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Watanabe R, Zyla D, Parekh D, Hong C, Jones Y, Schendel SL, Wan W, Castillon G, Saphire EO. Intracellular Ebola virus nucleocapsid assembly revealed by in situ cryo-electron tomography. Cell 2024:S0092-8674(24)00973-5. [PMID: 39293445 DOI: 10.1016/j.cell.2024.08.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/04/2024] [Accepted: 08/21/2024] [Indexed: 09/20/2024]
Abstract
Filoviruses, including the Ebola and Marburg viruses, cause hemorrhagic fevers with up to 90% lethality. The viral nucleocapsid is assembled by polymerization of the nucleoprotein (NP) along the viral genome, together with the viral proteins VP24 and VP35. We employed cryo-electron tomography of cells transfected with viral proteins and infected with model Ebola virus to illuminate assembly intermediates, as well as a 9 Å map of the complete intracellular assembly. This structure reveals a previously unresolved third and outer layer of NP complexed with VP35. The intrinsically disordered region, together with the C-terminal domain of this outer layer of NP, provides the constant width between intracellular nucleocapsid bundles and likely functions as a flexible tether to the viral matrix protein in the virion. A comparison of intracellular nucleocapsids with prior in-virion nucleocapsid structures reveals that the nucleocapsid further condenses vertically in the virion. The interfaces responsible for nucleocapsid assembly are highly conserved and offer targets for broadly effective antivirals.
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Affiliation(s)
- Reika Watanabe
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Dawid Zyla
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Diptiben Parekh
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Connor Hong
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Ying Jones
- Electron Microscopy Core, University of California, San Diego, La Jolla, CA 92037, USA
| | - Sharon L Schendel
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - William Wan
- Vanderbilt University Center for Structural Biology, Nashville, TN 37235, USA
| | - Guillaume Castillon
- Electron Microscopy Core, University of California, San Diego, La Jolla, CA 92037, USA
| | - Erica Ollmann Saphire
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
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2
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Jimah JR, Kundu N, Stanton AE, Sochacki KA, Canagarajah B, Chan L, Strub MP, Wang H, Taraska JW, Hinshaw JE. Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission. Dev Cell 2024; 59:1783-1793.e5. [PMID: 38663399 PMCID: PMC11265984 DOI: 10.1016/j.devcel.2024.04.008] [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: 06/08/2023] [Revised: 12/29/2023] [Accepted: 04/04/2024] [Indexed: 07/25/2024]
Abstract
Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the plasma membrane. Although atomic models of the dynamin helical polymer bound to guanosine triphosphate (GTP) analogs define earlier stages of membrane constriction, there are no atomic models of the assembled state post-GTP hydrolysis. Here, we used cryo-EM methods to determine atomic structures of the dynamin helical polymer assembled on lipid tubules, akin to necks of budding endocytic vesicles, in a guanosine diphosphate (GDP)-bound, super-constricted state. In this state, dynamin is assembled as a 2-start helix with an inner lumen of 3.4 nm, primed for spontaneous fission. Additionally, by cryo-electron tomography, we trapped dynamin helical assemblies within HeLa cells using the GTPase-defective dynamin K44A mutant and observed diverse dynamin helices, demonstrating that dynamin can accommodate a range of assembled complexes in cells that likely precede membrane fission.
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Affiliation(s)
- John R Jimah
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Nidhi Kundu
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abigail E Stanton
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kem A Sochacki
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bertram Canagarajah
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lieza Chan
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marie-Paule Strub
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jenny E Hinshaw
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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3
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Sanchez JC, Baumgardt JK, Wright ER. Purification and Cryo-Electron Microscopy Analysis of Bacterial Appendages. Bio Protoc 2024; 14:e5032. [PMID: 39100595 PMCID: PMC11292135 DOI: 10.21769/bioprotoc.5032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/14/2024] [Accepted: 06/30/2024] [Indexed: 08/06/2024] Open
Abstract
A number of extracellular helical protein polymers are crucial for supporting bacterial motility. The bacterial flagellum is a polymeric appendage used to support cellular motility. Historically, structural studies of flagellar and other filaments were limited to those present as or locked into straightened states. Here, we present a robust workflow that produces biologically relevant high-resolution cryo-electron microscopy (cryo-EM) structures of bacterial flagellar filaments. We highlight how a simple purification method, centered around several centrifugation steps, exploits the process of filament ejection in Caulobacter crescentus and results in isolated filaments amenable to transmission electron microscopy (TEM) studies. The quality of the sample is validated by SDS-PAGE and negative stain TEM analysis before a sample is vitrified for cryogenic electron microscopy (cryo-EM) data collection. We provide a detailed protocol for reconstructing either straight or curved flagellar filaments by cryo-EM helical reconstruction methods, followed by an overview of model building and validation. In our hands, this workflow resulted in several flagellar structures below 3 Å resolution, with one data set reaching a global resolution of 2.1 Å. The application of this workflow supports structure-function studies to better understand the molecular interactions that regulate filament architecture in biologically relevant states. Future work will not only examine interactions that regulate bacterial flagellar and other filament organization but also provide a foundation for developing new helical biopolymers for biotech applications. Key features • Rapid high-quality purification of bacterial flagella via simple bacterial culturing, centrifugation, and resuspension methods. • High-throughput cryo-EM data collection of filamentous objects. • Use of cryoSPARC implementations of helical reconstruction algorithms to generate high-resolution 3D structures of bacterial flagella or other helical polymers.
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Affiliation(s)
- Juan C. Sanchez
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- Biotechnology Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Joseph K. Baumgardt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
- Biotechnology Training Program, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, UW-Madison, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Morgridge Institute for Research, UW-Madison, Madison, WI, USA
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4
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Fernandez A, Hoq MR, Hallinan GI, Li D, Bharath SR, Vago FS, Zhang X, Ozcan KA, Newell KL, Garringer HJ, Jiang W, Ghetti B, Vidal R. Cryo-EM structures of amyloid-β and tau filaments in Down syndrome. Nat Struct Mol Biol 2024; 31:903-909. [PMID: 38553642 PMCID: PMC11189299 DOI: 10.1038/s41594-024-01252-3] [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: 05/11/2023] [Accepted: 02/09/2024] [Indexed: 04/10/2024]
Abstract
Adult individuals with Down syndrome (DS) develop Alzheimer disease (AD). Whether there is a difference between AD in DS and AD regarding the structure of amyloid-β (Aβ) and tau filaments is unknown. Here we report the structure of Aβ and tau filaments from two DS brains. We found two Aβ40 filaments (types IIIa and IIIb) that differ from those previously reported in sporadic AD and two types of Aβ42 filaments (I and II) identical to those found in sporadic and familial AD. Tau filaments (paired helical filaments and straight filaments) were identical to those in AD, supporting the notion of a common mechanism through which amyloids trigger aggregation of tau. This knowledge is important for understanding AD in DS and assessing whether adults with DS could be included in AD clinical trials.
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Affiliation(s)
- Anllely Fernandez
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Md Rejaul Hoq
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Grace I Hallinan
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Daoyi Li
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Sakshibeedu R Bharath
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Frank S Vago
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Xiaoqi Zhang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Kadir A Ozcan
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Holly J Garringer
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wen Jiang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA.
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.
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5
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Cingolani G, Iglesias S, Hou CF, Lemire S, Soriaga A, Kyme P. Cryo-EM analysis of Pseudomonas phage Pa193 structural components. RESEARCH SQUARE 2024:rs.3.rs-4189479. [PMID: 38659960 PMCID: PMC11042391 DOI: 10.21203/rs.3.rs-4189479/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various clinical settings, commonly called phage therapy, to address this growing public health crisis. Here, we describe a high-resolution structural atlas of a therapeutic, contractile-tailed Pseudomonas phage, Pa193. We used bioinformatics, proteomics, and cryogenic electron microscopy single particle analysis to identify, annotate, and build atomic models for 21 distinct structural polypeptide chains forming the icosahedral capsid, neck, contractile tail, and baseplate. We identified a putative scaffolding protein stabilizing the interior of the capsid 5-fold vertex. We also visualized a large portion of Pa193 ~ 500 Å long tail fibers and resolved the interface between the baseplate and tail fibers. The work presented here provides a framework to support a better understanding of phages as biomedicines for phage therapy and inform engineering opportunities.
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6
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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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7
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Ouyang R, Costa AR, Cassidy CK, Otwinowska A, Williams VCJ, Latka A, Stansfeld PJ, Drulis-Kawa Z, Briers Y, Pelt DM, Brouns SJJ, Briegel A. High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers. Nat Commun 2022; 13:7241. [PMID: 36433970 PMCID: PMC9700779 DOI: 10.1038/s41467-022-34972-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combine cryo-electron microscopy methods, protein structure prediction methods, molecular simulations, microbiological and machine learning approaches to explore the capsid, tail, and tail fibers of ϕKp24. We determine the structure of the capsid and tail at 4.1 Å and 3.0 Å resolution. We observe the tail fibers are branched and rearranged dramatically upon cell surface attachment. This complex configuration involves fourteen putative tail fibers with depolymerase activity that provide ϕKp24 with the ability to infect a broad panel of capsular polysaccharide (CPS) types of Klebsiella pneumoniae. Our study provides structural and functional insight into how ϕKp24 adapts to the variable surfaces of capsulated bacterial pathogens, which is useful for the development of phage therapy approaches against pan-drug resistant K. pneumoniae strains.
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Affiliation(s)
- Ruochen Ouyang
- grid.43169.390000 0001 0599 1243MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xianning West Road 28, Xi’an, 710049 China ,grid.5132.50000 0001 2312 1970Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ana Rita Costa
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands ,grid.5292.c0000 0001 2097 4740Kavli Institute of Nanoscience, Delft, The Netherlands
| | - C. Keith Cassidy
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, UK
| | - Aleksandra Otwinowska
- grid.8505.80000 0001 1010 5103Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63-77, 51-148 Wroclaw, Poland
| | - Vera C. J. Williams
- grid.5132.50000 0001 2312 1970Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Agnieszka Latka
- grid.8505.80000 0001 1010 5103Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63-77, 51-148 Wroclaw, Poland ,grid.5342.00000 0001 2069 7798Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Phill J. Stansfeld
- grid.7372.10000 0000 8809 1613School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
| | - Zuzanna Drulis-Kawa
- grid.8505.80000 0001 1010 5103Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63-77, 51-148 Wroclaw, Poland
| | - Yves Briers
- grid.5342.00000 0001 2069 7798Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Daniël M. Pelt
- grid.5132.50000 0001 2312 1970Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333CA Leiden, The Netherlands
| | - Stan J. J. Brouns
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands ,grid.5292.c0000 0001 2097 4740Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Ariane Briegel
- grid.5132.50000 0001 2312 1970Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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