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Borodavka A, Acker J. Seeing Biomolecular Condensates Through the Lens of Viruses. Annu Rev Virol 2023; 10:163-182. [PMID: 37040799 DOI: 10.1146/annurev-virology-111821-103226] [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: 04/13/2023]
Abstract
Phase separation of viral biopolymers is a key factor in the formation of cytoplasmic viral inclusions, known as sites of virus replication and assembly. This review describes the mechanisms and factors that affect phase separation in viral replication and identifies potential areas for future research. Drawing inspiration from studies on cellular RNA-rich condensates, we compare the hierarchical coassembly of ribosomal RNAs and proteins in the nucleolus to the coordinated coassembly of viral RNAs and proteins taking place within viral factories in viruses containing segmented RNA genomes. We highlight the common characteristics of biomolecular condensates in viral replication and how this new understanding is reshaping our views of virus assembly mechanisms. Such studies have the potential to uncover unexplored antiviral strategies targeting these phase-separated states.
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Affiliation(s)
- Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom;
| | - Julia Acker
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom;
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2
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Asensio-Cob D, Rodríguez JM, Luque D. Rotavirus Particle Disassembly and Assembly In Vivo and In Vitro. Viruses 2023; 15:1750. [PMID: 37632092 PMCID: PMC10458742 DOI: 10.3390/v15081750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Rotaviruses (RVs) are non-enveloped multilayered dsRNA viruses that are major etiologic agents of diarrheal disease in humans and in the young in a large number of animal species. The viral particle is composed of three different protein layers that enclose the segmented dsRNA genome and the transcriptional complexes. Each layer defines a unique subparticle that is associated with a different phase of the replication cycle. Thus, while single- and double-layered particles are associated with the intracellular processes of selective packaging, genome replication, and transcription, the viral machinery necessary for entry is located in the third layer. This modular nature of its particle allows rotaviruses to control its replication cycle by the disassembly and assembly of its structural proteins. In this review, we examine the significant advances in structural, molecular, and cellular RV biology that have contributed during the last few years to illuminating the intricate details of the RV particle disassembly and assembly processes.
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Affiliation(s)
- Dunia Asensio-Cob
- Department of Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G0A4, Canada;
| | - Javier M. Rodríguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Daniel Luque
- Electron Microscopy Unit UCCT/ISCIII, 28220 Majadahonda, Spain
- School of Biomedical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052, Australia
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3
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Hagan MF, Mohajerani F. Self-assembly coupled to liquid-liquid phase separation. PLoS Comput Biol 2023; 19:e1010652. [PMID: 37186597 PMCID: PMC10212142 DOI: 10.1371/journal.pcbi.1010652] [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: 10/12/2022] [Revised: 05/25/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Liquid condensate droplets with distinct compositions of proteins and nucleic acids are widespread in biological cells. While it is known that such droplets, or compartments, can regulate irreversible protein aggregation, their effect on reversible self-assembly remains largely unexplored. In this article, we use kinetic theory and solution thermodynamics to investigate the effect of liquid-liquid phase separation on the reversible self-assembly of structures with well-defined sizes and architectures. We find that, when assembling subunits preferentially partition into liquid compartments, robustness against kinetic traps and maximum achievable assembly rates can be significantly increased. In particular, both the range of solution conditions leading to productive assembly and the corresponding assembly rates can increase by orders of magnitude. We analyze the rate equation predictions using simple scaling estimates to identify effects of liquid-liquid phase separation as a function of relevant control parameters. These results may elucidate self-assembly processes that underlie normal cellular functions or pathogenesis, and suggest strategies for designing efficient bottom-up assembly for nanomaterials applications.
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Affiliation(s)
- Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
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4
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Zhang L, Liu W, Wu N, Wang H, Zhang Z, Liu Y, Wang X. Southern rice black-streaked dwarf virus induces incomplete autophagy for persistence in gut epithelial cells of its vector insect. PLoS Pathog 2023; 19:e1011134. [PMID: 36706154 PMCID: PMC9907856 DOI: 10.1371/journal.ppat.1011134] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/08/2023] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Autophagy plays an important role in virus infection of the host, because viral components and particles can be degraded by the host's autophagy and some viruses may be able to hijack and subvert autophagy for its benefit. However, details on the mechanisms that govern autophagy for immunity against viral infections or benefit viral survival remain largely unknown. Plant reoviruses such as southern rice black-streaked dwarf virus (SRBSDV), which seriously threaten crop yield, are only transmitted by vector insects. Here, we report a novel mechanism by which SRBSDV induces incomplete autophagy by blocking autophagosome-lysosome fusion, resulting in viral accumulation in gut epithelial cells of its vector, white-backed planthopper (Sogatella furcifera). SRBSDV infection leads to stimulation of the c-Jun N-terminal kinase (JNK) signaling pathway, which further activates autophagy. Mature and assembling virions were found close to the edge7 of the outer membrane of autophagosomes. Inhibition autophagy leads to the decrease of autophagosomes, which resulting in impaired maturation of virions and the decrease of virus titer, whereas activation of autophagy facilitated virus titer. Further, SRBSDV inhibited fusion of autophagosomes and lysosomes by interacting with lysosomal-associated membrane protein 1 (LAMP1) using viral P10. Thus, SRBSDV not only avoids being degrading by lysosomes, but also further hijacks these non-fusing autophagosomes for its subsistence. Our findings reveal a novel mechanism of reovirus persistence, which can explain why SRBSDV can be acquired and transmitted rapidly by its insect vector.
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Affiliation(s)
- Lu Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (WL); (XW)
| | - Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhongkai Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Key Laboratory of Agricultural Biotechnology, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (WL); (XW)
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5
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Strauss S, Acker J, Papa G, Desirò D, Schueder F, Borodavka A, Jungmann R. Principles of RNA recruitment to viral ribonucleoprotein condensates in a segmented dsRNA virus. eLife 2023; 12:e68670. [PMID: 36700549 PMCID: PMC9925054 DOI: 10.7554/elife.68670] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 01/26/2023] [Indexed: 01/27/2023] Open
Abstract
Rotaviruses transcribe 11 distinct RNAs that must be co-packaged prior to their replication to make an infectious virion. During infection, nontranslating rotavirus transcripts accumulate in cytoplasmic protein-RNA granules known as viroplasms that support segmented genome assembly and replication via a poorly understood mechanism. Here, we analysed the RV transcriptome by combining DNA-barcoded smFISH of rotavirus-infected cells. Rotavirus RNA stoichiometry in viroplasms appears to be distinct from the cytoplasmic transcript distribution, with the largest transcript being the most enriched in viroplasms, suggesting a selective RNA enrichment mechanism. While all 11 types of transcripts accumulate in viroplasms, their stoichiometry significantly varied between individual viroplasms. Accumulation of transcripts requires the presence of 3' untranslated terminal regions and viroplasmic localisation of the viral polymerase VP1, consistent with the observed lack of polyadenylated transcripts in viroplasms. Our observations reveal similarities between viroplasms and other cytoplasmic RNP granules and identify viroplasmic proteins as drivers of viral RNA assembly during viroplasm formation.
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Affiliation(s)
| | - Julia Acker
- Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
| | - Guido Papa
- Molecular Immunology Laboratory, International Centre for Genetic Engineering and BiotechnologyTriesteItaly
| | - Daniel Desirò
- Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
| | - Florian Schueder
- Max Planck Institute of BiochemistryMunichGermany
- Department of Physics and Center for Nanoscience, Ludwig Maximilian UniversityMunichGermany
| | | | - Ralf Jungmann
- Max Planck Institute of BiochemistryMunichGermany
- Department of Physics and Center for Nanoscience, Ludwig Maximilian UniversityMunichGermany
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6
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Torres-García E, Pinto-Cámara R, Linares A, Martínez D, Abonza V, Brito-Alarcón E, Calcines-Cruz C, Valdés-Galindo G, Torres D, Jabloñski M, Torres-Martínez HH, Martínez JL, Hernández HO, Ocelotl-Oviedo JP, Garcés Y, Barchi M, D’Antuono R, Bošković A, Dubrovsky JG, Darszon A, Buffone MG, Morales RR, Rendon-Mancha JM, Wood CD, Hernández-García A, Krapf D, Crevenna ÁH, Guerrero A. Extending resolution within a single imaging frame. Nat Commun 2022; 13:7452. [PMID: 36460648 PMCID: PMC9718789 DOI: 10.1038/s41467-022-34693-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 10/27/2022] [Indexed: 12/05/2022] Open
Abstract
The resolution of fluorescence microscopy images is limited by the physical properties of light. In the last decade, numerous super-resolution microscopy (SRM) approaches have been proposed to deal with such hindrance. Here we present Mean-Shift Super Resolution (MSSR), a new SRM algorithm based on the Mean Shift theory, which extends spatial resolution of single fluorescence images beyond the diffraction limit of light. MSSR works on low and high fluorophore densities, is not limited by the architecture of the optical setup and is applicable to single images as well as temporal series. The theoretical limit of spatial resolution, based on optimized real-world imaging conditions and analysis of temporal image stacks, has been measured to be 40 nm. Furthermore, MSSR has denoising capabilities that outperform other SRM approaches. Along with its wide accessibility, MSSR is a powerful, flexible, and generic tool for multidimensional and live cell imaging applications.
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Affiliation(s)
- Esley Torres-García
- grid.412873.b0000 0004 0484 1712Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos Mexico ,grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Raúl Pinto-Cámara
- grid.412873.b0000 0004 0484 1712Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos Mexico ,grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Alejandro Linares
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico ,grid.144532.5000000012169920XAnalytical and Quantitative Light Microscopy, Marine Biological Laboratory, Woods Hole, MA USA
| | - Damián Martínez
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Víctor Abonza
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Eduardo Brito-Alarcón
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Carlos Calcines-Cruz
- grid.9486.30000 0001 2159 0001Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Gustavo Valdés-Galindo
- grid.9486.30000 0001 2159 0001Departamento de Química de Biomacromoléculas, Instituto de Química. Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - David Torres
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Martina Jabloñski
- grid.464644.00000 0004 0637 7271Instituto de Biología y Medicina Experimental (IBYME‐CONICET), Buenos Aires, Argentina
| | - Héctor H. Torres-Martínez
- grid.9486.30000 0001 2159 0001Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - José L. Martínez
- grid.9486.30000 0001 2159 0001Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Haydee O. Hernández
- grid.9486.30000 0001 2159 0001Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - José P. Ocelotl-Oviedo
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Yasel Garcés
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico ,grid.9486.30000 0001 2159 0001Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Marco Barchi
- grid.6530.00000 0001 2300 0941Department of Biomedicine and Prevention, Faculty of Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | - Ana Bošković
- grid.418924.20000 0004 0627 3632Neurobiology and Epigenetics Unit, European Molecular Biology Laboratory, Monterotondo, Rome Italy
| | - Joseph G. Dubrovsky
- grid.9486.30000 0001 2159 0001Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Alberto Darszon
- grid.9486.30000 0001 2159 0001Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Mariano G. Buffone
- grid.464644.00000 0004 0637 7271Instituto de Biología y Medicina Experimental (IBYME‐CONICET), Buenos Aires, Argentina
| | - Roberto Rodríguez Morales
- grid.472559.80000 0004 0498 8706Instituto de Cibernética, Matemática y Física, Ciudad de la Habana, Cuba
| | - Juan Manuel Rendon-Mancha
- grid.412873.b0000 0004 0484 1712Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos Mexico
| | - Christopher D. Wood
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Armando Hernández-García
- grid.9486.30000 0001 2159 0001Departamento de Química de Biomacromoléculas, Instituto de Química. Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Diego Krapf
- grid.47894.360000 0004 1936 8083Electrical and Computer Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO USA
| | - Álvaro H. Crevenna
- grid.418924.20000 0004 0627 3632Neurobiology and Epigenetics Unit, European Molecular Biology Laboratory, Monterotondo, Rome Italy
| | - Adán Guerrero
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
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7
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Alva A, Brito-Alarcón E, Linares A, Torres-García E, Hernández HO, Pinto-Cámara R, Martínez D, Hernández-Herrera P, D'Antuono R, Wood C, Guerrero A. Fluorescence fluctuation based super resolution microscopy, basic concepts for an easy start. J Microsc 2022; 288:218-241. [PMID: 35896096 PMCID: PMC10087389 DOI: 10.1111/jmi.13135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 11/27/2022]
Abstract
Due to the wave nature of light, optical microscopy has a lower-bound lateral resolution limit of approximately half of the wavelength of visible light, i.e., within the range of 200 to 350 nm. Fluorescence Fluctuation based Super Resolution Microscopy (FF-SRM) is a term used to encompass a collection of image analysis techniques which rely on the statistical processing of temporal variations of the fluorescence signal. FF-SRM aims to reduce the uncertainty of the location of fluorophores within an image, often improving spatial resolution to several tens of nanometers. FF-SRM is suitable for live-cell imaging due to its compatibility with most fluorescent probes and relatively simple instrumental and experimental requirements, which are mostly camera-based epifluorescence instruments. Each FF-SRM approach has strengths and weaknesses, which depend directly on the underlying statistical principles through which enhanced spatial resolution is achieved. In this review, the basic concepts and principles behind a range of FF-SRM methods published to date are described. Their operational parameters are explained and guidance for its selection is provided. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Alma Alva
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Eduardo Brito-Alarcón
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Alejandro Linares
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Esley Torres-García
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.,Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Haydee O Hernández
- Posgrado en Ciencia e Ingeniería de la Computación, Universidad Nacional Autónoma de México, México City, México
| | - Raúl Pinto-Cámara
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.,Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Damián Martínez
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Paul Hernández-Herrera
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Rocco D'Antuono
- Crick Advanced Light Microscopy Science and Technology Platform, The Francis Crick Institute, London, UK
| | - Christopher Wood
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Adán Guerrero
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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8
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Geiger F, Acker J, Papa G, Wang X, Arter WE, Saar KL, Erkamp NA, Qi R, Bravo JPK, Strauss S, Krainer G, Burrone OR, Jungmann R, Knowles TPJ, Engelke H, Borodavka A. Liquid-liquid phase separation underpins the formation of replication factories in rotaviruses. EMBO J 2021; 40:e107711. [PMID: 34524703 PMCID: PMC8561643 DOI: 10.15252/embj.2021107711] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 12/29/2022] Open
Abstract
RNA viruses induce the formation of subcellular organelles that provide microenvironments conducive to their replication. Here we show that replication factories of rotaviruses represent protein-RNA condensates that are formed via liquid-liquid phase separation of the viroplasm-forming proteins NSP5 and rotavirus RNA chaperone NSP2. Upon mixing, these proteins readily form condensates at physiologically relevant low micromolar concentrations achieved in the cytoplasm of virus-infected cells. Early infection stage condensates could be reversibly dissolved by 1,6-hexanediol, as well as propylene glycol that released rotavirus transcripts from these condensates. During the early stages of infection, propylene glycol treatments reduced viral replication and phosphorylation of the condensate-forming protein NSP5. During late infection, these condensates exhibited altered material properties and became resistant to propylene glycol, coinciding with hyperphosphorylation of NSP5. Some aspects of the assembly of cytoplasmic rotavirus replication factories mirror the formation of other ribonucleoprotein granules. Such viral RNA-rich condensates that support replication of multi-segmented genomes represent an attractive target for developing novel therapeutic approaches.
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Affiliation(s)
- Florian Geiger
- Department of ChemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Julia Acker
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Guido Papa
- International Center for Genetic Engineering and BiotechnologyTriesteItaly
- Present address:
Medical Research Council Laboratory of Molecular Biology (MRC LMB)CambridgeUK
| | - Xinyu Wang
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Kadi L Saar
- Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Nadia A Erkamp
- Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Runzhang Qi
- Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Jack PK Bravo
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Present address:
Department of Molecular BiosciencesUniversity of Texas at AustinAustinTXUSA
| | - Sebastian Strauss
- Department of Physics and Center for NanoscienceMax Planck Institute of BiochemistryMunichGermany
| | - Georg Krainer
- Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Oscar R Burrone
- International Center for Genetic Engineering and BiotechnologyTriesteItaly
| | - Ralf Jungmann
- Department of Physics and Center for NanoscienceMax Planck Institute of BiochemistryMunichGermany
| | | | - Hanna Engelke
- Department of ChemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Institute of Pharmaceutical SciencesKarl‐Franzens‐Universität GrazGrazAustria
| | - Alexander Borodavka
- Department of ChemistryLudwig‐Maximilians‐Universität MünchenMunichGermany
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Department of Physics and Center for NanoscienceMax Planck Institute of BiochemistryMunichGermany
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9
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Abstract
Viruses have evolved precise mechanisms for using the cellular physiological pathways for their perpetuation. These virus-driven biochemical events must be separated in space and time from those of the host cell. In recent years, granular structures, known for over a century for rabies virus, were shown to host viral gene function and were named using terms such as viroplasms, replication sites, inclusion bodies, or viral factories (VFs). More recently, these VFs were shown to be liquid-like, sharing properties with membrane-less organelles driven by liquid–liquid phase separation (LLPS) in a process widely referred to as biomolecular condensation. Some of the best described examples of these structures come from negative stranded RNA viruses, where micrometer size VFs are formed toward the end of the infectious cycle. We here discuss some basic principles of LLPS in connection with several examples of VFs and propose a view, which integrates viral replication mechanisms with the biochemistry underlying liquid-like organelles. In this view, viral protein and RNA components gradually accumulate up to a critical point during infection where phase separation is triggered. This yields an increase in transcription that leads in turn to increased translation and a consequent growth of initially formed condensates. According to chemical principles behind phase separation, an increase in the concentration of components increases the size of the condensate. A positive feedback cycle would thus generate in which crucial components, in particular nucleoproteins and viral polymerases, reach their highest levels required for genome replication. Progress in understanding viral biomolecular condensation leads to exploration of novel therapeutics. Furthermore, it provides insights into the fundamentals of phase separation in the regulation of cellular gene function given that virus replication and transcription, in particular those requiring host polymerases, are governed by the same biochemical principles.
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10
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Caddy S, Papa G, Borodavka A, Desselberger U. Rotavirus research: 2014-2020. Virus Res 2021; 304:198499. [PMID: 34224769 DOI: 10.1016/j.virusres.2021.198499] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 02/09/2023]
Abstract
Rotaviruses are major causes of acute gastroenteritis in infants and young children worldwide and also cause disease in the young of many other mammalian and of avian species. During the recent 5-6 years rotavirus research has benefitted in a major way from the establishment of plasmid only-based reverse genetics systems, the creation of human and other mammalian intestinal enteroids, and from the wide application of structural biology (cryo-electron microscopy, cryo-EM tomography) and complementary biophysical approaches. All of these have permitted to gain new insights into structure-function relationships of rotaviruses and their interactions with the host. This review follows different stages of the viral replication cycle and summarizes highlights of structure-function studies of rotavirus-encoded proteins (both structural and non-structural), molecular mechanisms of viral replication including involvement of cellular proteins and lipids, the spectrum of viral genomic and antigenic diversity, progress in understanding of innate and acquired immune responses, and further developments of prevention of rotavirus-associated disease.
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Affiliation(s)
- Sarah Caddy
- Cambridge Institute for Therapeutic Immunology and Infectious Disease Jeffery Cheah Biomedical Centre, Cambridge, CB2 0AW, UK.
| | - Guido Papa
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
| | - Ulrich Desselberger
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
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11
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Rotavirus viroplasm biogenesis involves microtubule-based dynein transport mediated by an interaction between NSP2 and dynein intermediate chain. J Virol 2021; 95:e0124621. [PMID: 34379449 DOI: 10.1128/jvi.01246-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Rotaviruses are the causative agents of severe and dehydrating gastroenteritis in children, piglets, and many other young animals. They replicate their genomes and assemble double-layered particles in cytoplasmic electron-dense inclusion bodies called 'viroplasms'. The formation of viroplasms is reportedly associated with the stability of microtubules. Although material transport is an important function of microtubules, whether and how microtubule-based transport influences the formation of viroplasms is still unclear. Here, we demonstrate that the small viroplasms move and fuse in living cells. We show that microtubule-based dynein transport affects rotavirus infection, viroplasm formation, and the assembly of transient enveloped particles (TEPs) and triple-layered particles (TLPs). The dynein intermediate chain (DIC) is shown to localize in the viroplasm and to interact directly with non-structural protein 2 (NSP2), indicating that DIC is responsible for connecting the viroplasm to dynein. The WD40 repeat domain of DIC regulates the interaction between DIC and NSP2, and the knockdown of DIC inhibited rotaviral infection, viroplasm formation, and the assembly of TEPs and TLPs. Our findings show that rotavirus viroplasms hijack dynein transport for fusion events, required for maximal assembly of infectious viral progeny. This study provides novel insights into the intracellular transport of viroplasms, which is involved in their biogenesis. Importance Because the viroplasm is the viral factory for rotavirus replication, viroplasm formation undoubtedly determines the effective production of progeny rotavirus. Therefore, understanding the virus-host interactions involved in the biogenesis of the viroplasm is critical for the future development of prophylactic and therapeutic strategies. Previous studies have reported that the formation of viroplasms is associated with the stability of microtubules, whereas little is known about its specific mechanism. Here, we demonstrate that rotavirus viroplasm formation takes advantage of microtubule-based dynein transport mediated by an interaction between NSP2 and DIC. These findings provide new insight into the intracellular transport of viroplasms.
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Abstract
Group A rotaviruses (RVAs) are the major cause of severe acute gastroenteritis (AGE) in children under 5 years of age, annually resulting in nearly 130,000 deaths worldwide. Social conditions in developing countries that contribute to decreased oral rehydration and vaccine efficacy and the lack of approved antiviral drugs position RVA as a global health concern. In this minireview, we present an update in the field of antiviral compounds, mainly in relation to the latest findings in RVA virion structure and the viral replication cycle. In turn, we attempt to provide a perspective on the possible treatments for RVA-associated AGE, with special focus on novel approaches, such as those representing broad-spectrum therapeutic options. In this context, the modulation of host factors, lipid droplets, and the viral polymerase, which is highly conserved among AGE-causing viruses, are analyzed as possible drug targets.
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13
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Arnold MM, Dijk A, López S. Double‐stranded RNA Viruses. Virology 2021. [DOI: 10.1002/9781119818526.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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14
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Arista-Romero M, Pujals S, Albertazzi L. Towards a Quantitative Single Particle Characterization by Super Resolution Microscopy: From Virus Structures to Antivirals Design. Front Bioeng Biotechnol 2021; 9:647874. [PMID: 33842446 PMCID: PMC8033170 DOI: 10.3389/fbioe.2021.647874] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
In the last year the COVID19 pandemic clearly illustrated the potential threat that viruses pose to our society. The characterization of viral structures and the identification of key proteins involved in each step of the cycle of infection are crucial to develop treatments. However, the small size of viruses, invisible under conventional fluorescence microscopy, make it difficult to study the organization of protein clusters within the viral particle. The applications of super-resolution microscopy have skyrocketed in the last years, converting this group into one of the leading techniques to characterize viruses and study the viral infection in cells, breaking the diffraction limit by achieving resolutions up to 10 nm using conventional probes such as fluorescent dyes and proteins. There are several super-resolution methods available and the selection of the right one it is crucial to study in detail all the steps involved in the viral infection, quantifying and creating models of infection for relevant viruses such as HIV-1, Influenza, herpesvirus or SARS-CoV-1. Here we review the use of super-resolution microscopy (SRM) to study all steps involved in the viral infection and antiviral design. In light of the threat of new viruses, these studies could inspire future assays to unveil the viral mechanism of emerging viruses and further develop successful antivirals against them.
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Affiliation(s)
- Maria Arista-Romero
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Silvia Pujals
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, Universitat de Barcelona, Barcelona, Spain
| | - Lorenzo Albertazzi
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
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15
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Hernandez-Gonzalez M, Larocque G, Way M. Viral use and subversion of membrane organization and trafficking. J Cell Sci 2021; 134:jcs252676. [PMID: 33664154 PMCID: PMC7610647 DOI: 10.1242/jcs.252676] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Membrane trafficking is an essential cellular process conserved across all eukaryotes, which regulates the uptake or release of macromolecules from cells, the composition of cellular membranes and organelle biogenesis. It influences numerous aspects of cellular organisation, dynamics and homeostasis, including nutrition, signalling and cell architecture. Not surprisingly, malfunction of membrane trafficking is linked to many serious genetic, metabolic and neurological disorders. It is also often hijacked during viral infection, enabling viruses to accomplish many of the main stages of their replication cycle, including entry into and egress from cells. The appropriation of membrane trafficking by viruses has been studied since the birth of cell biology and has helped elucidate how this integral cellular process functions. In this Review, we discuss some of the different strategies viruses use to manipulate and take over the membrane compartments of their hosts to promote their replication, assembly and egress.
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Affiliation(s)
- Miguel Hernandez-Gonzalez
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gabrielle Larocque
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michael Way
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Infectious Disease, Imperial College, London W2 1PG, UK
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16
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Criglar JM, Crawford SE, Zhao B, Smith HG, Stossi F, Estes MK. A Genetically Engineered Rotavirus NSP2 Phosphorylation Mutant Impaired in Viroplasm Formation and Replication Shows an Early Interaction between vNSP2 and Cellular Lipid Droplets. J Virol 2020; 94:e00972-20. [PMID: 32461314 PMCID: PMC7375380 DOI: 10.1128/jvi.00972-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/18/2022] Open
Abstract
Many RNA viruses replicate in cytoplasmic compartments (virus factories or viroplasms) composed of viral and cellular proteins, but the mechanisms required for their formation remain largely unknown. Rotavirus (RV) replication in viroplasms requires interactions between virus nonstructural proteins NSP2 and NSP5, which are associated with components of lipid droplets (LDs). We previously identified two forms of NSP2 in RV-infected cells, a cytoplasmically dispersed form (dNSP2) and a viroplasm-specific form (vNSP2), which interact with hypophosphorylated and hyperphosphorylated NSP5, respectively, indicating that a coordinated phosphorylation cascade controls viroplasm assembly. The cellular kinase CK1α phosphorylates NSP2 on serine 313, triggering the localization of vNSP2 to sites of viroplasm assembly and its association with hyperphosphorylated NSP5. Using reverse genetics, we generated a rotavirus with a phosphomimetic NSP2 (S313D) mutation to directly evaluate the role of CK1α NSP2 phosphorylation in viroplasm formation. Recombinant rotavirus NSP2 S313D (rRV NSP2 S313D) is significantly delayed in viroplasm formation and in virus replication and interferes with wild-type RV replication in coinfection. Taking advantage of the delay in viroplasm formation, the NSP2 phosphomimetic mutant was used as a tool to observe very early events in viroplasm assembly. We show that (i) viroplasm assembly correlates with NSP5 hyperphosphorylation and (ii) vNSP2 S313D colocalizes with RV-induced LDs without NSP5, suggesting that vNSP2 phospho-S313 is sufficient for interacting with LDs and may be the virus factor required for RV-induced LD formation. Further studies with the rRV NSP2 S313D virus are expected to reveal new aspects of viroplasm and LD initiation and assembly.IMPORTANCE Reverse genetics was used to generate a recombinant rotavirus with a single phosphomimetic mutation in nonstructural protein 2 (NSP2 S313D) that exhibits delayed viroplasm formation, delayed replication, and an interfering phenotype during coinfection with wild-type rotavirus, indicating the importance of this amino acid during virus replication. Exploiting the delay in viroplasm assembly, we found that viroplasm-associated NSP2 colocalizes with rotavirus-induced lipid droplets prior to the accumulation of other rotavirus proteins that are required for viroplasm formation and that NSP5 hyperphosphorylation is required for viroplasm assembly. These data suggest that NSP2 phospho-S313 is sufficient for interaction with lipid droplets and may be the virus factor that induces lipid droplet biogenesis in rotavirus-infected cells. Lipid droplets are cellular organelles critical for the replication of many viral and bacterial pathogens, and thus, understanding the mechanism of NSP2-mediated viroplasm/lipid droplet initiation and interaction will lead to new insights into this important host-pathogen interaction.
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Affiliation(s)
- Jeanette M Criglar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Hunter G Smith
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Integrated Microscopy Core, Baylor College of Medicine, Houston, Texas, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Division of Infectious Diseases, Baylor College of Medicine, Houston, Texas, USA
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17
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Abid N, Chillemi G, Salemi M. Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach. Genes (Basel) 2019; 11:genes11010028. [PMID: 31878331 PMCID: PMC7016848 DOI: 10.3390/genes11010028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 12/10/2019] [Accepted: 12/19/2019] [Indexed: 01/12/2023] Open
Abstract
Rotavirus remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious question. The distribution of unusual genotypes subject to viral fitness is influenced by interactions among viral proteins. The present work aimed at analyzing the genetic constellation and the coevolution of rotavirus coding genes for the available rotavirus genotypes. Seventy-two full genome sequences of different genetic constellations were analyzed using a genetic algorithm. The results revealed an extensive genome-wide covariance network among the 12 viral proteins. Altogether, the emergence of new genotypes represents a challenge to the outcome and success of vaccination and the coevolutionary analysis of rotavirus proteins may boost efforts to better understand the interaction networks of proteins during viral replication/transcription.
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Affiliation(s)
- Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, Monastir 5000, Tunisia
- High Institute of Biotechnology of Sidi Thabet, Department of Biotechnology, University Manouba, BP-66, Ariana-Tunis 2020, Tunisia
- Correspondence: or ; Tel.: +216-92–974-000
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest systems, DIBAF, University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy;
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, Via Giovanni Amendola, 122/O, 70126 Bari, Italy
| | - Marco Salemi
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Emerging Pathogens Institute, P.O. Box 100009, Gainesville, FL 32610-3633, USA;
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