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Correlative super-resolution fluorescence and electron cryo-microscopy based on cryo-SOFI. Methods Cell Biol 2020; 162:253-271. [PMID: 33707015 DOI: 10.1016/bs.mcb.2020.10.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The combination of super-resolution fluorescence microscopy and electron microscopy at ambient temperatures has become an established technique and a broad variety of modalities are now available to the cell biology community. In contrast, correlative cryogenic super-resolution fluorescence and electron microscopy (super-resolution cryo-CLEM) is just emerging. Aside from technical challenges, one of the major issues is the risk of devitrification of the specimen caused by the laser intensities required for super-resolution imaging. Cryo-SOFI (cryogenic super-resolution optical fluctuation imaging) allows the reconstruction of super-resolution images at particularly low laser intensities. It is fully compatible with the standard sample preparation for cryogenic electron microscopy (cryo-EM) and fairly easy to implement in any standard cryogenic fluorescence microscope.
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52
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Prabhakar N, Peurla M, Shenderova O, Rosenholm JM. Fluorescent and Electron-Dense Green Color Emitting Nanodiamonds for Single-Cell Correlative Microscopy. Molecules 2020; 25:E5897. [PMID: 33322105 PMCID: PMC7764487 DOI: 10.3390/molecules25245897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/07/2020] [Accepted: 12/12/2020] [Indexed: 02/07/2023] Open
Abstract
Correlative light and electron microscopy (CLEM) is revolutionizing how cell samples are studied. CLEM provides a combination of the molecular and ultrastructural information about a cell. For the execution of CLEM experiments, multimodal fiducial landmarks are applied to precisely overlay light and electron microscopy images. Currently applied fiducials such as quantum dots and organic dye-labeled nanoparticles can be irreversibly quenched by electron beam exposure during electron microscopy. Generally, the sample is therefore investigated with a light microscope first and later with an electron microscope. A versatile fiducial landmark should offer to switch back from electron microscopy to light microscopy while preserving its fluorescent properties. Here, we evaluated green fluorescent and electron dense nanodiamonds for the execution of CLEM experiments and precisely correlated light microscopy and electron microscopy images. We demonstrated that green color emitting fluorescent nanodiamonds withstand electron beam exposure, harsh chemical treatments, heavy metal straining, and, importantly, their fluorescent properties remained intact for light microscopy.
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Affiliation(s)
- Neeraj Prabhakar
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
| | - Markus Peurla
- Institute of Biomedicine, Faculty of Medicine, University of Turku, 20520 Turku, Finland;
- Cancer Research Laboratory FICAN West, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Olga Shenderova
- Adámas Nanotechnologies, Inc., 8100 Brownleigh Drive, Suite 120, Raleigh, NC 27617, USA;
| | - Jessica M. Rosenholm
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
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53
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Harne S, Gayathri P, Béven L. Exploring Spiroplasma Biology: Opportunities and Challenges. Front Microbiol 2020; 11:589279. [PMID: 33193251 PMCID: PMC7609405 DOI: 10.3389/fmicb.2020.589279] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/28/2020] [Indexed: 11/13/2022] Open
Abstract
Spiroplasmas are cell-wall-deficient helical bacteria belonging to the class Mollicutes. Their ability to maintain a helical shape in the absence of cell wall and their motility in the absence of external appendages have attracted attention from the scientific community for a long time. In this review we compare and contrast motility, shape determination and cytokinesis mechanisms of Spiroplasma with those of other Mollicutes and cell-walled bacteria. The current models for rod-shape determination and cytokinesis in cell-walled bacteria propose a prominent role for the cell wall synthesis machinery. These models also involve the cooperation of the actin-like protein MreB and FtsZ, the bacterial homolog of tubulin. However the exact role of the cytoskeletal proteins is still under much debate. Spiroplasma possess MreBs, exhibit a rod-shape dependent helical morphology, and divide by an FtsZ-dependent mechanism. Hence, spiroplasmas represent model organisms for deciphering the roles of MreBs and FtsZ in fundamental mechanisms of non-spherical shape determination and cytokinesis in bacteria, in the absence of a cell wall. Identification of components implicated in these processes and deciphering their functions would require genetic experiments. Challenges in genetic manipulations in spiroplasmas are a major bottleneck in understanding their biology. We discuss advancements in genome sequencing, gene editing technologies, super-resolution microscopy and electron cryomicroscopy and tomography, which can be employed for addressing long-standing questions related to Spiroplasma biology.
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Affiliation(s)
- Shrikant Harne
- Indian Institute of Science Education and Research, Pune, India
| | | | - Laure Béven
- INRAE, UMR 1332, Biologie du Fruit et Pathologie, University of Bordeaux, Bordeaux, France
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54
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A. Matthay Z, Zumwinkle Kornblith L. Platelet Imaging. Platelets 2020. [DOI: 10.5772/intechopen.91736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The knowledge gained through imaging platelets has formed the backbone of our understanding of their biology in health and disease. Early investigators relied on conventional light microscopy with limited resolution and were primarily able to identify the presence and basic morphology of platelets. The advent of high resolution technologies, in particular, electron microscopy, accelerated our understanding of the dynamics of platelet ultrastructure dramatically. Further refinements and improvements in our ability to localize and reliably identify platelet structures have included the use of immune-labeling techniques, correlative-fluorescence light and electron microscopy, and super-resolution microscopies. More recently, the expanded development and application of intravital microscopy in animal models has enhanced our knowledge of platelet functions and thrombus formation in vivo, as these experimental systems most closely replicate native biological environments. Emerging improvements in our ability to characterize platelets at the ultrastructural and organelle levels include the use of platelet cryogenic electron tomography with quantitative, unbiased imaging analysis, and the ability to genetically label platelet features with electron dense markers for analysis by electron microscopy.
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55
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Li X, Park D, Chang Y, Radhakrishnan A, Wu H, Wang P, Liu J. A mammalian system for high-resolution imaging of intact cells by cryo-electron tomography. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 160:87-96. [PMID: 33058942 DOI: 10.1016/j.pbiomolbio.2020.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 09/17/2020] [Accepted: 09/20/2020] [Indexed: 10/23/2022]
Abstract
Mammalian cells contain an elaborate network of organelles and molecular machines that orchestrate essential cellular processes. Visualization of this network at a molecular level is vital for understanding these cellular processes. Here we present a model system based on nerve growth factor (NGF)-differentiated PC12 cells (PC12+) and suitable for high resolution imaging of organelles and molecular machines in situ. We detail an optimized imaging pipeline that effectively combines correlative light and electron microscopy (CLEM), cryo-focused ion beam (cryo-FIB), cryo-electron tomography (cryo-ET), and sub-tomogram averaging to produce three-dimensional and molecular resolution snapshots of organelles and molecular machines in near-native cellular environments. Our studies demonstrate that cryo-ET imaging of PC12+ systems provides an accessible and highly efficient avenue for dissecting specific cellular processes in mammalian cells at high resolution.
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Affiliation(s)
- Xia Li
- Department of Microbial Pathogenesis and Microbial Science Institute, Yale School of Medicine, New Haven, CT, 06516, USA; Institute of Special Environmental Medicine and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, 226000, China.
| | - Donghyun Park
- Department of Microbial Pathogenesis and Microbial Science Institute, Yale School of Medicine, New Haven, CT, 06516, USA
| | - Yunjie Chang
- Department of Microbial Pathogenesis and Microbial Science Institute, Yale School of Medicine, New Haven, CT, 06516, USA
| | | | - Hangjun Wu
- Center of Cryo Electron Microscopy and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Pei Wang
- Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China
| | - Jun Liu
- Department of Microbial Pathogenesis and Microbial Science Institute, Yale School of Medicine, New Haven, CT, 06516, USA.
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56
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Keevend K, Coenen T, Herrmann IK. Correlative cathodoluminescence electron microscopy bioimaging: towards single protein labelling with ultrastructural context. NANOSCALE 2020; 12:15588-15603. [PMID: 32677648 DOI: 10.1039/d0nr02563a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The understanding of living systems and their building blocks relies heavily on the assessment of structure-function relationships at the nanoscale. Ever since the development of the first optical microscope, the reliance of scientists across disciplines on microscopy has increased. The development of the first electron microscope and with it the access to information at the nanoscale has prompted numerous disruptive discoveries. While fluorescence imaging allows identification of specific entities based on the labelling with fluorophores, the unlabelled constituents of the samples remain invisible. In electron microscopy on the other hand, structures can be comprehensively visualized based on their distinct electron density and geometry. Although electron microscopy is a powerful tool, it does not implicitly provide information on the location and activity of specific organic molecules. While correlative light and electron microscopy techniques have attempted to unify the two modalities, the resolution mismatch between the two data sets poses major challenges. Recent developments in optical super resolution microscopy enable high resolution correlative light and electron microscopy, however, with considerable constraints due to sample preparation requirements. Labelling of specific structures directly for electron microscopy using small gold nanoparticles (i.e. immunogold) has been used extensively. However, identification of specific entities solely based on electron contrast, and the differentiation from endogenous dense granules, remains challenging. Recently, the use of correlative cathodoluminescence electron microscopy (CCLEM) imaging based on luminescent inorganic nanocrystals has been proposed. While nanometric resolution can be reached for both the electron and the optical signal, high energy electron beams are potentially damaging to the sample. In this review, we discuss the opportunities of (volumetric) multi-color single protein labelling based on correlative cathodoluminescence electron microscopy, and its prospective impact on biomedical research in general. We elaborate on the potential challenges of correlative cathodoluminescence electron microscopy-based bioimaging and benchmark CCLEM against alternative high-resolution correlative imaging techniques.
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Affiliation(s)
- Kerda Keevend
- Laboratory for Particles Biology Interactions, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, CH-9014, St Gallen, Switzerland.
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57
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Kounatidis I, Stanifer ML, Phillips MA, Paul-Gilloteaux P, Heiligenstein X, Wang H, Okolo CA, Fish TM, Spink MC, Stuart DI, Davis I, Boulant S, Grimes JM, Dobbie IM, Harkiolaki M. 3D Correlative Cryo-Structured Illumination Fluorescence and Soft X-ray Microscopy Elucidates Reovirus Intracellular Release Pathway. Cell 2020; 182:515-530.e17. [PMID: 32610083 PMCID: PMC7391008 DOI: 10.1016/j.cell.2020.05.051] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/14/2020] [Accepted: 05/28/2020] [Indexed: 01/15/2023]
Abstract
Imaging of biological matter across resolution scales entails the challenge of preserving the direct and unambiguous correlation of subject features from the macroscopic to the microscopic level. Here, we present a correlative imaging platform developed specifically for imaging cells in 3D under cryogenic conditions by using X-rays and visible light. Rapid cryo-preservation of biological specimens is the current gold standard in sample preparation for ultrastructural analysis in X-ray imaging. However, cryogenic fluorescence localization methods are, in their majority, diffraction-limited and fail to deliver matching resolution. We addressed this technological gap by developing an integrated, user-friendly platform for 3D correlative imaging of cells in vitreous ice by using super-resolution structured illumination microscopy in conjunction with soft X-ray tomography. The power of this approach is demonstrated by studying the process of reovirus release from intracellular vesicles during the early stages of infection and identifying intracellular virus-induced structures.
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Affiliation(s)
- Ilias Kounatidis
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Megan L Stanifer
- Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Michael A Phillips
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Perrine Paul-Gilloteaux
- Université de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France; Nantes Université, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS3556, Nantes, France
| | | | - Hongchang Wang
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Chidinma A Okolo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Thomas M Fish
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Matthew C Spink
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - David I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Ilan Davis
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Steeve Boulant
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; Research Group "Cellular polarity and viral infection," German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jonathan M Grimes
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Ian M Dobbie
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
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58
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KUBA JAKUB, MITCHELS JOHN, HOVORKA MILOŠ, ERDMANN PHILIPP, BERKA LUKÁŠ, KIRMSE ROBERT, KÖNIG JULIA, DE BOCK JAN, GOETZE BERNHARD, RIGORT ALEXANDER. Advanced cryo‐tomography workflow developments – correlative microscopy, milling automation and cryo‐lift‐out. J Microsc 2020; 281:112-124. [DOI: 10.1111/jmi.12939] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/22/2020] [Accepted: 06/16/2020] [Indexed: 01/13/2023]
Affiliation(s)
- JAKUB KUBA
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | - JOHN MITCHELS
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | - MILOŠ HOVORKA
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | - PHILIPP ERDMANN
- Department of Molecular Structural Biology Max Planck Institute of Biochemistry Martinsried Germany
| | - LUKÁŠ BERKA
- Thermo Fisher Scientific Brno s.r.o. Brno Czech Republic
| | | | | | - JAN DE BOCK
- Leica Microsystems CMS GmbH Mannheim Germany
| | - BERNHARD GOETZE
- Thermo Fisher Scientific FEI Deutschland GmbH Planegg Germany
| | - ALEXANDER RIGORT
- Department of Molecular Structural Biology Max Planck Institute of Biochemistry Martinsried Germany
- Thermo Fisher Scientific FEI Deutschland GmbH Planegg Germany
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59
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Dahlberg PD, Saurabh S, Sartor AM, Wang J, Mitchell PG, Chiu W, Shapiro L, Moerner WE. Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter. Proc Natl Acad Sci U S A 2020; 117:13937-13944. [PMID: 32513734 PMCID: PMC7321984 DOI: 10.1073/pnas.2001849117] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Superresolution fluorescence microscopy and cryogenic electron tomography (CET) are powerful imaging methods for exploring the subcellular organization of biomolecules. Superresolution fluorescence microscopy based on covalent labeling highlights specific proteins and has sufficient sensitivity to observe single fluorescent molecules, but the reconstructions lack detailed cellular context. CET has molecular-scale resolution but lacks specific and nonperturbative intracellular labeling techniques. Here, we describe an imaging scheme that correlates cryogenic single-molecule fluorescence localizations with CET reconstructions. Our approach achieves single-molecule localizations with an average lateral precision of 9 nm, and a relative registration error between the set of localizations and CET reconstruction of ∼30 nm. We illustrate the workflow by annotating the positions of three proteins in the bacterium Caulobacter crescentus: McpA, PopZ, and SpmX. McpA, which forms a part of the chemoreceptor array, acts as a validation structure by being visible under both imaging modalities. In contrast, PopZ and SpmX cannot be directly identified in CET. While not directly discernable, PopZ fills a region at the cell poles that is devoid of electron-dense ribosomes. We annotate the position of PopZ with single-molecule localizations and confirm its position within the ribosome excluded region. We further use the locations of PopZ to provide context for localizations of SpmX, a low-copy integral membrane protein sequestered by PopZ as part of a signaling pathway that leads to an asymmetric cell division. Our correlative approach reveals that SpmX localizes along one side of the cell pole and its extent closely matches that of the PopZ region.
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Affiliation(s)
- Peter D Dahlberg
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Saumya Saurabh
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Annina M Sartor
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jiarui Wang
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Patrick G Mitchell
- Division of Cryo-EM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Wah Chiu
- Division of Cryo-EM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305;
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60
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Böhning J, Bharat TAM. Towards high-throughput in situ structural biology using electron cryotomography. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 160:97-103. [PMID: 32579969 DOI: 10.1016/j.pbiomolbio.2020.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 01/11/2023]
Abstract
Electron cryotomography is a rapidly evolving method for imaging macromolecules directly within the native environment of cells and tissues. Combined with sub-tomogram averaging, it allows structural and cell biologists to obtain sub-nanometre resolution structures in situ. However, low throughput in cryo-ET sample preparation and data acquisition, as well as difficulties in target localisation and sub-tomogram averaging image processing, limit its widespread usability. In this review, we discuss new advances in the field that address these throughput and technical problems. We focus on recent efforts made to resolve issues in sample thinning, improvement in data collection speed at the microscope, strategies for localisation of macromolecules using correlated light and electron microscopy and advancements made to improve resolution in sub-tomogram averaging. These advances will considerably decrease the amount of time and effort required for cryo-ET and sub-tomogram averaging, ushering in a new era of structural biology where in situ macromolecular structure determination will be routine.
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Affiliation(s)
- Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom.
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61
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Jun S, Ro HJ, Bharda A, Kim SI, Jeoung D, Jung HS. Advances in Cryo-Correlative Light and Electron Microscopy: Applications for Studying Molecular and Cellular Events. Protein J 2020; 38:609-615. [PMID: 31396855 DOI: 10.1007/s10930-019-09856-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cryo-correlative light and electron microscopy (Cryo-CLEM) is materializing as a widespread approach amalgamating the advantages of both fluorescence light microscopy (FLM) as well as three dimensional (3D) cryo-electron tomography (cryo-ET) to reveal the ultrastructure of significant target molecules with specific cellular functions. Cryo-CLEM allows imaging of cells by means of fluorescence microscopy exhibiting the location of the destined molecule at high temporal and spatial resolution while cryo-ET is employed to analyze the 3D structure at a molecular resolution in close-to-physiological condition. Present review focuses upon the practical strategies for Cryo-CLEM and recent technical developments that will assist the broad implementation of this technique to investigate and answer questions pertaining to various biological events occurring in the cell.
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Affiliation(s)
- Sangmi Jun
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea. .,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea. .,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea.
| | - Hyun-Joo Ro
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Anahita Bharda
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea
| | - Seung Il Kim
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Dooil Jeoung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea.
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62
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Hoffman DP, Shtengel G, Xu CS, Campbell KR, Freeman M, Wang L, Milkie DE, Pasolli HA, Iyer N, Bogovic JA, Stabley DR, Shirinifard A, Pang S, Peale D, Schaefer K, Pomp W, Chang CL, Lippincott-Schwartz J, Kirchhausen T, Solecki DJ, Betzig E, Hess HF. Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. Science 2020; 367:eaaz5357. [PMID: 31949053 PMCID: PMC7339343 DOI: 10.1126/science.aaz5357] [Citation(s) in RCA: 205] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/20/2019] [Indexed: 12/27/2022]
Abstract
Within cells, the spatial compartmentalization of thousands of distinct proteins serves a multitude of diverse biochemical needs. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) can elucidate protein spatial relationships to global ultrastructure, but has suffered from tradeoffs of structure preservation, fluorescence retention, resolution, and field of view. We developed a platform for three-dimensional cryogenic SR and focused ion beam-milled block-face EM across entire vitreously frozen cells. The approach preserves ultrastructure while enabling independent SR and EM workflow optimization. We discovered unexpected protein-ultrastructure relationships in mammalian cells including intranuclear vesicles containing endoplasmic reticulum-associated proteins, web-like adhesions between cultured neurons, and chromatin domains subclassified on the basis of transcriptional activity. Our findings illustrate the value of a comprehensive multimodal view of ultrastructural variability across whole cells.
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Affiliation(s)
- David P Hoffman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Gleb Shtengel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Kirby R Campbell
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Melanie Freeman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Lei Wang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - H Amalia Pasolli
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Nirmala Iyer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - John A Bogovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Daniel R Stabley
- Neuroimaging Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Abbas Shirinifard
- Bioimage Analysis Core, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Song Pang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - David Peale
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Kathy Schaefer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Wim Pomp
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Chi-Lun Chang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | | | - Tom Kirchhausen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - David J Solecki
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Physics, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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63
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Ng CT, Gan L. Investigating eukaryotic cells with cryo-ET. Mol Biol Cell 2020; 31:87-100. [PMID: 31935172 PMCID: PMC6960407 DOI: 10.1091/mbc.e18-05-0329] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 01/06/2023] Open
Abstract
The interior of eukaryotic cells is mysterious. How do the large communities of macromolecular machines interact with each other? How do the structures and positions of these nanoscopic entities respond to new stimuli? Questions like these can now be answered with the help of a method called electron cryotomography (cryo-ET). Cryo-ET will ultimately reveal the inner workings of a cell at the protein, secondary structure, and perhaps even side-chain levels. Combined with genetic or pharmacological perturbation, cryo-ET will allow us to answer previously unimaginable questions, such as how structure, biochemistry, and forces are related in situ. Because it bridges structural biology and cell biology, cryo-ET is indispensable for structural cell biology-the study of the 3-D macromolecular structure of cells. Here we discuss some of the key ideas, strategies, auxiliary techniques, and innovations that an aspiring structural cell biologist will consider when planning to ask bold questions.
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Affiliation(s)
- Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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64
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Ho S, Tirrell DA. Enzymatic Labeling of Bacterial Proteins for Super-resolution Imaging in Live Cells. ACS CENTRAL SCIENCE 2019; 5:1911-1919. [PMID: 31893220 PMCID: PMC6935894 DOI: 10.1021/acscentsci.9b00617] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Indexed: 06/10/2023]
Abstract
Methods that enable the super-resolution imaging of intracellular proteins in live bacterial cells provide powerful tools for the study of prokaryotic cell biology. Photoswitchable organic dyes exhibit many of the photophysical properties needed for super-resolution imaging, including high brightness, photostability, and photon output, but most such dyes require organisms to be fixed and permeabilized if intracellular targets are to be labeled. We recently reported a general strategy for the chemoenzymatic labeling of bacterial proteins with azide-bearing fatty acids in live cells using the eukaryotic enzyme N-myristoyltransferase. Here we demonstrate the labeling of proteins in live Escherichia coli using cell-permeant bicyclononyne-functionalized photoswitchable rhodamine spirolactams. Single-molecule fluorescence measurements on model rhodamine spirolactam salts show that these dyes emit hundreds of photons per switching event. Super-resolution imaging was performed on bacterial chemotaxis proteins Tar and CheA and cell division proteins FtsZ and FtsA. High-resolution imaging of Tar revealed a helical pattern; imaging of FtsZ yielded banded patterns dispersed throughout the cell. The precision of radial and axial localization in reconstructed images approaches 15 and 30 nm, respectively. The simplicity of the method, which does not require redox imaging buffers, should make this approach broadly useful for imaging intracellular bacterial proteins in live cells with nanometer resolution.
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65
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mEosEM withstands osmium staining and Epon embedding for super-resolution CLEM. Nat Methods 2019; 17:55-58. [PMID: 31611693 DOI: 10.1038/s41592-019-0613-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 09/16/2019] [Indexed: 12/22/2022]
Abstract
Super-resolution correlative light and electron microscopy (SR-CLEM) is a powerful approach for imaging specific molecules at the nanoscale in the context of the cellular ultrastructure. Epon epoxy resin embedding offers advantages for SR-CLEM, including ultrastructural preservation and high quality sectioning. However, Epon embedding eliminates fluorescence from most fluorescent proteins. We describe a photocontrollable fluorescent protein, mEosEM, that can survive Epon embedding after osmium tetroxide (OsO4) treatment for improved SR-CLEM.
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66
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Choi J, Grosely R, Puglisi EV, Puglisi JD. Expanding single-molecule fluorescence spectroscopy to capture complexity in biology. Curr Opin Struct Biol 2019; 58:233-240. [PMID: 31213390 PMCID: PMC6778503 DOI: 10.1016/j.sbi.2019.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/08/2019] [Indexed: 11/16/2022]
Abstract
Fundamental biological processes are driven by diverse molecular machineries. In recent years, single-molecule fluorescence spectroscopy has matured as a unique tool in biology to study how structural dynamics of molecular complexes drive various biochemical reactions. In this review, we highlight underlying developments in single-molecule fluorescence methods that enable deep biological investigations. Recent progress in these methods points toward increasing complexity of measurements to capture biological processes in a living cell, where multiple processes often occur simultaneously and are mechanistically coupled.
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Affiliation(s)
- Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305-4090, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Elisabetta V Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
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67
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Yang W, Briegel A. Diversity of Bacterial Chemosensory Arrays. Trends Microbiol 2019; 28:68-80. [PMID: 31473052 DOI: 10.1016/j.tim.2019.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/15/2019] [Accepted: 08/01/2019] [Indexed: 02/01/2023]
Abstract
Chemotaxis is crucial for the survival of bacteria, and the signaling systems associated with it exhibit a high level of evolutionary conservation. The architecture of the chemosensory array and the signal transduction mechanisms have been extensively studied in Escherichia coli. More recent studies have revealed a vast diversity of the chemosensory system among bacteria. Unlike E. coli, some bacteria assemble more than one chemosensory array and respond to a broader spectrum of environmental and internal stimuli. These chemosensory arrays exhibit a great variability in terms of protein composition, cellular localization, and functional variability. Here, we present recent findings that emphasize the extent of diversity in chemosensory arrays and highlight the importance of studying chemosensory arrays in bacteria other than the common model organisms.
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Affiliation(s)
- Wen Yang
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Ariane Briegel
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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68
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Metskas LA, Briggs JAG. Fluorescence-Based Detection of Membrane Fusion State on a Cryo-EM Grid using Correlated Cryo-Fluorescence and Cryo-Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2019; 25:942-949. [PMID: 31084637 PMCID: PMC6624127 DOI: 10.1017/s1431927619000606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Correlated light and electron microscopy (CLEM) has become a popular technique for combining the protein-specific labeling of fluorescence with electron microscopy, both at room and cryogenic temperatures. Fluorescence applications at cryo-temperatures have typically been limited to localization of tagged protein oligomers due to known issues of extended triplet state duration, spectral shifts, and reduced photon capture through cryo-CLEM objectives. Here, we consider fluorophore characteristics and behaviors that could enable more extended applications. We describe how dialkylcarbocanine DiD, and its autoquenching by resonant energy transfer (RET), can be used to distinguish the fusion state of a lipid bilayer at cryo-temperatures. By adapting an established fusion assay to work under cryo-CLEM conditions, we identified areas of fusion between influenza virus-like particles and fluorescently labeled lipid vesicles on a cryo-EM grid. This result demonstrates that cryo-CLEM can be used to localize functions in addition to tagged proteins, and that fluorescence autoquenching by RET can be incorporated successfully into cryo-CLEM approaches. In the case of membrane fusion applications, this method provides both an orthogonal confirmation of functional state independent of the morphological description from cryo-EM and a way to bridge room-temperature kinetic assays and the cryo-EM images.
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Affiliation(s)
- Lauren Ann Metskas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory,69117 Heidelberg,Germany
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory,69117 Heidelberg,Germany
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69
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Lin R, Zeng X, Kitani K, Xu M. Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms. Bioinformatics 2019; 35:i260-i268. [PMID: 31510673 PMCID: PMC6612867 DOI: 10.1093/bioinformatics/btz364] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
MOTIVATION Since 2017, an increasing amount of attention has been paid to the supervised deep learning-based macromolecule in situ structural classification (i.e. subtomogram classification) in cellular electron cryo-tomography (CECT) due to the substantially higher scalability of deep learning. However, the success of such supervised approach relies heavily on the availability of large amounts of labeled training data. For CECT, creating valid training data from the same data source as prediction data is usually laborious and computationally intensive. It would be beneficial to have training data from a separate data source where the annotation is readily available or can be performed in a high-throughput fashion. However, the cross data source prediction is often biased due to the different image intensity distributions (a.k.a. domain shift). RESULTS We adapt a deep learning-based adversarial domain adaptation (3D-ADA) method to timely address the domain shift problem in CECT data analysis. 3D-ADA first uses a source domain feature extractor to extract discriminative features from the training data as the input to a classifier. Then it adversarially trains a target domain feature extractor to reduce the distribution differences of the extracted features between training and prediction data. As a result, the same classifier can be directly applied to the prediction data. We tested 3D-ADA on both experimental and realistically simulated subtomogram datasets under different imaging conditions. 3D-ADA stably improved the cross data source prediction, as well as outperformed two popular domain adaptation methods. Furthermore, we demonstrate that 3D-ADA can improve cross data source recovery of novel macromolecular structures. AVAILABILITY AND IMPLEMENTATION https://github.com/xulabs/projects. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ruogu Lin
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiangrui Zeng
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kris Kitani
- Robotics Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
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70
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An efficient protocol of cryo-correlative light and electron microscopy for the study of neuronal synapses. BIOPHYSICS REPORTS 2019. [DOI: 10.1007/s41048-019-0092-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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71
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Taraska JW. A primer on resolving the nanoscale structure of the plasma membrane with light and electron microscopy. J Gen Physiol 2019; 151:974-985. [PMID: 31253697 PMCID: PMC6683668 DOI: 10.1085/jgp.201812227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Taraska reviews the imaging methods that are being used to understand the structure of the plasma membrane at the molecular level. The plasma membrane separates a cell from its external environment. All materials and signals that enter or leave the cell must cross this hydrophobic barrier. Understanding the architecture and dynamics of the plasma membrane has been a central focus of general cellular physiology. Both light and electron microscopy have been fundamental in this endeavor and have been used to reveal the dense, complex, and dynamic nanoscale landscape of the plasma membrane. Here, I review classic and recent developments in the methods used to image and study the structure of the plasma membrane, particularly light, electron, and correlative microscopies. I will discuss their history and use for mapping the plasma membrane and focus on how these tools have provided a structural framework for understanding the membrane at the scale of molecules. Finally, I will describe how these studies provide a roadmap for determining the nanoscale architecture of other organelles and entire cells in order to bridge the gap between cellular form and function.
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Affiliation(s)
- Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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72
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Kramm K, Endesfelder U, Grohmann D. A Single-Molecule View of Archaeal Transcription. J Mol Biol 2019; 431:4116-4131. [PMID: 31207238 DOI: 10.1016/j.jmb.2019.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/27/2019] [Accepted: 06/06/2019] [Indexed: 01/03/2023]
Abstract
The discovery of the archaeal domain of life is tightly connected to an in-depth analysis of the prokaryotic RNA world. In addition to Carl Woese's approach to use the sequence of the 16S rRNA gene as phylogenetic marker, the finding of Karl Stetter and Wolfram Zillig that archaeal RNA polymerases (RNAPs) were nothing like the bacterial RNAP but are more complex enzymes that resemble the eukaryotic RNAPII was one of the key findings supporting the idea that archaea constitute the third major branch on the tree of life. This breakthrough in transcriptional research 40years ago paved the way for in-depth studies of the transcription machinery in archaea. However, although the archaeal RNAP and the basal transcription factors that fine-tune the activity of the RNAP during the transcription cycle are long known, we still lack information concerning the architecture and dynamics of archaeal transcription complexes. In this context, single-molecule measurements were instrumental as they provided crucial insights into the process of transcription initiation, the architecture of the initiation complex and the dynamics of mobile elements of the RNAP. In this review, we discuss single-molecule approaches suitable to examine molecular mechanisms of transcription and highlight findings that shaped our understanding of the archaeal transcription apparatus. We furthermore explore the possibilities and challenges of next-generation single-molecule techniques, for example, super-resolution microscopy and single-molecule tracking, and ask whether these approaches will ultimately allow us to investigate archaeal transcription in vivo.
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Affiliation(s)
- Kevin Kramm
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 16, 35043 Marburg, Germany
| | - Dina Grohmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
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73
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Anwar MN, Li ZF, Gong Y, Singh RP, Li YZ. Omics Studies Revealed the Factors Involved in the Formation of Colony Boundary in Myxococcus xanthus. Cells 2019; 8:E530. [PMID: 31163575 PMCID: PMC6627406 DOI: 10.3390/cells8060530] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 12/20/2022] Open
Abstract
Two unrecognizable strains of the same bacterial species form a distinct colony boundary. During growth as colonies, Myxococcus xanthus uses multiple factors to establish cooperation between recognized strains and prevent interactions with unrecognized strains of the same species. Here, ΔMXAN_0049 is a mutant strain deficient in immunity for the paired nuclease gene, MXAN_0050, that has a function in the colony-merger incompatibility of Myxococcus xanthus DK1622. With the aim to investigate the factors involved in boundary formation, a proteome and metabolome study was employed. Visualization of the boundary between DK1622 and ΔMXAN_0049 was done scanning electron microscope (SEM), which displayed the presence of many damaged cells in the boundary. Proteome analysis of the DK1622- boundary disclosed many possible proteins, such as cold shock proteins, cell shape-determining protein MreC, along with a few pathways, such as RNA degradation, phenylalanine, tyrosine and tryptophan biosynthesis, and Type VI secretion system (T6SS), which may play major roles in the boundary formation. Metabolomics studies revealed various secondary metabolites that were significantly produced during boundary formation. Overall, the results concluded that multiple factors participated in the boundary formation in M. xanthus, leading to cellular damage that is helpful in solving the mystery of the boundary formation mechanism.
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Affiliation(s)
- Mian Nabeel Anwar
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Zhi Feng Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Ya Gong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Raghvendra Pratap Singh
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
- Department of Research and Development, Uttaranchal University, Dehradun 248007, India.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
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74
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Cryo-SOFI enabling low-dose super-resolution correlative light and electron cryo-microscopy. Proc Natl Acad Sci U S A 2019; 116:4804-4809. [PMID: 30808803 PMCID: PMC6421404 DOI: 10.1073/pnas.1810690116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Correlative light and electron cryo-microscopy (cryo-CLEM) combines information from the specific labeling of fluorescence cryo-microscopy (cryo-FM) with the high resolution in environmental context of electron cryo-microscopy (cryo-EM). Exploiting super-resolution methods for cryo-FM is advantageous, as it enables the identification of rare events within the environmental background of cryo-EM at a sensitivity and resolution beyond that of conventional methods. However, due to the need for relatively high laser intensities, current super-resolution cryo-CLEM methods require cryo-protectants or support films which can severely reduce image quality in cryo-EM and are not compatible with many samples, such as mammalian cells. Here, we introduce cryogenic super-resolution optical fluctuation imaging (cryo-SOFI), a low-dose super-resolution imaging scheme based on the SOFI principle. As cryo-SOFI does not require special sample preparation, it is fully compatible with conventional cryo-EM specimens, and importantly, it does not affect the quality of cryo-EM imaging. By applying cryo-SOFI to a variety of biological application examples, we demonstrate resolutions up to ∼135 nm, an improvement of up to three times compared with conventional cryo-FM, while maintaining the specimen in a vitrified state for subsequent cryo-EM. Cryo-SOFI presents a general solution to the problem of specimen devitrification in super-resolution cryo-CLEM. It does not require a complex optical setup and can easily be implemented in any existing cryo-FM system.
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75
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Xu M, Singla J, Tocheva EI, Chang YW, Stevens RC, Jensen GJ, Alber F. De Novo Structural Pattern Mining in Cellular Electron Cryotomograms. Structure 2019; 27:679-691.e14. [PMID: 30744995 DOI: 10.1016/j.str.2019.01.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/27/2018] [Accepted: 01/14/2019] [Indexed: 11/16/2022]
Abstract
Electron cryotomography enables 3D visualization of cells in a near-native state at molecular resolution. The produced cellular tomograms contain detailed information about a plethora of macromolecular complexes, their structures, abundances, and specific spatial locations in the cell. However, extracting this information in a systematic way is very challenging, and current methods usually rely on individual templates of known structures. Here, we propose a framework called "Multi-Pattern Pursuit" for de novo discovery of different complexes from highly heterogeneous sets of particles extracted from entire cellular tomograms without using information of known structures. These initially detected structures can then serve as input for more targeted refinement efforts. Our tests on simulated and experimental tomograms show that our automated method is a promising tool for supporting large-scale template-free visual proteomics analysis.
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Affiliation(s)
- Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Jitin Singla
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raymond C Stevens
- Department of Biological Sciences and Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA
| | - Frank Alber
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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76
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Tuijtel MW, Koster AJ, Jakobs S, Faas FGA, Sharp TH. Correlative cryo super-resolution light and electron microscopy on mammalian cells using fluorescent proteins. Sci Rep 2019; 9:1369. [PMID: 30718653 PMCID: PMC6362030 DOI: 10.1038/s41598-018-37728-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/12/2018] [Indexed: 11/22/2022] Open
Abstract
Sample fixation by vitrification is critical for the optimal structural preservation of biomolecules and subsequent high-resolution imaging by cryo-correlative light and electron microscopy (cryoCLEM). There is a large resolution gap between cryo fluorescence microscopy (cryoFLM), ~400-nm, and the sub-nanometre resolution achievable with cryo-electron microscopy (cryoEM), which hinders interpretation of cryoCLEM data. Here, we present a general approach to increase the resolution of cryoFLM using cryo-super-resolution (cryoSR) microscopy that is compatible with successive cryoEM investigation in the same region. We determined imaging parameters to avoid devitrification of the cryosamples without the necessity for cryoprotectants. Next, we examined the applicability of various fluorescent proteins (FPs) for single-molecule localisation cryoSR microscopy and found that all investigated FPs display reversible photoswitchable behaviour, and demonstrated cryoSR on lipid nanotubes labelled with rsEGFP2 and rsFastLime. Finally, we performed SR-cryoCLEM on mammalian cells expressing microtubule-associated protein-2 fused to rsEGFP2 and performed 3D cryo-electron tomography on the localised areas. The method we describe exclusively uses commercially available equipment to achieve a localisation precision of 30-nm. Furthermore, all investigated FPs displayed behaviour compatible with cryoSR microscopy, making this technique broadly available without requiring specialised equipment and will improve the applicability of this emerging technique for cellular and structural biology.
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Affiliation(s)
- Maarten W Tuijtel
- Section Electron Microscopy, Dept. of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Abraham J Koster
- Section Electron Microscopy, Dept. of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
- NeCEN, Gorlaeus Laboratories, Leiden University, 2333 CC, Leiden, The Netherlands
| | - Stefan Jakobs
- Max Planck Institute for Biophysical Chemistry, Dept. of NanoBiophotonics and University Medical Center of Göttingen, Dept. of Neurology, Am Faßberg 11, 37077, Göttingen, Germany
| | - Frank G A Faas
- Section Electron Microscopy, Dept. of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
| | - Thomas H Sharp
- Section Electron Microscopy, Dept. of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
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77
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Pujals S, Feiner-Gracia N, Delcanale P, Voets I, Albertazzi L. Super-resolution microscopy as a powerful tool to study complex synthetic materials. Nat Rev Chem 2019. [DOI: 10.1038/s41570-018-0070-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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78
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Weber MS, Wojtynek M, Medalia O. Cellular and Structural Studies of Eukaryotic Cells by Cryo-Electron Tomography. Cells 2019; 8:E57. [PMID: 30654455 PMCID: PMC6356268 DOI: 10.3390/cells8010057] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 11/23/2022] Open
Abstract
The architecture of protein assemblies and their remodeling during physiological processes is fundamental to cells. Therefore, providing high-resolution snapshots of macromolecular complexes in their native environment is of major importance for understanding the molecular biology of the cell. Cellular structural biology by means of cryo-electron tomography (cryo-ET) offers unique insights into cellular processes at an unprecedented resolution. Recent technological advances have enabled the detection of single impinging electrons and improved the contrast of electron microscopic imaging, thereby significantly increasing the sensitivity and resolution. Moreover, various sample preparation approaches have paved the way to observe every part of a eukaryotic cell, and even multicellular specimens, under the electron beam. Imaging of macromolecular machineries at high resolution directly within their native environment is thereby becoming reality. In this review, we discuss several sample preparation and labeling techniques that allow the visualization and identification of macromolecular assemblies in situ, and demonstrate how these methods have been used to study eukaryotic cellular landscapes.
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Affiliation(s)
- Miriam Sarah Weber
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland.
| | - Matthias Wojtynek
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland.
- Department of Biology, Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland.
| | - Ohad Medalia
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland.
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84120, Israel.
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80
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Schermelleh L, Ferrand A, Huser T, Eggeling C, Sauer M, Biehlmaier O, Drummen GPC. Super-resolution microscopy demystified. Nat Cell Biol 2019; 21:72-84. [PMID: 30602772 DOI: 10.1038/s41556-018-0251-8] [Citation(s) in RCA: 540] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/12/2018] [Indexed: 02/08/2023]
Abstract
Super-resolution microscopy (SRM) bypasses the diffraction limit, a physical barrier that restricts the optical resolution to roughly 250 nm and was previously thought to be impenetrable. SRM techniques allow the visualization of subcellular organization with unprecedented detail, but also confront biologists with the challenge of selecting the best-suited approach for their particular research question. Here, we provide guidance on how to use SRM techniques advantageously for investigating cellular structures and dynamics to promote new discoveries.
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Affiliation(s)
- Lothar Schermelleh
- Micron Oxford Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Christian Eggeling
- MRC Human Immunology Unit and Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Institute for Applied Optics, Friedrich-Schiller-University Jena & Leibniz Institute of Photonic Technology, Jena, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Oliver Biehlmaier
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Gregor P C Drummen
- Advanced Bio-Imaging Program, Bio&Nano Solutions‒LAB3BIO, Bielefeld, Germany.
- ICON-Europe.org, Exxilon Scientific Events, Steinhagen, Germany.
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81
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Ho SH, Tirrell DA. N-Myristoyl Transferase (NMT)-Catalyzed Labeling of Bacterial Proteins for Imaging in Fixed and Live Cells. Methods Mol Biol 2019; 2012:315-326. [PMID: 31161515 DOI: 10.1007/978-1-4939-9546-2_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Methods for selective protein imaging are critical for elucidating how cells orchestrate fundamental biological processes. We recently developed a chemoenzymatic method to modify bacterial proteins in situ for fluorescence imaging using N-myristoyl transferase (NMT). Target proteins outfitted with an N-terminal NMT recognition sequence are covalently modified with an azido fatty acid. Subsequent strain-promoted azide-alkyne cycloaddition allows for conjugation to cell-permeant fluorophores and imaging by fluorescence microscopy. Here we describe sample preparation and labeling protocols for imaging bacterial proteins in fixed and live cells.
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Affiliation(s)
- Samuel H Ho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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82
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In Situ Imaging and Structure Determination of Bacterial Toxin Delivery Systems Using Electron Cryotomography. Methods Mol Biol 2019; 1921:249-265. [PMID: 30694497 DOI: 10.1007/978-1-4939-9048-1_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Determining the three-dimensional structure of biomacromolecules at high resolution in their native cellular environment is a major challenge for structural biology. Toward this end, electron cryotomography (ECT) allows large bio-macromolecular assemblies to be imaged directly in their hydrated physiological milieu to ~4 nm resolution. Combining ECT with other techniques like fluorescent imaging, immunogold labeling, and genetic manipulation has allowed the in situ investigation of complex biological processes at macromolecular resolution. Furthermore, the advent of cryogenic focused ion beam (FIB) milling has extended the domain of ECT to include regions even deep within thick eukaryotic cells. Anticipating two audiences (scientists who just want to understand the potential and general workflow involved and scientists who are learning how to do the work themselves), here we present both a broad overview of this kind of work and a step-by-step example protocol for ECT and subtomogram averaging using the Legionella pneumophila Dot/Icm type IV secretion system (T4SS) as a case study. While the general workflow is presented in step-by-step detail, we refer to online tutorials, user's manuals, and other training materials for the essential background understanding needed to perform each step.
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83
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Huebinger J, Spindler J, Holl KJ, Koos B. Quantification of protein mobility and associated reshuffling of cytoplasm during chemical fixation. Sci Rep 2018; 8:17756. [PMID: 30532039 PMCID: PMC6288139 DOI: 10.1038/s41598-018-36112-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/14/2018] [Indexed: 01/21/2023] Open
Abstract
To understand cellular functionalities, it is essential to unravel spatio-temporal patterns of molecular distributions and interactions within living cells. The technological progress in fluorescence microscopy now allows in principle to measure these patterns with sufficient spatial resolution. However, high resolution imaging comes with long acquisition times and high phototoxicity. Therefore, physiological live cell imaging is often unfeasible and chemical fixation is employed. Yet, fixation methods have not been rigorously investigated, in terms of pattern preservation, at the resolution at which cells can now be imaged. A key parameter for this is the time required until fixation is complete. During this time, cells are under unphysiological conditions and patterns decay. We demonstrate here that formaldehyde fixation takes more than one hour for cytosolic proteins in cultured cells. Other small aldehydes, glyoxal and acrolein, did not perform better. Associated with this, we found a distinct displacement of proteins and lipids, including their loss from cells. Fixations using glutaraldehyde were faster than four minutes and retained most cytoplasmic proteins. Surprisingly, autofluorescence produced by glutaraldehyde was almost completely absent with supplementary addition of formaldehyde without compromising fixation speed. These findings indicate, which cellular processes can actually be reliably imaged after a certain chemical fixation.
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Affiliation(s)
- Jan Huebinger
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227, Dortmund, Germany.
| | - Jessica Spindler
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227, Dortmund, Germany
| | - Kristin J Holl
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227, Dortmund, Germany
| | - Björn Koos
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227, Dortmund, Germany
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84
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Sun R, Chen X, Yin CY, Qi L, Lau PM, Han H, Bi GQ. Correlative light and electron microscopy for complex cellular structures on PDMS substrates with coded micro-patterns. LAB ON A CHIP 2018; 18:3840-3848. [PMID: 30417906 DOI: 10.1039/c8lc00703a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fluorescence light microscopy (FLM) is commonly used for localizing specific cellular and subcellular targets. Electron microscopy (EM), on the other hand, can reveal ultrastructural details of cellular architectures beyond the limit of optical resolution. Correlative light and electron microscopy (CLEM) that combines the two techniques has proven valuable in various cell biological applications that require both specificity and resolution. Here, we report an efficient and easy-to-use CLEM system, and its applications in studying neuronal synapses. The system utilizes patterned symbols to encode coordinates on micro-fabricated polydimethylsiloxane (PDMS) substrates, on which dissociated primary hippocampal neurons grow and form synaptic connections. After imaging and localizing specifically labeled synapses with FLM, samples are embedded in resin blocks and sectioned for EM analysis. The patterned symbols on PDMS substrates provide coordinate information, allowing efficient co-registration between FLM and EM images with high precision. A custom-developed software package achieves automated EM image collection, FLM/EM alignment, and EM navigation. With this CLEM system, we have obtained high quality electron tomograms of fluorescently labeled synapses along dendrites of hippocampal neurons and analyzed docking statistics of synaptic vesicles (SVs) in different subtypes of excitatory synapses. This technique provides an efficient approach to combine functional studies with ultrastructural analysis of heterogeneous neuronal synapses, as well as other subcellular structures in general.
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Affiliation(s)
- Rong Sun
- Center for Integrative Imaging, National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
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85
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Ng CT, Deng L, Chen C, Lim HH, Shi J, Surana U, Gan L. Electron cryotomography analysis of Dam1C/DASH at the kinetochore-spindle interface in situ. J Cell Biol 2018; 218:455-473. [PMID: 30504246 PMCID: PMC6363454 DOI: 10.1083/jcb.201809088] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 01/01/2023] Open
Abstract
In dividing cells, depolymerizing spindle microtubules move chromosomes by pulling at their kinetochores. While kinetochore subcomplexes have been studied extensively in vitro, little is known about their in vivo structure and interactions with microtubules or their response to spindle damage. Here we combine electron cryotomography of serial cryosections with genetic and pharmacological perturbation to study the yeast chromosome segregation machinery in vivo. Each kinetochore microtubule has one (rarely, two) Dam1C/DASH outer kinetochore assemblies. Dam1C/DASH contacts the microtubule walls and does so with its flexible "bridges"; there are no contacts with the protofilaments' curved tips. In metaphase, ∼40% of the Dam1C/DASH assemblies are complete rings; the rest are partial rings. Ring completeness and binding position along the microtubule are sensitive to kinetochore attachment and tension, respectively. Our study and those of others support a model in which each kinetochore must undergo cycles of conformational change to couple microtubule depolymerization to chromosome movement.
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Affiliation(s)
- Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Li Deng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Chen Chen
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Hong Hwa Lim
- Institute of Molecular and Cell Biology Agency for Science Technology and Research, Singapore.,Bioprocessing Technology Institute, Agency for Science Technology and Research, Singapore
| | - Jian Shi
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Uttam Surana
- Institute of Molecular and Cell Biology Agency for Science Technology and Research, Singapore.,Bioprocessing Technology Institute, Agency for Science Technology and Research, Singapore.,Department of Pharmacology, National University of Singapore, Singapore
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
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86
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Ando T, Bhamidimarri SP, Brending N, Colin-York H, Collinson L, De Jonge N, de Pablo PJ, Debroye E, Eggeling C, Franck C, Fritzsche M, Gerritsen H, Giepmans BNG, Grunewald K, Hofkens J, Hoogenboom JP, Janssen KPF, Kaufman R, Klumpermann J, Kurniawan N, Kusch J, Liv N, Parekh V, Peckys DB, Rehfeldt F, Reutens DC, Roeffaers MBJ, Salditt T, Schaap IAT, Schwarz US, Verkade P, Vogel MW, Wagner R, Winterhalter M, Yuan H, Zifarelli G. The 2018 correlative microscopy techniques roadmap. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:443001. [PMID: 30799880 PMCID: PMC6372154 DOI: 10.1088/1361-6463/aad055] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/14/2018] [Accepted: 07/01/2018] [Indexed: 05/19/2023]
Abstract
Developments in microscopy have been instrumental to progress in the life sciences, and many new techniques have been introduced and led to new discoveries throughout the last century. A wide and diverse range of methodologies is now available, including electron microscopy, atomic force microscopy, magnetic resonance imaging, small-angle x-ray scattering and multiple super-resolution fluorescence techniques, and each of these methods provides valuable read-outs to meet the demands set by the samples under study. Yet, the investigation of cell development requires a multi-parametric approach to address both the structure and spatio-temporal organization of organelles, and also the transduction of chemical signals and forces involved in cell-cell interactions. Although the microscopy technologies for observing each of these characteristics are well developed, none of them can offer read-out of all characteristics simultaneously, which limits the information content of a measurement. For example, while electron microscopy is able to disclose the structural layout of cells and the macromolecular arrangement of proteins, it cannot directly follow dynamics in living cells. The latter can be achieved with fluorescence microscopy which, however, requires labelling and lacks spatial resolution. A remedy is to combine and correlate different readouts from the same specimen, which opens new avenues to understand structure-function relations in biomedical research. At the same time, such correlative approaches pose new challenges concerning sample preparation, instrument stability, region of interest retrieval, and data analysis. Because the field of correlative microscopy is relatively young, the capabilities of the various approaches have yet to be fully explored, and uncertainties remain when considering the best choice of strategy and workflow for the correlative experiment. With this in mind, the Journal of Physics D: Applied Physics presents a special roadmap on the correlative microscopy techniques, giving a comprehensive overview from various leading scientists in this field, via a collection of multiple short viewpoints.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | | | | | - H Colin-York
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
| | | | - Niels De Jonge
- INM-Leibniz Institute for New Materials, 66123 Saarbrücken, Germany
- Saarland University, 66123 Saarbrücken, Germany
| | - P J de Pablo
- Dpto. Física de la Materia Condensada Universidad Autónoma de Madrid 28049, Madrid, Spain
- Instituto de Física de la Materia Condensada IFIMAC, Universidad Autónoma de Madrid 28049, Madrid, Spain
| | - Elke Debroye
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
- Institute of Applied Optics, Friedrich-Schiller University, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - Christian Franck
- Department of Mechanical Engineering, University of Wisconsin-Madison, 1513 University Ave, Madison, WI 53706, United States of America
| | - Marco Fritzsche
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Hans Gerritsen
- Debye Institute, Utrecht University, Utrecht, Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Kay Grunewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Centre of Structural Systems Biology Hamburg and University of Hamburg, Hamburg, Germany
- Heinrich-Pette-Institute, Leibniz Institute of Virology, Hamburg, Germany
| | - Johan Hofkens
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | | | | | - Rainer Kaufman
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Centre of Structural Systems Biology Hamburg and University of Hamburg, Hamburg, Germany
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Judith Klumpermann
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, Netherlands
| | - Nyoman Kurniawan
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, Netherlands
| | - Viha Parekh
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Diana B Peckys
- Faculty of Medicine, Saarland University, 66421 Homburg, Germany
| | - Florian Rehfeldt
- University of Göttingen, Third Institute of Physics-Biophysics, 37077 Göttingen, Germany
| | - David C Reutens
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Tim Salditt
- University of Göttingen, Institute for X-Ray Physics, 37077 Göttingen, Germany
| | - Iwan A T Schaap
- SmarAct GmbH, Schütte-Lanz-Str. 9, D-26135 Oldenburg, Germany
| | - Ulrich S Schwarz
- Institute for Theoretical Physics and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Michael W Vogel
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard Wagner
- Department of Life Sciences & Chemistry, Jacobs University, Bremen, Germany
| | | | - Haifeng Yuan
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | - Giovanni Zifarelli
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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87
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Ultra-stable super-resolution fluorescence cryo-microscopy for correlative light and electron cryo-microscopy. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1312-1319. [PMID: 30426455 DOI: 10.1007/s11427-018-9380-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/17/2018] [Indexed: 11/27/2022]
Abstract
Remarkable progress in correlative light and electron cryo-microscopy (cryo-CLEM) has been made in the past decade. A crucial component for cryo-CLEM is a dedicated cryo-fluorescence microscope (cryo-FM). Here, we describe an ultra-stable super-resolution cryo-FM that exhibits excellent thermal and mechanical stability. The temperature fluctuations in 10 h are less than 0.06 K, and the mechanical drift over 5 h is less than 200 nm in three dimensions. We have demonstrated the super-resolution imaging capability of this system (average single molecule localization accuracy of ∼13.0 nm). The results suggest that our system is particularly suitable for long-term observations, such as single molecule localization microscopy (SMLM) and cryogenic super-resolution correlative light and electron microscopy (csCLEM).
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88
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Pfeffer S, Mahamid J. Unravelling molecular complexity in structural cell biology. Curr Opin Struct Biol 2018; 52:111-118. [PMID: 30339965 DOI: 10.1016/j.sbi.2018.08.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/18/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Structural and cell biology have traditionally been separate disciplines and employed techniques that were well defined within the realm of either one or the other. Recent technological breakthroughs propelled electron microscopy of frozen hydrated specimens (cryo-EM) followed by single-particle analysis (SPA) to become a widely applied approach for obtaining near-atomic resolution structures of purified macromolecules. In parallel, ongoing developments on sample preparation are increasingly successful in bringing molecular views into cell biology. Cryo-electron tomography (cryo-ET) has so far served as the main imaging modality employed in these efforts towards obtaining three-dimensional (3D) volumes of heterogeneous molecular assemblies. We review the state-of-the-art in cryo-ET and computational processing and describe the current opportunities and frontiers for in-cell applications.
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Affiliation(s)
- Stefan Pfeffer
- Centre for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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89
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Dahlberg P, Sartor AM, Wang J, Saurabh S, Shapiro L, Moerner WE. Identification of PAmKate as a Red Photoactivatable Fluorescent Protein for Cryogenic Super-Resolution Imaging. J Am Chem Soc 2018; 140:12310-12313. [PMID: 30222332 PMCID: PMC6174896 DOI: 10.1021/jacs.8b05960] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Indexed: 11/30/2022]
Abstract
Single-molecule super-resolution fluorescence microscopy conducted in vitrified samples at cryogenic temperatures offers enhanced localization precision due to reduced photobleaching rates, a chemical-free and rapid fixation method, and the potential of correlation with cryogenic electron microscopy. Achieving cryogenic super-resolution microscopy requires the ability to control the sparsity of emissive labels at cryogenic temperatures. Obtaining this control presents a key challenge for the development of this technique. In this work, we identify a red photoactivatable protein, PAmKate, which remains activatable at cryogenic temperatures. We characterize its activation as a function of temperature and find that activation is efficient at cryogenic and room temperatures. We perform cryogenic super-resolution experiments in situ, labeling PopZ, a protein known to assemble into a microdomain at the poles of the model bacterium Caulobacter crescentus. We find improved localization precision at cryogenic temperatures compared to room temperature by a factor of 4, attributable to reduced photobleaching.
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Affiliation(s)
- Peter
D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Annina M. Sartor
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jiarui Wang
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Developmental Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Saumya Saurabh
- Department
of Developmental Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Lucy Shapiro
- Department
of Developmental Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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90
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Hulleman CN, Huisman M, Moerland RJ, Grünwald D, Stallinga S, Rieger B. Fluorescence Polarization Control for On-Off Switching of Single Molecules at Cryogenic Temperatures. SMALL METHODS 2018; 2:1700323. [PMID: 31240238 PMCID: PMC6592266 DOI: 10.1002/smtd.201700323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Light microscopy, allowing sub-diffraction-limited resolution, has been among the fastest developing techniques at the interface of biology, chemistry, and physics. Intriguingly no theoretical limit exists on how far the underlying measurement uncertainty can be lowered. In particular data fusion of large amounts of images can reduce the measurement error to match the resolution of structural methods like cryo-electron microscopy. Fluorescence, although reliant on a reporter molecule and therefore not the first choice to obtain ultraresolution structures, brings highly specific labeling of molecules in a large assembly to the table and inherently allows the detection of multiple colors, which enables the interrogation of multiple molecular species at the same time in the same sample. Here, the problems to be solved in the coming years, with the aim of higher resolution, are discussed, and what polarization depletion of fluorescence at cryogenic temperatures can contribute for fluorescence imaging of biological samples, like whole cells, is described.
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Affiliation(s)
- Christiaan N Hulleman
- Department of Imaging Physics Delft University of Technology Delft 2628, CJ, The Netherlands
| | - Maximiliaan Huisman
- RNA Therapeutics Institute University of Massachusetts Medical School Worcester, MA 01605, USA
| | - Robert J Moerland
- Department of Imaging Physics Delft University of Technology Delft 2628, CJ, The Netherlands
| | - David Grünwald
- RNA Therapeutics Institute University of Massachusetts Medical School Worcester, MA 01605, USA
| | - Sjoerd Stallinga
- Department of Imaging Physics Delft University of Technology Delft 2628, CJ, The Netherlands
| | - Bernd Rieger
- Department of Imaging Physics Delft University of Technology Delft 2628, CJ, The Netherlands
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91
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Möbius W, Posthuma G. Sugar and ice: Immunoelectron microscopy using cryosections according to the Tokuyasu method. Tissue Cell 2018; 57:90-102. [PMID: 30201442 DOI: 10.1016/j.tice.2018.08.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/26/2018] [Accepted: 08/22/2018] [Indexed: 11/29/2022]
Abstract
Since the pioneering work of Kiyoteru Tokuyasu in the 70ths the use of thawed cryosections prepared according to the "Tokuyasu-method" for immunoelectron microscopy did not lose popularity. We owe this method a whole subcellular world described by discrete gold particles pointing at cargo, receptors and organelle markers on delicate images of the inner life of a cell. Here we explain the procedure of sample preparation, sectioning and immunolabeling in view of recent developments and the reasoning behind protocols including some historical perspective. Cryosections are prepared from chemically fixed and sucrose infiltrated samples and labeled with affinity probes and electron dense markers. These sections are ideal substrates for immunolabeling, since antigens are not exposed to organic solvent dehydration or masked by resin. Instead, the structures remain fully hydrated throughout the labeling procedure. Furthermore, target molecules inside dense intercellular structural elements, cells and organelles are accessible to antibodies from the section surface. For the validation of antibody specificity several approaches are recommended including knock-out tissue and reagent controls. Correlative light and electron microscopy strategies involving correlative probes are possible as well as correlation of live imaging with the underlying ultrastructure. By applying stereology, gold labeling can be quantified and evaluated for specificity.
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Affiliation(s)
- Wiebke Möbius
- Electron Microscopy Core Unit, Department of Neurogenetics, Max Planck Institute of Experimental Medicine, 37075, Göttingen, Germany; Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany.
| | - George Posthuma
- Department of Cell Biology, Cell Microscopy Core, University Medical Center Utrecht, Utrecht University, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands.
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92
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Melia CE, Bharat TAM. Locating macromolecules and determining structures inside bacterial cells using electron cryotomography. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:973-981. [PMID: 29908328 PMCID: PMC6052677 DOI: 10.1016/j.bbapap.2018.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/30/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Electron cryotomography (cryo-ET) is an imaging technique uniquely suited to the study of bacterial ultrastructure and cell biology. Recent years have seen a surge in structural and cell biology research on bacteria using cryo-ET. This research has driven major technical developments in the field, with applications emerging to address a wide range of biological questions. In this review, we explore the diversity of cryo-ET approaches used for structural and cellular microbiology, with a focus on in situ localization and structure determination of macromolecules. The first section describes strategies employed to locate target macromolecules within large cellular volumes. Next, we explore methods to study thick specimens by sample thinning. Finally, we review examples of macromolecular structure determination in a cellular context using cryo-ET. The examples outlined serve as powerful demonstrations of how the cellular location, structure, and function of any bacterial macromolecule of interest can be investigated using cryo-ET.
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Affiliation(s)
- Charlotte E Melia
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; Central Oxford Structural and Molecular Imaging Centre, University of Oxford, Oxford OX1 3RE, United Kingdom.
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93
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Gong Y, Zhang Z, Liu Y, Zhou X, Anwar MN, Li Z, Hu W, Li Y. A nuclease‐toxin and immunity system for kin discrimination inMyxococcus xanthus. Environ Microbiol 2018; 20:2552-2567. [DOI: 10.1111/1462-2920.14282] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 05/14/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Ya Gong
- State Key Laboratory of Microbial Technology, School of Life ScienceShandong University Jinan 250100 China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, School of Life ScienceShandong University Jinan 250100 China
| | - Ya Liu
- State Key Laboratory of Microbial Technology, School of Life ScienceShandong University Jinan 250100 China
| | - Xiu‐Wen Zhou
- State Key Laboratory of Microbial Technology, School of Life ScienceShandong University Jinan 250100 China
| | - Mian Nabeel Anwar
- State Key Laboratory of Microbial Technology, School of Life ScienceShandong University Jinan 250100 China
| | - Ze‐Shuo Li
- State Key Laboratory of Microbial Technology, School of Life ScienceShandong University Jinan 250100 China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, School of Life ScienceShandong University Jinan 250100 China
| | - Yue‐Zhong Li
- State Key Laboratory of Microbial Technology, School of Life ScienceShandong University Jinan 250100 China
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94
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Cai S, Böck D, Pilhofer M, Gan L. The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin. Mol Biol Cell 2018; 29:2450-2457. [PMID: 30091658 PMCID: PMC6233054 DOI: 10.1091/mbc.e18-05-0331] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The in situ three-dimensional organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography to determine the in situ structures of HeLa nucleosomes, which have canonical core structures and asymmetric, flexible linker DNA. Subtomogram remapping suggests that sequential nucleosomes in heterochromatin follow irregular paths at the oligonucleosome level. This basic principle of higher-order repressive chromatin folding is compatible with the conformational variability of the two linker DNAs at the single-nucleosome level.
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Affiliation(s)
- Shujun Cai
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Désirée Böck
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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95
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Dillard RS, Hampton CM, Strauss JD, Ke Z, Altomara D, Guerrero-Ferreira RC, Kiss G, Wright ER. Biological Applications at the Cutting Edge of Cryo-Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2018; 24:406-419. [PMID: 30175702 PMCID: PMC6265046 DOI: 10.1017/s1431927618012382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is a powerful tool for macromolecular to near-atomic resolution structure determination in the biological sciences. The specimen is maintained in a near-native environment within a thin film of vitreous ice and imaged in a transmission electron microscope. The images can then be processed by a number of computational methods to produce three-dimensional information. Recent advances in sample preparation, imaging, and data processing have led to tremendous growth in the field of cryo-EM by providing higher resolution structures and the ability to investigate macromolecules within the context of the cell. Here, we review developments in sample preparation methods and substrates, detectors, phase plates, and cryo-correlative light and electron microscopy that have contributed to this expansion. We also have included specific biological applications.
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Affiliation(s)
- Rebecca S Dillard
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Cheri M Hampton
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Joshua D Strauss
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Zunlong Ke
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Deanna Altomara
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Ricardo C Guerrero-Ferreira
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Gabriella Kiss
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Elizabeth R Wright
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
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96
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97
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Microscopy in Infectious Disease Research-Imaging Across Scales. J Mol Biol 2018; 430:2612-2625. [PMID: 29908150 DOI: 10.1016/j.jmb.2018.06.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/03/2018] [Accepted: 06/08/2018] [Indexed: 12/18/2022]
Abstract
A comprehensive understanding of host-pathogen interactions requires quantitative assessment of molecular events across a wide range of spatiotemporal scales and organizational complexities. Due to recent technical developments, this is currently only achievable with microscopy. This article is providing a general perspective on the importance of microscopy in infectious disease research, with a focus on new imaging modalities that promise to have a major impact in biomedical research in the years to come. Every major technological breakthrough in light microscopy depends on, and is supported by, advancements in computing and information technologies. Bioimage acquisition and analysis based on machine learning will pave the way toward more robust, automated and objective implementation of new imaging modalities and in biomedical research in general. The combination of novel imaging technologies with machine learning and near-physiological model systems promises to accelerate discoveries and breakthroughs in our understanding of infectious diseases, from basic research all the way to clinical applications.
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98
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Huebinger J, Grabenbauer M. Self-Pressurized Rapid Freezing as Cryo-Fixation Method for Electron Microscopy and Cryopreservation of Living Cells. ACTA ACUST UNITED AC 2018; 79:e47. [PMID: 29924483 DOI: 10.1002/cpcb.47] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Reduction or complete prevention of ice crystal formation during freezing of biological specimens is mandatory for two important biological applications: (1) cryopreservation of living cells or tissues for long-term storage, and (2) cryo-fixation for ultrastructural investigations by electron microscopy. Here, a protocol that is fast, easy-to-use, and suitable for both cryo-fixation and cryopreservation is described. Samples are rapidly cooled in tightly sealed metal tubes of high thermal diffusivity and then plunged into a liquid cryogen. Due to the fast cooling speed and high-pressure buildup internally in the confined volume of the metal tubes, ice crystal formation is reduced or completely prevented, resulting in vitrification of the sample. For cryopreservation, however, a similar principle applies to prevent ice crystal formation during re-warming. A detailed description of procedures for cooling (and re-warming) of biological samples using this technique is provided. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jan Huebinger
- Department of Systemic Cell Biology, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Markus Grabenbauer
- Institute for Anatomy and Cell Biology, University of Heidelberg, Heidelberg, Germany
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99
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Sigmund F, Massner C, Erdmann P, Stelzl A, Rolbieski H, Desai M, Bricault S, Wörner TP, Snijder J, Geerlof A, Fuchs H, Hrabĕ de Angelis M, Heck AJR, Jasanoff A, Ntziachristos V, Plitzko J, Westmeyer GG. Bacterial encapsulins as orthogonal compartments for mammalian cell engineering. Nat Commun 2018; 9:1990. [PMID: 29777103 PMCID: PMC5959871 DOI: 10.1038/s41467-018-04227-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/16/2018] [Indexed: 01/06/2023] Open
Abstract
We genetically controlled compartmentalization in eukaryotic cells by heterologous expression of bacterial encapsulin shell and cargo proteins to engineer enclosed enzymatic reactions and size-constrained metal biomineralization. The shell protein (EncA) from Myxococcus xanthus auto-assembles into nanocompartments inside mammalian cells to which sets of native (EncB,C,D) and engineered cargo proteins self-target enabling localized bimolecular fluorescence and enzyme complementation. Encapsulation of the enzyme tyrosinase leads to the confinement of toxic melanin production for robust detection via multispectral optoacoustic tomography (MSOT). Co-expression of ferritin-like native cargo (EncB,C) results in efficient iron sequestration producing substantial contrast by magnetic resonance imaging (MRI) and allowing for magnetic cell sorting. The monodisperse, spherical, and iron-loading nanoshells are also excellent genetically encoded reporters for electron microscopy (EM). In general, eukaryotically expressed encapsulins enable cellular engineering of spatially confined multicomponent processes with versatile applications in multiscale molecular imaging, as well as intriguing implications for metabolic engineering and cellular therapy. Artificial compartments have been expressed in prokaryotes and yeast, but similar capabilities have been missing for mammalian cell engineering. Here the authors use bacterial encapsulins to engineer genetically controlled multifunctional orthogonal compartments in mammalian cells.
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Affiliation(s)
- Felix Sigmund
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.,Department of Nuclear Medicine, Technical University of Munich, Ismaninger Straße 22, Munich, 81675, Germany
| | - Christoph Massner
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.,Department of Nuclear Medicine, Technical University of Munich, Ismaninger Straße 22, Munich, 81675, Germany
| | - Philipp Erdmann
- Department of Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Anja Stelzl
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Hannes Rolbieski
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Mitul Desai
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, Massachusetts, USA
| | - Sarah Bricault
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, Massachusetts, USA
| | - Tobias P Wörner
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands.,Snijder Bioscience, Spijkerstraat 114-4, Arnhem, 6828 DN, The Netherlands
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Martin Hrabĕ de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - Alan Jasanoff
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, Massachusetts, USA.,Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, Massachusetts, USA.,Department of Nuclear Science & Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, Massachusetts, USA
| | - Vasilis Ntziachristos
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany.,Chair for Biological Imaging, Technical University of Munich, Ismaninger Straße 22, Munich, 81675, Germany
| | - Jürgen Plitzko
- Department of Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Gil G Westmeyer
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany. .,Institute of Developmental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany. .,Department of Nuclear Medicine, Technical University of Munich, Ismaninger Straße 22, Munich, 81675, Germany.
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100
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Hulleman CN, Li W, Gregor I, Rieger B, Enderlein J. Photon Yield Enhancement of Red Fluorophores at Cryogenic Temperatures. Chemphyschem 2018; 19:1774-1780. [PMID: 29659104 DOI: 10.1002/cphc.201800131] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Indexed: 11/10/2022]
Abstract
Single Molecule Localization Microscopy has become one of the most successful and widely applied methods of Super-resolution Fluorescence Microscopy. Its achievable resolution strongly depends on the number of detectable photons from a single molecule until photobleaching. By cooling a sample from room temperature down to liquid nitrogen temperatures, the photostability of dyes can be enhanced by more than 100 fold, which results in an improvement in localization precision greater than 10 times. Here, we investigate a variety of fluorescent dyes in the red spectral region, and we find an average photon yield between 3.5 ⋅ 106 to 11 ⋅ 106 photons before bleaching at liquid nitrogen temperatures, corresponding to a theoretical localization precision around 0.1 nm.
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Affiliation(s)
- Christiaan N Hulleman
- Department of Imaging Physics, Delft University of Technology, Lorentzweg 1, 2628CJ, Delft, The Netherlands
| | - Weixing Li
- III. Physical Institute Biophysics/Complex Systems, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany.,Current Address: Institute of Biophysics, Chinese Academy of Sciences, Datun Road 15, 100101, Beijing, China
| | - Ingo Gregor
- III. Physical Institute Biophysics/Complex Systems, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Bernd Rieger
- Department of Imaging Physics, Delft University of Technology, Lorentzweg 1, 2628CJ, Delft, The Netherlands
| | - Jörg Enderlein
- III. Physical Institute Biophysics/Complex Systems, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
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