation mechanisms by electron cryo-tomography. Curr Opin Struct Biol 2022; 77:102464. [PMID: 36174286 DOI: 10.1016/j.sbi.2022.102464] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 12/14/2022]
Abstract
Membrane modulation is a key part of cellular life. Critical to processes like energy production, cell division, trafficking, migration and even pathogen entry, defects in membrane modulation are often associated with diseases. Studying the molecular mechanisms of membrane modulation is challenging due to the highly dynamic nature of the oligomeric assemblies involved, which adopt multiple conformations depending on the precise event they are participating in. With the development of electron cryo-tomography and subtomogram averaging, many of these challenges are being resolved as it is now possible to observe complex macromolecular assemblies inside a cell at nanometre to sub-nanometre resolutions. Here, we review the different ways electron cryo-tomography is being used to help uncover the molecular mechanisms used by cells to shape their membranes.
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Affiliation(s)
- Davide Zabeo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Karen M Davies
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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24
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New opportunities in integrative structural modeling. Curr Opin Struct Biol 2022; 77:102488. [PMID: 36279817 DOI: 10.1016/j.sbi.2022.102488] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 12/14/2022]
Abstract
Integrative structural modeling enables structure determination of macromolecules and their complexes by integrating data from multiple sources. It has been successfully used to characterize macromolecular structures when a single structural biology technique was insufficient. Recent developments in cellular structural biology, including in-cell cryo-electron tomography and artificial intelligence-based structure prediction, have created new opportunities for integrative structural modeling. Here, we will review these opportunities along with the latest developments in integrative modeling methods and their applications. We also highlight open challenges and directions for further development.
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25
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Guaita M, Watters SC, Loerch S. Recent advances and current trends in cryo-electron microscopy. Curr Opin Struct Biol 2022; 77:102484. [PMID: 36323134 DOI: 10.1016/j.sbi.2022.102484] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/13/2022] [Accepted: 09/21/2022] [Indexed: 12/14/2022]
Abstract
All steps of cryogenic electron-microscopy (cryo-EM) workflows have rapidly evolved over the last decade. Advances in both single-particle analysis (SPA) cryo-EM and cryo-electron tomography (cryo-ET) have facilitated the determination of high-resolution biomolecular structures that are not tractable with other methods. However, challenges remain. For SPA, these include improved resolution in an additional dimension: time. For cryo-ET, these include accessing difficult-to-image areas of a cell and finding rare molecules. Finally, there is a need for automated and faster workflows, as many projects are limited by throughput. Here, we review current developments in SPA cryo-EM and cryo-ET that push these boundaries. Collectively, these advances are poised to propel our spatial and temporal understanding of macromolecular processes.
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Affiliation(s)
- Margherita Guaita
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Scott C Watters
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Sarah Loerch
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA.
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26
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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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27
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Russo CJ, Dickerson JL, Naydenova K. Cryomicroscopy in situ: what is the smallest molecule that can be directly identified without labels in a cell? Faraday Discuss 2022; 240:277-302. [PMID: 35913392 PMCID: PMC9642008 DOI: 10.1039/d2fd00076h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Electron cryomicroscopy (cryoEM) has made great strides in the last decade, such that the atomic structure of most biological macromolecules can, at least in principle, be determined. Major technological advances - in electron imaging hardware, data analysis software, and cryogenic specimen preparation technology - continue at pace and contribute to the exponential growth in the number of atomic structures determined by cryoEM. It is now conceivable that within the next decade we will have structures for hundreds of thousands of unique protein and nucleic acid molecular complexes. But the answers to many important questions in biology would become obvious if we could identify these structures precisely inside cells with quantifiable error. In the context of an abundance of known structures, it is appropriate to consider the current state of electron cryomicroscopy for frozen specimens prepared directly from cells, and try to answer to the question of the title, both now and in the foreseeable future.
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Affiliation(s)
- Christopher J Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Joshua L Dickerson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Katerina Naydenova
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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28
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Lovatt M, Leistner C, Frank RAW. Bridging length scales from molecules to the whole organism by cryoCLEM and cryoET. Faraday Discuss 2022; 240:114-126. [PMID: 35959706 PMCID: PMC9642002 DOI: 10.1039/d2fd00081d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Resolving atomic structures of isolated proteins has uncovered mechanisms and fundamental processes in biology. However, many functions can only be tested in the context of intact cells and tissues that are many orders of magnitude larger than the macromolecules on which they depend. Therefore, methods that interrogate macromolecular structure in situ provide a means of directly relating structure to function across length scales. Here, we developed several workflows using cryogenic correlated light and electron microscopy (cryoCLEM) and electron tomography (cryoET) that can bridge this gap to reveal the molecular infrastructure that underlies higher order functions within cells and tissues. We also describe experimental design considerations, including cryoCLEM labelling, sample preparation, and quality control, for determining the in situ molecular architectures within native, hydrated cells and tissues.
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Affiliation(s)
- Megan Lovatt
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of LeedsLS2 9JTUK
| | - Conny Leistner
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of LeedsLS2 9JTUK
| | - René A. W. Frank
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of LeedsLS2 9JTUK
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29
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Digitalizing neuronal synapses with cryo-electron tomography and correlative microscopy. Curr Opin Neurobiol 2022; 76:102595. [DOI: 10.1016/j.conb.2022.102595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/22/2022] [Accepted: 05/24/2022] [Indexed: 11/22/2022]
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30
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Segev-Zarko LA, Dahlberg PD, Sun SY, Pelt DM, Kim CY, Egan ES, Sethian JA, Chiu W, Boothroyd JC. Cryo-electron tomography with mixed-scale dense neural networks reveals key steps in deployment of Toxoplasma invasion machinery. PNAS NEXUS 2022; 1:pgac183. [PMID: 36329726 PMCID: PMC9615128 DOI: 10.1093/pnasnexus/pgac183] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/30/2022] [Indexed: 01/29/2023]
Abstract
Host cell invasion by intracellular, eukaryotic parasites within the phylum Apicomplexa is a remarkable and active process involving the coordinated action of apical organelles and other structures. To date, capturing how these structures interact during invasion has been difficult to observe in detail. Here, we used cryogenic electron tomography to image the apical complex of Toxoplasma gondii tachyzoites under conditions that mimic resting parasites and those primed to invade through stimulation with calcium ionophore. Through the application of mixed-scale dense networks for image processing, we developed a highly efficient pipeline for annotation of tomograms, enabling us to identify and extract densities of relevant subcellular organelles and accurately analyze features in 3-D. The results reveal a dramatic change in the shape of the anteriorly located apical vesicle upon its apparent fusion with a rhoptry that occurs only in the stimulated parasites. We also present information indicating that this vesicle originates from the vesicles that parallel the intraconoidal microtubules and that the latter two structures are linked by a novel tether. We show that a rosette structure previously proposed to be involved in rhoptry secretion is associated with apical vesicles beyond just the most anterior one. This result, suggesting multiple vesicles are primed to enable rhoptry secretion, may shed light on the mechanisms Toxoplasma employs to enable repeated invasion attempts. Using the same approach, we examine Plasmodium falciparum merozoites and show that they too possess an apical vesicle just beneath a rosette, demonstrating evolutionary conservation of this overall subcellular organization.
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Affiliation(s)
- Li-av Segev-Zarko
- Department of Microbiology and Immunology, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305, USA
| | - Peter D Dahlberg
- Department of Chemistry, Stanford University, 450 Serra Mall, Stanford, CA 94305, USA
| | - Stella Y Sun
- Department of Bioengineering, Stanford University, 450 Serra Mall, Stanford, CA 94305, USA,Department of Structural Biology, University of Pittsburgh, 4200 Fifth Ave, Pittsburgh, PA 15260, USA
| | - Daniël M Pelt
- Leiden Institute of Advanced Computer Science, Leiden University, Rapenburg 70, 2311 EZ Leiden, The Netherlands
| | - Chi Yong Kim
- Department of Microbiology and Immunology, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305, USA,Department of Pediatrics––Infectious Diseases, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305, USA
| | - Elizabeth S Egan
- Department of Microbiology and Immunology, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305, USA,Department of Pediatrics––Infectious Diseases, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305, USA
| | - James A Sethian
- Department of Mathematics, University of California, Berkeley, CA 94720, USA,Center for Advanced Mathematics for Energy Research Application (CAMERA), Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Wah Chiu
- To whom correspondence should be addressed:
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31
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Perez D, Dahlberg PD, Wang J, Sartor AM, Borden JS, Shapiro L, Moerner WE. Identification and demonstration of roGFP2 as an environmental sensor for cryogenic correlative light and electron microscopy. J Struct Biol 2022; 214:107881. [PMID: 35811036 PMCID: PMC9452478 DOI: 10.1016/j.jsb.2022.107881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 10/17/2022]
Abstract
Cryogenic correlative light and electron microscopy (cryo-CLEM) seeks to leverage orthogonal information present in two powerful imaging modalities. While recent advances in cryogenic electron microscopy (cryo-EM) allow for the visualization and identification of structures within cells at the nanometer scale, information regarding the cellular environment, such as pH, membrane potential, ionic strength, etc., which influences the observed structures remains absent. Fluorescence microscopy can potentially be used to reveal this information when specific labels, known as fluorescent biosensors, are used, but there has been minimal use of such biosensors in cryo-CLEM to date. Here we demonstrate the applicability of one such biosensor, the fluorescent protein roGFP2, for cryo-CLEM experiments. At room temperature, the ratio of roGFP2 emission brightness when excited at 425 nm or 488 nm is known to report on the local redox potential. When samples containing roGFP2 are rapidly cooled to 77 K in a manner compatible with cryo-EM, the ratio of excitation peaks remains a faithful indicator of the redox potential at the time of freezing. Using purified protein in different oxidizing/reducing environments, we generate a calibration curve which can be used to analyze in situ measurements. As a proof-of-principle demonstration, we investigate the oxidation/reduction state within vitrified Caulobacter crescentus cells. The polar organizing protein Z (PopZ) localizes to the polar regions of C. crescentus where it is known to form a distinct microdomain. By expressing an inducible roGFP2-PopZ fusion we visualize individual microdomains in the context of their redox environment.
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Affiliation(s)
- Davis Perez
- Department of Chemistry, Stanford University, United States
| | - Peter D Dahlberg
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, United States
| | - Jiarui Wang
- Department of Chemistry, Stanford University, United States; Department of Developmental Biology, Stanford University, United States
| | | | - Julia S Borden
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University, United States
| | - W E Moerner
- Department of Chemistry, Stanford University, United States
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32
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Varsano N, Wolf SG. Electron microscopy of cellular ultrastructure in three dimensions. Curr Opin Struct Biol 2022; 76:102444. [PMID: 36041268 DOI: 10.1016/j.sbi.2022.102444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/05/2022] [Accepted: 07/19/2022] [Indexed: 11/03/2022]
Abstract
Electron microscopy in three dimensions (3D) of cells and tissues can be essential for understanding the ultrastructural aspects of biological processes. The quest for 3D information reveals challenges at many stages of the workflow, from sample preparation, to imaging, data analysis and segmentation. Here, we outline several available methods, including volume SEM imaging, cryo-TEM and cryo-STEM tomography, each one occupying a different domain in the basic tradeoff between field-of-view and resolution. We discuss the considerations for choosing a suitable method depending on research needs and highlight recent developments that are essential for making 3D volume imaging of cells and tissues a standard tool for cellular and structural biologists.
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Affiliation(s)
- Neta Varsano
- Department of Chemical Research Support, Weizmann Institute of Science, 234 Herzl St., Rehovot 76100, Israel
| | - Sharon Grayer Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, 234 Herzl St., Rehovot 76100, Israel.
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33
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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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34
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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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35
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Kwon J, Elgawish MS, Shim S. Bleaching-Resistant Super-Resolution Fluorescence Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2101817. [PMID: 35088584 PMCID: PMC8948665 DOI: 10.1002/advs.202101817] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 01/07/2022] [Indexed: 05/08/2023]
Abstract
Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.
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Affiliation(s)
- Jiwoong Kwon
- Department of Biophysics and Biophysical ChemistryJohns Hopkins UniversityBaltimoreMD21205USA
| | - Mohamed Saleh Elgawish
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
- Medicinal Chemistry DepartmentFaculty of PharmacySuez Canal UniversityIsmailia41522Egypt
| | - Sang‐Hee Shim
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
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36
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Wang J, Han M, Roy AR, Wang H, Möckl L, Zeng L, Moerner W, Qi LS. Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection. CELL REPORTS METHODS 2022; 2:100170. [PMID: 35128513 PMCID: PMC8806145 DOI: 10.1016/j.crmeth.2022.100170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/19/2021] [Accepted: 01/26/2022] [Indexed: 12/20/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third human coronavirus within 20 years that gave rise to a life-threatening disease and the first to reach pandemic spread. To make therapeutic headway against current and future coronaviruses, the biology of coronavirus RNA during infection must be precisely understood. Here, we present a robust and generalizable framework combining high-throughput confocal and super-resolution microscopy imaging to study coronavirus infection at the nanoscale. Using the model human coronavirus HCoV-229E, we specifically labeled coronavirus genomic RNA (gRNA) and double-stranded RNA (dsRNA) via multi-color RNA immunoFISH and visualized their localization patterns within the cell. The 10-nm resolution achieved by our approach uncovers a striking spatial organization of gRNA and dsRNA into three distinct structures and enables quantitative characterization of the status of the infection after antiviral drug treatment. Our approach provides a comprehensive imaging framework that will enable future investigations of coronavirus fundamental biology and therapeutic effects.
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Affiliation(s)
- Jiarui Wang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Mengting Han
- Departments of Bioengineering, Chemical and Systems Biology, and ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Anish R. Roy
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Haifeng Wang
- Departments of Bioengineering, Chemical and Systems Biology, and ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Leonhard Möckl
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Leiping Zeng
- Departments of Bioengineering, Chemical and Systems Biology, and ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - W.E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Lei S. Qi
- Departments of Bioengineering, Chemical and Systems Biology, and ChEM-H, Stanford University, Stanford, CA 94305, USA
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37
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Abstract
Super-resolution microscopy techniques, and specifically single-molecule localization microscopy (SMLM), are approaching nanometer resolution inside cells and thus have great potential to complement structural biology techniques such as electron microscopy for structural cell biology. In this review, we introduce the different flavors of super-resolution microscopy, with a special emphasis on SMLM and MINFLUX (minimal photon flux). We summarize recent technical developments that pushed these localization-based techniques to structural scales and review the experimental conditions that are key to obtaining data of the highest quality. Furthermore, we give an overview of different analysis methods and highlight studies that used SMLM to gain structural insights into biologically relevant molecular machines. Ultimately, we give our perspective on what is needed to push the resolution of these techniques even further and to apply them to investigating dynamic structural rearrangements in living cells. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Sheng Liu
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany;
| | - Philipp Hoess
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany;
| | - Jonas Ries
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany;
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38
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Bond C, Santiago-Ruiz AN, Tang Q, Lakadamyali M. Technological advances in super-resolution microscopy to study cellular processes. Mol Cell 2022; 82:315-332. [PMID: 35063099 PMCID: PMC8852216 DOI: 10.1016/j.molcel.2021.12.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 01/22/2023]
Abstract
Since its initial demonstration in 2000, far-field super-resolution light microscopy has undergone tremendous technological developments. In parallel, these developments have opened a new window into visualizing the inner life of cells at unprecedented levels of detail. Here, we review the technical details behind the most common implementations of super-resolution microscopy and highlight some of the recent, promising advances in this field.
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Affiliation(s)
- Charles Bond
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adriana N. Santiago-Ruiz
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qing Tang
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Correspondence should be sent to M.L.:
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39
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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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40
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Smit R, Ristanović Z, Kozankiewicz B, Orrit M. Reverse Intersystem Crossing of Single Deuterated Perylene Molecules in a Dibenzothiophene Matrix. Chemphyschem 2021; 23:e202100679. [PMID: 34780094 PMCID: PMC9299031 DOI: 10.1002/cphc.202100679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Indexed: 11/11/2022]
Abstract
Intersystem crossing to the long-lived metastable triplet state is often a strong limitation on fluorescence brightness of single molecules, particularly for perylene in various matrices. In this paper, we report on a strong excitation-induced reverse intersystem crossing (rISC), a process where single perylene molecules in a dibenzothiophene matrix recover faster from the triplet state, turning into bright emitters at saturated excitation powers. With a detailed study of single-molecule fluorescence autocorrelations, we quantify the effect of rISC. The intrinsic lifetimes found for the two effective triplet states (8.5±0.4 ms and 64±12 ms) become significantly shorter, into the sub-millisecond range, as the excitation power increases and fluorescence brightness is ultimately enhanced at least fourfold. Our results are relevant for the understanding of triplet state manipulation of single-molecule quantum emitters and for markedly improving their brightness.
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Affiliation(s)
- Robert Smit
- Huygens-Kamerlingh Onnes Laboratory, LION, Postbus 9504, 2300 RA, Leiden, The Netherlands
| | - Zoran Ristanović
- Huygens-Kamerlingh Onnes Laboratory, LION, Postbus 9504, 2300 RA, Leiden, The Netherlands
| | - Bolesław Kozankiewicz
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668, Warsaw, Poland
| | - Michel Orrit
- Huygens-Kamerlingh Onnes Laboratory, LION, Postbus 9504, 2300 RA, Leiden, The Netherlands
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41
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Grillo CA, Holford M, Walter NG. From Flatland to Jupiter: Searching for Rules of Interaction Across Biological Scales. Integr Comp Biol 2021; 61:2048-2052. [PMID: 34254127 DOI: 10.1093/icb/icab159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/12/2022] Open
Abstract
In this future-spanning perspective, we examine how an agent based model could be used to define general rules for interactions across biological systems and evolutionary time. To date there have been a number of attempts to simulate the emergence of ecological communities using agent-based models of individuals that have evolving traits. Here we speculate whether it is possible to use this computational modeling to simulate self-organizing systems and, importantly, to decipher universal principles that govern biological interactions. This perspective is a thought exercise, meant to extrapolate from current knowledge to how we may make Jupiter-shot leaps to further advance the biosciences in the 21st century.
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Affiliation(s)
- Claudia A Grillo
- Department of Pharmacology, Physiology and Neuroscience, University of South Carolina
| | - Mandë Holford
- Department of Chemistry, Hunter College; Programs in Chemistry, Biochemistry, and Biology CUNY Graduate Center; Department of invertebrate zoology, American Museum of Natural History, Department of Biochemistry, Weill Cornell Medicine
| | - Nils G Walter
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan
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42
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Maier J, Weller T, Thelakkat M, Köhler J. Long-term switching of single photochromic triads based on dithienylcyclopentene and fluorophores at cryogenic temperatures. J Chem Phys 2021; 155:014901. [PMID: 34241405 DOI: 10.1063/5.0056815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Photochromic molecules can be reversibly converted between two bistable forms by light. These systems have been intensively studied for applications as molecular memories, sensing devices, or super-resolution optical microscopy. Here, we study the long-term switching behavior of single photochromic triads under oxygen-free conditions at 10 K. The triads consist of a photochromic unit that is covalently linked to two strong fluorophores that were employed for monitoring the light-induced conversions of the switch via changes in the fluorescence intensity from the fluorophores. As dyes we use either perylene bisimide or boron-dipyrromethen, and as photochromic switch we use dithienylcyclopentene (DCP). Both types of triads showed high fatigue resistance allowing for up to 6000 switching cycles of a single triad corresponding to time durations in the order of 80 min without deterioration. Long-term analysis of the switching cycles reveals that the probability that an intensity change in the emission from the dyes can be assigned to an externally stimulated conversion of the DCP (rather than to stochastic blinking of the dye molecules) amounts to 0.7 ± 0.1 for both types of triads. This number is far too low for optical data storage using single triads and implications concerning the miniaturization of optical memories based on such systems will be discussed. Yet, together with the high fatigue resistance, this number is encouraging for applications in super-resolution optical microscopy on frozen biological samples.
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Affiliation(s)
- Johannes Maier
- Spectroscopy of Soft Matter, University of Bayreuth, 95440 Bayreuth, Germany
| | - Tina Weller
- Applied Functional Materials, University of Bayreuth, 95440 Bayreuth, Germany
| | - Mukundan Thelakkat
- Applied Functional Materials, University of Bayreuth, 95440 Bayreuth, Germany
| | - Jürgen Köhler
- Spectroscopy of Soft Matter, University of Bayreuth, 95440 Bayreuth, Germany
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43
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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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