1
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Egelman EH. Helical reconstruction, again. Curr Opin Struct Biol 2024; 85:102788. [PMID: 38401399 PMCID: PMC10923117 DOI: 10.1016/j.sbi.2024.102788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/23/2024] [Accepted: 02/02/2024] [Indexed: 02/26/2024]
Abstract
Many protein and nucleoprotein complexes exist as helical polymers. As a result, much effort has been invested in developing methods for using electron microscopy to determine the structure of these assemblies. With the revolution in cryo-electron microscopy (cryo-EM), it has now become routine to reach a near-atomic level of resolution for these structures, and it is the exception when this is not possible. However, the greatest challenge is frequently determining the correct symmetry. This review focuses on why this can be so difficult and the current absence of a better approach than trial-and-error.
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Affiliation(s)
- Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22903, USA.
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2
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Mann D, Fromm SA, Martinez-Sanchez A, Gopaldass N, Choy R, Mayer A, Sachse C. Atg18 oligomer organization in assembled tubes and on lipid membrane scaffolds. Nat Commun 2023; 14:8086. [PMID: 38057304 DOI: 10.1038/s41467-023-43460-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/09/2023] [Indexed: 12/08/2023] Open
Abstract
Autophagy-related protein 18 (Atg18) participates in the elongation of early autophagosomal structures in concert with Atg2 and Atg9 complexes. How Atg18 contributes to the structural coordination of Atg2 and Atg9 at the isolation membrane remains to be understood. Here, we determined the cryo-EM structures of Atg18 organized in helical tubes, Atg18 oligomers in solution as well as on lipid membrane scaffolds. The helical assembly is composed of Atg18 tetramers forming a lozenge cylindrical lattice with remarkable structural similarity to the COPII outer coat. When reconstituted with lipid membranes, using subtomogram averaging we determined tilted Atg18 dimer structures bridging two juxtaposed lipid membranes spaced apart by 80 Å. Moreover, lipid reconstitution experiments further delineate the contributions of Atg18's FRRG motif and the amphipathic helical extension in membrane interaction. The observed structural plasticity of Atg18's oligomeric organization and membrane binding properties provide a molecular framework for the positioning of downstream components of the autophagy machinery.
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Affiliation(s)
- Daniel Mann
- Ernst-Ruska Centre 3/Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
- Institute for Biological Information Processing 6/Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
| | - Simon A Fromm
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antonio Martinez-Sanchez
- Department of Information and Communications Engineering, Faculty of Computers Sciences, University of Murcia, Murcia, Spain
| | - Navin Gopaldass
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Ramona Choy
- Ernst-Ruska Centre 3/Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
- Institute for Biological Information Processing 6/Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
| | - Andreas Mayer
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Carsten Sachse
- Ernst-Ruska Centre 3/Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany.
- Institute for Biological Information Processing 6/Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany.
- Department of Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, Germany.
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3
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Bethel NP, Borst AJ, Parmeggiani F, Bick MJ, Brunette TJ, Nguyen H, Kang A, Bera AK, Carter L, Miranda MC, Kibler RD, Lamb M, Li X, Sankaran B, Baker D. Precisely patterned nanofibres made from extendable protein multiplexes. Nat Chem 2023; 15:1664-1671. [PMID: 37667012 PMCID: PMC10695826 DOI: 10.1038/s41557-023-01314-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/04/2023] [Indexed: 09/06/2023]
Abstract
Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C2 to C8 and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.
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Affiliation(s)
- Neville P Bethel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Andrew J Borst
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Fabio Parmeggiani
- School of Chemistry, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
- Bristol Biodesign Institute, University of Bristol, Bristol, UK
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ryan D Kibler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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4
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Li D, Jiang W. Classification of helical polymers with deep-learning language models. J Struct Biol 2023; 215:108041. [PMID: 37939748 PMCID: PMC10843845 DOI: 10.1016/j.jsb.2023.108041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/11/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Many macromolecules in biological systems exist in the form of helical polymers. However, the inherent polymorphism and heterogeneity of samples complicate the reconstruction of helical polymers from cryo-EM images. Currently, available 2D classification methods are effective at separating particles of interest from contaminants, but they do not effectively differentiate between polymorphs, resulting in heterogeneity in the 2D classes. As such, it is crucial to develop a method that can computationally divide a dataset of polymorphic helical structures into homogenous subsets. In this work, we utilized deep-learning language models to embed the filaments as vectors in hyperspace and group them into clusters. Tests with both simulated and experimental datasets have demonstrated that our method - HLM (Helical classification with Language Model) can effectively distinguish different types of filaments, in the presence of many contaminants and low signal-to-noise ratios. We also demonstrate that HLM can isolate homogeneous subsets of particles from a publicly available dataset, resulting in the discovery of a previously unreported filament variant with an extra density around the tau filaments.
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Affiliation(s)
- Daoyi Li
- Department of Biological Sciences, Purdue University
| | - Wen Jiang
- Department of Biological Sciences, Purdue University.
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5
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Gu Y, Guberman-Pfeffer MJ, Srikanth V, Shen C, Giska F, Gupta K, Londer Y, Samatey FA, Batista VS, Malvankar NS. Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity. Nat Microbiol 2023; 8:284-298. [PMID: 36732469 PMCID: PMC9999484 DOI: 10.1038/s41564-022-01315-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 12/20/2022] [Indexed: 02/04/2023]
Abstract
OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm-1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome essential for the formation of high-current-density biofilms that require long-distance (>10 µm) extracellular electron transport. However, the mechanisms underlying OmcZ nanowire assembly and high conductivity are unknown. Here we report a 3.5-Å-resolution cryogenic electron microscopy structure for OmcZ nanowires. Our structure reveals linear and closely stacked haems that may account for conductivity. Surface-exposed haems and charge interactions explain how OmcZ nanowires bind to diverse extracellular electron acceptors and how organization of nanowire network re-arranges in different biochemical environments. In vitro studies explain how G. sulfurreducens employ a serine protease to control the assembly of OmcZ monomers into nanowires. We find that both OmcZ and serine protease are widespread in environmentally important bacteria and archaea, thus establishing a prevalence of nanowire biogenesis across diverse species and environments.
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Affiliation(s)
- Yangqi Gu
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- PNAC division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Matthew J Guberman-Pfeffer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Microbiology, Yale University, New Haven, CT, USA
| | - Fabian Giska
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Kallol Gupta
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Yuri Londer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Fadel A Samatey
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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6
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Azad K, Guilligay D, Boscheron C, Maity S, De Franceschi N, Sulbaran G, Effantin G, Wang H, Kleman JP, Bassereau P, Schoehn G, Roos WH, Desfosses A, Weissenhorn W. Structural basis of CHMP2A-CHMP3 ESCRT-III polymer assembly and membrane cleavage. Nat Struct Mol Biol 2023; 30:81-90. [PMID: 36604498 DOI: 10.1038/s41594-022-00867-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/12/2022] [Indexed: 01/07/2023]
Abstract
The endosomal sorting complex required for transport (ESCRT) is a highly conserved protein machinery that drives a divers set of physiological and pathological membrane remodeling processes. However, the structural basis of ESCRT-III polymers stabilizing, constricting and cleaving negatively curved membranes is yet unknown. Here we present cryo-EM structures of membrane-coated CHMP2A-CHMP3 filaments from Homo sapiens of two different diameters at 3.3 and 3.6 Å resolution. The structures reveal helical filaments assembled by CHMP2A-CHMP3 heterodimers in the open ESCRT-III conformation, which generates a partially positive charged membrane interaction surface, positions short N-terminal motifs for membrane interaction and the C-terminal VPS4 target sequence toward the tube interior. Inter-filament interactions are electrostatic, which may facilitate filament sliding upon VPS4-mediated polymer remodeling. Fluorescence microscopy as well as high-speed atomic force microscopy imaging corroborate that VPS4 can constrict and cleave CHMP2A-CHMP3 membrane tubes. We therefore conclude that CHMP2A-CHMP3-VPS4 act as a minimal membrane fission machinery.
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Affiliation(s)
- Kimi Azad
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Delphine Guilligay
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Cecile Boscheron
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Nicola De Franceschi
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France.,Curie Institute, Laboratory of Physical Chemistry Curie, University of PSL, Sorbonne University, CNRS, Paris, France
| | - Guidenn Sulbaran
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Gregory Effantin
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Haiyan Wang
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Jean-Philippe Kleman
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Patricia Bassereau
- Curie Institute, Laboratory of Physical Chemistry Curie, University of PSL, Sorbonne University, CNRS, Paris, France
| | - Guy Schoehn
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Ambroise Desfosses
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Winfried Weissenhorn
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France.
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7
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Gaines MC, Isupov MN, Sivabalasarma S, Haque RU, McLaren M, Mollat CL, Tripp P, Neuhaus A, Gold VAM, Albers SV, Daum B. Electron cryo-microscopy reveals the structure of the archaeal thread filament. Nat Commun 2022; 13:7411. [PMID: 36456543 PMCID: PMC9715654 DOI: 10.1038/s41467-022-34652-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/02/2022] [Indexed: 12/05/2022] Open
Abstract
Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal gene transfer. The model archaeaon Sulfolobus acidocaldarius assembles three filaments of the type-IV pilus superfamily (archaella, archaeal adhesion pili and UV-inducible pili), as well as a so-far uncharacterised fourth filament, named "thread". Here, we report on the cryo-EM structure of the archaeal thread. The filament is highly glycosylated and consists of subunits of the protein Saci_0406, arranged in a head-to-tail manner. Saci_0406 displays structural similarity, but low sequence homology, to bacterial type-I pilins. Thread subunits are interconnected via donor strand complementation, a feature reminiscent of bacterial chaperone-usher pili. However, despite these similarities in overall architecture, archaeal threads appear to have evolved independently and are likely assembled by a distinct mechanism.
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Affiliation(s)
- Matthew C Gaines
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, EX4 4QD, Exeter, UK
| | - Shamphavi Sivabalasarma
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Risat Ul Haque
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Clara L Mollat
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Patrick Tripp
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Alexander Neuhaus
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Sonja-Verena Albers
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBBS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK.
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK.
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8
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Pillay N, Mariotti L, Zaleska M, Inian O, Jessop M, Hibbs S, Desfosses A, Hopkins PCR, Templeton CM, Beuron F, Morris EP, Guettler S. Structural basis of tankyrase activation by polymerization. Nature 2022; 612:162-169. [PMID: 36418402 PMCID: PMC9712121 DOI: 10.1038/s41586-022-05449-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/13/2022] [Indexed: 11/25/2022]
Abstract
The poly-ADP-ribosyltransferase tankyrase (TNKS, TNKS2) controls a wide range of disease-relevant cellular processes, including WNT-β-catenin signalling, telomere length maintenance, Hippo signalling, DNA damage repair and glucose homeostasis1,2. This has incentivized the development of tankyrase inhibitors. Notwithstanding, our knowledge of the mechanisms that control tankyrase activity has remained limited. Both catalytic and non-catalytic functions of tankyrase depend on its filamentous polymerization3-5. Here we report the cryo-electron microscopy reconstruction of a filament formed by a minimal active unit of tankyrase, comprising the polymerizing sterile alpha motif (SAM) domain and its adjacent catalytic domain. The SAM domain forms a novel antiparallel double helix, positioning the protruding catalytic domains for recurring head-to-head and tail-to-tail interactions. The head interactions are highly conserved among tankyrases and induce an allosteric switch in the active site within the catalytic domain to promote catalysis. Although the tail interactions have a limited effect on catalysis, they are essential to tankyrase function in WNT-β-catenin signalling. This work reveals a novel SAM domain polymerization mode, illustrates how supramolecular assembly controls catalytic and non-catalytic functions, provides important structural insights into the regulation of a non-DNA-dependent poly-ADP-ribosyltransferase and will guide future efforts to modulate tankyrase and decipher its contribution to disease mechanisms.
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Affiliation(s)
- Nisha Pillay
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Laura Mariotti
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Mariola Zaleska
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Oviya Inian
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Matthew Jessop
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Sam Hibbs
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Ambroise Desfosses
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Paul C R Hopkins
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Catherine M Templeton
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Sebastian Guettler
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK.
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK.
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9
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Gambelli L, Isupov M, Daum B. Escaping the symmetry trap in helical reconstruction. Faraday Discuss 2022; 240:303-311. [PMID: 35929538 PMCID: PMC9642006 DOI: 10.1039/d2fd00051b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Helical reconstruction is the method of choice for obtaining 3D structures of filaments from electron cryo-microscopy (cryoEM) projections. This approach relies on applying helical symmetry parameters deduced from Fourier-Bessel or real space analysis, such as sub-tomogram averaging. While helical reconstruction continues to provide invaluable structural insights into filaments, its inherent dependence on imposing a pre-defined helical symmetry can also introduce bias. The applied helical symmetry produces structures that are infinitely straight along the filament's axis and can average out biologically important heterogeneities. Here, we describe a simple workflow aimed at overcoming these drawbacks in order to provide truer representations of filamentous structures.
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Affiliation(s)
- Lavinia Gambelli
- College of Engineering, Mathematics and Physical Sciences, University of ExeterExeterEX4 4QFUK,Living Systems Institute, University of ExeterExeterEX4 4QDUK
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of ExeterExeterEX4 4QDUK
| | - Bertram Daum
- Living Systems Institute, University of ExeterExeterEX4 4QDUK,College of Life and Environmental Sciences, University of ExeterExeterEX4 4QDUK
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10
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Abstract
While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Armin Solemanifar
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
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11
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Lazić I, Wirix M, Leidl ML, de Haas F, Mann D, Beckers M, Pechnikova EV, Müller-Caspary K, Egoavil R, Bosch EGT, Sachse C. Single-particle cryo-EM structures from iDPC-STEM at near-atomic resolution. Nat Methods 2022; 19:1126-1136. [PMID: 36064775 PMCID: PMC9467914 DOI: 10.1038/s41592-022-01586-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 07/19/2022] [Indexed: 11/09/2022]
Abstract
In electron cryomicroscopy (cryo-EM), molecular images of vitrified biological samples are obtained by conventional transmission microscopy (CTEM) using large underfocuses and subsequently computationally combined into a high-resolution three-dimensional structure. Here, we apply scanning transmission electron microscopy (STEM) using the integrated differential phase contrast mode also known as iDPC-STEM to two cryo-EM test specimens, keyhole limpet hemocyanin (KLH) and tobacco mosaic virus (TMV). The micrographs show complete contrast transfer to high resolution and enable the cryo-EM structure determination for KLH at 6.5 Å resolution, as well as for TMV at 3.5 Å resolution using single-particle reconstruction methods, which share identical features with maps obtained by CTEM of a previously acquired same-sized TMV data set. These data show that STEM imaging in general, and in particular the iDPC-STEM approach, can be applied to vitrified single-particle specimens to determine near-atomic resolution cryo-EM structures of biological macromolecules.
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Affiliation(s)
- Ivan Lazić
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands.
| | - Maarten Wirix
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands
| | - Max Leo Leidl
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Jülich, Germany.,Department of Chemistry and Centre for NanoScience, Ludwig-Maximilians-University Munich, Munich, Germany.,Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-1): Physics of Nanoscale Systems, Jülich, Germany.,Institute for Biological Information Processing (IBI-6): Cellular Structural Biology, Jülich, Germany
| | - Felix de Haas
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands
| | - Daniel Mann
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Jülich, Germany.,Institute for Biological Information Processing (IBI-6): Cellular Structural Biology, Jülich, Germany
| | - Maximilian Beckers
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Jülich, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Evgeniya V Pechnikova
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands
| | - Knut Müller-Caspary
- Department of Chemistry and Centre for NanoScience, Ludwig-Maximilians-University Munich, Munich, Germany.,Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-1): Physics of Nanoscale Systems, Jülich, Germany
| | - Ricardo Egoavil
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands
| | - Eric G T Bosch
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands
| | - Carsten Sachse
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Jülich, Germany. .,Institute for Biological Information Processing (IBI-6): Cellular Structural Biology, Jülich, Germany. .,Department of Biology, Heinrich Heine University, Düsseldorf, Germany.
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12
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Pakharukova N, Malmi H, Tuittila M, Dahlberg T, Ghosal D, Chang YW, Myint SL, Paavilainen S, Knight SD, Lamminmäki U, Uhlin BE, Andersson M, Jensen G, Zavialov AV. Archaic chaperone-usher pili self-secrete into superelastic zigzag springs. Nature 2022; 609:335-340. [PMID: 35853476 PMCID: PMC9452303 DOI: 10.1038/s41586-022-05095-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 07/08/2022] [Indexed: 11/23/2022]
Abstract
Adhesive pili assembled through the chaperone-usher pathway are hair-like appendages that mediate host tissue colonization and biofilm formation of Gram-negative bacteria1-3. Archaic chaperone-usher pathway pili, the most diverse and widespread chaperone-usher pathway adhesins, are promising vaccine and drug targets owing to their prevalence in the most troublesome multidrug-resistant pathogens1,4,5. However, their architecture and assembly-secretion process remain unknown. Here, we present the cryo-electron microscopy structure of the prototypical archaic Csu pilus that mediates biofilm formation of Acinetobacter baumannii-a notorious multidrug-resistant nosocomial pathogen. In contrast to the thick helical tubes of the classical type 1 and P pili, archaic pili assemble into an ultrathin zigzag architecture secured by an elegant clinch mechanism. The molecular clinch provides the pilus with high mechanical stability as well as superelasticity, a property observed for the first time, to our knowledge, in biomolecules, while enabling a more economical and faster pilus production. Furthermore, we demonstrate that clinch formation at the cell surface drives pilus secretion through the outer membrane. These findings suggest that clinch-formation inhibitors might represent a new strategy to fight multidrug-resistant bacterial infections.
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Affiliation(s)
- Natalia Pakharukova
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Henri Malmi
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Minna Tuittila
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Tobias Dahlberg
- Department of Physics, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Si Lhyam Myint
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Sari Paavilainen
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Stefan David Knight
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Bernt Eric Uhlin
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Magnus Andersson
- Department of Physics, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Grant Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anton V Zavialov
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland.
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13
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Nadeem A, Berg A, Pace H, Alam A, Toh E, Ådén J, Zlatkov N, Myint SL, Persson K, Gröbner G, Sjöstedt A, Bally M, Barandun J, Uhlin BE, Wai SN. Protein-lipid interaction at low pH induces oligomerization of the MakA cytotoxin from Vibrio cholerae. eLife 2022; 11:73439. [PMID: 35131030 PMCID: PMC8824476 DOI: 10.7554/elife.73439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 01/19/2022] [Indexed: 12/29/2022] Open
Abstract
The α-pore-forming toxins (α-PFTs) from pathogenic bacteria damage host cell membranes by pore formation. We demonstrate a remarkable, hitherto unknown mechanism by an α-PFT protein from Vibrio cholerae. As part of the MakA/B/E tripartite toxin, MakA is involved in membrane pore formation similar to other α-PFTs. In contrast, MakA in isolation induces tube-like structures in acidic endosomal compartments of epithelial cells in vitro. The present study unravels the dynamics of tubular growth, which occurs in a pH-, lipid-, and concentration-dependent manner. Within acidified organelle lumens or when incubated with cells in acidic media, MakA forms oligomers and remodels membranes into high-curvature tubes leading to loss of membrane integrity. A 3.7 Å cryo-electron microscopy structure of MakA filaments reveals a unique protein-lipid superstructure. MakA forms a pinecone-like spiral with a central cavity and a thin annular lipid bilayer embedded between the MakA transmembrane helices in its active α-PFT conformation. Our study provides insights into a novel tubulation mechanism of an α-PFT protein and a new mode of action by a secreted bacterial toxin.
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Affiliation(s)
- Aftab Nadeem
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Alexandra Berg
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.,Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Hudson Pace
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Athar Alam
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Eric Toh
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Jörgen Ådén
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Chemistry, Umeå University, Umeå, Sweden
| | - Nikola Zlatkov
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Si Lhyam Myint
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Karina Persson
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Chemistry, Umeå University, Umeå, Sweden
| | - Gerhard Gröbner
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Chemistry, Umeå University, Umeå, Sweden
| | - Anders Sjöstedt
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Marta Bally
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Jonas Barandun
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Bernt Eric Uhlin
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Sun Nyunt Wai
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
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14
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Zhang X. Python-based Helix Indexer: A graphical user interface program for finding symmetry of helical assembly through Fourier-Bessel indexing of electron microscopic data. Protein Sci 2022; 31:107-117. [PMID: 34529294 PMCID: PMC8740834 DOI: 10.1002/pro.4186] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/07/2021] [Accepted: 09/07/2021] [Indexed: 01/03/2023]
Abstract
Many macromolecules form helical assemblies to carry out their functions. Helical reconstruction from electron microscopic images is a powerful approach for solving high-resolution structures of such assemblies. Determination of the symmetry parameters of the helical assemblies is a prerequisite step in helical reconstruction. The most widely used method for deducing the symmetry is through Fourier-Bessel indexing the diffraction pattern of the helical assemblies. This method, however, often leads to incorrect solutions, due to intrinsic ambiguities in indexing helical diffraction patterns. Here, we present Python-based Helix Indexer (PyHI), which provides a graphical user interface (GUI) to guide the users through the process of symmetry determination. Diffraction patterns can be read into the program directly or calculated on the fly from two-dimensional class averages of helical assemblies. PyHI allows deducing the Bessel orders of diffraction peaks by using both the amplitudes and phases of the diffraction data. Based on the Bessel orders of two unit vectors, the Fourier space lattice is constructed with minimal user inputs. The program then uses a refinement algorithm to optimize the Fourier space lattice, and subsequently generate the helical assembly in real space. The program provides both a publication-quality graphic representation of the helical assembly and the symmetry parameters required for subsequent helical reconstruction steps.
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Affiliation(s)
- Xuewu Zhang
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTexas,Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexas
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15
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Pradhan B, Liedtke J, Sleutel M, Lindbäck T, Zegeye ED, O´Sullivan K, Llarena A, Brynildsrud O, Aspholm M, Remaut H. Endospore Appendages: a novel pilus superfamily from the endospores of pathogenic Bacilli. EMBO J 2021; 40:e106887. [PMID: 34031903 PMCID: PMC8408608 DOI: 10.15252/embj.2020106887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/29/2021] [Accepted: 04/16/2021] [Indexed: 11/09/2022] Open
Abstract
Bacillus cereus sensu lato is a group of Gram-positive endospore-forming bacteria with high ecological diversity. Their endospores are decorated with micrometer-long appendages of unknown identity and function. Here, we isolate endospore appendages (Enas) from the food poisoning outbreak strain B. cereus NVH 0075-95 and find proteinaceous fibers of two main morphologies: S- and L-Ena. By using cryoEM and 3D helical reconstruction of S-Enas, we show these to represent a novel class of Gram-positive pili. S-Enas consist of single domain subunits with jellyroll topology that are laterally stacked by β-sheet augmentation. S-Enas are longitudinally stabilized by disulfide bonding through N-terminal connector peptides that bridge the helical turns. Together, this results in flexible pili that are highly resistant to heat, drought, and chemical damage. Phylogenomic analysis reveals a ubiquitous presence of the ena-gene cluster in the B. cereus group, which include species of clinical, environmental, and food importance. We propose Enas to represent a new class of pili specifically adapted to the harsh conditions encountered by bacterial spores.
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Affiliation(s)
- Brajabandhu Pradhan
- Structural and Molecular MicrobiologyVIB‐VUB Center for Structural Biology, VIBBrusselsBelgium
- Department of Bioengineering SciencesStructural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
| | - Janine Liedtke
- Department of Paraclinical SciencesFaculty of Veterinary MedicineThe Norwegian University of Life SciencesÅsNorway
| | - Mike Sleutel
- Structural and Molecular MicrobiologyVIB‐VUB Center for Structural Biology, VIBBrusselsBelgium
- Department of Bioengineering SciencesStructural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
| | - Toril Lindbäck
- Department of Paraclinical SciencesFaculty of Veterinary MedicineThe Norwegian University of Life SciencesÅsNorway
| | - Ephrem Debebe Zegeye
- Department of Paraclinical SciencesFaculty of Veterinary MedicineThe Norwegian University of Life SciencesÅsNorway
| | - Kristin O´Sullivan
- Department of Paraclinical SciencesFaculty of Veterinary MedicineThe Norwegian University of Life SciencesÅsNorway
| | - Ann‐Katrin Llarena
- Department of Paraclinical SciencesFaculty of Veterinary MedicineThe Norwegian University of Life SciencesÅsNorway
| | - Ola Brynildsrud
- Department of Paraclinical SciencesFaculty of Veterinary MedicineThe Norwegian University of Life SciencesÅsNorway
- Division of Infection Control and Environmental HealthNorwegian Institute of Public HealthOsloNorway
| | - Marina Aspholm
- Department of Paraclinical SciencesFaculty of Veterinary MedicineThe Norwegian University of Life SciencesÅsNorway
| | - Han Remaut
- Structural and Molecular MicrobiologyVIB‐VUB Center for Structural Biology, VIBBrusselsBelgium
- Department of Bioengineering SciencesStructural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
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16
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Structure of Geobacter pili reveals secretory rather than nanowire behaviour. Nature 2021; 597:430-434. [PMID: 34471289 PMCID: PMC9127704 DOI: 10.1038/s41586-021-03857-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/28/2021] [Indexed: 02/07/2023]
Abstract
Extracellular electron transfer by Geobacter species through surface appendages known as microbial nanowires1 is important in a range of globally important environmental phenomena2, as well as for applications in bio-remediation, bioenergy, biofuels and bioelectronics. Since 2005, these nanowires have been thought to be type 4 pili composed solely of the PilA-N protein1. However, previous structural analyses have demonstrated that, during extracellular electron transfer, cells do not produce pili but rather nanowires made up of the cytochromes OmcS2,3 and OmcZ4. Here we show that Geobacter sulfurreducens binds PilA-N to PilA-C to assemble heterodimeric pili, which remain periplasmic under nanowire-producing conditions that require extracellular electron transfer5. Cryo-electron microscopy revealed that C-terminal residues of PilA-N stabilize its copolymerization with PilA-C (to form PilA-N-C) through electrostatic and hydrophobic interactions that position PilA-C along the outer surface of the filament. PilA-N-C filaments lack π-stacking of aromatic side chains and show a conductivity that is 20,000-fold lower than that of OmcZ nanowires. In contrast with surface-displayed type 4 pili, PilA-N-C filaments show structure, function and localization akin to those of type 2 secretion pseudopili6. The secretion of OmcS and OmcZ nanowires is lost when pilA-N is deleted and restored when PilA-N-C filaments are reconstituted. The substitution of pilA-N with the type 4 pili of other microorganisms also causes a loss of secretion of OmcZ nanowires. As all major phyla of prokaryotes use systems similar to type 4 pili, this nanowire translocation machinery may have a widespread effect in identifying the evolution and prevalence of diverse electron-transferring microorganisms and in determining nanowire assembly architecture for designing synthetic protein nanowires.
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17
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Zielinski M, Röder C, Schröder GF. Challenges in sample preparation and structure determination of amyloids by cryo-EM. J Biol Chem 2021; 297:100938. [PMID: 34224730 PMCID: PMC8335658 DOI: 10.1016/j.jbc.2021.100938] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/12/2023] Open
Abstract
Amyloids share a common architecture but play disparate biological roles in processes ranging from bacterial defense mechanisms to protein misfolding diseases. Their structures are highly polymorphic, which makes them difficult to study by X-ray diffraction or NMR spectroscopy. Our understanding of amyloid structures is due in large part to recent advances in the field of cryo-EM, which allows for determining the polymorphs separately. In this review, we highlight the main stepping stones leading to the substantial number of high-resolution amyloid fibril structures known today as well as recent developments regarding automation and software in cryo-EM. We discuss that sample preparation should move closer to physiological conditions to understand how amyloid aggregation and disease are linked. We further highlight new approaches to address heterogeneity and polymorphism of amyloid fibrils in EM image processing and give an outlook to the upcoming challenges in researching the structural biology of amyloids.
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Affiliation(s)
- Mara Zielinski
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Christine Röder
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Physics Department, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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18
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Junglas B, Huber ST, Heidler T, Schlösser L, Mann D, Hennig R, Clarke M, Hellmann N, Schneider D, Sachse C. PspA adopts an ESCRT-III-like fold and remodels bacterial membranes. Cell 2021; 184:3674-3688.e18. [PMID: 34166616 DOI: 10.1016/j.cell.2021.05.042] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 03/01/2021] [Accepted: 05/26/2021] [Indexed: 12/31/2022]
Abstract
PspA is the main effector of the phage shock protein (Psp) system and preserves the bacterial inner membrane integrity and function. Here, we present the 3.6 Å resolution cryoelectron microscopy (cryo-EM) structure of PspA assembled in helical rods. PspA monomers adopt a canonical ESCRT-III fold in an extended open conformation. PspA rods are capable of enclosing lipids and generating positive membrane curvature. Using cryo-EM, we visualized how PspA remodels membrane vesicles into μm-sized structures and how it mediates the formation of internalized vesicular structures. Hotspots of these activities are zones derived from PspA assemblies, serving as lipid transfer platforms and linking previously separated lipid structures. These membrane fusion and fission activities are in line with the described functional properties of bacterial PspA/IM30/LiaH proteins. Our structural and functional analyses reveal that bacterial PspA belongs to the evolutionary ancestry of ESCRT-III proteins involved in membrane remodeling.
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Affiliation(s)
- Benedikt Junglas
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Stefan T Huber
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Thomas Heidler
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Lukas Schlösser
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Daniel Mann
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Raoul Hennig
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Mairi Clarke
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany; Institute of Molecular Physiology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany.
| | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Department of Biology, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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19
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Self-association of MreC as a regulatory signal in bacterial cell wall elongation. Nat Commun 2021; 12:2987. [PMID: 34016967 PMCID: PMC8137920 DOI: 10.1038/s41467-021-22957-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 03/18/2021] [Indexed: 02/03/2023] Open
Abstract
The elongasome, or Rod system, is a protein complex that controls cell wall formation in rod-shaped bacteria. MreC is a membrane-associated elongasome component that co-localizes with the cytoskeletal element MreB and regulates the activity of cell wall biosynthesis enzymes, in a process that may be dependent on MreC self-association. Here, we use electron cryo-microscopy and X-ray crystallography to determine the structure of a self-associated form of MreC from Pseudomonas aeruginosa in atomic detail. MreC monomers interact in head-to-tail fashion. Longitudinal and lateral interfaces are essential for oligomerization in vitro, and a phylogenetic analysis of proteobacterial MreC sequences indicates the prevalence of the identified interfaces. Our results are consistent with a model where MreC's ability to alternate between self-association and interaction with the cell wall biosynthesis machinery plays a key role in the regulation of elongasome activity.
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20
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Thurber KR, Yin Y, Tycko R. Automated picking of amyloid fibrils from cryo-EM images for helical reconstruction with RELION. J Struct Biol 2021; 213:107736. [PMID: 33831509 DOI: 10.1016/j.jsb.2021.107736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/16/2022]
Abstract
Cryogenic electron microscopy (cryo-EM) is an important tool for determining the molecular structure of proteins and protein assemblies, including helical assemblies such as amyloid fibrils. In reconstruction of amyloid fibril structures from cryo-EM images, an important early step is the selection of fibril locations. This fibril picking step is typically done by hand, a tedious process when thousands of images need to be analyzed. Here we present a computer program called FibrilFinder that identifies the locations and directions of fibril segments in cryo-EM images, by using the properties that the fibrils should be linear objects and have widths within a specified range. The program outputs the fibril locations in text files compatible with the RELION density reconstruction program. After RELION is used to extract the particle image boxes contained in the fibril segments identified by FibrilFinder, a second program called FibrilFixer removes boxes that contain more than one fibril, for instance because two fibrils cross each other. As concrete and realistic examples, we describe the application of the two programs to cryo-EM images of two different amyloid fibrils, namely 40-residue amyloid-β fibrils derived from human brain tissue by seeded growth and fibrils formed by the C-terminal half of the low-complexity domain of the RNA-binding protein FUS. Both examples of amyloid fibrils can be picked from cryo-EM images using the same set of FibrilFinder and FibrilFixer parameters, showing that this software does not require re-optimization for each sample. A set of 1337 cryo-EM images was analyzed in 17 min with one multi-core computer. The new fibril picking software should enable the rapid analysis and comparison of more helical structures using cryo-EM, and perhaps serve as part of the greater automation of the entire structure determination process.
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Affiliation(s)
- Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
| | - Yi Yin
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford OX3 9DU, UK
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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21
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Pothula KR, Geraets JA, Ferber II, Schröder GF. Clustering polymorphs of tau and IAPP fibrils with the CHEP algorithm. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 160:16-25. [PMID: 33556421 DOI: 10.1016/j.pbiomolbio.2020.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 01/03/2023]
Abstract
Recent steps towards automation have improved the quality and efficiency of the entire cryo-electron microscopy workflow, from sample preparation to image processing. Most of the image processing steps are now quite automated, but there are still a few steps which need the specific intervention of researchers. One such step is the identification and separation of helical protein polymorphs at early stages of image processing. Here, we tested and evaluated our recent clustering approach on three datasets containing amyloid fibrils, demonstrating that the proposed unsupervised clustering method automatically and effectively identifies the polymorphs from cryo-EM images. As an automated polymorph separation method, it has the potential to complement automated helical picking, which typically cannot easily distinguish between polymorphs with subtle differences in morphology, and is therefore a useful tool for the image processing and structure determination of helical proteins.
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Affiliation(s)
- Karunakar R Pothula
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - James A Geraets
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Inda I Ferber
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany; Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
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22
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Flagellar Structures from the Bacterium Caulobacter crescentus and Implications for Phage ϕ CbK Predation of Multiflagellin Bacteria. J Bacteriol 2021; 203:JB.00399-20. [PMID: 33288623 DOI: 10.1128/jb.00399-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/02/2020] [Indexed: 02/06/2023] Open
Abstract
Caulobacter crescentus is a Gram-negative alphaproteobacterium that commonly lives in oligotrophic fresh- and saltwater environments. C. crescentus is a host to many bacteriophages, including ϕCbK and ϕCbK-like bacteriophages, which require interaction with the bacterial flagellum and pilus complexes during adsorption. It is commonly thought that the six paralogs of the flagellin gene present in C. crescentus are important for bacteriophage evasion. Here, we show that deletion of specific flagellins in C. crescentus can indeed attenuate ϕCbK adsorption efficiency, although no single deletion completely ablates ϕCbK adsorption. Thus, the bacteriophage ϕCbK likely recognizes a common motif among the six known flagellins in C. crescentus with various degrees of efficiency. Interestingly, we observe that most deletion strains still generate flagellar filaments, with the exception of a strain that contains only the most divergent flagellin, FljJ, or a strain that contains only FljN and FljO. To visualize the surface residues that are likely recognized by ϕCbK, we determined two high-resolution structures of the FljK filament, with and without an amino acid substitution that induces straightening of the filament. We observe posttranslational modifications on conserved surface threonine residues of FljK that are likely O-linked glycans. The possibility of interplay between these modifications and ϕCbK adsorption is discussed. We also determined the structure of a filament composed of a heterogeneous mixture of FljK and FljL, the final resolution of which was limited to approximately 4.6 Å. Altogether, this work builds a platform for future investigations of how phage ϕCbK infects C. crescentus at the molecular level.IMPORTANCE Bacterial flagellar filaments serve as an initial attachment point for many bacteriophages to bacteria. Some bacteria harbor numerous flagellin genes and are therefore able to generate flagellar filaments with complex compositions, which is thought to be important for evasion from bacteriophages. This study characterizes the importance of the six flagellin genes in C. crescentus for infection by bacteriophage ϕCbK. We find that filaments containing the FljK flagellin are the preferred substrate for bacteriophage ϕCbK. We also present a high-resolution structure of a flagellar filament containing only the FljK flagellin, which provides a platform for future studies on determining how bacteriophage ϕCbK attaches to flagellar filaments at the molecular level.
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23
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The native structure of the assembled matrix protein 1 of influenza A virus. Nature 2020; 587:495-498. [PMID: 32908308 DOI: 10.1038/s41586-020-2696-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/19/2020] [Indexed: 02/03/2023]
Abstract
Influenza A virus causes millions of severe cases of disease during annual epidemics. The most abundant protein in influenza virions is matrix protein 1 (M1), which mediates virus assembly by forming an endoskeleton beneath the virus membrane1. The structure of full-length M1, and how it oligomerizes to mediate the assembly of virions, is unknown. Here we determine the complete structure of assembled M1 within intact virus particles, as well as the structure of M1 oligomers reconstituted in vitro. We find that the C-terminal domain of M1 is disordered in solution but can fold and bind in trans to the N-terminal domain of another M1 monomer, thus polymerizing M1 into linear strands that coat the interior surface of the membrane of the assembling virion. In the M1 polymer, five histidine residues-contributed by three different monomers of M1-form a cluster that can serve as the pH-sensitive disassembly switch after entry into a target cell. These structures therefore reveal mechanisms of influenza virus assembly and disassembly.
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24
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Huber ST, Mostafavi S, Mortensen SA, Sachse C. Structure and assembly of ESCRT-III helical Vps24 filaments. SCIENCE ADVANCES 2020; 6:eaba4897. [PMID: 32875105 PMCID: PMC7438092 DOI: 10.1126/sciadv.aba4897] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
ESCRT-III proteins mediate a range of cellular membrane remodeling activities such as multivesicular body biogenesis, cytokinesis, and viral release. Critical to these processes is the assembly of ESCRT-III subunits into polymeric structures. In this study, we determined the cryo-EM structure of a helical assembly of Saccharomyces cerevisiae Vps24 at 3.2-Å resolution and found that Vps24 adopts an elongated open conformation. Vps24 forms a domain-swapped dimer extended into protofilaments that associate into a double-stranded apolar filament. We demonstrate that, upon binding negatively charged lipids, Vps24 homopolymer filaments undergo partial disassembly into shorter filament fragments and oligomers. Upon the addition of Vps24, Vps2, and Snf7, liposomes are deformed into neck and tubular structures by an ESCRT-III heteropolymer coat. The filamentous Vps24 homopolymer assembly structure and interaction studies reveal how Vps24 could introduce unique geometric properties to mixed-type ESCRT-III heteropolymers and contribute to the process of membrane scission events.
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Affiliation(s)
- Stefan T. Huber
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Siavash Mostafavi
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, 52425 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Simon A. Mortensen
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, 52425 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
- European Molecular Biology Laboratory (EMBL) Hamburg c/o DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Carsten Sachse
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, 52425 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
- Department of Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
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25
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Hardy JM, Dunstan RA, Grinter R, Belousoff MJ, Wang J, Pickard D, Venugopal H, Dougan G, Lithgow T, Coulibaly F. The architecture and stabilisation of flagellotropic tailed bacteriophages. Nat Commun 2020; 11:3748. [PMID: 32719311 PMCID: PMC7385642 DOI: 10.1038/s41467-020-17505-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 07/01/2020] [Indexed: 12/31/2022] Open
Abstract
Flagellotropic bacteriophages engage flagella to reach the bacterial surface as an effective means to increase the capture radius for predation. Structural details of these viruses are of great interest given the substantial drag forces and torques they face when moving down the spinning flagellum. We show that the main capsid and auxiliary proteins form two nested chainmails that ensure the integrity of the bacteriophage head. Core stabilising structures are conserved in herpesviruses suggesting their ancestral origin. The structure of the tail also reveals a robust yet pliable assembly. Hexameric rings of the tail-tube protein are braced by the N-terminus and a β-hairpin loop, and interconnected along the tail by the splayed β-hairpins. By contrast, we show that the β-hairpin has an inhibitory role in the tail-tube precursor, preventing uncontrolled self-assembly. Dyads of acidic residues inside the tail-tube present regularly-spaced motifs well suited to DNA translocation into bacteria through the tail.
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Affiliation(s)
- Joshua M Hardy
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Rhys A Dunstan
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Rhys Grinter
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Matthew J Belousoff
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Jiawei Wang
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Hariprasad Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia.
| | - Fasséli Coulibaly
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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26
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Neuhaus A, Selvaraj M, Salzer R, Langer JD, Kruse K, Kirchner L, Sanders K, Daum B, Averhoff B, Gold VAM. Cryo-electron microscopy reveals two distinct type IV pili assembled by the same bacterium. Nat Commun 2020; 11:2231. [PMID: 32376942 PMCID: PMC7203116 DOI: 10.1038/s41467-020-15650-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/19/2020] [Indexed: 12/19/2022] Open
Abstract
Type IV pili are flexible filaments on the surface of bacteria, consisting of a helical assembly of pilin proteins. They are involved in bacterial motility (twitching), surface adhesion, biofilm formation and DNA uptake (natural transformation). Here, we use cryo-electron microscopy and mass spectrometry to show that the bacterium Thermus thermophilus produces two forms of type IV pilus ('wide' and 'narrow'), differing in structure and protein composition. Wide pili are composed of the major pilin PilA4, while narrow pili are composed of a so-far uncharacterized pilin which we name PilA5. Functional experiments indicate that PilA4 is required for natural transformation, while PilA5 is important for twitching motility.
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Affiliation(s)
- Alexander Neuhaus
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Muniyandi Selvaraj
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
- Laboratory of Structural Biology, Helsinki Institute of Life Science, 00014 University of Helsinki, Helsinki, Finland
| | - Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
- Structural Studies Division, Medical Research Council-Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - Julian D Langer
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
- Proteomics, Max Planck Institute for Brain Research, Max-von-Laue Str. 4, 60438, Frankfurt am Main, Germany
| | - Kerstin Kruse
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Lennart Kirchner
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Kelly Sanders
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Beate Averhoff
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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27
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Wang K, Yu Q. Simulation analysis of 3D medical image reconstruction based on ant colony optimization algorithm. JOURNAL OF INTELLIGENT & FUZZY SYSTEMS 2020. [DOI: 10.3233/jifs-179613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Kailing Wang
- Modern Education Technology Center, Qiqihar Medical University, China
| | - Qinglian Yu
- Modern Education Technology Center, Qiqihar Medical University, China
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28
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Ruskamo S, Krokengen OC, Kowal J, Nieminen T, Lehtimäki M, Raasakka A, Dandey VP, Vattulainen I, Stahlberg H, Kursula P. Cryo-EM, X-ray diffraction, and atomistic simulations reveal determinants for the formation of a supramolecular myelin-like proteolipid lattice. J Biol Chem 2020; 295:8692-8705. [PMID: 32265298 DOI: 10.1074/jbc.ra120.013087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/31/2020] [Indexed: 12/15/2022] Open
Abstract
Myelin protein P2 is a peripheral membrane protein of the fatty acid-binding protein family that functions in the formation and maintenance of the peripheral nerve myelin sheath. Several P2 gene mutations cause human Charcot-Marie-Tooth neuropathy, but the mature myelin sheath assembly mechanism is unclear. Here, cryo-EM of myelin-like proteolipid multilayers revealed an ordered three-dimensional (3D) lattice of P2 molecules between stacked lipid bilayers, visualizing supramolecular assembly at the myelin major dense line. The data disclosed that a single P2 layer is inserted between two bilayers in a tight intermembrane space of ∼3 nm, implying direct interactions between P2 and two membrane surfaces. X-ray diffraction from P2-stacked bicelle multilayers revealed lateral protein organization, and surface mutagenesis of P2 coupled with structure-function experiments revealed a role for both the portal region of P2 and its opposite face in membrane interactions. Atomistic molecular dynamics simulations of P2 on model membrane surfaces suggested that Arg-88 is critical for P2-membrane interactions, in addition to the helical lid domain. Negatively charged lipid headgroups stably anchored P2 on the myelin-like bilayer surface. Membrane binding may be accompanied by opening of the P2 β-barrel structure and ligand exchange with the apposing bilayer. Our results provide an unprecedented view into an ordered, multilayered biomolecular membrane system induced by the presence of a peripheral membrane protein from human myelin. This is an important step toward deciphering the 3D assembly of a mature myelin sheath at the molecular level.
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Affiliation(s)
- Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
| | - Oda C Krokengen
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, 4058 Basel, Switzerland
| | - Tuomo Nieminen
- Computational Physics Laboratory, Tampere University, 33014 Tampere, Finland
| | - Mari Lehtimäki
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Venkata P Dandey
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, 4058 Basel, Switzerland
| | - Ilpo Vattulainen
- Computational Physics Laboratory, Tampere University, 33014 Tampere, Finland; Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, 4058 Basel, Switzerland
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; Biocenter Oulu, University of Oulu, 90014 Oulu, Finland; Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
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29
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Beckers M, Palmer CM, Sachse C. Confidence maps: statistical inference of cryo-EM maps. Acta Crystallogr D Struct Biol 2020; 76:332-339. [PMID: 32254057 PMCID: PMC7137106 DOI: 10.1107/s2059798320002995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/03/2020] [Indexed: 11/11/2022] Open
Abstract
Confidence maps provide complementary information for interpreting cryo-EM densities as they indicate statistical significance with respect to background noise. They can be thresholded by specifying the expected false-discovery rate (FDR), and the displayed volume shows the parts of the map that have the corresponding level of significance. Here, the basic statistical concepts of confidence maps are reviewed and practical guidance is provided for their interpretation and usage inside the CCP-EM suite. Limitations of the approach are discussed and extensions towards other error criteria such as the family-wise error rate are presented. The observed map features can be rendered at a common isosurface threshold, which is particularly beneficial for the interpretation of weak and noisy densities. In the current article, a practical guide is provided to the recommended usage of confidence maps.
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Affiliation(s)
- Maximilian Beckers
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Colin M. Palmer
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Carsten Sachse
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons 3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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30
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Nguyen HC, Talledge N, McCullough J, Sharma A, Moss FR, Iwasa JH, Vershinin MD, Sundquist WI, Frost A. Membrane constriction and thinning by sequential ESCRT-III polymerization. Nat Struct Mol Biol 2020; 27:392-399. [PMID: 32251413 PMCID: PMC7343221 DOI: 10.1038/s41594-020-0404-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/05/2020] [Indexed: 01/04/2023]
Abstract
The endosomal sorting complexes required for transport (ESCRTs) mediate diverse membrane remodeling events. These typically require ESCRT-III proteins to stabilize negatively curved membranes; however, recent work has indicated that certain ESCRT-IIIs also participate in positive-curvature membrane-shaping reactions. ESCRT-IIIs polymerize into membrane-binding filaments, but the structural basis for negative versus positive membrane remodeling by these proteins remains poorly understood. To learn how certain ESCRT-IIIs shape positively curved membranes, we determined structures of human membrane-bound CHMP1B-only, membrane-bound CHMP1B + IST1, and IST1-only filaments by cryo-EM. Our structures show how CHMP1B first polymerizes into a single-stranded helical filament, shaping membranes into moderate-curvature tubules. Subsequently, IST1 assembles a second strand on CHMP1B, further constricting the membrane tube and reducing its diameter nearly to the fission point. Each step of constriction thins the underlying bilayer, lowering the barrier to membrane fission. Our structures reveal how a two-component, sequential polymerization mechanism drives membrane tubulation, constriction and bilayer thinning.
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Affiliation(s)
- Henry C Nguyen
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Nathaniel Talledge
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
- Institute for Molecular Virology, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - John McCullough
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Abhimanyu Sharma
- Department of Physics & Astronomy, University of Utah, Salt Lake City, UT, USA
| | - Frank R Moss
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Janet H Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Michael D Vershinin
- Department of Physics & Astronomy, University of Utah, Salt Lake City, UT, USA
- Department of Biology, University of Utah, Salt Lake City, UT, USA
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, USA
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
| | - Adam Frost
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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31
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New insights on the structure of alpha-synuclein fibrils using cryo-electron microscopy. Curr Opin Neurobiol 2020; 61:89-95. [DOI: 10.1016/j.conb.2020.01.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 01/08/2023]
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32
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Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake. Nat Commun 2020; 11:440. [PMID: 31974402 PMCID: PMC6978347 DOI: 10.1038/s41467-020-14343-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022] Open
Abstract
p62/SQSTM1 is an autophagy receptor and signaling adaptor with an N-terminal PB1 domain that forms the scaffold of phase-separated p62 bodies in the cell. The molecular determinants that govern PB1 domain filament formation in vitro remain to be determined and the role of p62 filaments inside the cell is currently unclear. We here determine four high-resolution cryo-EM structures of different human and Arabidopsis PB1 domain assemblies and observed a filamentous ultrastructure of p62/SQSTM1 bodies using correlative cellular EM. We show that oligomerization or polymerization, driven by a double arginine finger in the PB1 domain, is a general requirement for lysosomal targeting of p62. Furthermore, the filamentous assembly state of p62 is required for autophagosomal processing of the p62-specific cargo KEAP1. Our results show that using such mechanisms, p62 filaments can be critical for cargo uptake in autophagy and are an integral part of phase-separated p62 bodies. PB1-mediated oligomerization of p62/SQSTM1 is essential for its function as a selective autophagy receptor. Here the authors present the cryo-EM structures of human and Arabidopsis PB1 domain helical assemblies and find that a conserved double arginine finger in the PB1 domain is important for p62 polymerisation and lysosomal targeting of p62.
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Desfosses A, Venugopal H, Joshi T, Felix J, Jessop M, Jeong H, Hyun J, Heymann JB, Hurst MRH, Gutsche I, Mitra AK. Atomic structures of an entire contractile injection system in both the extended and contracted states. Nat Microbiol 2019; 4:1885-1894. [PMID: 31384001 PMCID: PMC6817355 DOI: 10.1038/s41564-019-0530-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023]
Abstract
Contractile injection systems are sophisticated multiprotein nanomachines that puncture target cell membranes. While the amount of atomic resolution insights into contractile bacteriophage tails, bacterial type six secretion systems and R-pyocins is rapidly increasing, structural information about contraction of bacterial phage-like protein-translocation structures directed towards eukaryotic hosts is scarce. Here we characterise the antifeeding prophage AFP from Serratia entomophila by cryo-electron microscopy. We present the high-resolution structure of the entire AFP particle in the extended state, trace 11 protein chains de novo from the apical cap to the needle tip, describe localisation variants and perform specific structural comparisons with related systems. We analyse intersubunit interactions and highlight their universal conservation within contractile injection systems while revealing the specificities of AFP. Furthermore, we provide the structure of the AFP sheath-baseplate complex in a contracted state. This study reveals atomic details of interaction networks that accompany and define the contraction mechanism of toxin-delivery tailocins, offering a comprehensive framework for understanding their mode of action and for their possible adaptation as biocontrol agents.
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Affiliation(s)
- Ambroise Desfosses
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Hariprasad Venugopal
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Ramaciotti Centre for Cryo Electron Microscopy, Monash University, Melbourne, Victoria, Australia
| | - Tapan Joshi
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jan Felix
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Matthew Jessop
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Hyengseop Jeong
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju-si, Republic of Korea
| | - Jaekyung Hyun
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju-si, Republic of Korea.,Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - J Bernard Heymann
- Laboratory for Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mark R H Hurst
- Forage Science, AgResearch, Lincoln Research Centre, Christchurch, New Zealand. .,Bio-Protection Research Centre, Christchurch, New Zealand.
| | - Irina Gutsche
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Alok K Mitra
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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Structures of autoinhibited and polymerized forms of CARD9 reveal mechanisms of CARD9 and CARD11 activation. Nat Commun 2019; 10:3070. [PMID: 31296852 PMCID: PMC6624267 DOI: 10.1038/s41467-019-10953-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/06/2019] [Indexed: 12/30/2022] Open
Abstract
CARD9 and CARD11 drive immune cell activation by nucleating Bcl10 polymerization, but are held in an autoinhibited state prior to stimulation. Here, we elucidate the structural basis for this autoinhibition by determining the structure of a region of CARD9 that includes an extensive interface between its caspase recruitment domain (CARD) and coiled-coil domain. We demonstrate, for both CARD9 and CARD11, that disruption of this interface leads to hyperactivation in cells and to the formation of Bcl10-templating filaments in vitro, illuminating the mechanism of action of numerous oncogenic mutations of CARD11. These structural insights enable us to characterize two similar, yet distinct, mechanisms by which autoinhibition is relieved in the course of canonical CARD9 or CARD11 activation. We also dissect the molecular determinants of helical template assembly by solving the structure of the CARD9 filament. Taken together, these findings delineate the structural mechanisms of inhibition and activation within this protein family.
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35
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Meshcheryakov VA, Shibata S, Schreiber MT, Villar-Briones A, Jarrell KF, Aizawa SI, Wolf M. High-resolution archaellum structure reveals a conserved metal-binding site. EMBO Rep 2019; 20:embr.201846340. [PMID: 30898768 PMCID: PMC6500986 DOI: 10.15252/embr.201846340] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 02/16/2019] [Accepted: 02/27/2019] [Indexed: 01/09/2023] Open
Abstract
Many archaea swim by means of archaella. While the archaellum is similar in function to its bacterial counterpart, its structure, composition, and evolution are fundamentally different. Archaella are related to archaeal and bacterial type IV pili. Despite recent advances, our understanding of molecular processes governing archaellum assembly and stability is still incomplete. Here, we determine the structures of Methanococcus archaella by X‐ray crystallography and cryo‐EM. The crystal structure of Methanocaldococcus jannaschii FlaB1 is the first and only crystal structure of any archaellin to date at a resolution of 1.5 Å, which is put into biological context by a cryo‐EM reconstruction from Methanococcus maripaludis archaella at 4 Å resolution created with helical single‐particle analysis. Our results indicate that the archaellum is predominantly composed of FlaB1. We identify N‐linked glycosylation by cryo‐EM and mass spectrometry. The crystal structure reveals a highly conserved metal‐binding site, which is validated by mass spectrometry and electron energy‐loss spectroscopy. We show in vitro that the metal‐binding site, which appears to be a widespread property of archaellin, is required for filament integrity.
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Affiliation(s)
- Vladimir A Meshcheryakov
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
| | - Satoshi Shibata
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
| | - Makoto Tokoro Schreiber
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
| | - Alejandro Villar-Briones
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
| | - Kenneth F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Shin-Ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima, Japan
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
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36
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Assembly and cryo-EM structures of RNA-specific measles virus nucleocapsids provide mechanistic insight into paramyxoviral replication. Proc Natl Acad Sci U S A 2019; 116:4256-4264. [PMID: 30787192 DOI: 10.1073/pnas.1816417116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Assembly of paramyxoviral nucleocapsids on the RNA genome is an essential step in the viral cycle. The structural basis of this process has remained obscure due to the inability to control encapsidation. We used a recently developed approach to assemble measles virus nucleocapsid-like particles on specific sequences of RNA hexamers (poly-Adenine and viral genomic 5') in vitro, and determined their cryoelectron microscopy maps to 3.3-Å resolution. The structures unambiguously determine 5' and 3' binding sites and thereby the binding-register of viral genomic RNA within nucleocapsids. This observation reveals that the 3' end of the genome is largely exposed in fully assembled measles nucleocapsids. In particular, the final three nucleotides of the genome are rendered accessible to the RNA-dependent RNA polymerase complex, possibly enabling efficient RNA processing. The structures also reveal local and global conformational changes in the nucleoprotein upon assembly, in particular involving helix α6 and helix α13 that form edges of the RNA binding groove. Disorder is observed in the bound RNA, localized at one of the two backbone conformational switch sites. The high-resolution structure allowed us to identify putative nucleobase interaction sites in the RNA-binding groove, whose impact on assembly kinetics was measured using real-time NMR. Mutation of one of these sites, R195, whose sidechain stabilizes both backbone and base of a bound nucleic acid, is thereby shown to be essential for nucleocapsid-like particle assembly.
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37
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Raasakka A, Ruskamo S, Kowal J, Han H, Baumann A, Myllykoski M, Fasano A, Rossano R, Riccio P, Bürck J, Ulrich AS, Stahlberg H, Kursula P. Molecular structure and function of myelin protein P0 in membrane stacking. Sci Rep 2019; 9:642. [PMID: 30679613 PMCID: PMC6345808 DOI: 10.1038/s41598-018-37009-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022] Open
Abstract
Compact myelin forms the basis of nerve insulation essential for higher vertebrates. Dozens of myelin membrane bilayers undergo tight stacking, and in the peripheral nervous system, this is partially enabled by myelin protein zero (P0). Consisting of an immunoglobulin (Ig)-like extracellular domain, a single transmembrane helix, and a cytoplasmic extension (P0ct), P0 harbours an important task in ensuring the integrity of compact myelin in the extracellular compartment, referred to as the intraperiod line. Several disease mutations resulting in peripheral neuropathies have been identified for P0, reflecting its physiological importance, but the arrangement of P0 within the myelin ultrastructure remains obscure. We performed a biophysical characterization of recombinant P0ct. P0ct contributes to the binding affinity between apposed cytoplasmic myelin membrane leaflets, which not only results in changes of the bilayer properties, but also potentially involves the arrangement of the Ig-like domains in a manner that stabilizes the intraperiod line. Transmission electron cryomicroscopy of native full-length P0 showed that P0 stacks lipid membranes by forming antiparallel dimers between the extracellular Ig-like domains. The zipper-like arrangement of the P0 extracellular domains between two membranes explains the double structure of the myelin intraperiod line. Our results contribute to the understanding of PNS myelin, the role of P0 therein, and the underlying molecular foundation of compact myelin stability in health and disease.
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Affiliation(s)
- Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Switzerland
| | - Huijong Han
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anne Baumann
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Matti Myllykoski
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anna Fasano
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Rocco Rossano
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Paolo Riccio
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
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38
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Pothula KR, Smyrnova D, Schröder GF. Clustering cryo-EM images of helical protein polymers for helical reconstructions. Ultramicroscopy 2018; 203:132-138. [PMID: 30591222 DOI: 10.1016/j.ultramic.2018.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/04/2018] [Accepted: 12/16/2018] [Indexed: 02/02/2023]
Abstract
Helical protein polymers are often dynamic and complex assemblies, with many conformations and flexible domains possible within the helical assembly. During cryo-electron microscopy reconstruction, classification of the image data into homogeneous subsets is a critical step for achieving high resolution, resolving different conformations and elucidating functional mechanisms. Hence, methods aimed at improving the homogeneity of these datasets are becoming increasingly important. In this paper, we introduce a new algorithm that uses results from 2D image classification to sort 2D classes into groups of similar helical polymers. We show that our approach is able to distinguish helical polymers that differ in conformation, composition, and helical symmetry. Our results on test and experimental cases - actin filaments and amyloid fibrils - illustrate how our approach can be useful to improve the homogeneity of a data set. This method is exclusively applicable to helical polymers and other limitations are discussed.
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Affiliation(s)
- Karunakar R Pothula
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Daryna Smyrnova
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gunnar F Schröder
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany; Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
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39
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Gong Q, Long Z, Zhong FL, Teo DET, Jin Y, Yin Z, Boo ZZ, Zhang Y, Zhang J, Yang R, Bhushan S, Reversade B, Li Z, Wu B. Structural basis of RIP2 activation and signaling. Nat Commun 2018; 9:4993. [PMID: 30478312 PMCID: PMC6255760 DOI: 10.1038/s41467-018-07447-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 11/02/2018] [Indexed: 01/08/2023] Open
Abstract
Signals arising from bacterial infections are detected by pathogen recognition receptors (PRRs) and are transduced by specialized adapter proteins in mammalian cells. The Receptor-interacting-serine/threonine-protein kinase 2 (RIPK2 or RIP2) is such an adapter protein that is critical for signal propagation of the Nucleotide-binding-oligomerization-domain-containing proteins 1/2 (NOD1 and NOD2). Dysregulation of this signaling pathway leads to defects in bacterial detection and in some cases autoimmune diseases. Here, we show that the Caspase-activation-and-recruitment-domain (CARD) of RIP2 (RIP2-CARD) forms oligomeric structures upon stimulation by either NOD1-CARD or NOD2-2CARD. We reconstitute this complex, termed the RIPosome in vitro and solve the cryo-EM filament structure of the active RIP2-CARD complex at 4.1 Å resolution. The structure suggests potential mechanisms by which CARD domains from NOD1 and NOD2 initiate the oligomerization process of RIP2-CARD. Together with structure guided mutagenesis experiments at the CARD-CARD interfaces, we demonstrate molecular mechanisms how RIP2 is activated and self-propagating such signal.
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Affiliation(s)
- Qin Gong
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Ziqi Long
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | | | | | - Yibo Jin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Zhan Yin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore.,Medical Research Council, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Zhao Zhi Boo
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Yaming Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Jiawen Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Renliang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Bruno Reversade
- Institute of Medical Biology, A*STAR, Singapore, Singapore.,Department of Paediatrics, National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore.,Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey.,Reproductive Biology Laboratory, Academic Medical Center (AMC), Amsterdam-Zuidoost, The Netherlands
| | - Zongli Li
- Department of Biological Chemistry & Molecular Pharmacology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore. .,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore.
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40
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Sugita Y, Matsunami H, Kawaoka Y, Noda T, Wolf M. Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex at 3.6 Å resolution. Nature 2018; 563:137-140. [PMID: 30333622 DOI: 10.1038/s41586-018-0630-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/21/2018] [Indexed: 11/09/2022]
Abstract
Ebola virus causes haemorrhagic fever with a high fatality rate in humans and non-human primates. It belongs to the family Filoviridae in the order Mononegavirales, which are viruses that contain linear, non-segmented, negative-sense, single-stranded genomic RNA1,2. The enveloped, filamentous virion contains the nucleocapsid, consisting of the helical nucleoprotein-RNA complex, VP24, VP30, VP35 and viral polymerase1,3. The nucleoprotein-RNA complex acts as a scaffold for nucleocapsid formation and as a template for RNA replication and transcription by condensing RNA into the virion4,5. RNA binding and nucleoprotein oligomerization are synergistic and do not readily occur independently6. Although recent cryo-electron tomography studies have revealed the overall architecture of the nucleocapsid core4,5, there has been no high-resolution reconstruction of the nucleocapsid. Here we report the structure of a recombinant Ebola virus nucleoprotein-RNA complex expressed in mammalian cells without chemical fixation, at near-atomic resolution using single-particle cryo-electron microscopy. Our structure reveals how the Ebola virus nucleocapsid core encapsidates its viral genome, its sequence-independent coordination with RNA by nucleoprotein, and the dynamic transition between the RNA-free and RNA-bound states. It provides direct structural evidence for the role of the N terminus of nucleoprotein in subunit oligomerization, and for the hydrophobic and electrostatic interactions that lead to the formation of the helical assembly. The structure is validated as representative of the native biological assembly of the nucleocapsid core by consistent dimensions and symmetry with the full virion5. The atomic model provides a detailed mechanistic basis for understanding nucleocapsid assembly and highlights key structural features that may serve as targets for anti-viral drug development.
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Affiliation(s)
- Yukihiko Sugita
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.,Laboratory of Advanced Protein Characterization, Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hideyuki Matsunami
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
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41
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RIP2 filament formation is required for NOD2 dependent NF-κB signalling. Nat Commun 2018; 9:4043. [PMID: 30279485 PMCID: PMC6168553 DOI: 10.1038/s41467-018-06451-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/06/2018] [Indexed: 11/08/2022] Open
Abstract
Activation of the innate immune pattern recognition receptor NOD2 by the bacterial muramyl-dipeptide peptidoglycan fragment triggers recruitment of the downstream adaptor kinase RIP2, eventually leading to NF-κB activation and proinflammatory cytokine production. Here we show that full-length RIP2 can form long filaments mediated by its caspase recruitment domain (CARD), in common with other innate immune adaptor proteins. We further show that the NOD2 tandem CARDs bind to one end of the RIP2 CARD filament, suggesting a mechanism for polar filament nucleation by activated NOD2. We combine X-ray crystallography, solid-state NMR and high-resolution cryo-electron microscopy to determine the atomic structure of the helical RIP2 CARD filament, which reveals the intermolecular interactions that stabilize the assembly. Using structure-guided mutagenesis, we demonstrate the importance of RIP2 polymerization for the activation of NF-κB signalling by NOD2. Our results could be of use to develop new pharmacological strategies to treat inflammatory diseases characterised by aberrant NOD2 signalling.
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42
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Molecular architecture and regulation of BCL10-MALT1 filaments. Nat Commun 2018; 9:4041. [PMID: 30279415 PMCID: PMC6168461 DOI: 10.1038/s41467-018-06573-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023] Open
Abstract
The CARD11-BCL10-MALT1 (CBM) complex triggers the adaptive immune response in lymphocytes and lymphoma cells. CARD11/CARMA1 acts as a molecular seed inducing BCL10 filaments, but the integration of MALT1 and the assembly of a functional CBM complex has remained elusive. Using cryo-EM we solved the helical structure of the BCL10-MALT1 filament. The structural model of the filament core solved at 4.9 Å resolution identified the interface between the N-terminal MALT1 DD and the BCL10 caspase recruitment domain. The C-terminal MALT1 Ig and paracaspase domains protrude from this core to orchestrate binding of mediators and substrates at the filament periphery. Mutagenesis studies support the importance of the identified BCL10-MALT1 interface for CBM complex assembly, MALT1 protease activation and NF-κB signaling in Jurkat and primary CD4 T-cells. Collectively, we present a model for the assembly and architecture of the CBM signaling complex and how it functions as a signaling hub in T-lymphocytes. The BCL10-MALT1 complex is a central signaling hub in lymphocytes and linked to various human immune pathologies. Here the authors present the cryo-EM structure of the BCL10-MALT1 filament core and verify the identified BCL10/MALT1 interface with mutagenesis studies.
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43
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Holliday MJ, Ferrao R, de Leon Boenig G, Estevez A, Helgason E, Rohou A, Dueber EC, Fairbrother WJ. Picomolar zinc binding modulates formation of Bcl10-nucleating assemblies of the caspase recruitment domain (CARD) of CARD9. J Biol Chem 2018; 293:16803-16817. [PMID: 30206119 DOI: 10.1074/jbc.ra118.004821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/04/2018] [Indexed: 12/28/2022] Open
Abstract
The caspase recruitment domain-containing protein 9 (CARD9)-B-cell lymphoma/leukemia 10 (Bcl10) signaling axis is activated in myeloid cells during the innate immune response to a variety of diverse pathogens. This signaling pathway requires a critical caspase recruitment domain (CARD)-CARD interaction between CARD9 and Bcl10 that promotes downstream activation of factors, including NF-κB and the mitogen-activated protein kinase (MAPK) p38. Despite these insights, CARD9 remains structurally uncharacterized, and little mechanistic understanding of its regulation exists. We unexpectedly found here that the CARD in CARD9 binds to Zn2+ with picomolar affinity-a concentration comparable with the levels of readily accessible Zn2+ in the cytosol. NMR solution structures of the CARD9-CARD in the apo and Zn2+-bound states revealed that Zn2+ has little effect on the ground-state structure of the CARD; yet the stability of the domain increased considerably upon Zn2+ binding, with a concomitant reduction in conformational flexibility. Moreover, Zn2+ binding inhibited polymerization of the CARD9-CARD into helical assemblies. Here, we also present a 20-Å resolution negative-stain EM (NS-EM) structure of these filamentous assemblies and show that they adopt a similar helical symmetry as reported previously for filaments of the Bcl10 CARD. Using both bulk assays and direct NS-EM visualization, we further show that the CARD9-CARD assemblies can directly template and thereby nucleate Bcl10 polymerization, a capacity considered critical to propagation of the CARD9-Bcl10 signaling cascade. Our findings indicate that CARD9 is a potential target of Zn2+-mediated signaling that affects Bcl10 polymerization in innate immune responses.
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Affiliation(s)
| | - Ryan Ferrao
- Structural Biology Department, Genentech, South San Francisco, California 94080
| | | | - Alberto Estevez
- Structural Biology Department, Genentech, South San Francisco, California 94080
| | | | - Alexis Rohou
- Structural Biology Department, Genentech, South San Francisco, California 94080
| | - Erin C Dueber
- From the Early Discovery Biochemistry Department and
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Varlakhanova NV, Alvarez FJD, Brady TM, Tornabene BA, Hosford CJ, Chappie JS, Zhang P, Ford MGJ. Structures of the fungal dynamin-related protein Vps1 reveal a unique, open helical architecture. J Cell Biol 2018; 217:3608-3624. [PMID: 30087125 PMCID: PMC6168280 DOI: 10.1083/jcb.201712021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 05/26/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022] Open
Abstract
How specific dynamin-related proteins (DRPs) are tailored to their cellular targets is an open question. Varlakhanova et al. present structures of the fungal DRP Vps1, which functions at the endosomal compartment. The crystal and cryoEM structures reveal a unique DRP architecture that highlights structural flexibilities of DRP self-assembly. Dynamin-related proteins (DRPs) are large multidomain GTPases required for diverse membrane-remodeling events. DRPs self-assemble into helical structures, but how these structures are tailored to their cellular targets remains unclear. We demonstrate that the fungal DRP Vps1 primarily localizes to and functions at the endosomal compartment. We present crystal structures of a Vps1 GTPase–bundle signaling element (BSE) fusion in different nucleotide states to capture GTP hydrolysis intermediates and concomitant conformational changes. Using cryoEM, we determined the structure of full-length GMPPCP-bound Vps1. The Vps1 helix is more open and flexible than that of dynamin. This is due to further opening of the BSEs away from the GTPase domains. A novel interface between adjacent GTPase domains forms in Vps1 instead of the contacts between the BSE and adjacent stalks and GTPase domains as seen in dynamin. Disruption of this interface abolishes Vps1 function in vivo. Hence, Vps1 exhibits a unique helical architecture, highlighting structural flexibilities of DRP self-assembly.
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Affiliation(s)
| | - Frances J D Alvarez
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Tyler M Brady
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Bryan A Tornabene
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Marijn G J Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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Jenni S, Harrison SC. Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-microtubule interface. Science 2018; 360:552-558. [PMID: 29724956 DOI: 10.1126/science.aar6436] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/15/2018] [Indexed: 12/13/2022]
Abstract
Kinetochores connect mitotic-spindle microtubules with chromosomes, allowing microtubule depolymerization to pull chromosomes apart during anaphase while resisting detachment as the microtubule shortens. The heterodecameric DASH/Dam1 complex (DASH/Dam1c), an essential component of yeast kinetochores, assembles into a microtubule-encircling ring. The ring associates with rodlike Ndc80 complexes to organize the kinetochore-microtubule interface. We report the cryo-electron microscopy structure (at ~4.5-angstrom resolution) of a DASH/Dam1c ring and a molecular model of its ordered components, validated by evolutionary direct-coupling analysis. Integrating this structure with that of the Ndc80 complex and with published interaction data yields a molecular picture of kinetochore-microtubule attachment, including how flexible, C-terminal extensions of DASH/Dam1c subunits project and contact widely separated sites on the Ndc80 complex rod and how phosphorylation at previously identified sites might regulate kinetochore assembly.
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Affiliation(s)
- Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA. .,Howard Hughes Medical Institute, Harvard University, 250 Longwood Avenue, Boston, MA 02115, USA
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Abstract
We have developed new open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cisTEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k – 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cisTEM is available for download from cistem.org.
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Affiliation(s)
- Timothy Grant
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Alexis Rohou
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
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48
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Huber ST, Kuhm T, Sachse C. Automated tracing of helical assemblies from electron cryo-micrographs. J Struct Biol 2017; 202:1-12. [PMID: 29191673 PMCID: PMC5847486 DOI: 10.1016/j.jsb.2017.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/24/2017] [Accepted: 11/26/2017] [Indexed: 01/17/2023]
Abstract
Structure determination of helical specimens commonly requires datasets from thousands of micrographs often obtained by automated cryo-EM data acquisition. Interactive tracing of helical assemblies from such a number of micrographs is labor-intense and time-consuming. Here, we introduce an automated tracing tool MicHelixTrace that precisely locates helix traces from micrographs of rigid as well as very flexible helical assemblies with small numbers of false positives. The computer program is fast and has low computational requirements. In addition to helix coordinates required for a subsequent helical reconstruction work-flow, we determine the persistence length of the polymer ensemble. This information provides a useful measure to characterize mechanical properties of helical assemblies and to evaluate the potential for high-resolution structure determination.
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Affiliation(s)
- Stefan T Huber
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tanja Kuhm
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Carsten Sachse
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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49
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Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging. Nat Commun 2017; 8:1436. [PMID: 29127347 PMCID: PMC5681674 DOI: 10.1038/s41467-017-01668-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/05/2017] [Indexed: 12/13/2022] Open
Abstract
Archaeal viruses have evolved to infect hosts often thriving in extreme conditions such as high temperatures. However, there is a paucity of information on archaeal virion structures, genome packaging, and determinants of temperature resistance. The rod-shaped virus APBV1 (Aeropyrum pernix bacilliform virus 1) is among the most thermostable viruses known; it infects a hyperthermophile Aeropyrum pernix, which grows optimally at 90 °C. Here we report the structure of APBV1, determined by cryo-electron microscopy at near-atomic resolution. Tight packing of the major virion glycoprotein (VP1) is ensured by extended hydrophobic interfaces, and likely contributes to the extreme thermostability of the helical capsid. The double-stranded DNA is tightly packed in the capsid as a left-handed superhelix and held in place by the interactions with positively charged residues of VP1. The assembly is closed by specific capping structures at either end, which we propose to play a role in DNA packing and delivery. The rod-shaped virus APBV1 is among the most thermostable viruses known. Here, Ptchelkine et al. determine its structure at near-atomic resolution, show that the DNA is packed as left-handed superhelix and identify extended hydrophobic interfaces that likely contribute to the extreme thermostability of the capsid.
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TORC1 organized in inhibited domains (TOROIDs) regulate TORC1 activity. Nature 2017; 550:265-269. [PMID: 28976958 PMCID: PMC5640987 DOI: 10.1038/nature24021] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 08/21/2017] [Indexed: 12/17/2022]
Abstract
The Target of Rapamycin (TOR) is a eukaryotic serine/threonine protein kinase that functions in two distinct complexes, TORC1 and TORC2, to regulate growth and metabolism1,2. GTPases, responding to signals generated by abiotic stressors, nutrients, and, in metazoans, growth factors, play an important3, but poorly understood role in TORC1 regulation. Here, we report that, in budding yeast, glucose withdrawal, which leads to an acute loss of TORC1 kinase activity4, triggers a similarly rapid Rag GTPase-dependent redistribution of TORC1 from being semi-uniform around the vacuolar membrane to a single, vacuole-associated cylindrical structure visible by super-resolution optical microscopy. 3D reconstructions of cryo-electron micrograph images of these purified cylinders demonstrate that TORC1 oligomerizes into a higher-level hollow helical assembly which we name a TOROID (TORC1 Organised in Inhibited Domain). Fitting of the recently described mammalian TORC1 structure into our helical map revealed that oligomerisation leads to steric occlusion of the active site. Guided by the implications from our reconstruction, we present a TOR1 allele that prevents both TOROID formation and TORC1 inactivation in response to glucose withdrawal demonstrating that oligomerisation is necessary for TORC1 inactivation. Our results reveal a novel mechanism by which Rag-GTPases regulate TORC1 activity and suggest that the reversible assembly/disassembly of higher-level structure may be a new paradigm for the regulation of protein kinases.
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