101
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Correlative light and scanning electron microscopy (CLSEM) for analysis of bacterial infection of polarized epithelial cells. Sci Rep 2019; 9:17079. [PMID: 31745114 PMCID: PMC6863815 DOI: 10.1038/s41598-019-53085-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/16/2019] [Indexed: 12/11/2022] Open
Abstract
Infection of mammalian host cells by bacterial pathogens is a highly dynamic process and microscopy is instrumental to reveal the cellular and molecular details of host-pathogen interactions. Correlative light and electron microscopy (CLEM) combines the advantages of three-dimensional live cell imaging with ultrastructural analysis. The analyses of adhesion to, and invasion of polarized epithelial cells by pathogens often deploys scanning electron microscopy (SEM), since surface structures of the apical brush border can be analyzed in detail. Most available CLEM approaches focus on relocalization of separated single cells in different imaging modalities, but are not readily applicable to polarized epithelial cell monolayers, since orientation marks on substrate are overgrown during differentiation. To address this problem, we developed a simple and convenient workflow for correlative light and scanning electron microscopy (CLSEM), using gold mesh grids as carrier for growth of epithelial cell monolayers, and for imaging infection. The approach allows fast live cell imaging of bacterial infection of polarized cells with subsequent analyses by SEM. As examples for CLSEM applications, we investigated trigger invasion by Salmonella enterica, zipper invasion by Listeria monocytogenes, and the enterocyte attachment and effacement phenotype of enteropathogenic Escherichia coli. Our study demonstrates the versatile use of gold mesh grids for CLSEM of the interaction of bacterial pathogens with the apical side of polarized epithelial cells.
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102
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Hoffmann PC, Bharat TAM, Wozny MR, Boulanger J, Miller EA, Kukulski W. Tricalbins Contribute to Cellular Lipid Flux and Form Curved ER-PM Contacts that Are Bridged by Rod-Shaped Structures. Dev Cell 2019; 51:488-502.e8. [PMID: 31743663 PMCID: PMC6863393 DOI: 10.1016/j.devcel.2019.09.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 08/06/2019] [Accepted: 09/25/2019] [Indexed: 11/25/2022]
Abstract
Lipid flow between cellular organelles occurs via membrane contact sites. Extended-synaptotagmins, known as tricalbins in yeast, mediate lipid transfer between the endoplasmic reticulum (ER) and plasma membrane (PM). How these proteins regulate membrane architecture to transport lipids across the aqueous space between bilayers remains unknown. Using correlative microscopy, electron cryo-tomography, and high-throughput genetics, we address the interplay of architecture and function in budding yeast. We find that ER-PM contacts differ in protein composition and membrane morphology, not in intermembrane distance. In situ electron cryo-tomography reveals the molecular organization of tricalbin-mediated contacts, suggesting a structural framework for putative lipid transfer. Genetic analysis uncovers functional overlap with cellular lipid routes, such as maintenance of PM asymmetry. Further redundancies are suggested for individual tricalbin protein domains. We propose a modularity of molecular and structural functions of tricalbins and of their roles within the cellular network of lipid distribution pathways.
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Affiliation(s)
- Patrick C Hoffmann
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, UK
| | - Michael R Wozny
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jerome Boulanger
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Elizabeth A Miller
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Wanda Kukulski
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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103
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Asam C, Buerger K, Felthaus O, Brébant V, Rachel R, Prantl L, Witzgall R, Haerteis S, Aung T. Subcellular localization of the chemotherapeutic agent doxorubicin in renal epithelial cells and in tumor cells using correlative light and electron microscopy. Clin Hemorheol Microcirc 2019; 73:157-167. [DOI: 10.3233/ch-199212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Claudia Asam
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Germany
| | - Korbinian Buerger
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Germany
| | - Oliver Felthaus
- Centre of Plastic, Aesthetic, Hand and Reconstructive Surgery, University of Regensburg, Regensburg, Germany
| | - Vanessa Brébant
- Centre of Plastic, Aesthetic, Hand and Reconstructive Surgery, University of Regensburg, Regensburg, Germany
| | - Reinhard Rachel
- Centre for Electron Microscopy, Faculty of Biology and Preclinical Medicine, University of Regensburg, Germany
| | - Lukas Prantl
- Centre of Plastic, Aesthetic, Hand and Reconstructive Surgery, University of Regensburg, Regensburg, Germany
| | - Ralph Witzgall
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Germany
| | - Silke Haerteis
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Germany
| | - Thiha Aung
- Centre of Plastic, Aesthetic, Hand and Reconstructive Surgery, University of Regensburg, Regensburg, Germany
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104
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Hampoelz B, Schwarz A, Ronchi P, Bragulat-Teixidor H, Tischer C, Gaspar I, Ephrussi A, Schwab Y, Beck M. Nuclear Pores Assemble from Nucleoporin Condensates During Oogenesis. Cell 2019; 179:671-686.e17. [PMID: 31626769 PMCID: PMC6838685 DOI: 10.1016/j.cell.2019.09.022] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 08/09/2019] [Accepted: 09/20/2019] [Indexed: 02/02/2023]
Abstract
The molecular events that direct nuclear pore complex (NPC) assembly toward nuclear envelopes have been conceptualized in two pathways that occur during mitosis or interphase, respectively. In gametes and embryonic cells, NPCs also occur within stacked cytoplasmic membrane sheets, termed annulate lamellae (AL), which serve as NPC storage for early development. The mechanism of NPC biogenesis at cytoplasmic membranes remains unknown. Here, we show that during Drosophila oogenesis, Nucleoporins condense into different precursor granules that interact and progress into NPCs. Nup358 is a key player that condenses into NPC assembly platforms while its mRNA localizes to their surface in a translation-dependent manner. In concert, Microtubule-dependent transport, the small GTPase Ran and nuclear transport receptors regulate NPC biogenesis in oocytes. We delineate a non-canonical NPC assembly mechanism that relies on Nucleoporin condensates and occurs away from the nucleus under conditions of cell cycle arrest.
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Affiliation(s)
- Bernhard Hampoelz
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Andre Schwarz
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Paolo Ronchi
- European Molecular Biology Laboratory, Electron Microscopy Core Facility, Heidelberg, Germany
| | | | - Christian Tischer
- Center for Bioimage Analysis, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Imre Gaspar
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg, Germany
| | - Anne Ephrussi
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg, Germany
| | - Yannick Schwab
- European Molecular Biology Laboratory, Electron Microscopy Core Facility, Heidelberg, Germany; European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Max Planck Institute of Biophysics, Frankfurt am Main, Germany; European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany.
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105
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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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106
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Sachse M, Fernández de Castro I, Tenorio R, Risco C. The viral replication organelles within cells studied by electron microscopy. Adv Virus Res 2019; 105:1-33. [PMID: 31522702 PMCID: PMC7112055 DOI: 10.1016/bs.aivir.2019.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Transmission electron microscopy (TEM) has been crucial to study viral infections. As a result of recent advances in light and electron microscopy, we are starting to be aware of the variety of structures that viruses assemble inside cells. Viruses often remodel cellular compartments to build their replication factories. Remarkably, viruses are also able to induce new membranes and new organelles. Here we revise the most relevant imaging technologies to study the biogenesis of viral replication organelles. Live cell microscopy, correlative light and electron microscopy, cryo-TEM, and three-dimensional imaging methods are unveiling how viruses manipulate cell organization. In particular, methods for molecular mapping in situ in two and three dimensions are revealing how macromolecular complexes build functional replication complexes inside infected cells. The combination of all these imaging approaches is uncovering the viral life cycle events with a detail never seen before.
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Affiliation(s)
- Martin Sachse
- Unité Technologie et service BioImagerie Ultrastructurale, Institut Pasteur, Paris, France.
| | | | - Raquel Tenorio
- Cell Structure Laboratory, National Center for Biotechnology, CSIC, Madrid, Spain
| | - Cristina Risco
- Cell Structure Laboratory, National Center for Biotechnology, CSIC, Madrid, Spain.
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107
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Manenschijn HE, Picco A, Mund M, Rivier-Cordey AS, Ries J, Kaksonen M. Type-I myosins promote actin polymerization to drive membrane bending in endocytosis. eLife 2019; 8:44215. [PMID: 31385806 PMCID: PMC6684269 DOI: 10.7554/elife.44215] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 07/23/2019] [Indexed: 12/24/2022] Open
Abstract
Clathrin-mediated endocytosis in budding yeast requires the formation of a dynamic actin network that produces the force to invaginate the plasma membrane against the intracellular turgor pressure. The type-I myosins Myo3 and Myo5 are important for endocytic membrane reshaping, but mechanistic details of their function remain scarce. Here, we studied the function of Myo3 and Myo5 during endocytosis using quantitative live-cell imaging and genetic perturbations. We show that the type-I myosins promote, in a dose-dependent way, the growth and expansion of the actin network, which controls the speed of membrane and coat internalization. We found that this myosin-activity is independent of the actin nucleation promoting activity of myosins, and cannot be compensated for by increasing actin nucleation. Our results suggest a new mechanism for type-I myosins to produce force by promoting actin filament polymerization.
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Affiliation(s)
- Hetty E Manenschijn
- Department of Biochemistry, University of Geneva, Geneva, Switzerland.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andrea Picco
- Department of Biochemistry, University of Geneva, Geneva, Switzerland.,NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Markus Mund
- Department of Biochemistry, University of Geneva, Geneva, Switzerland.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Marko Kaksonen
- Department of Biochemistry, University of Geneva, Geneva, Switzerland.,NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
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108
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Bykov YS, Cohen N, Gabrielli N, Manenschijn H, Welsch S, Chlanda P, Kukulski W, Patil KR, Schuldiner M, Briggs JAG. High-throughput ultrastructure screening using electron microscopy and fluorescent barcoding. J Cell Biol 2019; 218:2797-2811. [PMID: 31289126 PMCID: PMC6683748 DOI: 10.1083/jcb.201812081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/28/2019] [Accepted: 06/11/2019] [Indexed: 01/24/2023] Open
Abstract
Genetic screens using high-throughput fluorescent microscopes have generated large datasets, contributing many cell biological insights. Such approaches cannot tackle questions requiring knowledge of ultrastructure below the resolution limit of fluorescent microscopy. Electron microscopy (EM) reveals detailed cellular ultrastructure but requires time-consuming sample preparation, limiting throughput. Here we describe a robust method for screening by high-throughput EM. Our approach uses combinations of fluorophores as barcodes to uniquely mark each cell type in mixed populations and correlative light and EM (CLEM) to read the barcode of each cell before it is imaged by EM. Coupled with an easy-to-use software workflow for correlation, segmentation, and computer image analysis, our method, called "MultiCLEM," allows us to extract and analyze multiple cell populations from each EM sample preparation. We demonstrate several uses for MultiCLEM with 15 different yeast variants. The methodology is not restricted to yeast, can be scaled to higher throughput, and can be used in multiple ways to enable EM to become a powerful screening technique.
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Affiliation(s)
- Yury S Bykov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Nir Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Natalia Gabrielli
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hetty Manenschijn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sonja Welsch
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Petr Chlanda
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Wanda Kukulski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kiran R Patil
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - John A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany .,Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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109
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Gorelick S, Buckley G, Gervinskas G, Johnson TK, Handley A, Caggiano MP, Whisstock JC, Pocock R, de Marco A. PIE-scope, integrated cryo-correlative light and FIB/SEM microscopy. eLife 2019; 8:e45919. [PMID: 31259689 PMCID: PMC6609333 DOI: 10.7554/elife.45919] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/26/2019] [Indexed: 11/14/2022] Open
Abstract
Cryo-electron tomography (cryo-ET) is emerging as a revolutionary method for resolving the structure of macromolecular complexes in situ. However, sample preparation for in situ Cryo-ET is labour-intensive and can require both cryo-lamella preparation through cryo-focused ion beam (FIB) milling and correlative light microscopy to ensure that the event of interest is present in the lamella. Here, we present an integrated cryo-FIB and light microscope setup called the Photon Ion Electron microscope (PIE-scope) that enables direct and rapid isolation of cellular regions containing protein complexes of interest. Specifically, we demonstrate the versatility of PIE-scope by preparing targeted cryo-lamellae from subcellular compartments of neurons from transgenic Caenorhabditis elegans and Drosophila melanogaster expressing fluorescent proteins. We designed PIE-scope to enable retrofitting of existing microscopes, which will increase the throughput and accuracy on projects requiring correlative microscopy to target protein complexes. This new approach will make cryo-correlative workflow safer and more accessible.
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Affiliation(s)
- Sergey Gorelick
- ARC Centre of Excellence in Advanced Molecular ImagingMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
| | - Genevieve Buckley
- ARC Centre of Excellence in Advanced Molecular ImagingMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
| | | | | | - Ava Handley
- Department of Anatomy and Developmental Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
| | - Monica Pia Caggiano
- ARC Centre of Excellence in Advanced Molecular ImagingMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
| | - James C Whisstock
- ARC Centre of Excellence in Advanced Molecular ImagingMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
- University of WarwickCoventryUnited Kingdom
- EMBL AustraliaClaytonAustralia
| | - Roger Pocock
- Department of Anatomy and Developmental Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
| | - Alex de Marco
- ARC Centre of Excellence in Advanced Molecular ImagingMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
- University of WarwickCoventryUnited Kingdom
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110
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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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111
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Abdellatif MEA, Hipp L, Plessner M, Walther P, Knöll B. Indirect visualization of endogenous nuclear actin by correlative light and electron microscopy (CLEM) using an actin-directed chromobody. Histochem Cell Biol 2019; 152:133-143. [PMID: 31154480 PMCID: PMC6675784 DOI: 10.1007/s00418-019-01795-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 12/14/2022]
Abstract
Actin fulfills important cytoplasmic but also nuclear functions in eukaryotic cells. In the nucleus, actin modulates gene expression and chromatin remodeling. Monomeric (G-actin) and polymerized actin (F-actin) have been analyzed by fluorescence microscopy in the nucleus; however, the resolution at the ultrastructural level has not been investigated in great detail. We provide a first documentation of nuclear actin in mouse fibroblasts by electron microscopy (EM). For this, we employed correlative light and electron microscopy on the same section using actin-directed nanobodies recognizing endogenous monomeric and polymeric actin proteins (so-called nuclear Actin-chromobody-GFP; nAC-GFP). Indeed, using this strategy, we could identify actin proteins present in the nucleus. Here, immunogold-labeled actin proteins were spread throughout the entire nucleoplasm. Of note, nuclear actin was complementarily localized to DAPI-positive areas, the latter marking preferentially transcriptionally inactive heterochromatin. Since actin aggregates in rod structures upon cell stress including neurodegeneration, we analyzed nuclear actin at the ultrastructural level after DMSO or UV-mediated cell damage. In those cells the ratio between cytoplasmic and nuclear gold-labeled actin proteins was altered compared to untreated control cells. In summary, this EM analysis (i) confirmed the presence of endogenous nuclear actin at ultrastructural resolution, (ii) revealed the actin abundance in less chromatin-dense regions potentially reflecting more transcriptionally active euchromatin rather than transcriptionally inactive heterochromatin and (iii) showed an altered abundance of actin-associated gold particles upon cell stress.
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Affiliation(s)
- Mohamed E A Abdellatif
- Central Facility for Electron Microscopy, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Lisa Hipp
- Institute of Physiological Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Matthias Plessner
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Bernd Knöll
- Institute of Physiological Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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112
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Schorb M, Haberbosch I, Hagen WJH, Schwab Y, Mastronarde DN. Software tools for automated transmission electron microscopy. Nat Methods 2019; 16:471-477. [PMID: 31086343 PMCID: PMC7000238 DOI: 10.1038/s41592-019-0396-9] [Citation(s) in RCA: 269] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 03/15/2019] [Indexed: 11/09/2022]
Abstract
The demand for high-throughput data collection in electron microscopy is increasing for applications in structural and cellular biology. Here we present a combination of software tools that enable automated acquisition guided by image analysis for a variety of transmission electron microscopy acquisition schemes. SerialEM controls microscopes and detectors and can trigger automated tasks at multiple positions with high flexibility. Py-EM interfaces with SerialEM to enact specimen-specific image-analysis pipelines that enable feedback microscopy. As example applications, we demonstrate dose reduction in cryo-electron microscopy experiments, fully automated acquisition of every cell in a plastic section and automated targeting on serial sections for 3D volume imaging across multiple grids.
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Affiliation(s)
- Martin Schorb
- Electron Microscopy Core Facility, EMBL, Heidelberg, Germany.
| | - Isabella Haberbosch
- Department of Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg Research Center for Molecular Medicine, EMBL, Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - Wim J H Hagen
- Structural and Computational Biology Unit and Cryo-Electron Microscopy Service Platform, EMBL, Heidelberg, Germany
| | - Yannick Schwab
- Electron Microscopy Core Facility, EMBL, Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - David N Mastronarde
- Department of Molecular, Cellular & Developmental Biology, University of Colorado, Boulder, CO, USA.
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113
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VAN HEST J, AGRONSKAIA A, FOKKEMA J, MONTANARELLA F, GREGORIO PUIG A, DE MELLO DONEGA C, MEIJERINK A, BLAB G, GERRITSEN H. Towards robust and versatile single nanoparticle fiducial markers for correlative light and electron microscopy. J Microsc 2019; 274:13-22. [PMID: 30648740 PMCID: PMC6849797 DOI: 10.1111/jmi.12778] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 12/18/2018] [Accepted: 12/27/2018] [Indexed: 01/10/2023]
Abstract
Fiducial markers are used in correlated light and electron microscopy (CLEM) to enable accurate overlaying of fluorescence and electron microscopy images. Currently used fiducial markers, e.g. dye-labelled nanoparticles and quantum dots, suffer from irreversible quenching of the luminescence after electron beam exposure. This limits their use in CLEM, since samples have to be studied with light microscopy before the sample can be studied with electron microscopy. Robust fiducial markers, i.e. luminescent labels that can (partially) withstand electron bombardment, are interesting because of the recent development of integrated CLEM microscopes. In addition, nonintegrated CLEM setups may benefit from such fiducial markers. Such markers would allow switching back from EM to LM and are not available yet. Here, we investigate the robustness of various luminescent nanoparticles (NPs) that have good contrast in electron microscopy; 130 nm gold-core rhodamine B-labelled silica particles, 15 nm CdSe/CdS/ZnS core-shell-shell quantum dots (QDs) and 230 nm Y2 O3 :Eu3+ particles. Robustness is studied by measuring the luminescence of (single) NPs after various cycles of electron beam exposure. The gold-core rhodamine B-labelled silica NPs and QDs are quenched after a single exposure to 60 ke- nm-2 with an energy of 120 keV, while Y2 O3 :Eu3+ NPs are robust and still show luminescence after five doses of 60 ke- nm-2 . In addition, the luminescence intensity of Y2 O3 :Eu3+ NPs is investigated as function of electron dose for various electron fluxes. The luminescence intensity initially drops to a constant value well above the single particle detection limit. The intensity loss does not depend on the electron flux, but on the total electron dose. The results indicate that Y2 O3 :Eu3+ NPs are promising as robust fiducial marker in CLEM. LAY DESCRIPTION: Luminescent particles are used as fiducial markers in correlative light and electron microscopy (CLEM) to enable accurate overlaying of fluorescence and electron microscopy images. The currently used fiducial markers, e.g. dyes and quantum dots, loose their luminescence after exposure to the electron beam of the electron microscope. This limits their use in CLEM, since samples have to be studied with light microscopy before the sample can be studied with electron microscopy. Robust fiducial markers, i.e. luminescent labels that can withstand electron exposure, are interesting because of recent developments in integrated CLEM microscopes. Also nonintegrated CLEM setups may benefit from such fiducial markers. Such markers would allow for switching back to fluorescence imaging after the recording of electron microscopy imaging and are not available yet. Here, we investigate the robustness of various luminescent nanoparticles (NPs) that have good contrast in electron microscopy; dye-labelled silica particles, quantum dots and lanthanide-doped inorganic particles. Robustness is studied by measuring the luminescence of (single) NPs after various cycles of electron beam exposure. The dye-labelled silica NPs and QDs are quenched after a single exposure to 60 ke- nm-2 with an energy of 120 keV, while lanthanide-doped inorganic NPs are robust and still show luminescence after five doses of 60 ke- nm-2 . In addition, the luminescence intensity of lanthanide-doped inorganic NPs is investigated as function of electron dose for various electron fluxes. The luminescence intensity initially drops to a constant value well above the single particle detection limit. The intensity loss does not depend on the electron flux, but on the total electron dose. The results indicate that lanthanide-doped NPs are promising as robust fiducial marker in CLEM.
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Affiliation(s)
- J.J.H.A. VAN HEST
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
- Molecular Biophysics, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - A.V. AGRONSKAIA
- Molecular Biophysics, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - J. FOKKEMA
- Molecular Biophysics, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - F. MONTANARELLA
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
- Soft Condensed Matter, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - A. GREGORIO PUIG
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - C. DE MELLO DONEGA
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - A. MEIJERINK
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - G.A. BLAB
- Molecular Biophysics, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
| | - H.C. GERRITSEN
- Molecular Biophysics, Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrechtThe Netherlands
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114
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Mohammadian S, Fokkema J, Agronskaia AV, Liv N, de Heus C, van Donselaar E, Blab GA, Klumperman J, Gerritsen HC. High accuracy, fiducial marker-based image registration of correlative microscopy images. Sci Rep 2019; 9:3211. [PMID: 30824844 PMCID: PMC6397213 DOI: 10.1038/s41598-019-40098-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 01/28/2019] [Indexed: 12/03/2022] Open
Abstract
Fluorescence microscopy (FM) and electron microscopy (EM) are complementary techniques. FM affords examination of large fields of view and identifying regions of interest but has a low resolution. EM exhibits excellent resolution over a limited field of view. The combination of these two techniques, correlative microscopy, received considerable interest in the past years and has proven its potential in biology and material science. Accurate correlation of FM and EM images is, however, challenging due to the differences in contrast mechanism, size of field of view and resolution. We report an accurate, fast and robust method to correlate FM and EM images using low densities of fiducial markers. Here, 120 nm diameter fiducial markers consisting of fluorescently labelled silica coated gold nanoparticles are used. The method relies on recording FM, low magnification EM and high magnification EM images. Two linear transformation matrices are constructed, FM to low magnification EM and low magnification EM to high magnification EM. Combination of these matrices results in a high accuracy transformation of FM to high magnification EM coordinates. The method was tested using two different transmission electron microscopes and different Tokuyasu and Lowicryl sections. The overall accuracy of the correlation method is high, 5-30 nm.
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Affiliation(s)
- Sajjad Mohammadian
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Jantina Fokkema
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Alexandra V Agronskaia
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cecilia de Heus
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elly van Donselaar
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gerhard A Blab
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hans C Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
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115
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van Haren J, Wittmann T. Microtubule Plus End Dynamics - Do We Know How Microtubules Grow?: Cells boost microtubule growth by promoting distinct structural transitions at growing microtubule ends. Bioessays 2019; 41:e1800194. [PMID: 30730055 PMCID: PMC7021488 DOI: 10.1002/bies.201800194] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/22/2018] [Indexed: 12/31/2022]
Abstract
Microtubules form a highly dynamic filament network in all eukaryotic cells. Individual microtubules grow by tubulin dimer subunit addition and frequently switch between phases of growth and shortening. These unique dynamics are powered by GTP hydrolysis and drive microtubule network remodeling, which is central to eukaryotic cell biology and morphogenesis. Yet, our knowledge of the molecular events at growing microtubule ends remains incomplete. Here, recent ultrastructural, biochemical and cell biological data are integrated to develop a realistic model of growing microtubule ends comprised of structurally distinct but biochemically overlapping zones. Proteins that recognize microtubule lattice conformations associated with specific tubulin guanosine nucleotide states may independently control major structural transitions at growing microtubule ends. A model is proposed in which tubulin dimer addition and subsequent closure of the MT wall are optimized in cells to achieve rapid physiological microtubule growth.
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Affiliation(s)
- Jeffrey van Haren
- Department of Cell and Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Torsten Wittmann
- Department of Cell and Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
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116
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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: 85] [Impact Index Per Article: 17.0] [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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117
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Ader NR, Hoffmann PC, Ganeva I, Borgeaud AC, Wang C, Youle RJ, Kukulski W. Molecular and topological reorganizations in mitochondrial architecture interplay during Bax-mediated steps of apoptosis. eLife 2019; 8:40712. [PMID: 30714902 PMCID: PMC6361589 DOI: 10.7554/elife.40712] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/22/2019] [Indexed: 12/25/2022] Open
Abstract
During apoptosis, Bcl-2 proteins such as Bax and Bak mediate the release of pro-apoptotic proteins from the mitochondria by clustering on the outer mitochondrial membrane and thereby permeabilizing it. However, it remains unclear how outer membrane openings form. Here, we combined different correlative microscopy and electron cryo-tomography approaches to visualize the effects of Bax activity on mitochondria in human cells. Our data show that Bax clusters localize near outer membrane ruptures of highly variable size. Bax clusters contain structural elements suggesting a higher order organization of their components. Furthermore, unfolding of inner membrane cristae is coupled to changes in the supramolecular assembly of ATP synthases, particularly pronounced at membrane segments exposed to the cytosol by ruptures. Based on our results, we propose a comprehensive model in which molecular reorganizations of the inner membrane and sequestration of outer membrane components into Bax clusters interplay in the formation of outer membrane ruptures. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Nicholas R Ader
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Patrick C Hoffmann
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Iva Ganeva
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Alicia C Borgeaud
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Chunxin Wang
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Wanda Kukulski
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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118
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Consideration of sample motion in cryo-tomography based on alignment residual interpolation. J Struct Biol 2019; 205:1-6. [PMID: 30690142 DOI: 10.1016/j.jsb.2019.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 11/24/2022]
Abstract
Recently, it has been shown that the resolution in cryo-tomography could be improved by considering the sample motion in tilt-series alignment and reconstruction, where a set of quadratic polynomials were used to model this motion. One requirement of this polynomial method is the optimization of a large number of parameters, which may limit its practical applicability. In this work, we propose an alternative method for modeling the sample motion. Starting from the standard fiducial-based tilt-series alignment, the method uses the alignment residual as local estimates of the sample motion at the 3D fiducial positions. Then, a scattered data interpolation technique characterized by its smoothness and a closed-form solution is applied to model the sample motion. The motion model is then integrated in the tomographic reconstruction. The new method improves the tomogram quality similar to the polynomial one, with the important advantage that the determination of the motion model is greatly simplified, thereby overcoming one of the major limitations of the polynomial model. Therefore, the new method is expected to make the beam-induced motion correction methodology more accessible to the cryoET community.
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119
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Liu M, Heimlicher MB, Bächler M, Ibeneche-Nnewihe CC, Florin EL, Brunner D, Hoenger A. Glucose starvation triggers filamentous septin assemblies in an S. pombe septin-2 deletion mutant. Biol Open 2019; 8:8/1/bio037622. [PMID: 30602528 PMCID: PMC6361201 DOI: 10.1242/bio.037622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Using correlative light and electron microscopy (CLEM), we studied the intracellular organization by of glucose-starved fission yeast cells (Schizosaccharomyces pombe) with regards to the localization of septin proteins throughout the cytoplasm. Thereby, we found that for cells carrying a deletion of the gene encoding septin-2 (spn2Δ), starvation causes a GFP-tagged version of septin-3 (spn3-GFP) and family members, to assemble into a single, prominent filamentous structure. It was previously shown that during exponential growth, spn2Δ cells form septin-3 polymers. However, the polymers we observed during exponential growth are different from the spn3p-GFP structure we observed in starved cells. Using CLEM, in combination with anti-GFP immunolabeling on plastic-sections, we could assign spn3p-GFP to the filaments we have found in EM pictures. Besides septin-3, these filamentous assemblies most likely also contain septin-1 as an RFP-tagged version of this protein forms a very similar structure in starved spn2Δ cells. Our data correlate phase-contrast and fluorescence microscopy with electron micrographs of plastic-embedded cells, and further on with detailed views of tomographic 3D reconstructions. Cryo-electron microscopy of spn2Δ cells in vitrified sections revealed a very distinct overall morphology of the spn3p-GFP assembly. The fine-structured, regular density pattern suggests the presence of assembled septin-3 filaments that are clearly different from F-actin bundles. Furthermore, we found that starvation causes substantial mitochondria fission, together with massive decoration of their outer membrane by ribosomes.
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Affiliation(s)
- Minghua Liu
- University of Colorado at Boulder, Department of Molecular, Cellular and Developmental Biology, UCB-0347, Boulder, CO 80309, USA
| | - Maria B Heimlicher
- University of Zürich, Department of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Mirjam Bächler
- University of Zürich, Department of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Chieze C Ibeneche-Nnewihe
- University of Texas at Austin, Center for Nonlinear Dynamics and Department of Physics, Austin, TX 78712, USA
| | - Ernst-Ludwig Florin
- University of Texas at Austin, Center for Nonlinear Dynamics and Department of Physics, Austin, TX 78712, USA
| | - Damian Brunner
- University of Zürich, Department of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Andreas Hoenger
- University of Colorado at Boulder, Department of Molecular, Cellular and Developmental Biology, UCB-0347, Boulder, CO 80309, USA
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120
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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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121
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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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122
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Porrati F, Grewe D, Seybert A, Frangakis AS, Eltsov M. FIB-SEM imaging properties of Drosophila melanogaster tissues embedded in Lowicryl HM20. J Microsc 2018; 273:91-104. [PMID: 30417390 DOI: 10.1111/jmi.12764] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 09/17/2018] [Accepted: 10/12/2018] [Indexed: 11/27/2022]
Abstract
Lowicryl resins enable processing of biological material for electron microscopy at the lowest temperatures compatible with resin embedding. When combined with high-pressure freezing and freeze-substitution, Lowicryl embedding supports preservation of fine structural details and fluorescent markers. Here, we analysed the applicability of Lowicryl HM20 embedding for focused ion beam (FIB) scanning electron microscopy (SEM) tomography of Drosophila melanogaster embryonic and larval model systems. We show that the freeze-substitution with per-mill concentrations of uranyl acetate provided sufficient contrast and an image quality of SEM imaging in the range of similar samples analysed by transmission electron microscopy (TEM). Preservation of genetically encoded fluorescent proteins allowed correlative localization of regions of interest (ROI) within the embedded tissue block. TEM on sections cut from the block face enabled evaluation of structural preservation to allow ROI ranking and thus targeted, time-efficient FIB-SEM tomography data collection. The versatility of Lowicryl embedding opens new perspectives for designing hybrid SEM-TEM workflows to comprehensively analyse biological structures. LAY DESCRIPTION: Focused ion beam scanning electron microscopy is becoming a widely used technique for the three-dimensional analysis of biological samples at fine structural details beyond levels feasible for light microscopy. To withstand the abrasion of material by the ion beam and the imaging by the scanning electron beam, biological samples have to be embedded into resins, most commonly these are very dense epoxy-based plastics. However, dense resins generate electron scattering which interferes with the signal from the biological specimen. Furthermore, to improve the imaging contrast, epoxy embedding requires chemical treatments with e.g. heavy metals, which deteriorate the ultrastructure of the biological specimen. In this study we explored the applicability of an electron lucent resin, Lowicryl HM 20, for focused ion beam scanning electron microscopy. The Lowicryl embedding workflow operates at milder chemical treatments and lower temperatures, thus preserving the sub-cellular and sub-organellar organization, as well as fluorescent markers visible by light microscopy. Here we show that focus ion beam scanning electron microscopy of Lowicryl-embedded fruit flies tissues provides reliable imaging revealing fine structural details. Our workflow benefited from use of transmission electron microscopy for the quality control of the ultrastructural preservation and fluorescent light microscopy for localization of regions of interest. The versatility of Lowicryl embedding opens up new perspectives for designing hybrid workflows combining fluorescent light, scanning, and transmission electron microscopy techniques to comprehensively analyze biological structures.
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Affiliation(s)
- F Porrati
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe-University, Frankfurt am Main, Germany
| | - D Grewe
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe-University, Frankfurt am Main, Germany
| | - A Seybert
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe-University, Frankfurt am Main, Germany
| | - A S Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe-University, Frankfurt am Main, Germany
| | - M Eltsov
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe-University, Frankfurt am Main, Germany
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123
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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: 79] [Impact Index Per Article: 13.2] [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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124
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Fokkema J, Fermie J, Liv N, van den Heuvel DJ, Konings TOM, Blab GA, Meijerink A, Klumperman J, Gerritsen HC. Fluorescently Labelled Silica Coated Gold Nanoparticles as Fiducial Markers for Correlative Light and Electron Microscopy. Sci Rep 2018; 8:13625. [PMID: 30206379 PMCID: PMC6133918 DOI: 10.1038/s41598-018-31836-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/22/2018] [Indexed: 11/09/2022] Open
Abstract
In this work, gold nanoparticles coated with a fluorescently labelled (rhodamine B) silica shell are presented as fiducial markers for correlative light and electron microscopy (CLEM). The synthesis of the particles is optimized to obtain homogeneous, spherical core-shell particles of arbitrary size. Next, particles labelled with different fluorophore densities are characterized to determine under which conditions bright and (photo)stable particles can be obtained. 2 and 3D CLEM examples are presented where optimized particles are used for correlation. In the 2D example, fiducials are added to a cryosection of cells whereas in the 3D example cells are imaged after endocytosis of the fiducials. Both examples demonstrate that the particles are clearly visible in both modalities and can be used for correlation. Additionally, the recognizable core-shell structure of the fiducials proves to be very powerful in electron microscopy: it makes it possible to irrefutably identify the particles and makes it easy to accurately determine the center of the fiducials.
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Affiliation(s)
- Jantina Fokkema
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Job Fermie
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Dave J van den Heuvel
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Tom O M Konings
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Gerhard A Blab
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Andries Meijerink
- Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hans C Gerritsen
- Soft Condensed Matter and Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
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125
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Santarella-Mellwig R, Haselmann U, Schieber NL, Walther P, Schwab Y, Antony C, Bartenschlager R, Romero-Brey I. Correlative Light Electron Microscopy (CLEM) for Tracking and Imaging Viral Protein Associated Structures in Cryo-immobilized Cells. J Vis Exp 2018. [PMID: 30247481 PMCID: PMC6235138 DOI: 10.3791/58154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Due to its high resolution, electron microscopy (EM) is an indispensable tool for virologists. However, one of the main difficulties when analyzing virus-infected or transfected cells via EM are the low efficiencies of infection or transfection, hindering the examination of these cells. In order to overcome this difficulty, light microscopy (LM) can be performed first to allocate the subpopulation of infected or transfected cells. Thus, taking advantage of the use of fluorescent proteins (FPs) fused to viral proteins, LM is used here to record the positions of the "positive-transfected" cells, expressing a FP and growing on a support with an alphanumeric pattern. Subsequently, cells are further processed for EM via high pressure freezing (HPF), freeze substitution (FS) and resin embedding. The ultra-rapid freezing step ensures excellent membrane preservation of the selected cells that can then be analyzed at the ultrastructural level by transmission electron microscopy (TEM). Here, a step-by-step correlative light electron microscopy (CLEM) workflow is provided, describing sample preparation, imaging and correlation in detail. The experimental design can be also applied to address many cell biology questions.
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Affiliation(s)
| | - Uta Haselmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University
| | | | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University
| | | | | | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University; Heidelberg Partner Site, German Center for Infection Research;
| | - Inés Romero-Brey
- Department of Infectious Diseases, Molecular Virology, Heidelberg University;
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126
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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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127
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Direct imaging of uncoated biological samples enables correlation of super-resolution and electron microscopy data. Sci Rep 2018; 8:11610. [PMID: 30072703 PMCID: PMC6072772 DOI: 10.1038/s41598-018-29970-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/23/2018] [Indexed: 11/08/2022] Open
Abstract
A simple method for imaging biological tissue samples by electron microscopy and its correlation with super-resolution light microscopy is presented. This room temperature protocol, based on protecting thin biological specimens with methylcellulose and imaging with low voltage scanning electron microscopy, circumvents complex classical electron microscopy sample preparation steps requiring dehydration, resin embedding and use of contrast agents. This technique facilitates visualization of subcellular structures e.g. synaptic clefts and synaptic vesicles in mouse brain tissue and the organization of mitochondrial cristae in the zebrafish retina. Application of immunogold protocols to these samples can determine the precise localization of synaptic proteins and, in combination with super-resolution light microscopy methods clearly pinpoints the subcellular distribution of several proteins in the tissue. The simplicity of the method, including section collection on a silicon wafer, reduces artefacts and correlates protein location with sample morphology.
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128
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Dutta M. Recent Advances in Single Particle Cryo-electron Microscopy and Cryo-electron Tomography to Determine the Structures of Biological Macromolecules. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0087-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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129
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Clarke NI, Royle SJ. FerriTag is a new genetically-encoded inducible tag for correlative light-electron microscopy. Nat Commun 2018; 9:2604. [PMID: 29973588 PMCID: PMC6031641 DOI: 10.1038/s41467-018-04993-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 05/24/2018] [Indexed: 01/20/2023] Open
Abstract
A current challenge is to develop tags to precisely visualize proteins in cells by light and electron microscopy. Here, we introduce FerriTag, a genetically-encoded chemically-inducible tag for correlative light-electron microscopy. FerriTag is a fluorescent recombinant electron-dense ferritin particle that can be attached to a protein-of-interest using rapamycin-induced heterodimerization. We demonstrate the utility of FerriTag for correlative light-electron microscopy by labeling proteins associated with various intracellular structures including mitochondria, plasma membrane, and clathrin-coated pits and vesicles. FerriTagging has a good signal-to-noise ratio and a labeling resolution of approximately 10 nm. We demonstrate how FerriTagging allows nanoscale mapping of protein location relative to a subcellular structure, and use it to detail the distribution and conformation of huntingtin-interacting protein 1 related (HIP1R) in and around clathrin-coated pits.
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Affiliation(s)
- Nicholas I Clarke
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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130
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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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131
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Burel A, Lavault MT, Chevalier C, Gnaegi H, Prigent S, Mucciolo A, Dutertre S, Humbel BM, Guillaudeux T, Kolotuev I. A targeted 3D EM and correlative microscopy method using SEM array tomography. Development 2018; 145:dev.160879. [PMID: 29802150 DOI: 10.1242/dev.160879] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/16/2018] [Indexed: 12/15/2022]
Abstract
Using electron microscopy to localize rare cellular events or structures in complex tissue is challenging. Correlative light and electron microscopy procedures have been developed to link fluorescent protein expression with ultrastructural resolution. Here, we present an optimized scanning electron microscopy (SEM) workflow for volumetric array tomography for asymmetric samples and model organisms (Caenorhabditis elegans, Drosophila melanogaster, Danio rerio). We modified a diamond knife to simplify serial section array acquisition with minimal artifacts. After array acquisition, the arrays were transferred to a glass coverslip or silicon wafer support. Using light microscopy, the arrays were screened rapidly for initial recognition of global anatomical features (organs or body traits). Then, using SEM, an in-depth study of the cells and/or organs of interest was performed. Our manual and automatic data acquisition strategies make 3D data acquisition and correlation simpler and more precise than alternative methods. This method can be used to address questions in cell and developmental biology that require the efficient identification of a labeled cell or organelle.
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Affiliation(s)
- Agnes Burel
- University of Rennes 1, UMS Biosit, MRic, 35043 Rennes, France
| | | | | | | | - Sylvain Prigent
- University of Rennes 1, UMS Biosit, MRic, 35043 Rennes, France
| | - Antonio Mucciolo
- University of Lausanne, Faculté de biologie et de médecine, Electron Microscopy Facility, CH-1015 Lausanne, Switzerland
| | | | - Bruno M Humbel
- University of Lausanne, Faculté de biologie et de médecine, Electron Microscopy Facility, CH-1015 Lausanne, Switzerland
| | | | - Irina Kolotuev
- University of Rennes 1, UMS Biosit, MRic, 35043 Rennes, France .,University of Lausanne, Faculté de biologie et de médecine, Electron Microscopy Facility, CH-1015 Lausanne, Switzerland
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132
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Ripoll L, Heiligenstein X, Hurbain I, Domingues L, Figon F, Petersen KJ, Dennis MK, Houdusse A, Marks MS, Raposo G, Delevoye C. Myosin VI and branched actin filaments mediate membrane constriction and fission of melanosomal tubule carriers. J Cell Biol 2018; 217:2709-2726. [PMID: 29875258 PMCID: PMC6080934 DOI: 10.1083/jcb.201709055] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 03/16/2018] [Accepted: 05/09/2018] [Indexed: 01/19/2023] Open
Abstract
Vesicular and tubular transport intermediates regulate organellar cargo dynamics. Transport carrier release involves local and profound membrane remodeling before fission. Pinching the neck of a budding tubule or vesicle requires mechanical forces, likely exerted by the action of molecular motors on the cytoskeleton. Here, we show that myosin VI, together with branched actin filaments, constricts the membrane of tubular carriers that are then released from melanosomes, the pigment containing lysosome-related organelles of melanocytes. By combining superresolution fluorescence microscopy, correlative light and electron microscopy, and biochemical analyses, we find that myosin VI motor activity mediates severing by constricting the neck of the tubule at specific melanosomal subdomains. Pinching of the tubules involves the cooperation of the myosin adaptor optineurin and the activity of actin nucleation machineries, including the WASH and Arp2/3 complexes. The fission and release of these tubules allows for the export of components from melanosomes, such as the SNARE VAMP7, and promotes melanosome maturation and transfer to keratinocytes. Our data reveal a new myosin VI- and actin-dependent membrane fission mechanism required for organelle function.
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Affiliation(s)
- Léa Ripoll
- Structure and Membrane Compartments, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, Paris, France
| | - Xavier Heiligenstein
- Structure and Membrane Compartments, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, Paris, France
| | - Ilse Hurbain
- Structure and Membrane Compartments, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, Paris, France.,Cell and Tissue Imaging Facility, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, Paris, France
| | - Lia Domingues
- Structure and Membrane Compartments, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, Paris, France
| | - Florent Figon
- Structure and Membrane Compartments, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, Paris, France.,Master BioSciences, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Karl J Petersen
- Structural Motility, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, Paris, France
| | - Megan K Dennis
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Departments of Pathology and Laboratory Medicine and Physiology, University of Pennsylvania, Philadelphia, PA
| | - Anne Houdusse
- Structural Motility, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, Paris, France
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Departments of Pathology and Laboratory Medicine and Physiology, University of Pennsylvania, Philadelphia, PA
| | - Graça Raposo
- Structure and Membrane Compartments, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, Paris, France.,Cell and Tissue Imaging Facility, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, Paris, France
| | - Cédric Delevoye
- Structure and Membrane Compartments, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, Paris, France .,Cell and Tissue Imaging Facility, Institut Curie, Paris Sciences & Lettres Research University, Centre National de la Recherche Scientifique, UMR144, Paris, France
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133
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McIntosh JR, O'Toole E, Morgan G, Austin J, Ulyanov E, Ataullakhanov F, Gudimchuk N. Microtubules grow by the addition of bent guanosine triphosphate tubulin to the tips of curved protofilaments. J Cell Biol 2018; 217:2691-2708. [PMID: 29794031 PMCID: PMC6080942 DOI: 10.1083/jcb.201802138] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/17/2018] [Accepted: 05/07/2018] [Indexed: 11/22/2022] Open
Abstract
How microtubules (MTs) grow during the addition of guanosine triphosphate (GTP) tubulin is not clear. McIntosh et al. now show that MTs elongating either in vivo or in vitro end in bent protofilaments that curve out from the microtubule axis, suggesting that GTP-tubulin is bent in solution and must straighten to join the MT wall. We used electron tomography to examine microtubules (MTs) growing from pure tubulin in vitro as well as two classes of MTs growing in cells from six species. The tips of all these growing MTs display bent protofilaments (PFs) that curve away from the MT axis, in contrast with previously reported MTs growing in vitro whose tips are either blunt or sheetlike. Neither high pressure nor freezing is responsible for the PF curvatures we see. The curvatures of PFs on growing and shortening MTs are similar; all are most curved at their tips, suggesting that guanosine triphosphate–tubulin in solution is bent and must straighten to be incorporated into the MT wall. Variations in curvature suggest that PFs are flexible in their plane of bending but rigid to bending out of that plane. Modeling by Brownian dynamics suggests that PF straightening for MT growth can be achieved by thermal motions, providing a simple mechanism with which to understand tubulin polymerization.
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Affiliation(s)
- J Richard McIntosh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO
| | - Eileen O'Toole
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO
| | - Garry Morgan
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO
| | - Jotham Austin
- Advanced Electron Microscopy Facility, University of Chicago, Chicago, IL
| | - Evgeniy Ulyanov
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Fazoil Ataullakhanov
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia.,Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Nikita Gudimchuk
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia.,Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
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134
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Tsang TK, Bushong EA, Boassa D, Hu J, Romoli B, Phan S, Dulcis D, Su CY, Ellisman MH. High-quality ultrastructural preservation using cryofixation for 3D electron microscopy of genetically labeled tissues. eLife 2018; 7:35524. [PMID: 29749931 PMCID: PMC5988420 DOI: 10.7554/elife.35524] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/09/2018] [Indexed: 02/06/2023] Open
Abstract
Electron microscopy (EM) offers unparalleled power to study cell substructures at the nanoscale. Cryofixation by high-pressure freezing offers optimal morphological preservation, as it captures cellular structures instantaneously in their near-native state. However, the applicability of cryofixation is limited by its incompatibility with diaminobenzidine labeling using genetic EM tags and the high-contrast en bloc staining required for serial block-face scanning electron microscopy (SBEM). In addition, it is challenging to perform correlated light and electron microscopy (CLEM) with cryofixed samples. Consequently, these powerful methods cannot be applied to address questions requiring optimal morphological preservation. Here, we developed an approach that overcomes these limitations; it enables genetically labeled, cryofixed samples to be characterized with SBEM and 3D CLEM. Our approach is broadly applicable, as demonstrated in cultured cells, Drosophila olfactory organ and mouse brain. This optimization exploits the potential of cryofixation, allowing for quality ultrastructural preservation for diverse EM applications.
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Affiliation(s)
- Tin Ki Tsang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Eric A Bushong
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Daniela Boassa
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Junru Hu
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Benedetto Romoli
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, United States
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States
| | - Davide Dulcis
- Department of Psychiatry, School of Medicine, University of California, San Diego, La Jolla, United States
| | - Chih-Ying Su
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California, San Diego, La Jolla, United States.,Department of Neurosciences, School of Medicine, University of California, San Diego, La Jolla, United States
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135
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A Liquid to Solid Phase Transition Underlying Pathological Huntingtin Exon1 Aggregation. Mol Cell 2018; 70:588-601.e6. [PMID: 29754822 PMCID: PMC5971205 DOI: 10.1016/j.molcel.2018.04.007] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/08/2018] [Accepted: 04/05/2018] [Indexed: 12/31/2022]
Abstract
Huntington’s disease is caused by an abnormally long polyglutamine tract in the huntingtin protein. This leads to the generation and deposition of N-terminal exon1 fragments of the protein in intracellular aggregates. We combined electron tomography and quantitative fluorescence microscopy to analyze the structural and material properties of huntingtin exon1 assemblies in mammalian cells, in yeast, and in vitro. We found that huntingtin exon1 proteins can form reversible liquid-like assemblies, a process driven by huntingtin’s polyQ tract and proline-rich region. In cells and in vitro, the liquid-like assemblies converted to solid-like assemblies with a fibrillar structure. Intracellular phase transitions of polyglutamine proteins could play a role in initiating irreversible pathological aggregation. Aggregates of huntingtin exon1 exist in distinct liquid-like and solid-like forms Liquid-like assembly formation is driven by polyQ and proline-rich regions of exon1 The liquid-like assemblies convert into solid-like assemblies in vitro and in cells Electron tomography reveals liquid and solid assemblies have distinct structures
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136
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Bharat TAM, Hoffmann PC, Kukulski W. Correlative Microscopy of Vitreous Sections Provides Insights into BAR-Domain Organization In Situ. Structure 2018; 26:879-886.e3. [PMID: 29681471 PMCID: PMC5992340 DOI: 10.1016/j.str.2018.03.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/22/2018] [Accepted: 03/22/2018] [Indexed: 12/15/2022]
Abstract
Electron microscopy imaging of macromolecular complexes in their native cellular context is limited by the inherent difficulty to acquire high-resolution tomographic data from thick cells and to specifically identify elusive structures within crowded cellular environments. Here, we combined cryo-fluorescence microscopy with electron cryo-tomography of vitreous sections into a coherent correlative microscopy workflow, ideal for detection and structural analysis of elusive protein assemblies in situ. We used this workflow to address an open question on BAR-domain coating of yeast plasma membrane compartments known as eisosomes. BAR domains can sense or induce membrane curvature, and form scaffold-like membrane coats in vitro. Our results demonstrate that in cells, the BAR protein Pil1 localizes to eisosomes of varying membrane curvature. Sub-tomogram analysis revealed a dense protein coat on curved eisosomes, which was not present on shallow eisosomes, indicating that while BAR domains can assemble at shallow membranes in vivo, scaffold formation is tightly coupled to curvature generation. Cryo-fluorescence microscopy eases electron cryo-tomography of vitreous sections Elusive protein assemblies are localized in situ by correlative microscopy Yeast BAR-domain protein Pil1 binds to plasma membrane with varying curvature Scaffold-like coats are only seen when Pil1 is bound to high curvature membranes
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Affiliation(s)
- Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Central Oxford Structural and Molecular Imaging Centre, South Parks Road, Oxford OX1 3RE, UK; Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Patrick C Hoffmann
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Wanda Kukulski
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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137
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Atherton J, Stouffer M, Francis F, Moores CA. Microtubule architecture in vitro and in cells revealed by cryo-electron tomography. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:572-584. [PMID: 29872007 PMCID: PMC6096491 DOI: 10.1107/s2059798318001948] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/01/2018] [Indexed: 01/03/2023]
Abstract
Electron microscopy is a key methodology for studying microtubule structure and organization. Here, the results of cryo-electron tomography experiments on in vitro-polymerized microtubules and comparisons with microtubule ultrastructure in cells are described. The microtubule cytoskeleton is involved in many vital cellular processes. Microtubules act as tracks for molecular motors, and their polymerization and depolymerization can be harnessed to generate force. The structures of microtubules provide key information about the mechanisms by which their cellular roles are accomplished and the physiological context in which these roles are performed. Cryo-electron microscopy allows the visualization of in vitro-polymerized microtubules and has provided important insights into their overall morphology and the influence of a range of factors on their structure and dynamics. Cryo-electron tomography can be used to determine the unique three-dimensional structure of individual microtubules and their ends. Here, a previous cryo-electron tomography study of in vitro-polymerized GMPCPP-stabilized microtubules is revisited, the findings are compared with new tomograms of dynamic in vitro and cellular microtubules, and the information that can be extracted from such data is highlighted. The analysis shows the surprising structural heterogeneity of in vitro-polymerized microtubules. Lattice defects can be observed both in vitro and in cells. The shared ultrastructural properties in these different populations emphasize the relevance of three-dimensional structures of in vitro microtubules for understanding microtubule cellular functions.
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Affiliation(s)
- Joseph Atherton
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
| | | | - Fiona Francis
- INSERM UMR-S 839, 17 Rue du Fer à Moulin, 75005 Paris, France
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
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138
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Picco A, Kukulski W, Manenschijn HE, Specht T, Briggs JAG, Kaksonen M. The contributions of the actin machinery to endocytic membrane bending and vesicle formation. Mol Biol Cell 2018; 29:1346-1358. [PMID: 29851558 PMCID: PMC5994895 DOI: 10.1091/mbc.e17-11-0688] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Branched and cross-linked actin networks mediate cellular processes that move and shape membranes. To understand how actin contributes during the different stages of endocytic membrane reshaping, we analyzed deletion mutants of yeast actin network components using a hybrid imaging approach that combines live imaging with correlative microscopy. We could thus temporally dissect the effects of different actin network perturbations, revealing distinct stages of actin-based membrane reshaping. Our data show that initiation of membrane bending requires the actin network to be physically linked to the plasma membrane and to be optimally cross-linked. Once initiated, the membrane invagination process is driven by nucleation and polymerization of new actin filaments, independent of the degree of cross-linking and unaffected by a surplus of actin network components. A key transition occurs 2 s before scission, when the filament nucleation rate drops. From that time point on, invagination growth and vesicle scission are driven by an expansion of the actin network without a proportional increase of net actin amounts. The expansion is sensitive to the amount of filamentous actin and its cross-linking. Our results suggest that the mechanism by which actin reshapes the membrane changes during the progress of endocytosis, possibly adapting to varying force requirements.
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Affiliation(s)
- Andrea Picco
- Department of Biochemistry and NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Wanda Kukulski
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Hetty E Manenschijn
- Department of Biochemistry and NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Tanja Specht
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - John A G Briggs
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Marko Kaksonen
- Department of Biochemistry and NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
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139
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Increasing Diversity of Biological Membrane Fission Mechanisms. Trends Cell Biol 2018; 28:274-286. [DOI: 10.1016/j.tcb.2017.12.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/06/2017] [Accepted: 12/12/2017] [Indexed: 12/19/2022]
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140
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Tolić IM. Mitotic spindle: kinetochore fibers hold on tight to interpolar bundles. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2018; 47:191-203. [PMID: 28725997 PMCID: PMC5845649 DOI: 10.1007/s00249-017-1244-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/30/2017] [Accepted: 07/02/2017] [Indexed: 12/24/2022]
Abstract
When a cell starts to divide, it forms a spindle, a micro-machine made of microtubules, which separates the duplicated chromosomes. The attachment of microtubules to chromosomes is mediated by kinetochores, protein complexes on the chromosome. Spindle microtubules can be divided into three major classes: kinetochore microtubules, which form k-fibers ending at the kinetochore; interpolar microtubules, which extend from the opposite sides of the spindle and interact in the middle; and astral microtubules, which extend towards the cell cortex. Recent work in human cells has shown a close relationship between interpolar and kinetochore microtubules, where interpolar bundles are attached laterally to kinetochore fibers almost all along their length, acting as a bridge between sister k-fibers. Most of the interpolar bundles are attached to a pair of sister kinetochore fibers and vice versa. Thus, the spindle is made of modules consisting of a pair of sister kinetochore fibers and a bundle of interpolar microtubules that connects them. These interpolar bundles, termed bridging fibers, balance the forces acting at kinetochores and support the rounded shape of the spindle during metaphase. This review discusses the structure, function, and formation of kinetochore fibers and interpolar bundles, with an emphasis on how they interact. Their connections have an impact on the force balance in the spindle and on chromosome movement during mitosis because the forces in interpolar bundles are transmitted to kinetochore fibers and hence to kinetochores through these connections.
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Affiliation(s)
- Iva M Tolić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.
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141
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Cyrklaff M, Frischknecht F, Kudryashev M. Functional insights into pathogen biology from 3D electron microscopy. FEMS Microbiol Rev 2018; 41:828-853. [PMID: 28962014 DOI: 10.1093/femsre/fux041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/25/2017] [Indexed: 01/10/2023] Open
Abstract
In recent years, novel imaging approaches revolutionised our understanding of the cellular and molecular biology of microorganisms. These include advances in fluorescent probes, dynamic live cell imaging, superresolution light and electron microscopy. Currently, a major transition in the experimental approach shifts electron microscopy studies from a complementary technique to a method of choice for structural and functional analysis. Here we review functional insights into the molecular architecture of viruses, bacteria and parasites as well as interactions with their respective host cells gained from studies using cryogenic electron tomography and related methodologies.
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Affiliation(s)
- Marek Cyrklaff
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Mikhail Kudryashev
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt, Max-von-Laue Strasse 17, 60438 Frankfurt, Germany
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142
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Single cell polarity in liquid phase facilitates tumour metastasis. Nat Commun 2018; 9:887. [PMID: 29491397 PMCID: PMC5830403 DOI: 10.1038/s41467-018-03139-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/19/2018] [Indexed: 01/19/2023] Open
Abstract
Dynamic polarisation of tumour cells is essential for metastasis. While the role of polarisation during dedifferentiation and migration is well established, polarisation of metastasising tumour cells during phases of detachment has not been investigated. Here we identify and characterise a type of polarisation maintained by single cells in liquid phase termed single-cell (sc) polarity and investigate its role during metastasis. We demonstrate that sc polarity is an inherent feature of cells from different tumour entities that is observed in circulating tumour cells in patients. Functionally, we propose that the sc pole is directly involved in early attachment, thereby affecting adhesion, transmigration and metastasis. In vivo, the metastatic capacity of cell lines correlates with the extent of sc polarisation. By manipulating sc polarity regulators and by generic depolarisation, we show that sc polarity prior to migration affects transmigration and metastasis in vitro and in vivo. Polarisation of metastasising cancer cells in circulation has not been investigated before. Here the authors identify single cell polarity as a distinct polarisation state of single cells in liquid phase, and show that perturbing single cell polarity affects attachment, adhesion, transmigration and metastasis in vitro and in vivo.
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143
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Mak J, de Marco A. Recent advances in retroviruses via cryo-electron microscopy. Retrovirology 2018; 15:23. [PMID: 29471854 PMCID: PMC5824478 DOI: 10.1186/s12977-018-0405-6] [Citation(s) in RCA: 5] [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: 09/17/2017] [Accepted: 02/14/2018] [Indexed: 12/14/2022] Open
Abstract
Cryo-electron microscopy has undergone a revolution in recent years and it has contributed significantly to a number of different areas in biological research. In this manuscript, we will describe some of the recent advancements in cryo-electron microscopy focussing on the advantages that this technique can bring rather than on the technology. We will then conclude discussing how the field of retrovirology has benefited from cryo-electron microscopy.
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Affiliation(s)
- Johnson Mak
- Institute for Glycomics, Griffith University Gold Coast, Southport, QLD, Australia
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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144
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Chang HF, Mannebach S, Beck A, Ravichandran K, Krause E, Frohnweiler K, Fecher-Trost C, Schirra C, Pattu V, Flockerzi V, Rettig J. Cytotoxic granule endocytosis depends on the Flower protein. J Cell Biol 2018; 217:667-683. [PMID: 29288152 PMCID: PMC5800809 DOI: 10.1083/jcb.201706053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 11/09/2017] [Accepted: 11/29/2017] [Indexed: 12/23/2022] Open
Abstract
Cytotoxic T lymphocytes (CTLs) kill target cells by the regulated release of cytotoxic substances from granules at the immunological synapse. To kill multiple target cells, CTLs use endocytosis of membrane components of cytotoxic granules. We studied the potential calcium dependence of endocytosis in mouse CTLs on Flower, which mediates the calcium dependence of synaptic vesicle endocytosis in Drosophila melanogaster Flower is predominantly localized on intracellular vesicles that move to the synapse on target cell contact. Endocytosis is entirely blocked at an early stage in Flower-deficient CTLs and is rescued to wild-type level by reintroducing Flower or by raising extracellular calcium. A Flower mutant lacking binding sites for the endocytic adaptor AP-2 proteins fails to rescue endocytosis, indicating that Flower interacts with proteins of the endocytic machinery to mediate granule endocytosis. Thus, our data identify Flower as a key protein mediating granule endocytosis.
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Affiliation(s)
- Hsin-Fang Chang
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Stefanie Mannebach
- Department of Experimental and Clinical Pharmacology and Toxicology and Preclinical Center for Molecular Signaling, Saarland University, Homburg, Germany
| | - Andreas Beck
- Department of Experimental and Clinical Pharmacology and Toxicology and Preclinical Center for Molecular Signaling, Saarland University, Homburg, Germany
- Center of Human and Molecular Biology, Saarland University, Homburg, Germany
| | - Keerthana Ravichandran
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Elmar Krause
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Katja Frohnweiler
- Department of Experimental and Clinical Pharmacology and Toxicology and Preclinical Center for Molecular Signaling, Saarland University, Homburg, Germany
| | - Claudia Fecher-Trost
- Department of Experimental and Clinical Pharmacology and Toxicology and Preclinical Center for Molecular Signaling, Saarland University, Homburg, Germany
| | - Claudia Schirra
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Varsha Pattu
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
| | - Veit Flockerzi
- Department of Experimental and Clinical Pharmacology and Toxicology and Preclinical Center for Molecular Signaling, Saarland University, Homburg, Germany
| | - Jens Rettig
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
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145
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Fernandez JJ, Li S, Bharat TAM, Agard DA. Cryo-tomography tilt-series alignment with consideration of the beam-induced sample motion. J Struct Biol 2018; 202:200-209. [PMID: 29410148 PMCID: PMC5949096 DOI: 10.1016/j.jsb.2018.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 11/18/2022]
Abstract
Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal tilt-series alignment and thus deterioration of the reconstruction quality. Here we present a novel approach to tilt-series alignment and tomographic reconstruction that considers the beam-induced sample motion through the tilt-series. It extends the standard fiducial-based alignment approach in cryoET by introducing quadratic polynomials to model the sample motion. The model can be used during reconstruction to yield a motion-compensated tomogram. We evaluated our method on various datasets with different sample sizes. The results demonstrate that our method could be a useful tool to improve the quality of tomograms and the resolution in cryoET.
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Affiliation(s)
| | - Sam Li
- Dept. Biochemistry and Biophysics, University of California, San Francisco, USA
| | - Tanmay A M Bharat
- MRC Laboratory of Molecular Biology, Francis Crick Avenue Cambridge CB2 0QH, UK; Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - David A Agard
- Dept. Biochemistry and Biophysics, University of California, San Francisco, USA
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146
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Clarke NI, Royle SJ. Correlating light microscopy with serial block face scanning electron microscopy to study mitotic spindle architecture. Methods Cell Biol 2018; 145:29-43. [PMID: 29957210 DOI: 10.1016/bs.mcb.2018.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The mitotic spindle is a complex structure that coordinates the accurate segregation of chromosomes during cell division. To understand how the mitotic spindle operates at the molecular level, high resolution imaging is needed. Serial block face-scanning electron microscopy (SBF-SEM) is a technique that can be used to visualize the ultrastructure of entire cells, including components of the mitotic spindle such as microtubules, kinetochores, centrosomes, and chromosomes. Although transmission electron microscopy (TEM) has higher resolution, the reconstruction of large volumes using TEM and tomography is labor intensive, whereas SBF-SEM takes only days to process, image, and segment samples. SBF-SEM fills the resolution gap between light microscopy (LM) and TEM. When combined with LM, SBF-SEM provides a platform where dynamic cellular events can be selected and imaged at high resolution. Here we outline methods to use correlation and SBF-SEM to study mitotic spindle architecture in 3D with high resolution.
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Affiliation(s)
- Nicholas I Clarke
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, United Kingdom
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, United Kingdom.
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147
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Anderson KL, Page C, Swift MF, Hanein D, Volkmann N. Marker-free method for accurate alignment between correlated light, cryo-light, and electron cryo-microscopy data using sample support features. J Struct Biol 2018; 201:46-51. [PMID: 29113849 PMCID: PMC5748349 DOI: 10.1016/j.jsb.2017.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 12/30/2022]
Abstract
Combining fluorescence microscopy with electron cryo-tomography allows, in principle, spatial localization of tagged macromolecular assemblies and structural features within the cellular environment. To allow precise localization and scale integration between the two disparate imaging modalities, accurate alignment procedures are needed. Here, we describe a marker-free method for aligning images from light or cryo-light fluorescence microscopy and from electron cryo-microscopy that takes advantage of sample support features, namely the holes in the carbon film. We find that the accuracy of this method, as judged by prediction errors of the hole center coordinates, is better than 100 nm.
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Affiliation(s)
- Karen L Anderson
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA
| | - Christopher Page
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA
| | - Mark F Swift
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA
| | - Dorit Hanein
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA
| | - Niels Volkmann
- Sanford-Burnham-Prebys Medical Discovery Institute, Bioinformatics and Structural Biology Program, La Jolla, CA, USA.
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148
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Encinar Del Dedo J, Idrissi FZ, Fernandez-Golbano IM, Garcia P, Rebollo E, Krzyzanowski MK, Grötsch H, Geli MI. ORP-Mediated ER Contact with Endocytic Sites Facilitates Actin Polymerization. Dev Cell 2017; 43:588-602.e6. [PMID: 29173820 DOI: 10.1016/j.devcel.2017.10.031] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 09/11/2017] [Accepted: 10/27/2017] [Indexed: 11/18/2022]
Abstract
Oxysterol binding protein-related proteins (ORPs) are conserved lipid binding polypeptides, enriched at ER contacts sites. ORPs promote non-vesicular lipid transport and work as lipid sensors in the context of many cellular tasks, but the determinants of their distinct localization and function are not understood. Here, we demonstrate that the yeast endocytic invaginations associate with the ER and that this association specifically requires the ORPs Osh2 and Osh3, which bridge the endocytic myosin-I Myo5 to the ER integral-membrane VAMP-associated protein (VAP) Scs2. Disruption of the ER contact with endocytic sites using ORP, VAP, myosin-I, or reticulon mutants delays and weakens actin polymerization and interferes with vesicle scission. Finally, we provide evidence suggesting that ORP-dependent sterol transfer facilitates actin polymerization at endocytic sites.
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Affiliation(s)
- Javier Encinar Del Dedo
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Fatima-Zahra Idrissi
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | | | - Patricia Garcia
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Elena Rebollo
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Marek K Krzyzanowski
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Helga Grötsch
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Maria Isabel Geli
- Institute for Molecular Biology of Barcelona (CSIC), Baldiri Reixac 15, 08028 Barcelona, Spain.
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149
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Carter SD, Mageswaran SK, Farino ZJ, Mamede JI, Oikonomou CM, Hope TJ, Freyberg Z, Jensen GJ. Distinguishing signal from autofluorescence in cryogenic correlated light and electron microscopy of mammalian cells. J Struct Biol 2017; 201:15-25. [PMID: 29078993 DOI: 10.1016/j.jsb.2017.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 10/21/2017] [Accepted: 10/23/2017] [Indexed: 01/09/2023]
Abstract
In cryogenic correlated light and electron microscopy (cryo-CLEM), frozen targets of interest are identified and located on EM grids by fluorescence microscopy and then imaged at higher resolution by cryo-EM. Whilst working with these methods, we discovered that a variety of mammalian cells exhibit strong punctate autofluorescence when imaged under cryogenic conditions (80 K). Autofluorescence originated from multilamellar bodies (MLBs) and secretory granules. Here we describe a method to distinguish fluorescent protein tags from these autofluorescent sources based on the narrower emission spectrum of the former. The method is first tested on mitochondria and then applied to examine the ultrastructural variability of secretory granules within insulin-secreting pancreatic beta-cell-derived INS-1E cells.
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Affiliation(s)
- Stephen D Carter
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shrawan K Mageswaran
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zachary J Farino
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - João I Mamede
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | | | - Thomas J Hope
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Cell Biology, University of Pittsburgh, PA 15213, USA.
| | - Grant J Jensen
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute (HHMI), California Institute of Technology, Pasadena, CA 91125, USA.
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150
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Hoffmann PC, Kukulski W. Perspective on architecture and assembly of membrane contact sites. Biol Cell 2017; 109:400-408. [PMID: 28960356 DOI: 10.1111/boc.201700031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/21/2017] [Accepted: 09/21/2017] [Indexed: 01/25/2023]
Abstract
Membrane contact sites (MCS) are platforms of physical contact between different organelles. They are formed through interactions involving lipids and proteins, and function in processes such as calcium and lipid exchange, metabolism and organelle biogenesis. In this article, we discuss emerging questions regarding the architecture, organisation and assembly of MCS, such as: What is the contribution of different components to the interaction between organelles? How is the specific composition of different types of membrane contacts sites established and maintained? How are proteins and lipids spatially organised at MCS and how does that influence their function? How dynamic are MCS on the molecular and ultrastructural level? We highlight current state of research and point out experimental approaches that promise to contribute to a spatiomechanistic understanding of MCS functions.
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Affiliation(s)
- Patrick C Hoffmann
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Wanda Kukulski
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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