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Dong D, Song Y, Wu S, Wang B, Peng C, Zhang W, Kong W, Zhang Z, Song J, Hou LH, Li S. Molecular basis of Ad5-nCoV vaccine-induced immunogenicity. Structure 2025; 33:858-868.e5. [PMID: 40112804 DOI: 10.1016/j.str.2025.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 12/12/2024] [Accepted: 02/21/2025] [Indexed: 03/22/2025]
Abstract
Ad5-nCoV (Convidecia) is listed for emergency use against COVID-19 by the World Health Organization (WHO) and has been globally administered to millions of people. It utilizes human adenovirus 5 (Ad5) replication-incompetent vector to deliver the spike (S) protein gene from various SARS-CoV-2 strains. Despite promising clinical data, the molecular mechanism underlying its high immunogenicity and adverse reactions remain incompletely understood. Here, we primarily applied cryo-electron tomography (cryo-ET), fluorescence microscopy and mass spectrometry to analyze the Ad5-nCoV_Wu and Ad5-nCoV_O vaccine-induced S antigens. These antigens encode the unmodified SARS-CoV-2 Wuhan-Hu-1 S gene and the stabilized Omicron S gene, respectively. Our findings highlight the structural integrity, antigenicity, and dense distribution on cell membrane of the vaccine-induced S proteins. Ad5-nCoV_O induced S proteins exhibit improved stability and reduced syncytia formation among inoculated cells. Our work demonstrates that Ad5-nCoV is a prominent platform for antigen induction and cryo-ET can be a useful technique for vaccine characterization and development.
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Affiliation(s)
- Dongyang Dong
- Beijing Frontier Research Center for Biological Structure & Tsinghua-Peking Center for Life Sciences & State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yutong Song
- Beijing Frontier Research Center for Biological Structure & Tsinghua-Peking Center for Life Sciences & State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shipo Wu
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Busen Wang
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Cheng Peng
- Beijing Frontier Research Center for Biological Structure & Tsinghua-Peking Center for Life Sciences & State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weiping Zhang
- Beijing Frontier Research Center for Biological Structure & Tsinghua-Peking Center for Life Sciences & State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weizheng Kong
- Beijing Frontier Research Center for Biological Structure & Tsinghua-Peking Center for Life Sciences & State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zheyuan Zhang
- Beijing Frontier Research Center for Biological Structure & Tsinghua-Peking Center for Life Sciences & State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingwen Song
- Beijing Frontier Research Center for Biological Structure & Tsinghua-Peking Center for Life Sciences & State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li-Hua Hou
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Sai Li
- Beijing Frontier Research Center for Biological Structure & Tsinghua-Peking Center for Life Sciences & State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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2
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Usmani M, Coudray N, Riggi M, Raghu R, Ramchandani H, Bobe D, Kopylov M, Zhong ED, Iwasa JH, Ekiert DC, Bhabha G. Cryo-ET reveals the in situ architecture of the polar tube invasion apparatus from microsporidian parasites. Proc Natl Acad Sci U S A 2025; 122:e2415233122. [PMID: 40067903 PMCID: PMC11929483 DOI: 10.1073/pnas.2415233122] [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: 07/29/2024] [Accepted: 01/28/2025] [Indexed: 03/19/2025] Open
Abstract
Microsporidia are divergent fungal pathogens that employ a unique harpoon-like apparatus called the polar tube (PT) to invade host cells. The long PT is fired out of the microsporidian spore over the course of just a few hundred milliseconds. Once fired, the PT is thought to pierce the plasma membrane of a target cell and act as a conduit for the transfer of the parasite into the host cell, which initiates infection. The PT architecture and its association with neighboring organelles within the parasite cell remain poorly understood. Here, we use cryoelectron tomography to investigate the structural cell biology of the PT in dormant spores from the human-infecting microsporidian species, Encephalitozoon intestinalis. Segmentation and subtomogram averaging of the PT reveal at least four layers: two protein-based layers surrounded by a membrane layer and filled with a dense core. Regularly spaced protein filaments form the structural skeleton of the PT. Combining cryoelectron tomography with cellular modeling, we propose a model for the three-dimensional organization of the polaroplast, an organelle that surrounds the PT and is continuous with the outermost, membranous layer of the PT. Our results reveal the ultrastructure of the microsporidian invasion apparatus in situ, laying the foundation for understanding infection mechanisms.
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Affiliation(s)
- Mahrukh Usmani
- Department of Biology, Johns Hopkins University, Baltimore, MD21218
- Vilcek Institute of Graduate Biomedical Sciences, New York University School of Medicine, New York, NY10016
| | - Nicolas Coudray
- Department of Biology, Johns Hopkins University, Baltimore, MD21218
- Applied Bioinformatics Laboratories, Office of Science & Research, New York University School of Medicine, New York, NY10016
| | - Margot Riggi
- Department of Biochemistry, University of Utah, Salt Lake City, UT84132
| | - Rishwanth Raghu
- Department of Computer Science, Princeton University, Princeton, NJ08540
| | | | - Daija Bobe
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY10027
| | - Mykhailo Kopylov
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY10027
| | - Ellen D. Zhong
- Department of Computer Science, Princeton University, Princeton, NJ08540
| | - Janet H. Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT84132
| | - Damian C. Ekiert
- Department of Biology, Johns Hopkins University, Baltimore, MD21218
| | - Gira Bhabha
- Department of Biology, Johns Hopkins University, Baltimore, MD21218
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3
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Shah PNM, Sanchez-Garcia R, Stuart DI. TomoCPT: a generalizable model for 3D particle detection and localization in cryo-electron tomograms. Acta Crystallogr D Struct Biol 2025; 81:63-76. [PMID: 39902808 PMCID: PMC11804251 DOI: 10.1107/s2059798325000865] [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: 10/30/2024] [Accepted: 01/30/2025] [Indexed: 02/06/2025] Open
Abstract
Cryo-electron tomography is a rapidly developing field for studying macromolecular complexes in their native environments and has the potential to revolutionize our understanding of protein function. However, fast and accurate identification of particles in cryo-tomograms is challenging and represents a significant bottleneck in downstream processes such as subtomogram averaging. Here, we present tomoCPT (Tomogram Centroid Prediction Tool), a transformer-based solution that reformulates particle detection as a centroid-prediction task using Gaussian labels. Our approach, which is built upon the SwinUNETR architecture, demonstrates superior performance compared with both conventional binary labelling strategies and template matching. We show that tomoCPT effectively generalizes to novel particle types through zero-shot inference and can be significantly enhanced through fine-tuning with limited data. The efficacy of tomoCPT is validated using three case studies: apoferritin, achieving a resolution of 3.0 Å compared with 3.3 Å using template matching, SARS-CoV-2 spike proteins on cell surfaces, yielding an 18.3 Å resolution map where template matching proved unsuccessful, and rubisco molecules within carboxysomes, reaching 8.0 Å resolution. These results demonstrate the ability of tomoCPT to handle varied scenarios, including densely packed environments and membrane-bound proteins. The implementation of the tool as a command-line program, coupled with its minimal data requirements for fine-tuning, makes it a practical solution for high-throughput cryo-ET data-processing workflows.
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Affiliation(s)
- Pranav N. M. Shah
- Division of Structural BiologyUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUnited Kingdom
| | - Ruben Sanchez-Garcia
- School of Science and TechnologyIE UniversityPaseo de la Castellana 25928046MadridSpain
| | - David I. Stuart
- Division of Structural BiologyUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUnited Kingdom
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4
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de Jager L, Jansen KI, Hoogebeen R, Akhmanova A, Kapitein LC, Förster F, Howes SC. StableMARK-decorated microtubules in cells have expanded lattices. J Cell Biol 2025; 224:e202206143. [PMID: 39387699 PMCID: PMC11471893 DOI: 10.1083/jcb.202206143] [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: 06/30/2022] [Revised: 05/10/2024] [Accepted: 09/27/2024] [Indexed: 10/15/2024] Open
Abstract
Microtubules are crucial in cells and are regulated by various mechanisms like posttranslational modifications, microtubule-associated proteins, and tubulin isoforms. Recently, the conformation of the microtubule lattice has also emerged as a potential regulatory factor, but it has remained unclear to what extent different lattices co-exist within the cell. Using cryo-electron tomography, we find that, while most microtubules have a compacted lattice (∼41 Å monomer spacing), approximately a quarter of the microtubules displayed more expanded lattice spacings. The addition of the microtubule-stabilizing agent Taxol increased the lattice spacing of all microtubules, consistent with results on reconstituted microtubules. Furthermore, correlative cryo-light and electron microscopy revealed that the stable subset of microtubules labeled by StableMARK, a marker for stable microtubules, predominantly displayed a more expanded lattice spacing (∼41.9 Å), further suggesting a close connection between lattice expansion and microtubule stability. The coexistence of different lattices and their correlation with stability implicate lattice spacing as an important factor in establishing specific microtubule subsets.
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Affiliation(s)
- Leanne de Jager
- Structural Biochemistry, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Klara I. Jansen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Robin Hoogebeen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Stuart C. Howes
- Structural Biochemistry, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
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5
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Johnstone BA, Hardy JM, Ha J, Butkovic A, Koszalka P, Accurso C, Venugopal H, de Marco A, Krupovic M, Coulibaly F. The nucleocapsid architecture and structural atlas of the prototype baculovirus define the hallmarks of a new viral realm. SCIENCE ADVANCES 2024; 10:eado2631. [PMID: 39693434 DOI: 10.1126/sciadv.ado2631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 11/12/2024] [Indexed: 12/20/2024]
Abstract
Baculovirus is the most studied insect virus owing to a broad ecological distribution and ease of engineering for biotechnological applications. However, its structure and evolutionary place in the virosphere remain enigmatic. Using cryo-electron microscopy, we show that the nucleocapsid forms a covalently cross-linked helical tube protecting a highly compacted 134-kilobase pair DNA genome. The ends of the tube are sealed by the base and cap substructures, which share a 126-subunit hub but differ in components that promote actin tail-mediated propulsion and nuclear entry of the nucleocapsid, respectively. Unexpectedly, sensitive searches for hidden evolutionary links show that the morphogenetic machinery and conserved oral infectivity factors originated within the lineage of baculo-like viruses (class Naldaviricetes). The unique viral architecture and structural atlas of hallmark proteins firmly place these viruses into a separate new realm, the highest taxonomy rank, and provide a structural framework to expand their use as sustainable bioinsecticides and biomedical tools.
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Affiliation(s)
- Bronte A Johnstone
- Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Joshua M Hardy
- Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jungmin Ha
- Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Anamarija Butkovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015, Paris, France
| | - Paulina Koszalka
- Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Cathy Accurso
- Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Hariprasad Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Alex de Marco
- Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015, Paris, France
| | - Fasséli Coulibaly
- Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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6
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Kudryashev M. The big chill: Growth of in situ structural biology with cryo-electron tomography. QRB DISCOVERY 2024; 5:e10. [PMID: 39687233 PMCID: PMC11649376 DOI: 10.1017/qrd.2024.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/23/2024] [Accepted: 08/29/2024] [Indexed: 12/18/2024] Open
Abstract
In situ structural biology with cryo-electron tomography (cryo-ET) and subtomogram averaging (StA) is evolving as a major method to understand the structure, function, and interactions of biological molecules in cells in a single experiment. Since its inception, the method has matured with some stellar highlights and with further opportunities to broaden its applications. In this short review, I want to provide a personal perspective on the developments in cryo-ET as I have seen it for the last ~20 years and outline the major steps that led to its success. This perspective highlights cryo-ET with my eyes as a junior researcher and my view on the present and past developments in hardware and software for in situ structural biology with cryo-ET.
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Affiliation(s)
- Mikhail Kudryashev
- In situ Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Medical Physics and Biophysics, Charite–Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin and Humboldt Universitat zu Berlin, Institute for Medical Physics and Biophysics, Berlin, Germany
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7
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van Hoorn C, Carter AP. A cryo-electron tomography study of ciliary rootlet organization. eLife 2024; 12:RP91642. [PMID: 39641991 PMCID: PMC11623930 DOI: 10.7554/elife.91642] [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] [Indexed: 12/07/2024] Open
Abstract
Ciliary rootlets are striated bundles of filaments that connect the base of cilia to internal cellular structures. Rootlets are critical for the sensory and motile functions of cilia. However, the mechanisms underlying these functions remain unknown, in part due to a lack of structural information of rootlet organization. In this study, we obtain 3D reconstructions of membrane-associated and purified rootlets from mouse retina using cryo-electron tomography. We show that flexible protrusions on the rootlet surface, which emanate from the cross-striations, connect to intracellular membranes. In purified rootlets, the striations were classified into amorphous (A)-bands, associated with accumulations on the rootlet surface, and discrete (D)-bands corresponding to punctate lines of density that run through the rootlet. These striations connect a flexible network of longitudinal filaments. Subtomogram averaging suggests the filaments consist of two intertwined coiled coils. The rootlet's filamentous architecture, with frequent membrane-connecting cross-striations, lends itself well for anchoring large membranes in the cell.
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8
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Burt A, Toader B, Warshamanage R, von Kügelgen A, Pyle E, Zivanov J, Kimanius D, Bharat TAM, Scheres SHW. An image processing pipeline for electron cryo-tomography in RELION-5. FEBS Open Bio 2024; 14:1788-1804. [PMID: 39147729 PMCID: PMC11532982 DOI: 10.1002/2211-5463.13873] [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: 04/30/2024] [Revised: 06/20/2024] [Accepted: 07/16/2024] [Indexed: 08/17/2024] Open
Abstract
Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three-dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution for de novo atomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and interoperability represents a barrier for newcomers to the field. Here, we present an image processing pipeline for electron tomography data in RELION-5, with functionality ranging from the import of unprocessed movies to the automated building of atomic models in the final maps. Our explicit definition of metadata items that describe the steps of our pipeline has been designed for interoperability with other software tools and provides a framework for further standardisation.
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Affiliation(s)
- Alister Burt
- MRC Laboratory of Molecular Biology, Cambridge Biomedical CampusCambridgeUK
- Department of Structural BiologyGenentechSouth San FranciscoCAUSA
| | - Bogdan Toader
- MRC Laboratory of Molecular Biology, Cambridge Biomedical CampusCambridgeUK
| | - Rangana Warshamanage
- CCP‐EM, Scientific Computing DepartmentUKRI Science and Technology Facilities Council, Harwell CampusDidcotUK
- Department of PsychiatryUniversity of PittsburghPittsburghPAUSA
| | | | - Euan Pyle
- Institute of Structural and Molecular Biology, Birkbeck CollegeLondonUK
- The Francis Crick InstituteLondonUK
- Present address:
European Molecular Biology LaboratoryHeidelbergGermany
| | - Jasenko Zivanov
- MRC Laboratory of Molecular Biology, Cambridge Biomedical CampusCambridgeUK
| | - Dari Kimanius
- MRC Laboratory of Molecular Biology, Cambridge Biomedical CampusCambridgeUK
- Present address:
CZ Imaging InstituteRedwood CityCAUSA
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9
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Dahmane S, Schexnaydre E, Zhang J, Rosendal E, Chotiwan N, Kumari Singh B, Yau WL, Lundmark R, Barad B, Grotjahn DA, Liese S, Carlson A, Overby A, Carlson LA. Cryo-electron tomography reveals coupled flavivirus replication, budding and maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.13.618056. [PMID: 39416041 PMCID: PMC11482891 DOI: 10.1101/2024.10.13.618056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Flaviviruses replicate their genomes in replication organelles (ROs) formed as bud-like invaginations on the endoplasmic reticulum (ER) membrane, which also functions as the site for virion assembly. While this localization is well established, it is not known to what extent viral membrane remodeling, genome replication, virion assembly, and maturation are coordinated. Here, we imaged tick-borne flavivirus replication in human cells using cryo-electron tomography. We find that the RO membrane bud is shaped by a combination of a curvature-establishing coat and the pressure from intraluminal template RNA. A protein complex at the RO base extends to an adjacent membrane, where immature virions bud. Naturally occurring furin site variants determine whether virions mature in the immediate vicinity of ROs. We further visualize replication in mouse brain tissue by cryo-electron tomography. Taken together, these findings reveal a close spatial coupling of flavivirus genome replication, budding, and maturation.
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10
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Young LN, Sherrard A, Zhou H, Shaikh F, Hutchings J, Riggi M, Rosen MK, Giraldez AJ, Villa E. ExoSloNano: Multi-Modal Nanogold Tags for identification of Macromolecules in Live Cells & Cryo-Electron Tomograms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.12.617288. [PMID: 39416124 PMCID: PMC11482945 DOI: 10.1101/2024.10.12.617288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
In situ cryo-Electron Microscopy (cryo-EM) enables the direct interrogation of structure-function relationships by resolving macromolecular structures in their native cellular environment. Tremendous progress in sample preparation, imaging and data processing over the past decade has contributed to the identification and determination of large biomolecular complexes. However, the majority of proteins are of a size that still eludes identification in cellular cryo-EM data, and most proteins exist in low copy numbers. Therefore, novel tools are needed for cryo-EM to identify the vast majority of macromolecules across multiple size scales (from microns to nanometers). Here, we introduce and validate novel nanogold probes that enable the detection of specific proteins using cryo-ET (cryo-Electron Tomography) and resin-embedded correlated light and electron microscopy (CLEM). We demonstrate that these nanogold probes can be introduced into live cells, in a manner that preserves intact molecular networks and cell viability. We use this system to identify both cytoplasmic and nuclear proteins by room temperature EM, and resolve associated structures by cryo-ET. We further employ gold particles of different sizes to enable future multiplexed labeling and structural analysis. By providing high efficiency protein labeling in live cells and molecular specificity within cryo-ET tomograms, we establish a broadly enabling tool that significantly expands the proteome available to electron microscopy.
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Affiliation(s)
- Lindsey N Young
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Huabin Zhou
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Farhaz Shaikh
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Joshua Hutchings
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Margot Riggi
- Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Michael K Rosen
- University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Dallas, TX, USA
| | | | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, La Jolla, CA, USA
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11
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Marcink TC, Zipursky G, Sobolik EB, Golub K, Herman E, Stearns K, Greninger AL, Porotto M, Moscona A. How a paramyxovirus fusion/entry complex adapts to escape a neutralizing antibody. Nat Commun 2024; 15:8831. [PMID: 39396053 PMCID: PMC11470942 DOI: 10.1038/s41467-024-53082-y] [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: 03/26/2024] [Accepted: 09/27/2024] [Indexed: 10/14/2024] Open
Abstract
Paramyxoviruses including measles, Nipah, and parainfluenza viruses are public health threats with pandemic potential. Human parainfluenza virus type 3 (HPIV3) is a leading cause of illness in pediatric, older, and immunocompromised populations. There are no approved vaccines or therapeutics for HPIV3. Neutralizing monoclonal antibodies (mAbs) that target viral fusion are a potential strategy for mitigating paramyxovirus infection, however their utility may be curtailed by viral evolution that leads to resistance. Paramyxoviruses enter cells by fusing with the cell membrane in a process mediated by a complex consisting of a receptor binding protein (HN) and a fusion protein (F). Existing atomic resolution structures fail to reveal physiologically relevant interactions during viral entry. We present cryo-ET structures of pre-fusion HN-F complexes in situ on surfaces of virions that evolved resistance to an anti-HPIV3 F neutralizing mAb. Single mutations in F abolish mAb binding and neutralization. In these complexes, the HN protein that normally restrains F triggering has shifted to uncap the F apex. These complexes are more readily triggered to fuse. These structures shed light on the adaptability of the pre-fusion HN-F complex and mechanisms of paramyxoviral resistance to mAbs, and help define potential barriers to resistance for the design of mAbs.
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Affiliation(s)
- Tara C Marcink
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - Gillian Zipursky
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Elizabeth B Sobolik
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Kate Golub
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Emily Herman
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kyle Stearns
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Anne Moscona
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Microbiology & Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Physiology & Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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12
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Zheng T, Cai S. Recent technical advances in cellular cryo-electron tomography. Int J Biochem Cell Biol 2024; 175:106648. [PMID: 39181502 DOI: 10.1016/j.biocel.2024.106648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
Understanding the in situ structure, organization, and interactions of macromolecules is essential for elucidating their functions and mechanisms of action. Cellular cryo-electron tomography (cryo-ET) is a cutting-edge technique that reveals in situ molecular-resolution architectures of macromolecules in their lifelike states. It also provides insights into the three-dimensional distribution of macromolecules and their spatial relationships with various subcellular structures. Thus, cellular cryo-ET bridges the gap between structural biology and cell biology. With rapid advancements, this technique achieved substantial improvements in throughput, automation, and resolution. This review presents the fundamental principles and methodologies of cellular cryo-ET, highlighting recent developments in sample preparation, data collection, and image processing. We also discuss emerging trends and potential future directions. As cellular cryo-ET continues to develop, it is set to play an increasingly vital role in structural cell biology.
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Affiliation(s)
- Tianyu Zheng
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shujun Cai
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China.
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13
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Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. The molecular architecture of the nuclear basket. Cell 2024; 187:5267-5281.e13. [PMID: 39127037 DOI: 10.1016/j.cell.2024.07.020] [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: 03/28/2024] [Revised: 05/24/2024] [Accepted: 07/12/2024] [Indexed: 08/12/2024]
Abstract
The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of nucleoporins (Nups) in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.
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Affiliation(s)
- Digvijay Singh
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Neelesh Soni
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joshua Hutchings
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Farhaz Shaikh
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Madeleine Duquette
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sergey Suslov
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhixun Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P.R. China
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Kelly Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P.R. China
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Elizabeth Villa
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA.
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14
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Calcraft T, Stanke-Scheffler N, Nans A, Lindemann D, Taylor IA, Rosenthal PB. Integrated cryoEM structure of a spumaretrovirus reveals cross-kingdom evolutionary relationships and the molecular basis for assembly and virus entry. Cell 2024; 187:4213-4230.e19. [PMID: 39013471 DOI: 10.1016/j.cell.2024.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/26/2024] [Accepted: 06/11/2024] [Indexed: 07/18/2024]
Abstract
Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates for gene and oncolytic therapies. Structural studies of PFV contribute to the understanding of the mechanisms of FV replication, cell entry and infection, and retroviral evolution. Here we combine cryoEM and cryoET to determine high-resolution in situ structures of the PFV icosahedral capsid (CA) and envelope glycoprotein (Env), including its type III transmembrane anchor and membrane-proximal external region (MPER), and show how they are organized in an integrated structure of assembled PFV particles. The atomic models reveal an ancient retroviral capsid architecture and an unexpected relationship between Env and other class 1 fusion proteins of the Mononegavirales. Our results represent the de novo structure determination of an assembled retrovirus particle.
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Affiliation(s)
- Thomas Calcraft
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicole Stanke-Scheffler
- Institute of Medical Microbiology and Virology, University Hospital and Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Fetscherstr. 74, 01307 Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Dirk Lindemann
- Institute of Medical Microbiology and Virology, University Hospital and Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Fetscherstr. 74, 01307 Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany.
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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15
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Watson AJI, Bartesaghi A. Advances in cryo-ET data processing: meeting the demands of visual proteomics. Curr Opin Struct Biol 2024; 87:102861. [PMID: 38889501 PMCID: PMC11283971 DOI: 10.1016/j.sbi.2024.102861] [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: 02/13/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
Abstract
Cryogenic electron tomography (cryo-ET), a method that enables the viewing of biomolecules in near-native environments at high resolution, is rising in accessibility and applicability. Over the past several years, once slow sample preparation and data collection procedures have seen innovations which enable rapid collection of the large datasets required for attaining high resolution structures. Increased data availability has provided a driving force for exciting improvements in cryo-ET data processing methodologies throughout the entire processing pipeline and the development of accessible graphical user interfaces (GUIs) that enable individuals inexperienced in computational fields to convert raw tilt series into 3D structures. These advances in data processing are enabling cryo-ET to attain higher resolution and extending its applicability to more complex samples.
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Affiliation(s)
- Abigail J I Watson
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Alberto Bartesaghi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Computer Science, Duke University, Durham, NC, 27708, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA.
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16
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Usmani M, Coudray N, Riggi M, Raghu R, Ramchandani H, Bobe D, Kopylov M, Zhong ED, Iwasa JH, Ekiert DC, Bhabha G. Cryo-ET reveals the in situ architecture of the polar tube invasion apparatus from microsporidian parasites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603322. [PMID: 39026755 PMCID: PMC11257570 DOI: 10.1101/2024.07.13.603322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Microsporidia are divergent fungal pathogens that employ a harpoon-like apparatus called the polar tube (PT) to invade host cells. The PT architecture and its association with neighboring organelles remain poorly understood. Here, we use cryo-electron tomography to investigate the structural cell biology of the PT in dormant spores from the human-infecting microsporidian species, Encephalitozoon intestinalis . Segmentation and subtomogram averaging of the PT reveal at least four layers: two protein-based layers surrounded by a membrane, and filled with a dense core. Regularly spaced protein filaments form the structural skeleton of the PT. Combining cryo-electron tomography with cellular modeling, we propose a model for the 3-dimensional organization of the polaroplast, an organelle that is continuous with the membrane layer that envelops the PT. Our results reveal the ultrastructure of the microsporidian invasion apparatus in situ , laying the foundation for understanding infection mechanisms.
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17
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Chen S, Basiashvili T, Hutchings J, Murillo MS, Suarez AV, Louro JA, Leschziner AE, Villa E. Cryo-electron tomography reveals the microtubule-bound form of inactive LRRK2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599606. [PMID: 38948781 PMCID: PMC11212993 DOI: 10.1101/2024.06.18.599606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Parkinson's Disease (PD) is the second most common neurodegenerative disorder. Mutations in leucine-rich repeat kinase 2 (LRRK2), a multi-domain protein containing both a kinase and a GTPase, are a leading cause of the familial form of PD. Pathogenic LRRK2 mutations increase LRRK2 kinase activity. While the bulk of LRRK2 is found in the cytosol, the protein associates with membranes where its Rab GTPase substrates are found, and under certain conditions, with microtubules. Integrative structural studies using single-particle cryo-electron microscopy (cryo-EM) and in situ cryo-electron tomography (cryo-ET) have revealed the architecture of microtubule-associated LRRK2 filaments, and that formation of these filaments requires LRRK2's kinase to be in the active-like conformation. However, whether LRRK2 can interact with and form filaments on microtubules in its autoinhibited state, where the kinase domain is in the inactive conformation and the N-terminal LRR domain covers the kinase active site, was not known. Using cryo-ET, we show that full-length LRRK2 can oligomerize on microtubules in its autoinhibited state. Both WT-LRRK2 and PD-linked LRRK2 mutants formed filaments on microtubules. While these filaments are stabilized by the same interfaces seen in the active-LRRK2 filaments, we observed a new interface involving the N-terminal repeats that were disordered in the active-LRRK2 filaments. The helical parameters of the autoinhibited-LRRK2 filaments are different from those reported for the active-LRRK2 filaments. Finally, the autoinhibited-LRRK2 filaments are shorter and less regular, suggesting they are less stable.
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Affiliation(s)
- Siyu Chen
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Tamar Basiashvili
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Joshua Hutchings
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marta Sanz Murillo
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Amalia Villagran Suarez
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jaime Alegrio Louro
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Andres E. Leschziner
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Elizabeth Villa
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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18
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Maurer VJ, Siggel M, Kosinski J. What shapes template-matching performance in cryogenic electron tomography in situ? Acta Crystallogr D Struct Biol 2024; 80:410-420. [PMID: 38805246 PMCID: PMC11154592 DOI: 10.1107/s2059798324004303] [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: 02/22/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
The detection of specific biological macromolecules in cryogenic electron tomography data is frequently approached by applying cross-correlation-based 3D template matching. To reduce computational cost and noise, high binning is used to aggregate voxels before template matching. This remains a prevalent practice in both practical applications and methods development. Here, the relation between template size, shape and angular sampling is systematically evaluated to identify ribosomes in a ground-truth annotated data set. It is shown that at the commonly used binning, a detailed subtomogram average, a sphere and a heart emoji result in near-identical performance. These findings indicate that with current template-matching practices macromolecules can only be detected with high precision if their shape and size are sufficiently different from the background. Using theoretical considerations, the experimental results are rationalized and it is discussed why primarily low-frequency information remains at high binning and that template matching fails to be accurate because similarly shaped and sized macromolecules have similar low-frequency spectra. These challenges are discussed and potential enhancements for future template-matching methodologies are proposed.
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Affiliation(s)
- Valentin J. Maurer
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, 22607 Hamburg, Germany
| | - Marc Siggel
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, 22607 Hamburg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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19
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Galaz-Montoya JG. The advent of preventive high-resolution structural histopathology by artificial-intelligence-powered cryogenic electron tomography. Front Mol Biosci 2024; 11:1390858. [PMID: 38868297 PMCID: PMC11167099 DOI: 10.3389/fmolb.2024.1390858] [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: 02/24/2024] [Accepted: 05/08/2024] [Indexed: 06/14/2024] Open
Abstract
Advances in cryogenic electron microscopy (cryoEM) single particle analysis have revolutionized structural biology by facilitating the in vitro determination of atomic- and near-atomic-resolution structures for fully hydrated macromolecular complexes exhibiting compositional and conformational heterogeneity across a wide range of sizes. Cryogenic electron tomography (cryoET) and subtomogram averaging are rapidly progressing toward delivering similar insights for macromolecular complexes in situ, without requiring tags or harsh biochemical purification. Furthermore, cryoET enables the visualization of cellular and tissue phenotypes directly at molecular, nanometric resolution without chemical fixation or staining artifacts. This forward-looking review covers recent developments in cryoEM/ET and related technologies such as cryogenic focused ion beam milling scanning electron microscopy and correlative light microscopy, increasingly enhanced and supported by artificial intelligence algorithms. Their potential application to emerging concepts is discussed, primarily the prospect of complementing medical histopathology analysis. Machine learning solutions are poised to address current challenges posed by "big data" in cryoET of tissues, cells, and macromolecules, offering the promise of enabling novel, quantitative insights into disease processes, which may translate into the clinic and lead to improved diagnostics and targeted therapeutics.
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Affiliation(s)
- Jesús G. Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, United States
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20
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Gaifas L, Kirchner MA, Timmins J, Gutsche I. Blik is an extensible 3D visualisation tool for the annotation and analysis of cryo-electron tomography data. PLoS Biol 2024; 22:e3002447. [PMID: 38687779 PMCID: PMC11268629 DOI: 10.1371/journal.pbio.3002447] [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: 11/08/2023] [Revised: 07/24/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
Powerful, workflow-agnostic and interactive visualisation is essential for the ad hoc, human-in-the-loop workflows typical of cryo-electron tomography (cryo-ET). While several tools exist for visualisation and annotation of cryo-ET data, they are often integrated as part of monolithic processing pipelines, or focused on a specific task and offering limited reusability and extensibility. With each software suite presenting its own pros and cons and tools tailored to address specific challenges, seamless integration between available pipelines is often a difficult task. As part of the effort to enable such flexibility and move the software ecosystem towards a more collaborative and modular approach, we developed blik, an open-source napari plugin for visualisation and annotation of cryo-ET data (source code: https://github.com/brisvag/blik). blik offers fast, interactive, and user-friendly 3D visualisation thanks to napari, and is built with extensibility and modularity at the core. Data is handled and exposed through well-established scientific Python libraries such as numpy arrays and pandas dataframes. Reusable components (such as data structures, file read/write, and annotation tools) are developed as independent Python libraries to encourage reuse and community contribution. By easily integrating with established image analysis tools-even outside of the cryo-ET world-blik provides a versatile platform for interacting with cryo-ET data. On top of core visualisation features-interactive and simultaneous visualisation of tomograms, particle picks, and segmentations-blik provides an interface for interactive tools such as manual, surface-based and filament-based particle picking, and image segmentation, as well as simple filtering tools. Additional self-contained napari plugins developed as part of this work also implement interactive plotting and selection based on particle features, and label interpolation for easier segmentation. Finally, we highlight the differences with existing software and showcase blik's applicability in biological research.
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Affiliation(s)
- Lorenzo Gaifas
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Moritz A. Kirchner
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Joanna Timmins
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- Department of Chemistry, Umeå University, Umeå, Sweden
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21
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Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. The Molecular Architecture of the Nuclear Basket. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587068. [PMID: 38586009 PMCID: PMC10996695 DOI: 10.1101/2024.03.27.587068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of Nups in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.
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Affiliation(s)
- Digvijay Singh
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Neelesh Soni
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Hutchings
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Farhaz Shaikh
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Madeleine Duquette
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sergey Suslov
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhixun Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P. R. China
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Kelly Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P. R. China
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
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22
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Hernandez-Gonzalez M, Calcraft T, Nans A, Rosenthal PB, Way M. Palisade structure in intact vaccinia virions. mBio 2024; 15:e0313423. [PMID: 38171004 PMCID: PMC10865856 DOI: 10.1128/mbio.03134-23] [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: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Vaccinia virus assembly in the cytoplasm of infected cells involves the formation of a biconcave viral core inside the maturing viral particle. The boundary of the core is defined by a pseudohexagonal palisade layer, composed of trimers projecting from an inner wall. To understand the assembly of this complex core architecture, we obtained a subnanometer structure of the palisade trimer by cryo-electron tomography and subtomogram averaging of purified intact virions. Using AlphaFold2 structure predictions, we determined that the palisade is formed from trimers of the proteolytically processed form of the viral protein A10. In addition, we found that each A10 protomer associates with an α-helix (residues 24-66) of A4. Cellular localization assays outside the context of infection demonstrate that the A4 N-terminus is necessary and sufficient to interact with A10. The interaction between A4 and A10 provides insights into how the palisade layer might become tightly associated with the viral membrane during virion maturation. Reconstruction of the palisade layer reveals that, despite local hexagonal ordering, the A10/A4 trimers are widely spaced, suggesting that additional components organize the lattice. This spacing would, however, allow the adoption of the characteristic biconcave shape of the viral core. Finally, we also found that the palisade incorporates multiple copies of a hexameric portal structure. We suggest that these portals are formed by E6, a viral protein that is essential for virion assembly and required to release viral mRNA from the core early in infection.IMPORTANCEPoxviruses such as variola virus (smallpox) and monkeypox cause diseases in humans. Other poxviruses, including vaccinia and modified vaccinia Ankara, are used as vaccine vectors. Given their importance, a greater structural understanding of poxvirus virions is needed. We now performed cryo-electron tomography of purified intact vaccinia virions to study the structure of the palisade, a protein lattice that defines the viral core boundary. We identified the main viral proteins that form the palisade and their interaction surfaces and provided new insights into the organization of the viral core.
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Affiliation(s)
- Miguel Hernandez-Gonzalez
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Thomas Calcraft
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Peter B. Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Way
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, Imperial College, London, United Kingdom
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23
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Lolicato F, Steringer JP, Saleppico R, Beyer D, Fernandez-Sobaberas J, Unger S, Klein S, Riegerová P, Wegehingel S, Müller HM, Schmitt XJ, Kaptan S, Freund C, Hof M, Šachl R, Chlanda P, Vattulainen I, Nickel W. Disulfide bridge-dependent dimerization triggers FGF2 membrane translocation into the extracellular space. eLife 2024; 12:RP88579. [PMID: 38252473 PMCID: PMC10945597 DOI: 10.7554/elife.88579] [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] [Indexed: 01/23/2024] Open
Abstract
Fibroblast growth factor 2 (FGF2) exits cells by direct translocation across the plasma membrane, a type I pathway of unconventional protein secretion. This process is initiated by phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2)-dependent formation of highly dynamic FGF2 oligomers at the inner plasma membrane leaflet, inducing the formation of lipidic membrane pores. Cell surface heparan sulfate chains linked to glypican-1 (GPC1) capture FGF2 at the outer plasma membrane leaflet, completing FGF2 membrane translocation into the extracellular space. While the basic steps of this pathway are well understood, the molecular mechanism by which FGF2 oligomerizes on membrane surfaces remains unclear. In the current study, we demonstrate the initial step of this process to depend on C95-C95 disulfide-bridge-mediated FGF2 dimerization on membrane surfaces, producing the building blocks for higher FGF2 oligomers that drive the formation of membrane pores. We find FGF2 with a C95A substitution to be defective in oligomerization, pore formation, and membrane translocation. Consistently, we demonstrate a C95A variant of FGF2 to be characterized by a severe secretion phenotype. By contrast, while also important for efficient FGF2 secretion from cells, a second cysteine residue on the molecular surface of FGF2 (C77) is not involved in FGF2 oligomerization. Rather, we find C77 to be part of the interaction interface through which FGF2 binds to the α1 subunit of the Na,K-ATPase, the landing platform for FGF2 at the inner plasma membrane leaflet. Using cross-linking mass spectrometry, atomistic molecular dynamics simulations combined with a machine learning analysis and cryo-electron tomography, we propose a mechanism by which disulfide-bridged FGF2 dimers bind with high avidity to PI(4,5)P2 on membrane surfaces. We further propose a tight coupling between FGF2 secretion and the formation of ternary signaling complexes on cell surfaces, hypothesizing that C95-C95-bridged FGF2 dimers are functioning as the molecular units triggering autocrine and paracrine FGF2 signaling.
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Affiliation(s)
- Fabio Lolicato
- Heidelberg University Biochemistry CenterHeidelbergGermany
- Department of Physics, University of HelsinkiHelsinkiFinland
| | | | | | - Daniel Beyer
- Heidelberg University Biochemistry CenterHeidelbergGermany
| | | | | | - Steffen Klein
- Schaller Research Group, Department of Infectious Diseases-Virology, Heidelberg University HospitalHeidelbergGermany
| | - Petra Riegerová
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of SciencesPragueCzech Republic
| | | | | | - Xiao J Schmitt
- Institute for Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Shreyas Kaptan
- Department of Physics, University of HelsinkiHelsinkiFinland
| | - Christian Freund
- Institute for Chemistry and Biochemistry, Freie Universität BerlinBerlinGermany
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Radek Šachl
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Petr Chlanda
- Schaller Research Group, Department of Infectious Diseases-Virology, Heidelberg University HospitalHeidelbergGermany
| | | | - Walter Nickel
- Heidelberg University Biochemistry CenterHeidelbergGermany
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24
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Tai L, Yin G, Huang X, Sun F, Zhu Y. In-cell structural insight into the stability of sperm microtubule doublet. Cell Discov 2023; 9:116. [PMID: 37989994 PMCID: PMC10663601 DOI: 10.1038/s41421-023-00606-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 09/21/2023] [Indexed: 11/23/2023] Open
Abstract
The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. However, the intricate molecular architecture of intact sperm DMT remains elusive. Here, by in situ cryo-electron tomography, we solved the in-cell structure of mouse sperm DMT at 4.5-7.5 Å resolutions, and built its model with 36 kinds of MIPs in 48 nm periodicity. We identified multiple copies of Tektin5 that reinforce Tektin bundle, and multiple MIPs with different periodicities that anchor the Tektin bundle to tubulin wall. This architecture contributes to a superior stability of A-tubule than B-tubule of DMT, which was revealed by structural comparison of DMTs from the intact and deformed axonemes. Our work provides an overall molecular picture of intact sperm DMT in 48 nm periodicity that is essential to understand the molecular mechanism of sperm motility as well as the related ciliopathies.
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Affiliation(s)
- Linhua Tai
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guoliang Yin
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojun Huang
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fei Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China.
| | - Yun Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
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25
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Balyschew N, Yushkevich A, Mikirtumov V, Sanchez RM, Sprink T, Kudryashev M. Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR. Nat Commun 2023; 14:6543. [PMID: 37848413 PMCID: PMC10582028 DOI: 10.1038/s41467-023-42085-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 09/29/2023] [Indexed: 10/19/2023] Open
Abstract
Structures of macromolecules in their native state provide unique unambiguous insights into their functions. Cryo-electron tomography combined with subtomogram averaging demonstrated the power to solve such structures in situ at resolutions in the range of 3 Angstrom for some macromolecules. In order to be applicable to the structural determination of the majority of macromolecules observable in cells in limited amounts, processing of tomographic data has to be performed in a high-throughput manner. Here we present TomoBEAR-a modular configurable workflow engine for streamlined processing of cryo-electron tomographic data for subtomogram averaging. TomoBEAR combines commonly used cryo-EM packages with reasonable presets to provide a transparent ("white box") approach for data management and processing. We demonstrate applications of TomoBEAR to two data sets of purified macromolecular targets, to an ion channel RyR1 in a membrane, and the tomograms of plasma FIB-milled lamellae and demonstrate the ability to produce high-resolution structures. TomoBEAR speeds up data processing, minimizes human interventions, and will help accelerate the adoption of in situ structural biology by cryo-ET. The source code and the documentation are freely available.
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Affiliation(s)
- Nikita Balyschew
- Max Planck Institute of Biophysics, Frankfurt on Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt on Main, Frankfurt, Germany
| | - Artsemi Yushkevich
- In Situ Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Physics, Humboldt University of Berlin, Berlin, Germany
| | - Vasilii Mikirtumov
- Max Planck Institute of Biophysics, Frankfurt on Main, Germany
- In Situ Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ricardo M Sanchez
- Max Planck Institute of Biophysics, Frankfurt on Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt on Main, Frankfurt, Germany
- EMBL Heidelberg, Heidelberg, Germany
| | - Thiemo Sprink
- Core Facility for Cryo-Electron Microscopy, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Cryo-EM Facility, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Mikhail Kudryashev
- Max Planck Institute of Biophysics, Frankfurt on Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt on Main, Frankfurt, Germany.
- In Situ Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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26
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Talledge N, Yang H, Shi K, Coray R, Yu G, Arndt WG, Meng S, Baxter GC, Mendonça LM, Castaño-Díez D, Aihara H, Mansky LM, Zhang W. HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation. J Mol Biol 2023; 435:168143. [PMID: 37150290 PMCID: PMC10524356 DOI: 10.1016/j.jmb.2023.168143] [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: 09/02/2022] [Revised: 05/01/2023] [Accepted: 05/01/2023] [Indexed: 05/09/2023]
Abstract
Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus type 2 (HIV-2) immature particles possess a distinct and extensive Gag lattice morphology. To better understand the nature of the continuously curved hexagonal Gag lattice, we have used the single particle cryo-electron microscopy method to determine the HIV-2 Gag lattice structure for immature virions. The reconstruction map at 5.5 Å resolution revealed a stable, wineglass-shaped Gag hexamer structure with structural features consistent with other lentiviral immature Gag lattice structures. Cryo-electron tomography provided evidence for nearly complete ordered Gag lattice structures in HIV-2 immature particles. We also solved a 1.98 Å resolution crystal structure of the carboxyl-terminal domain (CTD) of the HIV-2 capsid (CA) protein that identified a structured helix 12 supported via an interaction of helix 10 in the absence of the SP1 region of Gag. Residues at the helix 10-12 interface proved critical in maintaining HIV-2 particle release and infectivity. Taken together, our findings provide the first 3D organization of HIV-2 immature Gag lattice and important insights into both HIV Gag lattice stabilization and virus maturation.
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Affiliation(s)
- Nathaniel Talledge
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA. https://twitter.com/BioChemTalledge
| | - Huixin Yang
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Comparative Molecular Biosciences Graduate Program, University of Minnesota - Twin Cities, St. Paul, MN 55108, USA
| | - Ke Shi
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Raffaele Coray
- BioEM Lab, Biozentrum, University of Basel - Basel, Switzerland
| | - Guichuan Yu
- Minnesota Supercomputing Institute, Office of the Vice President for Research, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Characterization Facility, College of Sciences and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - William G Arndt
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Shuyu Meng
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Molecular Pharmacology and Therapeutics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Gloria C Baxter
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota - Twin Cities, USA
| | - Luiza M Mendonça
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | | | - Hideki Aihara
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Comparative Molecular Biosciences Graduate Program, University of Minnesota - Twin Cities, St. Paul, MN 55108, USA; Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Molecular Pharmacology and Therapeutics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
| | - Wei Zhang
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Characterization Facility, College of Sciences and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
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27
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Laurent T, Carlson LA. The organization of double-stranded RNA in the chikungunya virus replication organelle. PLoS Negl Trop Dis 2023; 17:e0011404. [PMID: 37406010 DOI: 10.1371/journal.pntd.0011404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/22/2023] [Indexed: 07/07/2023] Open
Abstract
Alphaviruses are mosquito-borne, positive-sense single-stranded RNA viruses. Amongst the alphaviruses, chikungunya virus is notable as a large source of human illness, especially in tropical and subtropical regions. When they invade a cell, alphaviruses generate dedicated organelles for viral genome replication, so-called spherules. Spherules form as outward-facing buds at the plasma membrane, and it has recently been shown that the thin membrane neck that connects this membrane bud with the cytoplasm is guarded by a two-megadalton protein complex that contains all the enzymatic functions necessary for RNA replication. The lumen of the spherules contains a single copy of the negative-strand template RNA, present in a duplex with newly synthesized positive-sense RNA. Less is known about the organization of this double-stranded RNA as compared to the protein components of the spherule. Here, we analyzed cryo-electron tomograms of chikungunya virus spherules in terms of the organization of the double-stranded RNA replication intermediate. We find that the double-stranded RNA has a shortened apparent persistence length as compared to unconstrained double-stranded RNA. Around half of the genome is present in either of five conformations identified by subtomogram classification, each representing a relatively straight segment of ~25-32 nm. Finally, the RNA occupies the spherule lumen at a homogeneous density, but has a preferred orientation to be perpendicular to a vector pointing from the membrane neck towards the spherule center. Taken together, this analysis lays another piece of the puzzle of the highly coordinated alphavirus genome replication.
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Affiliation(s)
- Timothée Laurent
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå, Sweden
| | - Lars-Anders Carlson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå, Sweden
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28
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Lopez-Robles C, Scaramuzza S, Astorga-Simon EN, Ishida M, Williamson CD, Baños-Mateos S, Gil-Carton D, Romero-Durana M, Vidaurrazaga A, Fernandez-Recio J, Rojas AL, Bonifacino JS, Castaño-Díez D, Hierro A. Architecture of the ESCPE-1 membrane coat. Nat Struct Mol Biol 2023; 30:958-969. [PMID: 37322239 PMCID: PMC10352136 DOI: 10.1038/s41594-023-01014-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
Abstract
Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1), which rescues transmembrane proteins from the endolysosomal pathway for transport to the trans-Golgi network and the plasma membrane. This rescue entails the formation of recycling tubules through ESCPE-1 recruitment, cargo capture, coat assembly and membrane sculpting by mechanisms that remain largely unknown. Herein, we show that ESCPE-1 has a single-layer coat organization and suggest how synergistic interactions between ESCPE-1 protomers, phosphoinositides and cargo molecules result in a global arrangement of amphipathic helices to drive tubule formation. Our results thus define a key process of tubule-based endosomal sorting.
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Affiliation(s)
| | | | | | - Morié Ishida
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chad D Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | - David Gil-Carton
- CIC bioGUNE, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- BREM Basque Resource for Electron Microscopy, Leioa, Spain
| | - Miguel Romero-Durana
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | | | - Juan Fernandez-Recio
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | | | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Daniel Castaño-Díez
- BioEM Lab, Biozentrum, University of Basel, Basel, Switzerland.
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain.
| | - Aitor Hierro
- CIC bioGUNE, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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29
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Sexton D, Hashimi A, Beskrovnaya P, Sibanda L, Huan T, Tocheva E. The cell envelope of Thermotogae suggests a mechanism for outer membrane biogenesis. Proc Natl Acad Sci U S A 2023; 120:e2303275120. [PMID: 37094164 PMCID: PMC10160955 DOI: 10.1073/pnas.2303275120] [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: 03/03/2023] [Accepted: 03/29/2023] [Indexed: 04/26/2023] Open
Abstract
The presence of a cell membrane is one of the major structural components defining life. Recent phylogenomic analyses have supported the hypothesis that the last universal common ancestor (LUCA) was likely a diderm. Yet, the mechanisms that guided outer membrane (OM) biogenesis remain unknown. Thermotogae is an early-branching phylum with a unique OM, the toga. Here, we use cryo-electron tomography to characterize the in situ cell envelope architecture of Thermotoga maritima and show that the toga is made of extended sheaths of β-barrel trimers supporting small (~200 nm) membrane patches. Lipidomic analyses identified the same major lipid species in the inner membrane (IM) and toga, including the rare to bacteria membrane-spanning ether-bound diabolic acids (DAs). Proteomic analyses revealed that the toga was composed of multiple SLH-domain containing Ompα and novel β-barrel proteins, and homology searches detected variable conservations of these proteins across the phylum. These results highlight that, in contrast to the SlpA/OmpM superfamily of proteins, Thermotoga possess a highly diverse bipartite OM-tethering system. We discuss the implications of our findings with respect to other early-branching phyla and propose that a toga-like intermediate may have facilitated monoderm-to-diderm cell envelope transitions.
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Affiliation(s)
- Danielle L. Sexton
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
| | - Ameena Hashimi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
| | - Polina Beskrovnaya
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
| | - Lloyd Sibanda
- Department of Chemistry, University of British Columbia, Vancouver,V6T1Z1 BC, Canada
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver,V6T1Z1 BC, Canada
| | - Elitza I. Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
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30
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Kim HHS, Uddin MR, Xu M, Chang YW. Computational Methods Toward Unbiased Pattern Mining and Structure Determination in Cryo-Electron Tomography Data. J Mol Biol 2023; 435:168068. [PMID: 37003470 PMCID: PMC10164694 DOI: 10.1016/j.jmb.2023.168068] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/19/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023]
Abstract
Cryo-electron tomography can uniquely probe the native cellular environment for macromolecular structures. Tomograms feature complex data with densities of diverse, densely crowded macromolecular complexes, low signal-to-noise, and artifacts such as the missing wedge effect. Post-processing of this data generally involves isolating regions or particles of interest from tomograms, organizing them into related groups, and rendering final structures through subtomogram averaging. Template-matching and reference-based structure determination are popular analysis methods but are vulnerable to biases and can often require significant user input. Most importantly, these approaches cannot identify novel complexes that reside within the imaged cellular environment. To reliably extract and resolve structures of interest, efficient and unbiased approaches are therefore of great value. This review highlights notable computational software and discusses how they contribute to making automated structural pattern discovery a possibility. Perspectives emphasizing the importance of features for user-friendliness and accessibility are also presented.
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Affiliation(s)
- Hannah Hyun-Sook Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. https://twitter.com/hannahinthelab
| | - Mostofa Rafid Uddin
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA. https://twitter.com/duran_rafid
| | - Min Xu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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31
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Riechmann C, Zhang P. Recent structural advances in bacterial chemotaxis signalling. Curr Opin Struct Biol 2023; 79:102565. [PMID: 36868078 PMCID: PMC10460253 DOI: 10.1016/j.sbi.2023.102565] [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: 10/16/2022] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 03/05/2023]
Abstract
Bacterial chemosensory arrays have served as a model system for in-situ structure determination, clearly cataloguing the improvement of cryo-electron tomography (cryoET) over the past decade. In recent years, this has culminated in an accurately fitted atomistic model for the full-length core signalling unit (CSU) and numerous insights into the function of the transmembrane receptors responsible for signal transduction. Here, we review the achievements of the latest structural advances in bacterial chemosensory arrays and the developments which have made such advances possible.
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Affiliation(s)
- Carlos Riechmann
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
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32
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Dutka P, Metskas LA, Hurt RC, Salahshoor H, Wang TY, Malounda D, Lu GJ, Chou TF, Shapiro MG, Jensen GJ. Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET. Structure 2023; 31:518-528.e6. [PMID: 37040766 PMCID: PMC10185304 DOI: 10.1016/j.str.2023.03.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 03/01/2023] [Accepted: 03/16/2023] [Indexed: 04/13/2023]
Abstract
Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical properties of GVs have led to their use as genetically encodable contrast agents for ultrasound and MRI. Currently, however, the structure and assembly mechanism of GVs remain unknown. Here we employ cryoelectron tomography to reveal how the GV shell is formed by a helical filament of highly conserved GvpA subunits. This filament changes polarity at the center of the GV cylinder, a site that may act as an elongation center. Subtomogram averaging reveals a corrugated pattern of the shell arising from polymerization of GvpA into a β sheet. The accessory protein GvpC forms a helical cage around the GvpA shell, providing structural reinforcement. Together, our results help explain the remarkable mechanical properties of GVs and their ability to adopt different diameters and shapes.
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Affiliation(s)
- Przemysław Dutka
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lauren Ann Metskas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Robert C Hurt
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hossein Salahshoor
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ting-Yu Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dina Malounda
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - George J Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA.
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; College of Physical and Mathematical Sciences, Brigham Young University, Provo, UT 84602, USA.
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33
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Hernandez-Gonzalez M, Calcraft T, Nans A, Rosenthal PB, Way M. A succession of two viral lattices drives vaccinia virus assembly. PLoS Biol 2023; 21:e3002005. [PMID: 36862727 PMCID: PMC10013923 DOI: 10.1371/journal.pbio.3002005] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/14/2023] [Accepted: 01/19/2023] [Indexed: 03/03/2023] Open
Abstract
During its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IV) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped intracellular mature virions (IMV) that lack D13. Here, we performed cryo-electron tomography (cryo-ET) of frozen-hydrated vaccinia-infected cells to structurally characterise the maturation process in situ. During IMV formation, a new viral core forms inside IV with a wall consisting of trimeric pillars arranged in a new pseudohexagonal lattice. This lattice appears as a palisade in cross-section. As maturation occurs, which involves a 50% reduction in particle volume, the viral membrane becomes corrugated as it adapts to the newly formed viral core in a process that does not appear to require membrane removal. Our study suggests that the length of this core is determined by the D13 lattice and that the consecutive D13 and palisade lattices control virion shape and dimensions during vaccinia assembly and maturation.
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Affiliation(s)
- Miguel Hernandez-Gonzalez
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
| | - Thomas Calcraft
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Way
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, Imperial College, London, United Kingdom
- * E-mail:
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34
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Marcink TC, Zipursky G, Cheng W, Stearns K, Stenglein S, Golub K, Cohen F, Bovier F, Pfalmer D, Greninger AL, Porotto M, des Georges A, Moscona A. Subnanometer structure of an enveloped virus fusion complex on viral surface reveals new entry mechanisms. SCIENCE ADVANCES 2023; 9:eade2727. [PMID: 36763666 PMCID: PMC9917000 DOI: 10.1126/sciadv.ade2727] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
Paramyxoviruses-including important pathogens like parainfluenza, measles, and Nipah viruses-use a receptor binding protein [hemagglutinin-neuraminidase (HN) for parainfluenza] and a fusion protein (F), acting in a complex, to enter cells. We use cryo-electron tomography to visualize the fusion complex of human parainfluenza virus 3 (HN/F) on the surface of authentic clinical viruses at a subnanometer resolution sufficient to answer mechanistic questions. An HN loop inserts in a pocket on F, showing how the fusion complex remains in a ready but quiescent state until activation. The globular HN heads are rotated with respect to each other: one downward to contact F, and the other upward to grapple cellular receptors, demonstrating how HN/F performs distinct steps before F activation. This depiction of viral fusion illuminates potentially druggable targets for paramyxoviruses and sheds light on fusion processes that underpin wide-ranging biological processes but have not been visualized in situ or at the present resolution.
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Affiliation(s)
- Tara C. Marcink
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gillian Zipursky
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Wenjing Cheng
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kyle Stearns
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shari Stenglein
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kate Golub
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Frances Cohen
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Francesca Bovier
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Daniel Pfalmer
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli,” 81100 Caserta, Italy
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
- PhD Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - Anne Moscona
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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35
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Ermel UH, Arghittu SM, Frangakis AS. ArtiaX: An electron tomography toolbox for the interactive handling of sub-tomograms in UCSF ChimeraX. Protein Sci 2022; 31:e4472. [PMID: 36251681 PMCID: PMC9667824 DOI: 10.1002/pro.4472] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022]
Abstract
Cryo-electron tomography analysis involves the selection of macromolecular complexes to be used for subsequent sub-tomogram averaging and structure determination. Here, we describe a plugin developed for UCSF ChimeraX that allows for the display, selection, and editing of particles within tomograms. Positions and orientations of selected particles can be manually set, modified and inspected in real time, both on screen and in virtual reality, and exported to various file formats. The plugin allows for the parallel visualization of particles stored in several meta data lists, in the context of any three-dimensional image that can be opened with UCSF ChimeraX. The particles are rendered in user-defined colors or using colormaps, such that individual classes or groups of particles, cross-correlation coefficients, or other types of information can be highlighted to the user. The implemented functions are fast, reliable, and intuitive, exploring the broad range of features in UCSF ChimeraX. They allow for a fluent human-machine interaction, which enables an effective understanding of the sub-tomogram processing pipeline, even for non-specialist users.
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Affiliation(s)
- Utz H. Ermel
- Buchmann Institute for Molecular Life Sciences and Institute for BiophysicsGoethe University FrankfurtFrankfurtGermany
| | - Serena M. Arghittu
- Buchmann Institute for Molecular Life Sciences and Institute for BiophysicsGoethe University FrankfurtFrankfurtGermany
- Buchmann Institute for Molecular Life SciencesFrankfurt Institute for Advanced StudiesFrankfurtGermany
| | - Achilleas S. Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for BiophysicsGoethe University FrankfurtFrankfurtGermany
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36
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Pyle E, Hutchings J, Zanetti G. Strategies for picking membrane-associated particles within subtomogram averaging workflows. Faraday Discuss 2022; 240:101-113. [PMID: 35924570 PMCID: PMC9642003 DOI: 10.1039/d2fd00022a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cryo-electron tomography (cryo-ET) with subtomogram averaging (STA) has emerged as a key tool for determining macromolecular structure(s) in vitro and in situ. However, processing cryo-ET data with STA currently requires significant user expertise. Recent efforts have streamlined several steps in STA workflows; however, particle picking remains a time-consuming bottleneck for many projects and requires considerable user input. Here, we present several strategies for the time-efficient and accurate picking of membrane-associated particles using the COPII inner coat as a case study. We also discuss a range of particle cleaning solutions to remove both poor quality and false-positive particles from STA datasets. We provide a step-by-step guide and the necessary scripts for users to independently carry out the particle picking and cleaning strategies discussed.
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Affiliation(s)
- Euan Pyle
- Institute of Structural and Molecular Biology, Birkbeck CollegeMalet St.LondonWC1E 7HXUK
| | - Joshua Hutchings
- Division of Biological Sciences, University of California San DiegoLa JollaCAUSA
| | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck CollegeMalet St.LondonWC1E 7HXUK
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37
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Dahmane S, Kerviel A, Morado DR, Shankar K, Ahlman B, Lazarou M, Altan-Bonnet N, Carlson LA. Membrane-assisted assembly and selective secretory autophagy of enteroviruses. Nat Commun 2022; 13:5986. [PMID: 36216808 PMCID: PMC9550805 DOI: 10.1038/s41467-022-33483-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
Enteroviruses are non-enveloped positive-sense RNA viruses that cause diverse diseases in humans. Their rapid multiplication depends on remodeling of cytoplasmic membranes for viral genome replication. It is unknown how virions assemble around these newly synthesized genomes and how they are then loaded into autophagic membranes for release through secretory autophagy. Here, we use cryo-electron tomography of infected cells to show that poliovirus assembles directly on replication membranes. Pharmacological untethering of capsids from membranes abrogates RNA encapsidation. Our data directly visualize a membrane-bound half-capsid as a prominent virion assembly intermediate. Assembly progression past this intermediate depends on the class III phosphatidylinositol 3-kinase VPS34, a key host-cell autophagy factor. On the other hand, the canonical autophagy initiator ULK1 is shown to restrict virion production since its inhibition leads to increased accumulation of virions in vast intracellular arrays, followed by an increased vesicular release at later time points. Finally, we identify multiple layers of selectivity in virus-induced autophagy, with a strong selection for RNA-loaded virions over empty capsids and the segregation of virions from other types of autophagosome contents. These findings provide an integrated structural framework for multiple stages of the poliovirus life cycle.
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Affiliation(s)
- Selma Dahmane
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Adeline Kerviel
- Laboratory of Host-Pathogen Dynamics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dustin R Morado
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Kasturika Shankar
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Björn Ahlman
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Nihal Altan-Bonnet
- Laboratory of Host-Pathogen Dynamics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lars-Anders Carlson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden. .,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden. .,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
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38
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Navarro PP, Vettiger A, Ananda VY, Llopis PM, Allolio C, Bernhardt TG, Chao LH. Cell wall synthesis and remodelling dynamics determine division site architecture and cell shape in Escherichia coli. Nat Microbiol 2022; 7:1621-1634. [PMID: 36097171 PMCID: PMC9519445 DOI: 10.1038/s41564-022-01210-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 07/21/2022] [Indexed: 01/19/2023]
Abstract
The bacterial division apparatus catalyses the synthesis and remodelling of septal peptidoglycan (sPG) to build the cell wall layer that fortifies the daughter cell poles. Understanding of this essential process has been limited by the lack of native three-dimensional views of developing septa. Here, we apply state-of-the-art cryogenic electron tomography (cryo-ET) and fluorescence microscopy to visualize the division site architecture and sPG biogenesis dynamics of the Gram-negative bacterium Escherichia coli. We identify a wedge-like sPG structure that fortifies the ingrowing septum. Experiments with strains defective in sPG biogenesis revealed that the septal architecture and mode of division can be modified to more closely resemble that of other Gram-negative (Caulobacter crescentus) or Gram-positive (Staphylococcus aureus) bacteria, suggesting that a conserved mechanism underlies the formation of different septal morphologies. Finally, analysis of mutants impaired in amidase activation (ΔenvC ΔnlpD) showed that cell wall remodelling affects the placement and stability of the cytokinetic ring. Taken together, our results support a model in which competition between the cell elongation and division machineries determines the shape of cell constrictions and the poles they form. They also highlight how the activity of the division system can be modulated to help generate the diverse array of shapes observed in the bacterial domain.
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Affiliation(s)
- Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Andrea Vettiger
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Virly Y Ananda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Christoph Allolio
- Faculty of Mathematics and Physics, Mathematical Institute, Charles University, Prague, Czech Republic
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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39
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Marcink TC, Kicmal T, Armbruster E, Zhang Z, Zipursky G, Golub KL, Idris M, Khao J, Drew-Bear J, McGill G, Gallagher T, Porotto M, des Georges A, Moscona A. Intermediates in SARS-CoV-2 spike-mediated cell entry. SCIENCE ADVANCES 2022; 8:eabo3153. [PMID: 35984891 PMCID: PMC9390989 DOI: 10.1126/sciadv.abo3153] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 07/07/2022] [Indexed: 05/17/2023]
Abstract
SARS-CoV-2 cell entry is completed after viral spike (S) protein-mediated membrane fusion between viral and host cell membranes. Stable prefusion and postfusion S structures have been resolved by cryo-electron microscopy and cryo-electron tomography, but the refolding intermediates on the fusion pathway are transient and have not been examined. We used an antiviral lipopeptide entry inhibitor to arrest S protein refolding and thereby capture intermediates as S proteins interact with hACE2 and fusion-activating proteases on cell-derived target membranes. Cryo-electron tomography imaged both extended and partially folded intermediate states of S2, as well as a novel late-stage conformation on the pathway to membrane fusion. The intermediates now identified in this dynamic S protein-directed fusion provide mechanistic insights that may guide the design of CoV entry inhibitors.
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Affiliation(s)
- Tara C. Marcink
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Thomas Kicmal
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Emily Armbruster
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
| | - Zhening Zhang
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gillian Zipursky
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kate L. Golub
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Mohab Idris
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | | | - Jennifer Drew-Bear
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gael McGill
- Digizyme Inc., Brookline, MA, USA
- Center for Molecular and Cellular Dynamics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli,” 81100 Caserta, Italy
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - Anne Moscona
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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40
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A cytoskeletal vortex drives phage nucleus rotation during jumbo phage replication in E. coli. Cell Rep 2022; 40:111179. [PMID: 35977483 PMCID: PMC9891218 DOI: 10.1016/j.celrep.2022.111179] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/29/2022] [Accepted: 07/19/2022] [Indexed: 02/03/2023] Open
Abstract
Nucleus-forming jumbo phages establish an intricate subcellular organization, enclosing phage genomes within a proteinaceous shell called the phage nucleus. During infection in Pseudomonas, some jumbo phages assemble a bipolar spindle of tubulin-like PhuZ filaments that positions the phage nucleus at midcell and drives its intracellular rotation. This facilitates the distribution of capsids on its surface for genome packaging. Here we show that the Escherichia coli jumbo phage Goslar assembles a phage nucleus surrounded by an array of PhuZ filaments resembling a vortex instead of a bipolar spindle. Expression of a mutant PhuZ protein strongly reduces Goslar phage nucleus rotation, demonstrating that the PhuZ cytoskeletal vortex is necessary for rotating the phage nucleus. While vortex-like cytoskeletal arrays are important in eukaryotes for cytoplasmic streaming and nucleus alignment, this work identifies a coherent assembly of filaments into a vortex-like structure driving intracellular rotation within the prokaryotic cytoplasm.
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41
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Laughlin TG, Deep A, Prichard AM, Seitz C, Gu Y, Enustun E, Suslov S, Khanna K, Birkholz EA, Armbruster E, McCammon JA, Amaro RE, Pogliano J, Corbett KD, Villa E. Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Nature 2022; 608:429-435. [PMID: 35922510 PMCID: PMC9365700 DOI: 10.1038/s41586-022-05013-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/22/2022] [Indexed: 12/26/2022]
Abstract
Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems1. In response, one family of large bacteriophages uses a nucleus-like compartment to protect its replicating genomes by excluding host defence factors2-4. However, the principal composition and structure of this compartment remain unknown. Here we find that the bacteriophage nuclear shell assembles primarily from one protein, which we name chimallin (ChmA). Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin self-assembles as a flexible sheet into closed micrometre-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.
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Affiliation(s)
- Thomas G Laughlin
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Amy M Prichard
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Christian Seitz
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Eray Enustun
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Sergey Suslov
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kanika Khanna
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Erica A Birkholz
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily Armbruster
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
| | - Elizabeth Villa
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA.
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Hao Y, Wan X, Yan R, Liu Z, Li J, Zhang S, Cui X, Zhang F. VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 221:106871. [PMID: 35584579 DOI: 10.1016/j.cmpb.2022.106871] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/28/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND OBJECTIVE Cryo-electron tomography (cryo-ET) with subtomogram averaging (STA) is indispensable when studying macromolecule structures and functions in their native environments. Due to the low signal-to-noise ratio, the missing wedge artifacts in tomographic reconstructions, and multiple macromolecules of varied shapes and sizes, macromolecule localization and classification remain challenging. To tackle this bottleneck problem for structural determination by STA, we design an accurate macromolecule localization and classification method named voxelwise particle detector (VP-Detector). METHODS VP-Detector is a two-stage particle detection method based on a 3D multiscale dense convolutional neural network (3D MSDNet). The proposed network uses 3D hybrid dilated convolution (3D HDC) to avoid the resolution loss caused by scaling operations. Meanwhile, it uses 3D dense connectivity to encourage the reuse of feature maps to reduce trainable parameters. In addition, the weighted focal loss is proposed to focus more attention on difficult samples and rare classes, which relieves the class imbalance caused by multiple particles of various sizes. The performance of VP-Detector is evaluated on both simulated and real-world tomograms, and it shows that VP-Detector outperforms state-of-the-art methods. RESULTS The experiments show that VP-Detector outperforms the state-of-the-art methods on particle localization with an F1-score of 0.951 and a precision of 0.978. In addition, VP-Detector can replace manual particle picking in experiment on the real-world tomograms. Furthermore, it performs well in classifying large-, medium-, and small-weight proteins with accuracies of 1, 0.95, and 0.82, respectively. Finally, ablation studies demonstrate the effectiveness of 3D HDC, 3D dense connectivity, weighted focal loss, and training on small training sets. CONCLUSIONS VP-Detector can achieve high accuracy in particle detection with few trainable parameters and support training on small datasets. It can also relieve the class imbalance caused by multiple particles with various shapes and sizes.
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Affiliation(s)
- Yu Hao
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Xiaohua Wan
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Rui Yan
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhiyong Liu
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Jintao Li
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Shihua Zhang
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China.
| | - Xuefeng Cui
- School of Computer Science and Technology, Shandong University, Qingdao, China.
| | - Fa Zhang
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.
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43
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Chaikeeratisak V, Khanna K, Nguyen KT, Egan ME, Enustun E, Armbruster E, Lee J, Pogliano K, Villa E, Pogliano J. Subcellular organization of viral particles during maturation of nucleus-forming jumbo phage. SCIENCE ADVANCES 2022; 8:eabj9670. [PMID: 35507660 PMCID: PMC9067925 DOI: 10.1126/sciadv.abj9670] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 03/16/2022] [Indexed: 06/03/2023]
Abstract
Many eukaryotic viruses assemble mature particles within distinct subcellular compartments, but bacteriophages are generally assumed to assemble randomly throughout the host cell cytoplasm. Here, we show that viral particles of Pseudomonas nucleus-forming jumbo phage PhiPA3 assemble into a unique structure inside cells we term phage bouquets. We show that after capsids complete DNA packaging at the surface of the phage nucleus, tails assemble and attach to capsids, and these particles accumulate over time in a spherical pattern, with tails oriented inward and the heads outward to form bouquets at specific subcellular locations. Bouquets localize at the same fixed distance from the phage nucleus even when it is mispositioned, suggesting an active mechanism for positioning. These results mark the discovery of a pathway for organizing mature viral particles inside bacteria and demonstrate that nucleus-forming jumbo phages, like most eukaryotic viruses, are highly spatially organized during all stages of their lytic cycle.
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Affiliation(s)
- Vorrapon Chaikeeratisak
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katrina T Nguyen
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - MacKennon E Egan
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eray Enustun
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily Armbruster
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elizabeth Villa
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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44
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Nicolas WJ, Fäßler F, Dutka P, Schur FKM, Jensen G, Meyerowitz E. Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks. Curr Biol 2022; 32:2375-2389.e6. [PMID: 35508170 PMCID: PMC9240970 DOI: 10.1016/j.cub.2022.04.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 01/23/2023]
Abstract
One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall's mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed "meshing," which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is-at least in part-composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at -45° and +45° relative to the cell's long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.
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Affiliation(s)
- William J Nicolas
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 California Boulevard, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Florian Fäßler
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Przemysław Dutka
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 California Boulevard, Pasadena, CA 91125, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 California Boulevard, Pasadena, CA 91125, USA
| | - Florian K M Schur
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Grant Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 California Boulevard, Pasadena, CA 91125, USA; Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Elliot Meyerowitz
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 California Boulevard, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA.
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45
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Weiner E, Pinskey JM, Nicastro D, Otegui MS. Electron microscopy for imaging organelles in plants and algae. PLANT PHYSIOLOGY 2022; 188:713-725. [PMID: 35235662 PMCID: PMC8825266 DOI: 10.1093/plphys/kiab449] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/23/2021] [Indexed: 05/31/2023]
Abstract
Recent developments in both instrumentation and image analysis algorithms have allowed three-dimensional electron microscopy (3D-EM) to increase automated image collections through large tissue volumes using serial block-face scanning EM (SEM) and to achieve near-atomic resolution of macromolecular complexes using cryo-electron tomography (cryo-ET) and sub-tomogram averaging. In this review, we discuss applications of cryo-ET to cell biology research on plant and algal systems and the special opportunities they offer for understanding the organization of eukaryotic organelles with unprecedently resolution. However, one of the most challenging aspects for cryo-ET is sample preparation, especially for multicellular organisms. We also discuss correlative light and electron microscopy (CLEM) approaches that have been developed for ET at both room and cryogenic temperatures.
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Affiliation(s)
- Ethan Weiner
- Department of Botany, University of Wisconsin, Madison 53706, Wisconsin
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison 53706, Wisconsin
| | - Justine M Pinskey
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas 75390, Texas
| | - Daniela Nicastro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas 75390, Texas
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin, Madison 53706, Wisconsin
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison 53706, Wisconsin
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46
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Conley MJ, Short JM, Burns AM, Streetley J, Hutchings J, Bakker SE, Power BJ, Jaffery H, Haney J, Zanetti G, Murcia PR, Stewart M, Fearns R, Vijayakrishnan S, Bhella D. Helical ordering of envelope-associated proteins and glycoproteins in respiratory syncytial virus. EMBO J 2022; 41:e109728. [PMID: 34935163 PMCID: PMC8804925 DOI: 10.15252/embj.2021109728] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 12/20/2022] Open
Abstract
Human respiratory syncytial virus (RSV) causes severe respiratory illness in children and the elderly. Here, using cryogenic electron microscopy and tomography combined with computational image analysis and three-dimensional reconstruction, we show that there is extensive helical ordering of the envelope-associated proteins and glycoproteins of RSV filamentous virions. We calculated a 16 Å resolution sub-tomogram average of the matrix protein (M) layer that forms an endoskeleton below the viral envelope. These data define a helical lattice of M-dimers, showing how M is oriented relative to the viral envelope. Glycoproteins that stud the viral envelope were also found to be helically ordered, a property that was coordinated by the M-layer. Furthermore, envelope glycoproteins clustered in pairs, a feature that may have implications for the conformation of fusion (F) glycoprotein epitopes that are the principal target for vaccine and monoclonal antibody development. We also report the presence, in authentic virus infections, of N-RNA rings packaged within RSV virions. These data provide molecular insight into the organisation of the virion and the mechanism of its assembly.
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Affiliation(s)
- Michaela J Conley
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Judith M Short
- Medical Research Council Laboratory of Molecular BiologyCambridgeUK
| | - Andrew M Burns
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - James Streetley
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Joshua Hutchings
- Department of Biological SciencesBirkbeck CollegeLondonUK
- Present address:
Division of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Saskia E Bakker
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
- Present address:
School of Life SciencesUniversity of WarwickCoventryUK
| | - B Joanne Power
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
- Present address:
Department of Biochemistry and Molecular BiologyThe Huck Center for Malaria ResearchPennsylvania State UniversityUniversity ParkPAUSA
| | - Hussain Jaffery
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Joanne Haney
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Giulia Zanetti
- Department of Biological SciencesBirkbeck CollegeLondonUK
| | - Pablo R Murcia
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Murray Stewart
- Medical Research Council Laboratory of Molecular BiologyCambridgeUK
| | - Rachel Fearns
- Department of MicrobiologyBoston University School of MedicineBostonMAUSA
- National Emerging Infectious Diseases LaboratoriesBoston UniversityBostonMAUSA
| | | | - David Bhella
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
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47
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Depelteau JS, Renault L, Althof N, Cassidy CK, Mendonça LM, Jensen GJ, Resch GP, Briegel A. UVC inactivation of pathogenic samples suitable for cryo-EM analysis. Commun Biol 2022; 5:29. [PMID: 35017666 PMCID: PMC8752862 DOI: 10.1038/s42003-021-02962-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/07/2021] [Indexed: 12/22/2022] Open
Abstract
Cryo-electron microscopy has become an essential tool to understand structure and function of biological samples. Especially for pathogens, such as disease-causing bacteria and viruses, insights gained by cryo-EM can aid in developing cures. However, due to the biosafety restrictions of pathogens, samples are often treated by chemical fixation to render the pathogen inert, affecting the ultrastructure of the sample. Alternatively, researchers use in vitro or ex vivo models, which are non-pathogenic but lack the complexity of the pathogen of interest. Here we show that ultraviolet-C (UVC) radiation applied at cryogenic temperatures can be used to eliminate or dramatically reduce the infectivity of Vibrio cholerae and the bacterial virus, the ICP1 bacteriophage. We show no discernable structural impact of this treatment of either sample using two cryo-EM methods: cryo-electron tomography followed by sub-tomogram averaging, and single particle analysis (SPA). Additionally, we applied the UVC irradiation to the protein apoferritin (ApoF), which is a widely used test sample for high-resolution SPA studies. The UVC-treated ApoF sample resulted in a 2.1 Å structure indistinguishable from an untreated published map. This research demonstrates that UVC treatment is an effective and inexpensive addition to the cryo-EM sample preparation toolbox. Depelteau et al. present a new method to inactivate cryo-EM samples from pathogenic organisms before imaging using ultraviolet-C radiation in cryogenic conditions. This method allows for the inexpensive preparation of cryo-EM samples with no discernable structural impact of the treatment.
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Affiliation(s)
- Jamie S Depelteau
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Ludovic Renault
- Netherlands Centre for Electron Nanoscopy (NeCEN), Leiden University, Leiden, The Netherlands
| | - Nynke Althof
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Luiza M Mendonça
- Biology and Bioengineering Department, California Institute of Technology, Pasadena, CA, USA.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Grant J Jensen
- Biology and Bioengineering Department, California Institute of Technology, Pasadena, CA, USA and Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Guenter P Resch
- Nexperion e.U.-Solutions for Electron Microscopy, Vienna, Austria
| | - Ariane Briegel
- Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands. .,Netherlands Centre for Electron Nanoscopy (NeCEN), Leiden University, Leiden, The Netherlands.
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48
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De Rossi P, Lewis AJ, Furrer J, De Vos L, Demeter T, Zbinden A, Zhong W, Wiersma VI, Scialo C, Weber J, Guo Z, Scaramuzza S, Di Fabrizio M, Böing C, Castaño‐Díez D, Al‐Amoudi A, Pérez‐Berlanga M, Lashley T, Stahlberg H, Polymenidou M. FTLD-TDP assemblies seed neoaggregates with subtype-specific features via a prion-like cascade. EMBO Rep 2021; 22:e53877. [PMID: 34806807 PMCID: PMC8647015 DOI: 10.15252/embr.202153877] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022] Open
Abstract
Morphologically distinct TDP-43 aggregates occur in clinically different FTLD-TDP subtypes, yet the mechanism of their emergence and contribution to clinical heterogeneity are poorly understood. Several lines of evidence suggest that pathological TDP-43 follows a prion-like cascade, but the molecular determinants of this process remain unknown. We use advanced microscopy techniques to compare the seeding properties of pathological FTLD-TDP-A and FTLD-TDP-C aggregates. Upon inoculation of patient-derived aggregates in cells, FTLD-TDP-A seeds amplify in a template-dependent fashion, triggering neoaggregation more efficiently than those extracted from FTLD-TDP-C patients, correlating with the respective disease progression rates. Neoaggregates are sequentially phosphorylated with N-to-C directionality and with subtype-specific timelines. The resulting FTLD-TDP-A neoaggregates are large and contain densely packed fibrils, reminiscent of the pure compacted fibrils present within cytoplasmic inclusions in postmortem brains. In contrast, FTLD-TDP-C dystrophic neurites show less dense fibrils mixed with cellular components, and their respective neoaggregates are small, amorphous protein accumulations. These cellular seeding models replicate aspects of the patient pathological diversity and will be a useful tool in the quest for subtype-specific therapeutics.
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Affiliation(s)
- Pierre De Rossi
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Amanda J Lewis
- Laboratory of Biological Electron MicroscopyInstitute of Physics, SB, EPFLDepartment of Fundamental MicrobiologyFaculty of Biology and MedicineUNILLausanneSwitzerland
| | - Johanna Furrer
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Laura De Vos
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Tomas Demeter
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Aurélie Zbinden
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Weijia Zhong
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Vera I Wiersma
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Carlo Scialo
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Julien Weber
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Zhongning Guo
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Stefano Scaramuzza
- C‐CINABiozentrumUniversity of BaselBaselSwitzerland
- BioEM LabBiozentrumUniversity of BaselBaselSwitzerland
| | - Marta Di Fabrizio
- Laboratory of Biological Electron MicroscopyInstitute of Physics, SB, EPFLDepartment of Fundamental MicrobiologyFaculty of Biology and MedicineUNILLausanneSwitzerland
| | | | | | | | | | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological diseasesDepartment of Movement DisordersUCL Institute of NeurologyLondonUK
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
| | - Henning Stahlberg
- Laboratory of Biological Electron MicroscopyInstitute of Physics, SB, EPFLDepartment of Fundamental MicrobiologyFaculty of Biology and MedicineUNILLausanneSwitzerland
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49
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Studying bacterial chemosensory array with CryoEM. Biochem Soc Trans 2021; 49:2081-2089. [PMID: 34495335 PMCID: PMC8589424 DOI: 10.1042/bst20210080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 12/30/2022]
Abstract
Bacteria direct their movement in respond to gradients of nutrients and other stimuli in the environment through the chemosensory system. The behavior is mediated by chemosensory arrays that are made up of thousands of proteins to form an organized array near the cell pole. In this review, we briefly introduce the architecture and function of the chemosensory array and its core signaling unit. We describe the in vivo and in vitro systems that have been used for structural studies of chemosensory array by cryoEM, including reconstituted lipid nanodiscs, 2D lipid monolayer arrays, lysed bacterial ghosts, bacterial minicells and native bacteria cells. Lastly, we review recent advances in structural analysis of chemosensory arrays using state-of-the-art cryoEM and cryoET methodologies, focusing on the latest developments and insights with a perspective on current challenges and future directions.
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50
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Sanchez CP, Patra P, Chang SYS, Karathanasis C, Hanebutte L, Kilian N, Cyrklaff M, Heilemann M, Schwarz US, Kudryashev M, Lanzer M. KAHRP dynamically relocalizes to remodeled actin junctions and associates with knob spirals in Plasmodium falciparum-infected erythrocytes. Mol Microbiol 2021; 117:274-292. [PMID: 34514656 DOI: 10.1111/mmi.14811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/28/2022]
Abstract
The knob-associated histidine-rich protein (KAHRP) plays a pivotal role in the pathophysiology of Plasmodium falciparum malaria by forming membrane protrusions in infected erythrocytes, which anchor parasite-encoded adhesins to the membrane skeleton. The resulting sequestration of parasitized erythrocytes in the microvasculature leads to severe disease. Despite KAHRP being an important virulence factor, its physical location within the membrane skeleton is still debated, as is its function in knob formation. Here, we show by super-resolution microscopy that KAHRP initially associates with various skeletal components, including ankyrin bridges, but eventually colocalizes with remnant actin junctions. We further present a 35 Å map of the spiral scaffold underlying knobs and show that a KAHRP-targeting nanoprobe binds close to the spiral scaffold. Single-molecule localization microscopy detected ~60 KAHRP molecules/knob. We propose a dynamic model of KAHRP organization and a function of KAHRP in attaching other factors to the spiral scaffold.
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Affiliation(s)
- Cecilia P Sanchez
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Pintu Patra
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany.,BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
| | - Shih-Ying Scott Chang
- Max Planck Institute for Biophysics and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt, Frankfurt, Germany
| | - Christos Karathanasis
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Lukas Hanebutte
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Nicole Kilian
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Marek Cyrklaff
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Mike Heilemann
- BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany.,Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany
| | - Ulrich S Schwarz
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany.,BioQuant-Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
| | - Mikhail Kudryashev
- Max Planck Institute for Biophysics and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt, Frankfurt, Germany
| | - Michael Lanzer
- Center of Infectious Diseases, Parasitology, Universitätsklinikum Heidelberg, Heidelberg, Germany
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