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Girard J, Le Bihan O, Lai-Kee-Him J, Girleanu M, Bernard E, Castellarin C, Chee M, Neyret A, Spehner D, Holy X, Favier AL, Briant L, Bron P. In situ fate of Chikungunya virus replication organelles. J Virol 2024; 98:e0036824. [PMID: 38940586 DOI: 10.1128/jvi.00368-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/02/2024] [Indexed: 06/29/2024] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne pathogen responsible for an acute musculoskeletal disease in humans. Replication of the viral RNA genome occurs in specialized membranous replication organelles (ROs) or spherules, which contain the viral replication complex. Initially generated by RNA synthesis-associated plasma membrane deformation, alphavirus ROs are generally rapidly endocytosed to produce type I cytopathic vacuoles (CPV-I), from which nascent RNAs are extruded for cytoplasmic translation. By contrast, CHIKV ROs are poorly internalized, raising the question of their fate and functionality at the late stage of infection. Here, using in situ cryogenic-electron microscopy approaches, we investigate the outcome of CHIKV ROs and associated replication machinery in infected human cells. We evidence the late persistence of CHIKV ROs at the plasma membrane with a crowned protein complex at the spherule neck similar to the recently resolved replication complex. The unexpectedly heterogeneous and large diameter of these compartments suggests a continuous, dynamic growth of these organelles beyond the replication of a single RNA genome. Ultrastructural analysis of surrounding cytoplasmic regions supports that outgrown CHIKV ROs remain dynamically active in viral RNA synthesis and export to the cell cytosol for protein translation. Interestingly, rare ROs with a homogeneous diameter are also marginally internalized in CPV-I near honeycomb-like arrangements of unknown function, which are absent in uninfected controls, thereby suggesting a temporal regulation of this internalization. Altogether, this study sheds new light on the dynamic pattern of CHIKV ROs and associated viral replication at the interface with cell membranes in infected cells.IMPORTANCEThe Chikungunya virus (CHIKV) is a positive-stranded RNA virus that requires specialized membranous replication organelles (ROs) for its genome replication. Our knowledge of this viral cycle stage is still incomplete, notably regarding the fate and functional dynamics of CHIKV ROs in infected cells. Here, we show that CHIKV ROs are maintained at the plasma membrane beyond the first viral cycle, continuing to grow and be dynamically active both in viral RNA replication and in its export to the cell cytosol, where translation occurs in proximity to ROs. This contrasts with the homogeneous diameter of ROs during internalization in cytoplasmic vacuoles, which are often associated with honeycomb-like arrangements of unknown function, suggesting a regulated mechanism. This study sheds new light on the dynamics and fate of CHIKV ROs in human cells and, consequently, on our understanding of the Chikungunya viral cycle.
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Affiliation(s)
- Justine Girard
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS, INSERM, Montpellier, France
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
| | - Olivier Le Bihan
- Institut de Recherche Biomédicale des Armées (IRBA), Ministère des armées, Brétigny-sur-Orge, France
| | - Joséphine Lai-Kee-Him
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Maria Girleanu
- Institut de Recherche Biomédicale des Armées (IRBA), Ministère des armées, Brétigny-sur-Orge, France
| | - Eric Bernard
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
| | - Cedric Castellarin
- Institut de Recherche Biomédicale des Armées (IRBA), Ministère des armées, Brétigny-sur-Orge, France
| | - Matthew Chee
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Aymeric Neyret
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
| | - Danièle Spehner
- Institut de Recherche Biomédicale des Armées (IRBA), Ministère des armées, Brétigny-sur-Orge, France
| | - Xavier Holy
- Institut de Recherche Biomédicale des Armées (IRBA), Ministère des armées, Brétigny-sur-Orge, France
| | - Anne-Laure Favier
- Institut de Recherche Biomédicale des Armées (IRBA), Ministère des armées, Brétigny-sur-Orge, France
| | - Laurence Briant
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
| | - Patrick Bron
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS, INSERM, Montpellier, France
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Emelyanov A, Shtam T, Kamyshinsky R, Garaeva L, Verlov N, Miliukhina I, Kudrevatykh A, Gavrilov G, Zabrodskaya Y, Pchelina S, Konevega A. Cryo-electron microscopy of extracellular vesicles from cerebrospinal fluid. PLoS One 2020; 15:e0227949. [PMID: 31999742 PMCID: PMC6991974 DOI: 10.1371/journal.pone.0227949] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/03/2020] [Indexed: 12/19/2022] Open
Abstract
Extracellular vesicles (EVs) are membrane-enclosed vesicles which play important role for cell communication and physiology. EVs are found in many human biological fluids, including blood, breast milk, urine, cerebrospinal fluid (CSF), ejaculate, saliva etc. These nano-sized vesicles contain proteins, mRNAs, microRNAs, non-coding RNAs and lipids that are derived from producing cells. EVs deliver complex sets of biological information to recipient cells thereby modulating their behaviors by their molecular cargo. In this way EVs are involved in the pathological development and progression of many human disorders, including neurodegenerative diseases. In this study EVs purified by ultracentrifugation from CSF of patients with Parkinson's disease (PD) and individuals of the comparison group were characterized using nanoparticle tracking analysis, flow cytometry and cryo-electron microscopy. Vesicular size and the presence of exosomal marker CD9 on the surface provided evidence that most of the EVs were exosome-like vesicles. Cryo-electron microscopy allowed us to visualize a large spectrum of extracellular vesicles of various size and morphology with lipid bilayers and vesicular internal structures. Thus, we described the diversity and new characteristics of the vesicles from CSF suggesting that subpopulations of EVs with different and specific functions may exist.
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Affiliation(s)
- Anton Emelyanov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Tatiana Shtam
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Roman Kamyshinsky
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
| | - Luiza Garaeva
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Nikolai Verlov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Irina Miliukhina
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
- Institute of Experimental Medicine, St. Petersburg, Russia
| | - Anastasia Kudrevatykh
- Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
- Institute of Experimental Medicine, St. Petersburg, Russia
| | - Gaspar Gavrilov
- S.M. Kirov Saint-Petersburg Military Medical Academy, St. Petersburg, Russia
| | - Yulia Zabrodskaya
- Polenov Neurosurgical Institute–Branch of National Almazov Medical Research Centre, St. Petersburg, Russia
| | - Sofya Pchelina
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Institute of Experimental Medicine, St. Petersburg, Russia
| | - Andrey Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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3
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Ali MH, Elsherbiny ME, Emara M. Updates on Aptamer Research. Int J Mol Sci 2019; 20:E2511. [PMID: 31117311 PMCID: PMC6566374 DOI: 10.3390/ijms20102511] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023] Open
Abstract
For many years, different probing techniques have mainly relied on antibodies for molecular recognition. However, with the discovery of aptamers, this has changed. The science community is currently considering using aptamers in molecular targeting studies because of the many potential advantages they have over traditional antibodies. Some of these possible advantages are their specificity, higher binding affinity, better target discrimination, minimized batch-to-batch variation, and reduced side effects. Overall, these characteristics of aptamers have attracted scholars to use them as molecular probes in place of antibodies, with some aptamer-based targeting products being now available in the market. The present review is aimed at discussing the potential of aptamers as probes in molecular biology and in super-resolution microscopy.
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Affiliation(s)
- Mohamed H Ali
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
- current address: Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
| | - Marwa E Elsherbiny
- Department of Pharmacology and Toxicology, Ahram Canadian University, 6th of October City, Giza 12566, Egypt.
| | - Marwan Emara
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
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4
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Huang X, Li S, Gao S. Applying a Modified Wavelet Shrinkage Filter to Improve Cryo-Electron Microscopy Imaging. J Comput Biol 2018; 25:1050-1058. [DOI: 10.1089/cmb.2018.0060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Xinrui Huang
- Department of Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Sha Li
- Department of Medical Physics, School of Foundational Education, Peking University, Beijing, China
| | - Song Gao
- Department of Medical Physics, School of Foundational Education, Peking University, Beijing, China
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5
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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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6
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Benítez-Mateos AI, Nidetzky B, Bolivar JM, López-Gallego F. Single-Particle Studies to Advance the Characterization of Heterogeneous Biocatalysts. ChemCatChem 2018. [DOI: 10.1002/cctc.201701590] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ana I. Benítez-Mateos
- Heterogeneous Biocatalysis Group; CIC BiomaGUNE; Paseo Miramon 182 San Sebastian-Donostia 20014 Spain
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
- Austrian Centre of Industrial Biotechnology; Petersgasse 14 8010 Graz Austria
| | - Juan M. Bolivar
- Institute of Biotechnology and Biochemical Engineering; Graz University of Technology, NAWI Graz; Petersgasse 12 8010 Graz Austria
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Group; CIC BiomaGUNE; Paseo Miramon 182 San Sebastian-Donostia 20014 Spain
- IKERBASQUE; Basque Foundation for Science; Bilbao Spain
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7
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Liu S, Hattne J, Reyes FE, Sanchez-Martinez S, Jason de la Cruz M, Shi D, Gonen T. Atomic resolution structure determination by the cryo-EM method MicroED. Protein Sci 2016; 26:8-15. [PMID: 27452773 DOI: 10.1002/pro.2989] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Abstract
The electron cryo-microscopy (cryoEM) method MicroED has been rapidly developing. In this review we highlight some of the key steps in MicroED from crystal analysis to structure determination. We compare and contrast MicroED and the latest X-ray based diffraction method the X-ray free-electron laser (XFEL). Strengths and shortcomings of both MicroED and XFEL are discussed. Finally, all current MicroED structures are tabulated with a view to the future.
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Affiliation(s)
- Shian Liu
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Johan Hattne
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Francis E Reyes
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Silvia Sanchez-Martinez
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - M Jason de la Cruz
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
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8
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Kyne C, Crowley PB. Grasping the nature of the cell interior: fromPhysiological ChemistrytoChemical Biology. FEBS J 2016; 283:3016-28. [DOI: 10.1111/febs.13744] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/09/2016] [Accepted: 04/18/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Ciara Kyne
- School of Chemistry; National University of Ireland Galway; Ireland
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; Ireland
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9
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Hagen C, Dent KC, Zeev-Ben-Mordehai T, Grange M, Bosse JB, Whittle C, Klupp BG, Siebert CA, Vasishtan D, Bäuerlein FJB, Cheleski J, Werner S, Guttmann P, Rehbein S, Henzler K, Demmerle J, Adler B, Koszinowski U, Schermelleh L, Schneider G, Enquist LW, Plitzko JM, Mettenleiter TC, Grünewald K. Structural Basis of Vesicle Formation at the Inner Nuclear Membrane. Cell 2016; 163:1692-701. [PMID: 26687357 PMCID: PMC4701712 DOI: 10.1016/j.cell.2015.11.029] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/11/2015] [Accepted: 11/06/2015] [Indexed: 12/22/2022]
Abstract
Vesicular nucleo-cytoplasmic transport is becoming recognized as a general cellular mechanism for translocation of large cargoes across the nuclear envelope. Cargo is recruited, enveloped at the inner nuclear membrane (INM), and delivered by membrane fusion at the outer nuclear membrane. To understand the structural underpinning for this trafficking, we investigated nuclear egress of progeny herpesvirus capsids where capsid envelopment is mediated by two viral proteins, forming the nuclear egress complex (NEC). Using a multi-modal imaging approach, we visualized the NEC in situ forming coated vesicles of defined size. Cellular electron cryo-tomography revealed a protein layer showing two distinct hexagonal lattices at its membrane-proximal and membrane-distant faces, respectively. NEC coat architecture was determined by combining this information with integrative modeling using small-angle X-ray scattering data. The molecular arrangement of the NEC establishes the basic mechanism for budding and scission of tailored vesicles at the INM. Multimodal imaging reveals mechanism of vesicle formation at inner nuclear membrane Nucleo-cytoplasmic cargo vesicle coat in situ comprises two distinct lattices Lattices are formed by hexameric building blocks made of the nuclear egress complex Induction of membrane curvature based solely on heterodimeric interactions
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Affiliation(s)
- Christoph Hagen
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kyle C Dent
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Tzviya Zeev-Ben-Mordehai
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Michael Grange
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jens B Bosse
- Department of Molecular Biology, Princeton Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Cathy Whittle
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Barbara G Klupp
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
| | - C Alistair Siebert
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Daven Vasishtan
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Felix J B Bäuerlein
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Juliana Cheleski
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Stephan Werner
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Wilhelm-Conrad-Röntgen Campus, 12489 Berlin, Germany
| | - Peter Guttmann
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Wilhelm-Conrad-Röntgen Campus, 12489 Berlin, Germany
| | - Stefan Rehbein
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Wilhelm-Conrad-Röntgen Campus, 12489 Berlin, Germany
| | - Katja Henzler
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Wilhelm-Conrad-Röntgen Campus, 12489 Berlin, Germany
| | - Justin Demmerle
- Micron Oxford, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Barbara Adler
- Max von Pettenkofer-Institut, Ludwig-Maximilians-Universität München, Pettenkoferstr. 9a, 80336 Munich, Germany
| | - Ulrich Koszinowski
- Max von Pettenkofer-Institut, Ludwig-Maximilians-Universität München, Pettenkoferstr. 9a, 80336 Munich, Germany
| | - Lothar Schermelleh
- Micron Oxford, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Gerd Schneider
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Wilhelm-Conrad-Röntgen Campus, 12489 Berlin, Germany
| | - Lynn W Enquist
- Department of Molecular Biology, Princeton Neuroscience Institute, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Thomas C Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany.
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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10
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Abstract
Cryo-electron tomography (cryo-ET) has emerged as a leading technique for three-dimensional visualization of large macromolecular complexes and their conformational changes in their native cellular environment. However, the resolution and potential applications of cryo-ET are fundamentally limited by specimen thickness, preventing high-resolution in situ visualization of macromolecular structures in many bacteria (such as Escherichia coli and Salmonella enterica). Minicells, which were discovered nearly 50 years ago, have recently been exploited as model systems to visualize molecular machines in situ, due to their smaller size and other unique properties. In this review, we discuss strategies for producing minicells and highlight their use in the study of chemotactic signaling, protein secretion, and DNA translocation. In combination with powerful genetic tools and advanced imaging techniques, minicells provide a springboard for in-depth structural studies of bacterial macromolecular complexes in situ and therefore offer a unique approach for gaining novel structural insights into many important processes in microbiology.
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11
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Brown JR, Schwartz CL, Heumann JM, Dawson SC, Hoenger A. A detailed look at the cytoskeletal architecture of the Giardia lamblia ventral disc. J Struct Biol 2016; 194:38-48. [PMID: 26821343 DOI: 10.1016/j.jsb.2016.01.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 01/21/2016] [Accepted: 01/24/2016] [Indexed: 11/16/2022]
Abstract
Giardia lamblia is a protistan parasite that infects and colonizes the small intestine of mammals. It is widespread and particularly endemic in the developing world. Here we present a detailed structural study by 3-D negative staining and cryo-electron tomography of a unique Giardia organelle, the ventral disc. The disc is composed of a regular array of microtubules and associated sheets, called microribbons that form a large spiral, held together by a myriad of mostly unknown associated proteins. In a previous study we analyzed by cryo-electron tomography the central microtubule portion (here called disc body) of the ventral disc and found a large portion of microtubule associated inner (MIPs) and outer proteins (MAPs) that render these microtubules hyper-stable. With this follow-up study we expanded our 3-D analysis to different parts of the disc such as the ventral and dorsal areas of the overlap zone, as well as the outer disc margin. There are intrinsic location-specific characteristics in the composition of microtubule-associated proteins between these regions, as well as large differences between the overall architecture of microtubules and microribbons. The lateral packing of microtubule-microribbon complexes varies substantially, and closer packing often comes with contracted lateral tethers that seem to hold the disc together. It appears that the marginal microtubule-microribbon complexes function as outer, laterally contractible lids that may help the cell to clamp onto the intestinal microvilli. Furthermore, we analyzed length, quantity, curvature and distribution between different zones of the disc, which we found to differ from previous publications.
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Affiliation(s)
- Joanna R Brown
- University of Colorado, Dept. MCD Biology, Boulder, CO 80309, USA
| | - Cindi L Schwartz
- University of Colorado, Dept. MCD Biology, Boulder, CO 80309, USA
| | - John M Heumann
- University of Colorado, Dept. MCD Biology, Boulder, CO 80309, USA
| | - Scott C Dawson
- University of California Davis, Dept. Microbiology and Molecular Genetics, Davis, CA 95616, USA
| | - Andreas Hoenger
- University of Colorado, Dept. MCD Biology, Boulder, CO 80309, USA.
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12
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Viral Infection at High Magnification: 3D Electron Microscopy Methods to Analyze the Architecture of Infected Cells. Viruses 2015; 7:6316-45. [PMID: 26633469 PMCID: PMC4690864 DOI: 10.3390/v7122940] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/16/2015] [Accepted: 11/16/2015] [Indexed: 02/06/2023] Open
Abstract
As obligate intracellular parasites, viruses need to hijack their cellular hosts and reprogram their machineries in order to replicate their genomes and produce new virions. For the direct visualization of the different steps of a viral life cycle (attachment, entry, replication, assembly and egress) electron microscopy (EM) methods are extremely helpful. While conventional EM has given important information about virus-host cell interactions, the development of three-dimensional EM (3D-EM) approaches provides unprecedented insights into how viruses remodel the intracellular architecture of the host cell. During the last years several 3D-EM methods have been developed. Here we will provide a description of the main approaches and examples of innovative applications.
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13
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Höög JL, Lötvall J. Diversity of extracellular vesicles in human ejaculates revealed by cryo-electron microscopy. J Extracell Vesicles 2015; 4:28680. [PMID: 26563734 PMCID: PMC4643196 DOI: 10.3402/jev.v4.28680] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/04/2015] [Accepted: 10/11/2015] [Indexed: 12/19/2022] Open
Abstract
Human ejaculates contain extracellular vesicles (EVs), that to a large extent are considered to originate from the prostate gland, and are often denominated “prostasomes.” These EVs are important for human fertility, for example by promoting sperm motility and by inducing immune tolerance of the female immune system to the spermatozoa. So far, the EVs present in human ejaculate have not been studied in their native state, inside the seminal fluid without prior purification and isolation procedures. Using cryo-electron microscopy and tomography, we performed a comprehensive inventory of human ejaculate EVs. The sample was neither centrifuged, fixed, filtered or sectioned, nor were heavy metals added. Approximately 1,500 extracellular structures were imaged and categorized. The extracellular environment of human ejaculate was found to be diverse, with 5 major subcategories of EVs and 6 subcategories of extracellular membrane compartments, including lamellar bodies. Furthermore, 3 morphological features, including electron density, double membrane bilayers and coated surface, are described in all subcategories. This study reveals that the extracellular environment in human ejaculate is multifaceted. Several novel morphological EV subcategories are identified and clues to their cellular origin may be found in their morphology. This inventory is therefore important for developing future experimental approaches, and to interpret previously published data to understand the role of EVs for human male fertility.
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Affiliation(s)
- Johanna L Höög
- Krefting Research Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden;
| | - Jan Lötvall
- Krefting Research Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Almo SC, Minor W. X-ray crystallography over the past decade for novel drug discovery - where are we heading next? Expert Opin Drug Discov 2015; 10:975-89. [PMID: 26177814 DOI: 10.1517/17460441.2015.1061991] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology. AREAS COVERED This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions. EXPERT OPINION X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible.
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Affiliation(s)
- Heping Zheng
- University of Virginia, Department of Molecular Physiology and Biological Physics , 1340 Jefferson Park Avenue, Charlottesville, VA 22908 , USA +1 434 243 6865 ; +1 434 243 2981 ;
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15
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Delgado L, Martínez G, López-Iglesias C, Mercadé E. Cryo-electron tomography of plunge-frozen whole bacteria and vitreous sections to analyze the recently described bacterial cytoplasmic structure, the Stack. J Struct Biol 2015; 189:220-9. [PMID: 25617813 DOI: 10.1016/j.jsb.2015.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/13/2015] [Indexed: 11/25/2022]
Abstract
Cryo-electron tomography (CET) of plunge-frozen whole bacteria and vitreous sections (CETOVIS) were used to revise and expand the structural knowledge of the "Stack", a recently described cytoplasmic structure in the Antarctic bacterium Pseudomonas deceptionensis M1(T). The advantages of both techniques can be complementarily combined to obtain more reliable insights into cells and their components with three-dimensional imaging at different resolutions. Cryo-electron microscopy (Cryo-EM) and CET of frozen-hydrated P. deceptionensis M1(T) cells confirmed that Stacks are found at different locations within the cell cytoplasm, in variable number, separately or grouped together, very close to the plasma membrane (PM) and oriented at different angles (from 35° to 90°) to the PM, thus establishing that they were not artifacts of the previous sample preparation methods. CET of plunge-frozen whole bacteria and vitreous sections verified that each Stack consisted of a pile of oval disc-like subunits, each disc being surrounded by a lipid bilayer membrane and separated from each other by a constant distance with a mean value of 5.2±1.3nm. FM4-64 staining and confocal microscopy corroborated the lipid nature of the membrane of the Stacked discs. Stacks did not appear to be invaginations of the PM because no continuity between both membranes was visible when whole bacteria were analyzed. We are still far from deciphering the function of these new structures, but a first experimental attempt links the Stacks with a given phase of the cell replication process.
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Affiliation(s)
- Lidia Delgado
- Cryo-Electron Microscopy, Scientific and Technological Centers, University of Barcelona, Barcelona, Spain; Department of Microbiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Gema Martínez
- Cryo-Electron Microscopy, Scientific and Technological Centers, University of Barcelona, Barcelona, Spain
| | - Carmen López-Iglesias
- Cryo-Electron Microscopy, Scientific and Technological Centers, University of Barcelona, Barcelona, Spain.
| | - Elena Mercadé
- Department of Microbiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain.
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16
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Wacker I, Chockley P, Bartels C, Spomer W, Hofmann A, Gengenbach U, Singh S, Thaler M, Grabher C, Schröder RR. Array tomography: characterizing FAC-sorted populations of zebrafish immune cells by their 3D ultrastructure. J Microsc 2015; 259:105-113. [PMID: 25611576 PMCID: PMC4670706 DOI: 10.1111/jmi.12223] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 12/23/2014] [Indexed: 11/29/2022]
Abstract
For 3D reconstructions of whole immune cells from zebrafish, isolated from adult animals by FAC-sorting we employed array tomography on hundreds of serial sections deposited on silicon wafers. Image stacks were either recorded manually or automatically with the newly released ZEISS Atlas 5 Array Tomography platform on a Zeiss FEGSEM. To characterize different populations of immune cells, organelle inventories were created by segmenting individual cells. In addition, arrays were used for quantification of cell populations with respect to the various cell types they contained. The detection of immunological synapses in cocultures of cell populations from thymus or WKM with cancer cells helped to identify the cytotoxic nature of these cells. Our results demonstrate the practicality and benefit of AT for high-throughput ultrastructural imaging of substantial volumes.
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Affiliation(s)
- Irene Wacker
- Centre for Advanced Materials, Universität Heidelberg, Heidelberg, Germany.,Heidelberg Karlsruhe Research Partnership, Heidelberg/Karlsruhe, Germany
| | - Peter Chockley
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Carolin Bartels
- Centre for Advanced Materials, Universität Heidelberg, Heidelberg, Germany
| | - Waldemar Spomer
- Heidelberg Karlsruhe Research Partnership, Heidelberg/Karlsruhe, Germany.,Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Andreas Hofmann
- Heidelberg Karlsruhe Research Partnership, Heidelberg/Karlsruhe, Germany.,Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ulrich Gengenbach
- Heidelberg Karlsruhe Research Partnership, Heidelberg/Karlsruhe, Germany.,Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sachin Singh
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | - Clemens Grabher
- Heidelberg Karlsruhe Research Partnership, Heidelberg/Karlsruhe, Germany.,Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Rasmus R Schröder
- Centre for Advanced Materials, Universität Heidelberg, Heidelberg, Germany.,Heidelberg Karlsruhe Research Partnership, Heidelberg/Karlsruhe, Germany.,Cryo-EM, CellNetworks, BioQuant Universitätsklinikum Heidelberg, Heidelberg, Germany
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17
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Wagenknecht T, Hsieh C, Marko M. Skeletal Muscle Triad Junction Ultrastructure by Focused-Ion-Beam Milling of Muscle and Cryo-Electron Tomography. Eur J Transl Myol 2015; 25:4823. [PMID: 26913145 PMCID: PMC4748973 DOI: 10.4081/ejtm.2015.4823] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/09/2015] [Accepted: 01/15/2015] [Indexed: 11/23/2022] Open
Abstract
Cryo-electron tomography (cryo-ET) has emerged as perhaps the only practical technique for revealing nanometer-level three-dimensional structural details of subcellular macromolecular complexes in their native context, inside the cell. As currently practiced, the specimen should be 0.1-0.2 microns in thickness to achieve optimal resolution. Thus, application of cryo-ET to intact frozen (vitreous) tissues, such as skeletal muscle, requires that they be sectioned. Cryo-ultramicrotomy is notoriously difficult and artifact-prone when applied to frozen cells and tissue, but a new technique, focused ion beam milling (cryo-FIB), shows great promise for “thinning” frozen biological specimens. Here we describe our initial results in applying cryo-FIB and cryo-ET to triad junctions of skeletal muscle.
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Affiliation(s)
- Terence Wagenknecht
- New York State Department of Health, Wadsworth Cente, Empire State Plaza, Albany, NY, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
| | - Chyongere Hsieh
- New York State Department of Health, Wadsworth Cente, Empire State Plaza, Albany, NY, USA
| | - Michael Marko
- New York State Department of Health, Wadsworth Cente, Empire State Plaza, Albany, NY, USA
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19
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Abstract
Correlative fluorescence and electron microscopy (CFEM) is a multimodal technique that combines dynamic and localization information from fluorescence methods with ultrastructural data from electron microscopy, to give new information about how cellular components change relative to the spatiotemporal dynamics within their environment. In this review, we will discuss some of the basic techniques and tools of the trade for utilizing this attractive research method, which is becoming a very powerful tool for biology labs. The information obtained from correlative methods has proven to be invaluable in creating consensus between the two types of microscopy, extending the capability of each, and cutting the time and expense associated with using each method separately for comparative analysis. The realization of the advantages of these methods in cell biology has led to rapid improvement in the protocols and has ushered in a new generation of instruments to reach the next level of correlation--integration.
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Affiliation(s)
- Randall T Schirra
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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