1
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Vieira Da Cruz A, Jiménez-Castellanos JC, Börnsen C, Van Maele L, Compagne N, Pradel E, Müller RT, Meurillon V, Soulard D, Piveteau C, Biela A, Dumont J, Leroux F, Deprez B, Willand N, Pos KM, Frangakis AS, Hartkoorn RC, Flipo M. Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against K. pneumoniae. EMBO Mol Med 2024; 16:93-111. [PMID: 38177534 PMCID: PMC10897476 DOI: 10.1038/s44321-023-00007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 01/06/2024] Open
Abstract
Antimicrobial resistance is a global problem, rendering conventional treatments less effective and requiring innovative strategies to combat this growing threat. The tripartite AcrAB-TolC efflux pump is the dominant constitutive system by which Enterobacterales like Escherichia coli and Klebsiella pneumoniae extrude antibiotics. Here, we describe the medicinal chemistry development and drug-like properties of BDM91288, a pyridylpiperazine-based AcrB efflux pump inhibitor. In vitro evaluation of BDM91288 confirmed it to potentiate the activity of a panel of antibiotics against K. pneumoniae as well as revert clinically relevant antibiotic resistance mediated by acrAB-tolC overexpression. Using cryo-EM, BDM91288 binding to the transmembrane region of K. pneumoniae AcrB was confirmed, further validating the mechanism of action of this inhibitor. Finally, proof of concept studies demonstrated that oral administration of BDM91288 significantly potentiated the in vivo efficacy of levofloxacin treatment in a murine model of K. pneumoniae lung infection.
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Affiliation(s)
- Anais Vieira Da Cruz
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Juan-Carlos Jiménez-Castellanos
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Clara Börnsen
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438, Frankfurt am Main, Germany
| | - Laurye Van Maele
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Nina Compagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Elizabeth Pradel
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Reinke T Müller
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438, Frankfurt am Main, Germany
| | - Virginie Meurillon
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Daphnée Soulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Alexandre Biela
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Julie Dumont
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, US 41-UAR 2014-PLBS, F-59000, Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Klaas M Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438, Frankfurt am Main, Germany.
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438, Frankfurt am Main, Germany.
| | - Ruben C Hartkoorn
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France.
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.
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2
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Sprankel L, Scheffer MP, Manger S, Ermel UH, Frangakis AS. Cryo-electron tomography reveals the binding and release states of the major adhesion complex from Mycoplasma genitalium. PLoS Pathog 2023; 19:e1011761. [PMID: 37939157 PMCID: PMC10659161 DOI: 10.1371/journal.ppat.1011761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/20/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023] Open
Abstract
The nap particle is an immunogenic surface adhesion complex from Mycoplasma genitalium. It is essential for motility and responsible for binding sialylated oligosaccharides on the surface of the host cell. The nap particle is composed of two P140-P110 heterodimers, the structure of which was recently solved. However, the interpretation of the mechanism by which the mycoplasma cells orchestrate adhesion remained challenging. Here, we provide cryo-electron tomography structures at ~11 Å resolution, which allow for the distinction between the bound and released state of the nap particle, displaying the in vivo conformational states. Fitting of the atomically resolved structures reveals that bound sialylated oligosaccharides are stabilized by both P110 and P140. Movement of the stalk domains allows for the transfer of conformational changes from the interior of the cell to the binding pocket, thus having the capability of an active release process. It is likely that the same mechanism can be transferred to other Mycoplasma species that belong to the pneumoniae cluster.
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Affiliation(s)
- Lasse Sprankel
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Margot P. Scheffer
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Sina Manger
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Utz H. Ermel
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Achilleas S. Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
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3
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Sprankel L, Vizarraga D, Martín J, Manger S, Meier-Credo J, Marcos M, Julve J, Rotllan N, Scheffer MP, Escolà-Gil JC, Langer JD, Piñol J, Fita I, Frangakis AS. Essential protein P116 extracts cholesterol and other indispensable lipids for Mycoplasmas. Nat Struct Mol Biol 2023; 30:321-329. [PMID: 36782049 PMCID: PMC10023570 DOI: 10.1038/s41594-023-00922-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/06/2023] [Indexed: 02/15/2023]
Abstract
Mycoplasma pneumoniae, responsible for approximately 30% of community-acquired human pneumonia, needs to extract lipids from the host environment for survival and proliferation. Here, we report a comprehensive structural and functional analysis of the previously uncharacterized protein P116 (MPN_213). Single-particle cryo-electron microscopy of P116 reveals a homodimer presenting a previously unseen fold, forming a huge hydrophobic cavity, which is fully accessible to solvent. Lipidomics analysis shows that P116 specifically extracts lipids such as phosphatidylcholine, sphingomyelin and cholesterol. Structures of different conformational states reveal the mechanism by which lipids are extracted. This finding immediately suggests a way to control Mycoplasma infection by interfering with lipid uptake.
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Affiliation(s)
- Lasse Sprankel
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - David Vizarraga
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Jesús Martín
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Sina Manger
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Marina Marcos
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Josep Julve
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau and CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Noemi Rotllan
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau and CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Margot P Scheffer
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Joan Carles Escolà-Gil
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau and CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Julian D Langer
- Proteomics, Max Planck Institute of Biophysics, Frankfurt, Germany
- Proteomics, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Jaume Piñol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Spain.
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany.
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4
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Ermel UH, Arghittu SM, Frangakis AS. ArtiaX: An Electron Tomography Toolbox for the Interactive Handling of Sub-Tomograms in UCSF ChimeraX. Protein Sci 2022; 31:e4472. [PMID: 36251681 DOI: 10.1002/pro.4472] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022]
Abstract
Cryo-electron tomography analysis involves the selection of macromolecular complexes to be used for subsequent sub-tomogram averaging and structure determination. Here, we describe a plugin developed for UCSF ChimeraX that allows for the display, selection, and editing of particles within tomograms. Positions and orientations of selected particles can be manually set, modified and inspected in real-time, both on screen and in virtual reality, and exported to various file formats. The plugin allows for the parallel visualization of particles stored in several meta data lists, in the context of any 3D image that can be opened with UCSF ChimeraX. The particles are rendered in user-defined colors or using colormaps, such that individual classes or groups of particles, cross-correlation coefficients or other types of information can be highlighted to the user. The implemented functions are fast, reliable and intuitive, exploring the broad range of features in UCSF ChimeraX. They allow for a fluent human-machine interaction, which enables an effective understanding of the sub-tomogram processing pipeline, even for non-specialist users. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Utz H Ermel
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Serena M Arghittu
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
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5
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Frangakis AS. Mean curvature motion facilitates the segmentation and surface visualization of electron tomograms. J Struct Biol 2022; 214:107833. [DOI: 10.1016/j.jsb.2022.107833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
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6
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Frangakis AS. It's noisy out there! A review of denoising techniques in cryo-electron tomography. J Struct Biol 2021; 213:107804. [PMID: 34732363 DOI: 10.1016/j.jsb.2021.107804] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022]
Abstract
Cryo-electron tomography is the only technique that can provide sub-nanometer resolved images of cell regions or even whole cells, without the need of labeling or staining methods. Technological advances over the past decade in electron microscope stability, cameras, stage precision and software have resulted in faster acquisition speeds and considerably improved resolution. In pursuit of even better image resolution, researchers seek to reduce noise - a crucial factor affecting the reliability of the tomogram interpretation and ultimately limiting the achieved resolution. Sub-tomogram averaging is the method of choice for reducing noise in repetitive objects. However, when averaging is not applicable, a trade-off between reducing noise and conserving genuine image details must be achieved. Thus, denoising is an important process that improves the interpretability of the tomogram not only directly but also by facilitating other downstream tasks, such as segmentation and 3D visualization. Here, I review contemporary denoising techniques for cryo-electron tomography by taking into account noise-specific properties of both reconstruction and detector noise. The outcomes of different techniques are compared, in order to help researchers select the most appropriate for each dataset and to achieve better and more reliable interpretation of the tomograms.
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Affiliation(s)
- Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany.
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7
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Manger S, Ermel UH, Frangakis AS. Ex vivo visualization of RNA polymerase III-specific gene activity with electron microscopy. Commun Biol 2021; 4:234. [PMID: 33608618 PMCID: PMC7895982 DOI: 10.1038/s42003-021-01752-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/24/2020] [Indexed: 11/09/2022] Open
Abstract
The direct study of transcription or DNA–protein-binding events, requires imaging of individual genes at molecular resolution. Electron microscopy (EM) can show local detail of the genome. However, direct visualization and analysis of specific individual genes is currently not feasible as they cannot be unambiguously localized in the crowded, landmark-free environment of the nucleus. Here, we present a method for the genomic insertion of gene clusters that can be localized and imaged together with their associated protein complexes in the EM. The method uses CRISPR/Cas9 technology to incorporate several genes of interest near the 35S rRNA gene, which is a frequently occurring, easy-to-identify genomic locus within the nucleolus that can be used as a landmark in micrographs. As a proof of principle, we demonstrate the incorporation of the locus-native gene RDN5 and the locus-foreign gene HSX1. This led to a greater than 7-fold enrichment of RNA polymerase III (Pol III) complexes associated with the genes within the field of view, allowing for a significant increase in the analysis yield. This method thereby allows for the insertion and direct visualization of gene clusters for a range of analyses, such as changes in gene activity upon alteration of cellular or external factors. Manger, Ermel, and Frangakis report the use of CRISPR/Cas9 to stably insert multiple copies of a particular gene-of-interest near the 35S rRNA gene, to allow direct visualization of gene clusters with electron microscopy. They achieve more than 7-fold enrichment of associated Pol III complexes within the field of view, demonstrating the utility of the approach.
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Affiliation(s)
- Sina Manger
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Utz H Ermel
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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8
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Bojkova D, Wagner JUG, Shumliakivska M, Aslan GS, Saleem U, Hansen A, Luxán G, Günther S, Pham MD, Krishnan J, Harter PN, Ermel UH, Frangakis AS, Milting H, Zeiher AM, Klingel K, Cinatl J, Dendorfer A, Eschenhagen T, Tschöpe C, Ciesek S, Dimmeler S. SARS-CoV-2 infects and induces cytotoxic effects in human cardiomyocytes. Cardiovasc Res 2020; 116:2207-2215. [PMID: 32966582 PMCID: PMC7543363 DOI: 10.1093/cvr/cvaa267] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 08/26/2020] [Accepted: 09/09/2020] [Indexed: 12/15/2022] Open
Abstract
Aims Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has emerged as a global pandemic. SARS-CoV-2 infection can lead to elevated markers of cardiac injury associated with higher risk of mortality. It is unclear whether cardiac injury is caused by direct infection of cardiomyocytes or is mainly secondary to lung injury and inflammation. Here, we investigate whether cardiomyocytes are permissive for SARS-CoV-2 infection. Methods and results Two strains of SARS-CoV-2 infected human induced pluripotent stem cell-derived cardiomyocytes (iPS-CMs) as demonstrated by detection of intracellular double-stranded viral RNA and viral spike glycoprotein expression. Increasing concentrations of viral RNA are detected in supernatants of infected cardiomyocytes, which induced infections in Caco-2 cell lines, documenting productive infections. SARS-COV-2 infection and induced cytotoxic and proapoptotic effects associated with it abolished cardiomyocyte beating. RNA sequencing confirmed a transcriptional response to viral infection as demonstrated by the up-regulation of genes associated with pathways related to viral response and interferon signalling, apoptosis, and reactive oxygen stress. SARS-CoV-2 infection and cardiotoxicity was confirmed in a 3D cardiosphere tissue model. Importantly, viral spike protein and viral particles were detected in living human heart slices after infection with SARS-CoV-2. Coronavirus particles were further observed in cardiomyocytes of a patient with COVID-19. Infection of iPS-CMs was dependent on cathepsins and angiotensin-converting enzyme 2 (ACE2), and was blocked by remdesivir. Conclusions This study demonstrates that SARS-CoV-2 infects cardiomyocytes in vitro in an ACE2- and cathepsin-dependent manner. SARS-CoV-2 infection of cardiomyocytes is inhibited by the antiviral drug remdesivir. Translational Perspective Although this study cannot address whether cardiac injury and dysfunction in COVID-19 patients is caused by direct infection of cardiomyocytes, the demonstration of direct cardiotoxicity in cardiomyocytes, organ mimics, human heart slices and human hearts warrants the further monitoring of cardiotoxic effects in COVID-19 patients.
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Affiliation(s)
- Denisa Bojkova
- Institute of Medical Virology, University of Frankfurt, Paul-Ehrlich-Str. 40, 60590 Frankfurt, Germany
| | - Julian U G Wagner
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt, Germany.,German Center for Cardiovascular Research (DZHK), Germany
| | - Mariana Shumliakivska
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Galip S Aslan
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Umber Saleem
- German Center for Cardiovascular Research (DZHK), Germany.,Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Arne Hansen
- German Center for Cardiovascular Research (DZHK), Germany.,Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Guillermo Luxán
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Stefan Günther
- Max Planck Institute Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim, Germany.,Cardiopulmonary Institute (CPI), Frankfurt, Germany
| | - Minh Duc Pham
- Department of Medicine, Cardiology, Goethe University Hospital, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Jaya Krishnan
- Cardiopulmonary Institute (CPI), Frankfurt, Germany.,Department of Medicine, Cardiology, Goethe University Hospital, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Patrick N Harter
- Neurological Institute (Edinger Institute), University of Frankfurt, Heinrich-Hoffmann Strasse 7, 60528 Frankfurt, Germany
| | - Utz H Ermel
- Institute of Biophysics and BMLS, University of Frankfurt, Campus Riedberg, Maxvon-Laue Strasse 15, 60438 Frankfurt, Germany
| | - Achilleas S Frangakis
- Institute of Biophysics and BMLS, University of Frankfurt, Campus Riedberg, Maxvon-Laue Strasse 15, 60438 Frankfurt, Germany
| | - Hendrik Milting
- Heart and Diabetes Center NRW, University Hospital of the Ruhr University Bochum, Clinic for Thoracic and Cardiovascular Surgery, Erich & Hanna Klessmann Institute, Georgstr. 11, 32545 Bad Oeyenhausen, Germany
| | - Andreas M Zeiher
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany.,Cardiopulmonary Institute (CPI), Frankfurt, Germany.,Department of Medicine, Cardiology, Goethe University Hospital, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Karin Klingel
- Cardiopathology, Institute for Pathology and Neuropathology, University Hospital Tuebingen, Liebermeisterstraße 8, 72076 Tuebingen, Germany
| | - Jindrich Cinatl
- Institute of Medical Virology, University of Frankfurt, Paul-Ehrlich-Str. 40, 60590 Frankfurt, Germany
| | - Andreas Dendorfer
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany.,Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Marchioninistr. 27, 81377 Munich, Germany
| | - Thomas Eschenhagen
- German Center for Cardiovascular Research (DZHK), Germany.,Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Carsten Tschöpe
- German Center for Cardiovascular Research (DZHK), Germany.,Department of Cardiology, Campus Virchow Klinikum (CVK), Charité, and Berlin Institute of Health (BIH), Berlin Brandenburger Center for Regenerative Therapies (BCRT), University Medicine Berlin, Berlin, Germany
| | - Sandra Ciesek
- Institute of Medical Virology, University of Frankfurt, Paul-Ehrlich-Str. 40, 60590 Frankfurt, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Theodor Stern Kai 7, 60590 Frankfurt, Germany.,German Centre for Infection Research (DZIF), External partner site, Frankfurt, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt, Germany.,German Center for Cardiovascular Research (DZHK), Germany.,Cardiopulmonary Institute (CPI), Frankfurt, Germany
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9
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Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau VV, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nat Commun 2020; 11:5569. [PMID: 33149120 PMCID: PMC7642426 DOI: 10.1038/s41467-020-19372-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/08/2020] [Indexed: 12/20/2022] Open
Abstract
Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.
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Affiliation(s)
- Linda Schulte
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany
| | - Jiafei Mao
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt, Germany
| | - Julian Reitz
- Institute for Biophysics, Buchmann Institute for Molecular Life Science, Goethe University Frankfurt, Frankfurt, Germany
| | - Sridhar Sreeramulu
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany
| | - Denis Kudlinzki
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany
| | - Victor-Valentin Hodirnau
- Institute for Biophysics, Buchmann Institute for Molecular Life Science, Goethe University Frankfurt, Frankfurt, Germany.,Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Krishna Saxena
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany
| | - Florian Buhr
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany.,Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | | | | | - Achilleas S Frangakis
- Institute for Biophysics, Buchmann Institute for Molecular Life Science, Goethe University Frankfurt, Frankfurt, Germany.
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt, Germany.
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University of Frankfurt, Frankfurt, Germany.
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10
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Vizarraga D, Kawamoto A, Matsumoto U, Illanes R, Pérez-Luque R, Martín J, Mazzolini R, Bierge P, Pich OQ, Espasa M, Sanfeliu I, Esperalba J, Fernández-Huerta M, Scheffer MP, Pinyol J, Frangakis AS, Lluch-Senar M, Mori S, Shibayama K, Kenri T, Kato T, Namba K, Fita I, Miyata M, Aparicio D. Immunodominant proteins P1 and P40/P90 from human pathogen Mycoplasma pneumoniae. Nat Commun 2020; 11:5188. [PMID: 33057023 PMCID: PMC7560827 DOI: 10.1038/s41467-020-18777-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Mycoplasma pneumoniae is a bacterial human pathogen that causes primary atypical pneumonia. M. pneumoniae motility and infectivity are mediated by the immunodominant proteins P1 and P40/P90, which form a transmembrane adhesion complex. Here we report the structure of P1, determined by X-ray crystallography and cryo-electron microscopy, and the X-ray structure of P40/P90. Contrary to what had been suggested, the binding site for sialic acid was found in P40/P90 and not in P1. Genetic and clinical variability concentrates on the N-terminal domain surfaces of P1 and P40/P90. Polyclonal antibodies generated against the mostly conserved C-terminal domain of P1 inhibited adhesion of M. pneumoniae, and serology assays with sera from infected patients were positive when tested against this C-terminal domain. P40/P90 also showed strong reactivity against human infected sera. The architectural elements determined for P1 and P40/P90 open new possibilities in vaccine development against M. pneumoniae infections.
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Affiliation(s)
- David Vizarraga
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Akihiro Kawamoto
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - U Matsumoto
- Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan
| | - Ramiro Illanes
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Rosa Pérez-Luque
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Jesús Martín
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Rocco Mazzolini
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Paula Bierge
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Oscar Q Pich
- Laboratori de Recerca en Microbiologia i Malalties Infeccioses, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain.,Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Mateu Espasa
- Departament de Microbiologia, Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Isabel Sanfeliu
- Departament de Microbiologia, Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, 08208, Sabadell, Spain
| | - Juliana Esperalba
- Departament de Microbiologia, Hospital Universitari Vall d´Hebron, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Miguel Fernández-Huerta
- Departament de Microbiologia, Hospital Universitari Vall d´Hebron, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Margot P Scheffer
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Jaume Pinyol
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Shigetarou Mori
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Kenri
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Makoto Miyata
- Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan. .,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, 558-8585, Japan.
| | - David Aparicio
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain.
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11
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Aparicio D, Scheffer MP, Marcos-Silva M, Vizarraga D, Sprankel L, Ratera M, Weber MS, Seybert A, Torres-Puig S, Gonzalez-Gonzalez L, Reitz J, Querol E, Piñol J, Pich OQ, Fita I, Frangakis AS. Structure and mechanism of the Nap adhesion complex from the human pathogen Mycoplasma genitalium. Nat Commun 2020; 11:2877. [PMID: 32513917 PMCID: PMC7280502 DOI: 10.1038/s41467-020-16511-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/06/2020] [Indexed: 11/09/2022] Open
Abstract
Mycoplasma genitalium is a human pathogen adhering to host target epithelial cells and causing urethritis, cervicitis and pelvic inflammatory disease. Essential for infectivity is a transmembrane adhesion complex called Nap comprising proteins P110 and P140. Here we report the crystal structure of P140 both alone and in complex with the N-terminal domain of P110. By cryo-electron microscopy (cryo-EM) and tomography (cryo-ET) we find closed and open Nap conformations, determined at 9.8 and 15 Å, respectively. Both crystal structures and the cryo-EM structure are found in a closed conformation, where the sialic acid binding site in P110 is occluded. By contrast, the cryo-ET structure shows an open conformation, where the binding site is accessible. Structural information, in combination with functional studies, suggests a mechanism for attachment and release of M. genitalium to and from the host cell receptor, in which Nap conformations alternate to sustain motility and guarantee infectivity.
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Affiliation(s)
- David Aparicio
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC) and Maria de Maeztu Unit of Excellence, Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Margot P Scheffer
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Marina Marcos-Silva
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - David Vizarraga
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC) and Maria de Maeztu Unit of Excellence, Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Lasse Sprankel
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Mercè Ratera
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC) and Maria de Maeztu Unit of Excellence, Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Miriam S Weber
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Anja Seybert
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Sergi Torres-Puig
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Luis Gonzalez-Gonzalez
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Julian Reitz
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany
| | - Enrique Querol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Jaume Piñol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Oscar Q Pich
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Ignacio Fita
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC) and Maria de Maeztu Unit of Excellence, Parc Científic de Barcelona, Baldiri Reixac 10, 08028, Barcelona, Spain.
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue Str. 15, 60438, Frankfurt, Germany.
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12
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Porrati F, Barth S, Sachser R, Dobrovolskiy OV, Seybert A, Frangakis AS, Huth M. Crystalline Niobium Carbide Superconducting Nanowires Prepared by Focused Ion Beam Direct Writing. ACS Nano 2019; 13:6287-6296. [PMID: 31046238 DOI: 10.1021/acsnano.9b00059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Superconducting planar nanostructures are widely used in applications, e.g., for highly sensitive magnetometers and in basic research, e.g., to study finite size effects or vortex dynamics. In contrast, 3D superconducting nanostructures, despite their potential in quantum information processing and nanoelectronics, have been addressed only in a few pioneering experiments. This is due to the complexity of fabricating 3D nanostructures by conventional techniques such as electron-beam lithography and to the scarce number of superconducting materials available for direct-writing techniques, which enable the growth of 3D free-standing nanostructures. Here, we present a comparative study of planar nanowires and free-standing 3D nanowires fabricated by focused electron- and ion (Ga+)-beam induced deposition (FEBID and FIBID) using the precursor Nb(NMe2)3(N- t-Bu). FEBID nanowires contain about 67 atomic percent C, 22 atomic percent N, and 11 atomic percent Nb, while FIBID samples are composed of 43 atomic percent C, 13 atomic percent N, 15.5 atomic percent Ga, and 28.5 atomic percent Nb. Transmission electron microscopy shows that FEBID samples are amorphous, while FIBID samples exhibit a fcc NbC polycrystalline structure, with grains about 15-20 nm in diameter. Electrical transport measurements show that FEBID nanowires are highly resistive following a variable-range-hopping behavior. In contradistinction, FIBID planar nanowires become superconducting at Tc ≈ 5 K. In addition, the critical temperature of free-standing 3D nanowires is as high as Tc ≈ 11 K, which is close to the value of bulk NbC. In conclusion, FIBID-NbC is a promising material for the fabrication of superconducting nanowire single-photon detectors (SNSPD) and for the development of 3D superconductivity with applications in quantum information processing and nanoelectronics.
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Affiliation(s)
- Fabrizio Porrati
- Physikalisches Institut , Goethe-Universität , Max-von-Laue-Strasse 1 , D-60438 Frankfurt am Main , Germany
| | - Sven Barth
- Institute of Materials Chemistry , TU Wien , Getreidemarkt 9/BC/02 , A-1060 Wien , Austria
| | - Roland Sachser
- Physikalisches Institut , Goethe-Universität , Max-von-Laue-Strasse 1 , D-60438 Frankfurt am Main , Germany
| | - Oleksandr V Dobrovolskiy
- Physikalisches Institut , Goethe-Universität , Max-von-Laue-Strasse 1 , D-60438 Frankfurt am Main , Germany
| | - Anja Seybert
- Buchmann Institute for Molecular Life Sciences , Goethe-Universität , Max-von-Laue-Strasse 15 , D-60438 Frankfurt am Main , Germany
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences , Goethe-Universität , Max-von-Laue-Strasse 15 , D-60438 Frankfurt am Main , Germany
| | - Michael Huth
- Physikalisches Institut , Goethe-Universität , Max-von-Laue-Strasse 1 , D-60438 Frankfurt am Main , Germany
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13
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Lewis JD, Caldara AL, Zimmer SE, Stahley SN, Seybold A, Strong NL, Frangakis AS, Levental I, Wahl JK, Mattheyses AL, Sasaki T, Nakabayashi K, Hata K, Matsubara Y, Ishida-Yamamoto A, Amagai M, Kubo A, Kowalczyk AP. The desmosome is a mesoscale lipid raft-like membrane domain. Mol Biol Cell 2019; 30:1390-1405. [PMID: 30943110 PMCID: PMC6724694 DOI: 10.1091/mbc.e18-10-0649] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Desmogleins (Dsgs) are cadherin family adhesion molecules essential for epidermal integrity. Previous studies have shown that desmogleins associate with lipid rafts, but the significance of this association was not clear. Here, we report that the desmoglein transmembrane domain (TMD) is the primary determinant of raft association. Further, we identify a novel mutation in the DSG1 TMD (G562R) that causes severe dermatitis, multiple allergies, and metabolic wasting syndrome. Molecular modeling predicts that this G-to-R mutation shortens the DSG1 TMD, and experiments directly demonstrate that this mutation compromises both lipid raft association and desmosome incorporation. Finally, cryo-electron tomography indicates that the lipid bilayer within the desmosome is ∼10% thicker than adjacent regions of the plasma membrane. These findings suggest that differences in bilayer thickness influence the organization of adhesion molecules within the epithelial plasma membrane, with cadherin TMDs recruited to the desmosome via the establishment of a specialized mesoscale lipid raft-like membrane domain.
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Affiliation(s)
- Joshua D Lewis
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322.,Department of Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322
| | - Amber L Caldara
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322.,Department of Graduate Program in Cancer Biology, Emory University School of Medicine, Atlanta, GA 30322
| | - Stephanie E Zimmer
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322.,Department of Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322
| | - Sara N Stahley
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322.,Department of Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322
| | - Anna Seybold
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60323 Frankfurt, Germany.,Institute for Biophysics, Goethe University Frankfurt, 60323 Frankfurt, Germany
| | - Nicole L Strong
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60323 Frankfurt, Germany.,Institute for Biophysics, Goethe University Frankfurt, 60323 Frankfurt, Germany
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - James K Wahl
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583
| | - Alexa L Mattheyses
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Takashi Sasaki
- Center for Supercentenarian Medical Research, Keio University School of Medicine, Tokyo 160-8582, Japan
| | | | - Kenichiro Hata
- National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yoichi Matsubara
- National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akemi Ishida-Yamamoto
- Department of Dermatology, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Masayuki Amagai
- Department of Dermatology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Akiharu Kubo
- Department of Dermatology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Andrew P Kowalczyk
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322.,Department of Dermatology, Emory University School of Medicine, Atlanta, GA 30322.,Department of Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322.,Department of Graduate Program in Cancer Biology, Emory University School of Medicine, Atlanta, GA 30322
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Hofbauer HF, Gecht M, Fischer SC, Seybert A, Frangakis AS, Stelzer EHK, Covino R, Hummer G, Ernst R. The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1. J Cell Biol 2018; 217:3109-3126. [PMID: 29941475 PMCID: PMC6122994 DOI: 10.1083/jcb.201802027] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/28/2018] [Accepted: 06/18/2018] [Indexed: 01/09/2023] Open
Abstract
Phosphatidic acid (PA) lipids have a dual role as building blocks for membrane biogenesis and as active signaling molecules. This study establishes the molecular details of selective PA recognition by the transcriptional regulator Opi1 from baker’s yeast. A key event in cellular physiology is the decision between membrane biogenesis and fat storage. Phosphatidic acid (PA) is an important intermediate at the branch point of these pathways and is continuously monitored by the transcriptional repressor Opi1 to orchestrate lipid metabolism. In this study, we report on the mechanism of membrane recognition by Opi1 and identify an amphipathic helix (AH) for selective binding of PA over phosphatidylserine (PS). The insertion of the AH into the membrane core renders Opi1 sensitive to the lipid acyl chain composition and provides a means to adjust membrane biogenesis. By rational design of the AH, we tune the membrane-binding properties of Opi1 and control its responsiveness in vivo. Using extensive molecular dynamics simulations, we identify two PA-selective three-finger grips that tightly bind the PA phosphate headgroup while interacting less intimately with PS. This work establishes lipid headgroup selectivity as a new feature in the family of AH-containing membrane property sensors.
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Affiliation(s)
- Harald F Hofbauer
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany .,Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany.,Institute of Medical Biochemistry and Molecular Biology, School of Medicine, University of Saarland, Homburg, Germany
| | - Michael Gecht
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany.,Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Sabine C Fischer
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany.,Physical Biology, Interdisciplinary Center for Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Anja Seybert
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Ernst H K Stelzer
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany.,Physical Biology, Interdisciplinary Center for Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Roberto Covino
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany.,Institute for Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Robert Ernst
- Institute of Medical Biochemistry and Molecular Biology, School of Medicine, University of Saarland, Homburg, Germany
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16
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Seybert A, Gonzalez-Gonzalez L, Scheffer MP, Lluch-Senar M, Mariscal AM, Querol E, Matthaeus F, Piñol J, Frangakis AS. Cryo-electron tomography analyses of terminal organelle mutants suggest the motility mechanism of Mycoplasma genitalium. Mol Microbiol 2018; 108:319-329. [PMID: 29470847 DOI: 10.1111/mmi.13938] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 11/28/2022]
Abstract
The terminal organelle of Mycoplasma genitalium is responsible for bacterial adhesion, motility and pathogenicity. Localized at the cell tip, it comprises an electron-dense core that is anchored to the cell membrane at its distal end and to the cytoplasm at its proximal end. The surface of the terminal organelle is also covered with adhesion proteins. We performed cellular cryoelectron tomography on deletion mutants of eleven proteins that are implicated in building the terminal organelle, to systematically analyze the ultrastructural effects. These data were correlated with microcinematographies, from which the motility patterns can be quantitatively assessed. We visualized diverse phenotypes, ranging from mild to severe cell adhesion, motility and segregation defects. Based on our observations, we propose a double-spring ratchet model for the motility mechanism that explains our current and previous observations. Our model, which expands and integrates the previously suggested inchworm model, allocates specific functions to each of the essential components of this unique bacterial motility system.
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Affiliation(s)
- Anja Seybert
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue Str. 15, Frankfurt 60438, Germany
| | - Luis Gonzalez-Gonzalez
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Margot P Scheffer
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue Str. 15, Frankfurt 60438, Germany
| | - Maria Lluch-Senar
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Ana M Mariscal
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Enrique Querol
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Franziska Matthaeus
- Faculty of Biological Sciences & FIAS, Goethe University Frankfurt, Ruth-Moufang-Straße 1, Frankfurt 60438, Germany
| | - Jaume Piñol
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue Str. 15, Frankfurt 60438, Germany
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17
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Dworak L, Roth S, Scheffer MP, Frangakis AS, Wachtveitl J. A thin CdSe shell boosts the electron transfer from CdTe quantum dots to methylene blue. Nanoscale 2018; 10:2162-2169. [PMID: 29327031 DOI: 10.1039/c7nr08287h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
CdTe core and CdTe/CdSe core/shell quantum dots (QD) are investigated with steady state and time-resolved spectroscopic methods. The coating of the CdTe core with a 0.7 nm thick CdSe shell shifts the lowest exciton absorption band to the red by more than 70 nm making the CdTe/CdSe QD an interesting candidate for application in solar energy conversion. Femtosecond transient absorption measurements are applied to study the photoinduced electron transfer (ET) to the molecular acceptor methylene blue (MB). ET times after single excitation of the QD are determined for different MB : QD ratios. The ET reaction is significantly faster in the case of the MB-CdTe/CdSe QD complexes, indicative of an altered charge distribution in the photoexcited heterostructure with a higher electron density in the CdSe shell. As a result of the efficient absorption of incoming light and the faster ET reaction, the amount of reduced MB in the time resolved experiments is higher for CdTe/CdSe QD compared to CdTe QD.
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Affiliation(s)
- L Dworak
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany.
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18
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Scheffer MP, Gonzalez-Gonzalez L, Seybert A, Ratera M, Kunz M, Valpuesta JM, Fita I, Querol E, Piñol J, Martín-Benito J, Frangakis AS. Structural characterization of the NAP; the major adhesion complex of the human pathogen Mycoplasma genitalium. Mol Microbiol 2017; 105:869-879. [PMID: 28671286 DOI: 10.1111/mmi.13743] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2017] [Indexed: 01/09/2023]
Abstract
Mycoplasma genitalium, the causative agent of non-gonococcal urethritis and pelvic inflammatory disease in humans, is a small eubacterium that lacks a peptidoglycan cell wall. On the surface of its plasma membrane is the major surface adhesion complex, known as NAP that is essential for adhesion and gliding motility of the organism. Here, we have performed cryo-electron tomography of intact cells and detergent permeabilized M. genitalium cell aggregates, providing sub-tomogram averages of free and cell-attached NAPs respectively, revealing a tetrameric complex with two-fold rotational (C2) symmetry. Each NAP has two pairs of globular lobes (named α and β lobes), arranged as a dimer of heterodimers with each lobe connected by a stalk to the cell membrane. The β lobes are larger than the α lobes by 20%. Classification of NAPs showed that the complex can tilt with respect to the cell membrane. A protein complex containing exclusively the proteins P140 and P110, was purified from M. genitalium and was structurally characterized by negative-stain single particle EM reconstruction. The close structural similarity found between intact NAPs and the isolated P140/P110 complexes, shows that dimers of P140/P110 heterodimers are the only components of the extracellular region of intact NAPs in M. genitalium.
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Affiliation(s)
- Margot P Scheffer
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Str. 15, Frankfurt 60438, Germany
| | - Luis Gonzalez-Gonzalez
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Anja Seybert
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Str. 15, Frankfurt 60438, Germany
| | - Mercè Ratera
- Parc Científic de Barcelona, Instituto de Biología Molecular de Barcelona del (IBMB-CSIC), Baldiri i Reixac 10, Barcelona 08028, Spain
| | - Michael Kunz
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Str. 15, Frankfurt 60438, Germany
| | - José M Valpuesta
- Department for Macromolecular Structures, Centro Nacional de Biotecnologıa (CNB-CSIC), Madrid 28049, Spain
| | - Ignacio Fita
- Parc Científic de Barcelona, Instituto de Biología Molecular de Barcelona del (IBMB-CSIC), Baldiri i Reixac 10, Barcelona 08028, Spain
| | - Enrique Querol
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Jaume Piñol
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Jaime Martín-Benito
- Department for Macromolecular Structures, Centro Nacional de Biotecnologıa (CNB-CSIC), Madrid 28049, Spain
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue Str. 15, Frankfurt 60438, Germany
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19
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Lahut S, Gispert S, Ömür Ö, Depboylu C, Seidel K, Domínguez-Bautista JA, Brehm N, Tireli H, Hackmann K, Pirkevi C, Leube B, Ries V, Reim K, Brose N, den Dunnen WF, Johnson M, Wolf Z, Schindewolf M, Schrempf W, Reetz K, Young P, Vadasz D, Frangakis AS, Schröck E, Steinmetz H, Jendrach M, Rüb U, Başak AN, Oertel W, Auburger G. Blood RNA biomarkers in prodromal PARK4 and rapid eye movement sleep behavior disorder show role of complexin 1 loss for risk of Parkinson's disease. Dis Model Mech 2017; 10:619-631. [PMID: 28108469 PMCID: PMC5451169 DOI: 10.1242/dmm.028035] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/12/2017] [Indexed: 12/30/2022] Open
Abstract
Parkinson's disease (PD) is a frequent neurodegenerative process in old age. Accumulation and aggregation of the lipid-binding SNARE complex component α-synuclein (SNCA) underlies this vulnerability and defines stages of disease progression. Determinants of SNCA levels and mechanisms of SNCA neurotoxicity have been intensely investigated. In view of the physiological roles of SNCA in blood to modulate vesicle release, we studied blood samples from a new large pedigree with SNCA gene duplication (PARK4 mutation) to identify effects of SNCA gain of function as potential disease biomarkers. Downregulation of complexin 1 (CPLX1) mRNA was correlated with genotype, but the expression of other Parkinson's disease genes was not. In global RNA-seq profiling of blood from presymptomatic PARK4 indviduals, bioinformatics detected significant upregulations for platelet activation, hemostasis, lipoproteins, endocytosis, lysosome, cytokine, Toll-like receptor signaling and extracellular pathways. In PARK4 platelets, stimulus-triggered degranulation was impaired. Strong SPP1, GZMH and PLTP mRNA upregulations were validated in PARK4. When analysing individuals with rapid eye movement sleep behavior disorder, the most specific known prodromal stage of general PD, only blood CPLX1 levels were altered. Validation experiments confirmed an inverse mutual regulation of SNCA and CPLX1 mRNA levels. In the 3'-UTR of the CPLX1 gene we identified a single nucleotide polymorphism that is significantly associated with PD risk. In summary, our data define CPLX1 as a PD risk factor and provide functional insights into the role and regulation of blood SNCA levels. The new blood biomarkers of PARK4 in this Turkish family might become useful for PD prediction.
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Affiliation(s)
- Suna Lahut
- Experimental Neurology, Goethe University Medical School, Frankfurt/Main 60590, Germany
- NDAL, Boğaziçi University, Istanbul 34342, Turkey
| | - Suzana Gispert
- Experimental Neurology, Goethe University Medical School, Frankfurt/Main 60590, Germany
| | - Özgür Ömür
- Experimental Neurology, Goethe University Medical School, Frankfurt/Main 60590, Germany
- NDAL, Boğaziçi University, Istanbul 34342, Turkey
| | - Candan Depboylu
- Department of Neurology, Philipps University, Baldingerstrasse, Marburg 35043, Germany
| | - Kay Seidel
- Dr Senckenberg Chronomedical Institute, Goethe University, Frankfurt/Main 60590, Germany
| | | | - Nadine Brehm
- Experimental Neurology, Goethe University Medical School, Frankfurt/Main 60590, Germany
| | - Hülya Tireli
- Department of Neurology, Haydarpaşa Numune Training and Research Hospital, Istanbul 34668, Turkey
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | | | - Barbara Leube
- Institute of Human Genetics, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Vincent Ries
- Department of Neurology, Philipps University, Baldingerstrasse, Marburg 35043, Germany
| | - Kerstin Reim
- Department of Molecular Neurobiology and Center for the Molecular Physiology of the Brain, Max Planck Institute of Experimental Medicine, Göttingen 37075, Germany
| | - Nils Brose
- Department of Molecular Neurobiology and Center for the Molecular Physiology of the Brain, Max Planck Institute of Experimental Medicine, Göttingen 37075, Germany
| | - Wilfred F den Dunnen
- Department of Pathology and Medical Biology, Medical Center, University, Groningen 9700 RB, The Netherlands
| | - Madrid Johnson
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University, Frankfurt/Main 60438, Germany
| | - Zsuzsanna Wolf
- Haemophilia Centre, Medical Clinic III, Institute of Immunohaematology and Transfusion Medicine, Goethe University, Frankfurt/Main 60590, Germany
| | - Marc Schindewolf
- Department of Internal Medicine, Division of Vascular Medicine and Hemostaseology, Goethe University, Frankfurt 60590, Germany
| | - Wiebke Schrempf
- Division of Neurodegenerative Diseases, Department of Neurology, Technische Universität, Dresden 01307, Germany
| | - Kathrin Reetz
- Department of Neurology, RWTH Aachen University Hospital, Aachen 52074, Germany
| | - Peter Young
- Department of Sleep Medicine and Neuromuscular Disorders, University Hospital Münster, Münster 48149, Germany
| | - David Vadasz
- Department of Neurology, Philipps University, Baldingerstrasse, Marburg 35043, Germany
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University, Frankfurt/Main 60438, Germany
| | - Evelin Schröck
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Helmuth Steinmetz
- Experimental Neurology, Goethe University Medical School, Frankfurt/Main 60590, Germany
| | - Marina Jendrach
- Experimental Neurology, Goethe University Medical School, Frankfurt/Main 60590, Germany
| | - Udo Rüb
- Dr Senckenberg Chronomedical Institute, Goethe University, Frankfurt/Main 60590, Germany
| | | | - Wolfgang Oertel
- Department of Neurology, Philipps University, Baldingerstrasse, Marburg 35043, Germany
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical School, Frankfurt/Main 60590, Germany
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20
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Grahammer F, Wigge C, Schell C, Kretz O, Patrakka J, Schneider S, Klose M, Kind J, Arnold SJ, Habermann A, Bräuniger R, Rinschen MM, Völker L, Bregenzer A, Rubbenstroth D, Boerries M, Kerjaschki D, Miner JH, Walz G, Benzing T, Fornoni A, Frangakis AS, Huber TB. A flexible, multilayered protein scaffold maintains the slit in between glomerular podocytes. JCI Insight 2016; 1:86177. [PMID: 27430022 DOI: 10.1172/jci.insight.86177] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Vertebrate life critically depends on renal filtration and excretion of low molecular weight waste products. This process is controlled by a specialized cell-cell contact between podocyte foot processes: the slit diaphragm (SD). Using a comprehensive set of targeted KO mice of key SD molecules, we provided genetic, functional, and high-resolution ultrastructural data highlighting a concept of a flexible, dynamic, and multilayered architecture of the SD. Our data indicate that the mammalian SD is composed of NEPHRIN and NEPH1 molecules, while NEPH2 and NEPH3 do not participate in podocyte intercellular junction formation. Unexpectedly, homo- and heteromeric NEPHRIN/NEPH1 complexes are rarely observed. Instead, single NEPH1 molecules appear to form the lower part of the junction close to the glomerular basement membrane with a width of 23 nm, while single NEPHRIN molecules form an adjacent junction more apically with a width of 45 nm. In both cases, the molecules are quasiperiodically spaced 7 nm apart. These structural findings, in combination with the flexibility inherent to the repetitive Ig folds of NEPHRIN and NEPH1, indicate that the SD likely represents a highly dynamic cell-cell contact that forms an adjustable, nonclogging barrier within the renal filtration apparatus.
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Affiliation(s)
- Florian Grahammer
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph Wigge
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Christoph Schell
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine.,Faculty of Biology, and
| | - Oliver Kretz
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,BIOSS Center for Biological Signalling Studies, Albert-Ludwigs University of Freiburg, Freiburg, Germany.,Institute of Anatomy, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jaakko Patrakka
- KI/AZ Integrated Cardio-Metabolic Center (ICMC), Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Simon Schneider
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Klose
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium and.,German Cancer Research Center, Heidelberg, Germany
| | - Julia Kind
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian J Arnold
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,BIOSS Center for Biological Signalling Studies, Albert-Ludwigs University of Freiburg, Freiburg, Germany.,Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anja Habermann
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Ricarda Bräuniger
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Markus M Rinschen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Linus Völker
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Andreas Bregenzer
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dennis Rubbenstroth
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Melanie Boerries
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium and.,German Cancer Research Center, Heidelberg, Germany
| | | | - Jeffrey H Miner
- Renal Division, Washington University, St. Louis, Missouri, USA
| | - Gerd Walz
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Alessia Fornoni
- Division of Nephrology and Katz Family Drug Discovery Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Tobias B Huber
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine.,BIOSS Center for Biological Signalling Studies, Albert-Ludwigs University of Freiburg, Freiburg, Germany.,FRIAS, Freiburg Institute for Advanced Studies and ZBSA, Center for Biological System Analysis, Albert-Ludwigs-University of Freiburg, Germany
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21
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Kunz M, Yu Z, Frangakis AS. M-free: Mask-independent scoring of the reference bias. J Struct Biol 2015; 192:307-11. [DOI: 10.1016/j.jsb.2015.08.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 11/25/2022]
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22
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McEwan DG, Richter B, Claudi B, Wigge C, Wild P, Farhan H, McGourty K, Coxon FP, Franz-Wachtel M, Perdu B, Akutsu M, Habermann A, Kirchof A, Helfrich MH, Odgren PR, Van Hul W, Frangakis AS, Rajalingam K, Macek B, Holden DW, Bumann D, Dikic I. PLEKHM1 regulates Salmonella-containing vacuole biogenesis and infection. Cell Host Microbe 2014; 17:58-71. [PMID: 25500191 DOI: 10.1016/j.chom.2014.11.011] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 10/21/2014] [Accepted: 11/14/2014] [Indexed: 01/13/2023]
Abstract
The host endolysosomal compartment is often manipulated by intracellular bacterial pathogens. Salmonella (Salmonella enterica serovar Typhimurium) secrete numerous effector proteins, including SifA, through a specialized type III secretion system to hijack the host endosomal system and generate the Salmonella-containing vacuole (SCV). To form this replicative niche, Salmonella targets the Rab7 GTPase to recruit host membranes through largely unknown mechanisms. We show that Pleckstrin homology domain-containing protein family member 1 (PLEKHM1), a lysosomal adaptor, is targeted by Salmonella through direct interaction with SifA. By binding the PLEKHM1 PH2 domain, Salmonella utilize a complex containing PLEKHM1, Rab7, and the HOPS tethering complex to mobilize phagolysosomal membranes to the SCV. Depletion of PLEKHM1 causes a profound defect in SCV morphology with multiple bacteria accumulating in enlarged structures and significantly dampens Salmonella proliferation in multiple cell types and mice. Thus, PLEKHM1 provides a critical interface between pathogenic infection and the host endolysosomal system.
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Affiliation(s)
- David G McEwan
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, D-60590 Frankfurt (Main), Germany
| | - Benjamin Richter
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, D-60590 Frankfurt (Main), Germany
| | - Beatrice Claudi
- Infection Biology, Biozentrum, University Basel, Klingelbergstr. 50/70, CH-4056 Basel, Switzerland
| | - Christoph Wigge
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 15, Goethe University 60438 Frankfurt am Main, Germany
| | - Philipp Wild
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, D-60590 Frankfurt (Main), Germany
| | - Hesso Farhan
- Infection Biology, Biozentrum, University Basel, Klingelbergstr. 50/70, CH-4056 Basel, Switzerland; Biotechnology Institute Thurga, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Kieran McGourty
- Centre for Molecular Microbiology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - Fraser P Coxon
- Musculoskeletal Research Programme, Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Bram Perdu
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43B, 2650 Edegem, Belgium
| | - Masato Akutsu
- Infection Biology, Biozentrum, University Basel, Klingelbergstr. 50/70, CH-4056 Basel, Switzerland
| | - Anja Habermann
- Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 15, Goethe University 60438 Frankfurt am Main, Germany
| | - Anja Kirchof
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, D-60590 Frankfurt (Main), Germany
| | - Miep H Helfrich
- Musculoskeletal Research Programme, Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Paul R Odgren
- Deptartment of Cell Biology, S7-242, University of Massachusetts Medical School, North Worcester, MA 01655, USA
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43B, 2650 Edegem, Belgium
| | - Achilleas S Frangakis
- Infection Biology, Biozentrum, University Basel, Klingelbergstr. 50/70, CH-4056 Basel, Switzerland
| | - Krishnaraj Rajalingam
- Molecular Signaling Unit, FZI, Institute for immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, Mainz 55131, Germany
| | - Boris Macek
- Proteome Center Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - David W Holden
- Centre for Molecular Microbiology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - Dirk Bumann
- Infection Biology, Biozentrum, University Basel, Klingelbergstr. 50/70, CH-4056 Basel, Switzerland.
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, D-60590 Frankfurt (Main), Germany; Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 15, Goethe University 60438 Frankfurt am Main, Germany; University of Split, School of Medicine, Department of Immunology and Medical Genetics, Soltanska 2, 21 000 Split, Croatia.
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23
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Kunz M, Frangakis AS. Super-sampling SART with ordered subsets. J Struct Biol 2014; 188:107-15. [DOI: 10.1016/j.jsb.2014.09.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 11/24/2022]
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24
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Yu Z, Frangakis AS. M-free: scoring the reference bias in sub-tomogram averaging and template matching. J Struct Biol 2014; 187:10-19. [PMID: 24859794 DOI: 10.1016/j.jsb.2014.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 04/23/2014] [Accepted: 05/15/2014] [Indexed: 11/27/2022]
Abstract
Cryo-electron tomography provides a snapshot of the cellular proteome. With template matching, the spatial positions of various macromolecular complexes within their native cellular context can be detected. However, the growing awareness of the reference bias introduced by the cross-correlation based approaches, and more importantly the lack of a reliable confidence measurement in the selection of these macromolecular complexes, has restricted the use of these applications. Here we propose a heuristic, in which the reference bias is measured in real space in an analogous way to the R-free value in X-ray crystallography. We measure the reference bias within the mask used to outline the area of the template, and do not modify the template itself. The heuristic works by splitting the mask into a working and a testing area in a volume ratio of 9:1. While the working area is used during the calculation of the cross-correlation function, the information from both areas is explored to calculate the M-free score. We show using artificial data, that the M-free score gives a reliable measure for the reference bias. The heuristic can be applied in template matching and in sub-tomogram averaging. We further test the applicability of the heuristic in tomograms of purified macromolecules, and tomograms of whole Mycoplasma cells.
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Affiliation(s)
- Zhou Yu
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str.15, 60438 Frankfurt am Main, Germany
| | - Achilleas S Frangakis
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str.15, 60438 Frankfurt am Main, Germany.
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25
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Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau VV, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. Correlative light- and electron microscopy with chemical tags. J Struct Biol 2014; 186:205-13. [PMID: 24698954 DOI: 10.1016/j.jsb.2014.03.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x-y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells.
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Affiliation(s)
- Mario Perkovic
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Michael Kunz
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Ulrike Endesfelder
- Goethe University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue Str. 13, 60438 Frankfurt am Main, Germany
| | - Stefanie Bunse
- Max-Planck-Institute for Brain Research, Max-von-Laue Str. 4, 60438 Frankfurt am Main, Germany
| | - Christoph Wigge
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Zhou Yu
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Victor-Valentin Hodirnau
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Margot P Scheffer
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Anja Seybert
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Sebastian Malkusch
- Goethe University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue Str. 13, 60438 Frankfurt am Main, Germany
| | - Erin M Schuman
- Max-Planck-Institute for Brain Research, Max-von-Laue Str. 4, 60438 Frankfurt am Main, Germany
| | - Mike Heilemann
- Goethe University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue Str. 13, 60438 Frankfurt am Main, Germany
| | - Achilleas S Frangakis
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany.
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26
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Geiss CP, Keramisanou D, Sekulic N, Scheffer MP, Black BE, Frangakis AS. CENP-A arrays are more condensed than canonical arrays at low ionic strength. Biophys J 2014; 106:875-82. [PMID: 24559990 PMCID: PMC3944588 DOI: 10.1016/j.bpj.2014.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/02/2014] [Accepted: 01/07/2014] [Indexed: 10/25/2022] Open
Abstract
The centromeric histone H3 variant centromeric protein A (CENP-A), whose sequence is the least conserved among all histone variants, is responsible for specifying the location of the centromere. Here, we present a comprehensive study of CENP-A nucleosome arrays by cryo-electron tomography. We see that CENP-A arrays have different biophysical properties than canonical ones under low ionic conditions, as they are more condensed with a 20% smaller average nearest-neighbor distance and a 30% higher nucleosome density. We find that CENP-A nucleosomes have a predominantly crossed DNA entry/exit site that is narrowed on average by 8°, and they have a propensity to stack face to face. We therefore propose that CENP-A induces geometric constraints at the nucleosome DNA entry/exit site to bring neighboring nucleosomes into close proximity. This specific property of CENP-A may be responsible for generating a fundamental process that contributes to increased chromatin fiber compaction that is propagated under physiological conditions to form centromeric chromatin.
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Affiliation(s)
| | | | - Nikolina Sekulic
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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27
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Al-Amoudi A, Frangakis AS. Three-dimensional visualization of the molecular architecture of cell-cell junctions in situ by cryo-electron tomography of vitreous sections. Methods Mol Biol 2013; 961:97-117. [PMID: 23325637 DOI: 10.1007/978-1-62703-227-8_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Cryo-electron tomography of vitreous sections is currently the only method for visualizing the eukaryotic ultrastructure at close to native state with molecular resolution. Here, we describe the detailed procedure of how to prepare suitable vitreous sections from mammalian skin for cryo-electron tomography, how to align the projection images of the tilt-series, and finally how to perform sub-tomogram averaging on macromolecular complexes with periodic arrangement such as desmosomes.
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Affiliation(s)
- Ashraf Al-Amoudi
- Deutsches Zentrum für Neurodegenerative Erkrankungen e.V, Bonn, Germany.
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28
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Hummel E, Guttmann P, Werner S, Tarek B, Schneider G, Kunz M, Frangakis AS, Westermann B. 3D Ultrastructural organization of whole Chlamydomonas reinhardtii cells studied by nanoscale soft x-ray tomography. PLoS One 2012; 7:e53293. [PMID: 23300909 PMCID: PMC3534036 DOI: 10.1371/journal.pone.0053293] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 11/27/2012] [Indexed: 11/30/2022] Open
Abstract
The complex architecture of their structural elements and compartments is a hallmark of eukaryotic cells. The creation of high resolution models of whole cells has been limited by the relatively low resolution of conventional light microscopes and the requirement for ultrathin sections in transmission electron microscopy. We used soft x-ray tomography to study the 3D ultrastructural organization of whole cells of the unicellular green alga Chlamydomonas reinhardtii at unprecedented spatial resolution. Intact frozen hydrated cells were imaged using the natural x-ray absorption contrast of the sample without any staining. We applied different fiducial-based and fiducial-less alignment procedures for the 3D reconstructions. The reconstructed 3D volumes of the cells show features down to 30 nm in size. The whole cell tomograms reveal ultrastructural details such as nuclear envelope membranes, thylakoids, basal apparatus, and flagellar microtubule doublets. In addition, the x-ray tomograms provide quantitative data from the cell architecture. Therefore, nanoscale soft x-ray tomography is a new valuable tool for numerous qualitative and quantitative applications in plant cell biology.
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Affiliation(s)
- Eric Hummel
- Institut für Zellbiologie, Universität Bayreuth, Bayreuth, Germany.
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29
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Saibil HR, Seybert A, Habermann A, Winkler J, Eltsov M, Perkovic M, Castaño-Diez D, Scheffer MP, Haselmann U, Chlanda P, Lindquist S, Tyedmers J, Frangakis AS. Heritable yeast prions have a highly organized three-dimensional architecture with interfiber structures. Proc Natl Acad Sci U S A 2012; 109:14906-14911. [PMID: 22927413 PMCID: PMC3443181 DOI: 10.1073/pnas.1211976109] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
Yeast prions constitute a "protein-only" mechanism of inheritance that is widely deployed by wild yeast to create diverse phenotypes. One of the best-characterized prions, [PSI(+)], is governed by a conformational change in the prion domain of Sup35, a translation-termination factor. When this domain switches from its normal soluble form to an insoluble amyloid, the ensuing change in protein synthesis creates new traits. Two factors make these traits heritable: (i) the amyloid conformation is self-templating; and (ii) the protein-remodeling factor heat-shock protein (Hsp)104 (acting together with Hsp70 chaperones) partitions the template to daughter cells with high fidelity. Prions formed by several other yeast proteins create their own phenotypes but share the same mechanistic basis of inheritance. Except for the amyloid fibril itself, the cellular architecture underlying these protein-based elements of inheritance is unknown. To study the 3D arrangement of prion assemblies in their cellular context, we examined yeast [PSI(+)] prions in the native, hydrated state in situ, taking advantage of recently developed methods for cryosectioning of vitrified cells. Cryo-electron tomography of the vitrified sections revealed the prion assemblies as aligned bundles of regularly spaced fibrils in the cytoplasm with no bounding structures. Although the fibers were widely spaced, other cellular complexes, such as ribosomes, were excluded from the fibril arrays. Subtomogram image averaging, made possible by the organized nature of the assemblies, uncovered the presence of an additional array of densities between the fibers. We suggest these structures constitute a self-organizing mechanism that coordinates fiber deposition and the regulation of prion inheritance.
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Affiliation(s)
- Helen R. Saibil
- Crystallography and Institute for Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Anja Seybert
- Institut für Biophysik and Frankfurt Institute for Molecular Life Sciences (FMLS), Johann Wolfgang Goethe Universität, D-60438 Frankfurt, Germany
| | - Anja Habermann
- Institut für Biophysik and Frankfurt Institute for Molecular Life Sciences (FMLS), Johann Wolfgang Goethe Universität, D-60438 Frankfurt, Germany
| | - Juliane Winkler
- Center for Molecular Biology of the University of Heidelberg and German Cancer Research Center, DKFZ-ZMBH Alliance, Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Mikhail Eltsov
- Institut für Biophysik and Frankfurt Institute for Molecular Life Sciences (FMLS), Johann Wolfgang Goethe Universität, D-60438 Frankfurt, Germany
- European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany; and
| | - Mario Perkovic
- Institut für Biophysik and Frankfurt Institute for Molecular Life Sciences (FMLS), Johann Wolfgang Goethe Universität, D-60438 Frankfurt, Germany
| | - Daniel Castaño-Diez
- European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany; and
| | - Margot P. Scheffer
- Institut für Biophysik and Frankfurt Institute for Molecular Life Sciences (FMLS), Johann Wolfgang Goethe Universität, D-60438 Frankfurt, Germany
- European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany; and
| | - Uta Haselmann
- European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany; and
| | - Petr Chlanda
- European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany; and
| | - Susan Lindquist
- Whitehead Institute and Howard Hughes Medical Institute (HHMI), Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Jens Tyedmers
- Center for Molecular Biology of the University of Heidelberg and German Cancer Research Center, DKFZ-ZMBH Alliance, Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Achilleas S. Frangakis
- Institut für Biophysik and Frankfurt Institute for Molecular Life Sciences (FMLS), Johann Wolfgang Goethe Universität, D-60438 Frankfurt, Germany
- European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany; and
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30
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Porrati F, Begun E, Winhold M, Schwalb CH, Sachser R, Frangakis AS, Huth M. Room temperature L1₀ phase transformation in binary CoPt nanostructures prepared by focused-electron-beam-induced deposition. Nanotechnology 2012; 23:185702. [PMID: 22499135 DOI: 10.1088/0957-4484/23/18/185702] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
CoPt-C binary alloys have been fabricated by focused-electron-beam-induced deposition by the simultaneous use of Co₂(CO)₈ and (CH₃)₃CH₃C₅H₄Pt as precursor gases. The alloys are made of CoPt nanoparticles embedded in a carbonaceous matrix. TEM investigations show that as-grown samples are in an amorphous phase. By means of a room temperature low-energy electron irradiation treatment the CoPt nanoparticles transform into face-centered tetragonal L1₀ nanocrystallites. In parallel, the system undergoes a transition from a superparamagnetic to a ferromagnetic state at room temperature. By variation of the post-growth irradiation dose the electrical and magneto-transport properties of the alloy can be continuously tuned.
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Affiliation(s)
- F Porrati
- Physikalisches Institut, Goethe-Universität, Max-von-Laue-Strasse 1, D-60438 Frankfurt am Main, Germany.
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31
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Nishino Y, Eltsov M, Joti Y, Ito K, Takata H, Takahashi Y, Hihara S, Frangakis AS, Imamoto N, Ishikawa T, Maeshima K. Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure. EMBO J 2012; 31:1644-53. [PMID: 22343941 DOI: 10.1038/emboj.2012.35] [Citation(s) in RCA: 219] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 01/26/2012] [Indexed: 12/28/2022] Open
Abstract
How a long strand of genomic DNA is compacted into a mitotic chromosome remains one of the basic questions in biology. The nucleosome fibre, in which DNA is wrapped around core histones, has long been assumed to be folded into a 30-nm chromatin fibre and further hierarchical regular structures to form mitotic chromosomes, although the actual existence of these regular structures is controversial. Here, we show that human mitotic HeLa chromosomes are mainly composed of irregularly folded nucleosome fibres rather than 30-nm chromatin fibres. Our comprehensive and quantitative study using cryo-electron microscopy and synchrotron X-ray scattering resolved the long-standing contradictions regarding the existence of 30-nm chromatin structures and detected no regular structure >11 nm. Our finding suggests that the mitotic chromosome consists of irregularly arranged nucleosome fibres, with a fractal nature, which permits a more dynamic and flexible genome organization than would be allowed by static regular structures.
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32
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Bouchet-Marquis C, Zuber B, Glynn AM, Eltsov M, Grabenbauer M, Goldie KN, Thomas D, Frangakis AS, Dubochet J, Chrétien D. Visualization of cell microtubules in their native state. Biol Cell 2012; 99:45-53. [PMID: 17049046 DOI: 10.1042/bc20060081] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND INFORMATION Over the past decades, cryo-electron microscopy of vitrified specimens has yielded a detailed understanding of the tubulin and microtubule structures of samples reassembled in vitro from purified components. However, our knowledge of microtubule structure in vivo remains limited by the chemical treatments commonly used to observe cellular architecture using electron microscopy. RESULTS We used cryo-electron microscopy and cryo-electron tomography of vitreous sections to investigate the ultrastructure of microtubules in their cellular context. Vitreous sections were obtained from organotypic slices of rat hippocampus and from Chinese-hamster ovary cells in culture. Microtubules revealed their protofilament ultrastructure, polarity and, in the most favourable cases, molecular details comparable with those visualized in three-dimensional reconstructions of microtubules reassembled in vitro from purified tubulin. The resolution of the tomograms was estimated to be approx. 4 nm, which enabled the detection of luminal particles of approx. 6 nm in diameter inside microtubules. CONCLUSIONS The present study provides a first step towards a description of microtubules, in addition to other macromolecular assemblies, in an unperturbed cellular context at the molecular level. As the resolution appears to be similar to that obtainable with plunge-frozen samples, it should allow for the in vivo identification of larger macromolecular assemblies in vitreous sections of whole cells and tissues.
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Affiliation(s)
- Cédric Bouchet-Marquis
- Laboratory for Ultrastructural Analysis, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland
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33
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Winhold M, Schwalb CH, Porrati F, Sachser R, Frangakis AS, Kämpken B, Terfort A, Auner N, Huth M. Binary Pt-Si nanostructures prepared by focused electron-beam-induced deposition. ACS Nano 2011; 5:9675-81. [PMID: 22050515 DOI: 10.1021/nn203134a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Binary systems of Pt-Si are prepared by electron-beam-induced deposition using the two precursors, trimethyl(methylcyclopentadienyl)platinum(IV) (MeCpPt(Me)(3)) and neopentasilane (Si(SiH(3))(4)), simultaneously. By varying the relative flux of the two precursors during deposition, we are able to study composites containing platinum and silicon in different ratios by means of energy-dispersive X-ray spectroscopy, atomic force microscopy, electrical transport measurements, and transmission electron microscopy. The results show strong evidence for the formation of a binary, metastable Pt(2)Si(3) phase, leading to a maximum in the conductivity for a Si/Pt ratio of 3:2.
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Affiliation(s)
- Marcel Winhold
- Physikalisches Institut, Goethe Universität, 60438 Frankfurt am Main, Germany
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34
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Scheffer MP, Eltsov M, Bednar J, Frangakis AS. Nucleosomes stacked with aligned dyad axes are found in native compact chromatin in vitro. J Struct Biol 2011; 178:207-14. [PMID: 22138167 DOI: 10.1016/j.jsb.2011.11.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 11/10/2011] [Accepted: 11/15/2011] [Indexed: 11/28/2022]
Abstract
In this study, electron tomograms of plunge-frozen isolated chromatin in both open and compacted form were recorded. We have resolved individual nucleosomes in these tomograms in order to provide a 3D view of the arrangement of nucleosomes within chromatin fibers at different compaction states. With an optimized template matching procedure we obtained accurate positions and orientations of nucleosomes in open chromatin in "low-salt" conditions (5 mM NaCl). The mean value of the planar angle between three consecutive nucleosomes is 70°, and the mean center-to-center distance between consecutive nucleosomes is 22.3 nm. Since the template matching approach was not effective in crowded conditions, for nucleosome detection in compact fibers (40 mM NaCl and 1 mM MgCl(2)) we developed the nucleosome detection procedure based on the watershed algorithm, followed by sub-tomogram alignment, averaging, and classification by Principal Components Analysis. We find that in compact chromatin the nucleosomes are arranged with a predominant face-to-face stacking organization, which has not been previously shown for native isolated chromatin. Although the path of the DNA cannot be directly seen in compact conditions, it is evident that the nucleosomes stack with their dyad axis aligned in forming a "double track" conformation which is a consequence of DNA joining adjacent nucleosome stacks. Our data suggests that nucleosome stacking is an important mechanism for generating chromatin compaction in vivo.
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Affiliation(s)
- Margot P Scheffer
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.
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35
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Yu Z, Frangakis AS. Classification of electron sub-tomograms with neural networks and its application to template-matching. J Struct Biol 2011; 174:494-504. [PMID: 21382496 DOI: 10.1016/j.jsb.2011.02.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 02/25/2011] [Accepted: 02/28/2011] [Indexed: 11/26/2022]
Abstract
Classification of electron sub-tomograms is a challenging task, due the missing-wedge and the low signal-to-noise ratio of the data. Classification algorithms tend to classify data according to their orientation to the missing-wedge, rather than to the underlying signal. Here we use a neural network approach, called the Kernel Density Estimator Self-Organizing Map (KerDenSOM3D), which we have implemented in three-dimensions (3D), also having compensated for the missing-wedge, and we comprehensively compare it to other classification methods. For this purpose, we use various simulated macromolecules, as well as tomographically reconstructed in vitro GroEL and GroEL/GroES molecules. We show that the performance of this classification method is superior to previously used algorithms. Furthermore, we show how this algorithm can be used to provide an initial cross-validation of template-matching approaches. For the example of sub-tomogram classification extracted from cellular tomograms of Mycoplasma pneumonia and Spiroplasma melliferum cells, we show the bias of template-matching, and by using differing search and classification areas, we demonstrate how the bias can be significantly reduced.
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Affiliation(s)
- Zhou Yu
- Frankfurt Institute for Molecular Life Sciences and Institute of Biophysics, Goethe University Frankfurt, Germany
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36
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Trépout S, Taveau JC, Benabdelhak H, Granier T, Ducruix A, Frangakis AS, Lambert O. Structure of reconstituted bacterial membrane efflux pump by cryo-electron tomography. Biochim Biophys Acta 2010; 1798:1953-60. [PMID: 20599691 DOI: 10.1016/j.bbamem.2010.06.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 06/07/2010] [Accepted: 06/18/2010] [Indexed: 11/19/2022]
Abstract
Complexes of OprM and MexA, two proteins of the MexA-MexB-OprM multidrug efflux pump from Pseudomonas aeruginosa, an opportunistic Gram-negative bacterium, were reconstituted into proteoliposomes by detergent removal. Stacks of protein layers with a constant height of 21nm, separated by lipid bilayers, were obtained at stoichiometry of 1:1 (w/w). Using cryo-electron microscopy and tomography, we showed that these protein layers were composed of MexA-OprM complexes self-assembled into regular arrays. Image processing of extracted sub-tomograms depicted the architecture of the bipartite complex sandwiched between two lipid bilayers, representing an environment close to that of the native whole pump (i.e. anchored between outer and inner membranes of P. aeruginosa). The MexA-OprM complex appeared as a cylindrical structure in which we were able to identify the OprM molecule and the MexA moiety. MexA molecules have a cylindrical shape prolonging the periplasmic helices of OprM, and widening near the lipid bilayer. The flared part is likely composed of two MexA domains adjacent to the lipid bilayer, although their precise organization was not reachable mainly due to their flexibility. Moreover, the intermembrane distance of 21nm indicated that the height of the bipartite complex is larger than that of the tripartite AcrA-AcrB-TolC built-up model in which TolC and AcrB are docked into contact. We proposed a model of MexA-OprM taking into account features of previous models based on AcrA-AcrB-TolC and our structural results providing clues to a possible mechanism of tripartite system assembly.
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Affiliation(s)
- Sylvain Trépout
- CBMN UMR 5248 CNRS-Université Bordeaux-ENITAB, IECB, Avenue des Facultés, F-33405 Talence, France
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37
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Castaño-Díez D, Scheffer M, Al-Amoudi A, Frangakis AS. Alignator: a GPU powered software package for robust fiducial-less alignment of cryo tilt-series. J Struct Biol 2010; 170:117-26. [PMID: 20117216 DOI: 10.1016/j.jsb.2010.01.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 01/21/2010] [Accepted: 01/23/2010] [Indexed: 11/17/2022]
Abstract
The robust alignment of tilt-series collected for cryo-electron tomography in the absence of fiducial markers, is a problem that, especially for tilt-series of vitreous sections, still represents a significant challenge. Here we present a complete software package that implements a cross-correlation-based procedure that tracks similar image features that are present in several micrographs and explores them implicitly as substitutes for fiducials like gold beads and quantum dots. The added value compared to previous approaches, is that the algorithm explores a huge number of random positions, which are tracked on several micrographs, while being able to identify trace failures, using a cross-validation procedure based on the 3D marker model of the tilt-series. Furthermore, this method allows the reliable identification of areas which behave as a rigid body during the tilt-series and hence addresses specific difficulties for the alignment of vitreous sections, by correcting practical caveats. The resulting alignments can attain sub-pixel precision at the local level and is able to yield a substantial number of usable tilt-series (around 60%). In principle, the algorithm has the potential to run in a fully automated fashion, and could be used to align any tilt-series directly from the microscope. Finally, we have significantly improved the user interface and implemented the source code on the graphics processing unit (GPU) to accelerate the computations.
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Affiliation(s)
- Daniel Castaño-Díez
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
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38
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Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC. Proteome organization in a genome-reduced bacterium. Science 2009; 326:1235-40. [PMID: 19965468 DOI: 10.1126/science.1176343] [Citation(s) in RCA: 354] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The genome of Mycoplasma pneumoniae is among the smallest found in self-replicating organisms. To study the basic principles of bacterial proteome organization, we used tandem affinity purification-mass spectrometry (TAP-MS) in a proteome-wide screen. The analysis revealed 62 homomultimeric and 116 heteromultimeric soluble protein complexes, of which the majority are novel. About a third of the heteromultimeric complexes show higher levels of proteome organization, including assembly into larger, multiprotein complex entities, suggesting sequential steps in biological processes, and extensive sharing of components, implying protein multifunctionality. Incorporation of structural models for 484 proteins, single-particle electron microscopy, and cellular electron tomograms provided supporting structural details for this proteome organization. The data set provides a blueprint of the minimal cellular machinery required for life.
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Affiliation(s)
- Sebastian Kühner
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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39
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Janes PW, Wimmer-Kleikamp SH, Frangakis AS, Treble K, Griesshaber B, Sabet O, Grabenbauer M, Ting AY, Saftig P, Bastiaens PI, Lackmann M. Cytoplasmic relaxation of active Eph controls ephrin shedding by ADAM10. PLoS Biol 2009; 7:e1000215. [PMID: 19823572 PMCID: PMC2753297 DOI: 10.1371/journal.pbio.1000215] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 09/01/2009] [Indexed: 11/18/2022] Open
Abstract
Novel imaging strategies reveal a conformational shift in a receptor tyrosine kinase domain that controls ligand shedding by an ADAM metalloprotease. Release of cell surface-bound ligands by A-Disintegrin-And-Metalloprotease (ADAM) transmembrane metalloproteases is essential for signalling by cytokine, cell adhesion, and tyrosine kinase receptors. For Eph receptor ligands, it provides the switch between cell-cell adhesion and repulsion. Ligand shedding is tightly controlled by intrinsic tyrosine kinase activity, which for Eph receptors relies on the release of an inhibitory interaction of the cytoplasmic juxtamembrane segment with the kinase domain. However, a mechanism linking kinase and sheddase activities had remained elusive. We demonstrate that it is a membrane-proximal localisation of the latent kinase domain that prevents ephrin ligand shedding in trans. Fluorescence lifetime imaging microscopy and electron tomography reveal that activation extends the Eph receptor tyrosine kinase intracellular domain away from the cell membrane into a conformation that facilitates productive association with ADAM10. Accordingly, EphA3 mutants with constitutively-released kinase domains efficiently support shedding, even when their kinase is disabled. Our data suggest that this phosphorylation-activated conformational switch of EphA3 directly controls ADAM-mediated shedding. The Eph transmembrane receptors are part of the receptor tyrosine kinase family and play important roles in communication between neighbouring cells. An Eph receptor binds to its ligand, membrane-tethered ephrin, on a neighbouring cell so as to form a stable complex and activate downstream signalling events. One such event is regulation of ADAM10, a transmembrane protease of the ADAM metalloprotease family, which provides a feedback mechanism to Eph signalling. ADAM10 is located on Eph-expressing cells and cleaves ephrin from its membrane tether on the opposite cell (through its so-called sheddase activity), thereby separating the cell-cell connection and allowing the signalling complex to internalise. In other biological contexts, activity of the ADAM metalloprotease family underlies signalling mechanisms such as oncogenic EGF-receptor transactivation, adhesion molecule shedding and cytokine/chemokine release. In general, ADAM function is enhanced when receptor tyrosine signalling is active and repressed when tyrosine kinase signalling is inhibited. However, the mechanism through which receptor tyrosine kinase signalling regulates ADAM10, have remained elusive. By combining fluorescence lifetime imaging microscopy (FLIM) and electron microscopic tomography of EphA3, we have demonstrated in live cells at molecular resolution that tyrosine phosphorylation of activated EphA3 triggers a measurable movement of the kinase domain away from the plasma membrane. Only this conformation of the EphA3 kinase domain away from the plasma membrane permits ADAM10 to come close enough to EphA3 so that it can reach its tightly EphA3-bound substrate, ephrin-A5. Our findings delineate a new regulatory concept in cell-cell communication, whereby control over proteolytic sheddase activity is provided by an activation-induced switch in the conformation of the cytoplasmic domain of a receptor tyrosine kinase, rather than by a cytosolic signalling pathway.
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Affiliation(s)
- Peter W. Janes
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
| | - Sabine H. Wimmer-Kleikamp
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
- European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Kane Treble
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
| | - Bettina Griesshaber
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
| | - Ola Sabet
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Markus Grabenbauer
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Alice Y. Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Paul Saftig
- Biochemical Institute, Christian-Albrecht-University, Kiel, Germany
| | - Philippe I. Bastiaens
- European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- * E-mail: (PIB); (ML)
| | - Martin Lackmann
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
- * E-mail: (PIB); (ML)
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40
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Pruggnaller S, Mayr M, Frangakis AS. A visualization and segmentation toolbox for electron microscopy. J Struct Biol 2008; 164:161-5. [DOI: 10.1016/j.jsb.2008.05.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 05/09/2008] [Accepted: 05/09/2008] [Indexed: 11/28/2022]
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41
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Castaño-Díez D, Al-Amoudi A, Glynn AM, Seybert A, Frangakis AS. Reprint of "Fiducial-less alignment of cryo-sections" [J. Struct. Biol. 159 (2007) 413-423]. J Struct Biol 2008; 161:249-59. [PMID: 18342740 DOI: 10.1016/s1047-8477(08)00060-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 04/17/2007] [Accepted: 04/24/2007] [Indexed: 11/27/2022]
Abstract
Cryo-electron tomography of vitreous sections is currently the most promising technique for visualizing arbitrary regions of eukaryotic cells or tissue at molecular resolution. Despite significant progress in the sample preparation techniques over the past few years, the three dimensional reconstruction using electron tomography is not as simple as in plunge frozen samples for various reasons, but mainly due to the effects of irradiation on the sections and the resulting poor alignment. Here, we present a new algorithm, which can provide a useful three-dimensional marker model after investigation of hundreds to thousands of observations calculated using local cross-correlation throughout the tilt series. The observations are chosen according to their coherence to a particular model and assigned to virtual markers. Through this type of measurement a merit figure can be calculated, precisely estimating the quality of the reconstruction. The merit figures of this alignment method are comparable to those obtained with plunge frozen samples using fiducial gold markers. An additional advantage of the algorithm is the implicit detection of areas in the sections that behave as rigid bodies and can thus be properly reconstructed.
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Affiliation(s)
- Daniel Castaño-Díez
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.
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42
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Al-Amoudi A, Díez DC, Betts MJ, Frangakis AS. The molecular architecture of cadherins in native epidermal desmosomes. Nature 2007; 450:832-7. [DOI: 10.1038/nature05994] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Accepted: 10/11/2007] [Indexed: 11/09/2022]
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43
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Förster F, Pruggnaller S, Seybert A, Frangakis AS. Classification of cryo-electron sub-tomograms using constrained correlation. J Struct Biol 2007; 161:276-86. [PMID: 17720536 DOI: 10.1016/j.jsb.2007.07.006] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 07/02/2007] [Accepted: 07/10/2007] [Indexed: 10/23/2022]
Abstract
Cryo-electron tomography (CET) is currently the only three-dimensional imaging technique capable of visualizing macromolecules in their cellular context at close-to-native conditions with a resolution in the nanometer range. An important component for the analysis of the data is their classification, which should discriminate among various macromolecules, conformational changes and interaction partners. Missing structure factors, typically in a wedge-shaped region in Fourier space if single-axis tilting is performed, hamper classification of cryo-electron tomographic data. Here, we describe a classification method for three-dimensional (3D) sub-tomograms extracted from cryo-electron tomograms, which takes the missing wedge into account and provides reliable results. The similarity of the individually aligned sub-tomograms is scored by constrained correlation. Subsequently, they are clustered based on their pairwise correlation values. In order to demonstrate the feasibility of this approach, we apply the proposed method to simulated tomographic data of the chaperone thermosome in different conformations. By comparison of the principal components of the resulting matrix we show that the proposed metric is significantly less prone to the orientation of the missing wedge compared to the unconstrained correlation. Moreover, we apply our classification method to an experimental dataset of GroEL with and without GroES, where we achieve a distinct discrimination between the putative GroEL and GroEL/GroES complexes.
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Affiliation(s)
- Friedrich Förster
- Max-Planck-Institut für Biochemie, Molekulare Strukturbiologie, Am Klopferspitz 18, 82152 Martinsried, Germany.
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44
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Castaño-Díez D, Al-Amoudi A, Glynn AM, Seybert A, Frangakis AS. Fiducial-less alignment of cryo-sections. J Struct Biol 2007; 159:413-23. [PMID: 17651988 DOI: 10.1016/j.jsb.2007.04.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 04/17/2007] [Accepted: 04/24/2007] [Indexed: 10/23/2022]
Abstract
Cryo-electron tomography of vitreous sections is currently the most promising technique for visualizing arbitrary regions of eukaryotic cells or tissue at molecular resolution. Despite significant progress in the sample preparation techniques over the past few years, the three dimensional reconstruction using electron tomography is not as simple as in plunge frozen samples for various reasons, but mainly due to the effects of irradiation on the sections and the resulting poor alignment. Here, we present a new algorithm, which can provide a useful three-dimensional marker model after investigation of hundreds to thousands of observations calculated using local cross-correlation throughout the tilt series. The observations are chosen according to their coherence to a particular model and assigned to virtual markers. Through this type of measurement a merit figure can be calculated, precisely estimating the quality of the reconstruction. The merit figures of this alignment method are comparable to those obtained with plunge frozen samples using fiducial gold markers. An additional advantage of the algorithm is the implicit detection of areas in the sections that behave as rigid bodies and can thus be properly reconstructed.
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Affiliation(s)
- Daniel Castaño-Díez
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.
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45
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Ravelli RBG, Haselmann-Weiss U, McGeehan JE, McCarthy AA, Marquez JA, Antony C, Frangakis AS, Stranzl G. Plastic-embedded protein crystals. J Synchrotron Radiat 2007; 14:128-32. [PMID: 17211079 DOI: 10.1107/s0909049506043111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Accepted: 10/17/2006] [Indexed: 05/13/2023]
Abstract
Rapid vitrification followed by the replacement of the vitrified water by a solvent (freeze substitution) and then resin is a widely used procedure for preparing biological samples for electron microscopy. The resulting plastic-embedded samples permit convenient room-temperature sectioning (microtomy) and can yield well preserved cellular structures. Here this procedure has been applied to crystalline protein samples, and it is shown that it is possible to freeze-substitute vitrified crystals while preserving some of their original diffraction properties. The plastic-embedded crystals were used to collect a series of complete room-temperature data sets at a powerful macromolecular crystallography synchrotron beamline. Whereas one normally observes specific damage to disulfide bonds upon X-ray radiation, no such damage was seen for the plastic-embedded sample. The X-ray diffraction data allowed an initial atomic analysis to be made of the effects of freeze-substitution and plastic embedding on biological samples.
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Affiliation(s)
- Raimond B G Ravelli
- EMBL Grenoble, 6 rue Jules Horowitz, BP 181, 38042 Grenoble CEDEX 9, France.
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46
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Castaño Díez D, Mueller H, Frangakis AS. Implementation and performance evaluation of reconstruction algorithms on graphics processors. J Struct Biol 2007; 157:288-95. [PMID: 17029985 DOI: 10.1016/j.jsb.2006.08.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Revised: 08/16/2006] [Accepted: 08/25/2006] [Indexed: 10/24/2022]
Abstract
The high-throughput needs in electron tomography and in single particle analysis have driven the parallel implementation of several reconstruction algorithms and software packages on computing clusters. Here, we report on the implementation of popular reconstruction algorithms as weighted backprojection, simultaneous iterative reconstruction technique (SIRT) and simultaneous algebraic reconstruction technique (SART) on common graphics processors (GPUs). The speed gain achieved on the GPUs is in the order of sixty (60x) to eighty (80x) times, compared to the performance of a single central processing unit (CPU), which is comparable to the acceleration achieved on a medium-range computing cluster. This acceleration of the reconstruction is caused by the highly specialized architecture of the GPU. Further, we show that the quality of the reconstruction on the GPU is comparable to the CPU. We present detailed flow-chart diagrams of the implementation. The reconstruction software does not require special hardware apart from the commercially available graphics cards and could be easily integrated in software packages like SPIDER, XMIPP, TOM-Package and others.
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Affiliation(s)
- Daniel Castaño Díez
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.
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47
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Seybert A, Herrmann R, Frangakis AS. Structural analysis of Mycoplasma pneumoniae by cryo-electron tomography. J Struct Biol 2006; 156:342-54. [PMID: 16875842 DOI: 10.1016/j.jsb.2006.04.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 04/24/2006] [Accepted: 04/28/2006] [Indexed: 11/21/2022]
Abstract
Bacteria of the genus Mycoplasma lack obvious homologs of prokaryotic or eukaryotic cytoskeletal, as well as motility-related genes (except FtsZ). Nevertheless, they maintain characteristic cell shapes and show adhesion and gliding abilities on both artificial surfaces and cells. Earlier genetic, biochemical, and electron microscopic analyses have shown that the tip structure, located at the tapered end of gliding mycoplasmas, is indispensable for this behavior. In this study, we have analyzed the fine structure of the Mycoplasma pneumoniae tip by cryo-electron tomography. We show that the central rod is surrounded by quasi-periodical electron-dense macromolecular complexes. Additional complexes are located at the distal end of the rod which connect the rod to the cytoplasmic membrane. Furthermore, we detect a structure at the proximal end of the rod that attaches the rod to the cell membrane. The surface protein complexes have been mapped in detail and their distribution on the cell surface has been visualized. Since the rod structures were detected at a close to native state of the cells, they allow us to build a hypothesis describing the motility mechanism of M. pneumoniae. Finally, we have evaluated the ribosome density of the organism by a template matching approach, whereby the reliability of the detection was supported by a comparative bioinformatics analysis.
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Affiliation(s)
- Anja Seybert
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
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48
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Abstract
While the absence of any cytoskeleton was once recognized as a distinguishing feature of prokaryotes, it is now clear that a number of different bacterial proteins do form filaments in vivo. Despite the critical roles these proteins play in cell shape, genome segregation and cell division, molecular mechanisms have remained obscure in part for lack of electron microscopy-resolution images where these filaments can be seen acting within their cellular context. Here, electron cryotomography was used to image the widely studied model prokaryote Caulobacter crescentus in an intact, near-native state, producing three-dimensional reconstructions of these cells with unprecedented clarity and fidelity. We observed many instances of large filament bundles in various locations throughout the cell and at different stages of the cell cycle. The bundles appear to fall into four major classes based on shape and location, referred to here as 'inner curvature', 'cytoplasmic', 'polar' and 'ring-like'. In an attempt to identify at least some of the filaments, we imaged cells where crescentin and MreB filaments would not be present. The inner curvature and cytoplasmic bundles persisted, which together with their localization patterns, suggest that they are composed of as-yet unidentified cytoskeletal proteins. Thus bacterial filaments are frequently found as bundles, and their variety and abundance is greater than previously suspected.
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Affiliation(s)
- Ariane Briegel
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
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Díez DC, Seybert A, Frangakis AS. Tilt-series and electron microscope alignment for the correction of the non-perpendicularity of beam and tilt-axis. J Struct Biol 2006; 154:195-205. [PMID: 16503168 DOI: 10.1016/j.jsb.2005.12.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 12/19/2005] [Accepted: 12/20/2005] [Indexed: 11/19/2022]
Abstract
In electron tomography the sample is tilted in the electron microscope and projections are recorded at different viewing angles. In the correct geometric setting, the tilt-axis of the object under scrutiny is perpendicular to the beam direction. However, we will demonstrate that this does not necessarily apply to all electron microscopes equipped with the default column alignment. The resulting effect is that a conical tilt is performed, which has to be considered in the reconstruction to avoid artifacts and to improve the resolution. A novel solution, with significantly improved convergence properties, will be introduced for calculating the three-dimensional marker model, which is necessary for the alignment of the tilt-series. Thereby, the angle between the beam direction and the tilt-axis is calculated, together with other geometrical distortions, like magnification and rotation changes, and incorporated in the reconstruction. Hereby, artifacts can be eliminated at the image processing basis, and the resolution can be significantly improved at the medium to high range frequencies. Synthetical and real data are used to demonstrate the obstructions caused by this effect and the quality improvement of the reconstructions. Finally, we also present a way to align the hardware of the microscope to correct for the non-perpendicularity between the beam direction and the tilt-axis, which is specifically tailored for tomographic applications.
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Affiliation(s)
- Daniel Castaño Díez
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.
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Abstract
Evidence has accumulated recently that not only eukaryotes but also bacteria can have a cytoskeleton. We used cryo-electron tomography to study the three-dimensional structure of Spiroplasma melliferum cells in a close-to-native state at approximately 4-nanometer resolution. We showed that these cells possess two types of filaments arranged in three parallel ribbons underneath the cell membrane. These two filamentous structures are built of the fibril protein and possibly the actin-like protein MreB. On the basis of our structural data, we could model the motility modes of these cells and explain how helical Mollicutes can propel themselves by means of coordinated length changes of their cytoskeletal ribbons.
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Affiliation(s)
- Julia Kürner
- Department of Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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